1
|
Ren Z, Gou R, Zhuo W, Chen Z, Yin X, Cao Y, Wang Y, Mi Y, Liu Y, Wang Y, Fan LM, Deng XW, Qian W. The MBD-ACD DNA methylation reader complex recruits MICRORCHIDIA6 to regulate ribosomal RNA gene expression in Arabidopsis. Plant Cell 2024; 36:1098-1118. [PMID: 38092516 PMCID: PMC10980342 DOI: 10.1093/plcell/koad313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 12/11/2023] [Indexed: 04/01/2024]
Abstract
DNA methylation is an important epigenetic mark implicated in selective rRNA gene expression, but the DNA methylation readers and effectors remain largely unknown. Here, we report a protein complex that reads DNA methylation to regulate variant-specific 45S ribosomal RNA (rRNA) gene expression in Arabidopsis (Arabidopsis thaliana). The complex, consisting of METHYL-CpG-BINDING DOMAIN PROTEIN5 (MBD5), MBD6, ALPHA-CRYSTALLIN DOMAIN PROTEIN15.5 (ACD15.5), and ACD21.4, directly binds to 45S rDNA. While MBD5 and MBD6 function redundantly, ACD15.5 and ACD21.4 are indispensable for variant-specific rRNA gene expression. These 4 proteins undergo phase separation in vitro and in vivo and are interdependent for their phase separation. The α-crystallin domain of ACD15.5 and ACD21.4, which is essential for their function, enables phase separation of the complex, likely by mediating multivalent protein interactions. The effector MICRORCHIDIA6 directly interacts with ACD15.5 and ACD21.4, but not with MBD5 and MBD6, and is recruited to 45S rDNA by the MBD-ACD complex to regulate variant-specific 45S rRNA expression. Our study reveals a pathway in Arabidopsis through which certain 45S rRNA gene variants are silenced, while others are activated.
Collapse
Affiliation(s)
- Zhitong Ren
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- College of Agronomy, Sichuan Agriculture University, Chengdu 611130, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Runyu Gou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Wanqing Zhuo
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhiyu Chen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xiaochang Yin
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yuxin Cao
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yingjie Mi
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Yannan Liu
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
- College of Life Sciences, Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou, Guangdong 510642, China
| | - Liu-Min Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Peking University Institute of advanced Agricultural Sciences, Weifang, Shandong 261325, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
2
|
Liu W, He G, Deng XW. Toward understanding and utilizing crop heterosis in the age of biotechnology. iScience 2024; 27:108901. [PMID: 38533455 PMCID: PMC10964264 DOI: 10.1016/j.isci.2024.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.
Collapse
Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| |
Collapse
|
3
|
Wang X, Yuan S, Wang C, Yan W, Xie G, Wang C, Qiu S, Wu J, Deng XW, Xu C, Tang X. Construction of a Female Sterility Maintaining System Based on a Novel Mutation of the MEL2 Gene. Rice (N Y) 2024; 17:12. [PMID: 38310612 PMCID: PMC10838886 DOI: 10.1186/s12284-024-00688-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2023] [Accepted: 01/19/2024] [Indexed: 02/06/2024]
Abstract
BACKGROUND Hybrid rice has significant yield advantage and stress tolerance compared with inbred rice. However, production of hybrid rice seeds requires extensive manual labors. Currently, hybrid rice seeds are produced by crosspollination of male sterile lines by fertile paternal lines. Because seeds from paternal lines can contaminate the hybrid seeds, mechanized production by mixed-seeding and mixed-harvesting is difficult. This problem can be solved if the paternal line is female sterile. RESULTS Here we identified a female infertile mutant named h569 carrying a novel mutation (A1106G) in the MEL2 gene that was previously reported to regulate meiosis entry both in male and female organs. h569 mutant is female infertile but male normal, suggesting that MEL2 regulates meiosis entry in male and female organs through distinct pathways. The MEL2 gene and h569 mutant gave us tools to construct female sterility maintaining systems that can be used for propagation of female sterile lines. We connected the wild-type MEL2 gene with pollen-killer gene ZmAA1 and seed-marker gene DsRed2 in one T-DNA cassette and transformed it into ZZH1607, a widely used restorer line. Transgenic line carrying a single transgene inserted in an intergenic region was selected to cross with h569 mutant. F2 progeny carrying homozygous A1106G mutation and hemizygous transgene displayed 1:1 segregation of fertile and infertile pollen grains and 1:1 segregation of fluorescent and non-fluorescent seeds upon self-fertilization. All of the non-fluorescent seeds generated female infertile plants, while the fluorescent seeds generated fertile plants that reproduced in the way as their previous generation. CONCLUSIONS These results indicated that the female sterility maintaining system constructed in the study can be used to breed and propagate paternal lines that are female infertile. The application of this system will enable mechanized production of hybrid rice seed by using the mixed-seeding and mixed harvesting approach, which will significantly reduce the cost in hybrid rice seed production.
Collapse
Affiliation(s)
- Xia Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Shuting Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, 518107, Shenzhen, China
| | - Changjian Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Gang Xie
- Shenzhen Institute of Molecular Crop Design, 518107, Shenzhen, China
| | - Cuifang Wang
- Shenzhen Institute of Molecular Crop Design, 518107, Shenzhen, China
| | - Shijun Qiu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop Design, 518107, Shenzhen, China.
- School of Advanced Agricultural Sciences, Peking University, 100871, Beijing, China.
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, 518107, Shenzhen, China.
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
- Shenzhen Institute of Molecular Crop Design, 518107, Shenzhen, China.
| |
Collapse
|
4
|
Gao Z, Su Y, Chang L, Jiao G, Ou Y, Yang M, Xu C, Liu P, Wang Z, Qi Z, Liu W, Sun L, He G, Deng XW, He H. Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids. J Integr Plant Biol 2024; 66:208-227. [PMID: 38326968 DOI: 10.1111/jipb.13620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/04/2024] [Indexed: 02/09/2024]
Abstract
In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.
Collapse
Affiliation(s)
- Zhaoxu Gao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yanning Su
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Le Chang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guanzhong Jiao
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Yang Ou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Mei Yang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Chao Xu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Pengtao Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zejia Wang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Zewen Qi
- College of Grassland Science, Beijing Forestry University, Beijing, 100083, China
| | - Wenwen Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Guangming He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang 261325, China
| |
Collapse
|
5
|
Sun L, Zhou J, Xu X, Liu Y, Ma N, Liu Y, Nie W, Zou L, Deng XW, He H. Mapping nucleosome-resolution chromatin organization and enhancer-promoter loops in plants using Micro-C-XL. Nat Commun 2024; 15:35. [PMID: 38167349 PMCID: PMC10762229 DOI: 10.1038/s41467-023-44347-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 12/10/2023] [Indexed: 01/05/2024] Open
Abstract
Although chromatin organizations in plants have been dissected at the scales of compartments and topologically associating domain (TAD)-like domains, there remains a gap in resolving fine-scale structures. Here, we use Micro-C-XL, a high-throughput chromosome conformation capture (Hi-C)-based technology that involves micrococcal nuclease (instead of restriction enzymes) and long cross-linkers, to dissect single nucleosome-resolution chromatin organization in Arabidopsis. Insulation analysis reveals more than 14,000 boundaries, which mostly include chromatin accessibility, epigenetic modifications, and transcription factors. Micro-C-XL reveals associations between RNA Pols and local chromatin organizations, suggesting that gene transcription substantially contributes to the establishment of local chromatin domains. By perturbing Pol II both genetically and chemically at the gene level, we confirm its function in regulating chromatin organization. Visible loops and stripes are assigned to super-enhancers and their targeted genes, thus providing direct insights for the identification and mechanistic analysis of distal CREs and their working modes in plants. We further investigate possible factors regulating these chromatin loops. Subsequently, we expand Micro-C-XL to soybean and rice. In summary, we use Micro-C-XL for analyses of plants, which reveal fine-scale chromatin organization and enhancer-promoter loops and provide insights regarding three-dimensional genomes in plants.
Collapse
Affiliation(s)
- Linhua Sun
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Jingru Zhou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Xiao Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Yi Liu
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
- PKU-Tsinghua-NIBS Graduate Program, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, 100871, China
| | - Yutong Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China
| | - Wenchao Nie
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Ling Zou
- Wuhan Frasergen Bioinformatics Co., Ltd., Wuhan, 430075, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Shandong, 261000, China.
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, 100871, China.
| |
Collapse
|
6
|
Han X, Zhang Y, Lou Z, Li J, Wang Z, Gao C, Liu Y, Ren Z, Liu W, Li B, Pan W, Zhang H, Sang Q, Wan M, He H, Deng XW. Time series single-cell transcriptional atlases reveal cell fate differentiation driven by light in Arabidopsis seedlings. Nat Plants 2023; 9:2095-2109. [PMID: 37903986 PMCID: PMC10724060 DOI: 10.1038/s41477-023-01544-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 09/19/2023] [Indexed: 11/01/2023]
Abstract
Light serves as the energy source for plants as well as a signal for growth and development during their whole life cycle. Seedling de-etiolation is the most dramatic manifestation of light-regulated plant development processes, as massive reprogramming of the plant transcriptome occurs at this time. Although several studies have reported about organ-specific development and expression induced by light, a systematic analysis of cell-type-specific differentiation and the associated transcriptional regulation is still lacking. Here we obtained single-cell transcriptional atlases for etiolated, de-etiolating and light-grown Arabidopsis thaliana seedlings. Informative cells from shoot and root tissues were grouped into 48 different cell clusters and finely annotated using multiple markers. With the determination of comprehensive developmental trajectories, we demonstrate light modulation of cell fate determination during guard cell specialization and vasculature development. Comparison of expression atlases between wild type and the pifq mutant indicates that phytochrome-interacting factors (PIFs) are involved in distinct developmental processes in endodermal and stomatal lineage cells via controlling cell-type-specific expression of target genes. These results provide information concerning the light signalling networks at the cell-type resolution, improving our understanding of how light regulates plant development at the cell-type and genome-wide levels. The obtained information could serve as a valuable resource for comprehensively investigating the molecular mechanism of cell development and differentiation in response to light.
Collapse
Affiliation(s)
- Xue Han
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Yilin Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zhiying Lou
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Zheng Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Chunlei Gao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Yi Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Zizheng Ren
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Weimin Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Bosheng Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Wenbo Pan
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Huawei Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Qing Sang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China
| | - Miaomiao Wan
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong, China.
- School of Advanced Agricultural Sciences and School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Peking University, Beijing, China.
| |
Collapse
|
7
|
Chen J, Yu R, Li N, Deng Z, Zhang X, Zhao Y, Qu C, Yuan Y, Pan Z, Zhou Y, Li K, Wang J, Chen Z, Wang X, Wang X, He SN, Dong J, Deng XW, Chen H. Amyloplast sedimentation repolarizes LAZYs to achieve gravity sensing in plants. Cell 2023; 186:4788-4802.e15. [PMID: 37741279 PMCID: PMC10615846 DOI: 10.1016/j.cell.2023.09.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/04/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Gravity controls directional growth of plants, and the classical starch-statolith hypothesis proposed more than a century ago postulates that amyloplast sedimentation in specialized cells initiates gravity sensing, but the molecular mechanism remains uncharacterized. The LAZY proteins are known as key regulators of gravitropism, and lazy mutants show striking gravitropic defects. Here, we report that gravistimulation by reorientation triggers mitogen-activated protein kinase (MAPK) signaling-mediated phosphorylation of Arabidopsis LAZY proteins basally polarized in root columella cells. Phosphorylation of LAZY increases its interaction with several translocons at the outer envelope membrane of chloroplasts (TOC) proteins on the surface of amyloplasts, facilitating enrichment of LAZY proteins on amyloplasts. Amyloplast sedimentation subsequently guides LAZY to relocate to the new lower side of the plasma membrane in columella cells, where LAZY induces asymmetrical auxin distribution and root differential growth. Together, this study provides a molecular interpretation for the starch-statolith hypothesis: the organelle-movement-triggered molecular polarity formation.
