1
|
He X, Wang Q, Pan J, Liu B, Ruan Y, Huang Y. Systematic analysis of JmjC gene family and stress--response expression of KDM5 subfamily genes in Brassica napus. PeerJ 2021; 9:e11137. [PMID: 33850662 PMCID: PMC8019318 DOI: 10.7717/peerj.11137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Background Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization by Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean. In JmjC proteins of Brassica species, the structure and function and its relationship with the parents and model plant Arabidopsis thaliana remain uncharacterized. Systematic identification and analysis for JmjC family in Brassica crops can facilitate the future functional characterization and oilseed crops improvement. Methods Basing on the conserved JmjC domain, JmjC homologs from the three Brassica species, B. rapa (AA), B. oleracea (CC) and B. napus, were identified from the Brassica database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of BnKDM5 subfamily genes were checked under abiotic stress by qRT-PCR. Results Sixty-five JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of B. napus JmjC genes (B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the BrKDM5 subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress. Conclusions This study provides the first genome-wide characterization of JmjC genes in Brassica species. The BnJmjC exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole B. napus genome. Furthermore, expression profiles of many genes indicated that BnKDM5 subfamily genes are involved in stress response to salt, drought and high temperature.
Collapse
Affiliation(s)
- Xinghui He
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Qianwen Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Jiao Pan
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Boyu Liu
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Ying Ruan
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Yong Huang
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| |
Collapse
|
4
|
Ayyappan V, Kalavacharla V, Thimmapuram J, Bhide KP, Sripathi VR, Smolinski TG, Manoharan M, Thurston Y, Todd A, Kingham B. Genome-Wide Profiling of Histone Modifications (H3K9me2 and H4K12ac) and Gene Expression in Rust (Uromyces appendiculatus) Inoculated Common Bean (Phaseolus vulgaris L.). PLoS One 2015; 10:e0132176. [PMID: 26167691 PMCID: PMC4500563 DOI: 10.1371/journal.pone.0132176] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Accepted: 06/10/2015] [Indexed: 01/12/2023] Open
Abstract
Histone modifications such as methylation and acetylation play a significant role in controlling gene expression in unstressed and stressed plants. Genome-wide analysis of such stress-responsive modifications and genes in non-model crops is limited. We report the genome-wide profiling of histone methylation (H3K9me2) and acetylation (H4K12ac) in common bean (Phaseolus vulgaris L.) under rust (Uromyces appendiculatus) stress using two high-throughput approaches, chromatin immunoprecipitation sequencing (ChIP-Seq) and RNA sequencing (RNA-Seq). ChIP-Seq analysis revealed 1,235 and 556 histone methylation and acetylation responsive genes from common bean leaves treated with the rust pathogen at 0, 12 and 84 hour-after-inoculation (hai), while RNA-Seq analysis identified 145 and 1,763 genes differentially expressed between mock-inoculated and inoculated plants. The combined ChIP-Seq and RNA-Seq analyses identified some key defense responsive genes (calmodulin, cytochrome p450, chitinase, DNA Pol II, and LRR) and transcription factors (WRKY, bZIP, MYB, HSFB3, GRAS, NAC, and NMRA) in bean-rust interaction. Differential methylation and acetylation affected a large proportion of stress-responsive genes including resistant (R) proteins, detoxifying enzymes, and genes involved in ion flux and cell death. The genes identified were functionally classified using Gene Ontology (GO) and EuKaryotic Orthologous Groups (KOGs). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified a putative pathway with ten key genes involved in plant-pathogen interactions. This first report of an integrated analysis of histone modifications and gene expression involved in the bean-rust interaction as reported here provides a comprehensive resource for other epigenomic regulation studies in non-model species under stress.
Collapse
Affiliation(s)
- Vasudevan Ayyappan
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America
| | - Venu Kalavacharla
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America
- Center for Integrated Biological and Environmental Research (CIBER), Delaware State University, Dover, Delaware, United States of America
| | - Jyothi Thimmapuram
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, United States of America
| | - Ketaki P. Bhide
- Bioinformatics Core, Purdue University, West Lafayette, Indiana, United States of America
| | - Venkateswara R. Sripathi
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America
| | - Tomasz G. Smolinski
- Computational Intelligence and Bio(logical)informatics Laboratory (CIBiL), Delaware State University, Dover, Delaware, United States of America
| | - Muthusamy Manoharan
- Department of Agriculture, University of Arkansas, Pine Bluff, Arkansas, United States of America
| | - Yaqoob Thurston
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America
| | - Antonette Todd
- Molecular Genetics and Epigenomics Laboratory, Delaware State University, Dover, Delaware, United States of America
| | - Bruce Kingham
- Sequencing and Genotyping Center, Delaware Biotechnology Institute, Newark, Delaware, United States of America
| |
Collapse
|
5
|
Sharma N, Bender Y, Boyle K, Fobert PR. High-level expression of sugar inducible gene2 (HSI2) is a negative regulator of drought stress tolerance in Arabidopsis. BMC PLANT BIOLOGY 2013; 13:170. [PMID: 24168327 PMCID: PMC3893512 DOI: 10.1186/1471-2229-13-170] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2012] [Accepted: 10/02/2013] [Indexed: 05/08/2023]
Abstract
BACKGROUND HIGH-LEVEL EXPRESSION OF SUGAR INDUCIBLE GENE2 (HSI2), also known as VAL1, is a B3 domain transcriptional repressor that acts redundantly with its closest relative, HSI2-LIKE1 (HSL1), to suppress the seed maturation program following germination. Mutant hsi2 hsl1 seedlings are arrested early in development and differentially express a number of abiotic stress-related genes. To test the potential requirement for HSI2 during abiotic stress, hsi2 single mutants and plants overexpressing HSI2 were subjected to simulated drought stress by withholding watering, and characterized through physiological, metabolic and gene expression studies. RESULTS The hsi2 mutants demonstrated reduced wilting and maintained higher relative water content than wild-type after withholding watering, while the overexpressing lines displayed the opposite phenotype. The hsi2 mutant displayed lower constitutive and ABA-induced stomatal conductance than wild-type and accumulated lower levels of ABA metabolites and several osmolytes and osmoprotectants following water withdrawal. Microarray comparisons between wild-type and the hsi2 mutant revealed that steady-state levels of numerous stress-induced genes were up-regulated in the mutant in the absence of stress but down-regulated at visible wilting. Plants with altered levels of HSI2 responded to exogenous application of ABA and a long-lived ABA analog, but the hsi2 mutant did not show altered expression of several ABA-responsive or ABA signalling genes 4 hr after application. CONCLUSIONS These results implicate HSI2 as a negative regulator of drought stress response in Arabidopsis, acting, at least in part, by regulating transpirational water loss. Metabolic and global transcript profiling comparisons of the hsi2 mutant and wild-type plants do not support a model whereby the greater drought tolerance observed in the hsi2 mutant is conferred by the accumulation of known osmolytes and osmoprotectants. Instead, data are consistent with mutants experiencing a relatively milder dehydration stress following water withdrawal.
