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, Xu97a, 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.

Genome
RepliconTotal GenesProtein GenesRNA GenesPseudogenesSize (bp)NCBI Link
chromosome4,7183,2741,444513,573,470RefSeq:NC_000911.1
plasmid pSYSM13113104119,895RefSeq:NC_005229.1
plasmid pSYSX11411400106,004RefSeq:NC_005232.1
plasmid pSYSA10010004103,307RefSeq:NC_005230.1
plasmid pSYSG43430344,343RefSeq:NC_005231.1
plasmid pCC5.255005,214RefSeq:NC_020290.1
plasmid pCA2.422002,378RefSeq:NC_020289.1
plasmid pCB2.433002,345RefSeq:NZ_L25424.1
Total:5,1793,6721,444623,956,956
Ortholog data available?Yes
Database Contents
Genes5,117
Pathways262
Enzymatic Reactions1,375
Transport Reactions83
Polypeptides3,691
Protein Complexes210
Enzymes860
Transporters234
Compounds976
Transcription Units3,354
tRNAs41
Transcriptional Regulation267
Protein Features12,390
GO Annotations27,924
Database Version29.6
Taxonomic Lineage cellular organisms
Bacteria <bacteria>
Bacillati
Cyanobacteriota/Melainabacteria group
Cyanobacteriota
Cyanophyceae
Synechococcales
Merismopediaceae
Synechocystis
unclassified Synechocystis
Synechocystis sp. PCC 6803
Synechocystis sp. PCC 6803 substr. Kazusa
Genetic Code Number 11 -- Bacterial, Archaeal and Plant Plastid (same as Standard, except for alternate initiation codons)
NCBI-Taxonomy1111708
Environmentfreshwater
Geographic LocationBerkeley, CA, USA
Collection Date1968
Relationship to Oxygenaerobe
Trophic Levelphotoautotroph
Temperature Rangemesophile
Biotic Relationshipfree-living
Ploidyhighly polyploid

References

Caspi18: Caspi R, Billington R, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Midford PE, Ong Q, Ong WK, Paley S, Subhraveti P, Karp PD (2018). "The MetaCyc database of metabolic pathways and enzymes." Nucleic Acids Res 46(D1);D633-D639. PMID: 29059334

Griese11: Griese M, Lange C, Soppa J (2011). "Ploidy in cyanobacteria." FEMS Microbiol Lett 323(2);124-31. PMID: 22092711

Grigorieva82: Grigorieva G, Shestakov S (1982). "Transformation in the cyanobacterium Synechocystis sp. 6803." FEMS Microbiology Letters 13(4);367-370.

Ikeuchi01: Ikeuchi M, Tabata S (2001). "Synechocystis sp. PCC 6803 - a useful tool in the study of the genetics of cyanobacteria." Photosynth Res 70(1);73-83. PMID: 16228363

Kaneko03: Kaneko T, Nakamura Y, Sasamoto S, Watanabe A, Kohara M, Matsumoto M, Shimpo S, Yamada M, Tabata S (2003). "Structural analysis of four large plasmids harboring in a unicellular cyanobacterium, Synechocystis sp. PCC 6803." DNA Res 10(5);221-8. PMID: 14686584

Kaneko95: Kaneko T, Tanaka A, Sato S, Kotani H, Sazuka T, Miyajima N, Sugiura M, Tabata S (1995). "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. I. Sequence features in the 1 Mb region from map positions 64% to 92% of the genome." DNA Res 2(4);153-66, 191-8. PMID: 8590279

Kaneko96: Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S, Kimura T, Hosouchi T, Matsuno A, Muraki A, Nakazaki N, Naruo K, Okumura S, Shimpo S, Takeuchi C, Wada T, Watanabe A, Yamada M, Yasuda M, Tabata S (1996). "Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions." DNA Res 1996;3(3);109-36. PMID: 8905231

Karp11: Karp PD, Latendresse M, Caspi R (2011). "The pathway tools pathway prediction algorithm." Stand Genomic Sci 5(3);424-9. PMID: 22675592

Karp16: Karp PD, Latendresse M, Paley SM, Krummenacker M, Ong QD, Billington R, Kothari A, Weaver D, Lee T, Subhraveti P, Spaulding A, Fulcher C, Keseler IM, Caspi R (2016). "Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology." Brief Bioinform 17(5);877-90. PMID: 26454094

Koskinen23: Koskinen S, Kurkela J, Linhartova M, Tyystjarvi T (2023). "The genome sequence of Synechocystis sp. PCC 6803 substrain GT-T and its implications for the evolution of PCC 6803 substrains." FEBS Open Bio 13(4);701-712. PMID: 36792971

Labarre89: Labarre J, Chauvat F, Thuriaux P (1989). "Insertional mutagenesis by random cloning of antibiotic resistance genes into the genome of the cyanobacterium Synechocystis strain PCC 6803." J Bacteriol 171(6);3449-57. PMID: 2498291

Miao23: Miao R, Jahn M, Shabestary K, Peltier G, Hudson EP (2023). "CRISPR interference screens reveal growth-robustness tradeoffs in Synechocystis sp. PCC 6803 across growth conditions." Plant Cell 35(11);3937-3956. PMID: 37494719

Stanier71: Stanier RY, Kunisawa R, Mandel M, Cohen-Bazire G (1971). "Purification and properties of unicellular blue-green algae (order Chroococcales)." Bacteriol Rev 35(2);171-205. PMID: 4998365

Tajima11: Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki NV, Kurokawa K, Ohta H, Kanesaki Y, Yoshikawa H, Tabata S, Ikeuchi M, Sato N (2011). "Genomic structure of the cyanobacterium Synechocystis sp. PCC 6803 strain GT-S." DNA Res 18(5);393-9. PMID: 21803841

Williams88: Williams, J. G. K. (1988). "Construction of specific mutations in photosystem II photosynthetic reaction center by genetic engineering methods in Synechocystis 6803." Methods in Enzymology 167:766-778.

Xu97a: Xu W, McFadden BA (1997). "Sequence analysis of plasmid pCC5.2 from cyanobacterium Synechocystis PCC 6803 that replicates by a rolling circle mechanism." Plasmid 37(2);95-104. PMID: 9169201

Yang93: Yang X, McFadden BA (1993). "A small plasmid, pCA2.4, from the cyanobacterium Synechocystis sp. strain PCC 6803 encodes a rep protein and replicates by a rolling circle mechanism." J Bacteriol 175(13);3981-91. PMID: 8320214

Yang94: Yang X, McFadden BA (1994). "The complete DNA sequence and replication analysis of the plasmid pCB2.4 from the cyanobacterium Synechocystis PCC 6803." Plasmid 31(2);131-7. PMID: 8029321

Zerulla16: Zerulla K, Ludt K, Soppa J (2016). "The ploidy level of Synechocystis sp. PCC 6803 is highly variable and is influenced by growth phase and by chemical and physical external parameters." Microbiology (Reading) 162(5);730-739. PMID: 26919857

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