1
|
Shao Z, Bai Y, Huq E, Qiao H. LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.01.583049. [PMID: 38496578 PMCID: PMC10942398 DOI: 10.1101/2024.03.01.583049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Ethylene signaling has been indicated as a potential positive regulator of plant warm ambient temperature response but its underlying molecular mechanisms are largely unknown. Here, we show that LHP1 and INO80 cooperate with ethylene signaling for warm ambient temperature response by activating specific bivalent genes. We found that the presence of warm ambient temperature activates ethylene signaling through EIN2 and EIN3, leading to an interaction between LHP1 and accumulated EIN2-C to co-regulate a subset of LHP1-bound genes marked by H3K27me3 and H3K4me3 bivalency. Furthermore, we demonstrate that INO80 is recruited to bivalent genes by interacting with EIN2-C and EIN3, promoting H3K4me3 enrichment and facilitating transcriptional activation in response to warm ambient temperature. Together, our findings illustrate a novel mechanism wherein ethylene signaling orchestrates LHP1 and INO80 to regulate warm ambient temperature response through activating specific bivalent genes in Arabidopsis.
Collapse
|
2
|
Wang K, Li M, Zhang B, Chang Y, An S, Zhao W. Sugar starvation activates the OsSnRK1a-OsbHLH111/OsSGI1-OsTPP7 module to mediate growth inhibition of rice. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2033-2046. [PMID: 37384619 PMCID: PMC10502754 DOI: 10.1111/pbi.14110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/29/2023] [Accepted: 06/15/2023] [Indexed: 07/01/2023]
Abstract
Sugar deficiency is the persistent challenge for plants during development. Trehalose-6-phosphate (T6P) is recognized as a key regulator in balancing plant sugar homeostasis. However, the underlying mechanisms by which sugar starvation limits plant development are unclear. Here, a basic helix-loop-helix (bHLH) transcription factor (OsbHLH111) was named starvation-associated growth inhibitor 1 (OsSGI1) and the focus is on the sugar shortage of rice. The transcript and protein levels of OsSGI1 were markedly increased during sugar starvation. The knockout mutants sgi1-1/2/3 exhibited increased grain size and promoted seed germination and vegetative growth, which were opposite to those of overexpression lines. The direct binding of OsSGI1 to sucrose non-fermenting-1 (SNF1)-related protein kinase 1a (OsSnRK1a) was enhanced during sugar shortage. Subsequently, OsSnRK1a-dependent phosphorylation of OsSGI1 enhanced the direct binding to the E-box of trehalose 6-phosphate phosphatase 7 (OsTPP7) promoter, thus rose the transcription inhibition on OsTPP7, then elevated trehalose 6-phosphate (Tre6P) content but decreased sucrose content. Meanwhile, OsSnRK1a degraded phosphorylated-OsSGI1 by proteasome pathway to prevent the cumulative toxicity of OsSGI1. Overall, we established the OsSGI1-OsTPP7-Tre6P loop with OsSnRK1a as center and OsSGI1 as forward, which is activated by sugar starvation to regulate sugar homeostasis and thus inhibits rice growth.
Collapse
Affiliation(s)
- Kun Wang
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
- College of Biological SciencesChina Agricultural UniversityBeijingChina
| | - Mengqi Li
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Bo Zhang
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Yanpeng Chang
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Shiheng An
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| | - Wenli Zhao
- College of Plant ProtectionHenan Agricultural UniversityZhengzhouHenanChina
| |
Collapse
|
3
|
Low nitrogen conditions accelerate flowering by modulating the phosphorylation state of FLOWERING BHLH 4 in Arabidopsis. Proc Natl Acad Sci U S A 2021; 118:2022942118. [PMID: 33963081 DOI: 10.1073/pnas.2022942118] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Nitrogen (N) is an essential nutrient that affects multiple plant developmental processes, including flowering. As flowering requires resources to develop sink tissues for reproduction, nutrient availability is tightly linked to this process. Low N levels accelerate floral transition; however, the molecular mechanisms underlying this response are not well understood. Here, we identify the FLOWERING BHLH 4 (FBH4) transcription factor as a key regulator of N-responsive flowering in Arabidopsis Low N-induced early flowering is compromised in fbh quadruple mutants. We found that FBH4 is a highly phosphorylated protein and that FBH4 phosphorylation levels decrease under low N conditions. In addition, decreased phosphorylation promotes FBH4 nuclear localization and transcriptional activation of the direct target CONSTANS (CO) and downstream florigen FLOWERING LOCUS T (FT) genes. Moreover, we demonstrate that the evolutionarily conserved cellular fuel sensor SNF1-RELATED KINASE 1 (SnRK1), whose kinase activity is down-regulated under low N conditions, directly phosphorylates FBH4. SnRK1 negatively regulates CO and FT transcript levels under high N conditions. Together, these results reveal a mechanism by which N levels may fine-tune FBH4 nuclear localization by adjusting the phosphorylation state to modulate flowering time. In addition to its role in flowering regulation, we also showed that FBH4 was involved in low N-induced up-regulation of nutrient recycling and remobilization-related gene expression. Thus, our findings provide insight into N-responsive growth phase transitions and optimization of plant fitness under nutrient-limited conditions.