Collapse
MESH Headings
- Abscisic Acid/pharmacology
- Adaptation, Physiological/drug effects
- Adaptation, Physiological/genetics
- Arabidopsis/drug effects
- Arabidopsis/genetics
- Arabidopsis/physiology
- Arabidopsis Proteins/genetics
- Arabidopsis Proteins/metabolism
- DNA, Bacterial/genetics
- Down-Regulation/drug effects
- Down-Regulation/genetics
- Droughts
- Gene Expression Regulation, Plant/drug effects
- Gene Ontology
- Kinetics
- Metabolome/drug effects
- Metabolome/genetics
- Molecular Sequence Annotation
- Mutagenesis, Insertional/drug effects
- Mutagenesis, Insertional/genetics
- Mutation/genetics
- Oligonucleotide Array Sequence Analysis
- Plant Stomata/drug effects
- Plant Stomata/genetics
- Plant Stomata/physiology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- Reproducibility of Results
- Stress, Physiological/drug effects
- Stress, Physiological/genetics
- Transcriptome/genetics
Collapse
Affiliation(s)
- Nirmala Sharma
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Yarnel Bender
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Kerry Boyle
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| | - Pierre R Fobert
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9, Canada
| |
Collapse
|
6
|
Heisel TJ, Li CY, Grey KM, Gibson SI. Mutations in HISTONE ACETYLTRANSFERASE1 affect sugar response and gene expression in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2013; 4:245. [PMID: 23882272 PMCID: PMC3713338 DOI: 10.3389/fpls.2013.00245] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 06/19/2013] [Indexed: 05/23/2023]
Abstract
Nutrient response networks are likely to have been among the first response networks to evolve, as the ability to sense and respond to the levels of available nutrients is critical for all organisms. Although several forward genetic screens have been successful in identifying components of plant sugar-response networks, many components remain to be identified. Toward this end, a reverse genetic screen was conducted in Arabidopsis thaliana to identify additional components of sugar-response networks. This screen was based on the rationale that some of the genes involved in sugar-response networks are likely to be themselves sugar regulated at the steady-state mRNA level and to encode proteins with activities commonly associated with response networks. This rationale was validated by the identification of hac1 mutants that are defective in sugar response. HAC1 encodes a histone acetyltransferase. Histone acetyltransferases increase transcription of specific genes by acetylating histones associated with those genes. Mutations in HAC1 also cause reduced fertility, a moderate degree of resistance to paclobutrazol and altered transcript levels of specific genes. Previous research has shown that hac1 mutants exhibit delayed flowering. The sugar-response and fertility defects of hac1 mutants may be partially explained by decreased expression of AtPV42a and AtPV42b, which are putative components of plant SnRK1 complexes. SnRK1 complexes have been shown to function as central regulators of plant nutrient and energy status. Involvement of a histone acetyltransferase in sugar response provides a possible mechanism whereby nutritional status could exert long-term effects on plant development and metabolism.
Collapse
Affiliation(s)
| | | | | | - Susan I. Gibson
- Department of Plant Biology, Microbial and Plant Genomics Institute, University of MinnesotaSaint Paul, MN, USA
| |
Collapse
|
7
|
Migicovsky Z, Kovalchuk I. Changes to DNA methylation and homologous recombination frequency in the progeny of stressed plants. Biochem Cell Biol 2013; 91:1-5. [PMID: 23442135 DOI: 10.1139/bcb-2012-0046] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Plants undergo changes in response to biotic and abiotic stresses that help them adjust and survive. Some of these changes may even be passed on to progeny and eventually lead to adaptive evolution. Transgenerational changes in response to stress include alterations in DNA methylation and changes in homologous recombination frequency (HRF). The progeny of plants that were stressed often show elevated HRF as well as genomic hypermethylation, although specific loci that are beneficial in times of stress may be hypomethylated. One of the possible mechanisms responsible for passing the memory to the progeny involves small interfering RNAs; Dicer-like proteins, DCL2 and DCL3, are in part required for this process. However, while epigenetic modifications are often present in the untreated progeny of stressed plants, they are not usually sustained for multiple unexposed generations. Still, transgenerational inheritance of such changes has already begun to provide evidence for an important role of epigenetics in enhancing stress resistance.
Collapse
Affiliation(s)
- Zoë Migicovsky
- University of Lethbridge, Department of Biological Sciences, Lethbridge, AB T1K 3M4, Canada
| | | |
Collapse
|