Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms

In the strictly anaerobic nitrate reducing bacterium Aromatoleum anaerobium, degradation of 1,3-dihydroxybenzene (1,3-DHB, resorcinol) is controlled by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2, which regulate the transcription of three σ-dependent promoters controlling expres...

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Autores: Pacheco-Sánchez, Daniel, Marín, Patricia, Molina-Fuentes, Á., Marqués, Silvia
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Consejo Superior de Investigaciones Científicas (CSIC)
Repositorio:DIGITAL.CSIC. Repositorio Institucional del CSIC
OAI Identifier:oai:digital.csic.es:10261/305876
Acceso en línea:http://hdl.handle.net/10261/305876
Access Level:acceso abierto
Palabra clave:1,3-dihydroxybenzene
Anaerobic
Aromatoleum
DoxX/D family
Heterohexamer
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repository_id_str
spelling Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanismsPacheco-Sánchez, DanielMarín, PatriciaMolina-Fuentes, Á.Marqués, Silvia1,3-dihydroxybenzeneAnaerobicAromatoleumDoxX/D familyHeterohexamerIn the strictly anaerobic nitrate reducing bacterium Aromatoleum anaerobium, degradation of 1,3-dihydroxybenzene (1,3-DHB, resorcinol) is controlled by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2, which regulate the transcription of three σ-dependent promoters controlling expression of the pathway. RedR1 and RedR2 are identical over their length except for their N-terminal tail which differ in sequence and length (six and eight residues, respectively), a single change in their N-terminal domain (NTD), and nine non-identical residues in their C-terminal domain (CTD). Their NTD is composed of a GAF and a PAS domain connected by a linker helix. We show that each regulator is controlled by a different mechanism: whilst RedR1 responds to the classical NTD-mediated negative regulation that is released by the presence of its effector, RedR2 activity is constitutive and controlled through interaction with BtdS, an integral membrane subunit of hydroxyhydroquinone dehydrogenase carrying out the second step in 1,3-DHB degradation. BtdS sequesters the RedR2 regulator to the membrane through its NTD, where a four-Ile track in the PAS domain, interrupted by a Thr in RedR1, and the N-terminal tail are involved. The presence of 1,3-DHB, which is metabolized to hydroxybenzoquinone, releases RedR2 from the membrane. Most bEBPs assemble into homohexamers to activate transcription; we show that hetero-oligomer formation between RedR1 and RedR2 is favoured over homo-oligomers. However, either an NTD-truncated version of RedR1 or a full-length RedR2 are capable of promoter activation on their own, suggesting they should assemble into homohexamers in vivo. We show that promoter DNA behaves as an allosteric effector through binding the CTD to control ΔNTD-RedR1 multimerization and activity. Overall, the regulation of the 1,3-DHB anaerobic degradation pathway can be described as a novel mode of bEBP activation and assembly.This work was supported by the European Regional Development Fund (ERDF) grant BIO2017-82242-R and by grant PID2020-113144RB-I00 funded by MCIN/AEI/10.13039/501100011033 and by “ERDF A way of making Europe”. We thank Javier I. Medina-Bellver for constructing plasmid pJBRedR2.John Wiley & SonsMinisterio de Ciencia e Innovación (España)European CommissionConsejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]2023202320222023info:eu-repo/semantics/articlehttp://purl.org/coar/resource_type/c_6501Publisher's versioninfo:eu-repo/semantics/publishedVersionhttp://hdl.handle.net/10261/305876reponame:DIGITAL.CSIC. Repositorio Institucional del CSICinstname:Consejo Superior de Investigaciones Científicas (CSIC)Inglés#PLACEHOLDER_PARENT_METADATA_VALUE##PLACEHOLDER_PARENT_METADATA_VALUE#info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2017-82242-Rinfo:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-113144RB-I00http://dx.doi.org/10.1111/febs.16576Síinfo:eu-repo/semantics/openAccessoai:digital.csic.es:10261/3058762026-05-22T06:33:51Z
dc.title.none.fl_str_mv Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
title Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
spellingShingle Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
Pacheco-Sánchez, Daniel
1,3-dihydroxybenzene
Anaerobic
Aromatoleum
DoxX/D family
Heterohexamer
title_short Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
title_full Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
title_fullStr Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
title_full_unstemmed Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
title_sort Subtle sequence differences between two interacting σ54-dependent regulators lead to different activation mechanisms
dc.creator.none.fl_str_mv Pacheco-Sánchez, Daniel
Marín, Patricia
Molina-Fuentes, Á.
