hide
show operations
Database Authors: Ron Caspi1, Douglas Campbell2, John Casey3, Jeff Elhai4, David Lea-Smith5, Tobias Pfennig6, Nicolas Schmelling, Annegret Wilde7, Lisa Moore1
1SRI International, 2Mount Allison University, 3Lawrence Livermore National Laboratory, 4Virginia Commonwealth University, 5University of East Anglia, School of Biological Sciences, 6RWTH Aachen University, Computational Life Science, Department of Biology, 7The University of Freiburg, Institute of Biology III
Summary:
Synechocystis sp. PCC 6803 is a unicellular, non-nitrogen-fixing, freshwater cyanobacterium that was isolated in 1968 from a lake at Berkeley, California by Riyo Kunisawa (back when cyanobacteria were known as blue-green algae)
[Stanier71]. At the time it was described as strain 6803 of the
Aphanocapsa genus. The original strain is deposited at the Pasteur Culture Collection of Cyanobacteria (PCC) as Synechocystis sp. PCC 6803 and at the American Type Culture Collection as ATCC 27184.
The original strain does not tolerate glucose in the light. However, as the organism is naturally competent and transformable by exogenous DNA [Grigorieva82, Ikeuchi01], glucose-tolerant substrains allowing photoheterotrophic, mixotrophic, and heterotrophic growth were constructed. A glucose-tolerant (GT) strain was generated from strain ATCC 27184 and designated the Williams GT strain [Williams88]. The chromosome of a derivative of that strain, known as GT-Kazusa, was sequenced in 1996, making it the first cyanobacterium and the fourth organism to have its chromosome completely sequenced. The sequencing was performed by a team at the Kazusa DNA Research Insitute [Kaneko95, Kaneko96]. In addition to the polyploid chromosome the organism has seven plasmids - four large ones (pSYSM/120 kb; pSYSX/106 kb; pSYSA/103 kb; pSYSG/44 kb) and three small ones (pCA2.4/2.4 kb; pCB2.4/2.4 kb; pCC5.2/5.2 kb).
In general, current strains of Synechocystis sp. PCC 6803 fall into two main clades: the GT clade comprises nonmotile, glucose-tolerant descendants of the Williams GT strain, whereas non-GT PCC strains are descendants of the original strain deposited in the Pasteur Culture Collection of Cyanobacteria [Koskinen23].
Synechocystis sp. PCC 6803 is highly polyploid, though its ploidy level is highly variable and is influenced by growth phase and other parameters [Zerulla16]. The motile wild-type strain was found to contain 218 genome copies in exponential phase and 58 genome copies in linear and in stationary growth phase, while the GT wild-type strain contains 142 genome copies in exponential phase and 42 genome copies in linear and stationary growth phase [Griese11]. An early study found only 12 genome copies in the Kazusa strain [Labarre89].
Synechocystis sp. PCC 6803 is one of the most extensively studied cyanobacterial species. The biochemical similarities between the plant chloroplasts and the organism make it an ideal system for studying the molecular mechanisms underlying stress responses and stress adaptation in higher plants. The cyanobacterium has also been used extensively as a host for metabolic engineering and synthetic biology studies. For many of the genes, we have included links to various additional research resources, such as the CRISPRi library used in [Miao23].
This Pathway/Genome database is based on chromosomal sequence obtained by [Kaneko95, Kaneko96] and plasmid sequences reported by [Yang93, Yang94, Xu97, Kaneko03]. The sequence was corrected based on limited resequencing performed in 2011 [Tajima11]. The sequences were annotated computationally by RefSeq, and the annotation was significantly modified by manual curation based on the professional literature.
This Pathway/Genome Database (PGDB) was generated by the PathoLogic component of Pathway Tools software version 27.0 [Karp11, Karp16] and MetaCyc version 27.1 [Caspi18] on 29-Mar-2023.
Taxonomic Lineage: cellular organisms, Bacteria <bacteria>, Terrabacteria group, Cyanobacteriota/Melainabacteria group, Cyanobacteriota, Cyanophyceae, Synechococcales, Merismopediaceae, Synechocystis, unclassified Synechocystis, Synechocystis sp. PCC 6803, Synechocystis sp. PCC 6803 substr. Kazusa
Synonyms: Synechocystis sp. PCC 6803 substr. Kazusa
Unification Links: NCBI-Taxonomy:1111708
| Organism or Sample Properties | |
| Environment: | freshwater lake |
| Geographic Location: | Berkeley, CA, USA |
| Collection Date: | 1968 |
| Relationship to Oxygen: | aerobe |
| Trophic Level: | photoautotroph |
| Temperature Range: | mesophile |
| Biotic Relationship: | free-living |
| Ploidy: | highly polyploid |
| Replicon | Total Genes | Protein Genes | RNA Genes | Pseudogenes | Size (bp) | NCBI Link |
| chromosome | 4,769 | 3,274 | 1,444 | 51 | 3,573,470 | NCBI-RefSeq:NC_000911.1 |
| plasmid pSYSM | 135 | 131 | 0 | 4 | 119,895 | NCBI-RefSeq:NC_005229.1 |
| plasmid pSYSX | 114 | 114 | 0 | 0 | 106,004 | NCBI-RefSeq:NC_005232.1 |
| plasmid pSYSA | 104 | 100 | 0 | 4 | 103,307 | NCBI-RefSeq:NC_005230.1 |
| plasmid pSYSG | 46 | 43 | 0 | 3 | 44,343 | NCBI-RefSeq:NC_005231.1 |
| plasmid pCC5.2 | 5 | 5 | 0 | 0 | 5,214 | NCBI-RefSeq:NC_020290.1 |
| plasmid pCA2.4 | 2 | 2 | 0 | 0 | 2,378 | NCBI-RefSeq:NC_020289.1 |
| plasmid pCB2.4 | 3 | 3 | 0 | 0 | 2,345 | NCBI-RefSeq:NZ_L25424.1 |
| Total: | 5,178 | 3,672 | 1,444 | 62 | 3,956,956 | |
| Ortholog data available? | Yes |
| Genes: | 5,179 | ||
| Pathways: | 262 | ||
| Enzymatic Reactions: | 1,377 | ||
| Transport Reactions: | 76 | ||
| Polypeptides: | 3,693 | ||
| Protein Complexes: | 202 | ||
| Enzymes: | 858 | ||
| Transporters: | 239 | ||
| Compounds: | 974 | ||
| Transcription Units: | 3,355 | ||
| tRNAs: | 41 | ||
| Transcriptional Regulation: | 137 | ||
| Protein Features: | 12,390 | ||
| GO Terms: | 25,516 |
Genetic Code Number:
11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
PGDB Unique ID: 2PN3
References
Report Errors or Provide Feedback
Page generated by Pathway Tools version 28.0 (software by SRI International) on Thu Jul 4, 2024, BIOCYC15.
