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Journal of Applied Phycology

, Volume 19, Issue 4, pp 333–346 | Cite as

Sequence analysis of Arthrospira maxima based on fosmid library

  • Na Ling
  • Yunxiang Mao
  • Xuecheng Zhang
  • Zhaolan Mo
  • Guangce Wang
  • Wei Liu
Article

Abstract

Arthrospira (Spirulina) (Setchell & Gardner) is an important cyanobacterium not only in its nutritional potential but in its special biological characteristics. An unbiased fosmid library of Arthrospira maxima FACHB438 that contains 4300 clones was constructed. The size distribution of insert fragments is from 15.5 to 48.9 kb and the average size is 37.6 kb. The recombination frequency is 100%. Therefore the library is 29.9 equivalents to the Arthrospira genome size of 5.4 Mb. A total of 719 sample clones were randomly chosen from the library and 602 available sequences, which consisted of 307,547 bases, covering 5.70% of the whole genome. The codon usage of A. maxima was not strongly biased. GC content at the first position of codons (46.9%) was higher than the second (39.8%) and the third (45.5%) positions. GC content of the genome was 43.6%. Of these sequences, 287 (47.7%) showed high similarities to known genes, 63 (10.5%) to hypothetical genes and the remaining 252 (41.8%) had no significant similarities. The assigned genes were classified into 22 categories with respect to different biological roles. Remarkably, the high presence of 25 sequences (4.2%) encoding reverse transcriptase indicates the RT gene may have multiple copies in the A. maxima genome and might play an important role in the evolutionary history and metabolic regulation. In addition, the sequences encoding the ATP-binding cassette transport system and the two-component signal transduction system were the second and third most frequent genes, respectively. These genomic features provide some clues as to the mechanisms by which this organism adapts to the high concentration of bicarbonate and to the high pH environment.

Key words

ABC transporter system Arthrospira maxima Codon usage Functional classification Reverse transcriptase TCST system 

Abbreviations

ABC

ATP-binding cassette

FIGE

Field inversion gel electrophoresis

KEGG

Kyoto Encyclopedia of Genes and Genomes

RT

Reverse transcriptase

TCST

Two-component signal transduction system

Notes

Acknowledgements

The work was supported by the National Natural Science Foundation of China (Grant No.30200208 and No.30571418) and the Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences. We thank Hangzhou Genomics Institute for performing the DNA sequencing under contract and Aruna kumara for valuable advice and critical reading of the manuscript.

