Skip to main content
Log in

Genome engineering in actinomycetes using site-specific recombinases

  • Mini-Review
  • Published:
Applied Microbiology and Biotechnology Aims and scope Submit manuscript

Abstract

The rational modification of the actinomycetes genomes has a variety of applications in research, medicine, and biotechnology. The use of site-specific recombinases allows generation of multiple mutations, large DNA deletions, integrations, and inversions and may lead to significant progress in all of these fields. Despite their huge potential, site-specific recombinase-based technologies have primarily been used for simple marker removal from a chromosome. In this review, we summarise the site-specific recombination approaches for genome engineering in various actinomycetes.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Fig. 1

Similar content being viewed by others

References

  • Alexander DC, Devlin DJ, Hewitt DD, Horan AC, Hosted TJ (2003) Development of the Micromonospora carbonacea var. africana ATCC 39149 bacteriophage pMLP1 integrase for site-specific integration in Micromonospora spp. Microbiology 149:2443–2453

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Anné J, Wohlleben W, Burkardt HJ, Springer R, Pühler A (1984) Morphological and molecular characterisation of several actinophages isolated from soil which lyse Streptomyces cattleya or Streptomyces venezuelae. J Gen Microbiol 130:2639–2649

    Google Scholar 

  • Baltz RH (1998) Genetic manipulation of antibiotic-producing Streptomyces. Trends Microbiol 6:76–83

    Article  CAS  Google Scholar 

  • Baltz RH (2012) Streptomyces temperate bacteriophage integration systems for stable genetic engineering of actinomycetes (and other organisms). J Ind Microbiol Biotechnol 39:661–672

    Article  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Boccard F, Smokvina T, Pernodet JL, Friedmann A, Guérineau M (1989a) Structural analysis of loci involved in pSAM2 site-specific integration in Streptomyces. Plasmid 21:59–70

    Article  CAS  Google Scholar 

  • Boccard F, Smokvina T, Pernodet JL, Friedmann A, Guérineau M (1989b) The integrated conjugative plasmid pSAM2 of Streptomyces ambofaciens is related to temperate bacteriophages. EMBO J 8:973–980

    CAS  Google Scholar 

  • Branda CS, Dymecki SM (2004) Talking about a revolution: the impact of site-specific recombinases on genetic analyses in mice. Dev Cell 6:7–28

    Article  CAS  Google Scholar 

  • Butler AR, Bate N, Kiehl DE, Kirst HA, Cundliffe E (2002) Genetic engineering of aminodeoxyhexose biosynthesis in Streptomyces fradiae. Nat Biotechnol 20:713–716

    Article  CAS  Google Scholar 

  • Chater KF, Carter AT (1979) A new, broad host-range, temperate bacteriophage (R4) of Streptomyces and its interaction with some restriction-modification systems. J Gen Microbiol 115:431–442

    Article  Google Scholar 

  • Chen L, Woo SL (2005) Complete and persistent phenotypic correction of phenylketonuria in mice by site-specific genome integration of murine phenylalanine hydroxylase cDNA. Proc Natl Acad Sci USA 102:15581–15586

    Article  CAS  Google Scholar 

  • Chen L, Woo SL (2008) Site-specific transgene integration in the human genome catalyzed by phiBT1 phage integrase. Hum Gene Ther 19:143–151

    Article  CAS  Google Scholar 

  • Chompoosri J, Fraser T, Rongsriyam Y, Komalamisra N, Siriyasatien P, Thavara U, Tawatsin A, Fraser MJ Jr (2009) Intramolecular integration assay validates integrase phiC31 and R4 potential in a variety of insect cells. Southeast Asian J Trop Med Public Health 40:1235–1253

    CAS  Google Scholar 

  • Combes P, Till R, Bee S, Smith MC (2002) The streptomyces genome contains multiple pseudo-attB sites for the (phi)C31-encoded site-specific recombination system. J Bacteriol 184:5746–5752

    Article  CAS  Google Scholar 

  • Dangel V, Westrich L, Smith MC, Heide L, Gust B (2010) Use of an inducible promoter for antibiotic production in a heterologous host. Appl Microbiol Biotechnol 87:261–269

    Article  CAS  Google Scholar 

  • Enríquez LL, Mendes MV, Antón N, Tunca S, Guerra SM, Martín JF, Aparicio JF (2006) An efficient gene transfer system for the pimaricin producer Streptomyces natalensis. FEMS Microbiol Lett 257:312–318