Collapse
Affiliation(s)
- Jiayue Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Renbo Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Key Laboratory of Vegetable Research Center, Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou 571101, China
| | - Na Li
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Zhaoguo Deng
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xinxin Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yaran Zhao
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Chengfu Qu
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yanfang Yuan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhexian Pan
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Yangyang Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Kunlun Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Jiajun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Zhiren Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Xiaoyi Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolian Wang
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Shu-Nan He
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China
| | - Juan Dong
- The Waksman Institute of Microbiology, Rutgers, the State University of New Jersey, Piscataway, NJ 08854, USA; Department of Plant Biology, Rutgers, the State University of New Jersey, New Brunswick, NJ 08901, USA
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haodong Chen
- Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China; State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Tsinghua-Peking Center for Life Sciences, Beijing 100084, China.
| |
Collapse
|
8
|
Kong L, Li Z, Liu Y, Zhang J, Chen M, Zhou Q, Qi X, Deng XW, Peng Y. A Generalized Deep Learning Method for Synthetic CT Generation. Int J Radiat Oncol Biol Phys 2023; 117:e472. [PMID: 37785502 DOI: 10.1016/j.ijrobp.2023.06.1681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) The application of deep learning to generate synthetic CT (sCT) has been widely studied in radiotherapy. Existing methods generally involve data from two different image modalities, such as CBCT-CT or MRI-CT, the quality of sCT is adversely affected by source image quality. We propose a unique method of synthesizing MRI and CBCT into sCT based on single-modal CT for training, and call it SmGAN. MATERIALS/METHODS We used planning CT of a group of 35 head and neck cases to as training data. We then applied two different spatial transformations to the planning CT image to produce the transformed CT1 and CT2. And We used a random style enhancement technique (Shuffle Remap) to modify the image distribution of CT1 which we termed CT1+E. CT1+E was used to simulate the patient's "image of the day" while CT2 to simulate the "planning image". After feeding both CT1+E and CT2 into the generator, we obtained the sCT predicted by the generator. The generator was trained using the Mean Absolute Error (MAE) loss between sCT and CT1. In the actual clinical process, we use the patient's CBCT or MRI instead of CT1+E and the patient's planning CT instead of CT2 as the input of the generator. After processing, we get an sCT that can maintain the spatial position of the image taken on the day, while presenting features similar to the planning CT. The evaluation data we have includes 10 pairs of MRI-Def_CT and 10 pairs of CBCT-Def_CT Head and Neck patients. Def_CT is obtained from the planning CT based on the spatial position deformation of MRI and CBCT. To evaluate the accuracy of sCT based on MRI and CBCT with Def CT, we use a range of metrics, including Hounsfield Unit (HU) difference, peak signal-to-noise ratio (PSNR), structural similarity (SSIM) and gamma pass rate. All results will be benchmarks against the advanced method RegGAN for comparison. RESULTS Compared to RegGAN, the results of SmGAN were significantly better. The mean absolute errors within the body were (44.7±216.2 HU vs. 36.7±131.4 HU) and (64.9±123.7 HU vs. 58.2±152.8 HU) for the CBCT-SCT and MRI-SCT, respectively (Table 1). In addition, experimental results show that SmGAN also outperforms RegGAN in dose calculation accuracy. For example, under the 10% threshold, SmGAN's gamma pass rate of 1mm and 1% is 0.926±0.02, compared with gamma rate of 0.896±0.02 for RegGAN. CONCLUSION We proposed a generalized deep learning model for synthetic CT generation, based on CBCT or MRI images. The proposed algorithm achieved high accuracy of dosimetric metrics, as well as excellent IMRT QA verification results. Compared to other existing synthetic CT generation methods, the proposed SmGAN required a single-modal image for training, which is considered as a major breakthrough in the industry, and is expected to have wide spread of clinical applications.
Collapse
Affiliation(s)
- L Kong
- Manteia Technologies Co., Ltd, Xiamen, 361001, People's Republic of China, Xiamen, Fujian, China
| | - Z Li
- Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan, China
| | - Y Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - J Zhang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - M Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, China
| | - Q Zhou
- Manteia Technologies Co., Ltd., Xiamen, China
| | - X Qi
- Dept. of Radiation Oncology, UCLA, Los Angeles, CA
| | - X W Deng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Y Peng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| |
Collapse
|
9
|
Wang J, Zhou C, Guan Z, Wang Q, Zhao J, Wang L, Zhang L, Zhang D, Deng XW, Ma L, Yin P. Plant phytochrome A in the Pr state assembles as an asymmetric dimer. Cell Res 2023; 33:802-805. [PMID: 37402899 PMCID: PMC10542778 DOI: 10.1038/s41422-023-00847-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Accepted: 06/24/2023] [Indexed: 07/06/2023] Open
Affiliation(s)
- Jiao Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Chen Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Qiang Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Jun Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Liuqing Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, Hubei, China.
| |
Collapse
|
10
|
Huang R, Miao J, Zhang L, Peng Y, Huang S, Han F, Wang L, Deng XW, Zhao C. Radiation-Induced Nasopharyngeal Necrosis in Locally-Recurrent Nasopharyngeal Carcinoma Patients after Re-Radiotherapy. Int J Radiat Oncol Biol Phys 2023; 117:e589-e590. [PMID: 37785783 DOI: 10.1016/j.ijrobp.2023.06.1938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Re-radiotherapy (re-RT) is the main treatment for locally recurrent nasopharyngeal carcinoma (lrNPC) patients, and commonly led to radiation-induced nasopharyngeal (NP) necrosis, which was lethal but rare study has focused on it. The aim of this study was to evaluate the cause and impact of radiation-induced NP necrosis in lrNPC patients who received re-RT. MATERIALS/METHODS Totally 252 lrNPC patients who received re-RT between January 2013 and December 2020 were retrospectively collected. The inclusion criteria were as follows: (1) no NP necrosis before re-RT; (2) complete medical records, including treatment, clinical and dosimetric information; (3) conventional fractionated radiotherapy. All patients received intensity-modulated radiotherapy ± chemotherapy. Radiation-induced NP necrosis was diagnosed by magnetic resonance imaging and/or electronic nasopharyngoscopy. Dosimetric factors of the planning target volume of primary tumor (PTVp) were extracted from the dose-volume histogram (DVH), which was rescaled to an equivalent dose of 2 Gy per fraction (EQD 2 Gy) using a linear quadratic model. Logistic regression was used to identify the independent prognostic factors for generating the nomogram. RESULTS With a median follow-up of 44.63 months (inter-quartile range [IQR], 27.70 - 69.20 months), 47.6% of patients (120/252) occurred radiation-induced NP necrosis, which mostly happened within 1 year post re-RT (median [IQR], 5.83 [3.37 - 11.57] months). The 3-year overall survival was 83.0% vs 39.7% (P<0.001) in lrNPC patients with or without radiation-induced NP necrosis. Except for the fractionated dose, other dosimetric factors of PTVp were not significantly different between two groups, including D98 (dose to 98% of PTVp), D50, D2 and homogeneity index (Table 1). Furthermore, multivariate analysis showed that continuous variable age (HR [95% CI]: 1.04 [1.02 - 1.07], P = 0.003) and tumor volume (HR [95% CI]: 1.02 [1.01 - 1.03], P<0.001), and fractionated dose > 2.22 Gy (HR [95% CI]: 2.36 [1.32 - 4.21], P = 0.004) were independent factors in predicting radiation-induced NP necrosis, which yielded a C-index of 0.742 (95% CI, 0.682 - 0.803) for OS in the nomogram. CONCLUSION The incidence of radiation-induced NP necrosis was high in lrNPC patients who received re-RT. Patients with older age, larger tumor volume or receiving fractionated dose over 2.22 Gy were more easily to suffer NP necrosis, which need to explore novel treatment strategies to improve patients' survivals.
Collapse
Affiliation(s)
- R Huang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - J Miao
- Department of Nasopharyngeal Carcinoma, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - L Zhang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - Y Peng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - S Huang
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - F Han
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - L Wang
- Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - X W Deng
- Department of Radiation Oncology, Sun Yat-Sen University Cancer Center, Guangzhou, China
| | - C Zhao
- Sun Yat-sen University Cancer Center, Guangzhou, China
| |
Collapse
|
11
|
Zhang Y, Lin X, Ma C, Zhao J, Shang X, Wang Z, Xu B, Gao N, Deng XW, Wang J. Structural insights into plant phytochrome A as a highly sensitized photoreceptor. Cell Res 2023; 33:806-809. [PMID: 37491602 PMCID: PMC10542756 DOI: 10.1038/s41422-023-00858-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/16/2023] [Indexed: 07/27/2023] Open
Affiliation(s)
- Yuxuan Zhang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaoli Lin
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Chengying Ma
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Jun Zhao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Xiaojin Shang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Zhengdong Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
| | - Bin Xu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China
| | - Ning Gao
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China
- State Key Laboratory of Membrane Biology, School of Life Sciences, Peking University, Beijing, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
- Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, China.
| | - Jizong Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences at Weifang, Weifang, Shandong, China.
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing, China.
| |
Collapse
|
12
|
Li H, Hua L, Zhao S, Hao M, Song R, Pang S, Liu Y, Chen H, Zhang W, Shen T, Gou JY, Mao H, Wang G, Hao X, Li J, Song B, Lan C, Li Z, Deng XW, Dubcovsky J, Wang X, Chen S. Cloning of the wheat leaf rust resistance gene Lr47 introgressed from Aegilops speltoides. Nat Commun 2023; 14:6072. [PMID: 37770474 PMCID: PMC10539295 DOI: 10.1038/s41467-023-41833-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 09/20/2023] [Indexed: 09/30/2023] Open
Abstract
Leaf rust, caused by Puccinia triticina Eriksson (Pt), is one of the most severe foliar diseases of wheat. Breeding for leaf rust resistance is a practical and sustainable method to control this devastating disease. Here, we report the identification of Lr47, a broadly effective leaf rust resistance gene introgressed into wheat from Aegilops speltoides. Lr47 encodes a coiled-coil nucleotide-binding leucine-rich repeat protein that is both necessary and sufficient to confer Pt resistance, as demonstrated by loss-of-function mutations and transgenic complementation. Lr47 introgression lines with no or reduced linkage drag are generated using the Pairing homoeologous1 mutation, and a diagnostic molecular marker for Lr47 is developed. The coiled-coil domain of the Lr47 protein is unable to induce cell death, nor does it have self-protein interaction. The cloning of Lr47 expands the number of leaf rust resistance genes that can be incorporated into multigene transgenic cassettes to control this devastating disease.
Collapse
Affiliation(s)
- Hongna Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Lei Hua
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuqing Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Rui Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Shuyong Pang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Yanna Liu
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Hong Chen
- Triticeae Research Institute, Sichuan Agricultural University, 611130, Chengdu, China
| | - Wenjun Zhang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Tao Shen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jin-Ying Gou
- Key Laboratory of Crop Heterosis and Utilization (MOE) and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, 100193, Beijing, China
| | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Guiping Wang
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Xiaohua Hao
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jian Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Caixia Lan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zaifeng Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA
| | - Xiaodong Wang
- State Key Laboratory of North China Crop Improvement and Regulation, College of Plant Protection, Hebei Agricultural University, 071000, Baoding, Hebei, China.
| | - Shisheng Chen
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, 261325, Shandong, China.
| |
Collapse
|
13
|
Song X, Guo P, Xia K, Wang M, Liu Y, Chen L, Zhang J, Xu M, Liu N, Yue Z, Xu X, Gu Y, Li G, Liu M, Fang L, Deng XW, Li B. Spatial transcriptomics reveals light-induced chlorenchyma cells involved in promoting shoot regeneration in tomato callus. Proc Natl Acad Sci U S A 2023; 120:e2310163120. [PMID: 37703282 PMCID: PMC10515167 DOI: 10.1073/pnas.2310163120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 08/09/2023] [Indexed: 09/15/2023] Open
Abstract
Callus is a reprogrammed cell mass involved in plant regeneration and gene transformation in crop engineering. Pluripotent callus cells develop into fertile shoots through shoot regeneration. The molecular basis of the shoot regeneration process in crop callus remains largely elusive. This study pioneers the exploration of the spatial transcriptome of tomato callus during shoot regeneration. The findings reveal the presence of highly heterogeneous cell populations within the callus, including epidermis, vascular tissue, shoot primordia, inner callus, and outgrowth shoots. By characterizing the spatially resolved molecular features of shoot primordia and surrounding cells, specific factors essential for shoot primordia formation are identified. Notably, chlorenchyma cells, enriched in photosynthesis-related processes, play a crucial role in promoting shoot primordia formation and subsequent shoot regeneration. Light is shown to promote shoot regeneration by inducing chlorenchyma cell development and coordinating sugar signaling. These findings significantly advance our understanding of the cellular and molecular aspects of shoot regeneration in tomato callus and demonstrate the immense potential of spatial transcriptomics in plant biology.
