Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803
Autor(a) principal: | |
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Data de Publicação: | 2017 |
Outros Autores: | , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
Texto Completo: | http://hdl.handle.net/10400.1/11759 |
Resumo: | In 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. |
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Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803Synechocystis Sp Pcc-6803Sigma-factor sigeSignal-transductionTarget predictionStrain Pcc-7942Gene-expressionRegulated genesRna-polymeraseSp Pcc6803In-VivoIn 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.Ministerio 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 DentistryOxford University PressSapientiaGiner-Lamia, JoaquinRobles-Rengel, RocioHernandez-Prieto, Miguel A.Isabel Muro-Pastor, M.Florencio, Francisco J.Futschik, Matthias E.2018-12-07T14:57:54Z20172017-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.1/11759eng0305-104810.1093/nar/gkx860info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-24T10:23:36Zoai:sapientia.ualg.pt:10400.1/11759Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T20:03:13.173507Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
dc.title.none.fl_str_mv |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
title |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
spellingShingle |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 Giner-Lamia, Joaquin Synechocystis Sp Pcc-6803 Sigma-factor sige Signal-transduction Target prediction Strain Pcc-7942 Gene-expression Regulated genes Rna-polymerase Sp Pcc6803 In-Vivo |
title_short |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
title_full |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
title_fullStr |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
title_full_unstemmed |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
title_sort |
Identification of the direct regulon of NtcA during early acclimation to nitrogen starvation in the cyanobacterium &ITSynechocystis&IT sp PCC 6803 |
author |
Giner-Lamia, Joaquin |
author_facet |
Giner-Lamia, Joaquin Robles-Rengel, Rocio Hernandez-Prieto, Miguel A. Isabel Muro-Pastor, M. Florencio, Francisco J. Futschik, Matthias E. |
author_role |
author |
author2 |
Robles-Rengel, Rocio Hernandez-Prieto, Miguel A. Isabel Muro-Pastor, M. Florencio, Francisco J. Futschik, Matthias E. |
author2_role |
author author author author author |
dc.contributor.none.fl_str_mv |
Sapientia |
dc.contributor.author.fl_str_mv |
Giner-Lamia, Joaquin Robles-Rengel, Rocio Hernandez-Prieto, Miguel A. Isabel Muro-Pastor, M. Florencio, Francisco J. Futschik, Matthias E. |
dc.subject.por.fl_str_mv |
Synechocystis Sp Pcc-6803 Sigma-factor sige Signal-transduction Target prediction Strain Pcc-7942 Gene-expression Regulated genes Rna-polymerase Sp Pcc6803 In-Vivo |
topic |
Synechocystis Sp Pcc-6803 Sigma-factor sige Signal-transduction Target prediction Strain Pcc-7942 Gene-expression Regulated genes Rna-polymerase Sp Pcc6803 In-Vivo |
description |
In 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. |
publishDate |
2017 |
dc.date.none.fl_str_mv |
2017 2017-01-01T00:00:00Z 2018-12-07T14:57:54Z |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.1/11759 |
url |
http://hdl.handle.net/10400.1/11759 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
0305-1048 10.1093/nar/gkx860 |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
application/pdf |
dc.publisher.none.fl_str_mv |
Oxford University Press |
publisher.none.fl_str_mv |
Oxford University Press |
dc.source.none.fl_str_mv |
reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
reponame_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
repository.mail.fl_str_mv |
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1799133266233524224 |