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Si J, Fan ZQ, Wu CJ, Yang YY, Shan W, Kuang JF, Lu WJ, Wei W, Chen JY. MaHsf24, a novel negative modulator, regulates cold tolerance in banana fruits by repressing the expression of HSPs and antioxidant enzyme genes. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38856080 DOI: 10.1111/pbi.14410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/29/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]
Abstract
Transcriptional regulation mechanisms underlying chilling injury (CI) development have been widely investigated in model plants and cold-sensitive fruits, such as banana (Musa acuminata). However, unlike the well-known NAC and WRKY transcription factors (TFs), the function and deciphering mechanism of heat shock factors (HSFs) involving in cold response are still fragmented. Here, we showed that hot water treatment (HWT) alleviated CI in harvested banana fruits accomplishing with reduced reactive oxygen species (ROS) accumulation and increased antioxidant enzyme activities. A cold-inducible but HWT-inhibited HSF, MaHsf24, was identified. Using DNA affinity purification sequencing (DAP-seq) combined with RNA-seq analyses, we found three heat shock protein (HSP) genes (MaHSP23.6, MaHSP70-1.1 and MaHSP70-1.2) and three antioxidant enzyme genes (MaAPX1, MaMDAR4 and MaGSTZ1) were the potential targets of MaHsf24. Subsequent electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation coupled with quantitative PCR (ChIP-qPCR) and dual-luciferase reporter (DLR) analyses demonstrated that MaHsf24 repressed the transcription of these six targets via directly binding to their promoters. Moreover, stably overexpressing MaHsf24 in tomatoes increased cold sensitivity by suppressing the expressions of HSPs and antioxidant enzyme genes, while HWT could recover cold tolerance, maintaining higher levels of HSPs and antioxidant enzyme genes, and activities of antioxidant enzymes. In contrast, transiently silencing MaHsf24 by virus-induced gene silencing (VIGS) in banana peels conferred cold resistance with the upregulation of MaHSPs and antioxidant enzyme genes. Collectively, our findings support the negative role of MaHsf24 in cold tolerance, and unravel a novel regulatory network controlling bananas CI occurrence, concerning MaHsf24-exerted inhibition of MaHSPs and antioxidant enzyme genes.
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Affiliation(s)
- Jia Si
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Zhong-Qi Fan
- Key Laboratory of Postharvest Biology of Subtropical Special Agricultural/Institute of Postharvest Technology of Agricultural Products, College of Food Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao-Jie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Ying-Ying Yang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jian-Fei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wang-Jin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
| | - Jian-Ye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou, China
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2
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Humphreys JL, Beveridge CA, Tanurdžić M. Strigolactone induces D14-dependent large-scale changes in gene expression requiring SWI/SNF chromatin remodellers. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38858857 DOI: 10.1111/tpj.16873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 06/12/2024]
Abstract
Strigolactones (SL) function as plant hormones in control of multiple aspects of plant development, mostly via the regulation of gene expression. Immediate early-gene regulation by SL remains unexplored due to difficulty in dissecting early from late gene expression responses to SL. We used synthetic SL, rac-GR24 treatment of protoplasts and RNA-seq to explore early SL-induced changes in gene expression over time (5-180 minutes) and discovered rapid, dynamic and SL receptor D14-dependent regulation of gene expression in response to rac-GR24. Importantly, we discovered a significant dependence of SL signalling on chromatin remodelling processes, as the induction of a key SL-induced transcription factor BRANCHED1 requires the SWI/SNF chromatin remodelling ATPase SPLAYED (SYD) and leads to upregulation of a homologue SWI/SNF ATPase BRAHMA. ATAC-seq profiling of genome-wide changes in chromatin accessibility in response to rac-GR24 identified large-scale changes, with over 1400 differentially accessible regions. These changes in chromatin accessibility often precede transcriptional changes and are likely to harbour SL cis-regulatory elements. Importantly, we discovered that this early and extensive modification of the chromatin landscape also requires SYD. This study, therefore, provides evidence that SL signalling requires regulation of chromatin accessibility, and it identifies genomic locations harbouring likely SL cis-regulatory sequences.
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Affiliation(s)
- Jazmine L Humphreys
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Christine A Beveridge
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
- ARC Centre for Plant Success in Nature and Agriculture, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Miloš Tanurdžić
- School of Biological Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
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3
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Hummel NFC, Markel K, Stefani J, Staller MV, Shih PM. Systematic identification of transcriptional activation domains from non-transcription factor proteins in plants and yeast. Cell Syst 2024:S2405-4712(24)00151-0. [PMID: 38866009 DOI: 10.1016/j.cels.2024.05.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 04/26/2024] [Accepted: 05/22/2024] [Indexed: 06/14/2024]
Abstract
Transcription factors can promote gene expression through activation domains. Whole-genome screens have systematically mapped activation domains in transcription factors but not in non-transcription factor proteins (e.g., chromatin regulators and coactivators). To fill this knowledge gap, we employed the activation domain predictor PADDLE to analyze the proteomes of Arabidopsis thaliana and Saccharomyces cerevisiae. We screened 18,000 predicted activation domains from >800 non-transcription factor genes in both species, confirming that 89% of candidate proteins contain active fragments. Our work enables the annotation of hundreds of nuclear proteins as putative coactivators, many of which have never been ascribed any function in plants. Analysis of peptide sequence compositions reveals how the distribution of key amino acids dictates activity. Finally, we validated short, "universal" activation domains with comparable performance to state-of-the-art activation domains used for genome engineering. Our approach enables the genome-wide discovery and annotation of activation domains that can function across diverse eukaryotes.
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Affiliation(s)
- Niklas F C Hummel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Biology, Technische Universität Darmstadt, 64287 Darmstadt, Germany
| | - Kasey Markel
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Jordan Stefani
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Max V Staller
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub-San Francisco, San Francisco, CA 9415, USA.
| | - Patrick M Shih
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA; Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608, USA; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA.
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4
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Wu X, Jia Y, Ma Q, Wang T, Xu J, Chen H, Wang M, Song H, Cao S. The transcription factor bZIP44 cooperates with MYB10 and MYB72 to regulate the response of Arabidopsis thaliana to iron deficiency stress. THE NEW PHYTOLOGIST 2024; 242:2586-2603. [PMID: 38523234 DOI: 10.1111/nph.19706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 03/09/2024] [Indexed: 03/26/2024]
Abstract
Nicotianamine (NA) plays a crucial role in transporting metal ions, including iron (Fe), in plants; therefore, NICOTIANAMINE SYNTHASE (NAS) genes, which control NA synthesis, are tightly regulated at the transcriptional level. However, the transcriptional regulatory mechanisms of NAS genes require further investigations. In this study, we determined the role of bZIP44 in mediating plant response to Fe deficiency stress by conducting transformation experiments and assays. bZIP44 positively regulated the response of Arabidopsis to Fe deficiency stress by interacting with MYB10 and MYB72 to enhance their abilities to bind at NAS2 and NAS4 promoters, thereby increasing NAS2 and NAS4 transcriptional levels and promote NA synthesis. In summary, the transcription activities of bZIP44, MYB10, and MYB72 were induced in response to Fe deficiency stress, which enhanced the interaction between bZIP44 and MYB10 or MYB72 proteins, synergistically activated the transcriptional activity of NAS2 and NAS4, promoted NA synthesis, and improved Fe transport, thereby enhancing plant tolerance to Fe deficiency stress.
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Affiliation(s)
- Xi Wu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Yafeng Jia
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Qian Ma
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Tingting Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Jiena Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hongli Chen
- Anhui Society for Horticultural Science, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Mingxia Wang
- Institute of Horticulture, Anhui Academy of Agricultural Sciences, Hefei, 230031, China
| | - Hui Song
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Shuqing Cao
- School of Food and Biological Engineering, Hefei University of Technology, Hefei, 230009, China
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5
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Ren Z, Zhang P, Su H, Xie X, Shao J, Ku L, Tian Z, Deng D, Wei L. Regulatory mechanisms used by ZmMYB39 to enhance drought tolerance in maize (Zea mays) seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 211:108696. [PMID: 38705046 DOI: 10.1016/j.plaphy.2024.108696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/14/2024] [Accepted: 05/01/2024] [Indexed: 05/07/2024]
Abstract
Drought is a significant abiotic stressor that limits maize (Zea mays L.) growth and development. Thus, enhancing drought tolerance is critical for promoting maize production. Our findings demonstrated that ZmMYB39 is an MYB transcription factor with transcriptional activation activity. Drought stress experiments involving ZmMYB39 overexpression and knockout lines indicated that ZmMYB39 positively regulated drought stress tolerance in maize. DAP-Seq, EMSA, dual-LUC, and RT-qPCR provided initial insights into the molecular regulatory mechanisms by which ZmMYB39 enhances drought tolerance in maize. ZmMYB39 directly promoted the expression of ZmP5CS1, ZmPOX1, ZmSOD2, ZmRD22, ZmNAC49, and ZmDREB2A, which are involved in stress resistance. ZmMYB39 enhanced drought tolerance by interacting with and promoting the expression of ZmFNR1, ZmHSP20, and ZmDOF6. Our study offers a theoretical basis for understanding the molecular regulatory networks involved in maize drought stress response. Furthermore, ZmMYB39 serves as a valuable genetic resource for breeding drought-resistant maize.
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Affiliation(s)
- Zhenzhen Ren
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Pengyu Zhang
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, China
| | - Huihui Su
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Xiaowen Xie
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China
| | - Jing Shao
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China
| | - Lixia Ku
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, 450046, China
| | - Zhiqiang Tian
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China.
| | | | - Li Wei
- Henna Technology Innovation Centre of Wheat, Henan Agricultural University, Zhengzhou, 450046, China.
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6
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Qiao Q, Cao Q, Zhang R, Wu M, Zheng Y, Xue L, Lei J, Sun H, Liston A, Zhang T. Genomic analyses provide insights into sex differentiation of tetraploid strawberry (Fragaria moupinensis). PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1552-1565. [PMID: 38184782 PMCID: PMC11123429 DOI: 10.1111/pbi.14286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/08/2024]
Abstract
The strawberry genus, Fragaria, exhibits a wide range of sexual systems and natural ploidy variation. Nearly, all polyploid strawberry species exhibit separate sexes (dioecy). Research has identified the sex-determining sequences as roughly conserved but with repeatedly changed genomic locations across octoploid strawberries. However, it remains unclear whether tetraploid wild strawberries evolved dioecy independently or shared a common origin with octoploid strawberries. In this study, we investigated the sex determinants of F. moupinensis, a dioecious plant with heterogametic females (ZW). Utilizing a combination of haplotype-resolved genome sequencing of the female F. moupinensis, k-mer-based and coverage-based genome-wide association studies (GWAS), and transcriptomic analysis, we discovered a non-recombining, approximately 33.6 kb W-specific region on chromosome 2a. Within this region, only one candidate sex-determining gene (FmoAFT) was identified. Furthermore, an extensive resequencing of the entire Fragaria genus indicated that the W-specific region displays conservative female specificity across all tetraploid species. This observation suggests that dioecy evolved independently in tetraploid and octoploid strawberries. Moreover, employing virus-induced gene silencing (VIGS), we knocked down the expression of the FmoAFT homologue transcript in cultivated strawberries, revealing its potential role in promoting female functions during early carpel development. We also applied DNA affinity purification sequencing (DAP-seq) and yeast one-hybrid assays to identify potential direct targets of FmoAFT. These insights shed new light on the genetic basis and evolutionary history of sex determination in strawberries, thereby facilitating the formulation of strategies to manipulate sex determination in breeding programs.
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Affiliation(s)
- Qin Qiao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Qiang Cao
- College of Horticulture and LandscapeYunnan Agricultural UniversityKunmingChina
| | - Rengang Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Mingzhao Wu
- School of AgricultureYunnan UniversityKunmingChina
| | | | - Li Xue
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Jiajun Lei
- College of HorticultureShenyang Agricultural UniversityShenyangChina
| | - Hang Sun
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
| | - Aaron Liston
- Department of Botany and Plant PathologyOregon State UniversityCorvallisOregonUSA
| | - Ticao Zhang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of Botany, Chinese Academy of SciencesKunmingChina
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7
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Pérez-Sancho J, Van den Broeck L, García-Caparros P, Sozzani R. Insights into multilevel spatial regulation within the root stem cell niche. Curr Opin Genet Dev 2024; 86:102200. [PMID: 38704928 DOI: 10.1016/j.gde.2024.102200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 05/07/2024]
Abstract
All differentiated root cells derive from stem cells spatially organized within the stem cell niche (SCN), a microenvironment located within the root tip. Here, we compiled recent advances in the understanding of how the SCN drives the establishment and maintenance of cell types. The quiescent center (QC) is widely recognized as the primary driver of cell fate determination, but it is recently considered a convergence center of multiple signals. Cell identity of the cortex endodermis initials is mainly driven by the regulatory feedback loops between transcription factors (TFs), acting as mobile signals between neighboring cells, including the QC. As exemplified in the vascular initials, the precise spatial expression of these regulatory TFs is connected with a dynamic hormonal interplay. Thus, stem cell maintenance and cell differentiation are regulated by a plethora of signals forming a complex, multilevel regulatory network. Integrating the transcriptional and post-translational regulations, protein-protein interactions, and mobile signals into models will be fundamental for the comprehensive understanding of SCN maintenance and differentiation.
