Oscillations in supercoiling drive circadian gene expression in cyanobacteria
Ontology highlight
ABSTRACT:
ORGANISM(S): Synechococcus elongatus PCC 7942 = FACHB-805
PROVIDER: GSE18902 | GEO | 2009/11/30
SECONDARY ACCESSION(S): PRJNA121309
REPOSITORIES: GEO
Similar Datasets
Project description:The cyanobacterium Synechococcus elongatus PCC 7942 exhibits oscillations in mRNA transcript abundance with 24-hour periodicity under continuous light conditions. The mechanism underlying these oscillations remains elusive â?? neither cis nor trans-factors controlling circadian gene expression phase have been identified. Here we show that the topological status of the chromosome is highly correlated with circadian gene expression state. We also demonstrate that DNA sequence characteristics of genes that appear monotonically activated and monotonically repressed by chromosomal relaxation during the circadian cycle are similar to those of supercoiling responsive genes in E. coli. Furthermore, perturbation of superhelical status within the physiological range elicits global changes in gene expression similar to those that occur during the normal circadian cycle. Synechococcus elongatus PCC 7942 was subjected to two consecutive light/dark cycles and released into continuous light (T = 0). Cells were sampled every 4 hours from T = 24 to T = 84 hours for microarray analysis to characterize circadian gene expression. In a separate experiment, to characterize the response of S. elongatus to immediate chromosome relaxation, cells were sampled at T = 56 and T = 64 hours, immediately followed by novobiocin treatment (0.1 ug/ml), and the resulting response was measured by microarray after 5, 10, 30, 90, and 150 minutes. This experiment was designed to test whether chromosomal relaxation is sufficient to induce gene expression changes similar to those observed during the circadian cycle.
2010-05-19 | E-GEOD-18902 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression in kaiA-overexpressor (Ptrc::[GTG]kaiA) strains under LL. KaiC has been proposed to globally activate gene expression, our analysis revealed that dawn expressing genes were downregulated by kaiA-overexpression, such that the clock was arrested at subjective dawn. IPTG-inducible kaiA-overexpressor (oxA) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a single experiment in oxA under LL in the presence or absence of an inducer, IPTG, from hour 24 to 48 in LL timecourse data (24~48 hours under continuous light) from Synechococcus elongatus PCC 7942 (inducible kaiA-overexpressor) strains
2013-12-31 | E-GEOD-47015 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to investigate comprehensive profiles of genome-wide Synechococcus gene expression in the kaiCEE mutant strains in which the KaiC phosphorylation cycling is abolished under LL.. In the kaiCEE mutant strain more than 23% of transcripts significantly oscillated with a period of about 48 h. 409 cyclic genes were shared with the wild type strains. kaiCEE mutant strain was analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: a single experiment in kaiCEE mutant under LL from hour 8 to 96 in LL timecourse data (8~96 hours under continuous light) from Synechococcus elongatus PCC 7942 (kaiCEE mutant) strains
2013-11-28 | E-GEOD-48901 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type, kaiABC-null and kaiC-overexpressor strains under LL and continuous dark (DD) conditions. In the wild type strain more than 30% of transcripts significantly oscillated in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was nullified in kaiABC-null strains. Although KaiC has been proposed to globally repress gene expression, our analysis revealed that dawn expressing genes were upregulated by kaiC-overexpression, such that the clock was arrested at subjective dawn. Transfer of cells to continuous dark (DD) conditions from LL immediately suppressed expression of most of genes, while the clock keeps time even in the absence of transcriptional feedback. Thus, the Synechococcus genome seems primarily regulated by the light/dark cycles and dramatically modified by the protein-based circadian oscillator. Keywords: timecourse data (~48 hours under continuous light or darkness) from Synechococcus elongatus PCC 7942 (wild type, kaiABC-null, and inducible kaiC-overexpressor) strains Wild type (WT), kaiABC-null (Dkai), and inducible kaiC-overexpressor (oxC) S. elongatus PCC 7942 strains were analyzed under continuous light (LL), continuous dark (DD) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: Two independent experiments in WT under LL (hours 0 to 52) and DD (hours 0 to 48); Two independent experiments in Dkai under LL (hours 0 to 48); Two independent experiments in oxC under LL in the presence or absence of an inducer, IPTG, from hour 25 to 33 in LL; a single experiment in WT under DD in the presence of an transcriptional inhibitor, rifampicin.
