Synechocystis sp. PCC 6803 is a model cyanobacterium, glucose-tolerant substrains of which are commonly used as laboratory strains. In recent years, it has become evident that 'wild-type' strains used in different laboratories show some differences in their phenotypes. We report here the chromosome sequence of our Synechocystis sp. PCC 6803 substrain, named substrain GT-T. The chromosome sequence of GT-T was compared to those of two other commonly used laboratory substrains, GT-S and PCC-M. We identified 11 specific mutations in the GT-T substrain, whose physiological consequences are discussed. We also provide an update on evolutionary relationships between different Synechocystis sp. PCC 6803 substrains.

Department of Life Sciences Molecular Plant Biology University of Turku Finland

Institute of Microbiology of the Czech Academy of Sciences Třeboň Czech Republic

Zobrazit více v PubMed

Stanier RY, Kunisawa R, Mandel M and Cohen‐Bazire G (1971) Purification and properties of unicellular blue‐green algae (order PubMed PMC

Kaneko T, Sato S, Kotani H, Tanaka A, Asamizu E, Nakamura Y, Miyajima N, Hirosawa M, Sugiura M, Sasamoto S PubMed

Ikeuchi M and Tabata S (2001) PubMed

Williams JGK (1988) Construction of specific mutations in photosystem II photosynthetic reaction center by genetic engineering methods in

Anderson SL and McIntosh L (1991) Light‐activated heterotrophic growth of the cyanobacterium PubMed PMC

Wilde A, Härtel H, Hübschmann T, Hoffmann P, Shestakov SV and Börner T (1995) Inactivation of a PubMed PMC

Ding Q, Chen G, Wang Y and Wei D (2015) Identification of specific variations in a non‐motile strain of cyanobacterium PubMed PMC

Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki NV, Kurokawa K, Ohta H, Kanesaki Y, Yoshikawa H, Tabata S PubMed PMC

Kanesaki Y, Shiwa Y, Tajima N, Suzuki M, Watanabe S, Sato N, Ikeuchi M and Yoshikawa H (2012) Identification of substrain‐specific mutations by massively parallel whole‐genome resequencing of PubMed PMC

Trautmann D, Voss B, Wilde A, Al‐Babili S and Hess WR (2012) Microevolution in cyanobacteria: re‐sequencing a motile substrain of PubMed PMC

Morris J, Crawford T, Jeffs A, Stockwell P, Eaton‐Rye J and Summerfield T (2014) Whole genome re‐sequencing of two ‘wild‐type’ strains of the model cyanobacterium

Tichý M, Bečková M, Kopečná J, Noda J, Sobotka R and Komenda J (2016) Strain of PubMed PMC

Mohamed A and Jansson C (1989) Influence of light on accumulation of photosynthesis‐specific transcripts in the cyanobacterium PubMed

Mäenpää P, Kallio T, Mulo P, Salih G, Aro E‐M, Tyystjärvi E and Jansson C (1993) Site‐specific mutations in the D1 polypeptide affect the susceptibility of PubMed

Jansson C, Debus RJ, Osiewacz HD, Gurevitz M and McIntosh L (1987) Construction of an obligate photoheterotrophic mutant of the cyanobacterium PubMed PMC

Ejima K, Kawaharada T, Inoue S, Kojima K and Nishiyama Y (2012) A change in the sensitivity of elongation factor G to oxidation protects photosystem II from photoinhibition in PubMed

Andrews S (2010) Fast QC: a quality control tool for high throughput sequence data. http://bioinformatics.babraham.ac.uk/projects/fastqc.

Li H and Durbin R (2009) Fast and accurate short read alignment with Burrows‐Wheeler transform. Bioinformatics 25, 1754–1760. PubMed PMC

Gunnelius L, Hakkila K, Kurkela J, Wada H, Tyystjärvi E and Tyystjärvi T (2014) The omega subunit of the RNA polymerase core directs transcription efficiency in cyanobacteria. Nucleic Acids Res 42, 4606–4614. PubMed PMC

Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R and 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079. PubMed PMC

Kallio MA, Tuimala JT, Hupponen T, Klemela P, Gentile M, Scheinin I, Koski M, Kaki J and Korpelainen EI (2011) Chipster: user‐friendly analysis software for microarray and other high‐throughput data. BMC Genomics 12, 507. PubMed PMC

Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP, Zaslavsky L, Lomsadze A, Pruitt KD, Borodovsky M and Ostell J (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44, 6614–6624. PubMed PMC

Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V, O'Neill K, Li W, Chitsaz F, Derbyshire MK, Gonzales NR PubMed PMC

Li W, O'Neill KR, Haft DH, DiCuccio M, Chetvernin V, Badretdin A, Coulouris G, Chitsaz F, Derbyshire MK, Durkin AS PubMed PMC

Mackinney G (1941) Absorption of light by chlorophyll solutions. J Biol Chem 140, 315–322.

