Characterization of the SOS meta-regulon in the human gut microbiome

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dc.contributorValencia, Alfonso
dc.contributor.authorCornish, Joseph P.
dc.contributor.authorSanchez-Alberola, Neus
dc.contributor.authorO’Neill, Patrick K.
dc.contributor.authorO’Keefe, Ronald
dc.contributor.authorGheba, Jameel
dc.contributor.authorErill, Ivan
dc.date.accessioned2018-10-11T13:29:17Z
dc.date.available2018-10-11T13:29:17Z
dc.date.issued2014-01-08
dc.description.abstractMotivation: Data from metagenomics projects remain largely untapped for the analysis of transcriptional regulatory networks. Here, we provide proof-of-concept that metagenomic data can be effectively leveraged to analyze regulatory networks by characterizing the SOS meta-regulon in the human gut microbiome. Results: We combine well-established in silico and in vitro techniques to mine the human gut microbiome data and determine the relative composition of the SOS network in a natural setting. Our analysis highlights the importance of translesion synthesis as a primary function of the SOS response. We predict the association of this network with three novel protein clusters involved in cell wall biogenesis, chromosome partitioning and restriction modification, and we confirm binding of the SOS response transcriptional repressor to sites in the promoter of a cell wall biogenesis enzyme, a phage integrase and a death-on-curing protein. We discuss the implications of these findings and the potential for this approach for metagenome analysis.en_US
dc.description.sponsorshipUMBC Office of Research through a Special Research Assistantship/Initiative Support (SRAIS) award and by US National Science Foundation [MCB-1158056]. Fundació Cellex (fellowship to N.S.A.). The UMBC High Performance Computing Facility is supported by the US National Science Foundation MRI [CNS-0821258, CNS-1228778] and SCREMS [DMS-0821311] programs and by the University of Maryland, Baltimore County (UMBC).en_US
dc.description.urihttps://academic.oup.com/bioinformatics/article/30/9/1193/234541en_US
dc.format.extent5 pagesen_US
dc.genrejournal article post-printen_US
dc.identifierdoi:10.13016/M2Q52FH36
dc.identifier.citationJoseph P. Cornish, Neus Sanchez-Alberola, Patrick K. O’Neill, Ronald O'Keefe, Jameel Gheba, Ivan Erill, Characterization of the SOS meta-regulon in the human gut microbiome, Bioinformatics, Volume 30, Issue 9, 1 May 2014, Pages 1193–1197, https://doi.org/10.1093/bioinformatics/btt753en_US
dc.identifier.urihttps://doi.org/10.1093/bioinformatics/btt753
dc.identifier.urihttp://hdl.handle.net/11603/11471
dc.language.isoen_USen_US
dc.publisherOxford University Pressen_US
dc.relation.isAvailableAtThe University of Maryland, Baltimore County (UMBC)
dc.relation.ispartofUMBC Biological Sciences Department
dc.relation.ispartofUMBC Faculty Collection
dc.rightsThis item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.*
dc.rightsAttribution 3.0 Unported (CC BY 3.0)*
dc.rights.urihttps://creativecommons.org/licenses/by/3.0/*
dc.subjectUMBC High Performance Computing Facility (HPCF)en_US
dc.subjectmetagenomicsen_US
dc.subjectSOS meta-regulonen_US
dc.subjectbiogenesis enzymeen_US
dc.subjectphage integraseen_US
dc.subjectdeath-on-curing proteinen_US
dc.subjectchromosome partitioningen_US
dc.subjectGenome analysisen_US
dc.titleCharacterization of the SOS meta-regulon in the human gut microbiomeen_US
dc.typeTexten_US

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