    Article  Google Scholar 

  • Eustaquio AS, Gust B, Galm U, Li SM, Chater KF, Heide L (2005) Heterologous expression of novobiocin and clorobiocin biosynthetic gene clusters. Appl Environ Microbiol 71:2452–2459

    Article  CAS  Google Scholar 

  • Farkašovská J, Godány A (2012) Analysis of the site-specific integration system of the Streptomyces aureofaciens phage μ1/6. Curr Microbiol 64:226–233

    Article  Google Scholar 

  • Farkasovská J, Klucar L, Vlcek C, Kokavec J, Godány A (2007) Complete genome sequence and analysis of the Streptomyces aureofaciens phage mu1/6. Folia Microbiol 52:347–358

    Article  Google Scholar 

  • Fedoryshyn M, Petzke L, Welle E, Bechthold A, Luzhetskyy A (2008a) Marker removal from actinomycetes genome using FLP recombinase. Gene 419:43–47

    Article  CAS  Google Scholar 

  • Fedoryshyn M, Welle E, Bechthold A, Luzhetskyy A (2008b) Functional expression of the Cre recombinase in actinomycetes. Appl Microbiol Biotechnol 78:1065–1070

    Article  CAS  Google Scholar 

  • 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 A(1), clorobiocin and caprazamycins in genetically modified Streptomyces coelicolor strains. Biopolymers 93:823–832

    Article  CAS  Google Scholar 

  • Galm U, Wang L, Wendt-Pienkowski E, Yang R, Liu W, Tao M, Coughlin JM, Shen B (2008) In vivo manipulation of the bleomycin biosynthetic gene cluster in Streptomyces verticillus ATCC15003 revealing new insights into its biosynthetic pathway. J Biol Chem 283:28236–28245

    Article  CAS  Google Scholar 

  • Gregory MA, Till R, Smith MC (2003) Integration site for Streptomyces phage phiBT1 and development of site-specific integrating vectors. J Bacteriol 185:5320–5323

    Article  CAS  Google Scholar 

  • Groth AC, Olivares EC, Thyagarajan B, Calos MP (2000) A phage integrase directs efficient site-specific integration in human cells. Proc Natl Acad Sci USA 97:5995–6000

    Article  CAS  Google Scholar 

  • Ha HS, Hwang YI, Choi SU (2008) Application of conjugation using phiC31 att/int system for Actinoplanes teichomyceticus, a producer of teicoplanin. Biotechnol Lett 30:1233–1238

    Article  CAS  Google Scholar 

  • Herrmann S, Siegl T, Luzhetska M, Petzke L, Jilg C, Welle E, Erb A, Leadlay PF, Bechthold A, Luzhetskyy A (2012) Site-specific recombinase strategies for engineering actinomycetes genome. Appl Environ Microbiol 78:1804–1812

    Article  CAS  Google Scholar 

  • Horbal L, Zaburannyy N, Ostash B, Shulga S, Fedorenko V (2012) Manipulating the regulatory genes for teicoplanin production in Actinoplanes teichomyceticus. World J Microbiol Biotechnol 28:2095–2100

    Article  CAS  Google Scholar 

  • Ichinose K, Taguchi T, Bedford DJ, Ebizuka Y, Hopwood DA (2001) Functional complementation of pyran ring formation in actinorhodin biosynthesis in Streptomyces coelicolor A3(2) by ketoreductase genes for granaticin biosynthesis. J Bacteriol 183:3247–3250

    Article  CAS  Google Scholar 

  • Jewett MC, Forster AC (2010) Update on disigning and building minimal cells. Curr Opin Biotechnol 21:697–703

    Article  CAS  Google Scholar 

  • Jiang J, Tetzlaff CN, Takamatsu S, Iwatsuki M, Komatsu M, Ikeda H, Cane DE (2009) Genome mining in Streptomyces avermitilis: a biochemical Baeyer–Villiger reaction and discovery of a new branch of the pentalenolactone family tree. Biochemistry 48:6431–6440

    Article  CAS  Google Scholar 

  • Khodakaramian G, Lissenden S, Gust B, Moir L, Hoskisson PA, Chater KF, Smith MC (2006) Expression of Cre recombinase during transient phage infection permits efficient marker removal in Streptomyces. Nucleic Acids Res 34:e20

    Article  Google Scholar 

  • Kim MK, Ha HS, Choi SU (2008) Conjugal transfer using the bacteriophage phiC31 att/int system and properties of the attB site in Streptomyces ambofaciens. Biotechnol Lett 30:695–699

