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Iron deprivation in synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling

2012-12Journal article Open access
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dc.contributor.authorHernandez-Prieto, Miguel A.
dc.contributor.authorSchoen, Verena
dc.contributor.authorGeorg, Jens
dc.contributor.authorBarreira, Luísa
dc.contributor.authorJ. C. or Varela J. or Varela J.C.S., Varela
dc.contributor.authorHess, Wolfgang R.
dc.contributor.authorFutschik, Matthias E.
dc.date.accessioned2018-12-07T14:52:53Z
dc.date.available2018-12-07T14:52:53Z
dc.date.issued2012-12
dc.description.abstractIron is an essential cofactor in many metabolic reactions. Mechanisms controlling iron homeostasis need to respond rapidly to changes in extracellular conditions, but they must also keep the concentration of intracellular iron under strict control to avoid the generation of damaging reactive oxygen species. Due to its role as a redox carrier in photosynthesis, the iron quota in cyanobacteria is about 10 times higher than in model enterobacteria. The molecular details of how such a high quota is regulated are obscure. Here we present experiments that shed light on the iron regulatory system in cyanobacteria. We measured time-resolved changes in gene expression after iron depletion in the cyanobacterium Synechocystis sp. PCC 6803 using a comprehensive microarray platform, monitoring both protein-coding and non-coding transcripts. In total, less than a fifth of all protein-coding genes were differentially expressed during the first 72 hr. Many of these proteins are associated with iron transport, photosynthesis, or ATP synthesis. Comparing our data with three previous studies, we identified a core set of 28 genes involved in iron stress response. Among them were genes important for assimilation of inorganic carbon, suggesting a link between the carbon and iron regulatory networks. Nine of the 28 genes have unknown functions and constitute key targets for further functional analysis. Statistical and clustering analyses identified 10 small RNAs, 62 antisense RNAs, four 59UTRs, and seven intragenic elements as potential novel components of the iron regulatory network in Synechocystis. Hence, our genome-wide expression profiling indicates an unprecedented complexity in the iron regulatory network of cyanobacteria.
dc.description.sponsorshipPortuguese Fundacao para a Ciencia e a Tecnologia (FCT) [PTDC/BIA-MIC/101036/2008]; Deutsche Forschungsgemeinschaft (DFG) Focus program "Sensory and regulatory RNAs in Prokaryotes [SPP1258]; FCT [PEst-OE/EQB/LA0023/2011]
dc.description.versioninfo:eu-repo/semantics/publishedVersion
dc.identifier.doi10.1534/g3.112.003863
dc.identifier.issn2160-1836
dc.identifier.urihttp://hdl.handle.net/10400.1/11251
dc.language.isoeng
dc.peerreviewedyes
dc.publisherGenetics Society America
dc.relationStrategic Project - LA 23 - 2011-2012
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectSp Pcc 6803
dc.subjectSp Strain Pcc-6803
dc.subjectCis antisense Rna
dc.subjectCyanobacterium synechocystis
dc.subjectGene expression
dc.subjectEscherichia coli
dc.subjectPhotosystem Ii
dc.subjectMicroarray data
dc.subjectStress conditions
dc.subjectOxidative stress
dc.titleIron deprivation in synechocystis: inference of pathways, non-coding RNAs, and regulatory elements from comprehensive expression profiling
dc.typejournal article
dspace.entity.typePublication
oaire.awardTitleStrategic Project - LA 23 - 2011-2012
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/3599-PPCDT/PTDC%2FBIA-MIC%2F101036%2F2008/PT
oaire.awardURIinfo:eu-repo/grantAgreement/FCT/6817 - DCRRNI ID/PEst-OE%2FEQB%2FLA0023%2F2011/PT
oaire.citation.endPage1495
oaire.citation.issue12
oaire.citation.startPage1475
oaire.citation.titleG3-Genes Genomes Genetics
oaire.citation.volume2
oaire.fundingStream3599-PPCDT
oaire.fundingStream6817 - DCRRNI ID
person.familyNameHernández-Prieto
person.familyNameBarreira
person.familyNameVarela
person.familyNameFutschik
person.givenNameMiguel Angel
person.givenNameLuísa
person.givenNameJoão
person.givenNameMatthias
person.identifier.ciencia-id6D1A-17E5-1400
person.identifier.ciencia-idA71B-AD01-3501
person.identifier.orcid0000-0001-7950-1526
person.identifier.orcid0000-0002-4077-855X
person.identifier.orcid0000-0003-3101-693X
person.identifier.orcid0000-0002-6245-8071
person.identifier.ridM-4223-2013
person.identifier.scopus-author-id26430696600
person.identifier.scopus-author-id55741416000
person.identifier.scopus-author-id14017989400
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.identifierhttp://doi.org/10.13039/501100001871
project.funder.nameFundação para a Ciência e a Tecnologia
project.funder.nameFundação para a Ciência e a Tecnologia
rcaap.rightsopenAccess
rcaap.typearticle
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