DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway

The facultative anaerobe Thauera aromatica strain AR-1 uses 3,5-dihydroxybenzoate (3,5-DHB) as a sole carbon and energy source under anoxic conditions using an unusual oxidative strategy to overcome aromatic ring stability. A 25-kb gene cluster organized in four main operons encodes the anaerobic de...

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Autores: Pacheco Sánchez, Daniel, Molina-Fuentes, Á., Marín, Patricia, Díaz-Romero, Alberto, Marqués, Silvia
Tipo de recurso: artículo
Fecha de publicación:2019
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/197850
Acceso en línea:http://hdl.handle.net/10261/197850
Access Level:acceso abierto
Palabra clave:Alfa-resorcylate
LTTR
Anaerobic biodegradation
Denitrifiers
Dihydroxylated aromatic
Transcriptional regulation
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network_name_str España
repository_id_str
dc.title.none.fl_str_mv DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
title DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
spellingShingle DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
Pacheco Sánchez, Daniel
Alfa-resorcylate
LTTR
Anaerobic biodegradation
Denitrifiers
Dihydroxylated aromatic
Transcriptional regulation
title_short DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
title_full DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
title_fullStr DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
title_full_unstemmed DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
title_sort DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathway
dc.creator.none.fl_str_mv Pacheco Sánchez, Daniel
Molina-Fuentes, Á.
Marín, Patricia
Díaz-Romero, Alberto
Marqués, Silvia
author Pacheco Sánchez, Daniel
author_facet Pacheco Sánchez, Daniel
Molina-Fuentes, Á.
Marín, Patricia
Díaz-Romero, Alberto
Marqués, Silvia
author_role author
author2 Molina-Fuentes, Á.
Marín, Patricia
Díaz-Romero, Alberto
Marqués, Silvia
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia y Tecnología (España)
Ministerio de Economía y Competitividad (España)
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv Alfa-resorcylate
LTTR
Anaerobic biodegradation
Denitrifiers
Dihydroxylated aromatic
Transcriptional regulation
topic Alfa-resorcylate
LTTR
Anaerobic biodegradation
Denitrifiers
Dihydroxylated aromatic
Transcriptional regulation
description The facultative anaerobe Thauera aromatica strain AR-1 uses 3,5-dihydroxybenzoate (3,5-DHB) as a sole carbon and energy source under anoxic conditions using an unusual oxidative strategy to overcome aromatic ring stability. A 25-kb gene cluster organized in four main operons encodes the anaerobic degradation pathway for this aromatic. The dbdR gene coding for a LysR-type transcriptional regulator (LTTR), which is present at the foremost end of the cluster, is required for anaerobic growth on 3,5-DHB and for the expression of the main pathway operons. A model structure of DbdR showed conserved key residues for effector binding with its closest relative TsaR for p-toluenesulfonate degradation. We found that DbdR controlled expression of three promoters upstream from the operons coding for the three main steps of the pathway. While one of them (P orf20 ) was only active in the presence of 3,5-DHB, the other two (P dbhL and P orf18 ) showed moderate basal levels that were further induced in the presence of the pathway substrate, which needed be converted to hydroxyhydroquinone to activate transcription. Both basal and induced activities were strictly dependent on DbdR, which was also required for transcription from its own promoter. DbdR basal expression was moderately high and, unlike most LTTR, increased 2-fold in response to the presence of the effector. DbdR was found to be a tetramer in solution, producing a single retardation complex in binding assays with the three enzymatic promoters, consistent with its tetrameric structure. The three promoters had a conserved organization with a clear putative primary (regulatory) binding site and a putative secondary (activating) binding site positioned at the expected distances from the transcription start site. In contrast, two protein-DNA complexes were observed for the P dbdR promoter, which also showed significant sequence divergence from those of the three other promoters. Taken together, our results show that a single LTTR coordinately controls expression of the entire 3,5-DHB anaerobic degradation pathway in Thauera aromatica AR-1, allowing a fast and optimized response to the presence of the aromatic.IMPORTANCEThauera aromatica AR-1 is a facultative anaerobe that is able to use 3,5-dihydroxybenzoat (3,5-DHB) as the sole carbon and energy source in a process that is dependent on nitrate respiration. We have shown that a single LysR-type regulator with unusual properties, DbdR, controls the expression of the pathway in response to the presence of the substrate; unlike other regulators of the family, DbdR does not repress but activates its own synthesis and is able to bind and activate three promoters directing the synthesis of the pathway enzymes. The promoter architecture is conserved among the three promoters but deviates from that of typical LTTR-dependent promoters. The substrate must be metabolized to an intermediate compound to activate transcription, which requires basal enzyme levels to always be present. The regulatory network present in this strain is designed to allow basal expression of the enzymatic machinery, which would rapidly metabolize the substrate when exposed to it, thus rendering the effector molecule. Once activated, the regulator induces the synthesis of the entire pathway through a positive feedback, increasing expression from all the target promoters to allow maximum growth.
