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General trends in organization and localization of crt-clusters in streptomycetes genomes
SUMMARY. The purpose of the work is to identify the existence of general principles in organization of crt-clusters of streptomycetes and their localization in genomes; to prove similarity in the organization of crt-clusters in phylogenetically related strains. The nucleotide sequences of crt-clusters of 100 strains of streptomycetes were analyzed using BLASTN programs. A number of schemes for organizing crt-clusters in streptomycetes were found. Several main trends in localization and organization of streptomycete crt-clusters were formu-lated. Òhe similarity of crt-cluster organizations in genomes of microorganisms belonging to different strains of same species of streptomycetes was shown. The ability to apply the organization of crp-clusters of Strep-tomyces (as an application to the genetic and phenotypic characteristics that are traditionally used) in the clas-sification of microorganisms within taxa of a lower order (clades, species, subspecies).
Key words: Streptomyces, crt-cluster, genome, scheme of cluster organization, BLASTN analysis
E-mail: LVPolishchuk ukr.net
1. Abdel-Haliem, M.E., Sakr, A.A., Ali, M.F., et al., Characterization of Streptomyces isolates causing colour changes of mural paintings in ancient Egyptian tombs, Microbiol. Res., 2013. https://doi.org/10.1016/j.micres.2013.02.004
2. Becerril, A., Alvarez, S., Braca, A.F., et al., Uncovering production of specialized metabolites by Streptomyces argillaceus: activation of cryptic biosynthesis gene clusters using nutritional and genetic approaches, PLoS One, 2018. https://doi.org/10.1371/journal.pone.0198145
3. Bentley, S.D. and Parkhill, J., Comparative genomic structure of prokaryotes, Annu. Rev. Genet., 2004. https://doi.org/10.1146/annurev.genet.38.072902.094318
4. Bianchi, M.L., Grein, A., Julita, P., et al., Streptomyces mediolani (Arcamone et al.) emend. Bianchi et al. and its production of carotenoids, Z. Allg. Mikrobiol., 1970. https://doi.org/10.1002/jobm.3630100402
5. Conn, H.J. and Conn, J.E., Value of pigmentation in classifying Actinomycetes, J. Bacteriol., 1941. https://doi.org/10.1146/annurev.genet.38.072902.094318
6. Iftime, D., Kulik, A., Hurtner, T., et al., Identification and activation of novel biosynthetic gene clusters by genome mining in the kirromycin producer Streptomyces collinus Tu 365, J. Industr. Microbiol. Biotechnol., 2016. https://doi.org/10.1007/s10295-015-1685-7
7. Kato, F., Akazai, M., Tanaka, M., et al., Mechanism of photo chromogenicity in Streptomyces canus ISP5017, Actinomycetology, 1989. https://doi.org/10.3209/saj.3_35
8. Kato, F., Hino, T., Nakaji, A., et al., Carotenoid synthesis in Streptomyces setonii ISP5395 is induced by the gene crtS, whose product is similar to a sigma factor, Mol. Gen. Genet., 1995. https://doi.org/10.1007/bf00293207
9. Kosyritzkaya, W.E. and Andreyuk, E.I., Production of lipids and carotinoids by yellow Streptomyces, Acta Biotechnol., 1984. https://doi.org/10.1002/abio.370040111
10. Krugel, H., Krubasik, P., Weber, K., et al., 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. https://doi.org/10.1016/s1388-1981(99)00075-x
11. Labeda, D.P., Goodfellow, M., and Brown, R., Phylogenetic study of the species within the family Streptomycetaceae, Antonie Van Leeuwenhoek, 2012. https://doi.org/10.1007/s10482-011-9656-0
12. Langeveld, S.A., van Mansfeld, A.D., Baas, P.D., et al., Nucleotide sequence of the origin of replication in bacteriophage phiX174 RF DNA, Nature, 1978. https://doi.org/10.1038/271417a0
13. Lee, H.S., Ohnishi, Y., and Horinouchi, S., A sigma B-like factor responsible for carotenoid biosynthesis in Streptomyces griseus, J. Mol. Microbiol. Biotechnol., 2001, vol. 3, no. 1, pp. 95–101.
