Bioreactor metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA266438 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1640762.fastq.gz | Fastqsanger.gz | |||
| SRR1640754.fastq.gz | Fastqsanger.gz | |||
| SRR1640755.fastq.gz | Fastqsanger.gz | |||
| SRR1640756.fastq.gz | Fastqsanger.gz | |||
| SRR1640757.fastq.gz | Fastqsanger.gz |
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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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and identified by:
MODEL1507180008.
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2015-07-30 | MODEL1507180008 | BioModels
Project description:HoxH is a subunit of hydrogenase in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed hoxH mutant strain, which the mRNA levels of hoxH reduced to 50% of the wild-type.
2016-06-01 | GSE76625 | GEO
Project description:Identification of the membrane and the soluble proteins in Synechocystis sp. PCC6803
2015-01-16 | PXD001246 | Pride
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:We compared transcriptomic changes, 5'-triphosphorylated (TSS) and 5'-monophosphorylated (PSS) RNA ends of a thermo-sensitive and a wild-typic RNase E mutant strain of the cyanobacterium Synechocystis sp. PCC6803 (rne(Ts) and rne(WT)) before and after a heat shock. Analysis of changing 5'-monophosphorylated ends revealed RNase E depedent processing sites on a transcriptome-wide level.
2021-07-30 | GSE180316 | GEO
Project description:NtcA regulates primary in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed an ntcA-overexpressing strain, named NOX10, by introducing the ntcA genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and NOX10 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed two times with biologically independent RNA.
2014-07-01 | GSE54487 | GEO
Project description:NtcA regulates primary in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed an ntcA-overexpressing strain, named NOX10, by introducing the ntcA genes fusing psbAII promoter by homologous recombination. The transcript profiles of parental wild-type strain GT and NOX10 were compared by microarray CyanoChip (Takrara bio.). Experiments were performed three times with biologically independent RNA.
2014-07-01 | GSE54485 | GEO
Project description:The production of biofuels in photosynthetic microalgae and cyanobacteria is considered a promising alternative to the generation of fuels from fossil resources. However, to be economically competitive, producer strains need to be established that synthesize the targeted product at high yield and over a long time. Engineering cyanobacteria to forced fuel producers should considerably interfere with overall cell homeostasis, which in turn might counteract productivity and sustainability of the process. Therefore, in-depth characterization of the cellular response upon long-term production is of high interest for the targeted improvement of a desired strain. Here we report the results of a monitoring experiment, in which the transcriptome-wide response to continuous ethanol production in the unicellular model cyanobacterium Synechocystis sp. PCC6803 was examined using high resolution microarrays. In two independent experiments, ethanol production rates of 0.0338% (v/v) EtOH d-1 M-BM-1 0.002 and 0.0303% (v/v) d-1 M-BM-1 0.002 were obtained over 18 consecutive days, measuring biological triplicates in fully automated photobioreactors. Ethanol production caused a significant (~40%) delay in biomass accumulation in the producer strains and the development of a bleaching phenotype. Absorption spectroscopy indicated in particular a down-regulation of light harvesting capacity. Microarray analyses performed at day 4, 7, 11 and 18 of the experiment revealed only three mRNAs with a strongly modified accumulation level throughout the course of the experiment. In addition to the overexpressed adhA (slr1192) gene, this was an about 4 fold reduction in cpcB (sll1577) and an about 3 to 6 fold increase in rps8 (sll1809) mRNA levels. Much weaker modifications of expression level or modifications restricted to day 18 of the experiment were observed for genes involved in carbon assimilation (Ribulose bisphosphate carboxylase and Glutamate decarboxylase). Molecular analysis of the reduced cpcB levels revealed a post-transcriptional operon discoordination in the cpcBA operon leaving a truncated mRNA cpcA* likely not competent for translation. Moreover, Western blots and zinc-enhanced bilin fluorescence blots confirmed a severe reduction in the amounts of both phycocyanin subunits, explaining the cause of the bleaching phenotype. We conclude that the changes in gene expression upon induction of long term ethanol production in Synechocystis sp. PCC6803 are highly specific. in particular we did not observe a comprehensive stress response contributing to a complex phenotype as might have been expected. Gene expression of Synechocystis sp. PCC 6803 WT (#621) and the isogenic ethanol producing strain #309 was monitored at 4, 7, 11 and 18 days after induction of ethanol production by copper depletion. Each condition was sampled in biological duplicates
2013-08-06 | E-GEOD-49552 | biostudies-arrayexpress
Project description:HoxH is a subunit of hydrogenase in a unicelluar cyanobacterium Synechocystis sp. PCC6803. We constructed hoxH mutant strain, which the mRNA levels of hoxH reduced to 50% of the wild-type. Total RNAs from three independent wilde-type (GT) and three independent hoxH mutant were labeled by Cy3 followed by hybridyzation on a microarry chip generated by Agilent Technologies (Design ID 036279). Microarray is designed by Prof. Tomohisa Hasunuma, Kobe University.
2016-06-01 | E-GEOD-76625 | biostudies-arrayexpress
Project description:The response of the model cyanobacterium Synechocystis sp. PCC6803 towards light and carbon limitation was systematically probed. To this end, Synechocystis sp. PCC6803 was cultivated in a photo-bioreactor driven in turbidostat-mode. The turbidostat is a continuous cultivation that enabled cells to adapt to a constant environment, leading to a stable and 'optimal' proteome for the respective condition. The major dataset in this project consisted of 5 different 'concentrations' for light and CO2. Changes in the proteome were determined using using liquid chromatography/mass spectrometry and it was found that carbon and light limitation induced gradual but broad responses in gene expression. With decreasing substrate concentration (increasing limitation) a decrease in growth rate and a gradually more severe response in the proteome was visible.
2018-09-12 | PXD009582 | Pride