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Pan-genome and methylome analysis reveals the diversity of restriction/modification systems in the gut commensal Bifidobacterium breve.

ABSTRACT: Bifidobacterium breve represents one of the most abundant (bifido)bacterial species in the gastro-intestinal tract of (breast-fed) infants, where their presence is believed to be beneficial. In the present study whole genome sequencing, employing PacBio’s 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 Restriction/Modification (R/M) systems constitute a substantial part of the B. breve variome. Availing of the methylome data generated by SMRT sequencing, combined with targeted Illumina bisulfite sequencing (BiSeq) 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, cloning of a selected methyltransferase-encoding gene validated the activity of the corresponding R/M system, and was shown to overcome the barrier they impose to genetic accessibility, thus allowing future genetic manipulation of members of this species.

ORGANISM(S): Bifidobacterium breve Bifidobacterium breve UCC2003

PROVIDER: GSE104927 | GEO | 2017/12/13

SECONDARY ACCESSION(S): PRJNA414173

REPOSITORIES: GEO

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2010-08-11 | E-GEOD-17604 | biostudies-arrayexpress

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Project description:Bifidobacterium breve Genome sequencing

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Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003

Project description:The recognition specificity and associated affinity of the RNA polymerase sigma subunit towards its cognate promoter sequence is one of the elements contributing to the modulation of gene expression in bacteria. In the present study we identified and assessed vegetative promoters of the bifidobacterial prototype Bifidobacterium breve UCC2003 employing a combination of tiling array analysis and RNA sequencing. By combining and comparing the outputs of these two distinct technologies we were able to identify a number of transcriptional units, including their initiation and termination signals, which correspond to promoters and terminators, respectively. Canonical -10 (TATAAT) and -35 (TTGACA) sequences were identified upstream of transcribed genes or operons, where deviations from this consensus correspond to transcription level variations. Using a Random Forest approach, we were able to define promoter characteristics that most substantially impact on transcription in B. breve. We observed that constitutively transcribed genes frequently encode house keeping functions that are part of the core and essential genome of this species. A comparative analysis between the tiling array-based and RNA-seq technologies allowed us to evaluate their performance and applicability for investigations on (regulation of) bifidobacterial gene expression.

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Discovering novel bile protection systems in Bifidobacterium breve UCC2003 through functional genomics

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2011-12-16 | E-GEOD-31032 | biostudies-arrayexpress

A two-component regulatory system controls serpin expression in Bifidobacterium breve UCC2003.

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