2009-07-31 | E-GEOD-14225 | biostudies-arrayexpress
Project description:In the unicellular cyanobacteriuIn the cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). Overexpression of clpX led to a decrease in kaiBC promoter activity, disruption of circadian rhythm, and eventually cell death. We found that overexpression of clpX upregulated mRNA levels of ribosomal protein subunits, after which expression of other genes containing the clock genes was decreased. Wild type (WT) and inducible clpX-overexpressor (ox-clpX) S. elongatus PCC 7942 strains were analyzed under continuous light (LL) using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: WT at hours 16 in LL (IPTG-free): WT under LL 20 in LL (addition of 100 µM IPTG for 4 hours): ox-clpX cells at hours 16 in LL (IPTG-free): ox-clpX cells at hours 20 in LL (addition of 100 µM IPTG for 4 hours)
2013-07-31 | E-GEOD-42542 | biostudies-arrayexpress
Project description:Previous molecular and mechanistic studies have identified several principles of prokaryotic transcription, but less is known about the global transcriptional architecture of bacterial genomes. Here we perform a comprehensive study of a cyanobacterial transcriptome, that of Synechococcus elongatus PCC 7942, generated by combining three high-resolution data sets: RNA sequencing, tiling expression microarrays, and RNA polymerase chromatin immunoprecipitation (ChIP) sequencing. We report absolute transcript levels, operon identification, and high-resolution mapping of 5' and 3' ends of transcripts. We identify several interesting features at promoters, within transcripts and in terminators relating to transcription initiation, elongation, and termination. Furthermore, we identify many putative non-coding transcripts. We provide a global analysis of a cyanobacterial transcriptome. Our results uncover insights that reinforce and extend the current views of bacterial transcription. RNA Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 RNA polymerase ChIP Sequencing of the cyanobacterium Synechococcus elongatus PCC 7942 Tiling Microarray of the cyanobacterium Synechococcus elongatus PCC 7942
2011-05-16 | E-GEOD-29264 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, most of genes are downregulated in the dark, while 10% of genes are upregulated. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type and kaiABC-null strains under continuous dark (DD) conditions. We found that expression profile of a subset of genes on the genome in DD was dramatically affected by kaiABC-nullification, and the magnitude of dark-induction was dependent on time when cells were transferred from light to DD Keywords: timecourse data (0-12 h) under continuous darkness after dark:light cycles from Synechococcus elongatus PCC 7942 wild type and kaiABC-null strains Wild type (WT) and kaiABC-null (DkaiABC) S. elongatus PCC 7942 strains were analyzed under continuous dark (DD) conditions after two 12h:12h light:dark (LD) cycles using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing predicted 2,515 protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also to the almost homologous strain, S. elongatus PCC 7942: Two independent experiments in WT and Dkai strains under DD (hours 0, 0.5, 1, 2, 4, 8 and 12).
2011-09-29 | E-GEOD-22468 | biostudies-arrayexpress
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, essentially all promoter activities are under the control of the circadian clock in continuous light (LL) conditions. Here, we employed high-density oligonucleotide arrays to explore comprehensive profiles of genome-wide Synechococcus gene expression in wild type, kaiABC-null and kaiC-overexpressor strains under LL and continuous dark (DD) conditions. In the wild type strain more than 30% of transcripts significantly oscillated in a circadian fashion, peaking at subjective dawn and dusk. Such circadian control was nullified in kaiABC-null strains. Although KaiC has been proposed to globally repress gene expression, our analysis revealed that dawn expressing genes were upregulated by kaiC-overexpression, such that the clock was arrested at subjective dawn. Transfer of cells to continuous dark (DD) conditions from LL immediately suppressed expression of most of genes, while the clock keeps time even in the absence of transcriptional feedback. Thus, the Synechococcus genome seems primarily regulated by the light/dark cycles and dramatically modified by the protein-based circadian oscillator. Keywords: timecourse data (~48 hours under continuous light or darkness) from Synechococcus elongatus PCC 7942 (wild type, kaiABC-null, and inducible kaiC-overexpressor) strains
2009-08-01 | GSE14225 | GEO
Project description:In the unicellular cyanobacterium, Synechococcus elongatus PCC 7942, most genes show rhythmic expression controlled by the Kai-based clock under continuous light conditions (LL). We found that rpoD6-null mutants impaired expression of clock-controlled genes peaking at hours 8-10 in LL, while sasA-null or rpaA-null mutants each arrested the expression profiles at subjective dawn. Time-course data (0-24 h) of wild type (WT), rpoD6-null, sasA-null and rpaA-null S. elongatus PCC 7942 strains analyzed under continuous light (LL) conditions after two 12h:12h light:dark (LD) cycles using Affymetrix high-density oligonucleotide microarrays (GeneChip CustomExpress Arrays) representing 2,515 predicted protein-coding genes on the genome of Synechococcus elongatus PCC 6301, which can be used also for the almost homologous strain, S. elongatus PCC 7942.
2012-03-01 | E-GEOD-28430 | biostudies-arrayexpress
Project description:The circadian clock of the cyanobacterium Synechococcus elongatus PCC 7942 drives oscillations in global mRNA abundances with 24 hour periodicity under constant light conditions. The transcription factor RpaA, a circadian clock-regulated transcription factor, controls the timing of circadian gene expression, but the mechanisms underlying this control are not well understood. Here we show that four RpaA-dependent sigma factors – RpoD2, RpoD6, RpoD5, and SigF2 – are sequentially activated downstream of active RpaA and are required for proper expression of circadian mRNAs. We find that RpoD6, RpoD5, and SigF2 exhibit circadian oscillations with different timing relative to each other at the level of mRNA expression and protein abundance. By measuring global gene expression in strains modified to individually lack rpoD2, rpoD6, rpoD5, and sigF2 we identify how expression of circadian mRNAs – including sigma factor mRNAs – is altered in the absence of each sigma factor. Broadly, our findings suggest that a single transcription factor, RpaA, is sufficient to generate complex circadian expression patterns in part by regulating an interdependent sigma factor cascade.
2019-05-20 | GSE114693 | GEO