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Strain improvement in actinomycetes in the postgenomic era

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Journal of Industrial Microbiology & Biotechnology

Abstract

With the recent advances in DNA sequencing technologies, it is now feasible to sequence multiple actinomycete genomes rapidly and inexpensively. An important observation that emerged from early Streptomyces genome sequencing projects was that each strain contains genes that encode 20 or more potential secondary metabolites, only a fraction of which are expressed during fermentation. More recently, this observation has been extended to many other actinomycetes with large genomes. The discovery of a wealth of orphan or cryptic secondary metabolite biosynthetic gene clusters has suggested that sequencing large numbers of actinomycete genomes may provide the starting materials for a productive new approach to discover novel secondary metabolites. The key issue for this approach to be successful is to find ways to turn on or turn up the expression of cryptic or poorly expressed pathways to provide material for structure elucidation and biological testing. In this review, I discuss several genetic approaches that are potentially applicable to many actinomycetes for this application.

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References

  1. Alexander DC, Rock J, He X, Miao V, Brian P, Baltz RH (2010) Development of genetic system for lipopeptide combinatorial biosynthesis in Streptomyces fradiae and heterologous expression of the A54145 biosynthetic gene cluster. Appl Environ Microbiol 76:6877–6887

    Article  PubMed  CAS  Google Scholar 

  2. Baltz RH (1986) Mutagenesis in Streptomyces. In: Demain AL, Soloman NA (eds) Manual of industrial microbiology and biotechnology. American Society for Microbiology, Washington, DC, pp 184–190

    Google Scholar 

  3. Baltz RH (1995) Gene expression in recombinant Streptomyces. Bioprocess Technol 22:309–381

    PubMed  CAS  Google Scholar 

  4. Baltz RH (1997) Molecular genetic approaches to yield improvement in actinomycetes. Drug Pharmaceutical Sci 82:49–62

    CAS  Google Scholar 

  5. Baltz RH (1998) New genetic methods to improve secondary metabolite production in Streptomyces. J Ind Microbiol Biotechnol 20:360–363

    Article  CAS  Google Scholar 

  6. Baltz RH (2001) Genetic methods and strategies for secondary metabolite yield improvement in actinomycetes. Antonie Van Leeuwenhoek 79:251–259

    Article  PubMed  CAS  Google Scholar 

  7. Baltz RH (2008) Renaissance in antibacterial discovery from actinomycetes. Curr Opin Pharmacol 8:1–7

    Article  Google Scholar 

  8. Baltz RH (2009) Biosynthesis and genetic engineering of lipopeptides in Streptomyces roseosporus. Methods Enzymol 458:511–531

    Article  PubMed  CAS  Google Scholar 

  9. Baltz RH (2010) Streptomyces and Saccharopolyspora hosts for heterologous expression of secondary metabolite gene clusters. J Ind Microbiol Biotechnol 37:759–772

    Article  PubMed  CAS  Google Scholar 

  10. Baltz RH, Nguyen KT, Alexander DC (2010) Genetic engineering of acidic lipopeptide antibiotics. In: Baltz RH, Davies JE, Demain AL (eds) Manual of industrial microbiology and biotechnology. American Society for Microbiology, Washington DC, pp 391–410

    Google Scholar 

  11. Bate N, Stratigopoulos G, Cundliffe E (2002) Differential roles of two SARP-encoding regulatory genes during tylosin biosynthesis. Mol Microbiol 43:449–458

    Article  PubMed  CAS  Google Scholar 

  12. Bate N, Bignell DRD, Cundliffe E (2006) Regulation of tylosin biosynthesis involving ‘SARP-helper’ activity. Mol Microbiol 62:148–156

    Article  PubMed  CAS  Google Scholar 

  13. Beltrametti F, Rossi R, Selva E, Marinelli F (2006) Antibiotic production improvement in the rare actinomycete Planobispora rosea by selection of mutants resistant to the aminoglycosides streptomycein and gentamycin and to rifamycin. J Ind Microbiol Biotechnol 33:283–288

    Article  PubMed  CAS  Google Scholar 

  14. Bentley SD, Chater KF, Cerdeño-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 (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147

    Article  PubMed  Google Scholar 

  15. Bibb MJ (2005) Regulation of secondary metabolism in streptomycetes. Curr Opin Microbiol 8:208–215

    Article  PubMed  CAS  Google Scholar 

  16. Bibb MJ, Hesketh A (2009) Analyzing the regulation of antibiotic production in streptomycetes. Methods Enzymol 458:93–116

