Skip to main content
SpringerLink
Log in

Recombineering-Mediated Genome Editing in Burkholderiales Strains

  • Protocol
  • First Online:
Recombineering

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2479))

Abstract

Red/ET recombineering is primarily mediated by the E. coli recombinase pair Redα/Redβ from λ phage or RecE/RecT from Rac prophage, which is applied in E. coli and also closely related Gram-negative bacteria for efficient genome editing. However, some distant bacterial species like Burkholderiales strains require host-specific Redα/Redβ recombinase pair for highly efficient genome editing. A pair of recombinases Redαβ7029 from the Burkholderiales strain DSM 7029, recently identified as Schlegelella brevitalea, were identified for efficient genetic manipulation in the native strain and several other Burkholderiales strains. In this chapter, we describe a detailed protocol for genome engineering in Burkholderiales strains via the Redγ-Redαβ7029 recombineering and Cre/loxP site-specific recombination.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Protocol
USD 49.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 139.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Depoorter E, Bull MJ, Peeters C, Coenye T, Vandamme P, Mahenthiralingam E (2016) Burkholderia: an update on taxonomy and biotechnological potential as antibiotic producers. Appl Microbiol Biotechnol 100:5215–5229

    Article  CAS  Google Scholar 

  2. Zhang W, Du L, Qu Z, Zhang X, Li F, Li Z, Qi F, Wang X, Jiang Y, Men P, Sun J, Cao S, Geng C, Qi F, Wan X, Liu C, Li S (2019) Compartmentalized biosynthesis of mycophenolic acid. Proc Natl Acad Sci U S A 116:13305–13310

    Article  CAS  Google Scholar 

  3. Partida-Martinez LP, Groth I, Schmitt I, Richter W, Roth M, Hertweck C (2007) Burkholderia rhizoxinica sp. nov. and Burkholderia endofungorum sp. nov., bacterial endosymbionts of the plant-pathogenic fungus Rhizopus microsporus. Int J Syst Evol Microbiol 57:2583–2590

    Article  CAS  Google Scholar 

  4. Esmaeel Q, Pupin M, Kieu NP, Chataigne G, Bechet M, Deravel J, Krier F, Hofte M, Jacques P, Leclere V (2016) Burkholderia genome mining for nonribosomal peptide synthetases reveals a great potential for novel siderophores and lipopeptides synthesis. Microbiol Open 5:512–526

    Article  CAS  Google Scholar 

  5. Minowa Y, Araki M, Kanehisa M (2007) Comprehensive analysis of distinctive polyketide and nonribosomal peptide structural motifs encoded in microbial genomes. J Mol Biol 368:1500–1517

    Article  CAS  Google Scholar 

  6. Hidalgo-Cantabrana C, Goh YJ, Barrangou R (2019) Characterization and repurposing of type I and type II CRISPR-Cas systems in bacteria. J Mol Biol 431:21–33

    Article  CAS  Google Scholar 

  7. Quin MB, Flynn CM, Schmidt-Dannert C (2014) Traversing the fungal terpenome. Nat Prod Rep 31:1449–1473

    Article  CAS  Google Scholar 

  8. Zhang MQ, Gaisser S, Nur EAM, Sheehan LS, Vousden WA, Gaitatzis N, Peck G, Coates NJ, Moss SJ, Radzom M, Foster TA, Sheridan RM, Gregory MA, Roe SM, Prodromou C, Pearl L, Boyd SM, Wilkinson B, Martin CJ (2008) Optimizing natural products by biosynthetic engineering: discovery of nonquinone Hsp90 inhibitors. J Med Chem 51:5494–5497

    Article  CAS  Google Scholar 

  9. Zhang Y, Muyrers JP, Rientjes J, Stewart AF (2003) Phage annealing proteins promote oligonucleotide-directed mutagenesis in Escherichia coli and mouse ES cells. BMC Mol Biol 4:1

    Article  Google Scholar 

  10. Weber T, Charusanti P, Musiol-Kroll EM, Jiang X, Tong Y, Kim HU, Lee SY (2015) Metabolic engineering of antibiotic factories: new tools for antibiotic production in actinomycetes. Trends Biotechnol 33:15–26

    Article  CAS  Google Scholar 

  11. Bunny K, Liu J, Roth J (2002) Phenotypes of lexA mutations in Salmonella enterica: evidence for a lethal lexA null phenotype due to the Fels-2 prophage. J Bacteriol 184:6235–6249

    Article  CAS  Google Scholar 

  12. Wei D, Wang M, Shi J, Hao J (2012) Red recombinase assisted gene replacement in Klebsiella pneumoniae. J Ind Microbiol Biotechnol 39:1219–1226

    Article  CAS  Google Scholar 

  13. Baltz RH, Miao V, Wrigley SK (2005) Natural products to drugs: daptomycin and related lipopeptide antibiotics. Nat Prod Rep 22:717–741

    Article  CAS  Google Scholar 

  14. Fais T, Delmas J, Barnich N, Bonnet R, Dalmasso G (2018) Colibactin: more than a new bacterial toxin. Toxins 10:E151

    Article  Google Scholar 

  15. Wang ZJ, Zhou H, Zhong G, Huo L, Tang YJ, Zhang Y, Bian X (2020) Genome mining and biosynthesis of primary amine-acylated desferrioxamines in a marine gliding bacterium. Org Lett 22:939–943

