Synechocystis sp. CACIAM 05
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PROVIDER: PRJNA360925 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Targeted proteome analysis of Synechocystis sp. PCC 6803 under photoautotrophic and mixotrophic conditions
2020-06-02 | PXD010010 | JPOST Repository
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Project description:Montagud2010 - Genome-scale metabolic network
of Synechocystis sp. PCC6803 (iSyn669)
This model is described in the article:
Reconstruction and analysis
of genome-scale metabolic model of a photosynthetic
bacterium.
Montagud A, Navarro E,
Fernández de Córdoba P, Urchueguía JF, Patil
KR.
BMC Syst Biol 2010; 4: 156
Abstract:
BACKGROUND: Synechocystis sp. PCC6803 is a cyanobacterium
considered as a candidate photo-biological production
platform--an attractive cell factory capable of using CO2 and
light as carbon and energy source, respectively. In order to
enable efficient use of metabolic potential of Synechocystis
sp. PCC6803, it is of importance to develop tools for
uncovering stoichiometric and regulatory principles in the
Synechocystis metabolic network. RESULTS: We report the most
comprehensive metabolic model of Synechocystis sp. PCC6803
available, iSyn669, which includes 882 reactions, associated
with 669 genes, and 790 metabolites. The model includes a
detailed biomass equation which encompasses elementary building
blocks that are needed for cell growth, as well as a detailed
stoichiometric representation of photosynthesis. We demonstrate
applicability of iSyn669 for stoichiometric analysis by
simulating three physiologically relevant growth conditions of
Synechocystis sp. PCC6803, and through in silico metabolic
engineering simulations that allowed identification of a set of
gene knock-out candidates towards enhanced succinate
production. Gene essentiality and hydrogen production potential
have also been assessed. Furthermore, iSyn669 was used as a
transcriptomic data integration scaffold and thereby we found
metabolic hot-spots around which gene regulation is dominant
during light-shifting growth regimes. CONCLUSIONS: iSyn669
provides a platform for facilitating the development of
cyanobacteria as microbial cell factories.
This model is hosted on
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MODEL1507180008.
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2015-07-30 | MODEL1507180008 | BioModels
Project description:Cyanobium sp. CACIAM 14 Genome sequencing and assembly
| PRJNA246088 | ENA
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:We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of different strains of the cyanobacterium Synechocystis sp. PCC6803. Comparison encompassed wild-type Synechocystis (WT), a strain overexpressing RNase E and RNase HII (rne(WT)) and a strain overexpressing 5’-sensing-deficient RNase E and RNase HII (rne(5p)). Analysis of changing 5'-monophosphorylated ends revealed 5’ sensing depedent processing sites on a transcriptome-wide level.
2023-01-20 | GSE184824 | 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