Linking Transcriptomic Organization to the Regulatory Landscape of Cyanobacteria through Context-Based Network Analysis
Ontology highlight
ABSTRACT:
ORGANISM(S): Picosynechococcus sp. PCC 7002
PROVIDER: GSE72880 | GEO | 2015/09/11
SECONDARY ACCESSION(S): PRJNA295259
REPOSITORIES: GEO
Similar Datasets
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.
2013-12-20 | E-GEOD-53360 | biostudies-arrayexpress
Project description:Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing the fast-growing response of Synechococcus sp. PCC 7002 response to variable irradience levels. We employed controlled cultivation and next-generation sequencing technology to identify transcriptional responses of euryhaline unicellular cyanobacterium Synechococcus sp. PCC 7002 grown under steady state conditions at six irradiance levels ranging from 33 to 760 µmol photons m-2 sec-1.
2015-09-04 | E-GEOD-72691 | biostudies-arrayexpress
Project description:We calculated global RNA half lives for all genes in the cyanobacteria Synechococcus sp. strain PCC 7002. Samples from three replicates of the WT strain were taken before and following the addition of the antibiotic rifampicin to stop nascent transcription. RNA spike-ins were added for normalization and using the number of RNA-sequencing reads we were able to calculate half lives for genes, transcripts, and for each position on the genome.
2019-01-01 | GSE109174 | GEO
Project description:Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method. DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803).
2013-07-19 | GSE48981 | GEO
Project description:Cyanobacteria are valuable organisms for studying the physiology of photosynthesis and carbon fixation as well as metabolic engineering for the production of fuels and chemicals. This work describes a novel counter selection method for the cyanobacterium Synechococcus sp. PCC 7002 based on organic acid toxicity. The organic acids acrylate, 3-hydroxypropionate, and propionate were shown to be inhibitory towards PCC 7002 and other cyanobacteria at low concentrations. Inhibition was overcome by a loss of function mutation in the gene acsA. Loss of AcsA function was used as a basis for an acrylate counter selection method. DNA fragments of interest were inserted into the acsA locus and strains harboring the insertion were isolated on selective medium containing acrylate. This methodology was also used to introduce DNA fragments into a pseudogene, glpK. Application of this method will allow for more advanced genetics and engineering studies in PCC 7002 including the construction of markerless gene deletions and insertions. The acrylate counter-selection could be applied to other cyanobacterial species where AcsA activity confers acrylate sensitivity (e.g. Synechocystis sp. PCC 6803). Cultures were grown in medium modified with 5mM acrylic acid at pH 8 and compared to cultures grown in unmodified medium. Samples were processed in duplicate.
2013-07-19 | E-GEOD-48981 | biostudies-arrayexpress
Project description:Metabolite Extractions data from the Strains Synechococcus sp. PCC 7002, Synechococcus elongatus PCC 11801 (New strain, Manuscript submitted) and Synechococcus elongatus PCC 7942
2018-09-08 | ST001057 | MetabolomicsWorkbench
Project description:Application of genome-scale 'omics approaches to dissect subcellular pathways and regulatory networks governing the fast-growing response of Synechococcus sp. PCC 7002 response to variable irradience levels.
2015-09-04 | GSE72691 | GEO
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 – 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.
2009-11-30 | GSE18902 | GEO
Project description:Cyanobacteria fix atmospheric CO2 to biomass and through metabolic engineering can also act as photosynthetic cell factories for sustainable productions of fuels and chemicals. The Calvin cycle is the primary pathway for CO2 fixation in cyanobacteria, algae and C3 plants, and several studies have shown that overexpression of a cyanobacterial Calvin cycle enzyme, bifunctional sedoheptulose-1,7-bisphosphatase/fructose-1,6-bisphosphatase (hereafter BiBPase), enhances CO2 fixation in both plants and algae, although its impact on cyanobacteria has not yet been rigorously studied. Here, we show that overexpression of BiBPase enhanced growth, cell size, and photosynthetic O2 evolution of the cyanobacterium Synechococcus sp. PCC 7002 in an environment with elevated CO2 concentration. Biochemical analysis, immunodetection, and proteomic analysis revealed that overexpression of BiBPase considerably elevated the cellular activities of two rate-limiting enzymes in the Calvin cycle, namely ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and aldolase, while it repressed several enzymes involved in the respiratory carbon metabolism (e.g. glycolysis and the oxidative pentose phosphate pathway) including glucose-6-phosphate dehydrogenase. Concomitantly, the content of glycogen was significantly reduced while the extracellular carbohydrate content increased. These results indicate that overexpression of BiBPase leads to global reprogramming of carbon metabolism in Synechococcus sp. PCC 7002, promoting photosynthetic carbon fixation and repressing the respiratory carbon catabolism, while altering carbohydrate partitioning.
2019-01-17 | PXD007963 | Pride
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