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Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803

2017Journal article Open access
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dc.contributor.authorGiner-Lamia, Joaquin
dc.contributor.authorRobles-Rengel, Rocio
dc.contributor.authorHernandez-Prieto, Miguel A.
dc.contributor.authorIsabel Muro-Pastor, M.
dc.contributor.authorFlorencio, Francisco J.
dc.contributor.authorFutschik, Matthias E.
dc.date.accessioned2018-12-07T14:57:54Z
dc.date.available2018-12-07T14:57:54Z
dc.date.issued2017
dc.description.abstractIn cyanobacteria, nitrogen homeostasis is maintained by an intricate regulatory network around transcription factor NtcA. Although mechanisms controlling NtcA activity appear to be well understood, its regulon remains poorly defined. To determine the NtcA regulon during the early stages of nitrogen starvation for the model cyanobacterium Synechocystis sp. PCC 6803, we performed chromatin immunoprecipitation, followed by sequencing (ChIP-seq), in parallel with transcriptome analysis (RNA-seq). Through combining these methods, we determined 51 genes activated and 28 repressed directly by NtcA. In addition to genes associated with nitrogen and carbon metabolism, a considerable number of genes without current functional annotation were among direct targets providing a rich reservoir for further studies. The NtcA regulon also included eight non-coding RNAs, of which Ncr1071, Syr6 and NsiR7 were experimentally validated, and their putative targets were computationally predicted. Surprisingly, we found substantial NtcA binding associated with delayed expression changes indicating that NtcA can reside in a poised state controlled by other factors. Indeed, a role of PipX as modulating factor in nitrogen regulation was confirmed for selected NtcA-targets. We suggest that the indicated poised state of NtcA enables a more differentiated response to nitrogen limitation and can be advantageous in native habitats of Synechocystis.
dc.description.sponsorshipMinisterio de Economia y Competitividad (MINECO) [BFU2013-41712, BIO2016-75634]; Junta de Andalucia-European Regional Funds (FEDER) [BIO-284, P12-BIO-1119]; FCT (Fundacao para a Ciencia e a Tecnologia) [PTDC/BIA-MIC/4418/2012, IF/00881/2013, UID/BIM/04773/2013-CBMR, UID/Multi/04326/2013-CCMAR]; School of Biomedical & Healthcare Sciences, Plymouth University Peninsula Schools of Medicine and Dentistry
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1093/nar/gkx860
dc.identifier.issn0305-1048
dc.identifier.issn1362-4962
dc.identifier.urihttp://hdl.handle.net/10400.1/11759
dc.language.isoeng
dc.peerreviewedyes
dc.publisherOxford University Press
dc.relationThe regulation of photosynthesis in cyanobacteria: A systems biology approach
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectSynechocystis Sp Pcc-6803
dc.subjectSigma-factor sige
dc.subjectSignal-transduction
dc.subjectTarget prediction
dc.subjectStrain Pcc-7942
dc.subjectGene-expression
dc.subjectRegulated genes
dc.subjectRna-polymerase
dc.subjectSp Pcc6803
dc.subjectIn-Vivo
dc.titleIdentification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleThe regulation of photosynthesis in cyanobacteria: A systems biology approach
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-MIC%2F4418%2F2012/PT
oaire.citation.endPage11820
oaire.citation.startPage11800
oaire.citation.titleNucleic Acids Research
oaire.citation.volume45
oaire.fundingStream3599-PPCDT
person.familyNameGiner
person.familyNameRobles Rengel
person.familyNameHernández-Prieto
person.familyNameMuro-Pastor
person.familyNameFlorencio
person.familyNameFutschik
person.givenNameJoaquin
person.givenNameRocío
person.givenNameMiguel Angel
person.givenNameM. Isabel
person.givenNameFrancisco J
person.givenNameMatthias
person.identifier336659
person.identifier74322
person.identifier.ciencia-idA71B-AD01-3501
person.identifier.orcid0000-0003-1553-8295
person.identifier.orcid0000-0002-5738-4880
person.identifier.orcid0000-0001-7950-1526
person.identifier.orcid0000-0001-7366-7904
person.identifier.orcid0000-0002-2068-7861
person.identifier.orcid0000-0002-6245-8071
person.identifier.ridC-6045-2015
person.identifier.ridK-7716-2014
person.identifier.scopus-author-id55329443800
person.identifier.scopus-author-id26430696600
person.identifier.scopus-author-id6602888228
person.identifier.scopus-author-id7004302600
person.identifier.scopus-author-id14017989400
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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