1
|
Jiang D, Berger F. Variation is important: Warranting chromatin function and dynamics by histone variants. CURRENT OPINION IN PLANT BIOLOGY 2023; 75:102408. [PMID: 37399781 DOI: 10.1016/j.pbi.2023.102408] [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: 03/23/2023] [Revised: 05/24/2023] [Accepted: 06/01/2023] [Indexed: 07/05/2023]
Abstract
The chromatin of flowering plants exhibits a wide range of sequence variants of the core and linker histones. Recent studies have demonstrated that specific histone variant enrichment, combined with post-translational modifications (PTMs) of histones, defines distinct chromatin states that impact specific chromatin functions. Chromatin remodelers are emerging as key regulators of histone variant dynamics, contributing to shaping chromatin states and regulating gene transcription in response to environment. Recognizing the histone variants by their specific readers, controlled by histone PTMs, is crucial for maintaining genome and chromatin integrity. In addition, various histone variants have been shown to play essential roles in remodeling chromatin domains to facilitate important programmed transitions throughout the plant life cycle. In this review, we discuss recent findings in this exciting field of research, which holds immense promise for many surprising discoveries related to the evolution of complexity in plant organization through a seemingly simple protein family.
Collapse
Affiliation(s)
- Danhua Jiang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy for Seed Design, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
| | - Frédéric Berger
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
2
|
Wan J, Zhang J, Zan X, Zhu J, Chen H, Li X, Zhou Z, Gao X, Chen R, Huang Z, Xu Z, Li L. Overexpression of Rice Histone H1 Gene Reduces Tolerance to Cold and Heat Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:2408. [PMID: 37446969 DOI: 10.3390/plants12132408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023]
Abstract
Temperature stresses, including low- and high-temperature stresses, are the main abiotic stresses affecting rice yield. Due to global climate change, the impact of temperature pressure on rice yield is gradually increasing, which is also a major concern for researchers. In this study, an H1 histone in Oryza sativa (OsHis1.1, LOC_Os04g18090) was cloned, and its role in rice's response to temperature stresses was functionally characterized. The GUS staining analysis of OsHis1.1 promoter-GUS transgenic rice showed that OsHis1.1 was widely expressed in various rice tissues. Transient expression demonstrated that OsHis1.1 was localized in the nucleus. The overexpression of OsHis1.1 reduces the tolerance to temperature stress in rice by inhibiting the expression of genes that are responsive to heat and cold stress. Under stress conditions, the POD activity and chlorophyll and proline contents of OsHis1.1-overexpression rice lines were significantly lower than those of the wild type, while the malondialdehyde content was higher than that of the wild type. Compared with Nip, OsHis1.1-overexpression rice suffered more serious oxidative stress and cell damage under temperature stress. Furthermore, OsHis1.1-overexpression rice showed changes in agronomic traits.
Collapse
Affiliation(s)
- Jiale Wan
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jia Zhang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaofei Zan
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Jiali Zhu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Hao Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaohong Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhanmei Zhou
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoling Gao
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Rongjun Chen
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Zhengjian Huang
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Zhengjun Xu
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| | - Lihua Li
- Rice Research Institute, Sichuan Agricultural University, Chengdu 611130, China
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Crop Ecophysiology and Cultivation Key Laboratory of Sichuan Province, Chengdu 611130, China
| |
Collapse
|
3
|
Wu X, Xu J, Meng X, Fang X, Xia M, Zhang J, Cao S, Fan T. Linker histone variant HIS1-3 and WRKY1 oppositely regulate salt stress tolerance in Arabidopsis. PLANT PHYSIOLOGY 2022; 189:1833-1847. [PMID: 35474141 PMCID: PMC9237719 DOI: 10.1093/plphys/kiac174] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Accepted: 11/03/2021] [Indexed: 06/12/2023]
Abstract
The salt overly sensitive (SOS) pathway plays an important role in plant salt stress; however, the transcriptional regulation of the genes in this pathway is unclear. In this study, we found that Linker histone variant HIS1-3 and WRKY1 oppositely regulate the salt stress response in Arabidopsis (Arabidopsis thaliana) through the transcriptional regulation of SOS genes. The expression of HIS1-3 was inhibited by salt stress, and the disruption of HIS1-3 resulted in enhanced salt tolerance. Conversely, the expression of WRKY1 was induced by salt stress, and the loss of WRKY1 function led to increased salt sensitivity. The expression of SOS1, SOS2, and SOS3 was repressed and induced by HIS1-3 and WRKY1, respectively, and HIS1-3 regulated the expression of SOS1 and SOS3 by occupying the WRKY1 binding sites on their promoters. Moreover, WRKY1 and HIS1-3 acted upstream of the SOS pathway. Together, our results indicate that HIS1-3 and WRKY1 oppositely modulate salt tolerance in Arabidopsis through transcriptional regulation of SOS genes.