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Affiliation(s)
| | - Lisa Van den Broeck
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA. https://twitter.com/@LisaVandenBroec
| | | | - Rosangela Sozzani
- Plant and Microbial Biology Department and NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC 27695, USA.
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8
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Liu L, Zhao L, Liu Y, Zhu Y, Chen S, Yang L, Li X, Chen W, Xu Z, Xu P, Wang H, Yu D. Transcription factor OsWRKY72 controls rice leaf angle by regulating LAZY1-mediated shoot gravitropism. PLANT PHYSIOLOGY 2024; 195:1586-1600. [PMID: 38478430 DOI: 10.1093/plphys/kiae159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 02/13/2024] [Indexed: 06/02/2024]
Abstract
Leaf angle is a major trait of ideal architecture, which is considered to influence rice (Oryza sativa) cultivation and grain yield. Although a few mutants with altered rice leaf inclination angles have been reported, the underlying molecular mechanism remains unclear. In this study, we showed that a WRKY transcription factor gene, OsWRKY72, was highly expressed in the leaf sheath and lamina joint. Phenotypic analyses showed that oswrky72 mutants had smaller leaf angles than the wild type, while OsWRKY72 overexpression lines exhibited an increased leaf angle. This observation suggests that OsWRKY72 functions as a positive regulator, promoting the enlargement of the leaf angle. Our bioinformatics analysis identified LAZY1 as the downstream gene of OsWRKY72. Electrophoretic mobility shift assays and dual-luciferase analysis revealed that OsWRKY72 directly inhibited LAZY1 by binding to its promoter. Moreover, knocking out OsWRKY72 enhanced shoot gravitropism, which contrasted with the phenotype of lazy1 plants. These results imply that OsWRKY72 regulates the leaf angle through gravitropism by reducing the expression of LAZY1. In addition, OsWRKY72 could directly regulate the expression of other leaf angle-related genes such as FLOWERING LOCUS T-LIKE 12 (OsFTL12) and WALL-ASSOCIATED KINASE 11 (OsWAK11). Our study indicates that OsWRKY72 contributes positively to the expansion of the leaf angle by interfering with shoot gravitropism in rice.
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Affiliation(s)
- Lei Liu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Lirong Zhao
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yunwei Liu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Yi Zhu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
| | - Shidie Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
| | - Lu Yang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Xia Li
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
| | - Wanqin Chen
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Zhiyu Xu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
| | - Peng Xu
- CAS Key Laboratory of Tropical Plant Resources and Sustainable Use, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, China
| | - Houping Wang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
| | - Diqiu Yu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, 650500 Kunming, China
- School of Life Sciences, Yunnan University, 650500 Kunming, China
- Southwest United Graduate School, 650092 Kunming, China
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9
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Yu Z, Chen X, Li Y, Shah SHA, Xiao D, Wang J, Hou X, Liu T, Li Y. ETHYLENE RESPONSE FACTOR 070 inhibits flowering in Pak-choi by indirectly impairing BcLEAFY expression. PLANT PHYSIOLOGY 2024; 195:986-1004. [PMID: 38269601 DOI: 10.1093/plphys/kiae021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/20/2023] [Accepted: 11/21/2023] [Indexed: 01/26/2024]
Abstract
APETALA2/ethylene responsive factors respond to ethylene and participate in many biological and physiological processes, such as plant morphogenesis, stress resistance, and hormone signal transduction. Ethylene responsive factor 070 (BcERF070) is important in flowering. However, the underlying molecular mechanisms of BcERF070 in floral transition in response to ethylene signaling have not been fully characterized. Herein, we explored the function of BcERF070 in Pak-choi [Brassica campestris (syn. Brassica rapa) ssp. chinensis]. Ethylene treatment induced BcERF070 expression and delayed flowering in Pak-choi. Silencing of BcERF070 induced flowering in Pak-choi. BcERF070 interacted with major latex protein-like 328 (BcMLP328), which forms a complex with helix-loop-helix protein 30 (BcbHLH30) to enhance the transcriptional activity of BcbHLH30 on LEAFY (BcLFY), ultimately promoting flowering. However, BcERF070 impaired the BcMLP328-BcbHLH30 complex activation of LEAFY (BcLFY), ultimately inhibiting flowering in Pak-choi. BcERF070 directly promoted the expression of the flowering inhibitor gene B-box 29 (BcBBX29) and delayed flowering by reducing FLOWERING LOCUS T (BcFT) expression. These results suggest that BcERF070 mediates ethylene-reduced flowering by impairing the BcMLP328-BcbHLH30 complex activation of BcLFY and by directly promoting the gene expression of the flowering inhibition factor BcBBX29 to repress BcFT expression. The findings contribute to understanding the molecular mechanisms underlying floral transition in response to ethylene in plants.
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Affiliation(s)
- Zhanghong Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaoshan Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yan Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sayyed Hamad Ahmad Shah
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Dong Xiao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianjun Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Tongkun Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China
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Dong J, Zhao X, Song X, Wang S, Zhao X, Liang B, Long Y, Xing Z. Identification of Eleutherococcus senticosus NAC transcription factors and their mechanisms in mediating DNA methylation of EsFPS, EsSS, and EsSE promoters to regulate saponin synthesis. BMC Genomics 2024; 25:536. [PMID: 38816704 PMCID: PMC11140872 DOI: 10.1186/s12864-024-10442-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 05/22/2024] [Indexed: 06/01/2024] Open
Abstract
BACKGROUND The formation of pharmacologically active components in medicinal plants is significantly impacted by DNA methylation. However, the exact mechanisms through which DNA methylation regulates secondary metabolism remain incompletely understood. Research in model species has demonstrated that DNA methylation at the transcription factor binding site within functional gene promoters can impact the binding of transcription factors to target DNA, subsequently influencing gene expression. These findings suggest that the interaction between transcription factors and target DNA could be a significant mechanism through which DNA methylation regulates secondary metabolism in medicinal plants. RESULTS This research conducted a comprehensive analysis of the NAC family in E. senticosus, encompassing genome-wide characterization and functional analysis. A total of 117 EsNAC genes were identified and phylogenetically divided into 15 subfamilies. Tandem duplications and chromosome segment duplications were found to be the primary replication modes of these genes. Motif 2 was identified as the core conserved motif of the genes, and the cis-acting elements, gene structures, and expression patterns of each EsNAC gene were different. EsJUB1, EsNAC047, EsNAC098, and EsNAC005 were significantly associated with the DNA methylation ratio in E. senticosus. These four genes were located in the nucleus or cytoplasm and exhibited transcriptional self-activation activity. DNA methylation in EsFPS, EsSS, and EsSE promoters significantly reduced their activity. The methyl groups added to cytosine directly hindered the binding of the promoters to EsJUB1, EsNAC047, EsNAC098, and EsNAC005 and altered the expression of EsFPS, EsSS, and EsSE genes, eventually leading to changes in saponin synthesis in E. senticosus. CONCLUSIONS NAC transcription factors that are hindered from binding by methylated DNA are found in E. senticosus. The incapacity of these NACs to bind to the promoter of the methylated saponin synthase gene leads to subsequent alterations in gene expression and saponin synthesis. This research is the initial evidence showcasing the involvement of EsNAC in governing the impact of DNA methylation on saponin production in E. senticosus.
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Affiliation(s)
- Jing Dong
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xuelei Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xin Song
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Shuo Wang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Xueying Zhao
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Baoxiang Liang
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China
| | - Yuehong Long
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
| | - Zhaobin Xing
- College of Life Sciences, North China University of Science and Technology, Tangshan, 063210, Hebei, China.
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Wang JD, Wang J, Huang LC, Kan LJ, Wang CX, Xiong M, Zhou P, Zhou LH, Chen C, Zhao DS, Fan XL, Zhang CQ, Zhou Y, Zhang L, Liu QQ, Li QF. ABA-mediated regulation of rice grain quality and seed dormancy via the NF-YB1-SLRL2-bHLH144 Module. Nat Commun 2024; 15:4493. [PMID: 38802342 PMCID: PMC11130328 DOI: 10.1038/s41467-024-48760-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 05/12/2024] [Indexed: 05/29/2024] Open
Abstract
Abscisic acid (ABA) plays a crucial role in promoting plant stress resistance and seed dormancy. However, how ABA regulates rice quality remains unclear. This study identifies a key transcription factor SLR1-like2 (SLRL2), which mediates the ABA-regulated amylose content (AC) of rice. Mechanistically, SLRL2 interacts with NF-YB1 to co-regulate Wx, a determinant of AC and rice quality. In contrast to SLR1, SLRL2 is ABA inducible but insensitive to GA. In addition, SLRL2 exhibits DNA-binding activity and directly regulates the expression of Wx, bHLH144 and MFT2. SLRL2 competes with NF-YC12 for interaction with NF-YB1. NF-YB1 also directly represses SLRL2 transcription. Genetic validation supports that SLRL2 functions downstream of NF-YB1 and bHLH144 in regulating rice AC. Thus, an NF-YB1-SLRL2-bHLH144 regulatory module is successfully revealed. Furthermore, SLRL2 regulates rice dormancy by modulating the expression of MFT2. In conclusion, this study revealed an ABA-responsive regulatory cascade that functions in both rice quality and seed dormancy.
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Affiliation(s)
- Jin-Dong Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Jing Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Li-Chun Huang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Li-Jun Kan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chu-Xin Wang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Min Xiong
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Peng Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Li-Hui Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chen Chen
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Dong-Sheng Zhao
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Xiao-Lei Fan
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Chang-Quan Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Yong Zhou
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Lin Zhang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China
| | - Qiao-Quan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
| | - Qian-Feng Li
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding/Zhongshan Biological Breeding Laboratory/ Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- Co-Innovation Center for Modern Production Technology of Grain Crops of Jiangsu Province, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
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Ou X, Sun L, Chen Y, Zhao Z, Jian W. Characteristics of NAC transcription factors in Solanaceae crops and their roles in responding to abiotic and biotic stresses. Biochem Biophys Res Commun 2024; 709:149840. [PMID: 38564941 DOI: 10.1016/j.bbrc.2024.149840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 03/23/2024] [Accepted: 03/26/2024] [Indexed: 04/04/2024]
Abstract
As one of the largest transcription factor (TF) families in plants, the NAC (NAM, ATAF1/2, and CUC2) family plays important roles in response pathways to various abiotic and biotic stresses, such as drought, high salinity, low temperature, and pathogen infection. Although, there are a number of reviews on the involvement of NAC TF in plant responses to biotic and abiotic stresses, most of them are focused on the model plants Arabidopsis thaliana and Oryza sativa, and there is a lack of systematic evaluation of specific species. Solanaceae, the world's third most significant cash crop, has been seriously affected by environmental disturbances in recent years in terms of yield and quality, posing a severe threat to global food security. This review focuses on the functional roles of NAC transcription factors in response to external stresses involved in five important Solanaceae crops: tomato, potato, pepper, eggplant and tobacco, and analyzes the affinities between them. It will provide resources for stress-resistant breeding of Solanaceae crops using transgenic technology.
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Affiliation(s)
- Xiaogang Ou
- Key Laboratory of Plant Environmental Adaptation Biology of Chongqing, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Lixinyu Sun
- Key Laboratory of Plant Environmental Adaptation Biology of Chongqing, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Yu Chen
- Key Laboratory of Plant Environmental Adaptation Biology of Chongqing, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Zhengwu Zhao
- Key Laboratory of Plant Environmental Adaptation Biology of Chongqing, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China
| | - Wei Jian
- Key Laboratory of Plant Environmental Adaptation Biology of Chongqing, College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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Fernández JD, Miño I, Canales J, Vidal EA. Gene regulatory networks underlying sulfate deficiency responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:2781-2798. [PMID: 38366662 DOI: 10.1093/jxb/erae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/14/2024] [Indexed: 02/18/2024]
Abstract
Sulfur (S) is an essential macronutrient for plants and its availability in soils is an important determinant for growth and development. Current regulatory policies aimed at reducing industrial S emissions together with changes in agronomical practices have led to a decline in S contents in soils worldwide. Deficiency of sulfate-the primary form of S accessible to plants in soil-has adverse effects on both crop yield and nutritional quality. Hence, recent research has increasingly focused on unraveling the molecular mechanisms through which plants detect and adapt to a limiting supply of sulfate. A significant part of these studies involves the use of omics technologies and has generated comprehensive catalogs of sulfate deficiency-responsive genes and processes, principally in Arabidopsis together with a few studies centering on crop species such as wheat, rice, or members of the Brassica genus. Although we know that sulfate deficiency elicits an important reprogramming of the transcriptome, the transcriptional regulators orchestrating this response are not yet well understood. In this review, we summarize our current knowledge of gene expression responses to sulfate deficiency and recent efforts towards the identification of the transcription factors that are involved in controlling these responses. We further compare the transcriptional response and putative regulators between Arabidopsis and two important crop species, rice and tomato, to gain insights into common mechanisms of the response to sulfate deficiency.
