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

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.