Collapse
Affiliation(s)
| | | | | | - Xue Fang
- School of Horticulture, Anhui Agricultural University, Hefei 230009, China
| | - Minghui Xia
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230009, China
| | - Jing Zhang
- 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
| | | |
Collapse
|
4
|
Abdelmoghny AM, Raghavendra KP, Sheeba JA, Santosh HB, Meshram JH, Singh SB, Kranthi KR, Waghmare VN. Morpho-physiological and molecular characterization of drought tolerance traits in Gossypium hirsutum genotypes under drought stress. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:2339-2353. [PMID: 33424151 PMCID: PMC7772122 DOI: 10.1007/s12298-020-00890-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/01/2020] [Accepted: 09/30/2020] [Indexed: 06/12/2023]
Abstract
Drought stress is one of the major abiotic stresses affecting lint yield and fibre quality in cotton. With increase in population, degrading natural resources and frequent drought occurrences, development of high yielding, drought tolerant cotton cultivars is critical for sustainable cotton production across countries. Six Gossypium hirsutum genotypes identified for drought tolerance, wider adaptability and better fibre quality traits were characterized for various morpho-physiological and biochemical characters and their molecular basis was investigated under drought stress. Under drought conditions, genotypes revealed statistically significant differences for all the morpho-physiological and biochemical traits. The interaction (genotype × treatment) effects were highly significant for root length, excised leaf water loss and cell membrane thermostability indicating differential interaction of genotypes under control and stress conditions. Correlation studies revealed that under drought stress, relative water content had significant positive correlation with root length and root-to-shoot ratio while it had significant negative correlation with excised leaf water loss, epicuticular wax, proline, potassium and total soluble sugar content. Analysis of expression of fourteen drought stress related genes under water stress indicated that both ABA dependent and ABA independent mechanisms of drought tolerance might be operating differentially in the studied genotypes. IC325280 and LRA5166 exhibited ABA mediated expression of stress responsive genes and traits. Molecular basis of drought tolerance in IC357406, Suraj, IC259637 and CNH 28I genotypes could be attributed to ABA independent pathway. Based on physiological phenotyping, the genotypes IC325280 and IC357406 were identified to possess better root traits and LRA5166 was found to have enhanced cellular level tolerance. Variety Suraj exhibited good osmotic adjustment and better root traits to withstand water stress. The identified drought component trait(s) in specific genotypes would pave way for their pyramiding through marker assisted cotton breeding.