    Article  PubMed  CAS  Google Scholar 

  17. Bierman M, Logan R, O’Brien K, Seno ET, Rao RN, Schoner BE (1992) Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp. Gene 116:43–49

    Article  PubMed  CAS  Google Scholar 

  18. Bignell DRD, Bate N, Cundliffe E (2007) Regulation of tylosin production: role of a TylP-interactive ligand. Mol Microbiol 63:838–847

    Article  PubMed  CAS  Google Scholar 

  19. Challis GL (2008) Mining microbial genomes for new natural products and biosynthetic pathways. Microbiology 154:1555–1569

    Article  PubMed  CAS  Google Scholar 

  20. Chen Y, Wendt-Pienkowski E, Shen B (2008) Identification and utility of FdmR1 as a Streptomyces antibiotic regulatory protein activator for fredericamycin production in Streptomyces griseus ATCC 49344 and heterologous hosts. J Bacteriol 190:5587–5596

    Article  PubMed  CAS  Google Scholar 

  21. Chen Y, Smanski MJ, Shen B (2010) Improvement of secondary metabolite production in Streptomyces by manipulating pathway regulation. Appl Microbiol Biotechnol 86:19–25

    Article  PubMed  CAS  Google Scholar 

  22. Chen X, Wei P, Fan L, Yang D, Zhu X, Shen W, Xu Z, Cen P (2009) Generation of high-yield rapamycin-producing strains through protoplasts-related techniques. Appl Microbiol Biotechnol 83:507–512

    Article  PubMed  CAS  Google Scholar 

  23. Corre C, Challis GL (2009) New natural product biosynthetic chemistry discovered by genome mining. Nat Prod Rep 26:977–986

    Article  PubMed  CAS  Google Scholar 

  24. Cundliffe E (2008) Control of tylosin biosynthesis in Streptomyces fradiae. J Microbiol Biotechnol 18:1485–1491

    PubMed  CAS  Google Scholar 

  25. Feng Z, Wang L, Rajski SR, Xu Z, Coëffet-LeGal MF, Shen B (2009) Engineered production of iso-migrastatin in heterologous Streptomyce hosts. Bioorg Med Chem 17:2147–2153

    Article  PubMed  CAS  Google Scholar 

  26. Flinspach K, Westrich L, Kaysser L, Siebenberg S, Gomez-Escribano JP, Bibb M, Gust B, Heide L (2010) Heterologous expression of the biosynthetic gene clusters of coumermycin A1, clorobiocin and caprazamycins in genetically modified Streptomyces coelicolor strains. Biopolymers 93:823–832

    Article  PubMed  CAS  Google Scholar 

  27. Foor F, Roberts GP, Morin N, Snyder L, Hwang M, Gibbons PH, Paradisio MJ, Stotish RL, Ruby CL, Wolanski B, Streiker SL (1985) Isolation and characterization of the Streptomyces cattleya temperate phage TG1. Gene 39:11–16

    Article  PubMed  CAS  Google Scholar 

  28. Gomez-Escribano JP, Bibb MJ (2011) Engineering Streptomyces coelicolor for heterologous expression of secondary metabolite gene clusters. Microb Biotechnol (in press)

  29. Gottelt M, Kol S, Gomez-Escribano JP, Bibb M, Takano E (2010) Deletion of a regulatory gene within the cpk gene cluster reveals novel antibacterial activity in Streptomyces coelicolor A3(2). Microbiology 156:2343–2353

    Article  PubMed  CAS  Google Scholar 

  30. Gregory MA, Till R, Smith MCM (2003) Integration site for Streptomyces phage ϕBT1 and development of site-specific integrating vectors. J Bacteriol 185:5320–5323

    Article  PubMed  CAS  Google Scholar 

  31. Gross H (2009) Genomic-mining—a concept for the discovery of new bioactive natural products. Curr Opin Drug Discov Devel 12:207–219

    PubMed  CAS  Google Scholar 

  32. Hosada T, Xu J, Ochi K (2006) Increased expression of ribosome recycling factor is responsible for the enhanced protein synthesis during the late growth phase in an antibiotic-overproducing Streptomyces coelicolor ribosomal rpsL mutant. Mol Microbiol 61:883–897

