Folia Microbiologica

, Volume 61, Issue 3, pp 209–220 | Cite as

Transcriptional regulators of GntR family in Streptomyces coelicolor A3(2): analysis in silico and in vivo of YtrA subfamily

  • O. Tsypik
  • O. Yushchuk
  • N. Zaburannyi
  • K. Flärdh
  • S. Walker
  • V. Fedorenko
  • B. Ostash
Article

Abstract

Transcriptional factors of the GntR family regulate numerous physiological and morphological processes in response to the nutrient state of bacterial cells. The number of GntR transcriptional factors in genomes of soil-dwelling actinomycetes is one of the highest among bacteria, reflecting both the large size of their chromosomes and the complex ecological niche that they occupy. However, very little is known about the roles of GntRs in actinomycete biology. Here, we analyzed the genome of model actinomycete, Streptomyces coelicolor A3(2), in an attempt to gain new insights into the function of GntR family. All 56 GntR proteins of M145 strain were classified into FadR, HutC, MocR, YtrA, and DevA subfamilies according to their secondary structure. We then checked for the presence of GntR orthologs in six other sequenced Streptomyces and one Kitasatospora genomes, revealing that 12 GntRs were conserved in all analyzed strains. Genomic analysis of the less studied YtrA type regulators revealed 160 sequences present in 88 members of Coriobacteridae, Rubrobacteridae, and Actinobacteridae subclasses. These proteins form seven dense clusters on the consensus phylogenetic tree and their genes are usually co-located with the genes for transport proteins. Probable operator sites were identified for orthologous groups of Sco0823 and Sco3812 proteins. All S. coelicolor YtrA-like regulatory genes (SCO0823, SCO1728, SCO3812) were analyzed at transcriptional level, knocked out, and introduced on moderate copy number plasmid in M145 strain. Also, gene SCO0824, a part of putative SCO0823 operon, was studied. Results of these experiments are discussed here.