    Article  CAS  Google Scholar 

  16. Knaggs AR (2003) The biosynthesis of shikimate metabolites. Nat Prod Rep 20:119–136

    Article  CAS  Google Scholar 

  17. Eichner S, Knobloch T, Floss HG, Fohrer J, Harmrolfs K, Hermane J, Schulz A, Sasse F, Spiteller P, Taft F, Kirschning A (2012) The interplay between mutasynthesis and semisynthesis: generation and evaluation of an ansamitocin library. Angew Chem 51:752–757

    Article  CAS  Google Scholar 

  18. Derbise A, Lesic B, Dacheux D, Ghigo JM, Carniel E (2003) A rapid and simple method for inactivating chromosomal genes in Yersinia. FEMS Immunol Med Microbiol 38:113–116

    Article  CAS  Google Scholar 

  19. van Kessel JC, Hatfull GF (2007) Recombineering in Mycobacterium tuberculosis. Nat Methods 4:147–152

    Article  Google Scholar 

  20. van Kessel JC, Hatfull GF (2008) Efficient point mutagenesis in mycobacteria using single-stranded DNA recombineering: characterization of antimycobacterial drug targets. Mol Microbiol 67:1094–1107

    Article  Google Scholar 

  21. van Pijkeren JP, Britton RA (2012) High efficiency recombineering in lactic acid bacteria. Nucleic Acids Res 40:e76

    Article  Google Scholar 

  22. Xin Y, Guo T, Mu Y, Kong J (2017) Identification and functional analysis of potential prophage-derived recombinases for genome editing in Lactobacillus casei. FEMS Microbiol Lett 364

    Google Scholar 

  23. Dong H, Tao W, Gong F, Li Y, Zhang Y (2014) A functional recT gene for recombineering of Clostridium. J Biotechnol 173:65–67

    Article  CAS  Google Scholar 

  24. Kang Y, Norris MH, Wilcox BA, Tuanyok A, Keim PS, Hoang TT (2011) Knockout and pullout recombineering for naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei. Nat Protoc 6:1085–1104

    Article  CAS  Google Scholar 

  25. Li JW, Vederas JC (2009) Drug discovery and natural products: end of an era or an endless frontier? Science 325:161–165

    Article  Google Scholar 

  26. Wang X, Zhou H, Chen H, Jing X, Zheng W, Li R, Sun T, Liu J, Fu J, Huo L, Li YZ, Shen Y, Ding X, Müller R, Bian X, Zhang Y (2018) Discovery of recombinases enables genome mining of cryptic biosynthetic gene clusters in Burkholderiales species. Proc Natl Acad Sci U S A 115:E4255–E4263

    CAS  PubMed  PubMed Central  Google Scholar 

  27. Zheng W, Wang X, Zhou H, Zhang Y, Li A, Bian X (2020) Establishment of recombineering genome editing system in Paraburkholderia megapolitana empowers activation of silent biosynthetic gene clusters. Microb Biotechnol 13:397–405

    Article  CAS  Google Scholar 

  28. Chen H, Zhou H, Sun T, Xu J, Tu Q, Yang J, Zhang Y, Bian X (2020) Identification of holrhizins E-Q reveals the diversity of nonribosomal lipopeptides in Paraburkholderia rhizoxinica. J Nat Prod 83:537–541

    Article  CAS  Google Scholar 

  29. Tang B, Yu Y, Zhang Y, Zhao G, Ding X (2015) Complete genome sequence of the glidobactin producing strain [Polyangium] brachysporum DSM 7029. J Biotechnol 210:83–84

    Article  CAS  Google Scholar 

  30. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Müller R, Stewart AF, Zhang Y (2012) Full-length RecE enhances linear-linear homologous recombination and facilitates direct cloning for bioprospecting. Nat Biotechnol 30:440–446

    Article  CAS  Google Scholar 

  31. Winn M, Fyans JK, Zhuo Y, Micklefield J (2016) Recent advances in engineering nonribosomal peptide assembly lines. Nat Prod Rep 33:317–347

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the National Key R&D Program of China (2017YFD0201400), the National Natural Science Foundation of China (31670098, 31670097), Shandong Provincial Natural Science Foundation (ZR2019JQ11), China Postdoctoral Science Foundation Grant (No.2019M652373), the Recruitment Program of Global Experts (1000 Plan), and the Qilu Youth Scholar Startup Funding of SDU.

Author information

Author notes

  1. Xue Wang and Jiaqi Liu contributed equally with all other contributors.

Authors and Affiliations

  1. Helmholtz International Lab for Anti-infectives, Shandong University-Helmholtz Institute of Biotechnology, State Key Laboratory of Microbial Technology, Shandong University, Qingdao, People’s Republic of China

    Xue Wang, Jiaqi Liu, Wentao Zheng, Youming Zhang & Xiaoying Bian

Authors
  1. Xue Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jiaqi Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Wentao Zheng
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Youming Zhang
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Xiaoying Bian
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Youming Zhang or Xiaoying Bian .

Editor information

Editors and Affiliations

  1. Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, USA

    Christopher R. Reisch

Rights and permissions

Reprints and permissions

Copyright information

© 2022 Springer Science+Business Media, LLC, part of Springer Nature

About this protocol

Check for updates. Verify currency and authenticity via CrossMark

Cite this protocol

Wang, X., Liu, J., Zheng, W., Zhang, Y., Bian, X. (2022). Recombineering-Mediated Genome Editing in Burkholderiales Strains. In: Reisch, C.R. (eds) Recombineering. Methods in Molecular Biology, vol 2479. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-2233-9_3

Download citation

  • DOI: https://doi.org/10.1007/978-1-0716-2233-9_3

  • Published:

  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-2232-2

  • Online ISBN: 978-1-0716-2233-9

  • eBook Packages: Springer Protocols

Publish with us

Policies and ethics

Search

Navigation