Comparative genomics reveals the regulatory complexity of Bifidobacterial arabinose and Arabino-oligosaccharide utilization

dc.contributor.authorArzamasov, Aleksandr A.
dc.contributor.authorvan Sinderen, Douwe
dc.contributor.authorRodionov, Dmitry A.
dc.contributor.funderRussian Science Foundation
dc.contributor.funderScience Foundation Ireland
dc.date.accessioned2018-05-31T11:56:25Z
dc.date.available2018-05-31T11:56:25Z
dc.description.abstractMembers of the genus Bifidobacterium are common inhabitants of the human gastrointestinal tract. Previously it was shown that arabino-oligosaccharides (AOS) might act as prebiotics and stimulate the bifidobacterial growth in the gut. However, despite the rapid accumulation of genomic data, the precise mechanisms by which these sugars are utilized and associated transcription control still remain unclear. In the current study, we used a comparative genomic approach to reconstruct arabinose and AOS utilization pathways in over 40 bacterial species belonging to the Bifidobacteriaceae family. The results indicate that the gene repertoire involved in the catabolism of these sugars is highly diverse, and even phylogenetically close species may differ in their utilization capabilities. Using bioinformatics analysis we identified potential DNA-binding motifs and reconstructed putative regulons for the arabinose and AOS utilization genes in the Bifidobacteriaceae genomes. Six LacI-family transcriptional factors (named AbfR, AauR, AauU1, AauU2, BauR1 and BauR2) and a TetR-family regulator (XsaR) presumably act as local repressors for AOS utilization genes encoding various alpha- or beta-L-arabinofuranosidases and predicted AOS transporters. The ROK-family regulator AraU and the LacI-family regulator AraQ control adjacent operons encoding putative arabinose transporters and catabolic enzymes, respectively. However, the AraQ regulator is universally present in all Bifidobacterium species including those lacking the arabinose catabolic genes araBDA, suggesting its control of other genes. Comparative genomic analyses of prospective AraQ-binding sites allowed the reconstruction of AraQ regulons and a proposed binary repression/activation mechanism. The conserved core of reconstructed AraQ regulons in bifidobacteria includes araBDA, as well as genes from the central glycolytic and fermentation pathways (pyk, eno, gap, tkt, tal, galM, ldh). The current study expands the range of genes involved in bifidobacterial arabinose/AOS utilization and demonstrates considerable variations in associated metabolic pathways and regulons. Detailed comparative and phylogenetic analyses allowed us to hypothesize how the identified reconstructed regulons evolved in bifidobacteria. Our findings may help to improve carbohydrate catabolic phenotype prediction and metabolic modeling, while it may also facilitate rational development of novel prebiotics.en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid776
dc.identifier.citationArzamasov, A. A., van Sinderen, D. and Rodionov, D. A. (2018) 'Comparative genomics reveals the regulatory complexity of Bifidobacterial arabinose and Arabino-oligosaccharide utilization', Frontiers in Microbiology, 9, 776 (17pp). doi: 10.3389/fmicb.2018.00776en
dc.identifier.doi10.3389/fmicb.2018.00776
dc.identifier.endpage17
dc.identifier.issn1664-302X
dc.identifier.issued2018
dc.identifier.journaltitleFrontiers in Microbiologyen
dc.identifier.startpage1
dc.identifier.urihttps://hdl.handle.net/10468/6213
dc.identifier.volume9
dc.language.isoenen
dc.publisherFrontiers Mediaen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.urihttps://www.frontiersin.org/articles/10.3389/fmicb.2018.00776/full
dc.rights© 2018, Arzamasov, 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) and the copyright owner 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.urihttps://creativecommons.org/licenses/by/4.0/
dc.subjectBifidobacteriaen
dc.subjectArabinoseen
dc.subjectArabino-oligosaccharidesen
dc.subjectPrebioticsen
dc.subjectRegulatory networksen
dc.subjectTranscription factorsen
dc.subjectComparative genomicsen
dc.titleComparative genomics reveals the regulatory complexity of Bifidobacterial arabinose and Arabino-oligosaccharide utilizationen
dc.typeArticle (peer-reviewed)en
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