DNA-(cytosine-C5) methyltransferases and demethylases in Theobroma cacao: insights into genomic features, phylogenetic relationships, and protein–protein interactions

IF 1.9 3区生物学 Q2 FORESTRY

Tree Genetics & Genomes Pub Date : 2024-02-14 DOI:10.1007/s11295-024-01640-2

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引用次数: 0

Abstract

DNA methylation is an important epigenetic mark that plays a crucial role in regulating various biological processes and adaptation to environmental conditions in both plants and animals. At present, there are no reports on the systematic analysis of the DNA-(cytosine-5) methyltransferase (C5-MTase) and demethylase (dMTase) gene families from the cacao (Theobroma cacao) genome. In this study, a comprehensive bioinformatic analysis identified the presence of seven C5-MTases (TcC5-MTases) and three dMTases (TcdMTases) in cacao. According to the sequence similarity, and conserved motif and domain architecture, TcC5-MTases were phylogenetically classified into METHYLTRANSFERASE 1 (TcMET1), CHROMOMETHYLASE (TcCMT1-3), DOMAINS REARRANGED METHYLASE (TcDRM1/2, TcDRM3), and de novo DNA METHYLTRANSFERASE 2 (TcDNMT2), and TcdMTases were classified into DEMETER (TcDME), REPRESSOR OF SILENCING 1 (TcROS1, also known as DEMETER-LIKE 1 (TcDML1)), and TcDML3 subfamilies. These genes were distributed randomly on six chromosomes. Moreover, most of the TcC5-MTases and TcdMTases were putatively localized in the nucleus, except TcDRM1/2 and TcDRM3, which were found in chloroplasts. Further analysis of cis-acting regulatory elements (CREs) in the promoter regions TcC5-MTase and TcdMTase genes inferred the presence of multiple CREs, especially stress-responsive, light-responsive, and hormone-responsive elements. Additionally, the analysis of protein–protein interaction networks revealed interactions among TcC5-MTases and with other proteins in T. cacao, such as S-adenosyl-L-homocysteine hydrolase and histone deacetylases, suggesting potential crosstalk among DNA methylation, the methionine cycle, and histone deacetylation. These interactions provide valuable insights into the complexity of regulating plant methylation levels. Collectively, the findings of this study provide a framework for further functional characterization of these genes and unravel the epigenetic mechanisms underlying growth and development, as well as adaptations to stress conditions in cacao.

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可可豆中的 DNA-（胞嘧啶-C5）甲基转移酶和脱甲基酶：对基因组特征、系统发育关系和蛋白质间相互作用的深入研究

摘要 DNA甲基化是一种重要的表观遗传标记，在调控动植物的各种生物过程和适应环境条件方面发挥着至关重要的作用。目前，还没有系统分析可可（Theobroma cacao）基因组中 DNA-（胞嘧啶-5）甲基转移酶（C5-MTase）和去甲基化酶（dMTase）基因家族的报道。在这项研究中，通过全面的生物信息学分析，确定了可可中存在 7 个 C5-MT 酶（TcC5-MT 酶）和 3 个 dMT 酶（TcdMT 酶）。根据序列相似性、保守的基序和结构域，TcC5-MTase 在系统发育上被分为 METHYLTRANSFERASE 1（TcMET1）、CHROMOMETHYLASE（TcCMT1-3）、DOMAINS REARRANGED METHYLASE（TcDRM1/2、TcdMT酶被分为 DEMETER（TcDME）、REPRESSOR OF SILENCING 1（TcROS1，又称 DEMETER-LIKE 1（TcDML1））和 TcDML3 亚家族。这些基因随机分布在六条染色体上。此外，除了 TcDRM1/2 和 TcDRM3 位于叶绿体外，大多数 TcC5-MT 酶和 TcdMT 酶都被推测定位于细胞核中。进一步分析 TcC5-MTase 和 TcdMTase 基因启动子区域的顺式调控元件（CRE），推断存在多个 CRE，尤其是胁迫响应元件、光响应元件和激素响应元件。此外，蛋白质-蛋白质相互作用网络分析还揭示了 TcC5-MT 酶之间以及与可可豆中其他蛋白质（如 S-腺苷-L-高半胱氨酸水解酶和组蛋白去乙酰化酶）之间的相互作用，表明 DNA 甲基化、蛋氨酸循环和组蛋白去乙酰化之间可能存在相互影响。这些相互作用为了解植物甲基化水平调控的复杂性提供了宝贵的见解。总之，本研究的发现为进一步确定这些基因的功能特征提供了一个框架，并揭示了可可生长和发育以及适应胁迫条件的表观遗传机制。

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来源期刊

Tree Genetics & Genomes 生物-林学

CiteScore

4.40

自引率

4.20%

发文量

审稿时长

2 months

期刊介绍： Tree Genetics and Genomes is an international, peer-reviewed journal, which provides for the rapid publication of high quality papers covering the areas of forest and horticultural tree genetics and genomics. Topics covered in this journal include: Structural, functional and comparative genomics Evolutionary, population and quantitative genetics Ecological and physiological genetics Molecular, cellular and developmental genetics Conservation and restoration genetics Breeding and germplasm development Bioinformatics and databases Tree Genetics and Genomes publishes four types of papers: (1) Original Paper (2) Review (3) Opinion Paper (4) Short Communication.