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Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve
Bottacini, Francesca; Morrissey, Ruth; Roberts, Richard John; James, Kieran; van Breen, Justin; Egan, Muireann; Lambert, Jolanda; van Limpt, Kees; Knol, Jan; O'Connell Motherway, Mary; van Sinderen, Douwe
Bifidobacterium breve represents one of the most abundant bifidobacterial species in the gastrointestinal tract of breast-fed infants, where their presence is believed to exert beneficial effects. In the present study whole genome sequencing, employing the PacBio Single Molecule, Real-Time (SMRT) sequencing platform, combined with comparative genome analysis allowed the most extensive genetic investigation of this taxon. Our findings demonstrate that genes encoding Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variable gene content (or variome). Using the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BS-seq) and comparative genome analysis, we were able to detect methylation recognition motifs and assign these to identified B. breve R/M systems, where in several cases such assignments were confirmed by restriction analysis. Furthermore, we show that R/M systems typically impose a very significant barrier to genetic accessibility of B. breve strains, and that cloning of a methyltransferase-encoding gene may overcome such a barrier, thus allowing future functional investigations of members of this species.
Keyword(s): Restriction-modification systems; DNA-microarray data; Gene-expression; Methyltransferases; UCC2003; Enzymes; Endonucleases; Mutagenesis; Microbiota; Algorithm
Publication Date:
2018
Type: Journal article
Peer-Reviewed: Yes
Language(s): English
Institution: University College Cork
Funder(s): Science Foundation Ireland; Health Research Board
Citation(s): Bottacini, F., Morrissey, R., Roberts, Richard J., James, K., van Breen, J., Egan, M., Lambert, J., van Limpt, K., Knol, J., O'Connell Motherway, M. and van Sinderen, D. (2018) 'Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve', Nucleic Acids Research, 46(4), pp. 1860-1877. doi: 10.1093/nar/gkx1289
Publisher(s): Oxford University Press
File Format(s): application/pdf
Related Link(s): https://academic.oup.com/nar/article/46/4/1860/4780163
First Indexed: 2018-06-16 06:30:34 Last Updated: 2018-07-13 06:30:59