Photophysiological and Genetic Factors Underlying Fast Photosynthetic Growth of Unicellular Cyanobacterium Synechococcus sp. PCC 7002
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ABSTRACT:
ORGANISM(S): Synechococcus sp. PCC 7942
SUBMITTER: Ryan McClure
PROVIDER: E-GEOD-72691 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing interspecies interactions is dependent, at least initially, on the availability of model systems with well-annotated genomes and tractable genetics. We employed controlled cultivation and next-generation sequencing technology to identify transcriptional responses of euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 and a marine facultative aerobe Shewanella putrefaciens W3-18-1 to investigate the effect of C sources and C flux directions on the interactions between these organisms.
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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).
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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 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
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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 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
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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.
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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.
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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)
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Project description:Marine Synechococcus, together with Prochlorococcus, contribute to a significant proportion of the primary production on Earth. The spatial distribution of these two groups of marine picocyanobacteria depends on different factors such as nutrients availability or temperature. Some Synechococcus ecotypes thrive in mesotrophic and moderately oligotrophic waters, where they exploit both oxidized and reduced forms of nitrogen. Here, we present a comprehensive study, which includes transcriptomic and proteomic analyses of the response of Synechococcus sp. strain WH7803 to nanomolar concentrations of nitrate, compared to ammonium or nitrogen starvation. We found that Synechococcus has a specific response to nanomolar nitrate concentration that differs to the response showed under nitrogen starvation or the presence of standard concentrations of either ammonium or nitrate. This fact suggests that the particular response to the uptake of nanomolar concentration of nitrate could be an evolutionary advantage for marine Synechococcus against Prochlorococcus in the natural field.
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