Transcriptional regulation of carbohydrate utilization pathways in the Bifidobacterium genus

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dc.contributor.author Khoroshkin, Matvei S.
dc.contributor.author Leyn, Semen A.
dc.contributor.author van Sinderen, Douwe
dc.contributor.author Rodionov., Dmitry A.
dc.date.accessioned 2017-02-23T15:46:38Z
dc.date.available 2017-02-23T15:46:38Z
dc.date.issued 2016-02-09
dc.identifier.citation Khoroshkin, M. S., Leyn, S. A., Van Sinderen, D. and Rodionov, D. A. (2016) 'Transcriptional Regulation of Carbohydrate Utilization Pathways in the Bifidobacterium Genus', Frontiers in Microbiology, 7(120). doi:10.3389/fmicb.2016.00120 en
dc.identifier.volume 7 en
dc.identifier.startpage 120-1 en
dc.identifier.endpage 120-14 en
dc.identifier.issn 1664-302X
dc.identifier.uri http://hdl.handle.net/10468/3680
dc.identifier.doi 10.3389/fmicb.2016.00120
dc.description.abstract Bifidobacteria, which represent common commensals of mammalian gut, are believed to have positive effects on human health. The influence of certain non-digestible carbohydrates (and their use as so-called prebiotics) on growth and metabolic activity of bifidobacteria is of increasing interest; however, mechanisms of transcriptional control of carbohydrate metabolism are poorly understood in these species. We used a comparative genomics approach to reconstruct carbohydrate utilization pathways and transcriptional regulons in 10 Bifidobacterium genomes. Analysis of regulatory gene regions revealed candidate DNA motifs and reconstructed regulons for 268 transcription factors from the LacI, ROK, DeoR, AraC, GntR, and TetR families that form 64 orthologous groups of regulators. Most of the reconstructed regulons are local and control specific catabolic pathways for host- and diet-derived glycans and monosaccharides. Mosaic distributions of many of these local regulators across Bifidobacterium species correlate with distribution of corresponding catabolic pathways. In contrast, the maltose, galactose, sucrose, and fructose regulons, as well as a novel global LacI-family regulator that is predicted to control the central carbohydrate metabolism and arabinose catabolism genes, are universally present in all 10 studied bifidobacteria. A novel group of TetR-family regulators presumably controls the glucoside and galactoside utilization pathways. Paralogs of the ribose repressor RbsR control the pyrimidine nucleoside utilization genes. Multiple paralogs of the maltose regulator MalR co-regulate large sets of genes involved in maltodextrin utilization. The inferred metabolic regulons provide new insights on diverse carbohydrate utilization networks in bifidobacteria that can be employed in metabolic modeling, phenotype prediction and the rational development of novel prebiotics. en
dc.description.sponsorship Russian Science Foundation (grant number 14-14-00289); National Institute of Health (grant number GM108527); Science Foundation Ireland (through the Irish Government’s National Development Plan (Grant number SFI/12/RC/2273)) en
dc.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher Frontiers Media en
dc.rights © 2016 Khoroshkin, Leyn, Van Sinderen and Rodionov. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. en
dc.rights.uri https://creativecommons.org/licenses/by/4.0/ en
dc.subject Carbohydrate metabolism en
dc.subject Sugar catabolism en
dc.subject Transcription factors en
dc.subject Regulatory networks en
dc.subject Regulatory sequences en
dc.subject Nucleic acid en
dc.subject Bifidobacteria en
dc.subject Comparative genomics en
dc.title Transcriptional regulation of carbohydrate utilization pathways in the Bifidobacterium genus en
dc.type Article (peer-reviewed) en
dc.internal.authorcontactother Douwe Van Sinderen, Microbiology, University College Cork, Cork, Ireland. +353-21-490-3000 Email: d.vansinderen@ucc.ie en
dc.internal.availability Full text available en
dc.date.updated 2017-02-23T15:27:27Z
dc.description.version Published Version en
dc.internal.rssid 384690877
dc.contributor.funder Russian Science Foundation en
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder National Institutes of Health en
dc.description.status Peer reviewed en
dc.identifier.journaltitle Frontiers In Microbiology en
dc.internal.copyrightchecked No !!CORA!! en
dc.internal.licenseacceptance Yes en
dc.internal.IRISemailaddress d.vansinderen@ucc.ie en


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© 2016 Khoroshkin, Leyn, Van Sinderen and Rodionov. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. Except where otherwise noted, this item's license is described as © 2016 Khoroshkin, Leyn, Van Sinderen and Rodionov. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
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