Supplementary material

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References

  1. Bilyk B, Weber S, Myronovskyi M, Bilyk O, Petzke L, Luzhetskyy A (2013) In vivo random mutagenesis of streptomycetes using mariner-based transposon Himar1. Appl Microbiol Biotechnol 97:351–359. doi:10.1007/s00253-012-4550-x CrossRefPubMedGoogle Scholar
  2. Bishop A, Fielding S, Dyson P, Herron P (2004) Systematic insertional mutagenesis of streptomycete genome: a link between osmoadaptation and antibiotic production. Genome Res 14:893–900. doi:10.1101/gr.1710304 CrossRefPubMedPubMedCentralGoogle Scholar
  3. Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL (2012) Domain enhanced lookup time accelerated BLAST. Biol Direct 7:12. doi:10.1186/1745-6150-7-12 CrossRefPubMedPubMedCentralGoogle Scholar
  4. Buchan DW, Ward SM, Lobley AE, Nugent TC, Bryson K, Jones DT (2010) Protein annotation and modelling servers at University College London. Nucl Acids Res 38(Suppl):W563–W568CrossRefPubMedPubMedCentralGoogle Scholar
  5. Chen L, Lu Y, Chen J, Zhang W, Shu D, Qin Z, Yang S, Jiang W (2008) Characterization of a negative regulator AveI for avermectin biosynthesis in Streptomyces avermitilis NRRL8165. Appl Microbiol Biotechnol 80:277–286. doi:10.1007/s00253-008-1545-8 CrossRefPubMedGoogle Scholar
  6. Cole C, Barber JD, Barton GJ (2008) The Jpred 3 secondary structure prediction server. Nucleic Acids Res 36:W197–201. doi:10.1093/nar/gkn238 CrossRefPubMedPubMedCentralGoogle Scholar
  7. Datsenko KA, Wanner BL (2000) One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645CrossRefPubMedPubMedCentralGoogle Scholar
  8. Dereeper A, Guignon V, Blanc G, Audic S et al (2008) Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 36:W465–9. doi:10.1093/nar/gkn180 CrossRefPubMedPubMedCentralGoogle Scholar
  9. Gust B, Chandra G, Jakimowicz D, Yuqing T, Bruton CJ, Chater KF (2004) Lambda red-mediated genetic manipulation of antibiotic-producing Streptomyces. Adv Appl Microbiol 54:107–128CrossRefPubMedGoogle Scholar
  10. Hillerich B, Westpheling J (2006) A new GntR family transcriptional regulator in Streptomyces coelicolor is required for morphogenesis and antibiotic production and controls transcription of an ABC transporter in response to carbon source. J Bacteriol 188(21):7477–87CrossRefPubMedPubMedCentralGoogle Scholar
  11. Horbal L, Kobylyanskyy A, Yushchuk O, Zaburannyi N, Luzhetskyy A, Ostash B, Marinelli F, Fedorenko V (2013) Evaluation of heterologous promoters for genetic analysis of Actinoplanes teichomyceticus—producer of teicoplanin, drug of last defense. J Biotechnol 168:367–372. doi:10.1016/j.jbiotec.2013.10.018 CrossRefPubMedGoogle Scholar
  12. Hoskisson PA, Rigali S (2009) Chapter 1: variation in form and function the helix-turn-helix regulators of the GntR superfamily. Adv Appl Microbiol 69:1–22. doi:10.1016/S0065-2164(09)69001-8 CrossRefPubMedGoogle Scholar
  13. Kelley LA, Sternberg MJ (2009) Protein structure prediction on the web: a case study using the phyre server. Nat Protoc 4(3):363–71. doi:10.1038/nprot.2009.2 CrossRefPubMedGoogle Scholar
  14. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical Streptomyces genetics. John Innes Foundation, NorwichGoogle Scholar
  15. Koster W (2005) Cytoplasmic membrane iron permease systems in the bacterial cell envelope. Front Biosci 10:462–477. doi:10.2741/1542 CrossRefPubMedGoogle Scholar
  16. Lewis RA, Shahi SK, Laing E, Bucca G, Efthimiou G, Bushell M, Smith CP (2011) Genome-wide transcriptomic analysis of the response to nitrogen limitation in Streptomyces coelicolor A3(2). BMC Res Notes 4:78. doi:10.1186/1756-0500-4-78 CrossRefPubMedPubMedCentralGoogle Scholar
  17. Liu G, Chater KF, Chandra G, Niu G, Tan H (2013) Molecular regulation of antibiotic biosynthesis in Streptomyces. Microbiol Mol Biol Rev 77(1):112–43. doi:10.1128/MMBR.00054-12 CrossRefPubMedPubMedCentralGoogle Scholar
  18. Magarvey N, He J, Aidoo KA, Vining LC (2001) The pdx genetic marker adjacent to the chloramphenicol biosynthesis gene cluster in Streptomyces venezuelae ISP5230: functional characterization. Microbiology 147(Pt 8):2103–12CrossRefPubMedGoogle Scholar
  19. Makitrynskyy R, Rebets Y, Ostash B, Zaburannyi N, Rabyk M, Walker S, Fedorenko V (2010) Genetic factors that influence moenomycin production in streptomycetes. J Ind Microbiol Biotechnol 37:559–566CrossRefPubMedPubMedCentralGoogle Scholar