Collapse
Affiliation(s)
- Xiehai Song
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Pengru Guo
- Beijing Genomics Institute Research, Beijing102601, China
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Keke Xia
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Meiling Wang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Yongqi Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Lichuan Chen
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Jinhui Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Mengyuan Xu
- Beijing Genomics Institute Research, Beijing102601, China
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Naixu Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Zhiliang Yue
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Xun Xu
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Ying Gu
- Beijing Genomics Institute Research, Shenzhen518083, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, Shandong271018, China
| | - Min Liu
- Baimaike Intelligent Manufacturing, Qingdao, Shandong266500, China
| | - Liang Fang
- Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong518005, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong261325, China
| |
Collapse
|
14
|
Cai Y, Liu Y, Fan Y, Li X, Yang M, Xu D, Wang H, Deng XW, Li J. MYB112 connects light and circadian clock signals to promote hypocotyl elongation in Arabidopsis. Plant Cell 2023; 35:3485-3503. [PMID: 37335905 PMCID: PMC10473211 DOI: 10.1093/plcell/koad170] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/05/2023] [Accepted: 06/13/2023] [Indexed: 06/21/2023]
Abstract
Ambient light and the endogenous circadian clock play key roles in regulating Arabidopsis (Arabidopsis thaliana) seedling photomorphogenesis. PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) acts downstream of both light and the circadian clock to promote hypocotyl elongation. Several members of the R2R3-MYB transcription factor (TF) family, the most common type of MYB TF family in Arabidopsis, have been shown to be involved in regulating photomorphogenesis. Nonetheless, whether R2R3-MYB TFs are involved in connecting the light and clock signaling pathways during seedling photomorphogenesis remains unknown. Here, we report that MYB112, a member of the R2R3-MYB family, acts as a negative regulator of seedling photomorphogenesis in Arabidopsis. The light signal promotes the transcription and protein accumulation of MYB112. myb112 mutants exhibit short hypocotyls in both constant light and diurnal cycles. MYB112 physically interacts with PIF4 to enhance the transcription of PIF4 target genes involved in the auxin pathway, including YUCCA8 (YUC8), INDOLE-3-ACETIC ACID INDUCIBLE 19 (IAA19), and IAA29. Furthermore, MYB112 directly binds to the promoter of LUX ARRHYTHMO (LUX), the central component of clock oscillators, to repress its expression mainly in the afternoon and relieve LUX-inhibited expression of PIF4. Genetic evidence confirms that LUX acts downstream of MYB112 in regulating hypocotyl elongation. Thus, the enhanced transcript accumulation and transcriptional activation activity of PIF4 by MYB112 additively promotes the expression of auxin-related genes, thereby increasing auxin synthesis and signaling and fine-tuning hypocotyl growth under diurnal cycles.
Collapse
Affiliation(s)
- Yupeng Cai
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- National Center for Transgenic Research in Plants, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yongting Liu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yangyang Fan
- Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing Engineering Research Center for Edible Mushroom, Beijing 100097, China
| | - Xitao Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- School of Life Science, Huizhou University, Huizhou 516007, China
| | - Maosheng Yang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou 510642, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking–Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
15
|
Li H, Zhou Y, Qin X, Peng J, Han R, Lv Y, Li C, Qi L, Qu GP, Yang L, Li Y, Terzaghi W, Li Z, Qin F, Gong Z, Deng XW, Li J. Reconstitution of phytochrome A-mediated light modulation of the ABA signaling pathways in yeast. Proc Natl Acad Sci U S A 2023; 120:e2302901120. [PMID: 37590408 PMCID: PMC10450666 DOI: 10.1073/pnas.2302901120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 07/06/2023] [Indexed: 08/19/2023] Open
Abstract
Abscisic acid (ABA), a classical plant hormone, plays an essential role in plant adaptation to environmental stresses. The ABA signaling mechanisms have been extensively investigated, and it was shown that the PYR1 (PYRABACTIN RESISTANCE1)/PYL (PYR1-LIKE)/RCAR (REGULATORY COMPONENT OF ABA RECEPTOR) ABA receptors, the PP2C coreceptors, and the SnRK2 protein kinases constitute the core ABA signaling module responsible for ABA perception and initiation of downstream responses. We recently showed that ABA signaling is modulated by light signals, but the underlying molecular mechanisms remain largely obscure. In this study, we established a system in yeast cells that was not only successful in reconstituting a complete ABA signaling pathway, from hormone perception to ABA-responsive gene expression, but also suitable for functionally characterizing the regulatory roles of additional factors of ABA signaling. Using this system, we analyzed the roles of several light signaling components, including the red and far-red light photoreceptors phytochrome A (phyA) and phyB, and the photomorphogenic central repressor COP1, in the regulation of ABA signaling. Our results showed that both phyA and phyB negatively regulated ABA signaling, whereas COP1 positively regulated ABA signaling in yeast cells. Further analyses showed that photoactivated phyA interacted with the ABA coreceptors ABI1 and ABI2 to decrease their interactions with the ABA receptor PYR1. Together, data from our reconstituted yeast ABA signaling system provide evidence that photoactivated photoreceptors attenuate ABA signaling by directly interacting with the key components of the core ABA signaling module, thus conferring enhanced ABA tolerance to light-grown plants.
Collapse
Affiliation(s)
- Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong261325, China
| | - Xinyan Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Jing Peng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Run Han
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Yang Lv
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Cong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Gao-Ping Qu
- Basic Forestry and Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou350002, China
| | - Li Yang
- Department of Plant Pathology, China Agricultural University, Beijing100193, China
| | - Yanjie Li
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT06520
| | | | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Feng Qin
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong261325, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, China Agricultural University, Beijing100193, China
| |
Collapse
|
16
|
Liu W, Ren D, Yang W, Xu M, Zhang Y, Wang X, He G, Deng XW. Genetic and molecular regulation of increased photosynthetic cell number contributes to leaf size heterosis in Arabidopsis. iScience 2023; 26:107366. [PMID: 37539024 PMCID: PMC10393828 DOI: 10.1016/j.isci.2023.107366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 05/31/2023] [Accepted: 07/10/2023] [Indexed: 08/05/2023] Open
Abstract
Heterosis is an important genetic phenomenon that has been observed and widely utilized in agriculture. However, the genetic and molecular bases of heterosis are unclear. Through transcriptome-wide association studies (TWAS) and expression quantitative trait locus (eQTL) analysis to integrate genome, transcriptome, and heterotic phenotype of a half-sibling Arabidopsis hybrid population, we report that the genetic and molecular bases of variations in leaf growth heterosis can be explained by the varied expression levels of growth-regulating genes resulting from distinct sets of heterozygous eQTLs carried by the half-sibling hybrids. In F1 versus parent, the degree of up-regulated gene expression in the cell cycle pathway in the shoot apex and the photosynthesis pathway in true leaf positively correlates with true leaf area heterosis level, and this is affected by the accumulation of superior heterozygous eQTLs. This was further corroborated by the major contribution of increased photosynthetic cell number to leaf area heterosis.
Collapse
Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Diqiu Ren
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Wenyi Yang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Miqi Xu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yi Zhang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xingwei Wang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| |
Collapse
|
17
|
Sun L, Cao Y, Li Z, Liu Y, Yin X, Deng XW, He H, Qian W. Conserved H3K27me3-associated chromatin looping mediates physical interactions of gene clusters in plants. J Integr Plant Biol 2023; 65:1966-1982. [PMID: 37154484 DOI: 10.1111/jipb.13502] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 04/26/2023] [Accepted: 05/06/2023] [Indexed: 05/10/2023]
Abstract
Higher-order chromatin organization is essential for transcriptional regulation, genome stability maintenance, and other genome functions. Increasing evidence has revealed significant differences in 3D chromatin organization between plants and animals. However, the extent, pattern, and rules of chromatin organization in plants are still unclear. In this study, we systematically identified and characterized long-range chromatin loops in the Arabidopsis 3D genome. We identified hundreds of long-range cis chromatin loops and found their anchor regions are closely associated with H3K27me3 epigenetic modifications. Furthermore, we demonstrated that these chromatin loops are dependent on Polycomb group (PcG) proteins, suggesting that the Polycomb repressive complex 2 (PRC2) complex is essential for establishing and maintaining these novel loops. Although most of these PcG-medicated chromatin loops are stable, many of these loops are tissue-specific or dynamically regulated by different treatments. Interestingly, tandemly arrayed gene clusters and metabolic gene clusters are enriched in anchor regions. Long-range H3K27me3-marked chromatin interactions are associated with the coregulation of specific gene clusters. Finally, we also identified H3K27me3-associated chromatin loops associated with gene clusters in Oryza sativa and Glycine max, indicating that these long-range chromatin loops are conserved in plants. Our results provide novel insights into genome evolution and transcriptional coregulation in plants.
Collapse
Affiliation(s)
- Linhua Sun
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Yuxin Cao
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Zhu Li
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Plant Science and Food Security, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Yi Liu
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xiaochang Yin
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| | - Weiqiang Qian
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, 261325, China
- School of Advanced Agriculture Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
18
|
Chai YF, Lin HB, Ding GH, Wang JW, Wang HY, Peng SY, Gao BX, Deng XW, Kong GL, Bao BY, Zhang LX. [Prevalence and treatment of anemia in chronic kidney disease patients based on regional medical big data]. Zhonghua Liu Xing Bing Xue Za Zhi 2023; 44:1046-1053. [PMID: 37482705 DOI: 10.3760/cma.j.cn112338-20221201-01028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Objective: To assess the prevalence, risk factors and treatment of anemia in patients with chronic kidney disease (CKD). Methods: A descriptive method was used to analyze the prevalence and treatment of anemia in CKD patients based on regional health data in Yinzhou District of Ningbo during 2012-2018. The multivariate logistic regression analysis was used to identify independent influence factors of anemia in the CKD patients. Results: In 52 619 CKD patients, 15 639 suffered from by anemia (29.72%), in whom 5 461 were men (26.41%) and 10 178 were women (31.87%), and anemia prevalence was higher in women than in men, the difference was significant (P<0.001). The prevalence of anemia increased with stage of CKD (24.77% in stage 1 vs. 69.42% in stage 5, trend χ2 test P<0.001). Multivariate logistic regression analysis revealed that being women (aOR=1.57, 95%CI: 1.50-1.63), CKD stage (stage 2: aOR=1.10, 95%CI: 1.04-1.16;stage 3: aOR=2.28,95%CI: 2.12-2.44;stage 4: aOR=4.49,95%CI :3.79-5.32;stage 5: aOR=6.31,95%CI: 4.74-8.39), age (18-30 years old: aOR=2.40,95%CI: 2.24-2.57, 61-75 years old: aOR=1.35,95%CI:1.28-1.42, ≥76 years old: aOR=2.37,95%CI:2.20-2.55), BMI (<18.5 kg/m2:aOR=1.29,95%CI: 1.18-1.41;23.0-24.9 kg/m2:aOR=0.79,95%CI: 0.75-0.83;≥25.0 kg/m2:aOR=0.70,95%CI: 0.66-0.74), abdominal obesity (aOR=0.91, 95%CI: 0.86-0.96), chronic obstructive pulmonary disease (aOR=1.15, 95%CI: 1.09-1.22), cancer (aOR=3.03, 95%CI: 2.84-3.23), heart failure (aOR=1.44, 95%CI: 1.35-1.54) and myocardial infarction (aOR=1.54, 95%CI:1.16-2.04) were independent risk factors of anemia in CKD patients. Among stage 3-5 CKD patients with anemia, 12.03% received iron therapy, and 4.78% received treatment with erythropoiesis-stimulating agent (ESA) within 12 months after anemia was diagnosed. Conclusions: The prevalence of anemia in CKD patients was high in Yinzhou. However, the treatment rate of iron therapy and ESA were low. More attention should be paid to the anemia management and treatment in CKD patients.
Collapse
Affiliation(s)
- Y F Chai
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China National Institute of Health Data Science, Peking University, Beijing 100191,China
| | - H B Lin
- Yinzhou District Center for Disease Control and Prevention of Ningbo, Ningbo 315199, China
| | - G H Ding
- School of Computer Science, Shenyang Aerospace University, Shenyang 110136, China
| | - J W Wang
- Department of Nephrology, Peking University First Hospital, Beijing 100034, China
| | - H Y Wang
- National Institute of Health Data Science, Peking University, Beijing 100191,China
| | - S Y Peng
- National Institute of Health Data Science, Peking University, Beijing 100191,China
| | - B X Gao
- Department of Nephrology, Peking University First Hospital, Beijing 100034, China
| | - X W Deng
- Department of Nephrology, Peking University First Hospital, Beijing 100034, China
| | - G L Kong
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China National Institute of Health Data Science, Peking University, Beijing 100191,China
| | - B Y Bao
- Ningbo Urology and Nephrology Hospital, Ningbo 315100, China
| | - L X Zhang
- National Institute of Health Data Science, Peking University, Beijing 100191,China Department of Nephrology, Peking University First Hospital, Beijing 100034, China
| |
Collapse
|
19
|
Yan W, Yuan S, Zu Y, Chang Z, Li Y, Chen Z, Xie G, Chen L, Lu C, Deng XW, Yang C, Xu C, Tang X. Ornithine δ-aminotransferase OsOAT is critical for male fertility and cold tolerance during rice plant development. Plant J 2023; 114:1301-1318. [PMID: 36932862 DOI: 10.1111/tpj.16194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/11/2023] [Indexed: 06/17/2023]
Abstract
Cold stress is a major factor limiting the production and geographical distribution of rice (Oryza sativa) varieties. However, the molecular mechanisms underlying cold tolerance remain to be elucidated. Here, we report that ornithine δ-aminotransferase (OsOAT) contributes to cold tolerance during the vegetative and reproductive development of rice. osoat mutant was identified as a temperature-sensitive male sterile mutant with deformed floral organs and seedlings sensitive to cold stress. Comparative transcriptome analysis showed that OsOAT mutation and cold treatment of the wild-type plant led to similar changes in the global gene expression profiles in anthers. OsOAT genes in indica rice Huanghuazhan (HHZ) and japonica rice Wuyungeng (WYG) are different in gene structure and response to cold. OsOAT is cold-inducible in WYG but cold-irresponsive in HHZ. Further studies showed that indica varieties carry both WYG-type and HHZ-type OsOAT, whereas japonica varieties mostly carry WYG-type OsOAT. Cultivars carrying HHZ-type OsOAT are mainly distributed in low-latitude regions, whereas varieties carrying WYG-type OsOAT are distributed in both low- and high-latitude regions. Moreover, indica varieties carrying WYG-type OsOAT generally have higher seed-setting rates than those carrying HHZ-type OsOAT under cold stress at reproductive stage, highlighting the favorable selection for WYG-type OsOAT during domestication and breeding to cope with low temperatures.
