The Journal of Microbiology

, Volume 46, Issue 1, pp 1–11 | Cite as

The use of the rare UUA codon to define “Expression Space” for genes involved in secondary metabolism, development and environmental adaptation in Streptomyces

  • Keith F. ChaterEmail author
  • Govind Chandra


In Streptomyces coelicolor, bldA encodes the only tRNA for a rare leucine codon, UUA. This tRNA is unnecessary for growth, but is required for some aspects of secondary metabolism and morphological development, as revealed by the phenotypes of bldA mutants in diverse streptomycetes. This article is a comprehensive review of out understanding of this unusual situation. Based on information from four sequenced genomes it now appears that, typically, about 2–3% of genes in any one streptomycete contain a TTA codon, most having been acquired through species-specific horizontal gene transfer. Among the few widely conserved TTA-containing genes, mutations in just one, the pleiotropic regulatory gene adpA, give an obvious phenotype: such mutants are defective in aerial growth and sporulation, but vary in the extent of their impairment in secondary metabolism in different streptomycetes. The TTA codon in adpA is largely responsible for the morphological phenotype of a bldA mutant of S. coelicolor. AdpA-dependent targets include several genes involved in the integrated action of extracellular proteases that, at least in some species, are involved in the conversion of primary biomass into spores. The effects of bldA mutations on secondary metabolism are mostly attributable to the presence of TTA codons in pathway-specific genes, particularly in transcriptional activator genes. This is not confined to S. coelicolor — it is true for about half of all known antibiotic biosynthetic gene sets from streptomycetes. Combined microarray and proteomic analysis of liquid (and therefore non-sporulating) S. coelicolor bldA mutant cultures revealed effects of the mutation during rapid growth, during transition phase, and in stationary phase. Some of these effects may be secondary consequences of changes in the pattern of ppGpp accumulation. It is argued that the preferential accumulation of the bldA tRNA under conditions in which growth is significantly constrained has evolved to favour the expression of genes that confer adaptive benefits in intermittently encountered sub-optimal environments. The evolution of this system may have been a secondary consequence of the selective pressure exerted by bacteriophage attack. Some biotechnological implications of bldA phenomenology are considered.


codon usage comparative genomics antibiotic production bacterial development horizontal gene transfer ecological adaptation 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Bentley, S.D., S. Brown, L.D. Murphy, D.E. Harris, M.A. Quail, J. Parkhill, B.G. Barrell, J.R. McCormick, R.I. Santamaria, R. Losick, M. Yamasaki, H. Kinashi, C.W. Chen, G. Chandra, D. Jakimowicz, H.M. Kieser, T. Kieser, and K.F. Chater. 2004. SCP1, a 356,023 bp linear plasmid adapted to the ecology and developmental biology of its host, Streptomyces coelicolor A3(2). Mol. Microbiol. 51, 1615–1628.PubMedCrossRefGoogle Scholar
  2. Bentley, S.D., K.F. Chater, A.M. Cerdeno-Tarraga, G.L. Challis, N.R. Thomson, K.D. James, D.E. Harris, M.A. Quail, H. Kieser, D. Harper, A. Bateman, S. Brown, G. Chandra, C.W. Chen, M. Collins, A. Cronin, A. Fraser, A. Goble, J. Hidalgo, T. Hornsby, et al. 2002. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147.PubMedCrossRefGoogle Scholar
