Biopolym. Cell. 2017; 33(3):206-213.
http://dx.doi.org/10.7124/bc.000952
Bioinformatics
Similarity and dissimilarity of primary structures of some Streptomyces spp. genomes and the Streptomyces globisporus 1912-2 chromosomal DNA.
1Polishchuk L. V.
  1. D. K. Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
    154, Academika Zabolotnoho Str., Kyiv, Ukraine, 03680

Abstract

Aim. To determine the similarity and dissimilarity of the nucleotide sequences of the S. globisporus 1912-2 chromosome and primary structures of genomes of some Streptomycetes strains. Methods. NCBI tools (BLAST: blastn and bl2seq: megablast) and Internet NCBI databases (Genome, Nucleotide) were used for in silico analysis of the primary structure contigs of S. grlobisporus 1912-2. Results. A few strains with significant identity of their DNA primary structures to the nucleotide sequences of the chromosomal DNA of S. globisporus 1912-2 (identity 88–97 %) and a degree of query cover (55–82 %) were identified. Primary structures of genomes of the strains S. globisporus C-1027 and S. griseus NBRC13350 were chosen as most identical to the nucleotide sequence of the S. globisporus 1912-2 chromosomal DNA. No fragments with a homologous primary structure to seven S. globisporus 1912-2 contigs were found in Streptomycetes spp. from the NCBI databases. Conclusions. S. globisporus 1912-2 strain is a member of the S. griseus clade. We detected a high biosynthetic potential of the strain S. globisporus 1912-2 due to many unique nucleotide sequences.
Keywords: Streptomyces, primary structure, genome, identity, in silico analysis, clade
Full text: (PDF, in English)