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Kuhn R, Torres RM (2002) Cre/loxP recombination system and gene targeting. Methods Mol Biol 180:175–204

    CAS  Google Scholar 

  • Kuhstoss S, Rao RN (1991) Analysis of the integration function of the streptomycete bacteriophage phiC31. J Mol Biol 222:897–908

    Article  CAS  Google Scholar 

  • Kuhstoss S, Richardson MA, Rao RN (1989) Site-specific integration in Streptomyces ambofaciens: localization of integration functions in S. ambofaciens plasmid pSAM2. J Bacteriol 171:16–23

    CAS  Google Scholar 

  • Kuhstoss S, Richardson MA, Rao RN (1991) Plasmid cloning vectors that integrate site-specifically in Streptomyces spp. Gene 97:143–146

    Article  CAS  Google Scholar 

  • Leibig M, Krismer B, Kolb M, Friede A, Götz F, Bertram R (2008) Marker removal in staphylococci via Cre recombinase and different lox sites. Appl Environ Microbiol 74:1316–1323

    Article  CAS  Google Scholar 

  • Li X, Zhou X, Deng Z (2003) Vector systems allowing efficient autonomous or integrative gene cloning in Micromonospora sp. strain 40027. Appl Environ Microbiol 69:3144–3151

    Article  CAS  Google Scholar 

  • Liao G, Li J, Li L, Yang H, Tian Y, Tan H (2010) Cloning, reassembling and integration of the entire nikkomycin biosynthetic gene cluster into Streptomyces ansochromogenes lead to an improved nikkomycin production. Microb Cell Fact 9:6

    Article  Google Scholar 

  • Liu H, Jiang H, Haltli B, Kulowski K, Muszynska E, Feng X, Summers M, Young M, Graziani E, Koehn F, Carter GT, He M (2009) Rapid cloning and heterologous expression of the meridamycin biosynthetic gene cluster using a versatile Escherichia coli-streptomyces artificial chromosome vector, pSBAC. J Nat Prod 72:389–395

    Article  CAS  Google Scholar 

  • Liu G, Ou HY, Wang T, Li L, Tan H, Zhou X, Rajakumar K, Deng Z, He X (2010) Cleavage of phosphorothioated DNA and methylated DNA by the type IV restriction endonuclease ScoMcrA. PLoS Genet 6:e1001253

    Article  CAS  Google Scholar 

  • Lomovskaya ND, Emeljanova LK, Alikhanian SI (1971) The genetic location of the prophage on Streptomyces coelicolor A3(2) chromosome. Genetics 68:341–347

    CAS  Google Scholar 

  • Luzhetskiĭ AN, Ostash BE, Fedorenko VA (2001) Interspecies conjugation of Escherichia coliStreptomyces globisporus 1912 using integrative plasmid pSET152 and its derivatives. Genetika 37:1340–1347

    Google Scholar 

  • Luzhetskyy A, Mayer A, Hoffmann J, Pelzer S, Holzenkämper M, Schmitt B, Wohlert SE, Vente A, Bechthold A (2007) Cloning and heterologous expression of the aranciamycin biosynthetic gene cluster revealed a new flexible glycosyltransferase. ChemBioChem 8:599–602

    Article  CAS  Google Scholar 

  • Marx CJ, Lidstrom ME (2002) Broad-host-range cre-lox system for antibiotic marker recycling in gram-negative bacteria. Biotechniques 33:1062–1067

    CAS  Google Scholar 

  • Matsuura M, Noguchi T, Yamaguchi D, Aida T, Asayama M, Takahashi H, Shirai M (1996) The sre gene (ORF469) encodes a site-specific recombinase responsible for integration of the R4 phage genome. J Bacteriol 178:3374–3376

    CAS  Google Scholar 

  • Miura T, Hosaka Y, Yan-Zhuo Y, Nishizawa T, Asayama M, Takahashi H, Shirai M (2011) In vivo and in vitro characterization of site-specific recombination of actinophage R4 integrase. J Gen Appl Microbiol 57:45–57

    Article  CAS  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Morita K, Yamamoto T, Fusada N, Komatsu M, Ikeda H, Hirano N, Takahashi H (2009b) In vitro characterization of the site-specific recombination system based on actinophage TG1 integrase. Mol Genet Genomics 282:607–616