Collapse
Affiliation(s)
- Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Shuting Yuan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Yazhou Zu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Zhenyi Chang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Yiqi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Gang Xie
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Lei Chen
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Changqing Lu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Xing Wang Deng
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen, 518055, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| |
Collapse
|
20
|
Li J, Wang C, Liang W, Zhang J, Jiang CK, Liu Y, Ren Z, Ci D, Chang J, Han S, Deng XW, Wang Y, Qian W. Functional importance and divergence of plant apurinic/apyrimidinic endonucleases in somatic and meiotic DNA repair. Plant Cell 2023; 35:2316-2331. [PMID: 36856605 PMCID: PMC10226563 DOI: 10.1093/plcell/koad056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 01/31/2023] [Accepted: 02/05/2023] [Indexed: 05/30/2023]
Abstract
Apurinic/apyrimidinic (AP) sites are one of the most abundant DNA lesions and are mainly repaired by AP endonucleases (APEs). While most eukaryotic genomes encode two APEs, plants usually possess three APEs, namely APE1L, APE2, and ARP. To date, the biological relevance and functional divergence of plant APEs are unclear. Here, we show that the three plant APEs have ancient origins, with the APE1L clade being plant-specific. In Arabidopsis thaliana, simultaneously mutating APE1L and APE2, but not ARP alone or in combination with either APE1L or APE2, results in clear developmental defects linked to genotoxic stress. Genetic analyses indicated that the three plant APEs have different substrate preferences in vivo. ARP is mainly responsible for AP site repair, while APE1L and APE2 prefer to repair 3'-blocked single-stranded DNA breaks. We further determined that APEs play an important role in DNA repair and the maintenance of genomic integrity in meiotic cells. The ape1l ape2 double mutant exhibited a greatly enhanced frequency of sporulation 1 (SPO11-1)-dependent and SPO11-1-independent double-stranded DNA breaks. The DNA damage response (DDR) was activated in ape1l ape2 to trigger pollen abortion. Our findings suggest functional divergence of plant APEs and reveal important roles of plant APEs during vegetative and reproductive development.
Collapse
Affiliation(s)
- Jinchao Li
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Cong Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Wenjie Liang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Jun Zhang
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Chen-Kun Jiang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Yi Liu
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhitong Ren
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Dong Ci
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| | - Jinjie Chang
- School of Life Sciences, Peking University, Beijing 100871, China
| | - Shangling Han
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| | - Yingxiang Wang
- Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
- State Key Laboratory of Genetic Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Shandong 261000, China
| |
Collapse
|
21
|
Zhou H, Deng XW, He H. Gene expression variations and allele-specific expression of two rice and their hybrid in caryopses at single-nucleus resolution. Front Plant Sci 2023; 14:1171474. [PMID: 37287712 PMCID: PMC10242081 DOI: 10.3389/fpls.2023.1171474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 04/26/2023] [Indexed: 06/09/2023]
Abstract
Seeds are an indispensable part of the flowering plant life cycle and a critical determinant of agricultural production. Distinct differences in the anatomy and morphology of seeds separate monocots and dicots. Although some progress has been made with respect to understanding seed development in Arabidopsis, the transcriptomic features of monocotyledon seeds at the cellular level are much less understood. Since most important cereal crops, such as rice, maize, and wheat, are monocots, it is essential to study transcriptional differentiation and heterogeneity during seed development at a finer scale. Here, we present single-nucleus RNA sequencing (snRNA-seq) results of over three thousand nuclei from caryopses of the rice cultivars Nipponbare and 9311 and their intersubspecies F1 hybrid. A transcriptomics atlas that covers most of the cell types present during the early developmental stage of rice caryopses was successfully constructed. Additionally, novel specific marker genes were identified for each nuclear cluster in the rice caryopsis. Moreover, with a focus on rice endosperm, the differentiation trajectory of endosperm subclusters was reconstructed to reveal the developmental process. Allele-specific expression (ASE) profiling in endosperm revealed 345 genes with ASE (ASEGs). Further pairwise comparisons of the differentially expressed genes (DEGs) in each endosperm cluster among the three rice samples demonstrated transcriptional divergence. Our research reveals differentiation in rice caryopsis from the single-nucleus perspective and provides valuable resources to facilitate clarification of the molecular mechanism underlying caryopsis development in rice and other monocots.
Collapse
Affiliation(s)
- Han Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, China
| |
Collapse
|
22
|
Zhao Y, Shi H, Pan Y, Lyu M, Yang Z, Kou X, Deng XW, Zhong S. Sensory circuitry controls cytosolic calcium-mediated phytochrome B phototransduction. Cell 2023; 186:1230-1243.e14. [PMID: 36931246 DOI: 10.1016/j.cell.2023.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/23/2022] [Accepted: 02/03/2023] [Indexed: 03/18/2023]
Abstract
Although Ca2+ has long been recognized as an obligatory intermediate in visual transduction, its role in plant phototransduction remains elusive. Here, we report a Ca2+ signaling that controls photoreceptor phyB nuclear translocation in etiolated seedlings during dark-to-light transition. Red light stimulates acute cytosolic Ca2+ increases via phyB, which are sensed by Ca2+-binding protein kinases, CPK6 and CPK12 (CPK6/12). Upon Ca2+ activation, CPK6/12 in turn directly interact with and phosphorylate photo-activated phyB at Ser80/Ser106 to initiate phyB nuclear import. Non-phosphorylatable mutation, phyBS80A/S106A, abolishes nuclear translocation and fails to complement phyB mutant, which is fully restored by combining phyBS80A/S106A with a nuclear localization signal. We further show that CPK6/12 function specifically in the early phyB-mediated cotyledon expansion, while Ser80/Ser106 phosphorylation generally governs phyB nuclear translocation. Our results uncover a biochemical regulatory loop centered in phyB phototransduction and provide a paradigm for linking ubiquitous Ca2+ increases to specific responses in sensory stimulus processing.
Collapse
Affiliation(s)
- Yan Zhao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Hui Shi
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing 100048, China
| | - Ying Pan
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Mohan Lyu
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Zhixuan Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoxia Kou
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China
| | - Shangwei Zhong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang 261325, China.
| |
Collapse
|
23
|
Wang Y, Fan Y, Fan D, Zhou X, Jiao Y, Deng XW, Zhu D. The noncoding RNA HIDDEN TREASURE 1 promotes phytochrome B-dependent seed germination by repressing abscisic acid biosynthesis. Plant Cell 2023; 35:700-716. [PMID: 36423345 PMCID: PMC9940872 DOI: 10.1093/plcell/koac334] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
Light is a major environmental factor for seed germination. Red light-activated phytochrome B (phyB) promotes seed germination by modulating the dynamic balance of two phytohormones, gibberellic acid (GA) and abscisic acid (ABA). How phyB modulates ABA biosynthesis after perceiving a light signal is not yet well understood. Here, we identified the noncoding RNA HIDDEN TREASURE 1 (HID1) as a repressor of ABA biosynthesis acting downstream of phyB during Arabidopsis thaliana seed germination. Loss of HID1 function led to delayed phyB-dependent seed germination. Photoactivated phyB promoted the accumulation of HID1 in the radicle within 48 h of imbibition. Our transcriptomics analysis showed that HID1 and phyB co-regulate the transcription of a common set of genes involved in ABA and GA metabolism. Through a forward genetic screen, we identified three ABA biosynthesis genes, ABA DEFICIENT 1 (ABA1), ABA2, and ABA3, as suppressors of HID1. We further demonstrated that HID1 directly inhibits the transcription of 9-CIS-EPOXYCAROTENOID DIOXYGENASE (NCED9), a gene encoding a key rate-limiting enzyme of ABA biosynthesis. HID1 interacts with ARABIDOPSIS TRITHORAX-RELATED7 (ATXR7), an H3K4me3 methyltransferase, inhibiting its occupancy and H3K4me3 modification at the NCED9 locus. Our study reveals a nuclear mechanism of phyB signaling transmitted through HID1 to control the internal homeostasis of ABA and GA, which gradually optimizes the transcriptional network during seed germination.
Collapse
Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yangyang Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - De Fan
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Xiaoli Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuntong Jiao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
24
|
Han X, Zhang Y, Zhang Q, Ma N, Liu X, Tao W, Lou Z, Zhong C, Deng XW, Li D, He H. Two haplotype-resolved, gap-free genome assemblies for Actinidia latifolia and Actinidia chinensis shed light on the regulatory mechanisms of vitamin C and sucrose metabolism in kiwifruit. Mol Plant 2023; 16:452-470. [PMID: 36588343 DOI: 10.1016/j.molp.2022.12.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/29/2022] [Accepted: 12/30/2022] [Indexed: 06/17/2023]
Abstract
Kiwifruit is a recently domesticated horticultural fruit crop with substantial economic and nutritional value, especially because of the high content of vitamin C in its fruit. In this study, we de novo assembled two telomere-to-telomere kiwifruit genomes from Actinidia chinensis var. 'Donghong' (DH) and Actinidia latifolia 'Kuoye' (KY), with total lengths of 608 327 852 and 640 561 626 bp for 29 chromosomes, respectively. With a burst of structural variants involving inversion, translocations, and duplications within 8.39 million years, the metabolite content of DH and KY exhibited differences in saccharides, lignans, and vitamins. A regulatory ERF098 transcription factor family has expanded in KY and Actinidia eriantha, both of which have ultra-high vitamin C content. With each assembly phased into two complete haplotypes, we identified allelic variations between two sets of haplotypes, leading to protein sequence variations in 26 494 and 27 773 gene loci and allele-specific expression of 4687 and 12 238 homozygous gene pairs. Synchronized metabolome and transcriptome changes during DH fruit development revealed the same dynamic patterns in expression levels and metabolite contents; free fatty acids and flavonols accumulated in the early stages, but sugar substances and amino acids accumulated in the late stages. The AcSWEET9b gene that exhibits allelic dominance was further identified to positively correlate with high sucrose content in fruit. Compared with wild varieties and other Actinidia species, AcSWEET9b promoters were selected in red-flesh kiwifruits that have increased fruit sucrose content, providing a possible explanation on why red-flesh kiwifruits are sweeter. Collectively, these two gap-free kiwifruit genomes provide a valuable genetic resource for investigating domestication mechanisms and genome-based breeding of kiwifruit.
Collapse
Affiliation(s)
- Xue Han
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Yilin Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Ni Ma
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaoying Liu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Wenjing Tao
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen 361102, China
| | - Zhiying Lou
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China
| | - Caihong Zhong
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China.
| | - Dawei Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, The Chinese Academy of Sciences, Wuhan, Hubei 430074, China.
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong 261325, China; School of Advanced Agricultural Sciences and School of Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
25
|
Wang J, Sun N, Zheng L, Zhang F, Xiang M, Chen H, Deng XW, Wei N. Brassinosteroids promote etiolated apical structures in darkness by amplifying the ethylene response via the EBF-EIN3/PIF3 circuit. Plant Cell 2023; 35:390-408. [PMID: 36321994 PMCID: PMC9806594 DOI: 10.1093/plcell/koac316] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Germinated plants grow in darkness until they emerge above the soil. To help the seedling penetrate the soil, most dicot seedlings develop an etiolated apical structure consisting of an apical hook and folded, unexpanded cotyledons atop a rapidly elongating hypocotyl. Brassinosteroids (BRs) are necessary for etiolated apical development, but their precise role and mechanisms remain unclear. Arabidopsis thaliana SMALL AUXIN UP RNA17 (SAUR17) is an apical-organ-specific regulator that promotes production of an apical hook and closed cotyledons. In darkness, ethylene and BRs stimulate SAUR17 expression by transcription factor complexes containing PHYTOCHROME-INTERACTING FACTORs (PIFs), ETHYLENE INSENSITIVE 3 (EIN3), and its homolog EIN3-LIKE 1 (EIL1), and BRASSINAZOLE RESISTANT1 (BZR1). BZR1 requires EIN3 and PIFs for enhanced DNA-binding and transcriptional activation of the SAUR17 promoter; while EIN3, PIF3, and PIF4 stability depends on BR signaling. BZR1 transcriptionally downregulates EIN3-BINDING F-BOX 1 and 2 (EBF1 and EBF2), which encode ubiquitin ligases mediating EIN3 and PIF3 protein degradation. By modulating the EBF-EIN3/PIF protein-stability circuit, BRs induce EIN3 and PIF3 accumulation, which underlies BR-responsive expression of SAUR17 and HOOKLESS1 and ultimately apical hook development. We suggest that in the etiolated development of apical structures, BRs primarily modulate plant sensitivity to darkness and ethylene.
