The Verrucomicrobia LexA-Binding Motif

The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its tran...

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Autores: Erill, Ivan|||0000-0002-7280-7191, Campoy Sánchez, Susana|||0000-0003-1369-0197, Kiliç, Sefa, Barbé García, Jordi|||0000-0003-4408-013X
Formato: artículo
Fecha de publicación:2016
País:España
Recursos:Universitat Autònoma de Barcelona
Repositorio:Dipòsit Digital de Documents de la UAB
Idioma:inglés
OAI Identifier:oai:ddd.uab.cat:185944
Acesso em linha:https://ddd.uab.cat/record/185944
https://dx.doi.org/urn:doi:10.3389/fmolb.2016.00033
Access Level:acceso abierto
Palavra-chave:SOS response
LexA regulon
DNA repair
Comparative genomics
Binding motif
Translesion synthesis
Uracil-dna glycosylase
Regulatory network evolution
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spelling The Verrucomicrobia LexA-Binding MotifInsights into the Evolutionary Dynamics of the SOS ResponseErill, Ivan|||0000-0002-7280-7191Campoy Sánchez, Susana|||0000-0003-1369-0197Kiliç, SefaBarbé García, Jordi|||0000-0003-4408-013XSOS responseLexA regulonDNA repairComparative genomicsBinding motifTranslesion synthesisUracil-dna glycosylaseRegulatory network evolutionThe SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls. 22016-01-0120162016-01-01Articlehttp://purl.org/coar/resource_type/c_6501VoRhttp://purl.org/coar/version/c_970fb48d4fbd8a85info:eu-repo/semantics/articleapplication/pdfhttps://ddd.uab.cat/record/185944https://dx.doi.org/urn:doi:10.3389/fmolb.2016.00033reponame:Dipòsit Digital de Documents de la UABinstname:Universitat Autònoma de BarcelonaInglésengopen accesshttp://purl.org/coar/access_right/c_abf2Aquest document està subjecte a una llicència d'ús Creative Commons. Es permet la reproducció total o parcial, la distribució, la comunicació pública de l'obra i la creació d'obres derivades, fins i tot amb finalitats comercials, sempre i quan es reconegui l'autoria de l'obra original.https://creativecommons.org/licenses/by/4.0/info:eu-repo/semantics/openAccessoai:ddd.uab.cat:1859442026-06-06T12:50:31Z
dc.title.none.fl_str_mv The Verrucomicrobia LexA-Binding Motif
Insights into the Evolutionary Dynamics of the SOS Response
title The Verrucomicrobia LexA-Binding Motif
spellingShingle The Verrucomicrobia LexA-Binding Motif
Erill, Ivan|||0000-0002-7280-7191
SOS response
LexA regulon
DNA repair
Comparative genomics
Binding motif
Translesion synthesis
Uracil-dna glycosylase
Regulatory network evolution
title_short The Verrucomicrobia LexA-Binding Motif
title_full The Verrucomicrobia LexA-Binding Motif
title_fullStr The Verrucomicrobia LexA-Binding Motif
title_full_unstemmed The Verrucomicrobia LexA-Binding Motif
title_sort The Verrucomicrobia LexA-Binding Motif
dc.creator.none.fl_str_mv Erill, Ivan|||0000-0002-7280-7191
Campoy Sánchez, Susana|||0000-0003-1369-0197
Kiliç, Sefa
Barbé García, Jordi|||0000-0003-4408-013X
author Erill, Ivan|||0000-0002-7280-7191
author_facet Erill, Ivan|||0000-0002-7280-7191
Campoy Sánchez, Susana|||0000-0003-1369-0197
Kiliç, Sefa
Barbé García, Jordi|||0000-0003-4408-013X
author_role author
author2 Campoy Sánchez, Susana|||0000-0003-1369-0197
Kiliç, Sefa
Barbé García, Jordi|||0000-0003-4408-013X
author2_role author
author
author
dc.subject.none.fl_str_mv SOS response
LexA regulon
DNA repair
Comparative genomics
Binding motif
Translesion synthesis
Uracil-dna glycosylase
Regulatory network evolution
topic SOS response
LexA regulon
DNA repair
Comparative genomics
Binding motif
Translesion synthesis
Uracil-dna glycosylase
Regulatory network evolution
description The SOS response is the primary bacterial mechanism to address DNA damage, coordinating multiple cellular processes that include DNA repair, cell division, and translesion synthesis. In contrast to other regulatory systems, the composition of the SOS genetic network and the binding motif of its transcriptional repressor, LexA, have been shown to vary greatly across bacterial clades, making it an ideal system to study the co-evolution of transcription factors and their regulons. Leveraging comparative genomics approaches and prior knowledge on the core SOS regulon, here we define the binding motif of the Verrucomicrobia, a recently described phylum of emerging interest due to its association with eukaryotic hosts. Site directed mutagenesis of the Verrucomicrobium spinosum recA promoter confirms that LexA binds a 14 bp palindromic motif with consensus sequence TGTTC-N4-GAACA. Computational analyses suggest that recognition of this novel motif is determined primarily by changes in base-contacting residues of the third alpha helix of the LexA helix-turn-helix DNA binding motif. In conjunction with comparative genomics analysis of the LexA regulon in the Verrucomicrobia phylum, electrophoretic shift assays reveal that LexA binds to operators in the promoter region of DNA repair genes and a mutagenesis cassette in this organism, and identify previously unreported components of the SOS response. The identification of tandem LexA-binding sites generating instances of other LexA-binding motifs in the lexA gene promoter of Verrucomicrobia species leads us to postulate a novel mechanism for LexA-binding motif evolution. This model, based on gene duplication, successfully addresses outstanding questions in the intricate co-evolution of the LexA protein, its binding motif and the regulatory network it controls.
publishDate 2016
dc.date.none.fl_str_mv 2
2016-01-01
2016
2016-01-01
dc.type.none.fl_str_mv Article
http://purl.org/coar/resource_type/c_6501
VoR
http://purl.org/coar/version/c_970fb48d4fbd8a85
dc.type.openaire.fl_str_mv info:eu-repo/semantics/article
format article
dc.identifier.none.fl_str_mv https://ddd.uab.cat/record/185944
https://dx.doi.org/urn:doi:10.3389/fmolb.2016.00033
url https://ddd.uab.cat/record/185944
https://dx.doi.org/urn:doi:10.3389/fmolb.2016.00033
dc.language.none.fl_str_mv Inglés
eng
language_invalid_str_mv Inglés
language eng
dc.rights.none.fl_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
dc.rights.openaire.fl_str_mv info:eu-repo/semantics/openAccess
rights_invalid_str_mv open access
http://purl.org/coar/access_right/c_abf2
https://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Dipòsit Digital de Documents de la UAB
instname:Universitat Autònoma de Barcelona
instname_str Universitat Autònoma de Barcelona
reponame_str Dipòsit Digital de Documents de la UAB
collection Dipòsit Digital de Documents de la UAB
repository.name.fl_str_mv
repository.mail.fl_str_mv
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