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

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Date
2017
Authors
Bottacini, Francesca
Zomer, Aldert
Milani, Christian
Ferrario, Chiara
Lugli, Gabriele A.
Egan, Muireann
Ventura, Marco
van Sinderen, Douwe
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Publisher
BioMed Central
Published Version
10.1186/s12864-017-4387-x
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Abstract
Background: Bifidobacterium breve represents a common member of the infant gut microbiota and its presence in the gut has been associated with host well being. For this reason it is relevant to investigate and understand the molecular mechanisms underlying the establishment, persistence and activities of this gut commensal in the host environment. Results: The assessment of vegetative promoters in the bifidobacterial prototype Bifidobacterium breve UCC2003 was performed employing a combination of RNA tiling array analysis and cDNA sequencing. 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. A Random Forest analysis assigned the −10 region of B. breve promoters as the element most impacting on the level of transcription, followed by the spacer length and the 5’-UTR length of transcripts. Furthermore, our transcriptome study also identified rho-independent termination as the most common and effective termination signal of highly and moderately transcribed operons in B. breve. Conclusion: The present study allowed us to identify genes and operons that are actively transcribed in this organism during logarithmic growth, and link promoter elements with levels of transcription of essential genes in this organism. As homologs of many of our identified genes are present across the whole genus Bifidobacterium, our dataset constitutes a transcriptomic reference to be used for future investigations of gene expression in members of this genus.
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Keywords
Gene expression , Bifidobacteria , Probiotics , Transcription
Citation
Bottacini, F., Zomer, A., Milani, C., Ferrario, C., Lugli, G. A., Egan, M., Ventura, M. and van Sinderen, D. (2017) 'Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003', BMC Genomics, 18(1), 991 (14pp). doi: 10.1186/s12864-017-4387-x
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https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4387-x
URI
https://hdl.handle.net/10468/5401
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Microbiology - Journal Articles
APC Microbiome Ireland - Journal Articles
Copyright
© 2017, the Authors. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.