    Article  CAS  Google Scholar 

  • Morita K, Morimura K, Fusada N, Komatsu M, Ikeda H, Hirano N, Takahashi H (2012) Site-specific genome integration in alphaproteobacteria mediated by TG1 integrase. Appl Microbiol Biotechnol 93:295–304

    Article  Google Scholar 

  • Myronovskyy M, Ostash B, Ostash I, Fedorenko V (2009) A gene cloning system for the siomycin producer Streptomyces producer Streptomyces sioyaensis NRRL-B5408. Folia Microbiol 54:91–96

    Article  CAS  Google Scholar 

  • Novakova R, Kutas P, Feckova L, Kormanec J (2010) The role of the TetR-family transcriptional regulator Aur1R in negative regulation of the auricin gene cluster in Streptomyces aureofaciens CCM 3239. Microbiology 156:2374–2383

    Article  CAS  Google Scholar 

  • Olivares EC, Hollis RP, Calos MP (2001) Phage R4 integrase mediates site-specific integration in human cells. Gene 278:167–176

    Article  CAS  Google Scholar 

  • Ostash B, Saghatelian A, Walker S (2007) A streamlined metabolic pathway for the biosynthesis of moenomycin A. Chem Biol 14:257–267

    Article  CAS  Google Scholar 

  • Ostash B, Makitrinskyy R, Walker S, Fedorenko V (2009) Identification and characterization of Streptomyces ghanaensis ATCC14672 integration sites for three actinophage-based plasmids. Plasmid 61:171–175

    Article  CAS  Google Scholar 

  • Paranthaman S, Dharmalingam K (2003) Intergeneric conjugation in Streptomyces peucetius and Streptomyces sp. strain C5: chromosomal integration and expression of recombinant plasmids carrying the chiC gene. Appl Environ Microbiol 69:84–91

    Article  CAS  Google Scholar 

  • Penn J, Li X, Whiting A, Latif M, Gibson T, Silva CJ, Brian P, Davies J, Miao V, Wrigley SK, Baltz RH (2006) Heterologous production of daptomycin in Streptomyces lividans. J Ind Microbiol Biotechnol 33:121–128

    Article  CAS  Google Scholar 

  • Rajeev L, Malanowska K, Gardner JF (2009) Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions. Microbiol Mol Biol Rev 73:300–309

    Article  CAS  Google Scholar 

  • Raynal A, Tuphile K, Gerbaud C, Luther T, Guérineau M, Pernodet JL (1998) Structure of the chromosomal insertion site for pSAM2: functional analysis in Escherichia coli. Mol Microbiol 28:333–342

    Article  CAS  Google Scholar 

  • Raynal A, Friedmann A, Tuphile K, Guerineau M, Pernodet JL (2002) Characterisation of the attP site of the integrative element pSAM2 from Streptomyces ambofaciens. Microbiology 148:61–67

    CAS  Google Scholar 

  • Raynal A, Karray F, Tuphile K, Darbon-Rongère E, Pernodet JL (2006) Excisable cassettes: new tools for functional analysis of Streptomyces genomes. Appl Environ Microbiol 72:4839–4844

    Article  CAS  Google Scholar 

  • 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  CAS  Google Scholar 

  • Sauer B, McDermott J (2004) DNA recombination with a heterospecific Cre homolog identified from comparison of the pac-c1 regions of P1-related phages. Nucleic Acids Res 32:6086–6095

    Article  CAS  Google Scholar 

  • Schweizer HP (2003) Applications of the Saccharomyces cerevisiae Flp-FRT system in bacterial genetics. J Mol Microbiol Biotechnol 5:67–77

    Google Scholar 

  • Sekurova ON, Brautaset T, Sletta H, Borgos SE, Jakobsen MØM, Ellingsen TE, Strøm AR, Valla S, Zotchev SB (2004) In vivo analysis of the regulatory genes in the nystatin biosynthetic gene cluster of Streptomyces noursei ATCC 11455 reveals their differential control over antibiotic biosynthesis. J Bacteriol 186:1345–1354

    Article  CAS  Google Scholar 

  • Seoane A, Navas J, García Lobo JM (1997) Targets for pSAM2 integrase mediated site-specific integration in the Mycobacterium smegmatis chromosome. Microbiology 143:3375–3380

    Article  CAS  Google Scholar 

  • Sezonov G, Duchêne AM, Friedmann A, Guérineau M, Pernodet JL (1998) Replicase, excisionase, and integrase genes of the Streptomyces element pSAM2 constitute an operon positively regulated by the pra gene. J Bacteriol 180:3056–3061