Pollari M, Rantamäki S, Huokko T, Kårlund‐Marttila A, Virjamo V, Tyystjärvi E and Tyystjärvi T (2011) Effects of deficiency and overdose of group 2 sigma factors in triple inactivation strains of PubMed PMC

Schneider CA, Rasband WS and Eliceiri KW (2012) NIH image to ImageJ: 25 years of image analysis. Nat Methods 9, 671–675. PubMed PMC

Bhaya D, Bianco NR, Bryant D and Grossman A (2000) Type IV pilus biogenesis and motility in the cyanobacterium PubMed

Yoshihara S, Geng X, Okamoto S, Yura K, Murata T, Go M, Ohmori M and Ikeuchi M (2001) Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium PubMed

Linhartová M (2021) Function of the Type IV pili proteins in the cyanobacterium

Oeser S, Wallner T, Schuergers N, Bučinská L, Sivabalasarma S, Bähre H, Albers S and Wilde A (2021) Minor pilins are involved in motility and natural competence in the cyanobacterium PubMed

Chen GE, Hitchcock A, Mareš J, Gong Y, Tichý M, Pilný J, Kovárová L, Zdvihalová B, Xu J, Hunter CN PubMed PMC

Takatani N, Uenosono M, Hara Y, Yamakawa H, Fujita Y and Omata T (2022) Chlorophyll and pheophytin dephytylating enzymes required for efficient repair of PSII in PubMed

Schmetterer GR (1990) Sequence conservation among the glucose transporter from the cyanobacterium PubMed

Tyystjärvi T, Aro E‐M, Jansson C and Mäenpää P (1994) Changes of amino acid sequence in PEST‐like area and QEEET motif affect degradation rate of D1 polypeptide in photosystem II. Plant Mol Biol 25, 517–526. PubMed

Laughlin TG, Bayne AN, Trempe J‐F, Savage DF and Davies KM (2019) Structure of the complex I‐like molecule NDH of oxygenic photosynthesis. Nature 566, 411–414. PubMed

Zhang P, Battchikova N, Jansen T, Appel J, Ogawa T and Aro E‐M (2004) Expression and functional roles of the two distinct NDH‐1 complexes and the carbon acquisition complex NdhD3/NdhF3/CupA/Sll1735 in PubMed PMC

Baier A, Winkler W, Korte T, Lockau W and Karradt A (2014) Degradation of phycobilisomes in PubMed PMC

Tillich UM, Wolter N, Franke P, Dühring U and Frohme M (2014) Screening and genetic characterization of thermo‐tolerant PubMed PMC

Antal T, Kurkela J, Parikainen M, Kårlund A, Hakkila K, Tyystjärvi E and Tyystjärvi T (2016) Roles of group 2 sigma factors in acclimation of the cyanobacterium PubMed

Inoue N, Taira Y, Emi T, Yamane Y, Kashino Y, Koike H and Satoh K (2001) Acclimation to the growth temperature and the high‐temperature effects on photosystem II and plasma membranes in a mesophilic cyanobacterium, PubMed

Tuominen I, Pollari M, Tyystjärvi E and Tyystjärvi T (2006) The SigB σ factor mediates high‐temperature responses in the cyanobacterium PubMed

Kamei A, Yuasa T, Orikawa K, Geng XX and Ikeuchi M (2001) A eukaryotic‐type protein kinase, SpkA, is required for normal motility of the unicellular cyanobacterium PubMed PMC

Panichkin VB, Arakawa‐Kobayashi S, Kanaseki T, Suzuki I, Los DA, Shestakov SV and Murata N (2006) Serine/threonine protein kinase SpkA in PubMed PMC

Trautner C and Vermaas WFJ (2013) The PubMed PMC

Koskinen S, Hakkila K, Kurkela J, Tyystjärvi E and Tyystjärvi T (2018) Inactivation of group 2 σ factors upregulates production of transcriptional and translational machineries in the cyanobacterium PubMed PMC

Pathak D, Jin KS, Tandukar S, Kim JH, Kwon E and Kim DY (2020) Structural insights into the regulation of SigB activity by RsbV and RsbW. IUCrJ 7, 737–747. PubMed PMC

Huckauf J, Nomura C, Forchhammer K and Hagemann M (2000) Stress responses of PubMed

Heilmann B, Hakkila K, Georg J, Tyystjarvi T, Hess WR, Axmann IM and Dienst D (2017) 6S RNA plays a role in recovery from nitrogen depletion in PubMed PMC

Mulo P, Tyystjärvi T, Tyystjärvi E, Govindjee MP and Aro E‐M (1997) Mutagenesis of the D‐E loop of photosystem II reaction centre protein D1. Function and assembly of photosystem II. Plant Mol Biol 33, 1059–1071. PubMed

Pollari M, Gunnelius L, Tuominen I, Ruotsalainen V, Tyystjärvi E, Salminen T and Tyystjärvi T (2008) Characterization of single and double inactivation strains reveals new physiological roles for group 2 σ factors in the cyanobacterium PubMed PMC

Koskinen S, Hakkila K, Gunnelius L, Kurkela J, Wada H and Tyystjärvi T (2016) PubMed

Osanai T, Oikawa A, Azuma M, Tanaka K, Saito K, Hirai MY and Ikeuchi M (2011) Genetic engineering of group 2 σ factor SigE widely activates expressions of sugar catabolic genes in PubMed PMC

Satyshur KA, Worzalla GA, Meyer LS, Heiniger EK, Aukema KG, Misic AM and Forest KT (2007) Crystal structures of the pilus retraction motor PilT suggest large domain movements and subunit cooperation drive motility. Structure 15, 363–376. PubMed PMC

Kurkela J, Hakkila K, Antal T and Tyystjärvi T (2017) Acclimation to high CO PubMed PMC

Gunnelius L, Kurkela J, Hakkila K, Koskinen S, Parikainen M and Tyystjärvi T (2014) The ω subunit of RNA polymerase is essential for thermal acclimation of the cyanobacterium PubMed PMC

Differences in photosystem II activity and carbon allocation during photomixotrophic growth in distinct wild-type strains of Synechocystis sp. PCC 6803

Cyanophycinase is required for heterotrophy in cyanobacteria

Zobrazit více v PubMed

RefSeq
CP094998