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The bacterial epigenome

Abstract

In all domains of life, genomes contain epigenetic information superimposed over the nucleotide sequence. Epigenetic signals control DNA–protein interactions and can cause phenotypic change in the absence of mutation. A nearly universal mechanism of epigenetic signalling is DNA methylation. In bacteria, DNA methylation has roles in genome defence, chromosome replication and segregation, nucleoid organization, cell cycle control, DNA repair and regulation of transcription. In many bacterial species, DNA methylation controls reversible switching (phase variation) of gene expression, a phenomenon that generates phenotypic cell variants. The formation of epigenetic lineages enables the adaptation of bacterial populations to harsh or changing environments and modulates the interaction of pathogens with their eukaryotic hosts.

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Fig. 1: Methylation, hemimethylation and passive demethylation of GATC sites in gammaproteobacteria.
Fig. 2: Control of bistable loci by the formation of alternative Dam methylation patterns.
Fig. 3: Formation of subpopulations controlled by Dam-dependent methylation.
Fig. 4: Mechanisms of switching and methylome diversification in phasevarions.

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Acknowledgements

Work in the authors’ laboratory is supported by grant BIO2016-75235-P from the Ministerio de Ciencia, Innovación y Universidades of Spain and the European Regional Fund. They are grateful to M. van der Woude and L. García-Pastor for discussions.

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J.C. and M.A.S.-R. contributed to discussion of the content, wrote the article, reviewed and edited the manuscript before submission, and researched data for the article.

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Glossary

Methylome

Overall DNA methylation pattern in a genome.

Adaptive value

In population genetics, the contribution of a phenotypic trait to the fitness of an individual or a population.

Restriction–modification (R-M) systems

Machine systems that eliminate foreign DNA molecules by endonucleolytic cleavage and protect the genome by modification of the cognate endonuclease target. A frequent type of protection is DNA methylation.

SOS regulon

Regulatory network that responds to DNA damage in gammaproteobacteria.

Homopolymeric nucleotide tract

DNA region that contains only AT or GC nucleotide pairs.

Transparent–opaque transition

Formation of phenotypic variants (phase variation) of Streptococcus pneumoniae that is involved in pneumococcal carriage and invasive infection.

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Sánchez-Romero, M.A., Casadesús, J. The bacterial epigenome. Nat Rev Microbiol 18, 7–20 (2020). https://doi.org/10.1038/s41579-019-0286-2

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