Cite this paper:
CHEN Jun, SHI Wenjun, LI Wenjun, CHEN Gao, QIN Song. Specific genetic variation in two non-motile substrains of the model cyanobacterium Synechocystis sp. PCC 6803[J]. HaiyangYuHuZhao, 2018, 36(6): 2322-2332

Specific genetic variation in two non-motile substrains of the model cyanobacterium Synechocystis sp. PCC 6803

CHEN Jun1,2, SHI Wenjun1,2, LI Wenjun1, CHEN Gao3, QIN Song1
1 Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China;
2 University of Chinese Academy of Sciences, Beijing 100049, China;
3 Biotechnology Research Centre, Shandong Academy of Agricultural Sciences, Jinan 250100, China
Synechocystis sp. PCC 6803 is a model organism widely used in cyanobacterium biology and biotechnology. To know the genetic background of substrains of Synechocystis sp. PCC 6803 is important for further research and application. In this study, we reported the genome sequences of two non-motile wild-type substrains of Synechocystis sp. PCC 6803 using whole genome resequencing. 55/56 putative single nucleotide polymorphisms (SNPs) and 8/9 Indels (insertion and deletion) were identified. Among these, 47 SNPs were found in both the GT-AR and GT-CH strains, and 8 were unique to GT-AR and 9 were unique to GT-CH. All of these variations were annotated in metabolism pathway referred to KEGG database. Meanwhile, the deletion in slr0332 gene was detected in these two strains, which attributed to the non-motile phenotype of them and suggested that the insertion in spkA gene was not essential for non-motile phenotype. These resequencing data provide the genetic background information of these two strains and highlighted the microevolution over decades of laboratory cultivation.
Key words:    Synechocystis sp. PCC 6803|genome resequencing|non-motile|genetic background   
Received: 2017-10-17   Revised:
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Allahverdiyeva Y, Ermakova M, Eisenhut M, Zhang P P, Richaud P, Hagemann M, Cournac L, Aro E M. 2011.Interplay between flavodiiron proteins and photorespiration in Synechocystis sp. PCC 6803. Journal of Biological Chemistry, 286(27):24 007-24 014.
Anderson S L, McIntosh L. 1991. Light-activated heterotrophic growth of the cyanobacterium Synechocystis sp. strain PCC6803:a blue-light-requiring process. Journal of Bacteriology, 173(9):2 761-2 767.
Bhaya D, Bianco N R, Bryant D, Grossman A. 2000. Type IV pilus biogenesis and motility in the cyanobacterium Synechocystis sp. PCC6803. Molecular Microbiology, 37(4):941-951.
Bhaya D, Watanabe N, Ogawa T, Grossman A R. 1999. The role of an alternative sigma factor in motility and pilus formation in the cyanobacterium Synechocystis sp. strain PCC6803. Proceedings of the National Academy of Sciences of the United States of America, 96(6):3 188-3 193.
Buchfink B, Xie C, Huson D H. 2015. Fast and sensitive protein alignment using DIAMOND. Nature Methods, 12(1):59-60.
Chen K, Wallis J W, McLellan M D, Larson D E, Kalicki J M, Pohl C S, McGrath S D, Wendl M C, Zhang Q Y, Locke D P, Shi X Q, Fulton R S, Ley T J, Wilson R K, Ding L, Mardis, E R. 2009. BreakDancer:an algorithm for highresolution mapping of genomic structural variation.Nature Methods, 6(9):677-681.
Dexter J, Fu P C. 2009. Metabolic engineering of cyanobacteria for ethanol production. Energy & Environmental Science., 2(8):857-864.
Ding Q L, Chen G, Wang Y L, Wei D. 2015. Identification of specific variations in a non-motile strain of cyanobacterium Synechocystis sp. PCC 6803 originated from ATCC 27184 by whole genome resequencing. International Journal of Molecular Sciences, 16(10):24 081-24 093.
Dismukes G C, Carrieri D, Bennette N, Ananyev G M, Posewitz M C. 2008. Aquatic phototrophs:efficient alternatives to land-based crops for biofuels. Current Opinion in Biotechnology, 19(3):235-240.
Gao Q Q, Wang W H, Zhao H, Lu X F. 2012. Effects of fatty acid activation on photosynthetic production of fatty acidbased biofuels in Synechocystis sp. PCC 6803.Biotechnology for Biofuels, 5:17.
Hihara Y, Ikeuchi M. 1997. Mutation in a novel gene required for photomixotrophic growth leads to enhanced photoautotrophic growth of Synechocystis sp. PCC 6803.Photosynthesis Research, 53(2-3):243-252.
Ikeuchi M, Tabata S. 2001. Synechocystis sp. PCC 6803-a useful tool in the study of the genetics of cyanobacteria.Photosynthesis Research, 70(1):73-83.
Imamura S, Yoshihara S, Nakano S, Shiozaki N, Yamada A, Tanaka K, Takahashi H, Asayama M, Shirai M. 2003.Purification, characterization, and gene expression of all sigma factors of RNA polymerase in a cyanobacterium.Journal of Molecular Biology, 325(5):857-872.
