Title |
The complete methylome of Helicobacter pylori UM032
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Published in |
BMC Genomics, June 2015
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DOI | 10.1186/s12864-015-1585-2 |
Pubmed ID | |
Authors |
Woon Ching Lee, Brian P Anton, Susana Wang, Primo Baybayan, Siddarth Singh, Meredith Ashby, Eng Guan Chua, Chin Yen Tay, Fanny Thirriot, Mun Fai Loke, Khean Lee Goh, Barry J Marshall, Richard J Roberts, Jamuna Vadivelu |
Abstract |
The genome of the human gastric pathogen Helicobacter pylori encodes a large number of DNA methyltransferases (MTases), some of which are shared among many strains, and others of which are unique to a given strain. The MTases have potential roles in the survival of the bacterium. In this study, we sequenced a Malaysian H. pylori clinical strain, designated UM032, by using a combination of PacBio Single Molecule, Real-Time (SMRT) and Illumina MiSeq next generation sequencing platforms, and used the SMRT data to characterize the set of methylated bases (the methylome). The N4-methylcytosine and N6-methyladenine modifications detected at single-base resolution using SMRT technology revealed 17 methylated sequence motifs corresponding to one Type I and 16 Type II restriction-modification (R-M) systems. Previously unassigned methylation motifs were now assigned to their respective MTases-coding genes. Furthermore, one gene that appears to be inactive in the H. pylori UM032 genome during normal growth was characterized by cloning. Consistent with previously-studied H. pylori strains, we show that strain UM032 contains a relatively large number of R-M systems, including some MTase activities with novel specificities. Additional studies are underway to further elucidating the biological significance of the R-M systems in the physiology and pathogenesis of H. pylori. |
X Demographics
Geographical breakdown
Country | Count | As % |
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United States | 5 | 71% |
United Kingdom | 1 | 14% |
Unknown | 1 | 14% |
Demographic breakdown
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Members of the public | 5 | 71% |
Scientists | 2 | 29% |
Mendeley readers
Geographical breakdown
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India | 2 | 3% |
Canada | 1 | 2% |
Unknown | 57 | 95% |
Demographic breakdown
Readers by professional status | Count | As % |
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Student > Ph. D. Student | 18 | 30% |
Researcher | 14 | 23% |
Student > Doctoral Student | 5 | 8% |
Student > Master | 4 | 7% |
Student > Bachelor | 3 | 5% |
Other | 8 | 13% |
Unknown | 8 | 13% |
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Biochemistry, Genetics and Molecular Biology | 18 | 30% |
Medicine and Dentistry | 3 | 5% |
Immunology and Microbiology | 2 | 3% |
Computer Science | 1 | 2% |
Other | 2 | 3% |
Unknown | 12 | 20% |