Marqués, Silvia
author Pacheco-Sánchez, Daniel
author_facet Pacheco-Sánchez, Daniel
Marín, Patricia
Molina-Fuentes, Á.
Marqués, Silvia
author_role author
author2 Marín, Patricia
Molina-Fuentes, Á.
Marqués, Silvia
author2_role author
author
author
dc.contributor.none.fl_str_mv Ministerio de Ciencia e Innovación (España)
European Commission
Consejo Superior de Investigaciones Científicas [https://ror.org/02gfc7t72]
dc.subject.none.fl_str_mv 1,3-dihydroxybenzene
Anaerobic
Aromatoleum
DoxX/D family
Heterohexamer
topic 1,3-dihydroxybenzene
Anaerobic
Aromatoleum
DoxX/D family
Heterohexamer
description In the strictly anaerobic nitrate reducing bacterium Aromatoleum anaerobium, degradation of 1,3-dihydroxybenzene (1,3-DHB, resorcinol) is controlled by two bacterial enhancer-binding proteins (bEBPs), RedR1 and RedR2, which regulate the transcription of three σ-dependent promoters controlling expression of the pathway. RedR1 and RedR2 are identical over their length except for their N-terminal tail which differ in sequence and length (six and eight residues, respectively), a single change in their N-terminal domain (NTD), and nine non-identical residues in their C-terminal domain (CTD). Their NTD is composed of a GAF and a PAS domain connected by a linker helix. We show that each regulator is controlled by a different mechanism: whilst RedR1 responds to the classical NTD-mediated negative regulation that is released by the presence of its effector, RedR2 activity is constitutive and controlled through interaction with BtdS, an integral membrane subunit of hydroxyhydroquinone dehydrogenase carrying out the second step in 1,3-DHB degradation. BtdS sequesters the RedR2 regulator to the membrane through its NTD, where a four-Ile track in the PAS domain, interrupted by a Thr in RedR1, and the N-terminal tail are involved. The presence of 1,3-DHB, which is metabolized to hydroxybenzoquinone, releases RedR2 from the membrane. Most bEBPs assemble into homohexamers to activate transcription; we show that hetero-oligomer formation between RedR1 and RedR2 is favoured over homo-oligomers. However, either an NTD-truncated version of RedR1 or a full-length RedR2 are capable of promoter activation on their own, suggesting they should assemble into homohexamers in vivo. We show that promoter DNA behaves as an allosteric effector through binding the CTD to control ΔNTD-RedR1 multimerization and activity. Overall, the regulation of the 1,3-DHB anaerobic degradation pathway can be described as a novel mode of bEBP activation and assembly.
publishDate 2022
dc.date.none.fl_str_mv 2022
2023
2023
2023
dc.type.none.fl_str_mv info:eu-repo/semantics/article
http://purl.org/coar/resource_type/c_6501
Publisher's version
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv http://hdl.handle.net/10261/305876
url http://hdl.handle.net/10261/305876
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv #PLACEHOLDER_PARENT_METADATA_VALUE#
#PLACEHOLDER_PARENT_METADATA_VALUE#
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2013-2016/BIO2017-82242-R
info:eu-repo/grantAgreement/AEI/Plan Estatal de Investigación Científica y Técnica y de Innovación 2017-2020/PID2020-113144RB-I00
http://dx.doi.org/10.1111/febs.16576
Sí
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv John Wiley & Sons
publisher.none.fl_str_mv John Wiley & Sons
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
repository.mail.fl_str_mv
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