Examination of gene expression levels in mutants of phytochrome-related protain
Ontology highlight
ABSTRACT:
ORGANISM(S): Synechocystis sp. PCC 6803
PROVIDER: GSE5391 | GEO | 2007/01/01
SECONDARY ACCESSION(S): PRJNA96185
REPOSITORIES: GEO
Similar Datasets
Project description:We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.
2018-08-15 | GSE115134 | GEO
Project description:We found that cyanobacterial RNA polymerase possesses very efficient intrinsic proofreading ability. This ability allows model species of cyanobacteria, Synechocystis sp PCC 6803 to keep in vivo level of transcriptional mistakes close to that of E.coli.
2018-08-15 | GSE115132 | GEO
Project description:Like many other organisms, cyanobacteria exhibit rhythmic gene expression with a period length of 24 hours to adapt to daily environmental changes. In the model organism Synechococcus elongatus PCC 7942 the central oscillator consists of three proteins: KaiA, KaiB and KaiC and utilizes the histidine kinase SasA and its response regulator RpaA as output-signaling pathway. Synechocystis sp. PCC 6803 contains two additional homologs of the kaiB and kaiC genes. Here we demonstrate that RpaA interacts with the core oscillator KaiAB1C1 of Synechocystis sp. PCC 6803 via SasA, similar to Synechococcus elongatus PCC 7942. However, interaction with the additional Kai homologs was not detected, suggesting different signal transduction components for the clock homologs. Inactivation of rpaA in Synechocystis sp. PCC 6803, lead to reduced viability of the mutant in light-dark cycles that aggravated under mixotrophic growth conditions. Chemoheterotrophic growth in the dark was abolished completely. In accordance, transcriptomic data revealed that RpaA is involved in the regulation of genes related to CO2‑acclimation and carbon metabolism under diurnal light conditions. Further, our results indicate that RpaA functions in the posttranslational regulation of glycogen metabolism as well, and a potential link between the circadian clock and motility was identified.
2018-10-01 | GSE116795 | GEO
Project description:Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells
2013-04-02 | GSE45667 | GEO
Project description:In cyanobacteria DNA supercoiling varies over the diurnal light/dark cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits gyrA, gyrB and overexpression of topoisomerase I (TopoI) topA and analyzed the transcriptional response to gyrase knock-downs (endpoint in triplicate) and topoisomerase I overexpression (endpoint in triplicate, and 19 time points time series before and after induction) in Synechocystis sp. PCC 6803 via RNA-seq of coding RNA. In detail, Illumina Ribo-Zero Plus rRNA Depletion Kit was used to remove the ribosomal RNA molecules from the isolated total RNA. Removal of rRNA was evaluated with the RNA Pico 6000 kit on the Agilent 2100 Bioanalyzer. RNA was free of detectable rRNA. Preparation of cDNA libraries was performed according to the manufacturer’s instructions for the TruSeq stranded mRNA kit (Illumina, San Diego, CA, United States). Subsequently, each cDNA library was sequenced on an Illumina NextSeq 500 system (2 x 75 nt PE high output v2.5).
2021-12-06 | E-MTAB-10949 | biostudies-arrayexpress
Project description:Extracellular proteins are involved in a remarkable number of fundamental processes in cyanobacteria. Yet, there is limited knowledge regarding the identity and function of these proteins. Here, we introduce a solid-phase enhanced protein aggregation workflow that enables description of the cyanobacterial exoproteome with unprecedented depth. Application to cyanobacteria from three distinct habitats, Synechocystis sp. PCC 6803, Synechcoccus sp. PCC 11901 and Nostoc punctiforme PCC 73102, allowed the identification of up to 62% of all predicted secreted proteins. The approach was then extended to compare the Synechocystis sp. PCC 6803 wild-type secretome with that of a bloom-like aggregated state and a secretion-impaired mutant. Finally, we demonstrate that the workflow can be miniaturized and adapted to a 96-well format for high-throughput secretome analysis. Collectively, these findings challenge the general belief that cyanobacteria lack secretory proteins and point to a functional conservation of the secretome across species from different environments. Our approach can be applied to microbes from a wide range of habitats, with the potential to open new avenues of investigation in microbial exoproteomics.
2024-08-29 | PXD047856 | Pride
Project description:In eubacteria, replacement of one σ factor in the RNA polymerase (RNAP) holoenzyme by another one changes the transcription pattern. Cyanobacteria are eubacteria characterized by oxygenic photosynthesis and they typically encode numerous group 2 σ factors that closely resemble the essential primary σ factor. A mutant strain of the model cyanobacterium Synechocystis sp. PCC 6803 without functional group 2 σ factors (named as ΔsigBCDE) could not acclimate to heat, high salt, or bright light stress but in standard conditions ΔsigBCDE grew only 9% slower than the control strain. One-fifth of the genes in ΔsigBCDE were differently expressed compared to the control strain in standard growth conditions and several physiological changes in photosynthesis, and pigment and lipid compositions were detected. To directly analyze the σ factor content of RNAP holoenzyme in vivo, a His-tag was added to the γ subunit of RNAP in Synechocystis and RNAPs were collected. The results revealed that all group 2 σ factors were recruited by RNAP in standard conditions, but recruitment of SigB and SigC increased in heat stress, SigD in bright light, SigE in darkness and SigB, SigC and SigE in high salt, explaining the poor acclimation of ΔsigBCDE to these stress conditions. Cells from cyanobacteria Synechocystis sp. PCC 6803 named as control strain (CS) and a mutant strain without any functional group 2 sigma factors, ΔsigBCDE, were harvested (A730=1, 40 mL) directly from standard growth conditions (continuous illumination at the PPFD of 40 µmol m-2s-1, 32°C, ambient CO2). From three to four independent experiments were performed at each conditions.
2015-09-15 | E-GEOD-69981 | biostudies-arrayexpress
Project description:Targeted proteome analysis of Synechocystis sp. PCC 6803 under photoautotrophic and mixotrophic conditions
2020-06-02 | PXD010010 | JPOST Repository
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