Collapse
Affiliation(s)
- Jiajun Wang
- School of Life Sciences, Southwest University, Chongqing 400715, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Ning Sun
- Key Laboratory of Growth Regulation and Transformation Research of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou 310024, China
| | - Lidan Zheng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Fangfang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Mengda Xiang
- School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and Life Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
26
|
Wang Y, Deng XW, Zhu D. From molecular basics to agronomic benefits: Insights into noncoding RNA-mediated gene regulation in plants. J Integr Plant Biol 2022; 64:2290-2308. [PMID: 36453685 DOI: 10.1111/jipb.13420] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 11/30/2022] [Indexed: 06/17/2023]
Abstract
The development of plants is largely dependent on their growth environment. To better adapt to a particular habitat, plants have evolved various subtle regulatory mechanisms for altering gene expression. Non coding RNAs (ncRNAs) constitute a major portion of the transcriptomes of eukaryotes. Various ncRNAs have been recognized as important regulators of the expression of genes involved in essential biological processes throughout the whole life cycles of plants. In this review, we summarize the current understanding of the biogenesis and contributions of small nucle olar RNA (snoRNA)- and regulatory long non coding RNA (lncRNA)-mediated gene regulation in plant development and environmental responses. Many regulatory ncRNAs appear to be associated with increased yield, quality and disease resistance of various species and cultivars. These ncRNAs may potentially be used as genetic resources for improving agronomic traits and for molecular breeding. The challenges in understanding plant ncRNA biology and the possibilities to make better use of these valuable gene resources in the future are discussed in this review.
Collapse
Affiliation(s)
- Yuqiu Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
- Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Peking University Institute of Advanced Agricultural Sciences, Weifang, 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
27
|
Lan H, Heng Y, Li J, Zhang M, Bian Y, Chu L, Jiang Y, Wang X, Xu D, Deng XW. COP1 SUPPRESSOR 6 represses the PIF4 and PIF5 action to promote light-inhibited hypocotyl growth. J Integr Plant Biol 2022; 64:2097-2110. [PMID: 36029156 DOI: 10.1111/jipb.13350] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 08/26/2022] [Indexed: 06/15/2023]
Abstract
Light signaling precisely controls photomorphogenic development in plants. PHYTOCHROME INTERACTING FACTOR 4 and 5 (PIF4 and PIF5) play critical roles in the regulation of this developmental process. In this study, we report CONSTITUTIVELY PHOTOMORPHOGENIC 1 SUPPRESSOR 6 (CSU6) functions as a key regulator of light signaling. Loss of CSU6 function largely rescues the cop1-6 constitutively photomorphogenic phenotype. CSU6 promotes hypocotyl growth in the dark, but inhibits hypocotyl elongation in the light. CSU6 not only associates with the promoter regions of PIF4 and PIF5 to inhibit their expression in the morning, but also directly interacts with both PIF4 and PIF5 to repress their transcriptional activation activity. CSU6 negatively controls a group of PIF4- and PIF5-regulated gene expressions. Mutations in PIF4 and/or PIF5 are epistatic to the loss of CSU6, suggesting that CSU6 acts upstream of PIF4 and PIF5. Taken together, CSU6 promotes light-inhibited hypocotyl elongation by negatively regulating PIF4 and PIF5 transcription and biochemical activity.
Collapse
Affiliation(s)
- Hongxia Lan
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yueqin Heng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Mengdi Zhang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Li Chu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Sciences, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| |
Collapse
|
28
|
Cao Y, Wang J, Wu S, Yin X, Shu J, Dai X, Liu Y, Sun L, Zhu D, Deng XW, Ye K, Qian W. The small nucleolar RNA SnoR28 regulates plant growth and development by directing rRNA maturation. Plant Cell 2022; 34:4173-4190. [PMID: 36005862 PMCID: PMC9614442 DOI: 10.1093/plcell/koac265] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Small nucleolar RNAs (snoRNAs) are noncoding RNAs (ncRNAs) that guide chemical modifications of structural RNAs, which are essential for ribosome assembly and function in eukaryotes. Although numerous snoRNAs have been identified in plants by high-throughput sequencing, the biological functions of most of these snoRNAs remain unclear. Here, we identified box C/D SnoR28.1s as important regulators of plant growth and development by screening a CRISPR/Cas9-generated ncRNA deletion mutant library in Arabidopsis thaliana. Deletion of the SnoR28.1 locus, which contains a cluster of three genes producing SnoR28.1s, resulted in defects in root and shoot growth. SnoR28.1s guide 2'-O-ribose methylation of 25S rRNA at G2396. SnoR28.1s facilitate proper and efficient pre-rRNA processing, as the SnoR28.1 deletion mutants also showed impaired ribosome assembly and function, which may account for the growth defects. SnoR28 contains a 7-bp antisense box, which is required for 2'-O-ribose methylation of 25S rRNA at G2396, and an 8-bp extra box that is complementary to a nearby rRNA methylation site and is partially responsible for methylation of G2396. Both of these motifs are required for proper and efficient pre-rRNA processing. Finally, we show that SnoR28.1s genetically interact with HIDDEN TREASURE2 and NUCLEOLIN1. Our results advance our understanding of the roles of snoRNAs in Arabidopsis.
Collapse
Affiliation(s)
- Yuxin Cao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jiayin Wang
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Songlin Wu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jia Shu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Dai
- Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha 410128, China
| | - Yannan Liu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiqiang Qian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China
| |
Collapse
|
29
|
Xu M, Wang X, Liu J, Jia A, Xu C, Deng XW, He G. Natural variation in the transcription factor REPLUMLESS contributes to both disease resistance and plant growth in Arabidopsis. Plant Commun 2022; 3:100351. [PMID: 35752937 PMCID: PMC9483108 DOI: 10.1016/j.xplc.2022.100351] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 06/06/2022] [Accepted: 06/21/2022] [Indexed: 05/05/2023]
Abstract
When attacked by pathogens, plants need to reallocate energy from growth to defense to fend off the invaders, frequently incurring growth penalties. This phenomenon is known as the growth-defense tradeoff and is orchestrated by a hardwired transcriptional network. Altering key factors involved in this network has the potential to increase disease resistance without growth or yield loss, but the mechanisms underlying such changes require further investigation. By conducting a genome-wide association study (GWAS) of leaves infected by the hemi-biotrophic bacterial pathogen Pseudomonas syringae pv. tomato (Pst) DC3000, we discovered that the Arabidopsis transcription factor REPLUMLESS (RPL) is necessary for bacterial resistance. More importantly, RPL functions in promoting both disease resistance and growth. Transcriptome analysis revealed a cluster of genes in the GRETCHEN HAGEN 3 (GH3) family that were significantly upregulated in rpl mutants, leading to the accumulation of indole-3-acetic acid-aspartic acid (IAA-Asp). Consistent with this observation, transcripts of virulence effector genes were activated by IAA-Asp accumulated in the rpl mutants. We found that RPL protein could directly bind to GH3 promoters and repress their expression. RPL also repressed flavonol synthesis by directly repressing CHI expression and thus activated the auxin transport pathway, which promotes plant growth. Therefore, RPL plays an important role in plant immunity and functions in the auxin pathway to optimize Arabidopsis growth and defense.
Collapse
Affiliation(s)
- Miqi Xu
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xuncheng Wang
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jing Liu
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Aolin Jia
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Chao Xu
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| | - Guangming He
- School of Life Sciences and School of Advanced Agricultural Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China.
| |
Collapse
|
30
|
Zhang Y, Fu J, Wang K, Han X, Yan T, Su Y, Li Y, Lin Z, Qin P, Fu C, Deng XW, Zhou D, Yang Y, He H. The telomere-to-telomere gap-free genome of four rice parents reveals SV and PAV patterns in hybrid rice breeding. Plant Biotechnol J 2022; 20:1642-1644. [PMID: 35748695 PMCID: PMC9398309 DOI: 10.1111/pbi.13880] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 06/19/2022] [Indexed: 05/02/2023]
Affiliation(s)
- Yilin Zhang
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
- Peking University Institute of Advanced Agricultural SciencesShandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangChina
| | - Jun Fu
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
| | - Kai Wang
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterChangshaChina
- College of Plant Science & TechnologyHuazhong Agricultural UniversityWuhanChina
| | - Xue Han
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
- Peking University Institute of Advanced Agricultural SciencesShandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangChina
| | - Tianze Yan
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
| | - Yanning Su
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
| | - Yanfeng Li
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
| | - Peng Qin
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
| | - Chenjian Fu
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
- Peking University Institute of Advanced Agricultural SciencesShandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangChina
| | - Degui Zhou
- Guangdong Key Laboratory of New Technology in Rice BreedingRice Research Institute, Guangdong Academy of Agricultural SciencesGuangzhouChina
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of Life SciencesSouth China Agricultural UniversityGuangzhouChina
| | - Yuanzhu Yang
- Peking University Institute of Advanced Agricultural SciencesShandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangChina
- Key Laboratory of Southern Rice Innovation & Improvement, Ministry of Agriculture and Rural Affairs, Hunan Engineering Laboratory of Disease and Pest Resistant Rice BreedingYuan Longping High‐Tech Agriculture Co., Ltd.ChangshaChina
- State Key Laboratory of Hybrid RiceHunan Hybrid Rice Research CenterChangshaChina
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene ResearchPeking UniversityBeijingChina
- Peking University Institute of Advanced Agricultural SciencesShandong Laboratory of Advanced Agricultural Sciences at WeifangWeifangChina
| |
Collapse
|
31
|
Deng Y, Liu S, Zhang Y, Tan J, Li X, Chu X, Xu B, Tian Y, Sun Y, Li B, Xu Y, Deng XW, He H, Zhang X. A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding. Mol Plant 2022; 15:1268-1284. [PMID: 35746868 DOI: 10.1016/j.molp.2022.06.010] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 05/30/2022] [Accepted: 06/19/2022] [Indexed: 06/15/2023]
Abstract
Watermelon, Citrullus lanatus, is the world's third largest fruit crop. Reference genomes with gaps and a narrow genetic base hinder functional genomics and genetic improvement of watermelon. Here, we report the assembly of a telomere-to-telomere gap-free genome of the elite watermelon inbred line G42 by incorporating high-coverage and accurate long-read sequencing data with multiple assembly strategies. All 11 chromosomes have been assembled into single-contig pseudomolecules without gaps, representing the highest completeness and assembly quality to date. The G42 reference genome is 369 321 829 bp in length and contains 24 205 predicted protein-coding genes, with all 22 telomeres and 11 centromeres characterized. Furthermore, we established a pollen-EMS mutagenesis protocol and obtained over 200 000 M1 seeds from G42 . In a sampling pool, 48 monogenic phenotypic mutations, selected from 223 M1 and 78 M2 mutants with morphological changes, were confirmed. The average mutation density was 1 SNP/1.69 Mb and 1 indel/4.55 Mb per M1 plant and 1 SNP/1.08 Mb and 1 indel/6.25 Mb per M2 plant. Taking advantage of the gap-free G42 genome, 8039 mutations from 32 plants sampled from M1 and M2 families were identified with 100% accuracy, whereas only 25% of the randomly selected mutations identified using the 97103v2 reference genome could be confirmed. Using this library and the gap-free genome, two genes responsible for elongated fruit shape and male sterility (ClMS1) were identified, both caused by a single base change from G to A. The validated gap-free genome and its EMS mutation library provide invaluable resources for functional genomics and genetic improvement of watermelon.