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 Research, 10(5):221-228.
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 Research, 3(3):109-136.
Kanesaki Y, Shiwa Y, Tajima N, Suzuki M, Watanabe S, Sato N, Ikeuchi M, Yoshikawa H. 2012. Identification of substrain-specific mutations by massively parallel wholegenome resequencing of Synechocystis sp. PCC 6803.DNA Research, 19(1):67-79.
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, Jones S J, Marra M A. 2009. Circos:an information aesthetic for comparative genomics. Genome Research, 19(9):1 639-1 645.
Li H, Durbin R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14):1 754-1 760.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup. 2009. The sequence alignment/map format and SAMtools. Bioinformatics, 25(16):2 078-2 079.
McCormick A J, Bombelli P, Lea-Smith D J, Bradley R W, Scott A M. Fisher A C, Smith A G, Howe C J. 2013.Hydrogen production through oxygenic photosynthesis using the cyanobacterium Synechocystis sp. PCC 6803 in a bio-photoelectrolysis cell (BPE) system. Energy & Environmental Science, 6(9):2 682-2 690.
Melis A. 2009. Solar energy conversion efficiencies in photosynthesis:minimizing the chlorophyll antennae to maximize efficiency. Plant Science, 177(4):272-280.
Morris J N, Crawford T S, Jeffs A, Stockwell P A, Eaton-Rye J J, Summerfield T C. 2014. Whole genome re-sequencing of two ‘wild-type’ strains of the model cyanobacterium Synechocystis sp. PCC 6803. New Zealand Journal of Botany, 52(1):36-47.
Nakajima T, Kajihata S, Yoshikawa K, Matsuda F, Furusawa C, Hirasawa T, Shimizu H. 2014. Integrated metabolic flux and omics analysis of Synechocystis sp. PCC 6803 under mixotrophic and photoheterotrophic conditions.Plant and Cell Physiology, 55(9):1 605-1 612.
Rippka R, Deruelles J, Waterbury J B, Herdman M, Stanier R Y. 1979. Generic assignments, strain histories and properties of pure cultures of cyanobacteria. Microbiology, 111(1):1-61.
Sambrook J, Russell D W. 2000. Molecular Cloning:A Laboratory Manual, 3 Vols. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York.
Stanier R Y, Kunisawa R, Mandel M, Cohen-Bazire G. 1971.Purification and properties of unicellular blue-green algae(order Chroococcales). Bacteriology Reviews, 35(2):171-205.
Tajima N, Sato S, Maruyama F, Kaneko T, Sasaki N V, 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 Research, 18(5):393-399.
Takahashi H, Uchimiya H, Hihara Y. 2008. Difference in metabolite levels between photoautotrophic and photomixotrophic cultures of Synechocystis sp. PCC 6803
examined by capillary electrophoresis electrospray ionization mass spectrometry. Journal of Experimental Botany, 59(11):3 009-3 018.
Tan X M, Yao L, Gao Q Q, Wang W H, Qi F X, Lu X F. 2011.Photosynthesis driven conversion of carbon dioxide to fatty alcohols and hydrocarbons in cyanobacteria.Metabolic Engineering, 13(2):169-176.
Trautmann D, Voß B, Wilde A, Al-Babili S, Hess W R. 2012.Microevolution in cyanobacteria:re-sequencing a motile substrain of Synechocystis sp. PCC 6803. DNA Research, 19(6):435-448.
Varman A M, Xiao Y, Pakrasi H B, Tang Y J. 2013. Metabolic engineering of Synechocystis sp. strain PCC 6803 for isobutanol production. Applied and Environmental Microbiology, 79(3):908-914.
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.
Xu W D, McFadden B A. 1997. Sequence analysis of plasmid pCC5.2 from cyanobacterium Synechocystis PCC 6803 that replicates by a rolling circle mechanism. Plasmid, 37(2):95-104.
Yang X Y, McFadden B A. 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. Journal of Bacteriology, 175(13):3 981-3 991.
Yang X Y, McFadden B A. 1994. The complete DNA sequence and replication analysis of the plasmid pCB2.4 from the cyanobacterium Synechocystis PCC 6803. Plasmid, 31(2):131-137.
Yoshihara S, Geng X X, Okamoto S, Yura K, Murata T, Go M, Ohmori M, Ikeuchi M. 2001. Mutational analysis of genes involved in pilus structure, motility and transformation competency in the unicellular motile cyanobacterium Synechocystis sp. PCC6803. Plant and Cell Physiology., 42(1):63-73.
Yoshikawa K, Hirasawa T, Ogawa K, Hidaka Y, Nakajima T, Furusawa C, Shimizu H. 2013. Integrated transcriptomic and metabolomic analysis of the central metabolism of Synechocystis sp. PCC 6803 under different trophic conditions. Biotechnology Journal, 8(5):571-580.