dc.contributor.author	Arzamasov, Aleksandr A.
dc.contributor.author	van Sinderen, Douwe
dc.contributor.author	Rodionov, Dmitry A.
dc.contributor.funder	Russian Science Foundation
dc.contributor.funder	Science Foundation Ireland
dc.date.accessioned	2018-05-31T11:56:25Z
dc.date.available	2018-05-31T11:56:25Z
dc.description.abstract	Members 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.status	Peer reviewed	en
dc.description.version	Published Version	en
dc.format.mimetype	application/pdf	en
dc.identifier.articleid	776
dc.identifier.citation	Arzamasov, 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.2018.00776	en
dc.identifier.doi	10.3389/fmicb.2018.00776
dc.identifier.endpage	17
dc.identifier.issn	1664-302X
dc.identifier.issued	2018
dc.identifier.journaltitle	Frontiers in Microbiology	en
dc.identifier.startpage	1
dc.identifier.uri	https://hdl.handle.net/10468/6213
dc.identifier.volume	9
dc.language.iso	en	en
dc.publisher	Frontiers Media	en
dc.relation.project	info:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.relation.uri	https://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.uri	https://creativecommons.org/licenses/by/4.0/
dc.subject	Bifidobacteria	en
dc.subject	Arabinose	en
dc.subject	Arabino-oligosaccharides	en
dc.subject	Prebiotics	en
dc.subject	Regulatory networks	en
dc.subject	Transcription factors	en
dc.subject	Comparative genomics	en
dc.title	Comparative genomics reveals the regulatory complexity of Bifidobacterial arabinose and Arabino-oligosaccharide utilization	en
dc.type	Article (peer-reviewed)	en

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

Files

Original bundle

Collections