  3. Bruton, C.J., E.P. Guthrie, and K.F. Chater. 1991. Phage vectors that allow monitoring of transcription of secondary metabolism genes in Streptomyces. Biotechnology 9, 652–656.PubMedCrossRefGoogle Scholar
  4. Chakraburtty, R. and M. Bibb. 1997. The ppGpp synthetase gene (relA) of Streptomyces coelicolor A3(2) plays a conditional role in antibiotic production and morphological differentiation. J. Bacteriol. 179, 5854–5861.PubMedGoogle Scholar
  5. Champness, W.C. 1988. New loci required for Streptomyces coelicolor morphological and physiological differentiation. J. Bacteriol. 170, 1168–1174.PubMedGoogle Scholar
  6. Champness, W.C. and K.F. Chater. 1994. The regulation and interaction of antibiotic production and morphological differentiation in Streptomyces spp. In P. Piggot, C. Moran, and P. Youngman. (eds.), Regulation of bacterial differentiation. Washington, American Society for Microbiology, 6193.Google Scholar
  7. Chater, K.F. 2001. Regulation of sporulation in Streptomyces coelicolor A3(2): a checkpoint multiplex? Curr. Opin. Microbiol. 4, 667–673.PubMedCrossRefGoogle Scholar
  8. Chater, K.F. 2006. Streptomyces inside out: a new perspective on the bacteria that provide us with antibiotics. Phil. Trans. R. Soc. Lond. B. Biol. Sci. 361, 761–768.CrossRefGoogle Scholar
  9. Chater, K.F. and G. Chandra. 2006. The evolution of development in Streptomyces analysed by genome comparisons. FEMS Microbiol. Rev. 30, 651–672.PubMedCrossRefGoogle Scholar
  10. Chater, K.F. and S. Horinouchi. 2003. Signalling early developmental events in two highly diverged Streptomyces species. Mol. Microbiol. 48, 9–15.PubMedCrossRefGoogle Scholar
  11. Crick, F. 1966. Codon-anticodon pairing: the wobble hypothesis. J. Mol. Biol. 19, 548–555.PubMedGoogle Scholar
  12. Distler, J., K. Mansouri, G. Mayer, M. Stockmann, and W. Piepersberg. 1992. Streptomycin biosynthesis and its regulation in streptomycetes. Gene 115, 105–111.PubMedCrossRefGoogle Scholar
  13. Elliot, M. and N.J. Talbot. 2004. Building filaments in the air: aerial morphogenesis in bacteria and fungi. Curr. Opin. Microbiol. 7, 594–601.PubMedCrossRefGoogle Scholar
  14. Eustaquio, A.S., B. Gust, U. Galm, S.M. Li, K.F. Chater, and L. Heide. 2005. Heterologous expression of novobiocin and clorobiocin biosynthetic gene clusters. Appl. Environ. Microbiol. 71, 2452–2459.PubMedCrossRefGoogle Scholar
  15. Fernandez-Moreno, M.A., J.L. Caballero, D.A. Hopwood, and F. Malpartida. 1991. The act cluster contains regulatory and antibiotic export genes, direct targets for translational control by the bldA tRNA gene of Streptomyces. Cell 66, 769–780.PubMedCrossRefGoogle Scholar
  16. Fuglsang, A. 2005. Intragenic position of UUA codons in streptomycetes. Microbiology 151, 3150–3152.PubMedCrossRefGoogle Scholar
  17. Gehring, A., J. Nodwell, S. Beverley, and R. Losick. 2000. Genomewide insertional mutagenesis in Streptomyces coelicolor reveals additional genes involved in morphological differentiation. Proc. Natl. Acad. Sci. USA 97, 9642–9647.PubMedCrossRefGoogle Scholar
  18. Gramajo, H.C., E. Takano, and M.J. Bibb. 1993. Stationary phase production of the antibiotic actinorhodin in Streptomyces coelicolor is transcriptionally regulated. Mol. Microbiol. 7, 837–845.PubMedCrossRefGoogle Scholar