Collapse
Affiliation(s)
- Yun Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Shoucheng Liu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yilin Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Jingsheng Tan
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiaopeng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xiao Chu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Binghua Xu
- Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science, Huaian, Jiangsu 223300, China
| | - Yao Tian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yudong Sun
- Jiangsu Xuhuai Area Huaiyin Institute of Agricultural Science, Huaian, Jiangsu 223300, China
| | - Bosheng Li
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Yunbi Xu
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China
| | - Xing Wang Deng
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China; School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China.
| | - Xingping Zhang
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences at Weifang, Weifang, Shandong 261000, China.
| |
Collapse
|
32
|
Irigoyen ML, Iniesto E, Rodriguez L, Puga MI, Yanagawa Y, Pick E, Strickland E, Paz-Ares J, Wei N, De Jaeger G, Rodriguez PL, Deng XW, Rubio V. Correction to: Targeted Degradation of Abscisic Acid Receptors Is Mediated by the Ubiquitin Ligase Substrate Adaptor DDA1 in Arabidopsis. Plant Cell 2022; 34:2807-2808. [PMID: 35348775 PMCID: PMC9252497 DOI: 10.1093/plcell/koac102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Accepted: 03/23/2022] [Indexed: 06/14/2023]
|
33
|
Zhou H, Zhu W, Wang X, Bian Y, Jiang Y, Li J, Wang L, Yin P, Deng XW, Xu D. A missense mutation in WRKY32 converts its function from a positive regulator to a repressor of photomorphogenesis. New Phytol 2022; 233:373-389. [PMID: 34935148 DOI: 10.1111/nph.17618] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/05/2021] [Indexed: 05/21/2023]
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mediates various cellular and physiological processes in plants by targeting a large number of substrates for ubiquitination and degradation. In this study, we reveal that a substitution of Pro for Leu at amino acid position 409 in WRKY32 largely suppresses the short hypocotyls and expanded cotyledon phenotypes of cop1-6. WRKY32P409L promotes hypocotyl growth and inhibits the opening of cotyledons in Arabidopsis. Loss of WRKY32 function mutant seedlings display elongated hypocotyls, whereas overexpression of WRKY32 leads to shortened hypocotyls. WRKY32 directly associates with the promoter regions of HY5 to activate its transcription. COP1 interacts with and targets WRKY32 for ubiquitination and degradation in darkness. WRKY32P409L exhibits enhanced DNA binding ability and affects the expression of more genes compared with WRKY32 in Arabidopsis. Our results not only reveal the basic role for WRKY32 in promoting photomorphogenesis, but also provide insights into manipulating plant growth by engineering key components of light signaling.
Collapse
Affiliation(s)
- Hua Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
34
|
Zhou H, Zhu W, Wang X, Bian Y, Jiang Y, Li J, Wang L, Yin P, Deng XW, Xu D. A missense mutation in WRKY32 converts its function from a positive regulator to a repressor of photomorphogenesis. New Phytol 2022; 235:111-125. [PMID: 34935148 DOI: 10.1111/nph.17932] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 12/08/2021] [Indexed: 06/14/2023]
Abstract
CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) mediates various cellular and physiological processes in plants by targeting a large number of substrates for ubiquitination and degradation. In this study, we reveal that a substitution of Pro for Leu at amino acid position 409 in WRKY32 largely suppresses the short hypocotyls and expanded cotyledon phenotypes of cop1-6. WRKY32P409L promotes hypocotyl growth and inhibits the opening of cotyledons in Arabidopsis. Loss of WRKY32 function mutant seedlings display elongated hypocotyls, whereas overexpression of WRKY32 leads to shortened hypocotyls. WRKY32 directly associates with the promoter regions of HY5 to activate its transcription. COP1 interacts with and targets WRKY32 for ubiquitination and degradation in darkness. WRKY32P409L exhibits enhanced DNA binding ability and affects the expression of more genes compared with WRKY32 in Arabidopsis. Our results not only reveal the basic role for WRKY32 in promoting photomorphogenesis, but also provide insights into manipulating plant growth by engineering key components of light signaling.
Collapse
Affiliation(s)
- Hua Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Wei Zhu
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environment Friendly Management on Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100097, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yan Jiang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|
35
|
Cui Y, Bian J, Lv Y, Li J, Deng XW, Liu X. Analysis of the Transcriptional Dynamics of Regulatory Genes During Peanut Pod Development Caused by Darkness and Mechanical Stress. Front Plant Sci 2022; 13:904162. [PMID: 35693161 PMCID: PMC9178256 DOI: 10.3389/fpls.2022.904162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 04/26/2022] [Indexed: 06/15/2023]
Abstract
Peanut is an oil crop with important economic value that is widely cultivated around the world. It blooms on the ground but bears fruit underground. When the peg penetrates the ground, it enters a dark environment, is subjected to mechanical stress from the soil, and develops into a normal pod. When a newly developed pod emerges from the soil, it turns green and stops growing. It has been reported that both darkness and mechanical stress are necessary for normal pod development. In this study, we investigated changes in gene expression during the reverse process of peg penetration: developmental arrest caused by pod (Pattee 3 pods) excavation. Bagging the aerial pods was used to simulate loss of mechanical pressure, while direct exposure of the aerial pods was used to simulate loss of both mechanical pressure and darkness. After the loss of mechanical stress and darkness, the DEGs were significantly enriched in photosynthesis, photosynthesis-antenna proteins, plant-pathogen interaction, DNA replication, and circadian rhythm pathways. The DNA replication pathway was enriched by down-regulated genes, and the other four pathways were enriched by upregulated genes. Upregulated genes were also significantly enriched in protein ubiquitination and calmodulin-related genes, highlighting the important role of ubiquitination and calcium signaling in pod development. Further analysis of DEGs showed that phytochrome A (Phy A), auxin response factor 9 (IAA9), and mechanosensitive ion channel protein played important roles in geocarpy. The expression of these two genes increased in subterranean pods but decreased in aerial pods. Based on a large number of chloroplast-related genes, calmodulin, kinases, and ubiquitin-related proteins identified in this study, we propose two possible signal transduction pathways involved in peanut geocarpy, namely, one begins in chloroplasts and signals down through phosphorylation, and the other begins during abiotic stress and signals down through calcium signaling, phosphorylation, and ubiquitination. Our study provides valuable information about putative regulatory genes for peanut pod development and contributes to a better understanding of the biological phenomenon of geocarpy.
Collapse
Affiliation(s)
- Yuanyuan Cui
- Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Jianxin Bian
- Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China
| | - Yuying Lv
- Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China
| | - Jihua Li
- Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China
| | - Xing Wang Deng
- Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China
- School of Advanced Agricultural Sciences, Peking University, Beijing, China
| | - Xiaoqin Liu
- Shandong Laboratory for Advanced Agricultural Sciences at Weifang, Peking University Institute of Advanced Agricultural Science, Weifang, China
| |
Collapse
|
36
|
Cao J, Liang Y, Yan T, Wang X, Zhou H, Chen C, Zhang Y, Zhang B, Zhang S, Liao J, Cheng S, Chu J, Huang X, Xu D, Li J, Deng XW, Lin F. The photomorphogenic repressors BBX28 and BBX29 integrate light and brassinosteroid signaling to inhibit seedling development in Arabidopsis. Plant Cell 2022; 34:2266-2285. [PMID: 35294019 PMCID: PMC9134050 DOI: 10.1093/plcell/koac092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/27/2022] [Indexed: 05/20/2023]
Abstract
B-box containing proteins (BBXs) integrate light and various hormonal signals to regulate plant growth and development. Here, we demonstrate that the photomorphogenic repressors BBX28 and BBX29 positively regulate brassinosteroid (BR) signaling in Arabidopsis thaliana seedlings. Treatment with the BR brassinolide stabilized BBX28 and BBX29, which partially depended on BR INSENSITIVE1 (BRI1) and BIN2. bbx28 bbx29 seedlings exhibited larger cotyledon aperture than the wild-type when treated with brassinazole in the dark, which partially suppressed the closed cotyledons of brassinazole resistant 1-1D (bzr1-1D). Consistently, overexpressing BBX28 and BBX29 partially rescued the short hypocotyls of bri1-5 and bin2-1 in both the dark and light, while the loss-of-function of BBX28 and BBX29 partially suppressed the long hypocotyls of bzr1-1D in the light. BBX28 and BBX29 physically interacted with BR-ENHANCED EXPRESSION1 (BEE1), BEE2, and BEE3 and enhanced their binding to and activation of their target genes. Moreover, BBX28 and BBX29 as well as BEE1, BEE2, and BEE3 increased BZR1 accumulation to promote the BR signaling pathway. Therefore, both BBX28 and BBX29 interact with BEE1, BEE2, and BEE3 to orchestrate light and BR signaling by facilitating the transcriptional activity of BEE target genes. Our study provides insights into the pivotal roles of BBX28 and BBX29 as signal integrators in ensuring normal seedling development.
Collapse
Affiliation(s)
| | | | | | - Xuncheng Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Hua Zhou
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chen Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingli Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Beihong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shuhao Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Juncheng Liao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shujing Cheng
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xing Wang Deng
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | | |
Collapse
|
37
|
Cui D, Zhou H, Ma X, Lin Z, Sun L, Han B, Li M, Sun J, Liu J, Jin G, Wang X, Cao G, Deng XW, He H, Han L. Genomic insights on the contribution of introgressions from Xian/Indica to the genetic improvement of Geng/Japonica rice cultivars. Plant Commun 2022; 3:100325. [PMID: 35576158 PMCID: PMC9251437 DOI: 10.1016/j.xplc.2022.100325] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/12/2022] [Accepted: 04/09/2022] [Indexed: 06/15/2023]
Abstract
Hybridization between Xian/indica (XI) and Geng/japonica (GJ) rice combined with utilization of plant ideotypes has greatly contributed to yield improvements in modern GJ rice in China over the past 50 years. To explore the genomic basis of improved yield and disease resistance in GJ rice, we conducted a large-scale genomic landscape analysis of 816 elite GJ cultivars representing multiple eras of germplasm from China. We detected consistently increasing introgressions from three XI subpopulations into GJ cultivars since the 1980s and found that the XI genome introgressions significantly increased the grain number per panicle (GN) and decreased the panicle number per plant. This contributed to the improvement of plant type during modern breeding, changing multi-tiller plants to moderate tiller plants with a large panicle size and increasing the blast resistance. Notably, we found that key gene haplotypes controlling plant architecture, yield components, and pest and disease resistance, including IPA1, SMG1, DEP3, Pib, Pi-d2, and Bph3, were introduced from XI rice by introgression. By GWAS analysis, we detected a GN-related gene Gnd5, which had been consistently introgressed from XI into GJ cultivars since the 1980s. Gnd5 is a GRAS transcription factor gene, and Gnd5 knockout mutants showed a significant reduction in GN. The estimated genetic effects of genes varied among different breeding locations, which explained the distinct introgression levels of XI gene haplotypes, including Gnd5, DEP3, etc., to these GJ breeding pedigrees. These findings reveal the genomic contributions of introgressions from XI to the trait improvements of GJ rice cultivars and provide new insights for future rice genomic breeding.
Collapse
Affiliation(s)
- Di Cui
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Han Zhou
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Xiaoding Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zechuan Lin
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Linhua Sun
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Bing Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Maomao Li
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jianchang Sun
- Institute of Crop Research, Ningxia Academy of Agricultural and Forestry Sciences, Yongning 750105, China
| | - Jin Liu
- Rice Research Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Guixiu Jin
- Rice Research Institute, Linyi Academy of Agricultural Sciences, Shandong Linyi 276012, China
| | - Xianju Wang
- Rice Research Institute of Liaoning Province, Shenyang 110161, China
| | - Guilan Cao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xing Wang Deng
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China
| | - Hang He
- School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong, 261325, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| |
Collapse
|
38
|
Wang Y, Wang L, Guan Z, Chang H, Ma L, Shen C, Qiu L, Yan J, Zhang D, Li J, Deng XW, Yin P. Structural insight into UV-B-activated UVR8 bound to COP1. Sci Adv 2022; 8:eabn3337. [PMID: 35442727 PMCID: PMC9020657 DOI: 10.1126/sciadv.abn3337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
The CONSTITUTIVE PHOTOMORPHOGENIC 1-SUPPRESSOR OF PHYA-105 (COP1-SPA) complex is a central repressor of photomorphogenesis. This complex acts as an E3 ubiquitin ligase downstream of various light signaling transduced from multiple photoreceptors in plants. How the COP1-SPA activity is regulated by divergent light-signaling pathways remains largely elusive. Here, we reproduced the regulation pathway of COP1-SPA in ultraviolet-B (UV-B) signaling in vitro and determined the cryo-electron microscopy structure of UV-B receptor UVR8 in complex with COP1. The complex formation is mediated by two-interface interactions between UV-B-activated UVR8 and COP1. Both interfaces are essential for the competitive binding of UVR8 against the signaling hub component HY5 to the COP1-SPA complex. We also show that RUP2 dissociates UVR8 from the COP1-SPA41-464-UVR8 complex and facilitates its redimerization. Our results support a UV-B signaling model that the COP1-SPA activity is repressed by UV-B-activated UVR8 and derepressed by RUP2, owing to competitive binding, and provide a framework for studying the regulatory roles of distinct photoreceptors on photomorphogenesis.
