Synechocystis sp. PCC 6803: Difference between revisions
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*[http://genome.kazusa.or.jp/cyanobase/Synechocystis/ CyanoBase]: Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. This database was originally developed by Makoto Hirosawa, Takakazu Kaneko and Satoshi Tabata, and the current version of CyanoBase has been developed and maintained by Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata at Kazusa DNA Research Institute. |
*[http://genome.kazusa.or.jp/cyanobase/Synechocystis/ CyanoBase]: Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. This database was originally developed by Makoto Hirosawa, Takakazu Kaneko and Satoshi Tabata, and the current version of CyanoBase has been developed and maintained by Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata at Kazusa DNA Research Institute. |
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*[http://string.embl.de/ STRING]: STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughpot Experiments, (Conserved) Coexpression, and Previous Knowledge. The database currently contains 1,513,782 proteins in 373 species. Especially, the database provides interactions for ''Synechocystis'' sp. PCC 6803. |
*[http://string.embl.de/ STRING]: STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughpot Experiments, (Conserved) Coexpression, and Previous Knowledge. The database currently contains 1,513,782 proteins in 373 species. Especially, the database provides interactions for ''Synechocystis'' sp. PCC 6803. |
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*[http://bioinformatics.zj.cn/cTFbase/index.php cTFbase]: cTFbase contains 1288 putative TFs identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domain and ortholog identification from any selected genomes. |
*[http://bioinformatics.zj.cn/cTFbase/index.php cTFbase]: cTFbase contains 1288 putative trascription factors (TFs) identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domain and ortholog identification from any selected genomes. |
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[[Category:Cyanobacteria]] |
[[Category:Cyanobacteria]] |
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Revision as of 21:43, 21 September 2014
| Synechocystis sp. PCC6803 | |
|---|---|
| Scientific classification | |
| Kingdom: | |
| Phylum: | |
| Order: | |
| Genus: | Synechocystis
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| Species: | S. sp. PCC6803
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| Binomial name | |
| Synechocystis sp. | |
Synechocystis is a genus of cyanobacteria primarily represented by the strain Synechocystis sp. PCC6803. S. sp. PCC6803 lives in freshwater and is capable of both phototrophic growth by oxygenic photosynthesis in sunlight and heterotrophic growth by glycolysis and oxidative phosphorylation during dark periods. It is able to effectively anticipate transitions of light and dark phases by using a circadian clock.
Growth and use as a model organism
Cyanobacteria are model microorganisms for the study of photosynthesis, carbon and nitrogen assimilation, evolution of plant plastids, and adaptability to environmental stresses. Synechocystis sp. PCC6803 is one of the most highly studied types of cyanobacteria as it can grow both autotrophically or heterotrophically in the absence of light. It was isolated from a freshwater lake in 1968 and is easily transformed by exogenous DNA. The photosynthetic apparatus is very similar to the one found in plants. This organism also exhibits phototactic movement.
Genome
The genome of Synechocystis sp. PCC6803 is contained within one chromosome (3.57 megabases), three small plasmids (5.2, 2.4, and 2.3 kilobases) and four large plasmids (120, 106, 103, and 44 kilobases).[1]
Light-activated heterotrophy
Synechocystis sp. PCC6803 can live completely heterotrophically in the dark, but for yet unknown reasons requires a minimum of 5 to 15 minutes (blue) light per day. This regulatory role of light is intact in both PSI and PSII deficient strains.[2]
NDH-2 is a regulatory quinone:NAD(P)H oxidoreductase[3] global analysis of circadian gene expression indicates that translation genes are expressed at the early subjective day.[4]
Some glycolytic genes are regulated by sll1330 under light and glucose-supplemented conditions. One of the most important glycolytic genes is fructose-1,6-bisphosphate aldolase (fbaA). The mRNA level of fbaA is increased under light and glucose-supplemented conditions. But in Δsll1330, fbaA is not increased under same conditions.[5]
References
- ^ Kaneko, T; Nakamura, Y; Sasamoto, S; Watanabe, A; Kohara, M; Matsumoto, M; Shimpo, S; Yamada, M; Tabata, S (Oct 31, 2003). "Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803". DNA research : an international journal for rapid publication of reports on genes and genomes. 10 (5): 221–8. doi:10.1093/dnares/10.5.221. PMID 14686584.