Collapse
Affiliation(s)
- A. M. Abdelmoghny
- Cotton Research Institute (CRI), Agricultural Research Center (ARC), Giza, Egypt
| | | | - J. Annie Sheeba
- ICAR - Central Institute for Cotton Research (CICR), Nagpur, India
| | - H. B. Santosh
- ICAR - Central Institute for Cotton Research (CICR), Nagpur, India
| | | | - Suman Bala Singh
- ICAR - Central Institute for Cotton Research (CICR), Nagpur, India
| | - K. R. Kranthi
- ICAR - Central Institute for Cotton Research (CICR), Nagpur, India
- International Cotton Advisory Committee (ICAC), Washington, DC USA
| | - V. N. Waghmare
- ICAR - Central Institute for Cotton Research (CICR), Nagpur, India
| |
Collapse
|
5
|
Gu W, Yu D, Guan Y, Wang H, Qin T, Sun P, Hu Y, Wei J, Zheng H. The dynamic transcriptome of waxy maize (Zea mays L. sinensis Kulesh) during seed development. Genes Genomics 2020; 42:997-1010. [PMID: 32676852 DOI: 10.1007/s13258-020-00967-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/03/2020] [Indexed: 11/28/2022]
Abstract
BACKGROUND Waxy maize (Zea mays L. sinensis Kulesh) is a mutant of maize (Zea mays L.) with a mutation at Waxy1 (Wx1) gene locus. The seed of waxy maize has higher viscosity compared to regular maize. By now, we know little about the expression patterns of genes that involved in the seed development of waxy maize. OBJECTIVE By analyzing the transcriptome data during waxy maize seed development, we attempt to dig out the genes that may influence the seed development of waxy maize. METHODS The seeds of waxy maize inbred line SWL01 from six phases after pollination were used to do RNA-seq. Bioinformatics methods were used to analyze the expression patterns of the expressed genes, to identify the genes involved in waxy maize seed development. RESULTS A total of 24,546 genes including 1611 transcription factors (TFs) were detected during waxy maize seed development. Coexpression analysis of expressed genes revealed the dynamic processes of waxy maize seed development. Particularly, 2457 genes including 177 TFs were specially expressed in waxy maize seed, some of which mainly involved in the process of seed dormancy and maturation. In addition, 2681, 5686, 4491, 4386, 3669 and 4624 genes were identified to be differential expressed genes (DEGs) at six phases compared to regular maize B73, and 113 DEGs among them may be key genes that lead the difference of seed development between waxy and regular maizes in milk stage. CONCLUSION In summary, we elucidated the expression patterns of expressed genes during waxy maize seed development globally. A series of genes that associated with seed development were identified in our research, which may provide an important resource for functional study of waxy maize seed development to help molecular assisted breeding.
Collapse
Affiliation(s)
- Wei Gu
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Diansi Yu
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Yuan Guan
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Hui Wang
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Tao Qin
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Pingdong Sun
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Yingxiong Hu
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Jihui Wei
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China
| | - Hongjian Zheng
- Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China. .,CIMMYT-China Specialty Maize Research Center, Shanghai Academy of Agricultural Sciences, Shanghai, 201403, China.
| |
Collapse
|
6
|
Jiang Z, Jin F, Shan X, Li Y. iTRAQ-Based Proteomic Analysis Reveals Several Strategies to Cope with Drought Stress in Maize Seedlings. Int J Mol Sci 2019; 20:ijms20235956. [PMID: 31779286 PMCID: PMC6928945 DOI: 10.3390/ijms20235956] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/19/2019] [Accepted: 11/25/2019] [Indexed: 12/11/2022] Open
Abstract
Drought stress, especially during the seedling stage, seriously limits the growth of maize and reduces production in the northeast of China. To investigate the molecular mechanisms of drought response in maize seedlings, proteome changes were analyzed. Using an isotopic tagging relative quantitation (iTRAQ) based method, a total of 207 differentially accumulated protein species (DAPS) were identified under drought stress in maize seedlings. The DAPS were classified into ten essential groups and analyzed thoroughly, which involved in signaling, osmotic regulation, protein synthesis and turnover, reactive oxygen species (ROS) scavenging, membrane trafficking, transcription related, cell structure and cell cycle, fatty acid metabolism, carbohydrate and energy metabolism, as well as photosynthesis and photorespiration. The enhancements of ROS scavenging, osmotic regulation, protein turnover, membrane trafficking, and photosynthesis may play important roles in improving drought tolerance of maize seedlings. Besides, the inhibitions of some protein synthesis and slowdown of cell division could reduce the growth rate and avoid excessive water loss, which is possible to be the main reasons for enhancing drought avoidance of maize seedlings. The incongruence between protein and transcript levels was expectedly observed in the process of confirming iTRAQ data by quantitative real-time polymerase chain reaction (qRT-PCR) analysis, which further indicated that the multiplex post-transcriptional regulation and post-translational modification occurred in drought-stressed maize seedlings. Finally, a hypothetical strategy was proposed that maize seedlings coped with drought stress by improving drought tolerance (via. promoting osmotic adjustment and antioxidant capacity) and enhancing drought avoidance (via. reducing water loss). Our study provides valuable insight to mechanisms underlying drought response in maize seedlings.