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Affiliation(s)
- José David Fernández
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, 8580745, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Programa de Doctorado en Genómica Integrativa, Vicerrectoría de Investigación, Universidad Mayor, 8580745, Santiago, Chile
| | - Ignacio Miño
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5110566, Valdivia, Chile
| | - Javier Canales
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Instituto de Bioquímica y Microbiología, Facultad de Ciencias, Universidad Austral de Chile, 5110566, Valdivia, Chile
| | - Elena A Vidal
- Centro de Genómica y Bioinformática, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, 8580745, Santiago, Chile
- Agencia Nacional de Investigación y Desarrollo - Millennium Science Initiative Program, Millennium Institute for Integrative Biology, 7500565, Santiago, Chile
- Escuela de Biotecnología, Facultad de Ciencias, Ingeniería y Tecnología, Universidad Mayor, 8580745, Santiago, Chile
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Yan Y, Wang P, He J, Shi H. KIN10-mediated HB16 protein phosphorylation and self-association improve cassava disease resistance by transcriptional activation of lignin biosynthesis genes. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 38768314 DOI: 10.1111/pbi.14386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 03/07/2024] [Accepted: 05/07/2024] [Indexed: 05/22/2024]
Abstract
Cassava bacterial blight significantly affects cassava yield worldwide, while major cassava cultivars are susceptible to this disease. Therefore, it is crucial to identify cassava disease resistance gene networks and defence molecules for the genetic improvement of cassava cultivars. In this study, we found that MeHB16 transcription factor as a differentially expressed gene in cassava cultivars with contrasting disease resistance, positively modulated disease resistance by modulating defence molecule lignin accumulation. Further investigation showed that MeHB16 physically interacted with itself via the leucine-Zippe domain (L-Zip), which was necessary for the transcriptional activation of downstream lignin biosynthesis genes. In addition, protein kinase MeKIN10 directly interacted with MeHB16 to promote its phosphorylation at Ser6, which in turn enhanced MeHB16 self-association and downstream lignin biosynthesis. In summary, this study revealed the molecular network of MeKIN10-mediated MeHB16 protein phosphorylation improved cassava bacterial blight resistance by fine-tuning lignin biosynthesis and provides candidate genes and the defence molecule for improving cassava disease resistance.
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Affiliation(s)
- Yu Yan
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
| | - Peng Wang
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
| | - Jiaoyan He
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
| | - Haitao Shi
- National Key Laboratory for Tropical Crop Breeding, School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Key Laboratory of Biotechnology of Salt Tolerant Crops of Hainan Province, School of Tropical Agriculture and Forestry, Hainan University, Hainan province, China
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15
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Chu J, Newman J, Cho J. Molecular Mimicry of Transposable Elements in Plants. PLANT & CELL PHYSIOLOGY 2024:pcae058. [PMID: 38808931 DOI: 10.1093/pcp/pcae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 04/06/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
Transposable elements (TEs) are mobile DNA elements that are particularly abundant in the plant genomes. They have long been considered as junk DNA; however, a growing body of evidence suggests that TE insertions promote genetic diversity that is essential for the adaptive evolution of a species. Thus far, studies have mainly investigated the cis-acting regulatory roles of TEs generated by their insertions nearby or within the host genes. However, the trans-acting effects of TE-derived RNA and DNA remained obscure to date. TEs contain various regulatory elements within their sequences that can accommodate the binding of specific RNAs and proteins. Recently, it was suggested that some of these cellular regulators are shared between TEs and the host genes, and the competition for the common host factors underlies the fine-tuned developmental reprogramming. In this review, we will highlight and discuss the latest discoveries on the biological functions of plant TEs, with a particular focus on their competitive binding with specific developmental regulators.
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Affiliation(s)
- Jie Chu
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, Beijing 200032, China
- University of Chinese Academy of Science, Beijing 100049, China
| | - Josephine Newman
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
| | - Jungnam Cho
- Department of Biosciences, Durham University, Durham, DH1 3LE, UK
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16
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Li H, Xue M, Zhang H, Zhao F, Li X, Yu S, Jiang D. A warm temperature-released negative feedback loop fine-tunes PIF4-mediated thermomorphogenesis in Arabidopsis. PLANT COMMUNICATIONS 2024; 5:100833. [PMID: 38327058 PMCID: PMC11121753 DOI: 10.1016/j.xplc.2024.100833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 12/24/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Plants can sense temperature changes and adjust their growth accordingly. In Arabidopsis, high ambient temperatures stimulate stem elongation by activating a key thermoresponsive regulator, PHYTOCHROME INTERACTING FACTOR 4 (PIF4). Here, we show that warmth promotes the nighttime transcription of GI, which is necessary for the high temperature-induced transcription of TOC1. Genetic analyses suggest that GI prevents excessive thermoresponsive growth by inhibiting PIF4, with this regulatory mechanism being partially reliant on TOC1. GI transcription is repressed by ELF3 and HY5, which concurrently inhibit PIF4 expression and activity. Temperature elevation causes the deactivation or degradation of ELF3 and HY5, leading to PIF4 activation and relief of GI transcriptional repression at high temperatures. This allows PIF4 to further activate GI transcription in response to elevated temperatures. GI, in turn, inhibits PIF4, establishing a negative feedback loop that fine-tunes PIF4 activity. In addition, we demonstrate that ELF3, HY5, and PIF4 regulate GI transcription by modulating the enrichment of histone variant H2A.Z at the GI locus. Together, our findings suggest that thermal release of a negative feedback loop finely adjusts plant thermomorphogenesis.
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Affiliation(s)
- Hui Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Mande Xue
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Huairen Zhang
- University of Chinese Academy of Sciences, Beijing, China
| | - Fengyue Zhao
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoyi Li
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Shuancang Yu
- Beijing Vegetable Research Center, Beijing Academy of Agriculture and Forestry Sciences (BAAFS), Beijing, China
| | - Danhua Jiang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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Maeo K, Nakaya Y, Mitsuda N, Ishiguro S. ACRE, a class of AP2/ERF transcription factors, activates the expression of sweet potato ß-amylase and sporamin genes through the sugar-responsible element CMSRE-1. PLANT MOLECULAR BIOLOGY 2024; 114:54. [PMID: 38714535 PMCID: PMC11076338 DOI: 10.1007/s11103-024-01450-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 04/04/2024] [Indexed: 05/10/2024]
Abstract
Sugars, synthesized by photosynthesis in source organs, are loaded and utilized as an energy source and carbon skeleton in sink organs, and also known to be important signal molecules regulating gene expression in higher plants. The expression of genes coding for sporamin and β-amylase, the two most abundant proteins in storage roots of sweet potato, is coordinately induced by sugars. We previously reported on the identification of the carbohydrate metabolic signal-responsible element-1 (CMSRE-1) essential for the sugar-responsible expression of two genes. However, transcription factors that bind to this sequence have not been identified. In this study, we performed yeast one-hybrid screening using the sugar-responsible minimal promoter region of the ß-amylase gene as bait and a library composed only transcription factor cDNAs of Arabidopsis. Two clones, named Activator protein binding to CMSRE-1 (ACRE), encoding AP2/ERF transcription factors were isolated. ACRE showed transactivation activity of the sugar-responsible minimal promoter in a CMSRE-1-dependent manner in Arabidopsis protoplasts. Electric mobility shift assay (EMSA) using recombinant proteins and transient co-expression assay in Arabidopsis protoplasts revealed that ACRE could actually act to the CMSRE-1. Among the DEHYDRATION -RESPONSIVE ELEMENT BINDING FACTOR (DREB) subfamily, almost all homologs including ACRE, could act on the DRE, while only three ACREs could act to the CMSRE-1. Moreover, ACRE-homologs of Japanese morning glory also have the same property of DNA-binding preference and transactivation activity through the CMSRE-1. These findings suggested that ACRE plays an important role in the mechanism regulating the sugar-responsible gene expression through the CMSRE-1 conserved across plant species.
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Affiliation(s)
- Kenichiro Maeo
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8601, Japan.
| | - Yuki Nakaya
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8601, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566, Japan
| | - Sumie Ishiguro
- Graduate School of Bioagricultural Sciences, Nagoya University, Furo-Cho, Chikusa-Ku, Nagoya, Aichi, 464-8601, Japan
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Guo C, Huang Z, Chen J, Yu G, Wang Y, Wang X. Identification of Novel Regulators of Leaf Senescence Using a Deep Learning Model. PLANTS (BASEL, SWITZERLAND) 2024; 13:1276. [PMID: 38732491 PMCID: PMC11085074 DOI: 10.3390/plants13091276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 04/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Deep learning has emerged as a powerful tool for investigating intricate biological processes in plants by harnessing the potential of large-scale data. Gene regulation is a complex process that transcription factors (TFs), cooperating with their target genes, participate in through various aspects of biological processes. Despite its significance, the study of gene regulation has primarily focused on a limited number of notable instances, leaving numerous aspects and interactions yet to be explored comprehensively. Here, we developed DEGRN (Deep learning on Expression for Gene Regulatory Network), an innovative deep learning model designed to decipher gene interactions by leveraging high-dimensional expression data obtained from bulk RNA-Seq and scRNA-Seq data in the model plant Arabidopsis. DEGRN exhibited a compared level of predictive power when applied to various datasets. Through the utilization of DEGRN, we successfully identified an extensive set of 3,053,363 high-quality interactions, encompassing 1430 TFs and 13,739 non-TF genes. Notably, DEGRN's predictive capabilities allowed us to uncover novel regulators involved in a range of complex biological processes, including development, metabolism, and stress responses. Using leaf senescence as an example, we revealed a complex network underpinning this process composed of diverse TF families, including bHLH, ERF, and MYB. We also identified a novel TF, named MAF5, whose expression showed a strong linear regression relation during the progression of senescence. The mutant maf5 showed early leaf decay compared to the wild type, indicating a potential role in the regulation of leaf senescence. This hypothesis was further supported by the expression patterns observed across four stages of leaf development, as well as transcriptomics analysis. Overall, the comprehensive coverage provided by DEGRN expands our understanding of gene regulatory networks and paves the way for further investigations into their functional implications.
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Affiliation(s)
| | | | | | | | | | - Xu Wang
- Shanghai Collaborative Innovation Center of Agri-Seeds, Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China; (C.G.); (Z.H.); (J.C.); (G.Y.); (Y.W.)
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Deng D, Guo Y, Guo L, Li C, Nie Y, Wang S, Wu W. Functional Divergence in Orthologous Transcription Factors: Insights from AtCBF2/3/1 and OsDREB1C. Mol Biol Evol 2024; 41:msae089. [PMID: 38723179 PMCID: PMC11119335 DOI: 10.1093/molbev/msae089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 04/19/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
Despite traditional beliefs of orthologous genes maintaining similar functions across species, growing evidence points to their potential for functional divergence. C-repeat binding factors/dehydration-responsive element binding protein 1s (CBFs/DREB1s) are critical in cold acclimation, with their overexpression enhancing stress tolerance but often constraining plant growth. In contrast, a recent study unveiled a distinctive role of rice OsDREB1C in elevating nitrogen use efficiency (NUE), photosynthesis, and grain yield, implying functional divergence within the CBF/DREB1 orthologs across species. Here, we delve into divergent molecular mechanisms of OsDREB1C and AtCBF2/3/1 by exploring their evolutionary trajectories across rice and Arabidopsis genomes, regulatomes, and transcriptomes. Evolutionary scrutiny shows discrete clades for OsDREB1C and AtCBF2/3/1, with the Poaceae-specific DREB1C clade mediated by a transposon event. Genome-wide binding profiles highlight OsDREB1C's preference for GCCGAC compared to AtCBF2/3/1's preference for A/GCCGAC, a distinction determined by R12 in the OsDREB1C AP2/ERF domain. Cross-species multiomic analyses reveal shared gene orthogroups (OGs) and underscore numerous specific OGs uniquely bound and regulated by OsDREB1C, implicated in NUE, photosynthesis, and early flowering, or by AtCBF2/3/1, engaged in hormone and stress responses. This divergence arises from gene gains/losses (∼16.7% to 25.6%) and expression reprogramming (∼62.3% to 66.2%) of OsDREB1C- and AtCBF2/3/1-regulated OGs during the extensive evolution following the rice-Arabidopsis split. Our findings illustrate the regulatory evolution of OsDREB1C and AtCBF2/3/1 at a genomic scale, providing insights on the functional divergence of orthologous transcription factors following gene duplications across species.
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Affiliation(s)
- Deyin Deng
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Yixin Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Chengyang Li
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Yuqi Nie
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
- Zhejiang International Science and Technology Cooperation Base for Plant Germplasm Resources Conservation and Utilization, Zhejiang A&F University, Hangzhou 311300, China
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20
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Coomey JH, MacKinnon KJM, McCahill IW, Khahani B, Handakumbura PP, Trabucco GM, Mazzola J, Leblanc NA, Kheam R, Hernandez-Romero M, Barry K, Liu L, Lee JE, Vogel JP, O’Malley RC, Chambers JJ, Hazen SP. Mechanically induced localisation of SECONDARY WALL INTERACTING bZIP is associated with thigmomorphogenic and secondary cell wall gene expression. QUANTITATIVE PLANT BIOLOGY 2024; 5:e5. [PMID: 38774130 PMCID: PMC11106548 DOI: 10.1017/qpb.2024.5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 05/24/2024]
Abstract
Plant growth requires the integration of internal and external cues, perceived and transduced into a developmental programme of cell division, elongation and wall thickening. Mechanical forces contribute to this regulation, and thigmomorphogenesis typically includes reducing stem height, increasing stem diameter, and a canonical transcriptomic response. We present data on a bZIP transcription factor involved in this process in grasses. Brachypodium distachyon SECONDARY WALL INTERACTING bZIP (SWIZ) protein translocated into the nucleus following mechanostimulation. Classical touch-responsive genes were upregulated in B. distachyon roots following touch, including significant induction of the glycoside hydrolase 17 family, which may be unique to grass thigmomorphogenesis. SWIZ protein binding to an E-box variant in exons and introns was associated with immediate activation followed by repression of gene expression. SWIZ overexpression resulted in plants with reduced stem and root elongation. These data further define plant touch-responsive transcriptomics and physiology, offering insights into grass mechanotranduction dynamics.
