Mikrobiol. Z. 2018; 80(6):28-40. Russian.
doi: https://doi.org/10.15407/microbiolj80.06.028

Organization of crt-Clusters of Strains from the Streptomyces albus Clade

Polishchuk L.V., Lukyanchuk V.V.

Zabolotny Institute of Microbiology and Virology, NAS of Ukraine
154 Akad. Zabolotny Str., Kyiv, 03143, Ukraine

The purpose of this study was to define the organization of crt-clusters of 8 strains from the S. albus clade. Show the possibility to use the organization of crt-clusters for classification of streptomycetes to taxons of lower hierarchy. Methods. Comparative analysis in silico of the primary structures of Streptomycetes genomes included in “Nucleotide collection” database on NCBI server was performed using programs (blastn and bl2seq) of the BLAST software package. Results. A number of similarities in organization of crtclusters of the 8 strains selected for the study, both recognized members of the S. albus group (J1074, DSM 41398, SM254, BK3-25), and related strains (S. sampsonii KJ40, Streptomyces sp. GBA 94-10, Streptomyces sp. PVA 94-07, Streptomyces sp. FR-008) were found. It was shown that all 8 crt-clusters consist of 2 convergent operons. They all do not maintain crtT-genes. All 8 clusters had inserts of additional genes whose products are not involved in carotenoid synthesis. They are usually located between operons. Exceptions are the crt-clusters of strains S. albus DSM 41398 and S. albus BK3-25, in which the additional genes are located between crtY and crtU genes. Conclusions. It is assumed that the characteristic features of Streptomycetes crt-cluster organization can be useful (in addition to the genetic and phenotypic characteristics already used) in microorganism classification to the taxa of the lower hierarchy (clades, species, subspecies).

Keywords: Streptomyces, in silico analysis, primary structure, genome, cluster, gene, clade, homology, overlap.

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  1. Takano H, Obitsu S, Beppu T, Ueda K. Light-induced carotenogenesis in Streptomyces coelicolor A3(2): identification of an extracytoplasmic function sigma factor that directs photodependent transcription of the carotenoid biosynthesis gene cluster. J Bacteriol. 2006; 187(5):1825−1832.
  2. 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; 247:387−390.
  3. Krugel H, Krubasik P, Weber K, Saluz HP, Sandmann G. Functional analysis of genes from Streptomyces griseus involved in the synthesis of isorenieratene, a carotenoid with aromatic end groups, revealed a novel type of carotenoid desaturase. Biochim Biophys Acta. 1999; 1439(1):57−64.
  4. Lee HS, Ohnishi Y, Horinouchi S. A sigma B-like factor responsible for carotenoid biosynthesis in Streptomyces griseus. J Mol Microbiol Biotechnol. 2001; 3(1):95−101.
  5. Matselyukh BP, Matselyukh DY, Golembiovska SL, Polishchuk LV, Lavrinchuk VY. Isolation of Streptomyces globisporus and Blakeslea trispora mutants with increased carotenoid content. Mikrobiol. Z. 2013; 75(6):10−16.
  6. Myronovskyi M, Tokovenko B, Brutz E, Ruckert C, Kalinowski J, Luzhetskyy A. Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation. Appl Microbiol Biotechnol. 2014; 98(2):795−806.
  7. Schumann G, Nurnberger H, Sandmann G, Krugel H. Activation and analysis of cryptic crt genes for carotenoid biosynthesis from Streptomyces griseus. Mol Gen Genet. 2006; 252(6):658−666.
  8. Takano H, Asker D, Beppu T, Ueda K. Genetic control for light-induced carotenoid production in non-phototrophic bacteria. J Ind Microbiol Biotechnol. 2006; 33(2):88−93.
  9. Abdel-Haliem ME, Sakr AA, Ali MF, Ghaly MF, Sohlenkamp C. Characterization of Streptomyces isolates causing color changes of mural paintings in ancient Egyptian tombs. Microbiol Res. 2013; 168(7):428−437.
  10. Kato F, Akazai M, Tanaka M, Koyama Y. Mechanism of photochromogenicity in Streptomyces canus ISP5017. Actinomycetology. 1989; 3:35−40.
  11. Myronovskyi M, Tokovenko B, Manderscheid N, Petzke L, Luzhetskyy A. Complete genome sequence of Streptomyces fulvissimus. J Biotechnol. 2013; 168(1):117−118.
  12. Zaburannyi N, Rabyk M, Ostash B, Fedorenko V, Luzhetskyy A. Insights into naturally minimized Streptomyces albus J1074 genome. BMC Genomics. 2014; 15:97. https://doi.org/10.1186/1471-2164-15-97
  13. Bentley SD, Chater KF, Cerdeco-Tarraga AM, Challis GL, et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 2002; 417(6885):141–147. https://doi.org/10.1038/417141a
  14. Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, et al. Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol. 2008; 190(11):4050–4060. https://doi.org/10.1128/JB.00204-08
  15. Shneyer S. On the species-specificity of DNA: fifty years later. Biochemistry (Moscow). 2007: 72(12):1377−1384.
  16. Goodfellow M, Kumar Y, Labeda DP, Sembiring L. The Streptomyces violaceusniger clade: a home for Streptomycetes with rugose ornamented spores. Antonie Van Leeuwenhoek. 2007; 92(2):173−199.
  17. Vandamme P, Pot B, Gillis M, de Vos P, Kersters K, Swings J. Polyphasic taxonomy, a consensus approach to bacterial systematics. Microbiol Rev. 1996; 60(2):407−438.