Comparative genome and methylome analysis reveals restriction/modification system diversity in the gut commensal Bifidobacterium breve
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Date
2018
Authors
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
Journal Title
Journal ISSN
Volume Title
Publisher
Oxford University Press
Published Version
Abstract
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.
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Keywords
Restriction-modification systems , DNA-microarray data , Gene-expression , Methyltransferases , UCC2003 , Enzymes , Endonucleases , Mutagenesis , Microbiota , Algorithm
Citation
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