ABSTRACT: Transcriptional profile of Synechocystis sp. PCC6803 and Chlorogloeopsis fritschii sp. PCC6912 exposed to an M-dwarf spectrum under anoxic atmosphere
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
BioModels Database
and identified by:
MODEL1507180008.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
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.
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.
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.
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.
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.