Collapse
|
4
|
Liu Z, Zheng L, Pu L, Ma X, Wang X, Wu Y, Ming H, Wang Q, Zhang G. ENO2 Affects the Seed Size and Weight by Adjusting Cytokinin Content and Forming ENO2-bZIP75 Complex in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2020; 11:574316. [PMID: 32983222 PMCID: PMC7479207 DOI: 10.3389/fpls.2020.574316] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 08/13/2020] [Indexed: 06/11/2023]
Abstract
Arabidopsis thaliana ENO2 (AtENO2) encodes two proteins AtENO2 (enolase) and AtMBP-1 (c-Myc binding protein 1-like). The loss of AtENO2 function causes the constitutive developmental defects which are correlated with reduced enolase activity, but not AtMBP-1 transcript abundance. However, the regulation mechanism of AtENO2 on the seed properties is still not clear. In this study, we found that the mutation of AtENO2 reduced the seed size and weight. The level of glucose in seed was significantly elevated but that of starch was decreased in AtENO2 mutants compared to WT plants. We also found that AtENO2 mutation reduced the content of cytokinin which resulted in smaller cotyledons. The RNA-seq data showed that there were 1892 differentially expressed genes and secondary metabolic pathways were significantly enriched. Instead of AtMBP-1, AtENO2 protein interacted with AtbZIP75 which may mediate the secondary metabolism. Therefore, ENO2 alters the size and weight of seeds which is not only regulated by the content of cytokinin and secondary metabolism, but may be affected by the interaction of ENO2 and bZIP57. These results are helpful to understand the novel function of AtENO2 which provide a foundation for further exploration of the key candidate genes for crop breeding.
Collapse
Affiliation(s)
- Zijin Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lamei Zheng
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Li Pu
- Biotechnology Research Institute, Chinese Academy of Agriculture Sciences, Beijing, China
| | - Xiaofeng Ma
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xing Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yu Wu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Hainan Ming
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Qing Wang
- Institute of Radiation Botany, Beijing Radiation Center, Beijing, China
| | - Genfa Zhang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| |
Collapse
|
5
|
Han J, Wang P, Wang Q, Lin Q, Chen Z, Yu G, Miao C, Dao Y, Wu R, Schnable JC, Tang H, Wang K. Genome-Wide Characterization of DNase I-Hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses. THE PLANT CELL 2020; 32:2457-2473. [PMID: 32471863 PMCID: PMC7401015 DOI: 10.1105/tpc.19.00716] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 05/11/2020] [Accepted: 05/23/2020] [Indexed: 05/05/2023]
Abstract
Deep sequencing of DNase-I treated chromatin (DNase-seq) can be used to identify DNase I-hypersensitive sites (DHSs) and facilitates genome-scale mining of de novo cis-regulatory DNA elements. Here, we adapted DNase-seq to generate genome-wide maps of DHSs using control and cold-treated leaf, stem, and root tissues of three widely studied grass species: Brachypodium distachyon, foxtail millet (Setaria italica), and sorghum (Sorghum bicolor). Functional validation demonstrated that 12 of 15 DHSs drove reporter gene expression in transiently transgenic B. distachyon protoplasts. DHSs under both normal and cold treatment substantially differed among tissues and species. Intriguingly, the putative DHS-derived transcription factors (TFs) are largely colocated among tissues and species and include 17 ubiquitous motifs covering all grass taxa and all tissues examined in this study. This feature allowed us to reconstruct a regulatory network that responds to cold stress. Ethylene-responsive TFs SHINE3, ERF2, and ERF9 occurred frequently in cold feedback loops in the tissues examined, pointing to their possible roles in the regulatory network. Overall, we provide experimental annotation of 322,713 DHSs and 93 derived cold-response TF binding motifs in multiple grasses, which could serve as a valuable resource for elucidating the transcriptional networks that function in the cold-stress response and other physiological processes.
