Exploring the roles of DNA methylation in the metal-reducing bacterium Shewanella oneidensis MR-1

Journal Article · Fri Aug 30 04:00:00 EDT 2013 · Journal of Bacteriology

DOI:https://doi.org/10.1128/JB.00935-13· OSTI ID:1241160

Bendall, Matthew L. ^[1]; Luong, Khai ^[2]; Wetmore, Kelly M. ^[1]; Blow, Matthew ^[1]; Korlach, Jonas ^[2]; Deutschbauer, Adam ^[1]; Malmstrom, Rex ^[1]

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1. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
2. Pacific Biosciences, Menlo Park, CA (United States)

We performed whole genome analyses of DNA methylation in Shewanella 17 oneidensis MR-1 to examine its possible role in regulating gene expression and 18 other cellular processes. Single-Molecule Real Time (SMRT) sequencing 19 revealed extensive methylation of adenine (N6mA) throughout the 20 genome. These methylated bases were located in five sequence motifs, 21 including three novel targets for Type I restriction/modification enzymes. The 22 sequence motifs targeted by putative methyltranferases were determined via 23 SMRT sequencing of gene knockout mutants. In addition, we found S. 24 oneidensis MR-1 cultures grown under various culture conditions displayed 25 different DNA methylation patterns. However, the small number of differentially 26 methylated sites could not be directly linked to the much larger number of 27 differentially expressed genes in these conditions, suggesting DNA methylation is 28 not a major regulator of gene expression in S. oneidensis MR-1. The enrichment 29 of methylated GATC motifs in the origin of replication indicate DNA methylation 30 may regulate genome replication in a manner similar to that seen in Escherichia 31 coli. Furthermore, comparative analyses suggest that many 32 Gammaproteobacteria, including all members of the Shewanellaceae family, may 33 also utilize DNA methylation to regulate genome replication.

• Research Organization: Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: AC02-05CH11231
• OSTI ID: 1241160
• Report Number(s): LBNL--7086E
• Journal Information: Journal of Bacteriology, Journal Name: Journal of Bacteriology Journal Issue: 21 Vol. 195; ISSN 0021-9193
• Publisher: American Society for Microbiology
• Country of Publication: United States
• Language: English

Related Subjects

99 GENERAL AND MISCELLANEOUS
DNA
Shewanella oneidensis MR-1
methylation