Gláucia C.B. Silva, Luciana R. Camillo, Dalma B. Santos, Maurício S. Amorim, Luana P. Gonçalves, Ana C.O. Barbosa, Dílson S. Rocha Junior, Grazielle M. Alcântara, Marcio G.C. Costa
{"title":"Identification of DEMETER-like DNA demethylase gene family in citrus and their role in drought stress-adaptive responses","authors":"Gláucia C.B. Silva, Luciana R. Camillo, Dalma B. Santos, Maurício S. Amorim, Luana P. Gonçalves, Ana C.O. Barbosa, Dílson S. Rocha Junior, Grazielle M. Alcântara, Marcio G.C. Costa","doi":"10.1016/j.compbiolchem.2024.108128","DOIUrl":null,"url":null,"abstract":"<div><p>DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the <em>DML</em> gene family in citrus is available to date. Here, a total of three <em>DML</em> genes in the genomes of <em>Citrus sinensis</em> (named <em>CsDML1–3</em>) and <em>C. clementina</em> (named <em>CcDML1–3</em>) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several <em>cis</em>-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus <em>DML</em>s in different plant tissues. <em>CsDML1</em> and <em>CsDML3</em> were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between <em>CsDML1</em> and <em>PHYTOENE SYNTHASE</em> (<em>PSY</em>) and between <em>CsDML3</em> and <em>ATP CITRATE LYASE</em>s (<em>ACL</em>s) and <em>ZETA-CAROTENE DESATURASE</em> (<em>ZDS</em>) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.</p></div>","PeriodicalId":10616,"journal":{"name":"Computational Biology and Chemistry","volume":null,"pages":null},"PeriodicalIF":2.6000,"publicationDate":"2024-06-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computational Biology and Chemistry","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1476927124001166","RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the DML gene family in citrus is available to date. Here, a total of three DML genes in the genomes of Citrus sinensis (named CsDML1–3) and C. clementina (named CcDML1–3) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several cis-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus DMLs in different plant tissues. CsDML1 and CsDML3 were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between CsDML1 and PHYTOENE SYNTHASE (PSY) and between CsDML3 and ATP CITRATE LYASEs (ACLs) and ZETA-CAROTENE DESATURASE (ZDS) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.
期刊介绍:
Computational Biology and Chemistry publishes original research papers and review articles in all areas of computational life sciences. High quality research contributions with a major computational component in the areas of nucleic acid and protein sequence research, molecular evolution, molecular genetics (functional genomics and proteomics), theory and practice of either biology-specific or chemical-biology-specific modeling, and structural biology of nucleic acids and proteins are particularly welcome. Exceptionally high quality research work in bioinformatics, systems biology, ecology, computational pharmacology, metabolism, biomedical engineering, epidemiology, and statistical genetics will also be considered.
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