    Article  Google Scholar 

  33. Hosada T, Ohnishi-Kameyama M, Muramatsu H, Murakami K, Tsurumi Y, Kodani S, Yoshida M, Fujie A, Ochi K (2009) Antibacterial discovery in actinomycetes strains with mutations in RNA polymerase or ribosomal protein S12. Nat Biotechnol 27:462–464

    Article  Google Scholar 

  34. Hu H, Ochi K (2001) Novel approach for improving the productivity of antibiotic-producing strains by inducing combined resistance mutations. Appl Environ Microbiol 67:1885–1892

    Article  PubMed  CAS  Google Scholar 

  35. Hu H, Zhang Q, Ochi K (2002) Activation of antibiotic biosynthesis by specified mutations in the rpoB gene (encoding the RNA polymerase β subunit) of Streptomyces lividans. J Bacteriol 184:3984–3991

    Article  PubMed  CAS  Google Scholar 

  36. Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Ōmura S (2003) Complete genome sequence of and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21:526–531

    Article  PubMed  Google Scholar 

  37. Ishikawa J, Chiba K, Kurita H, Satoh H (2006) Contribution of rpoB2 RNA polymerase subunit gene to rifampin resistance in Nocardia species. Antimicrob Agents Chemother 50:1342–1346

    Article  PubMed  CAS  Google Scholar 

  38. Komatsu M, Uchiyama T, Ōmura S, Cane D, Ikeda H (2010) Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci USA 107:2646–2651

    Article  PubMed  CAS  Google Scholar 

  39. Kustoss S, Rao RN (1991) Analysis of the integration function of the streptomycete bacteriophage ϕC31. J Mol Biol 222:897–908

    Article  Google Scholar 

  40. Lai C, Xu J, Tozawa Y, Okamoto-Hosoya Y, Yao X, Ochi K (2002) Genetic and physiological characterization of rpoB mutations that activate antibiotic production in Streptomyces lividans. Microbiology 148:3365–3373

    PubMed  CAS  Google Scholar 

  41. Li C, Hazzard C, Florova G, Reynolds KA (2009) High titer expression of tetracenomycins by heterologous expression of the pathway in a Streptomyces cinnamonensis industrial monensin producer strain. Metab Eng 11:319–327

    Article  PubMed  CAS  Google Scholar 

  42. Li L, Guo J, Wen Y, Chen Z, Song Y, Li J (2010) Overproduction of ribosome recycling factor causes increased production of avermectin in Streptomyces avermitilis strains. J Ind Microbiol Biotechnol 37:673–679

    Article  PubMed  CAS  Google Scholar 

  43. Lombo F, Velasco A, Castro A, de la Calle F, Brana AF, Sanchez-Puelles JM, Mendez C, Salas JA (2006) Deciphering the biosynthesis pathway of the antitumor thiocoraline from a marine actinomycete and its expression in two Streptomyces species. ChemBioChem 7:366–376

    Article  PubMed  CAS  Google Scholar 

  44. Makitrynskyy R, Rebets Y, Ostach B, Zaburannyi N, Rabyk M, Walker S, Federenko V (2010) Genetic factors that influence moenomycin production in streptomycetes. J Ind Microbiol Biotechnol 37:559–566

    Article  PubMed  CAS  Google Scholar 

  45. Matsushima P, Baltz RH (1986) Protoplast fusion. In: Demain AL, Soloman NA (eds) Manual of industrial microbiology and biotechnology. American Society for Microbiology, Washington, DC, pp 170–183

    Google Scholar 

  46. Morita K, Yamamoto T, Fusada N, Komatsu M, Ikeda H, Hirano N, Takahashi H (2009) The site-specific recombination system of actinophage TG1. FEMS Microbiol Lett 297:234–240

    Article  PubMed  CAS  Google Scholar 

  47. Nett M, Ikeda H, Moore BS (2009) Genomic basis for natural product biosynthetic diversity in the actinomycetes. Nat Prod Rep 26:1362–1384

    Article  PubMed  CAS  Google Scholar 

  48. Nguyen K, Ritz D, Gu J-Q, Alexander D, Chu M, Miao V, Brian P, Baltz RH (2006) Combinatorial biosynthesis of lipopeptide antibiotics related to daptomycin. Proc Natl Acad Sci USA 103:17462–17467