Collapse
Affiliation(s)
- Zhilei Jiang
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Changchun 130033, China; (Z.J.); (F.J.)
| | - Fengxue Jin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Changchun 130033, China; (Z.J.); (F.J.)
| | - Xiaohui Shan
- College of Plant Science, Jilin University, Changchun 130062, China
- Correspondence: (X.S.); (Y.L.)
| | - Yidan Li
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences/Jilin Provincial Key Laboratory of Agricultural Biotechnology, Changchun 130033, China; (Z.J.); (F.J.)
- Correspondence: (X.S.); (Y.L.)
| |
Collapse
|
7
|
Yin X, Komatsu S. Comprehensive analysis of response and tolerant mechanisms in early-stage soybean at initial-flooding stress. J Proteomics 2017; 169:225-232. [PMID: 28137666 DOI: 10.1016/j.jprot.2017.01.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/17/2017] [Accepted: 01/23/2017] [Indexed: 12/31/2022]
Abstract
Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, which markedly reduces its growth and yield. Morphological and biochemical changes such as an increase of fresh weight and a decrease of ATP content happen in early-stage soybean at initial-flooding stress, indicating that soybean responses to flooding stress are keys for its survival and seedling growth. Phosphoproteomics and nuclear proteomics are useful tools to detect protein-phosphorylation status and to identify transcriptional factors. In the review, the effect of flooding on soybean response to initial flooding stress is discussed based on recent results of proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies. In addition, soybean survival under flooding stress, which is defined as tolerance mechanism, is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. BIOLOGICAL SIGNIFICANCE Soybean is one of the most cultivated crops in the world; however, it is very sensitive to flooding stress, especially soybean responses to initial flooding stress is key for its survival and seedling growth. Recently, proteomic techniques are applied to investigate the response and tolerant mechanisms of soybean at initial flooding condition. In this review, the progress in proteomic, phosphoproteomic, nuclear proteomic, and nuclear phosphoproteomic studies about the initial-flooding response mechanism in early-stage soybean is presented. In addition, the tolerant mechanism in soybean is discussed with the results of comprehensive analysis in flooding-tolerant mutant line and abscisic acid-treated soybean. Through this review, the key proteins and genes involved in initial flooding response and tolerance at early stage soybean are summarized and they contribute greatly to uncover response and tolerance mechanism at early stage under stressful environmental conditions in soybean.
Collapse
Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba 305-8572, Japan; National Institute of Crop Science, National Agriculture and Food Research Organization, Tsukuba 305-8518, Japan.
| |
Collapse
|
8
|
Wang X, Cai X, Xu C, Wang Q, Dai S. Drought-Responsive Mechanisms in Plant Leaves Revealed by Proteomics. Int J Mol Sci 2016; 17:E1706. [PMID: 27763546 PMCID: PMC5085738 DOI: 10.3390/ijms17101706] [Citation(s) in RCA: 126] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/06/2016] [Accepted: 09/22/2016] [Indexed: 02/04/2023] Open
Abstract
Plant drought tolerance is a complex trait that requires a global view to understand its underlying mechanism. The proteomic aspects of plant drought response have been extensively investigated in model plants, crops and wood plants. In this review, we summarize recent proteomic studies on drought response in leaves to reveal the common and specialized drought-responsive mechanisms in different plants. Although drought-responsive proteins exhibit various patterns depending on plant species, genotypes and stress intensity, proteomic analyses show that dominant changes occurred in sensing and signal transduction, reactive oxygen species scavenging, osmotic regulation, gene expression, protein synthesis/turnover, cell structure modulation, as well as carbohydrate and energy metabolism. In combination with physiological and molecular results, proteomic studies in leaves have helped to discover some potential proteins and/or metabolic pathways for drought tolerance. These findings provide new clues for understanding the molecular basis of plant drought tolerance.
