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PLoS Genet. 2016 Feb 12;12(2):e1005854. doi: 10.1371/journal.pgen.1005854. eCollection 2016 Feb.

The Epigenomic Landscape of Prokaryotes.

Author information

1
Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
2
U.S. Department of Energy Joint Genome Institute, Walnut Creek, California, United States of America.
3
Pacific Biosciences, Menlo Park, California, United States of America.
4
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
5
New England Biolabs, Ipswich, Massachusetts, United States of America.

Abstract

DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.

PMID:
26870957
PMCID:
PMC4752239
DOI:
10.1371/journal.pgen.1005854
[Indexed for MEDLINE]
Free PMC Article

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