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Affiliation(s)
- Joshua H. Coomey
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Kirk J.-M. MacKinnon
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Ian W. McCahill
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Bahman Khahani
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Pubudu P. Handakumbura
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Gina M. Trabucco
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Jessica Mazzola
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | | | - Rithany Kheam
- Biology Department, University of Massachusetts, Amherst, MA, USA
| | - Miriam Hernandez-Romero
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
| | - Kerrie Barry
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Lifeng Liu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ji E. Lee
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - John P. Vogel
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ronan C. O’Malley
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - James J. Chambers
- Institute for Applied Life Science, University of Massachusetts, Amherst, MA, USA
| | - Samuel P. Hazen
- Biology Department, University of Massachusetts, Amherst, MA, USA
- Plant Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
- Molecular and Cellular Biology Graduate Program, University of Massachusetts, Amherst, MA, USA
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21
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Guo L, Wang S, Jiao X, Ye X, Deng D, Liu H, Li Y, Van de Peer Y, Wu W. Convergent and/or parallel evolution of RNA-binding proteins in angiosperms after polyploidization. THE NEW PHYTOLOGIST 2024; 242:1377-1393. [PMID: 38436132 DOI: 10.1111/nph.19656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 02/20/2024] [Indexed: 03/05/2024]
Abstract
Increasing studies suggest that the biased retention of stress-related transcription factors (TFs) after whole-genome duplications (WGDs) could rewire gene transcriptional networks, facilitating plant adaptation to challenging environments. However, the role of posttranscriptional factors (e.g. RNA-binding proteins, RBPs) following WGDs has been largely ignored. Uncovering thousands of RBPs in 21 representative angiosperm species, we integrate genomic, transcriptomic, regulatomic, and paleotemperature datasets to unravel their evolutionary trajectories and roles in adapting to challenging environments. We reveal functional enrichments of RBP genes in stress responses and identify their convergent retention across diverse angiosperms from independent WGDs, coinciding with global cooling periods. Numerous RBP duplicates derived from WGDs are then identified as cold-induced. A significant overlap of 29 orthogroups between WGD-derived and cold-induced RBP genes across diverse angiosperms highlights a correlation between WGD and cold stress. Notably, we unveil an orthogroup (Glycine-rich RNA-binding Proteins 7/8, GRP7/8) and relevant TF duplicates (CCA1/LHY, RVE4/8, CBF2/4, etc.), co-retained in different angiosperms post-WGDs. Finally, we illustrate their roles in rewiring circadian and cold-regulatory networks at both transcriptional and posttranscriptional levels during global cooling. Altogether, we underline the adaptive evolution of RBPs in angiosperms after WGDs during global cooling, improving our understanding of plants surviving periods of environmental turmoil.
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Affiliation(s)
- Liangyu Guo
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Shuo Wang
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xi Jiao
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Xiaoxue Ye
- Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, 571101, China
| | - Deyin Deng
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Hua Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yan Li
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, VIB - UGent Center for Plant Systems Biology, Ghent University, B-9052, Ghent, Belgium
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Wenwu Wu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
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22
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Liu L, He W, Xu P, Wei W, Wang J, Liu K. Contribution of the transcription factor SfGATAe to Bt Cry toxin resistance in Spodoptera frugiperda through reduction of ABCC2 expression. Int J Biol Macromol 2024; 267:131459. [PMID: 38593893 DOI: 10.1016/j.ijbiomac.2024.131459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 04/11/2024]
Abstract
Insect resistance evolution poses a significant threat to the advantages of biopesticides and transgenic crops utilizing insecticidal Cry-toxins from Bacillus thuringiensis (Bt). However, there is limited research on the relationship between transcriptional regulation of specific toxin receptors in lepidopteran insects and their resistance to Bt toxins. Here, we report the positive regulatory role of the SfGATAe transcription factor on the expression of the ABCC2 gene in Spodoptera frugiperda. DNA regions in the SfABCC2 promoter that are vital for regulation by SfGATAe, utilizing DAP-seq technology and promoter deletion mapping. Through yeast one-hybrid assays, DNA pull-down experiments, and site-directed mutagenesis, we confirmed that the transcription factor SfGATAe regulates the core control site PBS2 in the ABCC2 target gene. Tissue-specific expression analysis has revealed that SfGATAe is involved in the regulation and expression of midgut cells in the fall armyworm. Silencing SfGATAe in fall armyworm larvae resulted in reduced expression of SfABCC2 and decreased sensitivity to Cry1Ac toxin. Overall, this study elucidated the regulatory mechanism of the transcription factor SfGATAe on the expression of the toxin receptor gene SfABCC2 and this transcriptional control mechanism impacts the resistance of the fall armyworm to Bt toxins.
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Affiliation(s)
- Leilei Liu
- Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China.
| | - Wenfeng He
- Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Peiwen Xu
- Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Wei Wei
- Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China
| | - Jintao Wang
- Center of Applied Biotechnology, School of Life Sciences and Technology, Wuhan University of Bioengineering, Wuhan, Hubei, China
| | - Kaiyu Liu
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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23
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Spoel SH, Dong X. Salicylic acid in plant immunity and beyond. THE PLANT CELL 2024; 36:1451-1464. [PMID: 38163634 PMCID: PMC11062473 DOI: 10.1093/plcell/koad329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/19/2023] [Indexed: 01/03/2024]
Abstract
As the most widely used herbal medicine in human history and a major defence hormone in plants against a broad spectrum of pathogens and abiotic stresses, salicylic acid (SA) has attracted major research interest. With applications of modern technologies over the past 30 years, studies of the effects of SA on plant growth, development, and defence have revealed many new research frontiers and continue to deliver surprises. In this review, we provide an update on recent advances in our understanding of SA metabolism, perception, and signal transduction mechanisms in plant immunity. An overarching theme emerges that SA executes its many functions through intricate regulation at multiple steps: SA biosynthesis is regulated both locally and systemically, while its perception occurs through multiple cellular targets, including metabolic enzymes, redox regulators, transcription cofactors, and, most recently, an RNA-binding protein. Moreover, SA orchestrates a complex series of post-translational modifications of downstream signaling components and promotes the formation of biomolecular condensates that function as cellular signalling hubs. SA also impacts wider cellular functions through crosstalk with other plant hormones. Looking into the future, we propose new areas for exploration of SA functions, which will undoubtedly uncover more surprises for many years to come.
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Affiliation(s)
- Steven H Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, The King's Buildings, Edinburgh EH9 3BF, UK
| | - Xinnian Dong
- Department of Biology, Howard Hughes Medical Institute, Duke University, Durham, NC 27708, USA
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24
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Shanks CM, Rothkegel K, Brooks MD, Cheng CY, Alvarez JM, Ruffel S, Krouk G, Gutiérrez RA, Coruzzi GM. Nitrogen sensing and regulatory networks: it's about time and space. THE PLANT CELL 2024; 36:1482-1503. [PMID: 38366121 PMCID: PMC11062454 DOI: 10.1093/plcell/koae038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 02/18/2024]
Abstract
A plant's response to external and internal nitrogen signals/status relies on sensing and signaling mechanisms that operate across spatial and temporal dimensions. From a comprehensive systems biology perspective, this involves integrating nitrogen responses in different cell types and over long distances to ensure organ coordination in real time and yield practical applications. In this prospective review, we focus on novel aspects of nitrogen (N) sensing/signaling uncovered using temporal and spatial systems biology approaches, largely in the model Arabidopsis. The temporal aspects span: transcriptional responses to N-dose mediated by Michaelis-Menten kinetics, the role of the master NLP7 transcription factor as a nitrate sensor, its nitrate-dependent TF nuclear retention, its "hit-and-run" mode of target gene regulation, and temporal transcriptional cascade identified by "network walking." Spatial aspects of N-sensing/signaling have been uncovered in cell type-specific studies in roots and in root-to-shoot communication. We explore new approaches using single-cell sequencing data, trajectory inference, and pseudotime analysis as well as machine learning and artificial intelligence approaches. Finally, unveiling the mechanisms underlying the spatial dynamics of nitrogen sensing/signaling networks across species from model to crop could pave the way for translational studies to improve nitrogen-use efficiency in crops. Such outcomes could potentially reduce the detrimental effects of excessive fertilizer usage on groundwater pollution and greenhouse gas emissions.
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Affiliation(s)
- Carly M Shanks
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Karin Rothkegel
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Matthew D Brooks
- Global Change and Photosynthesis Research Unit, USDA-ARS, Urbana, IL 61801, USA
| | - Chia-Yi Cheng
- Department of Life Science, National Taiwan University, Taipei 10663, Taiwan
| | - José M Alvarez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Centro de Biotecnología Vegetal, Facultad de Ciencias, Universidad Andrés Bello, 8370035 Santiago, Chile
| | - Sandrine Ruffel
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Gabriel Krouk
- Institute for Plant Sciences of Montpellier (IPSiM), Centre National de la Recherche Scientifique (CNRS), Institut National de Recherche pour l’Agriculture, l’Alimentation, et l'Environnement (INRAE), Université de Montpellier, Montpellier 34090, France
| | - Rodrigo A Gutiérrez
- Agencia Nacional de Investigación y Desarrollo-Millennium Science Initiative Program, Millennium Institute for Integrative Biology (iBio), 7500565 Santiago, Chile
- Center for Genome Regulation (CRG), Institute of Ecology and Biodiversity (IEB), Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, 8331010 Santiago, Chile
| | - Gloria M Coruzzi
- Department of Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
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25
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van Butselaar T, Silva S, Lapin D, Bañales I, Tonn S, van Schie C, Van den Ackerveken G. The Role of Salicylic Acid in the Expression of RECEPTOR-LIKE PROTEIN 23 and Other Immunity-Related Genes. PHYTOPATHOLOGY 2024; 114:1097-1105. [PMID: 38684315 DOI: 10.1094/phyto-10-23-0413-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2024]
Abstract
The hormone salicylic acid (SA) plays a crucial role in plant immunity by activating responses that arrest pathogen ingress. SA accumulation also penalizes growth, a phenomenon visible in mutants that hyperaccumulate SA, resulting in strong growth inhibition. An important question, therefore, is why healthy plants produce basal levels of this hormone when defense responses are not activated. Here, we show that basal SA levels in unchallenged plants are needed for the expression of a number of immunity-related genes and receptors, such as RECEPTOR-LIKE PROTEIN 23 (RLP23). This was shown by depleting basal SA levels in transgenic Arabidopsis lines through the overexpression of the SA-inactivating hydroxylases DOWNY MILDEW-RESISTANT 6 (DMR6) or DMR6-LIKE OXYGENASE 1. RNAseq analysis revealed that the expression of a subset of immune receptor and signaling genes is strongly reduced in the absence of SA. The biological relevance of this was shown for RLP23: In SA-depleted and SA-insensitive plants, responses to the RLP23 ligand, the microbial pattern nlp24, were strongly reduced, whereas responses to flg22 remained unchanged. We hypothesize that low basal SA levels are needed for the expression of a subset of immune system components that enable early pathogen detection and activation of immunity.
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Affiliation(s)
- Tijmen van Butselaar
- Translational Plant Biology, Department of Biology, Institute of Environmental Biology, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Savani Silva
- Translational Plant Biology, Department of Biology, Institute of Environmental Biology, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Dmitry Lapin
- Translational Plant Biology, Department of Biology, Institute of Environmental Biology, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Iñigo Bañales
- Translational Plant Biology, Department of Biology, Institute of Environmental Biology, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Sebastian Tonn
- Translational Plant Biology, Department of Biology, Institute of Environmental Biology, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | | | - Guido Van den Ackerveken
- Translational Plant Biology, Department of Biology, Institute of Environmental Biology, Padualaan 8, 3584 CH Utrecht, the Netherlands
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26
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Yang W, Xin Z, Zhang Q, Zhang Y, Niu L. The tree peony DREB transcription factor PrDREB2D regulates seed α-linolenic acid accumulation. PLANT PHYSIOLOGY 2024; 195:745-761. [PMID: 38365221 DOI: 10.1093/plphys/kiae082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 01/11/2024] [Accepted: 01/17/2024] [Indexed: 02/18/2024]
Abstract
α-Linolenic acid (ALA), an essential fatty acid (FA) for human health, serves as the precursor of 2 nutritional benefits, docosahexaenoic acid and eicosapentaenoic acid, and can only be obtained from plant foods. We previously found that phospholipid:diacylglycerol acyltransferase 2 (PrPDAT2) derived from ALA-rich tree peony (Paeonia rockii) can promote seed ALA accumulation. However, the regulatory mechanism underlying its promoting effect on ALA accumulation remains unknown. Here, we revealed a tree peony dehydration-responsive element binding transcription factor, PrDREB2D, as an upstream regulator of PrPDAT2, which is involved in regulating seed ALA accumulation. Our findings demonstrated that PrDREB2D serves as a nucleus-localized transcriptional activator that directly activates PrPDAT2 expression. PrDREB2D altered the FA composition in transient overexpression Nicotiana benthamiana leaves and stable transgenic Arabidopsis (Arabidopsis thaliana) seeds. Repressing PrDREB2D expression in P. rockii resulted in decreased PrPDAT2 expression and ALA accumulation. In addition, PrDREB2D strengthened its regulation of ALA accumulation by recruiting the cofactor ABA-response element binding factor PrABF2b. Collectively, the study findings provide insights into the mechanism of seed ALA accumulation and avenues for enhancing ALA yield via biotechnological manipulation.