publishDate 2019
dc.date.none.fl_str_mv 2019
2020
2020
2020
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
format article
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/197850
url http://hdl.handle.net/10261/197850
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2014-54361-R
https://aem.asm.org/content/85/2/e02295-18.abstract
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv American Society for Microbiology
publisher.none.fl_str_mv American Society for Microbiology
dc.source.none.fl_str_mv reponame:DIGITAL.CSIC. Repositorio Institucional del CSIC
instname:Consejo Superior de Investigaciones Científicas (CSIC)
instname_str Consejo Superior de Investigaciones Científicas (CSIC)
reponame_str DIGITAL.CSIC. Repositorio Institucional del CSIC
collection DIGITAL.CSIC. Repositorio Institucional del CSIC
repository.name.fl_str_mv
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spelling DbdR, a new member of the LysR family of transcriptional regulators, coordinately controls four promoters in the Thauera aromatica AR-1 3,5-Dihydroxybenzoate anaerobic degradation pathwayPacheco Sánchez, DanielMolina-Fuentes, Á.Marín, PatriciaDíaz-Romero, AlbertoMarqués, SilviaAlfa-resorcylateLTTRAnaerobic biodegradationDenitrifiersDihydroxylated aromaticTranscriptional regulationThe facultative anaerobe Thauera aromatica strain AR-1 uses 3,5-dihydroxybenzoate (3,5-DHB) as a sole carbon and energy source under anoxic conditions using an unusual oxidative strategy to overcome aromatic ring stability. A 25-kb gene cluster organized in four main operons encodes the anaerobic degradation pathway for this aromatic. The dbdR gene coding for a LysR-type transcriptional regulator (LTTR), which is present at the foremost end of the cluster, is required for anaerobic growth on 3,5-DHB and for the expression of the main pathway operons. A model structure of DbdR showed conserved key residues for effector binding with its closest relative TsaR for p-toluenesulfonate degradation. We found that DbdR controlled expression of three promoters upstream from the operons coding for the three main steps of the pathway. While one of them (P orf20 ) was only active in the presence of 3,5-DHB, the other two (P dbhL and P orf18 ) showed moderate basal levels that were further induced in the presence of the pathway substrate, which needed be converted to hydroxyhydroquinone to activate transcription. Both basal and induced activities were strictly dependent on DbdR, which was also required for transcription from its own promoter. DbdR basal expression was moderately high and, unlike most LTTR, increased 2-fold in response to the presence of the effector. DbdR was found to be a tetramer in solution, producing a single retardation complex in binding assays with the three enzymatic promoters, consistent with its tetrameric structure. The three promoters had a conserved organization with a clear putative primary (regulatory) binding site and a putative secondary (activating) binding site positioned at the expected distances from the transcription start site. In contrast, two protein-DNA complexes were observed for the P dbdR promoter, which also showed significant sequence divergence from those of the three other promoters. Taken together, our results show that a single LTTR coordinately controls expression of the entire 3,5-DHB anaerobic degradation pathway in Thauera aromatica AR-1, allowing a fast and optimized response to the presence of the aromatic.IMPORTANCEThauera aromatica AR-1 is a facultative anaerobe that is able to use 3,5-dihydroxybenzoat (3,5-DHB) as the sole carbon and energy source in a process that is dependent on nitrate respiration. We have shown that a single LysR-type regulator with unusual properties, DbdR, controls the expression of the pathway in response to the presence of the substrate; unlike other regulators of the family, DbdR does not repress but activates its own synthesis and is able to bind and activate three promoters directing the synthesis of the pathway enzymes. The promoter architecture is conserved among the three promoters but deviates from that of typical LTTR-dependent promoters. The substrate must be metabolized to an intermediate compound to activate transcription, which requires basal enzyme levels to always be present. The regulatory network present in this strain is designed to allow basal expression of the enzymatic machinery, which would rapidly metabolize the substrate when exposed to it, thus rendering the effector molecule. Once activated, the regulator induces the synthesis of the entire pathway through a positive feedback, increasing expression from all the target promoters to allow maximum growth.This work was supported by FEDER and grants from the Spanish Ministry of Science and Technology (BIO2011-23615) and Ministry of Economy and Competitiveness (BIO2014-54361-R). Á. Molina-Fuentes was the recipient of an I3P contract from the European Social FundsPeer ReviewedAmerican Society for MicrobiologyMinisterio de Ciencia y Tecnología (España)Ministerio de Economía y Competitividad (España)Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2020202020192020info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501http://hdl.handle.net/10261/197850reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/MINECO/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2014-54361-Rhttps://aem.asm.org/content/85/2/e02295-18.abstractSíinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/1978502026-05-22T06:33:51Z
score 15,811543

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