Collapse
Affiliation(s)
- Xiaoli Wang
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Xiaofeng Cai
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Chenxi Xu
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Quanhua Wang
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| | - Shaojun Dai
- Development Centre of Plant Germplasm Resources, College of Life and Environmental Sciences, Shanghai Normal University, Shanghai 200234, China.
| |
Collapse
|
9
|
Jiang D, Berger F. Histone variants in plant transcriptional regulation. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:123-130. [PMID: 27412913 DOI: 10.1016/j.bbagrm.2016.07.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Revised: 06/18/2016] [Accepted: 07/03/2016] [Indexed: 12/28/2022]
Abstract
Chromatin based organization of eukaryotic genome plays a profound role in regulating gene transcription. Nucleosomes form the basic subunits of chromatin by packaging DNA with histone proteins, impeding the access of DNA to transcription factors and RNA polymerases. Exchange of histone variants in nucleosomes alters the properties of nucleosomes and thus modulates DNA exposure during transcriptional regulation. Growing evidence indicates the important function of histone variants in programming transcription during developmental transitions and stress response. Here we review how histone variants and their deposition machineries regulate the nucleosome stability and dynamics, and discuss the link between histone variants and transcriptional regulation in plants. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
Collapse
Affiliation(s)
- Danhua Jiang
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria
| | - Frédéric Berger
- Gregor Mendel Institute, Vienna Biocenter, Dr. Bohr-Gasse 3, 1030 Vienna, Austria.
| |
Collapse
|
10
|
Yin X, Komatsu S. Nuclear Proteomics Reveals the Role of Protein Synthesis and Chromatin Structure in Root Tip of Soybean during the Initial Stage of Flooding Stress. J Proteome Res 2016; 15:2283-98. [PMID: 27291164 DOI: 10.1021/acs.jproteome.6b00330] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
To identify the upstream events controlling the regulation of flooding-responsive proteins in soybean, proteomic analysis of nuclear proteins in root tip was performed. By using nuclear fractions, which were highly enriched, a total of 365 nuclear proteins were changed in soybean root tip at initial stage of flooding stress. Four exon-junction complex-related proteins and NOP1/NOP56, which function in upstream of 60S preribosome biogenesis, were decreased in flooded soybean. Furthermore, proteomic analysis of crude protein extract revealed that the protein translation was suppressed by continuous flooding stress. Seventeen chromatin structure-related nuclear proteins were decreased in response to flooding stress. Out of them, histone H3 was clearly decreased with protein abundance and mRNA expression levels at the initial flooding stress. Additionally, a number of protein synthesis-, RNA-, and DNA-related nuclear proteins were decreased in a time-dependent manner. mRNA expressions of genes encoding the significantly changed flooding-responsive nuclear proteins were inhibited by the transcriptional inhibitor, actinomycin D. These results suggest that protein translation is suppressed through inhibition of preribosome biogenesis- and mRNA processing-related proteins in nuclei of soybean root tip at initial flooding stress. In addition, flooding stress may regulate histone variants with gene expression in root tip.
Collapse
Affiliation(s)
- Xiaojian Yin
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
| | - Setsuko Komatsu
- Graduate School of Life and Environmental Sciences, University of Tsukuba , Tsukuba 305-8572, Japan
- National Institute of Crop Science, National Agriculture and Food Research Organization , Tsukuba 305-8518, Japan
| |
Collapse
|
11
|
Ranjan A, Sawant S. Genome-wide transcriptomic comparison of cotton (Gossypium herbaceum) leaf and root under drought stress. 3 Biotech 2015; 5:585-596. [PMID: 28324561 PMCID: PMC4522718 DOI: 10.1007/s13205-014-0257-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Accepted: 09/30/2014] [Indexed: 02/05/2023] Open
Abstract
In this study, the 454 pyrosequencing platform was used for analyzing the comparative transcriptomic profiles of leaf and root tissues of 1-month-old cotton (Gossypium herbaceum) plants under drought stress. A total of 56,354 and 49,308 reads were generated from leaf and root tissues, respectively, and clustered into 6,313 and 5,858 unigenes. The differentially expressed unigenes that showed up-regulation (≥2-fold) or down-regulation (2≤-fold) were considered for further analysis. A total of 3,517 unigenes were differentially expressed in both tissues. The 1,528 genes specific to leaves and 1,128 specific to roots were obtained. The 28 biological pathways in two tissues were found to respond significantly to drought stress. A total of 289 in leaf and 277 in root unknown (novel) unigenes were found to be remarkably regulated by drought stress. Some key regulatory genes involved in abiotic stress such as WRKY, ERF, AP2 EREBP, MYB, and LEA were highly expressed in leaves. The genes RHD3, LBD, and transcription factor WRKY75, known for root development under various stress conditions, were expressed specifically in root. The genes related to chlorophyll a/b binding protein and photosystem-related proteins showed significant higher expression in roots and as compared to leaves. It can be concluded that cotton leaves are distinct from roots in terms of molecular mechanisms for responses to drought stress.