Collapse
Affiliation(s)
- Yidong Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Lixia Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Zeyuan Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Hongfei Chang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Ling Ma
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Cuicui Shen
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Liang Qiu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Junjie Yan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Delin Zhang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Science, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Ping Yin
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
39
|
Liu W, Zhang Y, He H, He G, Deng XW. From hybrid genomes to heterotic trait output: Challenges and opportunities. Curr Opin Plant Biol 2022; 66:102193. [PMID: 35219140 DOI: 10.1016/j.pbi.2022.102193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/19/2021] [Accepted: 01/23/2022] [Indexed: 06/14/2023]
Abstract
Heterosis (or hybrid vigor) has been widely used in crop seed breeding to improve many key economic traits. Nevertheless, the genetic and molecular basis of this important phenomenon has long remained elusive, constraining its flexible and effective exploitation. Advanced genomic approaches are efficient in characterizing the mechanism of heterosis. Here, we review how the omics approaches, including genomic, transcriptomic, and population genetics methods such as genome-wide association studies, can reveal how hybrid genomes outperform parental genomes in plants. This information opens up opportunities for genomic exploration and manipulation of heterosis in crop breeding.
Collapse
Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yilin Zhang
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Hang He
- Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China.
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, China; Peking University Institute of Advanced Agricultural Sciences, 699 Binhu Road, Xiashan Ecological and Economic Development Zone, Weifang, Shandong, 261325, China.
| |
Collapse
|
40
|
Yan T, Heng Y, Wang W, Li J, Deng XW. SWELLMAP 2, a phyB-Interacting Splicing Factor, Negatively Regulates Seedling Photomorphogenesis in Arabidopsis. Front Plant Sci 2022; 13:836519. [PMID: 35222493 PMCID: PMC8867171 DOI: 10.3389/fpls.2022.836519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Light-triggered transcriptome reprogramming is critical for promoting photomorphogenesis in Arabidopsis seedlings. Nonetheless, recent studies have shed light on the importance of alternative pre-mRNA splicing (AS) in photomorphogenesis. The splicing factors splicing factor for phytochrome signaling (SFPS) and reduced red-light responses in cry1cry2 background1 (RRC1) are involved in the phytochrome B (phyB) signaling pathway and promote photomorphogenesis by controlling pre-mRNA splicing of light- and clock-related genes. However, splicing factors that serve as repressors in phyB signaling pathway remain unreported. Here, we report that the splicing factor SWELLMAP 2 (SMP2) suppresses photomorphogenesis in the light. SMP2 physically interacts with phyB and colocalizes with phyB in photobodies after light exposure. Genetic analyses show that SMP2 antagonizes phyB signaling to promote hypocotyl elongation in the light. The homologs of SMP2 in yeast and human belong to second-step splicing factors required for proper selection of the 3' splice site (3'SS) of an intron. Notably, SMP2 reduces the abundance of the functional REVEILLE 8 a (RVE8a) form, probably by determining the 3'SS, and thereby inhibits RVE8-mediated transcriptional activation of clock genes containing evening elements (EE). Finally, SMP2-mediated reduction of functional RVE8 isoform promotes phytochrome interacting factor 4 (PIF4) expression to fine-tune hypocotyl elongation in the light. Taken together, our data unveil a phyB-interacting splicing factor that negatively regulates photomorphogenesis, providing additional information for further mechanistic investigations regarding phyB-controlled AS of light- and clock-related genes.
Collapse
Affiliation(s)
- Tingting Yan
- Harbin Institute of Technology, Harbin, China
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Yueqin Heng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Wenwei Wang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Jian Li
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Xing Wang Deng
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Institute of Plant and Food Sciences, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences and School of Life Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| |
Collapse
|
41
|
Hao C, Yang Y, Du J, Deng XW, Li L. The PCY-SAG14 phytocyanin module regulated by PIFs and miR408 promotes dark-induced leaf senescence in Arabidopsis. Proc Natl Acad Sci U S A 2022; 119:e2116623119. [PMID: 35022242 PMCID: PMC8784109 DOI: 10.1073/pnas.2116623119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 12/08/2021] [Indexed: 11/21/2022] Open
Abstract
Leaf senescence is a critical process in plants and has a direct impact on many important agronomic traits. Despite decades of research on senescence-altered mutants via forward genetics and functional assessment of senescence-associated genes (SAGs) via reverse genetics, the senescence signal and the molecular mechanism that perceives and transduces the signal remain elusive. Here, using dark-induced senescence (DIS) of Arabidopsis leaf as the experimental system, we show that exogenous copper induces the senescence syndrome and transcriptomic changes in light-grown plants parallel to those in DIS. By profiling the transcriptomes and tracking the subcellular copper distribution, we found that reciprocal regulation of plastocyanin, the thylakoid lumen mobile electron carrier in the Z scheme of photosynthetic electron transport, and SAG14 and plantacyanin (PCY), a pair of interacting small blue copper proteins located on the endomembrane, is a common thread in different leaf senescence scenarios, including DIS. Genetic and molecular experiments confirmed that the PCY-SAG14 module is necessary and sufficient for promoting DIS. We also found that the PCY-SAG14 module is repressed by a conserved microRNA, miR408, which in turn is repressed by phytochrome interacting factor 3/4/5 (PIF3/4/5), the key trio of transcription factors promoting DIS. Together, these findings indicate that intracellular copper redistribution mediated by PCY-SAG14 has a regulatory role in DIS. Further deciphering the copper homeostasis mechanism and its interaction with other senescence-regulating pathways should provide insights into our understanding of the fundamental question of how plants age.
Collapse
Affiliation(s)
- Chen Hao
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China
| | - Yanzhi Yang
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
| | - Jianmei Du
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China;
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Lei Li
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China;
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| |
Collapse
|
42
|
Wu J, Qiu S, Wang M, Xu C, Deng XW, Tang X. Construction of a weight-based seed sorting system for the third-generation hybrid rice. Rice (N Y) 2021; 14:66. [PMID: 34255233 PMCID: PMC8276899 DOI: 10.1186/s12284-021-00510-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The third-generation hybrid rice technology can be constructed by transforming a recessive nuclear male sterile (NMS) mutant with a transgenic cassette containing three functional modules: the wild type male fertility gene to restore the fertility of the mutant, the pollen killer gene that specifically kills the pollen grains carrying the transgene, and the red fluorescence protein (RFP) gene to mark the transgenic seed (maintainer). The transgenic plant produces 1:1 NMS seeds and maintainer seeds that can be distinguished by the RFP signal. However, the RFP signals in the partially filled or pathogen-infected maintainer seeds are often too weak to be detected by RFP-based seed sorting machine, resulting in intermingling of the maintainer seeds with NMS seeds. RESULTS Here we constructed a weight-based seed sorting system for the third-generation hybrid rice technology by silencing the genes encoding ADP-glucose pyrophosphorylase (AGP) essential for endosperm starch biosynthesis via endosperm-specific expression of artificial microRNAs (amiRNAs). In this system, the NMS seeds have normal endosperm and are heavy, but the maintainer seeds have shrunken endosperms and are light-weighted. The maintainer seeds can be easily and accurately sorted out from the NMS seeds by weight-sorting machines, so pure and fully filled NMS seeds are available. CONCLUSIONS The weight-based seed sorting system shows obvious advantages over the RFP-based seed sorting system in accuracy, efficiency, and cost for propagation of pure male sterile seeds. These characteristics will significantly increase the value and transgenic safety of the third-generation hybrid rice technology.
Collapse
Affiliation(s)
- Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631 Guangzhou, China
| | - Shijun Qiu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631 Guangzhou, China
| | - Menglong Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631 Guangzhou, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, 518107 Shenzhen, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop Design, 518107 Shenzhen, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, 510631 Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, 518107 Shenzhen, China
| |
Collapse
|
43
|
Yan W, Deng XW, Yang C, Tang X. The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice. Front Plant Sci 2021; 12:579675. [PMID: 33841451 PMCID: PMC8025102 DOI: 10.3389/fpls.2021.579675] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
Ethyl methanesulfonate (EMS) is a chemical mutagen believed to mainly induce G/C to A/T transitions randomly in plant genomes. However, mutant screening for phenotypes often gets multiple alleles for one gene but no mutant for other genes. We investigated the potential EMS mutagenesis bias and the possible correlations with sequence context and chromatin structure using the whole genome resequencing data collected from 52 rice EMS mutants. We defined the EMS-induced single nucleotide polymorphic sites (SNPs) and explored the genomic factors associated with EMS mutagenesis bias. Compared with natural SNPs presented in the Rice3K project, EMS showed a preference on G/C sites with flanking sequences also higher in GC contents. The composition of local dinucleotides and trinucleotides was also associated with the efficiency of EMS mutagenesis. The biased distribution of EMS-induced SNPs was positively correlated with CpG numbers, transposable element contents, and repressive epigenetic markers but negatively with gene expression, the euchromatin marker DNase I hypersensitive sites, and active epigenetic markers, suggesting that sequence context and chromatin structure might correlate with the efficiency of EMS mutagenesis. Exploring the genome-wide features of EMS mutagenesis and correlations with epigenetic modifications will help in the understanding of DNA repair mechanism.
Collapse
Affiliation(s)
- Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, China
| | - Chengwei Yang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, China
| |
Collapse
|
44
|
Zhou JX, Yang J, Zhou YH, Henry SH, Qiu Q, Deng XW, Zhang JJ, Yu HJ. [Agreement of EV-A71 neutralization assay: serial 4-fold versus 2-fold dilution comparison]. Zhonghua Yu Fang Yi Xue Za Zhi 2021; 55:200-206. [PMID: 34645180 DOI: 10.3760/cma.j.cn112150-20200917-01211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Objective: To evaluate consistency between 2-fold serial and 4-fold serial diluted neutralization tests against Enterovirus A71 (EV-A71) in estimating titer, Geometric mean titer (GMT), seroprevalence, and seroincidence. Methods: Based on a prospective cohort of 1-9 years old children, mothers and infants established in Anhua County, Hunan Province, during 2013-2018, from which 92 participants with a total of 386 blood specimens were sampled and tested with a 2-fold serial dilution and a 4-fold serial dilution neutralization tests against EV-A71 at the same time. Agreement was estimated using the Bland-Altman method. Stratified analysis was conducted to estimate effect dilution approach on GMT, seroprevalence and seroincidence. Results: The mean difference (0.04, 95%CI:-0.02-0.10) between the two dilution approaches was not significant. However, the limits of agreement (LOA) (-1.12-1.21), with the 95% confidence interval of upper LOA (1.10-1.31) and of lower LOA (-1.22--1.02), significantly exceeded the Clinic accept interval (-1, 1) indicating insufficient agreement between the two approaches in practice. While the dilution approaches did not affect estimates of GMT of the total population and the positive population, and seroincidence with seroconversion only, the differences were 2, 6 and 2%, respectively (P>0.05). Estimates of seroincidence with at least 4-fold increase and seroconversion/4-fold increase were significantly higher using a 4-fold dilution neutralization test compared to the 2-fold dilution neutralization test with 8% (95%CI: 1%-12%) and 9% (95%CI: 1%-17%), respectively. Conclusion: The 2-dilution and 4-dilution neutralization tests yielded comparable results when estimating the population's GMT; however, the difference between the two is not negligible when assessing the seroincidence.
Collapse
Affiliation(s)
- J X Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| | - J Yang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| | - Y H Zhou
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| | - S H Henry
- Department of Biostatistics, School of Public Health, Fudan University, Shanghai 200032, China
| | - Qi Qiu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| | - X W Deng
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| | - J J Zhang
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| | - H J Yu
- School of Public Health, Fudan University, Key Laboratory of Public Health Safety, Ministry of Education, Shanghai 200032, China
| |
Collapse
|
45
|
Zhao P, Zhang X, Gong Y, Wang D, Xu D, Wang N, Sun Y, Gao L, Liu SS, Deng XW, Kliebenstein DJ, Zhou X, Fang RX, Ye J. Red-light is an environmental effector for mutualism between begomovirus and its vector whitefly. PLoS Pathog 2021; 17:e1008770. [PMID: 33428670 PMCID: PMC7822537 DOI: 10.1371/journal.ppat.1008770] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 01/22/2021] [Accepted: 10/31/2020] [Indexed: 01/04/2023] Open
Abstract
Environments such as light condition influence the spread of infectious diseases by affecting insect vector behavior. However, whether and how light affects the host defense which further affects insect preference and performance, remains unclear, nor has been demonstrated how pathogens co-adapt light condition to facilitate vector transmission. We previously showed that begomoviral βC1 inhibits MYC2-mediated jasmonate signaling to establish plant-dependent mutualism with its insect vector. Here we show red-light as an environmental catalyzer to promote mutualism of whitefly-begomovirus by stabilizing βC1, which interacts with PHYTOCHROME-INTERACTING FACTORS (PIFs) transcription factors. PIFs positively control plant defenses against whitefly by directly binding to the promoter of terpene synthase genes and promoting their transcription. Moreover, PIFs interact with MYC2 to integrate light and jasmonate signaling and regulate the transcription of terpene synthase genes. However, begomovirus encoded βC1 inhibits PIFs' and MYC2' transcriptional activity via disturbing their dimerization, thereby impairing plant defenses against whitefly-transmitted begomoviruses. Our results thus describe how a viral pathogen hijacks host external and internal signaling to enhance the mutualistic relationship with its insect vector.