  19. Guthrie, E.P. and K.F. Chater. 1990. The level of a transcript required for production of a Streptomyces coelicolor antibiotic is conditionally dependent on a tRNA gene. J. Bacteriol. 172, 6189–6193.PubMedGoogle Scholar
  20. Guthrie, E.P., C.S. Flaxman, J. White, D.A. Hodgson, M.J. Bibb, and K.F. Chater. 1998. A response-regulator-like activator of antibiotic synthesis from Streptomyces coelicolor A3(2) with an amino-terminal domain that lacks a phosphorylation pocket. Microbiology 144, 727–738.PubMedGoogle Scholar
  21. Hesketh, A., G. Bucca, E. Laing, F. Flett, G. Hotchkiss, C.P. Smith, and K.F. Chater. 2007. New pleiotropic effects of eliminating a rare tRNA from Streptomyces coelicolor, revealed by combined proteomic and transcriptomic analysis of liquid cultures. BMC Genomics 8, 261.PubMedCrossRefGoogle Scholar
  22. Hirano, S., J. Kato, Y. Ohnishi, and S. Horinouchi. 2006. Control of the Streptomyces subtilisin inhibitor gene by AdpA in the A-factor regulatory cascade in Streptomyces griseus. J. Bacteriol. 188, 6207–6216.PubMedCrossRefGoogle Scholar
  23. Hopwood, D. 1967. Genetic analysis and genome structure in Streptomyces coelicolor. Bacteriol. Rev. 31, 373–403.PubMedGoogle Scholar
  24. Horinouchi, S. 2002. A microbial hormone, A-factor, as a master switch for morphological differentiation and secondary metabolism in Streptomyces griseus. Front. Biosci. 7, D2045–D2057.PubMedCrossRefGoogle Scholar
  25. Ikeda, H., J. Ishikawa, A. Hanamoto, M. Shinose, H. Kikuchi, T. Shiba, Y. Sakaki, M. Hattori, and S. Omura. 2003. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat. Biotechnol. 21, 526–531.PubMedCrossRefGoogle Scholar
  26. Jayapal, K.P., W. Lian, F. Glod, and W.S. Hu. 2007. Comparative genome hybridizations reveal absence of large Streptomyces coelicolor genomic islands in Streptomyces lividans. BMC Genomics 8, 229.PubMedCrossRefGoogle Scholar
  27. Kataoka, M., S. Kosono, and G. Tsujimoto. 1999. Spatial and temporal regulation of protein expression by bldA within a Streptomyces lividans colony. FEBS Lett. 462, 425–429.PubMedCrossRefGoogle Scholar
  28. Kato, J., A. Suzuki, H. Yamazaki, Y. Ohnishi, and S. Horinouchi. 2002. Control by A-factor of a metalloendopeptidase gene involved in aerial mycelium formation in Streptomyces griseus. J. Bacteriol. 184, 6016–6025.PubMedCrossRefGoogle Scholar
  29. Kato, J.Y., I. Miyahisa, M. Mashiko, Y. Ohnishi, and S. Horinouchi. 2004. A single target is sufficient to account for the biological effects of the A-factor receptor protein of Streptomyces griseus. J. Bacteriol. 186, 2206–2211.PubMedCrossRefGoogle Scholar
  30. Kato, J.Y., W.J. Chi, Y. Ohnishi, S.K. Hong, and S. Horinouchi. 2005a. Transcriptional control by A-factor of two trypsin genes in Streptomyces griseus. J. Bacteriol. 187, 286–295.PubMedCrossRefGoogle Scholar
  31. Kato, J.Y., Y. Ohnishi, and S. Horinouchi. 2005b. Autorepression of AdpA of the AraC/XylS family, a key transcriptional activator in the A-factor regulatory cascade in Streptomyces griseus. J. Mol. Biol. 350, 12–26.PubMedCrossRefGoogle Scholar
  32. Kelemen, G.H. and M.J. Buttner. 1999. Initiation of aerial mycelium formation in Streptomyces. Curr. Opin. Microbiol. 2, 106–106(1).CrossRefGoogle Scholar
  33. Kim, I. and K.J. Lee. 1995. Physiological roles of leupeptin and extracellular proteases in mycelium development of Streptomyces exfoliatus SMF13. Microbiology 141, 1017–1025.PubMedGoogle Scholar