Collapse
Affiliation(s)
- Alok Ranjan
- Department of Biotechnology, Faculty of Science, Banaras Hindu University, Varanasi, 221005, UP, India.
| | - Samir Sawant
- National Botanical Research Institute, CSIR, Lucknow, 226001, UP, India
| |
Collapse
|
12
|
Xie F, Wang Q, Sun R, Zhang B. Deep sequencing reveals important roles of microRNAs in response to drought and salinity stress in cotton. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:789-804. [PMID: 25371507 PMCID: PMC4321542 DOI: 10.1093/jxb/eru437] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Drought and salinity are two major environmental factors adversely affecting plant growth and productivity. However, the regulatory mechanism is unknown. In this study, the potential roles of small regulatory microRNAs (miRNAs) in cotton response to those stresses were investigated. Using next-generation deep sequencing, a total of 337 miRNAs with precursors were identified, comprising 289 known miRNAs and 48 novel miRNAs. Of these miRNAs, 155 miRNAs were expressed differentially. Target prediction, Gene Ontology (GO)-based functional classification, and Kyoto Encyclopedia of Genes and Genomes (KEGG)-based functional enrichment show that these miRNAs might play roles in response to salinity and drought stresses through targeting a series of stress-related genes. Degradome sequencing analysis showed that at least 55 predicted target genes were further validated to be regulated by 60 miRNAs. CitationRank-based literature mining was employed to determinhe the importance of genes related to drought and salinity stress. The NAC, MYB, and MAPK families were ranked top under the context of drought and salinity, indicating their important roles for the plant to combat drought and salinity stress. According to target prediction, a series of cotton miRNAs are associated with these top-ranked genes, including miR164, miR172, miR396, miR1520, miR6158, ghr-n24, ghr-n56, and ghr-n59. Interestingly, 163 cotton miRNAs were also identified to target 210 genes that are important in fibre development. These results will contribute to cotton stress-resistant breeding as well as understanding fibre development.
Collapse
Affiliation(s)
- Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qinglian Wang
- Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, PR China
| | - Runrun Sun
- Department of Biology, East Carolina University, Greenville, NC 27858, USA Henan Institute of Sciences and Technology, Xinxiang, Henan 453003, PR China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| |
Collapse
|
13
|
Wang W, Wang Y, Du Y, Zhao Z, Zhu X, Jiang X, Shu Z, Yin Y, Li X. Overexpression of Camellia sinensis H1 histone gene confers abiotic stress tolerance in transgenic tobacco. PLANT CELL REPORTS 2014; 33:1829-41. [PMID: 25063323 DOI: 10.1007/s00299-014-1660-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2014] [Revised: 07/07/2014] [Accepted: 07/14/2014] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE Overexpression of CsHis in tobacco promoted chromatin condensation, but did not affect the phenotype. It also conferred tolerance to low-temperature, high-salinity, ABA, drought and oxidative stress in transgenic tobacco. H1 histone, as a major structural protein of higher-order chromatin, is associated with stress responses in plants. Here, we describe the functions of the Camellia sinensis H1 Histone gene (CsHis) to illustrate its roles in plant responses to stresses. Subcellular localization and prokaryotic expression assays showed that the CsHis protein is localized in the nucleus, and its molecular size is approximately 22.5 kD. The expression levels of CsHis in C. sinensis leaves under various conditions were investigated by qRT-PCR, and the results indicated that CsHis was strongly induced by various abiotic stresses such as low-temperature, high-salinity, ABA, drought and oxidative stress. Overexpression of CsHis in tobacco (Nicotiana tabacum) promoted chromatin condensation, while there were almost no changes in the growth and development of transgenic tobacco plants. Phylogenetic analysis showed that CsHis belongs to the H1C and H1D variants of H1 histones, which are stress-induced variants and not the key variants required for growth and development. Stress tolerance analysis indicated that the transgenic tobacco plants exhibited higher tolerance than the WT plants upon exposure to various abiotic stresses; the transgenic plants displayed reduced wilting and senescence and exhibited greater net photosynthetic rate (Pn), stomatal conductance (Gs) and maximal photochemical efficiency (Fv/Fm) values. All the above results suggest that CsHis is a stress-induced gene and that its overexpression improves the tolerance to various abiotic stresses in the transgenic tobacco plants, possibly through the maintenance of photosynthetic efficiency.
