The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

Fullmer, Matthew S.; Ouellette, Matthew; Louyakis, Artemis S.; Papke, R. Thane; Gogarten, Johann Peter

doi:10.3390/genes10030233

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The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

^1,2,†,

^1,†,

^1,†

^1,* and

Johann Peter Gogarten

^1,*

Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269-3125, USA

Bioinformatics Institute, School of Biological Sciences, The University of Auckland, Auckland 1010, New Zealand

Authors to whom correspondence should be addressed.

^†

These authors contributed equally.

Genes 2019, 10(3), 233; https://doi.org/10.3390/genes10030233

Received: 15 February 2019 / Revised: 13 March 2019 / Accepted: 14 March 2019 / Published: 19 March 2019

(This article belongs to the Special Issue Genetics of Halophilic Microorganisms)

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Abstract

Restriction–modification (RM) systems in bacteria are implicated in multiple biological roles ranging from defense against parasitic genetic elements, to selfish addiction cassettes, and barriers to gene transfer and lineage homogenization. In bacteria, DNA-methylation without cognate restriction also plays important roles in DNA replication, mismatch repair, protein expression, and in biasing DNA uptake. Little is known about archaeal RM systems and DNA methylation. To elucidate further understanding for the role of RM systems and DNA methylation in Archaea, we undertook a survey of the presence of RM system genes and related genes, including orphan DNA methylases, in the halophilic archaeal class Halobacteria. Our results reveal that some orphan DNA methyltransferase genes were highly conserved among lineages indicating an important functional constraint, whereas RM systems demonstrated patchy patterns of presence and absence. This irregular distribution is due to frequent horizontal gene transfer and gene loss, a finding suggesting that the evolution and life cycle of RM systems may be best described as that of a selfish genetic element. A putative target motif (CTAG) of one of the orphan methylases was underrepresented in all of the analyzed genomes, whereas another motif (GATC) was overrepresented in most of the haloarchaeal genomes, particularly in those that encoded the cognate orphan methylase. View Full-Text

Keywords: HGT; restriction; methylation; gene transfer; selfish genes; archaea; haloarchaea; DNA methylase; epigenetics

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MDPI and ACS Style

Fullmer, M.S.; Ouellette, M.; Louyakis, A.S.; Papke, R.T.; Gogarten, J.P. The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. Genes 2019, 10, 233. https://doi.org/10.3390/genes10030233

AMA Style

Fullmer MS, Ouellette M, Louyakis AS, Papke RT, Gogarten JP. The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria. Genes. 2019; 10(3):233. https://doi.org/10.3390/genes10030233

Chicago/Turabian Style

Fullmer, Matthew S., Matthew Ouellette, Artemis S. Louyakis, R. T. Papke, and Johann P. Gogarten. 2019. "The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria" Genes 10, no. 3: 233. https://doi.org/10.3390/genes10030233

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The Patchy Distribution of Restriction–Modification System Genes and the Conservation of Orphan Methyltransferases in Halobacteria

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