  20. Makitrynskyy R, Ostash B, Tsypik O, Rebets Y, Doud E, Meredith T, Luzhetskyy A, Bechthold A, Walker S, Fedorenko V (2013) Pleiotropic regulatory genes bldA, adpA and absB are implicated in production of phosphoglycolipid antibiotic moenomycin. Open Biol 3:130121. doi:10.1098/rsob.130121 CrossRefPubMedPubMedCentralGoogle Scholar
  21. McCormick JR, Flärdh K (2012) Signals and regulators that govern Streptomyces development. FEMS Microbiol Rev 36:206–231CrossRefPubMedPubMedCentralGoogle Scholar
  22. Muth G, Nussbaumer B, Wohlleben W, Pühler A (1989) A vector system with temperature-sensitive replication for gene disruption and mutational cloning in streptomycetes. Mol Gen Genet 6:1–8Google Scholar
  23. Myronovskyi M, Welle E, Fedorenko V, Luzhetskyy A (2011) Beta-glucuronidase as a sensitive and versatile reporter in actinomycetes. Appl Environ Microbiol 77(15):5370–83. doi:10.1128/AEM.00434-11 CrossRefPubMedPubMedCentralGoogle Scholar
  24. Myronovskyy M, Ostash B, Ostash I, Fedorenko V (2009) A gene cloning system for the siomycin producer Streptomyces sioyaensis NRRL-B5408. Folia Microbiol 54:91–96CrossRefGoogle Scholar
  25. Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26(11):1362–84. doi:10.1039/b817069j CrossRefPubMedPubMedCentralGoogle Scholar
  26. Novichkov PS, Rodionov DA, Stavrovskaya ED, Novichkova ES, Kazakov AE, Gelfand MS, Arkin AP, Mironov AA, Dubchak I (2011) RegPredict: an integrated system for regulon inference in prokaryotes by comparative genomics approach. Nucleic Acids Res 38:W299–307. doi:10.1093/nar/gkq531 CrossRefGoogle Scholar
  27. Ostash B, Rebets Y, Myronovskyy M, Tsypik O et al (2011) Identification and characterization of the Streptomyces globisporus 1912 regulatory gene lndYR that affects sporulation and antibiotic production. Microbiology 157(Pt 4):1240–9. doi:10.1099/mic.0.045088-0 CrossRefPubMedPubMedCentralGoogle Scholar
  28. Persson J, Chater KF, Flärdh K (2013) Molecular and cytological analysis of the expression of Streptomyces sporulation regulatory gene whiH. FEMS Microbiol Lett 341(2):96–105. doi:10.1111/1574-6968.12099 CrossRefPubMedGoogle Scholar
  29. Rigali S, Derouaux A, Giannotta F, Dusart J (2002) Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J Biol Chem 277(15):12507–15CrossRefPubMedGoogle Scholar
  30. Rigali S, Titgemeyer F, Barends S, Mulder S, Thomae AW, Hopwood DA, van Wezel GP (2008) Feast or famine: the global regulator DasR links nutrient stress to antibiotic production by Streptomyces. EMBO Rep 9(7):670–5. doi:10.1038/embor.2008.83 CrossRefPubMedPubMedCentralGoogle Scholar
  31. Salzberg LI, Luo Y, Hachmann AB, Mascher T, Helmann JD (2011) The Bacillus subtilis GntR family repressor YtrA responds to cell wall antibiotics. J Bacteriol 193(20):5793–801. doi:10.1128/JB.05862-11 CrossRefPubMedPubMedCentralGoogle Scholar
  32. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory, Cold Spring HarborGoogle Scholar
  33. Sezonov G, Possoz C, Friedmann A, Pernodet JL, Guérineau M (2000) KorSA from the Streptomyces integrative element pSAM2 is a central transcriptional repressor: target genes and binding sites. J Bacteriol 182(5):1243–1250CrossRefPubMedPubMedCentralGoogle Scholar
  34. Simossis VA, Heringa J (2003) The PRALINE online server: optimising progressive multiple alignment on the web. Comput Biol Chem 27(4–5):511–9CrossRefPubMedGoogle Scholar
  35. Söding J, Biegert A, Lupas AN (2005) The HHpred interactive server for protein homology detection and structure prediction. Nucleic Acids Res 33:W244–W248CrossRefPubMedPubMedCentralGoogle Scholar
  36. van Wezel GP, McDowall KJ (2011) The regulation of the secondary metabolism of Streptomyces: new links and experimental advances. Nat Prod Rep 28(7):1311–33. doi:10.1039/c1np00003a CrossRefPubMedGoogle Scholar
  37. Vindal V, Suma K, Ranjan A (2007a) GntR family of regulators in Mycobacterium smegmatis: a sequence and structure based characterization. BMC Genomics 23:289–301CrossRefGoogle Scholar
  38. Vindal V, Ranjan S, Ranjan A (2007b) In silico analysis and characterization of GntR family of regulators from Mycobacterium tuberculosis. Tuberculosis 87:242–247CrossRefPubMedGoogle Scholar

Copyright information

© Institute of Microbiology, Academy of Sciences of the Czech Republic, v.v.i. 2015

Authors and Affiliations

  1. 1.Department of Genetics and BiotechnologyIvan Franko National University of LvivLvivUkraine
  2. 2.Department of BiologyLund UniversityLundSweden
  3. 3.Department of Microbiology and ImmunobiologyHarvard Medical SchoolBostonUSA

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