14. Matselyukh, B.P., Matselyukh, D.Ya., Golembiovska, S.L., et al., Isolation of Streptomyces globisporus and Blakeslea trispora mutants with increased carotenoid content, Mikrobiol. Z., 2013. http://nbuv.gov.ua/ UJRN/MicroBiol_2013_75_6_3
15. Matselyukh, B.P., Identity of carotenoid biosynthetic genes of Streptomyces and their activation in S. globisporus 1912-4Crt, J. Genet. Genom., 2019, vol. 3, no. 1, pp. 122–126.
16. Myronovskyi, M., Tokovenko, B., Brötz, E., et al., Genome rearrangements of Streptomyces albus J1074 lead to the carotenoid gene cluster activation, Appl. Microbiol. Biotechnol., 2013. https://doi.org/10.1007/s00253-013-5440-6
17. Nefelova, M.V., Sverdlova, A.N., Feofilova, E.P., et al., Carotenoids synthesized by a culture of a mutant actinomycete strain, Mikrobiologiia, 1976, vol. 45, no. 2, pp. 306–309.
18. Omura, S., Ikeda, H., Ishikawa, J., et al., Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites, Proc. Natl. Acad. Sci. U. S. A., 2001. https://doi.org/10.1073/pnas.211433198
19. Polishchuk, L.V., Similarity and difference in crt-cluster organizations of strains from Streptomyces hygroscopicus clade, Slovak Int. Sci. J., 2018, vol. 1, no. 22, pp. 9–12.
20. Polishchuk, L.V., Organization of crt-clusters of 8 of strains of Streptomyces albus clade, Sci. Method., 2018a, vol. 1, no. 24, pp. 40–43.
21. Polishchuk, L.V. and Lukyanchuk, V.V., Organization of crt-clusters of strains from the Streptomyces griseus group, in The 10th Congress of UTGiS “Factors of Experimental Evolution of Organisms,” Inst. Mol. Biol. Genet. Natl. Acad. Sci. Ukr., Uman, October 2–6, 2017. https://doi.org/10.7124/FEEO.v20.790
22. Prozorov, A.A., Regularities of the location of genes having different functions and of some other nucleotide sequences in the bacterial chromosome, Microbiology, 2007. https://doi.org/10.1134/s0026261707040017
23. Ravin, N.V. and Shestakov, S.V., The genomes of prokaryotes, Vavilov J. Genet. Breed., 2013, vol. 17, no. 4, pp. 972–984.
24. Schumann, G., Nurnberger, H., Sandmann, G., et al., Activation and analysis of cryptic crt-genes for carotenoid biosynthesis from Streptomyces griseus, Mol. Gen. Genet., 2006. https://doi.org/10.1007/bf02173971
25. Stackebrandt, E., Frederiksen, W., and Garrity, G.M., Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology, Int. J. Syst. Evol. Microbiol., 2002. https://doi.org/10.1099/00207713-52-3-1043
26. Takano, H., Asker, D., Beppu, T., et al., Genetic control for light-induced carotenoid production in non-phototrophic bacteria, J. Ind. Microbiol. Biotechnol., 2006. https://doi.org/10.1007/s10295-005-0005-z
27. Takano, H., The regulatory mechanism underlying light-inducible production of carotenoids in nonphototrophic bacteria, Biosci. Biotechnol. Biochem., 2016. https://doi.org/10.1080/09168451.2016.1156478
28. Umeno, D.1., Tobias, A.V., and Arnold, F.H., Diversifying carotenoid biosynthetic pathways by directed evolution, Microbiol. Mol. Biol. Rev., 2005. https://doi.org/10.1128/MMBR.69.1.51-78.2005
29. Wang, M., Yang, H., Gao, J.-L., et al., Breeding of high-yield lycopene producing strains of Streptomyces rimosus and studies on its flask culture conditions, China Biotecnol., 2009. http://manu60.magtech.com.cn/biotech/Y2009/V29/I12/64
30. Waksman, S.A., On the classification of actinomycetes, J. Bacteriol., 1940. https://doi.org/10.1128/JB.39.5.549-558
31. Young, J.P., Crossman, L.C., and Johnston, A.W., The genome of Rhizobium leguminosarum has recognizable core and accessory components, Genome Biol., 2006. https://doi.org/10.1186/gb-2006-7-4-r34
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