  34. Kim, D.-W., K. Chater, K.-J. Lee, and A. Hesketh. 2005a. Changes in the extracellular proteome caused by the absence of the bldA gene product, a developmentally significant tRNA, reveal a new target for the pleiotropic regulator AdpA in Streptomyces coelicolor. J. Bacteriol. 187, 2957–2966.PubMedCrossRefGoogle Scholar
  35. Kim, D.-W., K. Chater, K.J. Lee, and A. Hesketh. 2005b. Effects of growth phase and the developmentally significant bldA-specified tRNA on the membrane-associated proteome of Streptomyces coelicolor. Microbiology 151, 2707–2720.PubMedCrossRefGoogle Scholar
  36. Kodani, S., M.E. Hudson, M.C. Durrant, M.J. Buttner, J.R. Nodwell, and J.M. Willey. 2004. The SapB morphogen is a lantibiotic-like peptide derived from the product of the developmental gene ramS in Streptomyces coelicolor. Proc. Natl. Acad. Set USA 101, 11448–11453.CrossRefGoogle Scholar
  37. Kwak, J., L.A. McCue, and K.E. Kendrick. 1996. Identification of bldA mutants of Streptomyces griseus. Gene 171, 75–78.PubMedCrossRefGoogle Scholar
  38. Lautru, S., R.J. Deeth, L.M. Bailey, and G.L. Challis. 2005. Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat. Chem. Biol. 1, 265–269.PubMedCrossRefGoogle Scholar
  39. Lawlor, E.J., H.A. Baylis, and K.F. Chater. 1987. Pleiotropic morphological and antibiotic deficiencies result from mutations in a gene encoding a transfer RNA-like product in Streptomyces coelicolor A3(2). Genes Dev. 1, 1305–1310.PubMedCrossRefGoogle Scholar
  40. Leskiw, B.K., E.J. Lawlor, J.M. FernandezAbalos, and K.F. Chater. 1991a. TTA codons in some genes prevent their expression in a class of developmental, antibiotic-negative, Streptomyces mutants. Proc. Natl. Acad. Sci. USA 88, 24612465.CrossRefGoogle Scholar
  41. Leskiw, B.K., M.J. Bibb, and K.F. Chater. 1991b. The use of a rare codon specifically during development? Mol. Microbiol. 5, 2861–2867.PubMedCrossRefGoogle Scholar
  42. Leskiw, B.K., R. Mah, E.J. Lawlor, and K.F. Chater. 1993. Accumulation of bldA-specified tRNA is temporally regulated in Streptomyces coelicolor A3(2). J. Bacteriol. 175, 1995–2005.PubMedGoogle Scholar
  43. Li, W., J. Wu, W. Tao, C. Zhao, Y. Wang, X. He, G. Chandra, X. Zhou, Z. Deng, K.F. Chater, and M. Tao. 2007. A genetic and bioinformatic analysis of Streptomyces coelicolor genes containing TTA codons, possible targets for regulation by a developmentally significant tRNA. FEMS Microbiol. Lett. 266, 20–28.PubMedCrossRefGoogle Scholar
  44. Manteca, A., M. Fernandez, and J. Sanchez. 2006. Cytological and biochemical evidence for an early cell dismantling event in surface cultures of Streptomyces antibioticus. Res. Microbiol. 157, 143–152.PubMedCrossRefGoogle Scholar
  45. Merrick, M. 1976. A morphological and genetic mapping study of bald colony mutants of Streptomyces coelicolor. J. Gen. Microbiol. 96, 299–315.PubMedGoogle Scholar
  46. Nguyen, K.T., J. Tenor, H. Stettler, L.T. Nguyen, L.D. Nguyen, and C.J. Thompson. 2003. Colonial differentiation in Streptomyces coelicolor depends on translation of a specific codon within the adpA gene. J. Bacteriol. 185, 7291–7296.PubMedCrossRefGoogle Scholar
  47. Ohnishi, Y., S. Kameyama, H. Onaka, and S. Horinouchi. 1999. The A-factor regulatory cascade leading to streptomycin biosynthesis in Streptomyces griseus: identification of a target gene of the A-factor receptor. Mol. Microbiol. 34, 102–111.PubMedCrossRefGoogle Scholar
