Diurnal gene expression in cyanobacteria
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB42778 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5211750.fastq.gz | Fastqsanger.gz | |||
| ERR5211760.fastq.gz | Fastqsanger.gz | |||
| ERR5211770.fastq.gz | Fastqsanger.gz | |||
| ERR5211751.fastq.gz | Fastqsanger.gz | |||
| ERR5211761.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 21 |
Similar Datasets
Project description:Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells
2013-04-02 | GSE45667 | 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:The model cyanobacterium Synechocystis sp. PCC encodes nine different σ factors. SigA is the essential primary σ factor that is mainly responsible for expression of housekeeping genes during normal growth. Group 2 σ factors are non-essential in standard conditions, and actually all single, double, triple and quadruple inactivation strains of group 2 factors grow well in standard growth conditions. The roles of group 2 σ factors in oxidative stress acclimation were studied using the ΔsigBCDE strain of Synechocystis sp. PCC 6803 which is devoid of all group 2 σ factors, and triple inactivation strains, each containing one group 2 σ factor. The ΔsigBCD strain contains only SigE, ΔsigBCE only SigD, ΔsigBDE only SigC and ΔsigCDE only SigB. The expression of genes encoding known players of oxidative stress tolerance in the triple and quadruple mutants were compared in standard growth conditions using DNA microarray analysis.
2018-11-12 | GSE117478 | GEO
Project description:The aim of this study was to find the cause for the previously reported inconsistency between oscillating transcription and constant protein levels under day-night growth conditions in cyanobacteria. To determine whether translational regulation counteracts transcriptional changes, Synechocystis sp. PCC 6803 was cultivated in an artificial day-night setting and the level of transcription, translation and protein was measured across the genome at different time points using mRNA sequencing, ribosome profiling and quantitative proteomics. This proteomics data set represents one layer of a larger data set covering three 'omics' levels.
2021-09-10 | PXD023812 | Pride
Project description:As photoautotrophic organisms, cyanobacteria are subjected to the natural diurnal rhythm. Thus, cyanobacteria face strong metabolomic changes that allow photosynthesis and glycogen anabolism throughout the day, while night phases require the adaption to a heterotrophic-like lifestyle, including glycogen catabolism. Previous studies highlighted the importance of both, SbtB and its effector molecule c-diAMP, for the nighttime survivability of Synechocystis through the regulation of glycogen synthesis. However, the extent of the cellular c-diAMP and SbtB impact for day/night survivability remained elusive. To get better understanding of cellular processes under SbtB or c-diAMP regulation, we compared metabolomic and proteomic characterizations of both a SbtB knockout (ΔsbtB) and a c-diAMP free (ΔdacA) mutant of the model strain Synechocystis sp. PCC 6803. While our data indicates that the cellular role of SbtB for nighttime survivability is solely restricted to carbon/glycogen metabolism, the diurnal lethality of ΔdacA seems to be a sum of cellular dysregulations among several metabolic processes. These processes include photosystem assembly and redox regulation, which leads to elevated levels of intracellular ROS and glutathione. Further, we were able to show an impact of c-diAMP on central carbon as well as nitrogen metabolism. The latter can be directly linked to reduced levels of NtcA, the global nitrogen transcription regulator. Thus, dysregulations of NtcA regulated proteins lead to an imbalance of the glutamine to glutamate ratio, reduced amounts of bioproducts of the ornithine pathway, such as arginine, and elevated levels of urea as a degradation product.
2025-08-21 | PXD045008 | Pride
Project description:Quantification of circadian gene expression in WT Synechocystis sp. PCC 6803 cells We quantified circadian gene expression of the wild type Synechocystis PCC6083 strain. Over a 24 h time course, 6 samples for RNA isolation were taken at the following time points: 30 minutes before and after light is switched off (sample 1 - CT 11.5 and sample 2 - CT 12.5), 30 minutes before midnight (sample 3 - CT 17.5), 348 30 minutes before and after light onset (sample 4 - CT 23.5 and sample 5 - CT 0.5) and 30 minutes before noon (sample 6 - CT 5.5).
2013-04-02 | E-GEOD-45667 | biostudies-arrayexpress
Project description:Deciphering structure, function and mechanism of a new lysine methyltransferase cKMT1 in model cyanobacterium Synechocystis sp. PCC 6803
2022-07-29 | PXD035617 |
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: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:To identify novel phototransduction pathways in cyanobacteria, mutants defective for phytochrome-related proteins in Synechocystis sp. PCC 6803 that exhibit increased or decreased gene expression levels. were screened. Keywords: array-based
2007-01-01 | GSE5391 | GEO