Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges

Abstract

The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation. Here, we present an overview of the multifaceted roles of DNA methylation in prokaryotes and suggest research directions and tools which can enable us to better understand the contribution of DNA methylation to prokaryotic genome evolution and adaptation. In particular, we emphasize the need to understand the presence and role of transgenerational inheritance, as well as the impact of epigenomic signatures on adaptation and genome evolution. Research directions and the importance of novel computational tools are underlined.

Keywords: bacterial epigenomics; bacterial genome evolution; prokaryotic DNA methylation.

Figure 1

Effects of DNA methylation on cellular functions, adaptation, and evolution. DNA methylation plays a pivotal role in the replication of DNA, marking the parental strand to prevent and allow for the correction of replication errors. DNA methylation plays different roles in the adaptation of prokaryotes to the environment (e.g., quorum sensing, antibiotic resistance, virulence and pathogenicity, and developmental processes), modeling the accessibility of genetic material to the transcriptional machinery and thus influencing the transcription of genes. R-M systems, as well as the presence of phasevarions, shape the methylation pattern of prokaryotic cells through the expression of DNA MTases, with effects on environmental adaptation and the exchange of genetic material.

Figure 2

An analysis of genome-wide DNA methylation data. Here, the MeStudio [68] workflow is shown. Starting from genome sequencing obtained by the SMRT sequencing technique and genome annotation file, the recurrent methylated DNA motifs identified are searched within the genome sequence(s). Three main outputs are obtained, a .gff3 file and .bed file with annotated methylated sequences and their occurrence with respect to genomic regions (e.g., coding sequences, promoters, etc.) and a file with statistics of the occurrence of motifs and the percentage of their methylation. Visual outputs shown as circus plots may allow us to easily identify regions with peculiar methylation patterns and are saved as PDF files.