References

[1] Actinomycetes in biotechnology. Eds. Goodfellow M, Williams ST, Mordarski M.. San Diego, New York, Boston, London, Sydney, Tokyo, Toronto: Academic press, 1988. 501 p.
[2] The biology of the Actinomycetes. Eds. Goodfellow M, Mordarski M, Williams ST. London, Orlando, San Diego, San Francisco, New York, Toronto, Montreal, Tokyo, San Palo: Academic press, 1984. 484 p.
[3] Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol. 2008; 190(11): 4050–60.
[4] Barbe V, Bouzon M, Mangenot S, Badet B, Poulain J, Segurens B, Vallenet D, Marliere P, Weissenbach J. Complete genome sequence of Streptomyces cattleya NRRL 8057, a producer of antibiotics and fluorometabolites. J Bacteriol. 2011; 193(18):5055-6.
[5] Li X, Lei X, Zhang C, Jiang Z, Shi Y, Wang S, Wang L, Hong B. Complete genome sequence of Streptomyces globisporus C-1027, the producer of an enediyne antibiotic lidamycin. J Biotechnol. 2016; 222:9-10.
[6] Yang H, He T, Wu W, Zhu W, Lu B. Sun W. Whole-genome shotgun assembly and analysis of the genome of Streptomyces mobaraensis DSM 40847, a strain for industrial production of microbial transglutaminase. Genome Announc. 2013; 1(2):e0014313
[7] Matselyukh B, Mohammadipanah F, Laatsch H, Rohr J, Efremenkova O, Khilya V. N-methylphenylalanyl-dehydrobutyrine diketopiperazine, an A-factor mimic that restores antibiotic biosynthesis and morphogenesis in Streptomyces globisporus 1912-B2 and Streptomyces griseus 1439. J Antibiot. 2015; 68(1):9-14.
[8] Harrison J, Studholme DJ. Recently published Streptomyces genome sequences. Microb Biotechnol. 2014; 7(5):373-80.
[9] Bentley SD, Chater KF, Cerde-o-Tárraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O'Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002; 417(6885):141–7.
[10] Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol. 2003; 21(5):526–31.
[11] Myronovskyi M, Tokovenko B, Manderscheid N, Petzke L, Luzhetskyy A. Complete genome sequence of Streptomyces fulvissimus. J Biotechnol. 2013; 168(1):117-8.
[12] Matselyukh BP, Polishchuk LV, Lukyanchuk VV, Golembiovska SA, Lavrenchuk VY. Molecular mechanism of the carotenoid biosynthesis activation in the producer Streptomyces globisporus 1912. Biotechnol Acta. 2014; 7(6):69-74.
[13] Ostash B, Doud EH, Lin C, Ostash I, Perlstein DL, Fuse S, Wolpert M, Kahne D, Walker S. Complete characterization of the seventeen step moenomycin biosynthetic pathway. Biochemistry. 2009; 48(37):8830–41.
[14] Subramaniam-Niehaus B, Schneider T, Metzger JW. Wohlleben W. Isolation and analysis of moenomycin and its biosynthetic intermediates from Streptomyces ghanaensis (ATCC 14672) wild type and selected mutants. Z Naturforsch C. 1997; 52(3-4):217–26.
[15] Tan GY, Peng Y, Lu C, Bai L, Zhong JJ. Engineering validamycin production by tandem deletion of γ-butyrolactone receptor genes in Streptomyces hygroscopicus 5008. Metab Eng. 2015; 28:74-81.
[16] Polishchuk LV. [Chromosomal fragmern from Streptomyves globisporus 1912-2 homologous to afsA-gene of S. griseus NBRC 13350]. The Bulletin of Vavilov Society of Geneticists and Breeders of Ukraine. 2015; 13(1):68-72.
[17] Paradkar A, Trefzer A, Chakraburtty R, Stassi D. Streptomyces genetics: a genomic perspective. Crit Rev Biotechnol. 2003; 23(1):1-27.
[18] Volff JN, Altenbuchner J. Genetic instability of the Streptomyces chromosome. Mol Microbiol. 1998; 27(2):239-46.
[19] Leblond P, Decaris B. New insights into the genetic instability of Streptomyces. FEMS Microbiol Lett. 1994; 123(3):225-32.
[20] Birch A, Häusler A, Rüttener C, Hütter R. Chromosomal deletion and rearrangement in Streptomyces glaucescens. J Bacteriol. 1991; 173(11):3531-8.
[21] Arber W. Genetic variation: molecular mechanisms and impact on microbial evolution. FEMS Microbiol Rev. 2000; 24(1):1-7.
[22] Smirnov VG. [Mechanisms for the acquisition and loss of genetic information by bacterial genomes]. Biology Bulletin Reviews. 2008; 128(1):52-76.
[23] Polishchuk LV, Matselyukh BP. [rRNA-genes of Actinomycetes, which are homologous to Streptomyces globisporus 1912-2 rRNA-clusters]. Factors of experimental evolution of organisms. 2014; 14: 129-33
[24] Rong X, Huang Y. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol. 2010; 60(3):696-703.
[25] Goodfellow M., Kumar Y., Labeda D.P., Sembiring L. The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores. Antonie Van Leeuwenhoek. 2007;92(2): 173-99.
[26] Ghiurcuta CG, Moret BM. Evaluating synteny for improved comparative studies. Bioinformatics. 2014; 30(12):i9-18.
[27] Polishchuk LV. [In silico seaching of Streptomyces globisporus 1912-2 gvp-cluster]. Factors of experimental evolution of organisms. 2015; 17: 325-9.
[28] Kato F, Hino T, Nakaji A, Tanaka M, Koyama Y. Carotenoid synthesis in Streptomyces setonii ISP5395 is induced by the gene crtS, whose product is similar to a sigma factor. Mol Gen Genet. 1995; 247(3):387-90.
[29] Schumann G, Nürnberger H, Sandmann G, Krügel H. Activation and analysis of cryptic crt genes for carotenoid biosynthesis from Streptomyces griseus. Mol Gen Genet. 1996; 252(6):658-66.