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Affiliation(s)
- Weizong Yang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling 712100, China
| | - Ziwei Xin
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling 712100, China
| | - Qingyu Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling 712100, China
| | - Yanlong Zhang
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling 712100, China
| | - Lixin Niu
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling 712100, China
- Oil Peony Engineering Technology Research Center of National Forestry Administration, Yangling 712100, China
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27
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Tsuji H, Sato M. The Function of Florigen in the Vegetative-to-Reproductive Phase Transition in and around the Shoot Apical Meristem. PLANT & CELL PHYSIOLOGY 2024; 65:322-337. [PMID: 38179836 PMCID: PMC11020210 DOI: 10.1093/pcp/pcae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 11/30/2023] [Accepted: 01/03/2024] [Indexed: 01/06/2024]
Abstract
Plants undergo a series of developmental phases throughout their life-cycle, each characterized by specific processes. Three critical features distinguish these phases: the arrangement of primordia (phyllotaxis), the timing of their differentiation (plastochron) and the characteristics of the lateral organs and axillary meristems. Identifying the unique molecular features of each phase, determining the molecular triggers that cause transitions and understanding the molecular mechanisms underlying these transitions are keys to gleaning a complete understanding of plant development. During the vegetative phase, the shoot apical meristem (SAM) facilitates continuous leaf and stem formation, with leaf development as the hallmark. The transition to the reproductive phase induces significant changes in these processes, driven mainly by the protein FT (FLOWERING LOCUS T) in Arabidopsis and proteins encoded by FT orthologs, which are specified as 'florigen'. These proteins are synthesized in leaves and transported to the SAM, and act as the primary flowering signal, although its impact varies among species. Within the SAM, florigen integrates with other signals, culminating in developmental changes. This review explores the central question of how florigen induces developmental phase transition in the SAM. Future research may combine phase transition studies, potentially revealing the florigen-induced developmental phase transition in the SAM.
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Affiliation(s)
- Hiroyuki Tsuji
- Bioscience and Biotechnology Center, Nagoya University, Furocho, Chikusa, Nagoya, Japan
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Moeko Sato
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
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28
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Xu Y, Tian W, Yin M, Cai Z, Zhang L, Yuan D, Yi H, Wu J. The miR159a-DUO1 module regulates pollen development by modulating auxin biosynthesis and starch metabolism in citrus. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024. [PMID: 38578168 DOI: 10.1111/jipb.13656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2023] [Accepted: 03/15/2024] [Indexed: 04/06/2024]
Abstract
Achieving seedlessness in citrus varieties is one of the important objectives of citrus breeding. Male sterility associated with abnormal pollen development is an important factor in seedlessness. However, our understanding of the regulatory mechanism underlying the seedlessness phenotype in citrus is still limited. Here, we determined that the miR159a-DUO1 module played an important role in regulating pollen development in citrus, which further indirectly modulated seed development and fruit size. Both the overexpression of csi-miR159a and the knocking out of DUO1 in Hong Kong kumquat (Fortunella hindsii) resulted in small and seedless fruit phenotypes. Moreover, pollen was severely aborted in both transgenic lines, with arrested pollen mitotic I and abnormal pollen starch metabolism. Through additional cross-pollination experiments, DUO1 was proven to be the key target gene for miR159a to regulate male sterility in citrus. Based on DNA affinity purification sequencing (DAP-seq), RNA-seq, and verified interaction assays, YUC2/YUC6, SS4 and STP8 were identified as downstream target genes of DUO1, those were all positively regulated by DUO1. In transgenic F. hindsii lines, the miR159a-DUO1 module down-regulated the expression of YUC2/YUC6, which decreased indoleacetic acid (IAA) levels and modulated auxin signaling to repress pollen mitotic I. The miR159a-DUO1 module reduced the expression of the starch synthesis gene SS4 and sugar transport gene STP8 to disrupt starch metabolism in pollen. Overall, this work reveals a new mechanism by which the miR159a-DUO1 module regulates pollen development and elucidates the molecular regulatory network underlying male sterility in citrus.
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Affiliation(s)
- Yanhui Xu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenxiu Tian
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Minqiang Yin
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhenmei Cai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Li Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Deyi Yuan
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees of the Ministry of Education and Key Laboratory of Non-Wood Forest Products of the Forestry Ministry, Central South University of Forestry and Technology, Changsha, 410004, China
| | - Hualin Yi
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
| | - Juxun Wu
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
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Dong X, Liu X, Cheng L, Li R, Ge S, Wang S, Cai Y, Liu Y, Meng S, Jiang CZ, Shi CL, Li T, Fu D, Qi M, Xu T. SlBEL11 regulates flavonoid biosynthesis, thus fine-tuning auxin efflux to prevent premature fruit drop in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2024; 66:749-770. [PMID: 38420861 DOI: 10.1111/jipb.13627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 01/13/2024] [Indexed: 03/02/2024]
Abstract
Auxin regulates flower and fruit abscission, but how developmental signals mediate auxin transport in abscission remains unclear. Here, we reveal the role of the transcription factor BEL1-LIKE HOMEODOMAIN11 (SlBEL11) in regulating auxin transport during abscission in tomato (Solanum lycopersicum). SlBEL11 is highly expressed in the fruit abscission zone, and its expression increases during fruit development. Knockdown of SlBEL11 expression by RNA interference (RNAi) caused premature fruit drop at the breaker (Br) and 3 d post-breaker (Br+3) stages of fruit development. Transcriptome and metabolome analysis of SlBEL11-RNAi lines revealed impaired flavonoid biosynthesis and decreased levels of most flavonoids, especially quercetin, which functions as an auxin transport inhibitor. This suggested that SlBEL11 prevents premature fruit abscission by modulating auxin efflux from fruits, which is crucial for the formation of an auxin response gradient. Indeed, quercetin treatment suppressed premature fruit drop in SlBEL11-RNAi plants. DNA affinity purification sequencing (DAP-seq) analysis indicated that SlBEL11 induced expression of the transcription factor gene SlMYB111 by directly binding to its promoter. Chromatin immunoprecipitation-quantitative polymerase chain reaction and electrophoretic mobility shift assay showed that S. lycopersicum MYELOBLASTOSIS VIRAL ONCOGENE HOMOLOG111 (SlMYB111) induces the expression of the core flavonoid biosynthesis genes SlCHS1, SlCHI, SlF3H, and SlFLS by directly binding to their promoters. Our findings suggest that the SlBEL11-SlMYB111 module modulates flavonoid biosynthesis to fine-tune auxin efflux from fruits and thus maintain an auxin response gradient in the pedicel, thereby preventing premature fruit drop.
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Affiliation(s)
- Xiufen Dong
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China
- Key Laboratory for Quality and Safety Control of Subtropical Fruits and Vegetables, Collaborative Innovation Center for Efficient and Green Production of Agriculture in Mountainous Areas of Zhejiang Province, Ministry of Agriculture and Rural Affairs, College of Horticulture Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xianfeng Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Lina Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Ruizhen Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Siqi Ge
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Sai Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Yue Cai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Yang Liu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Sida Meng
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Cai-Zhong Jiang
- Crops Pathology and Genetic Research Unit, United States Department of Agriculture Agricultural Research Service, Washington, DC, 20250, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | | | - Tianlai Li
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Daqi Fu
- Laboratory of Fruit Biology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
| | - Tao Xu
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
- Key Laboratory of Protected Horticulture of Ministry of Education, Shenyang, 110866, China
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Su H, Cao L, Ren Z, Sun W, Zhu B, Ma S, Sun C, Zhang D, Liu Z, Zeng H, Yang W, Liu Y, Zheng L, Yang Y, Wu Z, Zhu Y, Ku L, Chong L, Chen Y. ZmELF6-ZmPRR37 module regulates maize flowering and salt response. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:929-945. [PMID: 38009862 PMCID: PMC10955496 DOI: 10.1111/pbi.14236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 10/22/2023] [Accepted: 11/06/2023] [Indexed: 11/29/2023]
Abstract
The control of flowering time in maize is crucial for reproductive success and yield, and it can be influenced by environmental stresses. Using the approaches of Ac/Ds transposon and transposable element amplicon sequencing techniques, we identified a Ds insertion mutant in the ZmPRR37 gene. The Ds insertion showed a significant correlation with days to anthesis. Further research indicated that ZmPRR37-CR knockout mutants exhibited early flowering, whereas ZmPRR37-overexpression lines displayed delayed flowering compared to WT under long-day (LD) conditions. We demonstrated that ZmPRR37 repressed the expression of ZmNF-YC2 and ZmNF-YA3 to delay flowering. Association analysis revealed a significant correlation between flowering time and a SNP2071-C/T located upstream of ZmPRR37. The SNP2071-C/T impacted the binding capacity of ZmELF6 to the promoter of ZmPRR37. ZmELF6 also acted as a flowering suppressor in maize under LD conditions. Notably, our study unveiled that ZmPRR37 can enhance salt stress tolerance in maize by directly regulating the expression of ABA-responsive gene ZmDhn1. ZmDhn1 negatively regulated maize salt stress resistance. In summary, our findings proposed a novel pathway for regulating photoperiodic flowering and responding to salt stress based on ZmPRR37 in maize, providing novel insights into the integration of abiotic stress signals into floral pathways.
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Affiliation(s)
- Huihui Su
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Liru Cao
- The Shennong LaboratoryZhengzhouHenanChina
| | - Zhenzhen Ren
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Wenhao Sun
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Bingqi Zhu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Shixiang Ma
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Chongyu Sun
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Dongling Zhang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhixue Liu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Haixia Zeng
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Wenjing Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yingpeng Liu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Lingling Zheng
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yuwei Yang
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Zhendong Wu
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life SciencesHenan UniversityKaifengChina
| | - Lixia Ku
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Leelyn Chong
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
| | - Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, College of AgronomyHenan Agricultural UniversityZhengzhouHenanChina
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Zhang Y, Zeng Z, Hu H, Zhao M, Chen C, Ma X, Li G, Li J, Liu Y, Hao Y, Xu J, Xia R. MicroRNA482/2118 is lineage-specifically involved in gibberellin signalling via the regulation of GID1 expression by targeting noncoding PHAS genes and subsequently instigated phasiRNAs. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:819-832. [PMID: 37966709 PMCID: PMC10955497 DOI: 10.1111/pbi.14226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 10/05/2023] [Accepted: 10/22/2023] [Indexed: 11/16/2023]
Abstract
MicroRNA482/2118 (miR482/2118) is a 22-nt miRNA superfamily, with conserved functions in disease resistance and plant development. It usually instigates the production of phased small interfering RNAs (phasiRNAs) from its targets to expand or reinforce its silencing effect. Using a new high-quality reference genome sequence and comprehensive small RNA profiling, we characterized a newly evolved regulatory pathway of miR482/2118 in litchi. In this pathway, miR482/2118 cleaved a novel noncoding trans-acting gene (LcTASL1) and triggered phasiRNAs to regulate the expression of gibberellin (GA) receptor gene GIBBERELLIN INSENSITIVE DWARF1 (GID1) in trans; another trans-acting gene LcTASL2, targeted by LcTASL1-derived phasiRNAs, produced phasiRNAs as well to target LcGID1 to reinforce the silencing effect of LcTASL1. We found this miR482/2118-TASL-GID1 pathway was likely involved in fruit development, especially the seed development in litchi. In vivo construction of the miR482a-TASL-GID1 pathway in Arabidopsis could lead to defects in flower and silique development, analogous to the phenotype of gid1 mutants. Finally, we found that a GA-responsive transcription factor, LcGAMYB33, could regulate LcMIR482/2118 as a feedback mechanism of the sRNA-silencing pathway. Our results deciphered a lineage-specifically evolved regulatory module of miR482/2118, demonstrating the high dynamics of miR482/2118 function in plants.
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Affiliation(s)
- Yanqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Zaohai Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Huimin Hu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Minglei Zhao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Chengjie Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Xingshuai Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Guanliang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Jianguo Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Yuanlong Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Yanwei Hao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
| | - Jing Xu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
| | - Rui Xia
- State Key Laboratory for Conservation and Utilization of Subtropical Agro‐Bioresources, College of HorticultureSouth China Agricultural UniversityGuangzhouChina
- Guangdong Laboratory for Lingnan Modern AgricultureSouth China Agricultural UniversityGuangzhouChina
- Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture and Rural AffairsSouth China Agricultural UniversityGuangzhouChina
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Tao J, Pan Z, Kong W, Mo B, Chen X, Yu Y. miR319-TCPs-TGA9/TGA10/ROXY2 regulatory module controls cell fate specification in early anther development in Arabidopsis. SCIENCE CHINA. LIFE SCIENCES 2024; 67:839-842. [PMID: 37987941 DOI: 10.1007/s11427-023-2453-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Accepted: 09/15/2023] [Indexed: 11/22/2023]
Affiliation(s)
- Jinyuan Tao
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Zijie Pan
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Wenwen Kong
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Beixin Mo
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China
| | - Xuemei Chen
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, 100871, China
| | - Yu Yu
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Longhua Bioindustry and Innovation Research Institute, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, China.
- School of Life Sciences, Peking-Tsinghua Joint Center for Life Sciences, Peking University, Beijing, 100871, China.