  48. Ohnishi, Y., H. Yamazaki, J.Y. Kato, A. Tomono, and S. Horinouchi. 2005. AdpA, a central transcriptional regulator in the A-factor regulatory cascade that leads to morphological development and secondary metabolism in Streptomyces griseus. Biosci. Biotechnol. Biochem. 69, 431–439.PubMedCrossRefGoogle Scholar
  49. O’Rourke, S. 2003. Regulation of methylenomycin biosynthesis. Ph. D. thesis, University of East Anglia, Norwich, UK.Google Scholar
  50. Passantino, R., A.M. Puglia, and K.F. Chater. 1991. Additional copies of the actII regulatory gene induce actinorhodin production in pleiotropic bld mutants of Streptomyces coelicolor A3(2). J. Gen. Microbiol. 137, 20592064.Google Scholar
  51. Perez-Llarena, F.J., P. Liras, A. Rodriguez-Garcia, and J.F. Martin. 1997. A regulatory gene (ccaR) required for cephamycin and clavulanic acid production in Streptomyces clavuligerus: amplification results in overproduction of both beta-lactam compounds. J. Bacteriol. 179, 2053–2059.PubMedGoogle Scholar
  52. Piret, J.M. and K.F. Chater. 1985. Phage-mediated cloning of bldA, a region involved in Streptomyces coelicolor morphological development, and its analysis by genetic complementation. J. Bacteriol. 163, 965–972.PubMedGoogle Scholar
  53. Rebets, Y.V., B.O. Ostash, M. Fukuhara, T. Nakamura, and V.O. Fedorenko. 2006. Expression of the regulatory protein LndI for landomycin E production in Streptomyces globisporus 1912 is controlled by the availability of tRNA for the rare UUA codon. FEMS Microbiol. Lett. 256, 30–37.PubMedCrossRefGoogle Scholar
  54. Rozenski, J., P.F. Crain, and J.A. McCloskey. 1999. The RNA modification database: 1999 update. Nucleic Acids Res. 27, 196–197.PubMedCrossRefGoogle Scholar
  55. Song, L., F. Barona-Gomez, C. Corre, L. Xiang, D.W. Udwary, M.B. Austin, J.P. Noel, B.S. Moore, and G.L. Challis. 2006. Type III polyketide synthase β-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining. J. Am. Chem. Soc. 128, 14754–14755.PubMedCrossRefGoogle Scholar
  56. Strauch, E., E. Takano, H.A. Baylis, and M.J. Bibb. 1991. The stringent response in Streptomyces coelicolor A3(2). Mol. Microbiol. 5, 289–298.PubMedCrossRefGoogle Scholar
  57. Takano, E., M. Tao, F. Long, M.J. Bibb, L. Wang, W. Li, M.J. Buttner, Z.X. Deng, and K.F. Chater. 2003. A rare leucine codon in adpA is implicated in the morphological defect of bldA mutants of Streptomyces coelicolor. Mol. Microbiol. 50, 475–486.PubMedCrossRefGoogle Scholar
  58. Tao, W.F., J. Wu, Z.X. Deng, and M.F. Tao. 2007. Cloning of bldAa and the effect on morphological differentiation and avermectins production in Streptomyces avermitilis NRRL8165. Wei Sheng Wu Xue Bao (In Chinese) 47, 34–38.Google Scholar
  59. Tercero, J.A., J.C. Espinosa, and A. Jimenez. 1998. Expression of the Streptomyces alboniger pur cluster in Streptomyces lividans is dependent on the bldA-encoded tRNALeu. FEBS Lett. 421, 221–223.PubMedCrossRefGoogle Scholar
  60. Tomono, A., Y. Tsai, Y. Ohnishi, and S. Horinouchi. 2005. Three chymotrypsin genes are members of the AdpA regulon in the A-factor regulatory cascade in Streptomyces griseus. J. Bacteriol. 187, 6341–6353.PubMedCrossRefGoogle Scholar
  61. Trepanier, N.K., S. Jensen, D.C. Alexander, and B.K. Leskiw. 2002. The positive activator of cephamycin C and clavulanic acid production in Streptomyces clavuligerus is mistranslated in a bldA mutant. Microbiology 148, 643–656.PubMedGoogle Scholar