Collapse
Affiliation(s)
- Jinlei Han
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Pengxi Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qiongli Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Qingfang Lin
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Zhiyong Chen
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Guangrun Yu
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Chenyong Miao
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Yihang Dao
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Ruoxi Wu
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - James C Schnable
- Center for Plant Science Innovation, University of Nebraska, Lincoln, Nebraska 68588
| | - Haibao Tang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| | - Kai Wang
- Key Laboratory of Genetics, Breeding, and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, 350002 Fuzhou, China
| |
Collapse
|
6
|
Li X, Sanagi M, Lu Y, Nomura Y, Stolze SC, Yasuda S, Saijo Y, Schulze WX, Feil R, Stitt M, Lunn JE, Nakagami H, Sato T, Yamaguchi J. Protein Phosphorylation Dynamics Under Carbon/Nitrogen-Nutrient Stress and Identification of a Cell Death-Related Receptor-Like Kinase in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2020; 11:377. [PMID: 32308664 PMCID: PMC7145971 DOI: 10.3389/fpls.2020.00377] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/16/2020] [Indexed: 05/03/2023]
Abstract
Nutrient availability, in particular the availability of sugar [carbon (C)] and nitrogen (N), is important for the regulation of plant metabolism and development. In addition to independent utilization of C and N nutrients, plants sense and respond to the balance of C and N nutrients (C/N-nutrient) available to them. High C/low N-nutrient stress has been shown to arrest early post-germinative growth while promoting progression to senescence in Arabidopsis. Although several signaling components of the C/N-nutrient response have been identified, the inclusive molecular basis of plant C/N-nutrient response remains unclear. This proteome analysis evaluated phosphorylation dynamics in response to high C/low N-nutrient stress. Phosphoproteomics under conditions of C/N-nutrient stress showed a global change in the phosphorylation status of proteins, including plasma membrane H+-ATPase, carbon and nitrogen metabolic enzymes and signaling proteins such as protein kinases and transcription factors. Further analyses suggested that SNF1-related protein kinase 1 (SnRK1) is involved in primary C/N-nutrient signal mediation via the transcriptional regulation of C/N-regulatory kinases. We also identified a leucine-rich repeat receptor-like kinase with extracellular malectin-like domain, named as LMK1, which was shown to possess cell death induction activity in plant leaves. These results provide important insight into the C/N-nutrient signaling pathways connecting nutrition stress to various cellular and physiological processes in plants.
Collapse
Affiliation(s)
- Xingwen Li
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Miho Sanagi
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Lu
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| | - Yuko Nomura
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
| | | | - Shigetaka Yasuda
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Yusuke Saijo
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Japan
| | - Waltraud X. Schulze
- Department of Plant Systems Biology, University of Hohenheim, Stuttgart, Germany
| | - Regina Feil
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Mark Stitt
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - John E. Lunn
- Max Planck Institute of Molecular Plant Physiology, Golm, Germany
| | - Hirofumi Nakagami
- Plant Proteomics Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, Japan
- Max Planck Institute for Plant Breeding Research, Cologne, Germany
- *Correspondence: Hirofumi Nakagami,
| | - Takeo Sato
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
- Takeo Sato,
| | - Junji Yamaguchi
- Faculty of Science and Graduate School of Life Sciences, Hokkaido University, Sapporo, Japan
| |
Collapse
|
7
|
Luo Y, Aoyama S, Fukao Y, Chiba Y, Sato T, Yamaguchi J. Involvement of the membrane-localized ubiquitin ligase ATL8 in sugar starvation response in Arabidopsis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2019; 36:107-112. [PMID: 31768111 PMCID: PMC6847778 DOI: 10.5511/plantbiotechnology.19.0328a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 03/28/2019] [Indexed: 05/11/2023]
Abstract
As major components of the ubiquitin system, ubiquitin ligases mediate the transfer of ubiquitin to specific target substrates, thereby playing important roles in regulating a wide range of cellular processes. The Arabidopsis Tóxicos en Levadura (ATL) family is a group of plant-specific RING-type ubiquitin ligases with N-terminal transmembrane-like domains. To date, 91 ATL isoforms have been identified in the Arabidopsis genome, with some reported to regulate plant responses to environmental stresses. However, the functions of most ATLs remain unclear. This study showed that ATL8 is a sugar starvation response gene and that ATL8 expression was significantly increased by sugar starvation conditions but repressed by exogenous sugar supply. The ATL8 protein was found to possess ubiquitin ligase activity in vitro and to localize to membrane-bound compartments in plant cells. In addition, Starch Synthase 4 was identified as a putative interactor with ATL8, suggesting that ATL8 may be involved in modulating starch accumulation in response to sugar availability. These findings suggest that ATL8 functions as a membrane-localized ubiquitin ligase likely to be involved in the adaptation of Arabidopsis plants to sugar starvation stress.
Collapse
Affiliation(s)
- Yongming Luo
- Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shoki Aoyama
- Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoichiro Fukao
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Shiga 525-8577, Japan
| | - Yukako Chiba
- Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takeo Sato
- Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junji Yamaguchi
- Faculty of Science and Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| |
Collapse
|