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Wu C, Cai D, Li J, Lin Z, Wei W, Shan W, Chen J, Lu W, Su X, Kuang J. Banana MabHLH28 positively regulates the expression of softening-related genes to mediate fruit ripening independently or via cooperating with MaWRKY49/111. HORTICULTURE RESEARCH 2024; 11:uhae053. [PMID: 38706579 PMCID: PMC11069428 DOI: 10.1093/hr/uhae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 02/17/2024] [Indexed: 05/07/2024]
Abstract
Texture softening is a physiological indicator of fruit ripening, which eventually contributes to fruit quality and the consumer's acceptance. Despite great progress having been made in identification of the genes related to fruit softening, the upstream transcriptional regulatory pathways of these softening-related genes are not fully elucidated. Here, a novel bHLH gene, designated as MabHLH28, was identified because of its significant upregulation in banana fruit ripening. DAP-Seq analysis revealed that MabHLH28 bound to the core sequence of 'CAYGTG' presented in promoter regions of fruit softening-associated genes, such as the genes related to cell wall modification (MaPG3, MaPE1, MaPL5, MaPL8, MaEXP1, MaEXP2, MaEXPA2, and MaEXPA15) and starch degradation (MaGWD1 and MaLSF2), and these bindings were validated by EMSA and DLR assays. Transient overexpression and knockdown of MabHLH28 in banana fruit resulted in up- and down-regulation of softening-related genes, thereby hastening and postponing fruit ripening. Furthermore, overexpression of MabHLH28 in tomato accelerated the ripening process by elevating the accumulation of softening-associated genes. In addition, MabHLH28 showed interaction withMaWRKY49/111 and itself to form protein complexes, which could combinatorically strengthen the transcription of softening-associated genes. Taken together, our findings suggest that MabHLH28 mediates fruit softening by upregulating the expression of softening-related genes either alone or in combination with MaWRKY49/111.
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Affiliation(s)
- Chaojie Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Danling Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jun Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Zengxiang Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Wei
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wei Shan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Jianye Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Wangjin Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
| | - Xinguo Su
- Agronomy Dean, Guangdong AIB Polytechnic College, Guangzhou 510507, China
| | - Jianfei Kuang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Engineering Research Center of Southern Horticultural Products Preservation, Ministry of Education, College of Horticulture, South China Agricultural University, Guangzhou 510642, China
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Adhikari PB, Liu X, Huang C, Mitsuda N, Notaguchi M, Kasahara RD. Transcription Factors behind MYB98 Regulation: What Does the Discovery of SaeM Suggest? PLANTS (BASEL, SWITZERLAND) 2024; 13:1007. [PMID: 38611536 PMCID: PMC11013860 DOI: 10.3390/plants13071007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/15/2024] [Accepted: 03/27/2024] [Indexed: 04/14/2024]
Abstract
MYB98 is master regulator of the molecular network involved in pollen tube attraction. Until recently, it was unclear how this gene exhibits exclusively synergid cell-specific expression in ovule. Our recent study has established that a 16-bp-long SaeM element is crucial for its synergid cell-specific expression in ovule, and an 84-bp-long fragment harboring SaeM is sufficient to drive the process. In this study, we have developed a workflow to predict functional roles of potential transcription factors (TFs) putatively binding to the promoter region, taking MYB98 promoter as a test subject. After sequential assessment of co-expression pattern, network analysis, and potential master regulator identification, we have proposed a multi-TF model for MYB98 regulation. Our study suggests that ANL2, GT-1, and their respective homologs could be direct regulators of MYB98 and indicates that TCP15, TCP16, FRS9, and HB34 are likely master regulators of the majority of the TFs involved in its regulation. Comprehensive studies in the future are expected to offer more insights into such propositions. Developed workflow can be used while designing similar regulome-related studies for any other species and genes.
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Affiliation(s)
- Prakash B. Adhikari
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan;
| | - Xiaoyan Liu
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (C.H.)
| | - Chen Huang
- College of Life Science, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (X.L.); (C.H.)
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8560, Japan;
| | - Michitaka Notaguchi
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan;
| | - Ryushiro Dora Kasahara
- Biotechnology and Bioscience Research Center, Nagoya University, Nagoya 464-8601, Japan;
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Candela-Ferre J, Diego-Martin B, Pérez-Alemany J, Gallego-Bartolomé J. Mind the gap: Epigenetic regulation of chromatin accessibility in plants. PLANT PHYSIOLOGY 2024; 194:1998-2016. [PMID: 38236303 PMCID: PMC10980423 DOI: 10.1093/plphys/kiae024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 11/07/2023] [Accepted: 11/23/2023] [Indexed: 01/19/2024]
Abstract
Chromatin plays a crucial role in genome compaction and is fundamental for regulating multiple nuclear processes. Nucleosomes, the basic building blocks of chromatin, are central in regulating these processes, determining chromatin accessibility by limiting access to DNA for various proteins and acting as important signaling hubs. The association of histones with DNA in nucleosomes and the folding of chromatin into higher-order structures are strongly influenced by a variety of epigenetic marks, including DNA methylation, histone variants, and histone post-translational modifications. Additionally, a wide array of chaperones and ATP-dependent remodelers regulate various aspects of nucleosome biology, including assembly, deposition, and positioning. This review provides an overview of recent advances in our mechanistic understanding of how nucleosomes and chromatin organization are regulated by epigenetic marks and remodelers in plants. Furthermore, we present current technologies for profiling chromatin accessibility and organization.
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Affiliation(s)
- Joan Candela-Ferre
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Borja Diego-Martin
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Jaime Pérez-Alemany
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
| | - Javier Gallego-Bartolomé
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), CSIC-Universitat Politècnica de València, Valencia, 46022Spain
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Wu X, Wang Z, Du A, Gao H, Liang J, Yu W, Yu H, Fan S, Chen Q, Guo J, Xiao Y, Peng F. Transcription factor LBD16 targets cell wall modification/ion transport genes in peach lateral root formation. PLANT PHYSIOLOGY 2024; 194:2472-2490. [PMID: 38217865 DOI: 10.1093/plphys/kiae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/30/2023] [Accepted: 12/14/2023] [Indexed: 01/15/2024]
Abstract
LATERAL ORGAN BOUNDARIES DOMAIN/ASYMMETRIC LEAVES2-LIKEs (LBDs/ASLs) are plant-specific transcription factors that function downstream of auxin-regulated lateral root (LR) formation. Our previous research found that PpLBD16 positively regulates peach (Prunus persica) LR formation. However, the downstream regulatory network and target genes of PpLBD16 are still largely unknown. Here, we constructed a PpLBD16 homologous overexpression line and a PpLBD16 silenced line. We found that overexpressing PpLBD16 promoted peach root initiation, while silencing PpLBD16 inhibited peach root formation. Through RNA sequencing (RNA-seq) analysis of roots from PpLBD16 overexpression and silenced lines, we discovered that genes positively regulated by PpLBD16 were closely related to cell wall synthesis and degradation, ion/substance transport, and ion binding and homeostasis. To further detect the binding motifs and potential target genes of PpLBD16, we performed DNA-affinity purification sequencing (DAP-seq) analysis in vitro. PpLBD16 preferentially bound to CCNGAAANNNNGG (MEME-1), [C/T]TTCT[C/T][T/C] (MEME-2), and GCGGCGG (ABR1) motifs. By combined analysis of RNA-seq and DAP-seq data, we screened candidate target genes for PpLBD16. We demonstrated that PpLBD16 bound and activated the cell wall modification-related genes EXPANSIN-B2 (PpEXPB2) and SUBTILISIN-LIKE PROTEASE 1.7 (PpSBT1.7), the ion transport-related gene CYCLIC NUCLEOTIDE-GATED ION CHANNEL 1 (PpCNGC1) and the polyphenol oxidase (PPO)-encoding gene PpPPO, thereby controlling peach root organogenesis and promoting LR formation. Moreover, our results displayed that PpLBD16 and its target genes are involved in peach LR primordia development. Overall, this work reveals the downstream regulatory network and target genes of PpLBD16, providing insights into the molecular network of LBD16-mediated LR development.
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Affiliation(s)
- Xuelian Wu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Zhe Wang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Anqi Du
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Huaifeng Gao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Jiahui Liang
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Wenying Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Haixiang Yu
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Shihao Fan
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Qiuju Chen
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Jian Guo
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Yuansong Xiao
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
| | - Futian Peng
- College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An 271018, China
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Liu GS, Huang H, Grierson D, Gao Y, Ji X, Peng ZZ, Li HL, Niu XL, Jia W, He JL, Xiang LT, Gao HY, Qu GQ, Zhu HL, Zhu BZ, Luo YB, Fu DQ. NAC transcription factor SlNOR-like1 plays a dual regulatory role in tomato fruit cuticle formation. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1903-1918. [PMID: 37856192 DOI: 10.1093/jxb/erad410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 10/18/2023] [Indexed: 10/20/2023]
Abstract
The plant cuticle is an important protective barrier on the plant surface, constructed mainly by polymerized cutin matrix and a complex wax mixture. Although the pathway of plant cuticle biosynthesis has been clarified, knowledge of the transcriptional regulation network underlying fruit cuticle formation remains limited. In the present work, we discovered that tomato fruits of the NAC transcription factor SlNOR-like1 knockout mutants (nor-like1) produced by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9] displayed reduced cutin deposition and cuticle thickness, with a microcracking phenotype, while wax accumulation was promoted. Further research revealed that SlNOR-like1 promotes cutin deposition by binding to the promoters of glycerol-3-phosphate acyltransferase6 (SlGPAT6; a key gene for cutin monomer formation) and CUTIN DEFICIENT2 (SlCD2; a positive regulator of cutin production) to activate their expression. Meanwhile, SlNOR-like1 inhibits wax accumulation, acting as a transcriptional repressor by targeting wax biosynthesis, and transport-related genes 3-ketoacyl-CoA synthase1 (SlKCS1), ECERIFERUM 1-2 (SlCER1-2), SlWAX2, and glycosylphosphatidylinositol-anchored lipid transfer protein 1-like (SlLTPG1-like). In conclusion, SlNOR-like1 executes a dual regulatory effect on tomato fruit cuticle development. Our results provide a new model for the transcriptional regulation of fruit cuticle formation.
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Affiliation(s)
- Gang-Shuai Liu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hua Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences; Key Laboratory of South Subtropical Fruit Biology and Genetic Resource Utilization, Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of Tropical and Subtropical Fruit Tree Research, Guangzhou 510640, China
| | - Donald Grierson
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, UK
| | - Ying Gao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing 401331, China
| | - Xiang Ji
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Zhen-Zhen Peng
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hong-Li Li
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Xiao-Lin Niu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Wen Jia
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Jian-Lin He
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Lan-Ting Xiang
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hai-Yan Gao
- Key Laboratory of Post-Harvest Handing of Fruits, Ministry of Agriculture and Rural Affairs, Key Laboratory of Fruits and Vegetables Postharvest and Processing Technology Research of Zhejiang Province, Key Laboratory of Postharvest Preservation and Processing of Fruits and Vegetables, China National Light Industry, Food Science Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Gui-Qin Qu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Hong-Liang Zhu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Ben-Zhong Zhu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Yun-Bo Luo
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Da-Qi Fu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Jue D, Li Z, Zhang W, Tang J, Xie T, Sang X, Guo Q. Identification and functional analysis of the LEAFY gene in longan flower induction. BMC Genomics 2024; 25:308. [PMID: 38528464 DOI: 10.1186/s12864-024-10229-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/15/2024] [Indexed: 03/27/2024] Open
Abstract
BACKGROUND Flowering at the right time is a very important factor affecting the stable annual yield of longan. However, a lack of knowledge of the regulatory mechanism and key genes of longan flowering restricts healthy development of the longan industry. Therefore, identifying relevant genes and analysing their regulatory mechanism are essential for scientific research and longan industry development. RESULTS DlLFY (Dimocarpus longan LEAFY) contains a 1167 bp open reading frame and encodes 388 amino acids. The amino acid sequence has a typical LFY/FLO family domain. DlLFY was expressed in all tissues tested, except for the leaf, pericarp, and pulp, with the highest expression occurring in flower buds. Expression of DlLFY was significantly upregulated at the early flower induction stage in "SX" ("Shixia"). The results of subcellular localization and transactivation analysis showed that DlLFY is a typical transcription factor acting as a transcriptional activator. Moreover, overexpression of DlLFY in Arabidopsis promoted early flowering and restrained growth, resulting in reduced plant height and rosette leaf number and area in transgenic plants. DNA affinity purification sequencing (DAP-Seq) analysis showed that 13 flower-related genes corresponding to five homologous genes of Arabidopsis may have binding sites and be putative target genes. Among these five flower-related genes, only AtTFL1 (terminal flower 1) was strongly inhibited in transgenic lines. CONCLUSION Taken together, these results indicate that DlLFY plays a pivotal role in controlling longan flowering, possibly by interacting with TFL1.
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Affiliation(s)
- Dengwei Jue
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400715, Chongqing, Beibei, China
| | - Zhexin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Wenlin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Ting Xie
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China
| | - Xuelian Sang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing Engineering Research Center for Special Plant Seedling, Institute of Special Plants, Chongqing University of Arts and Sciences, 402160, Yongchuan, China.
| | - Qigao Guo
- Key Laboratory of Horticulture Science for Southern Mountains Regions of Ministry of Education, College of Horticulture and Landscape Architecture, Southwest University, 400715, Chongqing, Beibei, China.
