Synechocystis sp. PCC 6803
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PROVIDER: PRJNA209987 | ENA |
REPOSITORIES: ENA
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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: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:Acclimation to low CO2 conditions in cyanobacteria involves the coordinated regulation of genes mainly encoding components of the carbon concentration mechanism (CCM). Making use of several independent microarray datasets a core set of CO2-regulated genes was defined for the model strain Synechocystis sp. PCC 6803. On the transcriptional level, the CCM is mainly regulated by the well-characterized transcriptional regulators NdhR and CmpR, whereas the role of an additional regulatory protein, namely cyAbrB2 belonging to the widely distributed AbrB regulator family that was originally characterized in the genus Bacillus, is less defined. Here we present results of transcript profiling of the wild type and a ΔcyabrB2 mutant of Synechocystis sp. PCC 6803 after shifts from high CO2 (5% in air, HC) to low CO2 (0.04%, LC). Evaluation of the transcriptomic data revealed that cyAbrB2 is involved in the regulation of several CCM-related genes such as sbtA/B, ndhF3/ndhD3/cupA and cmpABCD under LC conditions, but apparently acts supplementary to the main regulators. Under HC conditions, cyAbrB2 deletion changes the expression of photosystem II subunits, light-harvesting components, and Calvin-Benson-Bassham cycle enzymes.
2016-09-19 | GSE82120 | GEO
Project description:Targeted proteome analysis of Synechocystis sp. PCC 6803 under photoautotrophic and mixotrophic conditions
2020-06-02 | PXD010010 | JPOST Repository
Project description:Synechocystis sp. PCC 6803 Genome sequencing
| PRJNA632699 | ENA
Project description:Synechocystis sp. PCC 6803 Genome sequencing
| PRJNA80481 | ENA
Project description:To investigate acclimation mechanisms employed under extreme high light conditions, gene expression analysis was performed using the model microalgae Synechocystis sp. PCC 6803 (PCC 6803) cultured under various light intensities. From the low to the mid light conditions, the expression of genes related to light harvesting systems was repressed, whereas that of CO2 fixation and of D1 protein turnover-related genes was induced. Gene expression data also revealed that the down-regulation of genes related to flagellum synthesis (pilA2), pyridine nucleotide transhydrogenase (pntA and pntB), and sigma factor (sigA and sigF) represents acclimation mechanisms of PCC 6803 under excessive high light conditions.
2018-03-06 | GSE111408 | GEO
Project description:The NDH1 complex fulfils numerous tasks in the cyanobacterial cell such as respiration, cyclic electron flow, and inorganic carbon concentration. Despite the immense progress in our understanding of structure/function relation of the cyanobacterial NDH1 complex, the subunits catalysing the NAD(P)H docking and oxidation are still missing. The gene sml0013 of Synechocystis 6803 encodes for a small protein of unknown function for that homologs exist in all completely known cyanobacterial genomes. The protein exhibits weak similarities to the NDF6 protein, which was reported from Arabidopsis chloroplasts as a NDH subunit (Ishikawa et al. 2008). A sml0013 inactivation mutant of Synechocystis 6803 was generated and characterized. It showed only weak differences regarding growth and pigmentation at various culture conditions; most remarkably it exhibited a glucose-sensitive phenotype in the light. The genome-wide expression pattern of the M-NM-^Tsml0013::Km mutant was almost identical to wild type when grown under high CO2 conditions as well as after shifts to low CO2 conditions. However, measurements of the photosystem I redox kinetic in cells of the M-NM-^Tsml0013::Km mutant revealed differences to wild type such as a decreased capability of cyclic electron flow as well as of utilization of electrons from catabolic processes. These results suggest that the Sml0013 protein (named NdhP) represent a novel subunit of the cyanobacterial NDH1 complex mediating its coupling to the respiratory or photosynthetic electron flow. Gene expression of Synechocystis sp. PCC 6803 WT and a M-NM-^Tsml0013::Km mutant was monitored at HC conditions (5% CO2) and at 24h after a shift to LC conditions (ambient air containing 0.035% CO2). Each condition was sampled in biological duplicates.
2013-06-29 | E-GEOD-48415 | biostudies-arrayexpress
Project description:Cyanobacteria are photoautotrophic prokaryotes with a plant-like photosynthetic machinery. Besides being able to grow photoautotrophically, some cyanobacteria are also capable to grow photoheterotrophically, where they use reduced organic compounds as carbon source, or even completely heterotrophically by using reduced organic compounds as carbon and energy source. The well characterized cyanobacterium Synechocystis sp. PCC 6803 can grow in darkness under light-activated heterotrophic growth (LAHG) conditions by using glucose as carbon and energy source. In the present work, we combined pre-fractioning of Synechocystis cellular membranes with a global proteome and lipidome analysis, to shift the analytical focus towards the rearrangement of the internal thylakoid membrane system observed in Synechocystis cells under LAHG conditions.
2015-03-03 | PXD000980 | Pride