Collapse
Affiliation(s)
- Weidong Wang
- Tea Science Research Institute, Nanjing Agricultural University, Nanjing, 210095, China,
| | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Talbert PB, Henikoff S. Environmental responses mediated by histone variants. Trends Cell Biol 2014; 24:642-50. [PMID: 25150594 DOI: 10.1016/j.tcb.2014.07.006] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 07/22/2014] [Accepted: 07/24/2014] [Indexed: 01/19/2023]
Abstract
Fluctuations in the ambient environment can trigger chromatin disruptions, involving replacement of nucleosomes or exchange of their histone subunits. Unlike canonical histones, which are available only during S-phase, replication-independent histone variants are present throughout the cell cycle and are adapted for chromatin repair. The H2A.Z variant mediates responses to environmental perturbations including fluctuations in temperature and seasonal variation. Phosphorylation of histone H2A.X rapidly marks double-strand DNA breaks for chromatin repair, which is mediated by both H2A and H3 histone variants. Other histones are used as weapons in conflicts between parasites and their hosts, which suggests broad involvement of histone variants in environmental responses beyond chromatin repair.
Collapse
Affiliation(s)
- Paul B Talbert
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA
| | - Steven Henikoff
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA; Howard Hughes Medical Institute, Seattle, WA 98109, USA.
| |
Collapse
|
15
|
Han SK, Wagner D. Role of chromatin in water stress responses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2785-99. [PMID: 24302754 PMCID: PMC4110454 DOI: 10.1093/jxb/ert403] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
As sessile organisms, plants are exposed to environmental stresses throughout their life. They have developed survival strategies such as developmental and morphological adaptations, as well as physiological responses, to protect themselves from adverse environments. In addition, stress sensing triggers large-scale transcriptional reprogramming directed at minimizing the deleterious effect of water stress on plant cells. Here, we review recent findings that reveal a role of chromatin in water stress responses. In addition, we discuss data in support of the idea that chromatin remodelling and modifying enzymes may be direct targets of stress signalling pathways. Modulation of chromatin regulator activity by these signaling pathways may be critical in minimizing potential trade-offs between growth and stress responses. Alterations in the chromatin organization and/or in the activity of chromatin remodelling and modifying enzymes may furthermore contribute to stress memory. Mechanistic insight into these phenomena derived from studies in model plant systems should allow future engineering of broadly drought-tolerant crop plants that do not incur unnecessary losses in yield or growth.
Collapse
Affiliation(s)
- Soon-Ki Han
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| |
Collapse
|
16
|
Over RS, Michaels SD. Open and closed: the roles of linker histones in plants and animals. MOLECULAR PLANT 2014; 7:481-91. [PMID: 24270504 PMCID: PMC3941478 DOI: 10.1093/mp/sst164] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 11/11/2013] [Indexed: 05/19/2023]
Abstract
Histones package DNA in all eukaryotes and play key roles in regulating gene expression. Approximately 150 base pairs of DNA wraps around an octamer of core histones to form the nucleosome, the basic unit of chromatin. Linker histones compact chromatin further by binding to and neutralizing the charge of the DNA between nucleosomes. It is well established that chromatin packing is regulated by a complex pattern of posttranslational modifications (PTMs) to core histones, but linker histone function is less well understood. In this review, we describe the current understanding of the many roles that linker histones play in cellular processes, including gene regulation, cell division, and development, while putting the linker histone in the context of other nuclear proteins. Although intriguing roles for plant linker histones are beginning to emerge, much of our current understanding comes from work in animal systems. Many unanswered questions remain and additional work is required to fully elucidate the complex processes mediated by linker histones in plants.