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Zhang Y, Hua C, Kiang JX, Shen L. A dephosphorylation-dependent molecular switch for FT repression mediates flowering in Arabidopsis. PLANT COMMUNICATIONS 2024; 5:100779. [PMID: 38115582 PMCID: PMC10943578 DOI: 10.1016/j.xplc.2023.100779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Revised: 11/23/2023] [Accepted: 12/15/2023] [Indexed: 12/21/2023]
Abstract
The reproductive success of flowering plants relies greatly on precise timing of the floral transition, which is finely modulated by a complex network of floral regulators. As a main floral integrator, FLOWERING LOCUS T (FT) is also an essential constituent of the florigen that is transported from leaves to shoot apices to induce flowering. FT is specifically transcribed in leaf vascular tissues, where its production is suppressed by many flowering repressors, including the MYB transcription factor EARLY FLOWERING MYB PROTEIN (EFM). Here, we show that a plant CTD phosphatase, C-TERMINAL DOMAIN PHOSPHATASE-LIKE 2 (CPL2), suppresses FT expression in leaf vascular tissues by modulating the binding activity of EFM. CPL2 interacts with and dephosphorylates EFM to facilitate the binding of dephosphorylated EFM to FT chromatin, thereby inhibiting flowering. Our results suggest that CPL2-mediated dephosphorylation of the floral repressor EFM serves as a molecular switch, adding another layer of regulation to fine-tune FT transcription and ensure that flowering occurs at an appropriate time.
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Affiliation(s)
- Yu Zhang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Changmei Hua
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore
| | - Jian Xuan Kiang
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore
| | - Lisha Shen
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore 117604, Singapore; Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117543, Singapore.
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Méndez-Gómez M, Sierra-Cacho D, Jiménez-Morales E, Guzmán P. Modulation of early gene expression responses to water deprivation stress by the E3 ubiquitin ligase ATL80: implications for retrograde signaling interplay. BMC PLANT BIOLOGY 2024; 24:180. [PMID: 38459432 PMCID: PMC10921668 DOI: 10.1186/s12870-024-04872-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024]
Abstract
BACKGROUND Primary response genes play a pivotal role in translating short-lived stress signals into sustained adaptive responses. In this study, we investigated the involvement of ATL80, an E3 ubiquitin ligase, in the dynamics of gene expression following water deprivation stress. We observed that ATL80 is rapidly activated within minutes of water deprivation stress perception, reaching peak expression around 60 min before gradually declining. ATL80, despite its post-translational regulation role, emerged as a key player in modulating early gene expression responses to water deprivation stress. RESULTS The impact of ATL80 on gene expression was assessed using a time-course microarray analysis (0, 15, 30, 60, and 120 min), revealing a burst of differentially expressed genes, many of which were associated with various stress responses. In addition, the diversity of early modulation of gene expression in response to water deprivation stress was significantly abolished in the atl80 mutant compared to wild-type plants. A subset of 73 genes that exhibited a similar expression pattern to ATL80 was identified. Among them, several are linked to stress responses, including ERF/AP2 and WRKY transcription factors, calcium signaling genes, MAP kinases, and signaling peptides. Promoter analysis predicts enrichment of binding sites for CAMTA1 and CAMTA5, which are known regulators of rapid stress responses. Furthermore, we have identified a group of differentially expressed ERF/AP2 transcription factors, proteins associated with folding and refolding, as well as pinpointed core module genes which are known to play roles in retrograde signaling pathways that cross-referenced with the early ATL80 transcriptome. CONCLUSIONS Based on these findings, we propose that ATL80 may target one or more components within the retrograde signaling pathways for degradation. In essence, ATL80 serves as a bridge connecting these signaling pathways and effectively functions as an alarm signal.
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Affiliation(s)
- Manuel Méndez-Gómez
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México
| | - Daniel Sierra-Cacho
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México
| | - Estela Jiménez-Morales
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México
| | - Plinio Guzmán
- Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN, Unidad Irapuato, Irapuato, 36824, Gto, México.
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Zheng L, Hu Y, Yang T, Wang Z, Wang D, Jia L, Xie Y, Luo L, Qi W, Lv Y, Beeckman T, Xuan W, Han Y. A root cap-localized NAC transcription factor controls root halotropic response to salt stress in Arabidopsis. Nat Commun 2024; 15:2061. [PMID: 38448433 PMCID: PMC10917740 DOI: 10.1038/s41467-024-46482-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/28/2024] [Indexed: 03/08/2024] Open
Abstract
Plants are capable of altering root growth direction to curtail exposure to a saline environment (termed halotropism). The root cap that surrounds root tip meristematic stem cells plays crucial roles in perceiving and responding to environmental stimuli. However, how the root cap mediates root halotropism remains undetermined. Here, we identified a root cap-localized NAC transcription factor, SOMBRERO (SMB), that is required for root halotropism. Its effect on root halotropism is attributable to the establishment of asymmetric auxin distribution in the lateral root cap (LRC) rather than to the alteration of cellular sodium equilibrium or amyloplast statoliths. Furthermore, SMB is essential for basal expression of the auxin influx carrier gene AUX1 in LRC and for auxin redistribution in a spatiotemporally-regulated manner, thereby leading to directional bending of roots away from higher salinity. Our findings uncover an SMB-AUX1-auxin module linking the role of the root cap to the activation of root halotropism.
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Affiliation(s)
- Lulu Zheng
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Yongfeng Hu
- Key Laboratory of Three Gorges Regional Plant Genetics and Germplasm Enhancement, Biotechnology Research Center, China Three Gorges University, Yichang, China
| | - Tianzhao Yang
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhen Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Daoyuan Wang
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Letian Jia
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Yuanming Xie
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China
| | - Long Luo
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Weicong Qi
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB-UGent Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Wei Xuan
- Sanya Institute of Nanjing Agricultural University, State Key Laboratory of Crop Genetics & Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, China.
| | - Yi Han
- National Engineering Laboratory of Crop Stress Resistence Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China.
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Rieu P, Beretta VM, Caselli F, Thévénon E, Lucas J, Rizk M, Franchini E, Caporali E, Paleni C, Nanao MH, Kater MM, Dumas R, Zubieta C, Parcy F, Gregis V. The ALOG domain defines a family of plant-specific transcription factors acting during Arabidopsis flower development. Proc Natl Acad Sci U S A 2024; 121:e2310464121. [PMID: 38412122 DOI: 10.1073/pnas.2310464121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/05/2023] [Indexed: 02/29/2024] Open
Abstract
The ALOG (Arabidopsis LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 (LSH1) and Oryza G1) proteins are conserved plant-specific Transcription Factors (TFs). They play critical roles in the development of various plant organs (meristems, inflorescences, floral organs, and nodules) from bryophytes to higher flowering plants. Despite the fact that the first members of this family were originally discovered in Arabidopsis, their role in this model plant has remained poorly characterized. Moreover, how these transcriptional regulators work at the molecular level is unknown. Here, we study the redundant function of the ALOG proteins LSH1,3,4 from Arabidopsis. We uncover their role in the repression of bract development and position them within a gene regulatory network controlling this process and involving the floral regulators LEAFY, BLADE-ON-PETIOLE, and PUCHI. Next, using in vitro genome-wide studies, we identified the conserved DNA motif bound by ALOG proteins from evolutionarily distant species (the liverwort Marchantia polymorpha and the flowering plants Arabidopsis, tomato, and rice). Resolution of the crystallographic structure of the ALOG DNA-binding domain in complex with DNA revealed the domain is a four-helix bundle with a disordered NLS and a zinc ribbon insertion between helices 2 and 3. The majority of DNA interactions are mediated by specific contacts made by the third alpha helix and the NLS. Taken together, this work provides the biochemical and structural basis for DNA-binding specificity of an evolutionarily conserved TF family and reveals its role as a key player in Arabidopsis flower development.
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Affiliation(s)
- Philippe Rieu
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | | | - Francesca Caselli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Emmanuel Thévénon
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Jérémy Lucas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Mahmoud Rizk
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Emanuela Franchini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Elisabetta Caporali
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Chiara Paleni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Max H Nanao
- Structural Biology Group, European Synchrotron Radiation Facility, Grenoble 38000, France
| | - Martin M Kater
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
| | - Renaud Dumas
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Chloe Zubieta
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - François Parcy
- Laboratoire Physiologie Cellulaire et Végétale, Université Grenoble Alpes, Centre national de la recherche scientifique, Commissariat à l'énergie atomique et aux énergies alternatives, Institut national de recherche pour l'agriculture, l'alimentation et l'environnement, Département de Biologie Structurale et Cellulaire intégrée, Grenoble F-38054, France
| | - Veronica Gregis
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milano 20133, Italy
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Liu H, Wu Z, Bao M, Gao F, Yang W, Abou-Elwafa SF, Liu Z, Ren Z, Zhu Y, Ku L, Su H, Chong L, Chen Y. ZmC2H2-149 negatively regulates drought tolerance by repressing ZmHSD1 in maize. PLANT, CELL & ENVIRONMENT 2024; 47:885-899. [PMID: 38164019 DOI: 10.1111/pce.14798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 12/17/2023] [Indexed: 01/03/2024]
Abstract
Drought is a major abiotic stress that limits maize production worldwide. Therefore, it is of great importance to improve drought tolerance in crop plants for sustainable agriculture. In this study, we examined the roles of Cys2 /His2 zinc-finger-proteins (C2H2-ZFPs) in maize's drought tolerance as C2H2-ZFPs have been implicated for plant stress tolerance. By subjecting 150 Ac/Ds mutant lines to drought stress, we successfully identified a Ds-insertion mutant, zmc2h2-149, which shows increased tolerance to drought stress. Overexpression of ZmC2H2-149 in maize led to a decrease in both drought tolerance and crop yield. DAP-Seq, RNA-Seq, Y1H and LUC assays additionally showed that ZmC2H2-149 directly suppresses the expression of a positive drought tolerance regulator, ZmHSD1 (hydroxysteroid dehydrogenase 1). Consistently, the zmhsd1 mutants exhibited decreased drought tolerance and grain yield under water deficit conditions compared to their respective wild-type plants. Our findings thus demonstrated that ZmC2H2-149 can regulate ZmHSD1 for drought stress tolerance in maize, offering valuable theoretical and genetic resources for maize breeding programmes that aim for improving drought tolerance.
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Affiliation(s)
- Huafeng Liu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhendong Wu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Miaomiao Bao
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Fengran Gao
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Wenjing Yang
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | | | - Zhixue Liu
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zhenzhen Ren
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yingfang Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Lixia Ku
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Huihui Su
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Leelyn Chong
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yanhui Chen
- College of Agronomy, National Key Laboratory of Wheat and Maize Crop Science and Key Laboratory of Regulating and Controlling Crop Growth and Development Ministry of Education, Henan Agricultural University, Zhengzhou, Henan, China
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Dong T, Hu Y, Wang J, Wang Y, Chen P, Xing J, Duan H. GhWRKY4 binds to the histone deacetylase GhHDA8 promoter to regulate drought and salt tolerance in Gossypium hirsutum. Int J Biol Macromol 2024; 262:129971. [PMID: 38354933 DOI: 10.1016/j.ijbiomac.2024.129971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/16/2024]
Abstract
Soil drought and salinization, caused by water deficiency, have become the greatest concerns limiting crop production. Up to now, the WRKY transcription factor and histone deacetylase have been shown to be involved in drought and salt responses. However, the molecular mechanism underlying their interaction remains unclear in cotton. Herein, we identified GhWRKY4, a member of WRKY gene family, which is induced by drought and salt stress and is located in the nucleus. The ectopic expression of GhWRKY4 in Arabidopsis enhanced drought and salt tolerance, and suppressing GhWRKY4 in cotton increased susceptibility to drought and salinity. Subsequently, DAP-seq analysis revealed that the W box element in the promoter of stress-induced genes could potentially be the binding target for GhWRKY4 protein. GhWRKY4 binds to the promoters of GhHDA8 and GhNHX7 via W box element, and the expression level of GhHDA8 was increased in GhWRKY4-silenced plants. In addition, GhHDA8-overexpressed Arabidopsis were found to be hypersensitive to drought and salt stress, while silencing of GhHDA8 enhanced drought and salt tolerance in cotton. The stress-related genes, such as GhDREB2A, GhRD22, GhP5CS, and GhNHX7, were induced in GhHDA8-silenced plants. Our findings indicate that the GhWRKY4-GhHDA8 module regulates drought and salt tolerance in cotton. Collectively, the results provide new insights into the coordination of transcription factors and histone deacetylases in regulating drought and salt stress responses in plants.
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Affiliation(s)
- Tianyu Dong
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Yueran Hu
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jiao Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Ying Wang
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Peilei Chen
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jingjing Xing
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China.
| | - Hongying Duan
- College of Life Sciences, Henan Normal University, Xinxiang 453007, China; Henan International Joint Laboratory of Aquatic Toxicology and Health Protection, College of Life Sciences, Henan Normal University, Xinxiang 453007, China.