  62. Trepanier, N.K., G.D. Nguyen, P.J. Leedell, and B.K. Leskiw. 1997. Use of polymerase chain reaction to identify a leucyl tRNA in Streptomyces coelicolor. Gene 193, 59–63.PubMedCrossRefGoogle Scholar
  63. Ueda, K., K.I. Oinuma, G. Ikeda, K. Hosono, Y. Ohnishi, S. Horinouchi, and T. Beppu. 2002. AmfS, an extracellular peptidic morphogen in Streptomyces griseus. J. Bacteriol. 184, 1488–1492.PubMedCrossRefGoogle Scholar
  64. Ueda, K., H. Takano, M. Nishimoto, H. Inaba, and T. Beppu. 2005. Dual transcriptional control of amfTSBA, which regulates the onset of cellular differentiation in Streptomyces griseus. J. Bacteriol. 187, 135–142.PubMedCrossRefGoogle Scholar
  65. Ventura, M., C. Canchaya, A. Tauch, G. Chandra, G.F. Fitzgerald, K.F. Chater, and D. Van Sinderen. 2007. Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum. Microbiol. Mol. Biol. Rev. 71, 495–548.PubMedCrossRefGoogle Scholar
  66. Vohradsky, J. and C.J. Thompson. 2006. Systems level analysis of protein synthesis patterns associated with bacterial growth and metabolic transitions. Proteomics 6, 785–793.PubMedCrossRefGoogle Scholar
  67. White, J. and M. Bibb. 1997. bldA dependence of undecylprodigiosin production in Streptomyces coelicolor A3(2) involves a pathway-specific regulatory cascade. J. Bacteriol. 179, 627–633.PubMedGoogle Scholar
  68. Widdick, D.A., H.M. Dodd, P. Barraille, J. White, T.H. Stein, K.F. Chater, M.J. Gasson, and M.J. Bibb. 2003. Cloning and engineering of the cinnamycin biosynthetic gene cluster from Streptomyces cinnamoneus cinnamoneus DSM 40005. Proc. Natl. Acad. Sci. USA 100, 4316–4321.PubMedCrossRefGoogle Scholar
  69. Willey, J., J. Schwedock, and R. Losick. 1993. Multiple extracellular signals govern the production of a morphogenetic protein involved in aerial mycelium formation by Streptomyces coelicolor. Genes Dev. 7, 895–903.PubMedCrossRefGoogle Scholar
  70. Willey, J., A. Willems, S. Kodani, and J.R. Nodwell. 2006. Morphogenetic surfactants and their role in the formation of aerial hyphae in Streptomyce coelicolor. Mol. Microbiol. 59, 731–742.PubMedCrossRefGoogle Scholar
  71. Yamazaki, H., Y. Ohnishi, and S. Horinouchi. 2000. An A-factor-dependent extracytoplasmic function sigma factor [oAdsA] that is essential for morphological development in Streptomyces griseus. J. Bacteriol. 182, 4596–4605.PubMedCrossRefGoogle Scholar
  72. Yamazaki, H., A. Takano, Y. Ohnishi, and S. Horinouchi. 2003a. amfR, an essential gene for aerial mycelium formation, is a member of the AdpA regulon in the A-factor regulatory cascade in Streptomyces griseus. Mol. Microbiol. 50, 1173–1187.PubMedCrossRefGoogle Scholar
  73. Yamazaki, H., Y. Ohnishi, and S. Horinouchi. 2003b. Transcriptional switch-on by A-factor of ssgA that is essential for spore septum formation in Streptomyces griseus. J. Bacteriol. 285, 1273–1283.CrossRefGoogle Scholar
  74. Yamazaki, H., A. Tomono, Y. Ohnishi, and S. Horinouchi. 2004. DNA-binding specificity of AdpA, a transcriptional activator in the A-factor regulatory cascade in Streptomyces griseus. Mol. Microbiol. 53, 555–572.PubMedCrossRefGoogle Scholar

Copyright information

© The Microbiological Society of Korea 2008

Authors and Affiliations

  1. 1.Department of Molecular MicrobiologyJohn Innes CentreNorwichUK

Personalised recommendations