{{cite journal}}: Unknown parameter|displayauthors=ignored (|display-authors=suggested) (help) - ^ Anderson SL and McIntosh L (May 1991). "Light-activated heterotrophic growth of the cyanobacterium Synechocystis sp. strain PCC 6803: a blue-light-requiring process". J Bacteriol. 173 (9): 2761–2767. PMC 207855. PMID 1902208.
- ^ Howitt CA, Udall PK, and Vermaas WF (July 1999). "Type 2 NADH dehydrogenases in the cyanobacterium Synechocystis sp. strain PCC 6803 are involved in regulation rather than respiration". J Bacteriol. 181 (13): 3994–4003. PMC 93889. PMID 10383967.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Kucho K, Okamoto K, Tsuchiya Y, Nomura S, Nango M, Kanehisa M, and Ishiura M (March 2005). "Global analysis of circadian expression in the cyanobacterium Synechocystis sp. strain PCC 6803". J Bacteriol. 187 (6): 2190–2199. doi:10.1128/JB.187.6.2190-2199.2005. PMC 1064041. PMID 15743968.
{{cite journal}}: CS1 maint: multiple names: authors list (link) - ^ Yusuke Tabei, Katsuhiko Okada and Mikio Tsuzuki (April 2007). "Sll1330 controls the expression of glycolytic genes in Synechocystis sp. PCC 6803". Biochem. Biophys. Res. Commun. 355 (4): 1045–1050. doi:10.1016/j.bbrc.2007.02.065. PMID 17331473.
Databases
- SynechoNET: integrated protein-protein interaction database of a model cyanobacterium Synechocystis sp. PCC 6803. SynechoNET is a specialized cyanobacterial protein-protein interaction database. It shows feasible cyanobacterial domain-domain interactions, as well as their protein level interactions using the model cyanobacterium, Synechocystis sp. PCC 6803. Additionally, SynechoNET provides transmembrane topology and domain information, as well as the interaction networks in graphical web interfaces.
- CyanoBase: Cyanobacteria carry a complete set of genes for oxygenic photosynthesis, which is the most fundamental life process on the earth. This organism is also interesting from an evolutional viewpoint, for it was born in a very ancient age and has survived in various environments. Chloroplast is believed to have evolved from cyanobacterial ancestors which developed an endosymbiontic relationship with a eukaryotic host cell. CyanoBase provides an easy way of accessing the sequences and all-inclusive annotation data on the structures of the cyanobacterial genomes. This database was originally developed by Makoto Hirosawa, Takakazu Kaneko and Satoshi Tabata, and the current version of CyanoBase has been developed and maintained by Yasukazu Nakamura, Takakazu Kaneko, and Satoshi Tabata at Kazusa DNA Research Institute.
- STRING: STRING is a database of known and predicted protein-protein interactions.The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: Genomic Context, High-throughpot Experiments, (Conserved) Coexpression, and Previous Knowledge. The database currently contains 1,513,782 proteins in 373 species. Especially, the database provides interactions for Synechocystis sp. PCC 6803.
- cTFbase: cTFbase contains 1288 putative trascription factors (TFs) identified from 21 fully sequenced cyanobacterial genomes. Through its user-friendly interactive interface, users can employ various criteria to retrieve all TF sequences and their detailed annotation information, including sequence features, domain architecture and sequence similarity against the linked databases. Furthermore, cTFbase also provides phylogenetic trees of individual TF family, multiple sequence alignments of the DNA-binding domain and ortholog identification from any selected genomes.