A survey of Type III restriction-modification systems reveals numerous, novel epigenetic regulators controlling phase-variable regulons; phasevarions. Issue 7 (15th March 2018)

• Record Type: Journal Article
• Authors: Atack, John M; Yang, Yuedong; Seib, Kate L; Zhou, Yaoqi; Jennings, Michael P
• Is Part Of: Nucleic acids research. Volume 46:Issue 7(2018)
• Page Start: 3532
• Page End: 3542
• Publication Date: 2018-03-15
• Subjects: Nucleic acids -- Periodicals; Molecular biology -- Periodicals; 572.805
• DOI: 10.1093/nar/gky192
• Languages: English
• ISSNs: 0305-1048

Abstract

Abstract: Many bacteria utilize simple DNA sequence repeats as a mechanism to randomly switch genes on and off. This process is called phase variation. Several phase-variable N 6 -adenine DNA-methyltransferases from Type III restriction-modification systems have been reported in bacterial pathogens. Random switching of DNA methyltransferases changes the global DNA methylation pattern, leading to changes in gene expression. These epigenetic regulatory systems are called phasevarions — phase-variable regulons. The extent of these phase-variable genes in the bacterial kingdom is unknown. Here, we interrogated a database of restriction-modification systems, REBASE, by searching for all simple DNA sequence repeats in mod genes that encode Type III N 6 -adenine DNA-methyltransferases. We report that 17.4% of Type III mod genes (662/3805) contain simple sequence repeats. Of these, only one-fifth have been previously identified. The newly discovered examples are widely distributed and include many examples in opportunistic pathogens as well as in environmental species. In many cases, multiple phasevarions exist in one genome, with examples of up to 4 independent phasevarions in some species. We found several new types of phase-variable mod genes, including the first example of a phase-variable methyltransferase in pathogenic Escherichia coli . Phasevarions are a common epigenetic regulation contingency strategy used by both pathogenic and non-pathogenic bacteria.