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45
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Mora‐Carrera E, Stubbs RL, Potente G, Yousefi N, Keller B, de Vos JM, Szövényi P, Conti E. Genomic analyses elucidate S-locus evolution in response to intra-specific losses of distyly in Primula vulgaris. Ecol Evol 2024; 14:e10940. [PMID: 38516570 PMCID: PMC10955462 DOI: 10.1002/ece3.10940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 12/02/2023] [Accepted: 01/03/2024] [Indexed: 03/23/2024] Open
Abstract
Distyly, a floral dimorphism that promotes outcrossing, is controlled by a hemizygous genomic region known as the S-locus. Disruptions of genes within the S-locus are responsible for the loss of distyly and the emergence of homostyly, a floral monomorphism that favors selfing. Using whole-genome resequencing data of distylous and homostylous individuals from populations of Primula vulgaris and leveraging high-quality reference genomes of Primula we tested, for the first time, predictions about the evolutionary consequences of transitions to selfing on S-genes. Our results reveal a previously undetected structural rearrangement in CYPᵀ associated with the shift to homostyly and confirm previously reported, homostyle-specific, loss-of-function mutations in the exons of the S-gene CYPᵀ. We also discovered that the promoter and intronic regions of CYPᵀ in distylous and homostylous individuals are conserved, suggesting that down-regulation of CYPᵀ via mutations in its promoter and intronic regions is not a cause of the shift to homostyly. Furthermore, we found that hemizygosity is associated with reduced genetic diversity in S-genes compared with their paralogs outside the S-locus. Additionally, the shift to homostyly lowers genetic diversity in both the S-genes and their paralogs, as expected in primarily selfing plants. Finally, we tested, for the first time, long-standing theoretical models of changes in S-locus genotypes during early stages of the transition to homostyly, supporting the assumption that two copies of the S-locus might reduce homostyle fitness.
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Affiliation(s)
- E. Mora‐Carrera
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - R. L. Stubbs
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - G. Potente
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - N. Yousefi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - B. Keller
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - J. M. de Vos
- Department of Environmental Sciences – BotanyUniversity of BaselBaselSwitzerland
| | - P. Szövényi
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
| | - E. Conti
- Department of Systematic and Evolutionary BotanyUniversity of ZurichZurichSwitzerland
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46
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Scacchi E, Paszkiewicz G, Thi Nguyen K, Meda S, Burian A, de Back W, Timmermans MCP. A diffusible small-RNA-based Turing system dynamically coordinates organ polarity. NATURE PLANTS 2024; 10:412-422. [PMID: 38409292 DOI: 10.1038/s41477-024-01634-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 01/26/2024] [Indexed: 02/28/2024]
Abstract
The formation of a flat and thin leaf presents a developmentally challenging problem, requiring intricate regulation of adaxial-abaxial (top-bottom) polarity. The patterning principles controlling the spatial arrangement of these domains during organ growth have remained unclear. Here we show that this regulation in Arabidopsis thaliana is achieved by an organ-autonomous Turing reaction-diffusion system centred on mobile small RNAs. The data illustrate how Turing dynamics transiently instructed by prepatterned information is sufficient to self-sustain properly oriented polarity in a dynamic, growing organ, presenting intriguing parallels to left-right patterning in the vertebrate embryo. Computational modelling demonstrates that this self-organizing system continuously adapts to coordinate the robust planar polarity of a flat leaf while affording flexibility to generate the tissue patterns of evolutionarily diverse organ shapes. Our findings identify a small-RNA-based Turing network as a dynamic regulator of organ polarity that accounts for leaf shape diversity at the level of the individual organ, plant or species.
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Affiliation(s)
- Emanuele Scacchi
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany.
| | - Gael Paszkiewicz
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Khoa Thi Nguyen
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
- NTT Hi-Tech Institute, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam
| | - Shreyas Meda
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Agata Burian
- Institute of Biology, Biotechnology and Environmental Protection, University of Silesia in Katowice, Katowice, Poland
| | - Walter de Back
- Institute for Medical Informatics and Biometry, Faculty of Medicine Carl Gustav Carus, TU Dresden, Dresden, Germany
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47
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Shi Y, Hu G, Wang Y, Liang Q, Su D, Lu W, Deng W, Bouzayen M, Liu Y, Li Z, Huang B. The SlGRAS9-SlZHD17 transcriptional cascade regulates chlorophyll and carbohydrate metabolism contributing to fruit quality traits in tomato. THE NEW PHYTOLOGIST 2024; 241:2540-2557. [PMID: 38263687 DOI: 10.1111/nph.19530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 12/12/2023] [Indexed: 01/25/2024]
Abstract
Some essential components of fleshy fruits are dependent on photosynthetic activity and carbohydrate metabolism. Nevertheless, the regulatory mechanisms linking chlorophyll and carbohydrate metabolism remain partially understood. Here, we uncovered the role of SlGRAS9 and SlZHD17 transcription factors in controlling chlorophyll and carbohydrate accumulation in tomato fruit. Knockout or knockdown of SlGRAS9 or SlZHD17 resulted in marked increase in chlorophyll content, reprogrammed chloroplast biogenesis and enhanced accumulation of starch and soluble sugars. Combined genome-wide transcriptomic profiling and promoter-binding experiments unveiled a complex mechanism in which the SlGRAS9/SlZHD17 regulatory module modulates the expression of chloroplast and sugar metabolism either via a sequential transcriptional cascade or through binding of both TFs to the same gene promoters, or, alternatively, via parallel pathways where each of the TFs act on different target genes. For instance, the regulation of SlAGPaseS1 and SlSUS1 is mediated by SlZHD17 whereas that of SlVI and SlGLK1 occurs only through SlGRAS9 without the intervention of SlZHD17. Both SlGRAS9 and SlZHD17 can also directly bind the promoter of SlPOR-B to regulate its expression. Taken together, our findings uncover two important regulators acting synergistically to manipulate chlorophyll and carbohydrate accumulation and provide new potential breeding targets for improving fruit quality in fleshy fruits.
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Affiliation(s)
- Yuan Shi
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Guojian Hu
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Laboratoire de Recherche en Sciences Vegetales - Genomique et Biotechnologie des Fruits - UMR5546, Universite de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, 31326, France
| | - Yan Wang
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Qin Liang
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Deding Su
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Wang Lu
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Wei Deng
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Mondher Bouzayen
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
- Laboratoire de Recherche en Sciences Vegetales - Genomique et Biotechnologie des Fruits - UMR5546, Universite de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, 31326, France
| | - Yudong Liu
- School of Agricultural Sciences, Zhengzhou University, Zhengzhou, 450001, China
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
| | - Baowen Huang
- Key Laboratory of Plant Hormones and Molecular Breeding of Chongqing, School of Life Sciences, Chongqing University, Chongqing, 401331, China
- Center of Plant Functional Genomics, Institute of Advanced Interdisciplinary Studies, Chongqing University, Chongqing, 401331, China
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48
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Song B, Buckler ES, Stitzer MC. New whole-genome alignment tools are needed for tapping into plant diversity. TRENDS IN PLANT SCIENCE 2024; 29:355-369. [PMID: 37749022 DOI: 10.1016/j.tplants.2023.08.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/19/2023] [Accepted: 08/23/2023] [Indexed: 09/27/2023]
Abstract
Genome alignment is one of the most foundational methods for genome sequence studies. With rapid advances in sequencing and assembly technologies, these newly assembled genomes present challenges for alignment tools to meet the increased complexity and scale. Plant genome alignment is technologically challenging because of frequent whole-genome duplications (WGDs) as well as chromosome rearrangements and fractionation, high nucleotide diversity, widespread structural variation, and high transposable element (TE) activity causing large proportions of repeat elements. We summarize classical pairwise and multiple genome alignment (MGA) methods, and highlight techniques that are widely used or are being developed by the plant research community. We also outline the remaining challenges for precise genome alignment and the interpretation of alignment results in plants.
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Affiliation(s)
- Baoxing Song
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agriculture Sciences in Weifang, Weifang, Shandong 261325, China; Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region of the Ministry of Agriculture, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Edward S Buckler
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Section of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853, USA; Agricultural Research Service, United States Department of Agriculture, Ithaca, NY 14853, USA
| | - Michelle C Stitzer
- Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA; Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.
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49
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Wang X, Wei J, Wu J, Shi B, Wang P, Alabd A, Wang D, Gao Y, Ni J, Bai S, Teng Y. Transcription factors BZR2/MYC2 modulate brassinosteroid and jasmonic acid crosstalk during pear dormancy. PLANT PHYSIOLOGY 2024; 194:1794-1814. [PMID: 38036294 DOI: 10.1093/plphys/kiad633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 10/27/2023] [Accepted: 10/29/2023] [Indexed: 12/02/2023]
Abstract
Bud dormancy is an important physiological process during winter. Its release requires a certain period of chilling. In pear (Pyrus pyrifolia), the abscisic acid (ABA)-induced expression of DORMANCY-ASSOCIATED MADS-box (DAM) genes represses bud break, whereas exogenous gibberellin (GA) promotes dormancy release. However, with the exception of ABA and GA, the regulatory effects of phytohormones on dormancy remain largely uncharacterized. In this study, we confirmed brassinosteroids (BRs) and jasmonic acid (JA) contribute to pear bud dormancy release. If chilling accumulation is insufficient, both 24-epibrassinolide (EBR) and methyl jasmonic acid (MeJA) can promote pear bud break, implying that they positively regulate dormancy release. BRASSINAZOLE RESISTANT 2 (BZR2), which is a BR-responsive transcription factor, inhibited PpyDAM3 expression and accelerated pear bud break. The transient overexpression of PpyBZR2 increased endogenous GA, JA, and JA-Ile levels. In addition, the direct interaction between PpyBZR2 and MYELOCYTOMATOSIS 2 (PpyMYC2) enhanced the PpyMYC2-mediated activation of Gibberellin 20-oxidase genes PpyGA20OX1L1 and PpyGA20OX2L2 transcription, thereby increasing GA3 contents and accelerating pear bud dormancy release. Interestingly, treatment with 5 μm MeJA increased the bud break rate, while also enhancing PpyMYC2-activated PpyGA20OX expression and increasing GA3,4 contents. The 100 μm MeJA treatment decreased the PpyMYC2-mediated activation of the PpyGA20OX1L1 and PpyGA20OX2L2 promoters and suppressed the inhibitory effect of PpyBZR2 on PpyDAM3 transcription, ultimately inhibiting pear bud break. In summary, our data provide insights into the crosstalk between the BR and JA signaling pathways that regulate the BZR2/MYC2-mediated pathway in the pear dormancy release process.
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Affiliation(s)
- Xuxu Wang
- Hainan Institute of Zhejiang University, Sanya, Hainan 572000, PR China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Jia Wei
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Jiahao Wu
- Hainan Institute of Zhejiang University, Sanya, Hainan 572000, PR China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Baojing Shi
- Hainan Institute of Zhejiang University, Sanya, Hainan 572000, PR China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Peihui Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Ahmed Alabd
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
- Department of Pomology, Faculty of Agriculture, Alexandria University, Alexandria 21545, Egypt
| | - Duanni Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Yuhao Gao
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Junbei Ni
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Songling Bai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
| | - Yuanwen Teng
- Hainan Institute of Zhejiang University, Sanya, Hainan 572000, PR China
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, Zhejiang 310058, PR China
- Zhejiang Provincial Key Laboratory of Integrative Biology of Horticultural Plants, Hangzhou 310058, Zhejiang, PR China
- The Key Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Ministry of Agriculture of China, Hangzhou 310058, Zhejiang, PR China
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Zhang X, Ekwealor JTB, Mishler BD, Silva AT, Yu L, Jones AK, Nelson ADL, Oliver MJ. Syntrichia ruralis: emerging model moss genome reveals a conserved and previously unknown regulator of desiccation in flowering plants. THE NEW PHYTOLOGIST 2024. [PMID: 38415863 DOI: 10.1111/nph.19620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 02/05/2024] [Indexed: 02/29/2024]
Abstract
Water scarcity, resulting from climate change, poses a significant threat to ecosystems. Syntrichia ruralis, a dryland desiccation-tolerant moss, provides valuable insights into survival of water-limited conditions. We sequenced the genome of S. ruralis, conducted transcriptomic analyses, and performed comparative genomic and transcriptomic analyses with existing genomes and transcriptomes, including with the close relative S. caninervis. We took a genetic approach to characterize the role of an S. ruralis transcription factor, identified in transcriptomic analyses, in Arabidopsis thaliana. The genome was assembled into 12 chromosomes encompassing 21 169 protein-coding genes. Comparative analysis revealed copy number and transcript abundance differences in known desiccation-associated gene families, and highlighted genome-level variation among species that may reflect adaptation to different habitats. A significant number of abscisic acid (ABA)-responsive genes were found to be negatively regulated by a MYB transcription factor (MYB55) that was upstream of the S. ruralis ortholog of ABA-insensitive 3 (ABI3). We determined that this conserved MYB transcription factor, uncharacterized in Arabidopsis, acts as a negative regulator of an ABA-dependent stress response in Arabidopsis. The new genomic resources from this emerging model moss offer novel insights into how plants regulate their responses to water deprivation.
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Affiliation(s)
- Xiaodan Zhang
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Jenna T B Ekwealor
- Department of Biology, Utah State University, Logan, UT, 84322, USA
- Department of Biology, San Francisco State University, San Francisco, CA, 94132, USA
| | - Brent D Mishler
- University and Jepson Herbaria, Berkeley, CA, 94720-2465, USA
- Department of Integrative Biology, University of California, Berkeley, CA, 94720-2465, USA
| | | | - Li'ang Yu
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Andrea K Jones
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Andrew D L Nelson
- The Boyce Thompson Institute, Cornell University, Ithaca, NY, 14853, USA
| | - Melvin J Oliver
- Division of Plant Sciences and Technology and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, 65211, USA
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