Transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration in R. sphaeroides
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ABSTRACT:
ORGANISM(S): Cereibacter sphaeroides 2.4.1
PROVIDER: GSE12269 | GEO | 2008/07/29
SECONDARY ACCESSION(S): PRJNA113653
REPOSITORIES: GEO
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Project description:we performed time series microarray analyses to investigate transcriptome dynamics during the transition from anaerobic photosynthesis to aerobic respiration. Published on J. Bacteriol., 190 (1), 286-299, 2008. Major changes in gene expression profiles occurred in the initial 15 min after the shift from anaerobic-light to aerobic-dark conditions, with changes continuing to occur up to 4 hours postshift. Those genes whose expression levels changed significantly during the time series were grouped into three major classes by clustering analysis. Class I contained genes, such as that for the aa3 cytochrome oxidase, whose expression levels increased after the shift. Class II contained genes, such as those for the photosynthetic apparatus and Calvin cycle enzymes, whose expression levels decreased after the shift. Class III contained genes whose expression levels temporarily increased during the time series. Keywords: time course R. sphaeroides 2.4.1 was grown in 800 ml of medium in 1-liter glass bottles under anaerobic photosynthesis conditions. When the optical density at 600 nm (OD600) reached approximately 0.2 to 0.3, the light was turned off and the composition of the gas mixture was abruptly changed for aerobic growth conditions. RNA was isolated from a 50-ml aliquot of the culture prior to the shift to aerobic conditions (0 min) and at 15 min, 30 min, 1 h, 2 h, and 4 h after the shift. The final OD600 at 4 h was approximately 0.3 to 0.4, representing not quite a culture doubling. The experiment was performed in quadruplicate independent cultures.
2008-07-28 | E-GEOD-12269 | biostudies-arrayexpress
Project description:Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria. Comparison of gene expression profiles of the wild type before and after sigC overexpression at the exponential phase. Three independent experiments were performed.
2016-08-22 | E-GEOD-72451 | biostudies-arrayexpress
Project description:Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.
2016-08-22 | GSE72452 | GEO
Project description:Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.
2016-08-22 | GSE72451 | GEO
Project description:Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria.
2016-08-22 | GSE72450 | GEO
Project description:Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria. ChIP-chip analyses using a strain expressing the FLAG-tagged SigC in the background of the wild type at two growth phases (exporenatial and stationary phases). Two independent experiments were performed.
2016-08-22 | E-GEOD-72452 | biostudies-arrayexpress
Project description:Bacteria modify expression of different types of terminal oxidase in response to oxygen availability. Corynebacterium glutamicum, a facultative anaerobic bacterium in Actinobacteria, possesses aa3-type cytochrome c oxidase and cytochrome bd-type quinol oxidase, the latter of which is induced upon oxygen limitation. We report here that an extracytoplasmic function sigma factor, SigC, is unprecedentedly responsible for the regulation. Chromatin immunoprecipitation in conjunction with microarray (ChIP-chip) analysis detected eight SigC-binding regions in the genome, leading to identification of a consensus promoter sequence for SigC recognition. The promoter sequences were found upstream of genes for cytochrome bd, heme a synthesis enzymes, and uncharacterized membrane proteins, all of which were upregulated by sigC overexpression. In contrast, that found on the antisense strand upstream of an operon encoding the cytochrome bc1 complex conferred a SigC-dependent negative effect on the operon expression. The SigC regulon was induced by cytochrome aa3 deficiency without modification of expression of sigC itself, but not by deficiency of the bc1 complex. These findings suggest that SigC is activated in response to impairment of electron transfer via cytochrome aa3, not directly to shift in oxygen levels. Our results provide a novel paradigm for transcriptional regulation of the aerobic respiratory system in bacteria. Gene expression profile of the wild type at the exponential phase was compared with that of the sigC deletion mutant. Two indepent experiments using two independent mutants were performed.
2016-08-22 | E-GEOD-72450 | biostudies-arrayexpress
Project description:Transcriptional expression of MG1655 and UTI89 harvested from various time points during aerobic or anaerobic growth in Luria-Bertani medium Keywords: time course analyses (aerobic and anaerobic)
2007-02-02 | GSE6425 | GEO
Project description:In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
2024-02-01 | GSE253350 | GEO
Project description:In this study, we provide a time-series analysis of the transcriptional response of Gemmatimonas phototrophica AP64T during the dark-to-light transition under aerobic and semiaerobic conditions. By analysing its transcriptome, focussing especially on PS-related genes, we tested the hypothesis that G. phototrophica might constitute an example of an anoxygenic phototroph on its evolutionary pathway from anaerobic to aerobic life-style.
2024-02-01 | GSE253349 | GEO