Reference

  1. Bateman A, Birney E, Cerruti L, Durbin R, Marshall M, Sonnhammer EL (2002) The Pfam protein family database. Nucleic Acids Res 30:276–280PubMedCrossRefGoogle Scholar
  2. Dhundale A, Lampson B, Furuichi T, Inouye M, Inouye S (1987) Structure of msDNA from Myxococcus xanthus: evidence for a long, self annealing RNA precursor for the covalently linked, branched RNA. Cell 51:1105–1112PubMedCrossRefGoogle Scholar
  3. Fath MJ, Kolter R (1993) ABC transporters: bacterial exporters. Microbiol Rev 57:995–1017PubMedGoogle Scholar
  4. Garcia-Dominguez M, Muro-Pastor MI, Reyesm JC, Florencio FJ (2000) Light-dependent regulation of cyanobacterial phytochrome expression. J Bacteriol 182:38–44PubMedGoogle Scholar
  5. Higgins CF (1992) ABC transporters: from microorganisms to man. Annu Rev Cell Biol 8:67–113PubMedCrossRefGoogle Scholar
  6. Inouye S, Hsu MY, Eagle S, Inouye M (1989) Reverse transcriptase associated with the branched RNA-linked msDNA in Myxococcus xanthus. Cell 56:709–717PubMedCrossRefGoogle Scholar
  7. Jitka M, Marcela F (2003) Retron reverse transcriptase rrtT is ubiquitous in strains of Salmonella enterica serovar Typhimurium. FEMS Microbiol Lett 223:281–286CrossRefGoogle Scholar
  8. Kaneko T, Sato S, Kotani H, Tanaka A, Tabata S (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136PubMedCrossRefGoogle Scholar
  9. Kaneko T, Nakamura Y, Wolk CP, Kuritz T, Sasamoto S, Tabata S (2001) Complete genomic sequence of the filamentous nitrogen-fixing cyanobacterium Anabaena sp. strain PCC 7120. DNA Res 8:205–213PubMedCrossRefGoogle Scholar
  10. Kawata Y, Yano S, Kojima H, Toyomizu M (2004) Transformation of Spirulina platensis strain C1 (Arthrospira sp. PCC 9438) with Tn5 transposase-transposon DNA-cation liposome complex. Mar Biotechnol 6:355–363PubMedCrossRefGoogle Scholar
  11. Kay RA (1991) Microalgae as food and supplement. Crit Rev Food Sci 30:555–573CrossRefGoogle Scholar
  12. Kojima H, Qin S, Thankappan AK, Kawata Y, Yano S (1998) Transposable genetic elements in Spirulina and potential applications for genetic engineering. Chin J Oceanol Limnol 16:30–39Google Scholar
  13. Lampson BC, Sun J, Inouye S, Inouye M (1989) Reverse transcriptase in a clinical strain of Escherichia coli: production of branched RNA-linked msDNA. Science 243:1033–1038PubMedCrossRefGoogle Scholar
  14. Lampson BC, Inouye M, Inouye S (1991) Survey of multicopy single-stranded DNAs and reverse transcriptase genes among natural isolates of Myxococcus xanthus. J Bacteriol 173:5363–5370PubMedGoogle Scholar
  15. Lanfaloni L, Trinei M, Russo M, Gualerzi CO (1991) Mutagenesis of the cyanobacterium Spirulina platensis by UV and nitrosoguanidine treatment. FEMS Microbiol Lett 83:85–90CrossRefGoogle Scholar
  16. Lim D, Maas WK (1989) Reverse transcriptase-dependent synthesis of a covalently linked, branched DNA-RNA compound in E.coli. Cell 56:891–904PubMedCrossRefGoogle Scholar
  17. Marmur J (1961) A procedure for the isolation of deoxyribonucleic acid from microorganisms. J Mol Biol 3:208–218CrossRefGoogle Scholar
  18. McClelland M, Wilson RK (1998) Comparison of sample sequences of the Salmonella typhi genome to the sequence of complete Escherichia coli K-12 genome. Infect Immun 66:4305–4312PubMedGoogle Scholar
  19. Meeks JC, Elhai J, Thiel T, Predki P, Atlas R (2001) An overview of the genome of Nostoc punctiforme, a multicellular, symbiotic cyanobacterium. Photosynth Res 70:85–106PubMedCrossRefGoogle Scholar
  20. Møller JV, Juul B, le Maire M (1996) Structural organization, ion transport, and energy transduction of ATPases. Biochim Biophys Acta 1286:1–51PubMedGoogle Scholar
  21. Palenik B, Brahamsha B, Land M, Hauser L, Chain P, Waterbury J (2003) The genome of a motile marine Synechococcus. Nature 424:1037–1042PubMedCrossRefGoogle Scholar
  22. Qin S (1993) Isolation of plasmid from the blue-green alga-Spirulina platensis. Chin J Occnol Limnol 11:285–288CrossRefGoogle Scholar
  23. Reumann S, Davila-Aponte J, Keegstra K (1999) The evolutionary origin of the protein-translocating channel of chloroplastic envelope membranes: identification of a cyanobacterial homolog. Proc Natl Acad Sci 96:784–789PubMedCrossRefGoogle Scholar
  24. Riccardi G, Savi A, Ciferri O (1981) Characterization of mutants of Spirulina platensis resistant to amino acid analogues. FEMS Microbiol Lett 12:333–336CrossRefGoogle Scholar
  25. Rice SA, Bieber J, Lampson BC (1993) Diversity of retron elements in a population of rhizobia and other Gram-negative bacteria. J Bacteriol 175:4250–4254PubMedGoogle Scholar
  26. Takakazu K, Shusei S, Hirokazu K, Ayako T, Erika A (1996) Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. PCC 6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 3:109–136CrossRefGoogle Scholar
  27. Toyomizu M, Suzuki K, Kawata Y, Kojima H, Akiba Y (2001) Effective transformation of the cyanobacterium Spirulina platensis using electroporation. J Appl Phycol 13:209–214CrossRefGoogle Scholar
  28. Vachhani AK, Vonshak A (1997) Genetics of Spirulina. In: Vonshak A (ed) Spirulina platensis (Arthrospira): Physiology, Cell-biology and Biotechnology. Taylor & Francis Ltd, London, pp 67–77Google Scholar
  29. Vinnemeier J, Hagemann M (1999) Identification of salt-regulated genes in the genome of the cyanobacterium Synechocystis sp. strain PCC 6803 by subtractive RNA hybridization. Arch Microbiol 172:377–386PubMedCrossRefGoogle Scholar
  30. Wang GG, Zhang BH, Mao YX, Zhang XC (2001) Axenic single cells preparation and regeneration of Spirulina platensis. High Tech Lett 4:9–13 (in Chinese)Google Scholar
  31. Xu H, He L, Zhu Y, Zhou Y (2003) EST pipeline system: detailed and automated EST data processing and mining. Geno Prot & Bioinfo 1:236–242Google Scholar
  32. Yeh KC, Wu SH, Murphy JT, Lagarias JC (1997) A cyanobacterial phytochrome two-component light sensory system. Science 277:1505–1508PubMedCrossRefGoogle Scholar
  33. Yura K, Toh H, Go M (1999) Putative mechanism of natural transformation as deduced from genome data. DNA Res 6:75–82PubMedCrossRefGoogle Scholar
  34. Zarrouk C (1966) Contribution à l’étude d’une cyanophycée. Influence de divers facteurs physiques et chimiques sur la croissance et photosynthèse de Spirulina maxima Geitler. Dissertation, University of Paris, FranceGoogle Scholar
  35. ZoBell CE (1946) Marine Microbiology. Chronica Botanica Company, Waltham, MAGoogle Scholar

Copyright information

© Springer Science+Business Media, Inc. 2007

Authors and Affiliations

  • Na Ling
    • 1
  • Yunxiang Mao
    • 1
  • Xuecheng Zhang
    • 1
  • Zhaolan Mo
    • 2
  • Guangce Wang
    • 2
  • Wei Liu
    • 1
  1. 1.Laboratory of Marine Genetics and Breeding, College of Marine Life SciencesOcean University of ChinaQingdaoChina
  2. 2.Key Laboratory of Experimental Marine Biology Institute of OceanologyChinese Academy of SciencesQingdaoChina

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