Unknown,Transcriptomics,Genomics,Proteomics

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A daily temporal program for rhythmic expression of protein-coding and non-coding genes in response to light and dark in Synechocystis sp. PCC 6803

ABSTRACT: We investigated Synechocystis high-density microarray data of three high-resolution time-series experiments with alternating light/dark rhythm, transition to continuous light, and transition to continuous darkness. Using M-bM-^@M-^Xleast oscillating setM-bM-^@M-^Y normalization and a clustering approach we found a daily temporal program for rhythmic expression of protein-coding and non-coding genes under light/dark conditions. All rhythms, however, damped out rapidly under continuous conditions. We quantified gene expression of wild type Synechocystis PCC 6083 over 48 hours under three different light regimes; 12:12-h light/dark cycle (LDLDL), transfer to continuous light (LDLLL), and transfer to continuous dark (LDDDD). Samples were taken every two hours starting at CT 5.5 with an extra sample 30 minutes after dawn. Before the transfer to continuous light/dark in the LDLLL and LDDDD experiment, samples were taken every 6 with an extra sample 30 minutes after dawn.

ORGANISM(S): Synechocystis sp. PCC 6803

SUBMITTER: Christian Beck

PROVIDER: E-GEOD-47482 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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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.

Dataset Information

A daily temporal program for rhythmic expression of protein-coding and non-coding genes in response to light and dark in Synechocystis sp. PCC 6803

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