Collapse
Affiliation(s)
- Pingzhi Zhao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Xuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yuqing Gong
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Duan Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China
| | - Ning Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Yanwei Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Lianbo Gao
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Shu-Sheng Liu
- Institute of Insect Sciences, Zhejiang University, Hangzhou, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Daniel J. Kliebenstein
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Xueping Zhou
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Rong-Xiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| | - Jian Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
46
|
Li G, Wang L, Yang J, He H, Jin H, Li X, Ren T, Ren Z, Li F, Han X, Zhao X, Dong L, Li Y, Song Z, Yan Z, Zheng N, Shi C, Wang Z, Yang S, Xiong Z, Zhang M, Sun G, Zheng X, Gou M, Ji C, Du J, Zheng H, Doležel J, Deng XW, Stein N, Yang Q, Zhang K, Wang D. A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes. Nat Genet 2021; 53:574-584. [PMID: 33737755 PMCID: PMC8035075 DOI: 10.1038/s41588-021-00808-z] [Citation(s) in RCA: 110] [Impact Index Per Article: 36.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/29/2021] [Indexed: 01/31/2023]
Abstract
Rye is a valuable food and forage crop, an important genetic resource for wheat and triticale improvement and an indispensable material for efficient comparative genomic studies in grasses. Here, we sequenced the genome of Weining rye, an elite Chinese rye variety. The assembled contigs (7.74 Gb) accounted for 98.47% of the estimated genome size (7.86 Gb), with 93.67% of the contigs (7.25 Gb) assigned to seven chromosomes. Repetitive elements constituted 90.31% of the assembled genome. Compared to previously sequenced Triticeae genomes, Daniela, Sumaya and Sumana retrotransposons showed strong expansion in rye. Further analyses of the Weining assembly shed new light on genome-wide gene duplications and their impact on starch biosynthesis genes, physical organization of complex prolamin loci, gene expression features underlying early heading trait and putative domestication-associated chromosomal regions and loci in rye. This genome sequence promises to accelerate genomic and breeding studies in rye and related cereal crops.
Collapse
Affiliation(s)
- Guangwei Li
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Lijian Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Jianping Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Hang He
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Huaibing Jin
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Xuming Li
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Tianheng Ren
- grid.80510.3c0000 0001 0185 3134Agronomy College, Sichuan Agricultural University, Chengdu, China
| | - Zhenglong Ren
- grid.80510.3c0000 0001 0185 3134Agronomy College, Sichuan Agricultural University, Chengdu, China
| | - Feng Li
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xue Han
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Xiaoge Zhao
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Lingli Dong
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yiwen Li
- grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Zhongping Song
- grid.80510.3c0000 0001 0185 3134Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Zehong Yan
- grid.80510.3c0000 0001 0185 3134Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Nannan Zheng
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Cuilan Shi
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Zhaohui Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Shuling Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Zijun Xiong
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Menglan Zhang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Guanghua Sun
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Xu Zheng
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Mingyue Gou
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Changmian Ji
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Junkai Du
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Hongkun Zheng
- grid.410751.6Biomarker Technologies Corporation, Beijing, China
| | - Jaroslav Doležel
- grid.454748.eInstitute of Experimental Botany of the Czech Academy of Sciences, Centre of the Region Hana for Biotechnological and Agricultural Research, Olomouc, Czech Republic
| | - Xing Wang Deng
- grid.11135.370000 0001 2256 9319Peking University Institute of Advanced Agricultural Sciences, Weifang, China ,grid.11135.370000 0001 2256 9319School of Advanced Agriculture Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking University, Beijing, China
| | - Nils Stein
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany ,grid.7450.60000 0001 2364 4210Center for Integrated Breeding Research (CiBreed), Department of Crop Sciences, Georg-August-University, Göttingen, Germany
| | - Qinghua Yang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Kunpu Zhang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| | - Daowen Wang
- grid.108266.b0000 0004 1803 0494College of Agronomy, Longzi Lake Campus, Henan Agricultural University, Zhengzhou, China ,grid.9227.e0000000119573309The State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China ,grid.108266.b0000 0004 1803 0494The State Key Laboratory of Wheat and Maize Crop Science, Center for Crop Genome Engineering, Henan Agricultural University, Zhengzhou, China
| |
Collapse
|
47
|
Wang J, Sun N, Zhang F, Yu R, Chen H, Deng XW, Wei N. SAUR17 and SAUR50 Differentially Regulate PP2C-D1 during Apical Hook Development and Cotyledon Opening in Arabidopsis. Plant Cell 2020; 32:3792-3811. [PMID: 33093148 PMCID: PMC7721335 DOI: 10.1105/tpc.20.00283] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 09/28/2020] [Accepted: 10/22/2020] [Indexed: 05/04/2023]
Abstract
Following germination in the dark, Arabidopsis (Arabidopsis thaliana) seedlings undergo etiolation and develop apical hooks, closed cotyledons, and rapidly elongating hypocotyls. Upon light perception, the seedlings de-etiolate, which includes the opening of apical hooks and cotyledons. Here, we identify Arabidopsis Small Auxin Up RNA17 (SAUR17) as a downstream effector of etiolation, which serves to bring about apical hook formation and closed cotyledons. SAUR17 is highly expressed in apical hooks and cotyledons and is repressed by light. The apical organs also express a group of light-inducing SAURs, as represented by SAUR50, which promote hook and cotyledon opening. The development of etiolated or de-etiolated apical structures requires asymmetric differential cell growth. We present evidence that the opposing actions of SAUR17 and SAUR50 on apical development largely result from their antagonistic regulation of Protein Phosphatase 2C D-clade 1 (PP2C-D1), a phosphatase that suppresses cell expansion and promotes apical hook development in the dark. SAUR50 inhibits PP2C-D1, whereas SAUR17 has a higher affinity for PP2C-D1 without inhibiting its activity. PP2C-D1 predominantly associates with SAUR17 in etiolated seedlings, which shields it from inhibitory SAURs such as SAUR50. Light signals turn off SAUR17 and upregulate a subgroup of SAURs including SAUR50 at the inner side of the hook and cotyledon cells, leading to cell expansion and unfolding of the hook and cotyledons.
Collapse
Affiliation(s)
- Jiajun Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, School of Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Ning Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, School of Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Fangfang Zhang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, School of Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Renbo Yu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, School of Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Haodong Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, School of Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, School of Life Sciences, and Academy for Advanced Interdisciplinary Studies, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- Institute of Plant and Food Science, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Ning Wei
- School of Life Sciences, Southwest University, Chongqing 400715, China
| |
Collapse
|
48
|
Zhang H, Wang M, Li Y, Yan W, Chang Z, Ni H, Chen Z, Wu J, Xu C, Deng XW, Tang X. GDSL esterase/lipases OsGELP34 and OsGELP110/OsGELP115 are essential for rice pollen development. J Integr Plant Biol 2020; 62:1574-1593. [PMID: 32068333 DOI: 10.1111/jipb.12919] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 02/17/2020] [Indexed: 05/27/2023]
Abstract
Pollen exine contains complex biopolymers of aliphatic lipids and phenolics. Abnormal development of pollen exine often leads to plant sterility. Molecular mechanisms regulating exine formation have been studied extensively but remain ambiguous. Here we report the analyses of three GDSL esterase/lipase protein genes, OsGELP34, OsGELP110, and OsGELP115, for rice exine formation. OsGELP34 was identified by cloning of a male sterile mutant gene. OsGELP34 encodes an endoplasmic reticulum protein and was mainly expressed in anthers during pollen exine formation. osgelp34 mutant displayed abnormal exine and altered expression of a number of key genes required for pollen development. OsGELP110 was previously identified as a gene differentially expressed in meiotic anthers. OsGELP110 was most homologous to OsGELP115, and the two genes showed similar gene expression patterns. Both OsGELP110 and OsGELP115 proteins were localized in peroxisomes. Individual knockout of OsGELP110 and OsGELP115 did not affect the plant fertility, but double knockout of both genes altered the exine structure and rendered the plant male sterile. OsGELP34 is distant from OsGELP110 and OsGELP115 in sequence, and osgelp34 and osgelp110/osgelp115 mutants were different in anther morphology despite both were male sterile. These results suggested that OsGELP34 and OsGELP110/OsGELP115 catalyze different compounds for pollen exine development.
Collapse
Affiliation(s)
- Huihui Zhang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
- School of Life Sciences, Capital Normal University, Beijing, 100048, China
| | - Menglong Wang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Yiqi Li
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Wei Yan
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Zhenyi Chang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Haoling Ni
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Zhufeng Chen
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Jianxin Wu
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
| | - Chunjue Xu
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| | - Xing Wang Deng
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
- School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xiaoyan Tang
- Guangdong Provincial Key Laboratory of Biotechnology for Plant Development, School of Life Sciences, South China Normal University, Guangzhou, 510631, China
- Shenzhen Institute of Molecular Crop Design, Shenzhen, 518107, China
| |
Collapse
|
49
|
Zhu W, Zhou H, Lin F, Zhao X, Jiang Y, Xu D, Deng XW. COLD-REGULATED GENE27 Integrates Signals from Light and the Circadian Clock to Promote Hypocotyl Growth in Arabidopsis. Plant Cell 2020; 32:3155-3169. [PMID: 32732313 PMCID: PMC7534470 DOI: 10.1105/tpc.20.00192] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/13/2020] [Accepted: 07/28/2020] [Indexed: 05/20/2023]
Abstract
Light and the circadian clock are two essential external and internal cues affecting seedling development. COLD-REGULATED GENE27 (COR27), which is regulated by cold temperatures and light signals, functions as a key regulator of the circadian clock. Here, we report that COR27 acts as a negative regulator of light signaling. COR27 physically interacts with the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-SUPPRESSOR OF PHYTOCHROME A1 (SPA1) E3 ubiquitin ligase complex and undergoes COP1-mediated degradation via the 26S proteasome system in the dark. cor27 mutant seedlings exhibit shorter hypocotyls, while transgenic lines overexpressing COR27 show elongated hypocotyls in the light. In addition, light induces the accumulation of COR27. On one hand, accumulated COR27 interacts with ELONGATED HYPOCOTYL5 (HY5) to repress HY5 DNA binding activity. On the other hand, COR27 associates with the chromatin at the PHYTOCHROME INTERACTING FACTOR4 (PIF4) promoter region and upregulates PIF4 expression in a circadian clock-dependent manner. Together, our findings reveal a mechanistic framework whereby COR27 represses photomorphogenesis in the light and provide insights toward how light and the circadian clock synergistically control hypocotyl growth.
Collapse
Affiliation(s)
- Wei Zhu
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Hua Zhou
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Fang Lin
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xianhai Zhao
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Yan Jiang
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xing Wang Deng
- Institute of Plant and Food Sciences, Department of Biology, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| |
Collapse
|
50
|
Song Z, Yan T, Liu J, Bian Y, Heng Y, Lin F, Jiang Y, Wang Deng X, Xu D. BBX28/BBX29, HY5 and BBX30/31 form a feedback loop to fine-tune photomorphogenic development. Plant J 2020; 104:377-390. [PMID: 32654323 DOI: 10.1111/tpj.14929] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 06/28/2020] [Accepted: 07/06/2020] [Indexed: 05/23/2023]
Abstract
Light is one of the key environmental cues controlling photomorphogenic development in plants. A group of B-box (BBX) proteins play critical roles in this developmental process through diverse regulatory mechanisms. In this study we report that BBX29 acts as a negative regulator of light signaling. BBX29 interacts with CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and undergoes COP1-mediated degradation in the dark. Mutant seedlings with loss of BBX29 function show shortened hypocotyls, while transgenic plants overexpressing BBX29 display elongated hypocotyls in the light. Both BBX28 and BBX29 interfere with the binding of ELONGATED HYPOCOTYL 5 (HY5) to the promoters of BBX30 and BBX31, consequently leading to the upregulation of their transcript levels. BBX30 and BBX31 associate with the promoter regions of BBX28 and BBX29, which in turn promotes the expression of these genes. Taken together, this study reveals a transcriptional feedback loop consisting of BBX28, BBX29, BBX30, BBX31, and HY5 that serves to fine-tune photomorphogenesis in response to light in plants.
Collapse
Affiliation(s)
- Zhaoqing Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Tingting Yan
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Jiujie Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yeting Bian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yueqin Heng
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Fang Lin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Yan Jiang
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Xing Wang Deng
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, 100871, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| |
Collapse
|