    CAS  Google Scholar 

  • Smith MC, Till R, Smith MC (2004) Switching the polarity of a bacteriophage integration system. Mol Microbiol 51:1719–1728

    Article  CAS  Google Scholar 

  • Smokvina T, Mazodier P, Boccard F, Thompson CJ, Guérineau M (1990) Construction of a series of pSAM2-based integrative vectors for use in actinomycetes. Gene 94:53–59

    Article  CAS  Google Scholar 

  • Stinchi S, Azimonti S, Donadio S, Sosio M (2003) A gene transfer system for the glycopeptide producer Nonomuraea sp. ATCC39727. FEMS Microbiol Lett 225:53–57

    Article  CAS  Google Scholar 

  • Suzuki N, Tsuge Y, Inui M, Yukawa H (2005) Cre/loxP-mediated deletion system for large genome rearrangements in Corynebacterium glutamicum. Appl Microbiol Biotechnol 67:225–233

    Article  CAS  Google Scholar 

  • Thomason LC, Calendar R, Ow DW (2001) Gene insertion replacement in Schizosaccharomyces pombe mediated by Streptomyces bacteriophage phiC31 site-specific recombination system. Mol Genet Genomics 265:1031–1038

    Article  CAS  Google Scholar 

  • Thorpe HM, Smith MC (1998) In vitro site-specific integration of bacteriophage DNA catalyzed by a recombinases of the resolvase/invertase family. Proc Natl Acad Sci USA 95:5505–5510

    Article  CAS  Google Scholar 

  • Van Mellaert L, Mei L, Lammertyn E, Schacht S, Anné J (1998) Site-specific integration of bacteriophage VWB genome into Streptomyces venezuelae and construction of a VWB-based integrative vector. Microbiology 144:3351–3358

    Article  Google Scholar 

  • Voeykova T, Emelyanova L, Tabakov V, Mkrtumyan N (1998) Transfer of plasmid pTO1 from Escherichia coli to various representatives of the order Actinomycetales by intergeneric conjugation. FEMS Microbiol Lett 162:47–52

    Article  CAS  Google Scholar 

  • Wang SB, Cantlay S, Nordberg N, Letek M, Gil JA, Flärdh K (2009) Domains involved in the in vivo function and oligomerization of apical growth determinant DivIVA in Streptomyces coelicolor. FEMS Microbiol Lett 297:101–109

    Article  CAS  Google Scholar 

  • Zelyas N, Tahlan K, Jensen SE (2009) Use of the native flp gene to generate in-frame unmarked mutations in Streptomyces spp. Gene 443:48–54

    Article  CAS  Google Scholar 

  • Zhang L, Ou X, Zhao G, Ding X (2008) Highly efficient in vitro site-specific recombination system based on streptomyces phage phiBT1 integrase. J Bacteriol 190:6392–6397

    Article  CAS  Google Scholar 

  • Zhang L, Wang L, Wang J, Ou X, Zhao G, Ding X (2010) DNA cleavage is independent of synapsis during Streptomyces phage phiBT1 integrase-mediated site-specific recombination. J Mol Cell Biol 2:264–275

    Article  CAS  Google Scholar 

  • Zhang L, Zhao G, Ding X (2011) Tandem assembly of the epothilone biosynthetic gene cluster by in vitro site-specific recombination. Sci Rep 1:141

    Google Scholar 

  • Zhao C, Huang T, Chen W, Deng Z (2010) Enhancement of the diversity of polyoxins by a thymine-7-hydroxylase homolog outside the polyoxin biosynthesis gene cluster. Appl Environ Microbiol 76:7343–7347

    Article  CAS  Google Scholar 

  • Zhou X, Wu H, Li Z, Zhou X, Bai L, Deng Z (2011) Over-expression of UDP-glucose pyrophosphorlyase increases validamycin A but decreases validoxylamine A production in Streptomyces hagroscopicus var. jinggangensis 5008. Metab Eng 13:768–776

    Article  CAS  Google Scholar 

Download references

Acknowledgments

The work in the laboratory of AL was supported by the BMBF (GenBioCom), DFG (Lu1524/2-1) and ERC (EXPLOGEN) grants.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Andriy Luzhetskyy.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Myronovskyi, M., Luzhetskyy, A. Genome engineering in actinomycetes using site-specific recombinases. Appl Microbiol Biotechnol 97, 4701–4712 (2013). https://doi.org/10.1007/s00253-013-4866-1

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00253-013-4866-1

Keywords

Navigation