Collapse
Affiliation(s)
| | - Scott D. Michaels
- To whom correspondence should be addressed. E-mail , fax 812-855-6082, tel. 812-856-0302
| |
Collapse
|
17
|
Tripathi P, Rabara RC, Rushton PJ. A systems biology perspective on the role of WRKY transcription factors in drought responses in plants. PLANTA 2014; 239:255-66. [PMID: 24146023 DOI: 10.1007/s00425-013-1985-y] [Citation(s) in RCA: 132] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 10/14/2013] [Indexed: 05/20/2023]
Abstract
Drought is one of the major challenges affecting crop productivity and yield. However, water stress responses are notoriously multigenic and quantitative with strong environmental effects on phenotypes. It is also clear that water stress often does not occur alone under field conditions but rather in conjunction with other abiotic stresses such as high temperature and high light intensities. A multidisciplinary approach with successful integration of a whole range of -omics technologies will not only define the system, but also provide new gene targets for both transgenic approaches and marker-assisted selection. Transcription factors are major players in water stress signaling and some constitute major hubs in the signaling webs. The main transcription factors in this network include MYB, bHLH, bZIP, ERF, NAC, and WRKY transcription factors. The role of WRKY transcription factors in abiotic stress signaling networks is just becoming apparent and systems biology approaches are starting to define their places in the signaling network. Using systems biology approaches, there are now many transcriptomic analyses and promoter analyses that concern WRKY transcription factors. In addition, reports on nuclear proteomics have identified WRKY proteins that are up-regulated at the protein level by water stress. Interactomics has started to identify different classes of WRKY-interacting proteins. What are often lacking are connections between metabolomics, WRKY transcription factors, promoters, biosynthetic pathways, fluxes and downstream responses. As more levels of the system are characterized, a more detailed understanding of the roles of WRKY transcription factors in drought responses in crops will be obtained.
Collapse
Affiliation(s)
- Prateek Tripathi
- Molecular and Computational Biology, Department of Biological Sciences, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, TRF 108, 3430 S Vermont Ave, Los Angeles, CA, 90089, USA,
| | | | | |
Collapse
|
18
|
Chi Y, Yang Y, Zhou Y, Zhou J, Fan B, Yu JQ, Chen Z. Protein-protein interactions in the regulation of WRKY transcription factors. MOLECULAR PLANT 2013; 6:287-300. [PMID: 23455420 DOI: 10.1093/mp/sst026] [Citation(s) in RCA: 201] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
It has been almost 20 years since the first report of a WRKY transcription factor, SPF1, from sweet potato. Great progress has been made since then in establishing the diverse biological roles of WRKY transcription factors in plant growth, development, and responses to biotic and abiotic stress. Despite the functional diversity, almost all analyzed WRKY proteins recognize the TTGACC/T W-box sequences and, therefore, mechanisms other than mere recognition of the core W-box promoter elements are necessary to achieve the regulatory specificity of WRKY transcription factors. Research over the past several years has revealed that WRKY transcription factors physically interact with a wide range of proteins with roles in signaling, transcription, and chromatin remodeling. Studies of WRKY-interacting proteins have provided important insights into the regulation and mode of action of members of the important family of transcription factors. It has also emerged that the slightly varied WRKY domains and other protein motifs conserved within each of the seven WRKY subfamilies participate in protein-protein interactions and mediate complex functional interactions between WRKY proteins and between WRKY and other regulatory proteins in the modulation of important biological processes. In this review, we summarize studies of protein-protein interactions for WRKY transcription factors and discuss how the interacting partners contribute, at different levels, to the establishment of the complex regulatory and functional network of WRKY transcription factors.
Collapse
Affiliation(s)
- Yingjun Chi
- Department of Horticulture, Zhejiang University, Hangzhou, China
| | | | | | | | | | | | | |
Collapse
|