    Article  PubMed  CAS  Google Scholar 

  49. Ochi K (2007) From microbial differentiation to ribosome engineering. Biosci Biotechnol Biochem 71:1373–1386

    Article  PubMed  CAS  Google Scholar 

  50. Ohnishi Y, Ishikawa J, Hara H, Suzuki H, Ikenoya M, Ikeda H, Yamashita A, Hattori M, Horinouchi S (2008) Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350. J Bacteriol 190:4050–4060

    Article  PubMed  CAS  Google Scholar 

  51. Olano C, Lombó F, Mendéz C, Salas JA (2008) Improving production of bioactive secondary metabolites in actinomycetes by metabolic engineering. Metab Eng 10:281–292

    Article  PubMed  CAS  Google Scholar 

  52. Oliynyk M, Samborskyy M, Lester JB, Mironenko T, Scott N, Dickens S, Haydock SF, Leadlay PF (2007) Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338. Nat Biotechnol 25:447–453

    Article  PubMed  CAS  Google Scholar 

  53. Peschke U, Schmidt H, Zhang HZ, Piepersberg W (1995) Molecular characterization of the lincolmycin-production gene cluster of Streptomyces lincolnensis 78-11. Mol Microbiol 16:1137–1156

    Article  PubMed  CAS  Google Scholar 

  54. Petković H, Cullum J, Hranueli D, Hunter IS, Perić-Concha N, Pigac J, Thamchaipenet A, Vujaklija D, Long PF (2006) Genetics of Streptomyces rimosus, the oxytetracycline producer. Microbiol Mol Biol Rev 70:704–728

    Article  PubMed  Google Scholar 

  55. Reeves CD, Ward SL, Revill WP, Suzuki H, Marcus M, Petrakovsky OV, Marquez S, Fu H, Dong SD, Katz L (2004) Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts. Chem Biol 11:1465–1472

    Article  PubMed  CAS  Google Scholar 

  56. Rodriguez E, Hu Z, Ou S, Volchegursky Y, Hutchinson CR, McDaniel R (2003) Rapid engineering of polyketide overproduction by gene transfer to industrially optimized strains. J Ind Microbiol Biotechnol 30:480–488

    Article  PubMed  CAS  Google Scholar 

  57. Rodriguez E, Ward S, Fu H, Revill WP, McDaniel R, Katz L (2004) Engineered biosynthesis of 16-membered macrolides that require methoxymalonyl-ACP precursors in Streptomyces fradiae. Appl Microbiol Biotechnol 66:85–91

    Article  PubMed  CAS  Google Scholar 

  58. Shirai M, Nara H, Sato A, Aida T, Takahashi H (1991) Site-specific integration of the actinophage R4 genome into the chromosome of Streptomyces parvulus upon lysogenization. J Bacteriol 173:4237–4239

    PubMed  CAS  Google Scholar 

  59. Smanski MJ, Peterson RM, Rajski SR, Shen B (2009) Engineered Streptomyces platensis strains that overproduce antibiotics platensimycin and platencin. Antimicrob Agents Chemother 53:1299–1304

    Article  PubMed  CAS  Google Scholar 

  60. Smith MCM, Brown WRA, McEwan AR, Rowley PA (2010) Site-specific recombination by ϕC31 integrase and other serine recombinases. Biochem Soc Trans 38:388–394

    Article  PubMed  CAS  Google Scholar 

  61. Stratigopoulos G, Cundliffe E (2002) Expression analysis of the tylosin-biosynthetic gene cluster: pivotal regulation role of the tylQ product. Chem Biol 9:71–78

    Article  PubMed  CAS  Google Scholar 

  62. Stratigopoulos G, Cundliffe E (2002) Inactivation of a transcriptional repressor during empirical improvement of the tylosin producer, Streptomyces fradiae. J Ind Microbiol Biotechnol 28:219–224

    Article  PubMed  CAS  Google Scholar 

  63. Stratigopoulos G, Gandecha AR, Cundliffe E (2002) Regulation of tylosin production and morphological differentiation in Streptomyces fradiae by TylP, a deduced γ-butyrolactone receptor. Mol Microbiol 45:735–744

    Article  PubMed  CAS  Google Scholar 

  64. Stratigopoulos G, Bate N, Cundliffe E (2004) Positive control of tylosin biosynthesis: pivotal role of TylR. Mol Microbiol 54:1326–1334

