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

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dc.contributor.author Bottacini, Francesca
dc.contributor.author Zomer, Aldert
dc.contributor.author Milani, Christian
dc.contributor.author Ferrario, Chiara
dc.contributor.author Lugli, Gabriele A.
dc.contributor.author Egan, Muireann
dc.contributor.author Ventura, Marco
dc.contributor.author van Sinderen, Douwe
dc.date.accessioned 2018-02-06T13:36:29Z
dc.date.available 2018-02-06T13:36:29Z
dc.date.issued 2017
dc.identifier.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 en
dc.identifier.volume 18
dc.identifier.startpage 1
dc.identifier.endpage 14
dc.identifier.uri http://hdl.handle.net/10468/5401
dc.identifier.doi 10.1186/s12864-017-4387-x
dc.description.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. en
dc.description.sponsorship Federation of European Microbiological Societies (FEMS-RG-2016-0103) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher BioMed Central en
dc.relation.uri https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-017-4387-x
dc.rights © 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. en
dc.rights.uri http://creativecommons.org/licenses/by/4.0/
dc.subject Gene expression en
dc.subject Bifidobacteria en
dc.subject Probiotics en
dc.subject Transcription en
dc.title Global transcriptional landscape and promoter mapping of the gut commensal Bifidobacterium breve UCC2003 en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother d.vansinderen@ucc.ie en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder European Society of Clinical Microbiology and Infectious Diseases
dc.contributor.funder Federation of European Microbiological Societies
dc.contributor.funder Ministero dell’Istruzione, dell’Università e della Ricerca
dc.contributor.funder European Commission
dc.contributor.funder Science Foundation Ireland
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Genomics en
dc.internal.IRISemailaddress Douwe van Sinderen, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: d.vansinderen@ucc.ie en
dc.identifier.articleid 991
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Strategic Research Cluster/08/SRC/B1393/IE/SRC AGRC: Glycoscience Research Cluster/
dc.relation.project info:eu-repo/grantAgreement/EC/H2020::CSA/696300/EU/The second coordination and support action for the JPI Healthy Diet for a Healthy Life/CSA JPI HDHL 2.0
dc.relation.project info:eu-repo/grantAgreement/SFI/SFI Technology and Innovation Development Award (TIDA) - Training Award/07/CE/B1368 TIDA Training 11/IE/Alimentary Pharmabiotic Centre - Second Term Funding/


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© 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. Except where otherwise noted, this item's license is described as © 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.
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