Context-dependent conservation of DNA methyltransferases in bacteria.

Nucleic Acids Research
Aswin S N SeshasayeeSandeep Krishna

Abstract

DNA methytransferases (MTs) in bacteria are best understood in the context of restriction-modification (R-M) systems, which act as bacterial immune systems against incoming DNA including phages, but have also been described as selfish elements. But several orphan MTs, which are not associated with any restriction enzyme, have also been characterized and may protect against parasitism by R-M systems. The occurrence of MTs in these two contexts, namely as part of R-M systems or as orphans, is poorly understood. Here we report the results of a comparative genomic survey of DNA MTs across ∼1000 bacterial genomes. We show that orphan MTs overwhelm R-M systems in their occurrence. In general, R-M MTs are poorly conserved, whereas orphans are nearly as conserved within a genus as any average gene. However, oligonucleotide usage and conservation patterns across genera suggest that both forms of MTs might have been horizontally acquired. We suggest that many orphan MTs might be 'degradation' products of R-M systems, based on the properties of orphan MTs encoded adjacent to highly diverged REs. In addition, several fully degraded R-M systems exist in which both the MT and the RE are highly divergent from their corresponding reference R-M...Continue Reading

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Citations

May 11, 2013·Molecular BioSystems·Rajalakshmi SrinivasanAswin Sai Narain Seshasayee
Sep 12, 2012·Nucleic Acids Research·Anna S ErshovaAndrei V Alexeevski
Aug 31, 2013·Nucleic Acids Research·Wil A M Loenen, Elisabeth A Raleigh
Aug 15, 2014·Nucleic Acids Research·Pedro H OliveiraEduardo P C Rocha
Oct 15, 2013·Applied and Environmental Microbiology·James MurphyDouwe van Sinderen
Aug 30, 2016·Indian Journal of Microbiology·Aniel Jessica Leticia Brambila-TapiaKatya Rodríguez-Vázquez
Mar 15, 2016·Journal of Bioinformatics and Computational Biology·Anna ErshovaAnna Karyagina
Jun 18, 2015·Frontiers in Microbiology·Kim SneppenSandeep Krishna
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Mar 14, 2018·Proceedings of the National Academy of Sciences of the United States of America·Tong TongShi Chen
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Oct 13, 2020·FEMS Microbiology Letters·Kevin T MilitelloRachel Knapp
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Jul 28, 2021·Annual Review of Microbiology·Brian P Anton, Richard J Roberts

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Software Mentioned

EMBOSS
AlienHunter
REBASE
LOESS
phmmer
Alien Hunter
HMMER
R

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