    Article  PubMed  CAS  Google Scholar 

  65. Talà A, Wang G, Zemanova M, Okamoto S, Ochi K, Alifano P (2009) Activation of dormant bacterial genes by Nonomuraea sp. strain ATCC 39727 mutant-type RNA polymerase. J Bacteriol 191:805–814

    Article  PubMed  Google Scholar 

  66. Tamehiro N, Hosaka T, Xu J, Hu H, Otake N, Ochi K (2002) Innovative approach for improvement of as antibiotic-overproducing industrial strain of Streptomyces albus. Appl Environ Microbiol 69:6412–6417

    Article  Google Scholar 

  67. Tanaka Y, Komatsu M, Okamoto S, Tokuyama S, Kaji A, Ikeda H, Ochi K (2009) Antibiotic overproduction by rpsL and rsmG mutants of various actinomycetes. Appl Environ Microbiol 75:4919–4922

    Article  PubMed  CAS  Google Scholar 

  68. Udwary DW, Zeigler L, Asolkar RN, Singan V, Lapidus A, Fenical W, Jensen PR, Moore BS (2007) Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinospora tropica. Proc Natl Acad Sci USA 104:10376–10381

    Article  PubMed  CAS  Google Scholar 

  69. Vigliotti G, Tredici SM, Damiano F, Montinaro MR, Pulimeno R, di Summa R, Massardo DR, Gnoni GV, Alifano P (2005) Natural merodiploidy involving duplicated rpoB alleles affects secondary metabolism in a producer actinomycete. Mol Microbiol 55:396–412

    Article  Google Scholar 

  70. Wang G, Hosaka T, Ochi K (2008) Dramatic activation of antibiotic production in Streptomyces coelicolor by cumulative drug resistance mutations. Appl Environ Microbiol 74:2834–2840

    Article  PubMed  CAS  Google Scholar 

  71. Ward SL, Hu Z, Schirmer A, Reid R, Revill P, Reeves CD, Petrakowsky OV, Dong SD, Katz L (2004) Chalcomycin biosynthesis gene cluster from Streptomyces bikiniensis: novel features of an unusual ketolide produced through expression of the chm polyketide synthase in Streptomyces fradiae. Antimicrob Agents Chemother 8:4703–4712

    Article  Google Scholar 

  72. Xu B, Jin Z, Wang H, Jin Q, Jin X, Cen P (2008) Evolution of Streptomyces pristinaespiralis for resistance and production of pristinamycin by genome shuffling. Appl Microbiol Biotechnol 80:261–267

    Article  PubMed  CAS  Google Scholar 

  73. Xu J, Tozawa Y, Lai C, Hayashi H, Ochi K (2002) A rifampin resistant mutation in the rpoB gene confers ppGpp-independent antibiotic production in Streptomyces coelicolor A3(2). Mol Gen Genet 268:179–189

    CAS  Google Scholar 

  74. Yanai K, Murakami T, Bibb MJ (2006) Amplification of the entire kanamycin biosynthetic gene cluster during empirical strain improvement. Proc Natl Acad Sci USA 103:9661–9666

    Article  PubMed  CAS  Google Scholar 

  75. Zhang Y-X, Perry K, Vinci VA, Powell K, Stemmer WPC, del Cardayré SB (2002) Genome shuffling leads to rapid phenotypic improvement on bacteria. Nature 415:644–646

    Article  PubMed  CAS  Google Scholar 

  76. Zhao W, Zhong Y, Yuan H, Wang J, Zheng H, Wang Y, Cen X, Xu F, Bai J, Han X, Lu G, Zhu Y, Shao Z, Yan H, Li C, Peng N, Zhang Z, Zhang Y, Lin W, Fan Y, Qin Z, Hu Y, Zhu B, Wang S, Ding X, Zhao GP (2010) Complete genome sequence of the rifamycin SV-producing Amycolatopsis mediterranei U32 revealed its genetic characteristics in phylogeny and metabolism. Cell Res 20:1096–1108

    Article  PubMed  CAS  Google Scholar 

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    Richard H. Baltz

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Baltz, R.H. Strain improvement in actinomycetes in the postgenomic era. J Ind Microbiol Biotechnol 38, 657–666 (2011). https://doi.org/10.1007/s10295-010-0934-z

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