An improved method for oriT-directed cloning and functionalization of large bacterial genomic regions

Applied and Environmental Microbiology

Volumn 79, Issue 16, 2013, Pages 4869-4878

  Kvitko, Brian H ^a,b   McMillan, Ian A ^a,c   Schweizer, Herbert P ^a  

^a Department of Environmental and Radiological Health Sciences   (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

^c UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOSYNTHETIC GENE CLUSTER; BURKHOLDERIA PSEUDOMALLEI; FUNCTIONALIZATIONS; GENETIC ANALYSIS; HETEROLOGOUS EXPRESSION; NATURALLY OCCURRING; OPEN READING FRAME; SITE-SPECIFIC RECOMBINATION;

DNA; ESCHERICHIA COLI; GENES;

CLONING;

CHROMOSOME; CLONE; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; MICROBIAL COMMUNITY; PLASMID;

ARTICLE; BACTERIAL GENOME; BURKHOLDERIA PSEUDOMALLEI; DNA SEQUENCE; ESCHERICHIA COLI; EVALUATION; GENE VECTOR; GENETICS; GENOMICS; METABOLISM; METHODOLOGY; MOLECULAR CLONING; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; PLASMID; SEQUENCE HOMOLOGY;

BURKHOLDERIA PSEUDOMALLEI; CLONING, MOLECULAR; ESCHERICHIA COLI; GENETIC VECTORS; GENOME, BACTERIAL; GENOMICS; MOLECULAR SEQUENCE DATA; OPEN READING FRAMES; PLASMIDS; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY;

EID: 84881011340     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.00994-13     Document Type: Article

References (36)

1. Bian X, Huang F, Stewart FA, Xia L, Zhang Y, Muller R. 2012. Direct cloning, genetic engineering, and heterologous expression of the syringolin biosynthetic gene cluster in E. coli through Red/ET recombineering. Chembiochem 13:1946-1952.
2. Fu J, Bian X, Hu S, Wang H, Huang F, Seibert PM, Plaza A, Xia L, Muller R, Stewart AF, Zhang Y. 2012. Full-length RecE enhances linearlinear homologous recombination and facilitates direct cloning for bioprospecting. Nat. Biotechnol. 30:440-446.
3. Wargacki AJ, Leonard E, Win MN, Regitsky DD, Santos CN, Kim PB, Cooper SR, Raisner RM, Herman A, Sivitz AB, Lakshmanaswamy A, Kashiyama Y, Baker D, Yoshikuni Y. 2012. An engineered microbial platform for direct biofuel production frombrownmacroalgae. Science 335:308-313.
4. Tuanyok A, Leadem BR, Auerbach RK, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Mayo M, Wuthiekanun V, Brettin TS, Nierman WC, Peacock SJ, Currie BJ, Wagner DM, Keim P. 2008. Genomic islands from five strains of Burkholderia pseudomallei. BMC Genomics 9:566.
5. Chain PS, Hernandez-Lucas I, Golding B, Finan TM. 2000. oriTdirected cloning of defined large regions from bacterial genomes: identification of the Sinorhizobium meliloti pExo megaplasmid replicator region. J. Bacteriol. 182:5486-5494.
6. Noskov VN, Kouprina N, Leem SH, Ouspenski I, Barrett JC, Larionov V. 2003. A general cloning system to selectively isolate any eukaryotic or prokaryotic genomic region in yeast. BMC Genomics 4:16.
7. Zeng C, Kouprina N, Zhu B, Cairo A, Hoek M, Cross G, Osoegawa K, Larionov V, de Jong P. 2001. Large-insert BAC/YAC libraries for selective re-isolation of genomic regions by homologous recombination in yeast. Genomics 77:27-34.
8. Muyrers JP, Zhang Y, Stewart AF. 2001. Techniques: recombinogenic engineering-new options for cloning and manipulating DNA. Trends Biochem. Sci. 26:325-331.
9. Lee EC, Yu D, Martinez de Velasco J, Tessarollo L, Swing DA, Court DL, Jenkins NA, Copeland NG. 2001. A highly efficient Escherichia colibased chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA. Genomics 73:56-65.
10. Wild J, Hradecna Z, Posfai G, Szybalski W. 1996. A broad-host-range in vivo pop-out and amplification system for generating large quantities of 50-to 100-kb genomic fragments for direct DNA sequencing. Gene 179:181-188.
11. Lanka E, Wilkins BM. 1995. DNA processing reactions in bacterial conjugation. Annu. Rev. Biochem. 64:141-169.
12. Peters JE, Craig NL. 2001. Tn7: smarter than we thought. Nat. Rev. Mol. Cell Biol. 2:806-814.
13. Parks AR, Peters JE. 2007. Transposon Tn7 is widespread in diverse bacteria and forms genomic islands. J. Bacteriol. 189:2170-2173.
14. Parks AR, Peters JE. 2009. Tn7 elements: engendering diversity from chromosomes to episomes. Plasmid 61:1-14.
15. Cheng AC, Currie BJ. 2005. Melioidosis: epidemiology, pathophysiology, and management. Clin. Microbiol. Rev. 18:383-416.
16. Wiersinga WJ, van der Poll T, White NJ, Day NP, Peacock SJ. 2006. Melioidosis: insights into the pathogenicity of Burkholderia pseudomallei. Nat. Rev. Microbiol. 4:272-282.
17. Rotz LD, Khan AS, Lillibridge SR, OstroffSM, Hughes JM. 2002. Public health assessment of potential biological terrorism agents. Emerg. Infect. Dis. 8:225-230.
18. Dance DAB. 2005. Melioidosis and glanders as possible biological weapons, p 99-145. In Fong W, Alibek K (ed), Bioterrorism and infectious agents. A new dilemma for the 21st century. Springer Science and Business Media, New York, NY.
19. Holden MT, Titball RW, Peacock SJ, Cerdeno-Tarraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J. 2004. Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei. Proc. Natl. Acad. Sci. U. S. A. 101:14240-14245.
20. Sim SH, Yu Y, Lin CH, Karuturi RK, Wuthiekanun V, Tuanyok A, Chua HH, Ong C, Paramalingam SS, Tan G, Tang L, Lau G, Ooi EE, Woods D, Feil E, Peacock SJ, Tan P. 2008. The core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis. PLoS Pathog. 4:e1000178. doi:10.1371/journal.ppat.1000178.
21. Ou K, Ong C, Koh SY, Rodrigues F, Sim SH, Wong D, Ooi CH, Ng KC, Jikuya H, Yau CC, Soon SY, Kesuma D, Lee MA, Tan P. 2005. Integrative genomic, transcriptional, and proteomic diversity in natural isolates of the human pathogen Burkholderia pseudomallei. J. Bacteriol. 187:4276-4285.
22. Sambrook J, Russell DW. 2001. Molecular cloning, a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
23. Choi KH, Mima T, Casart Y, Rholl D, Kumar A, Beacham IR, Schweizer HP. 2008. Genetic tools for select-agent-compliant manipulation of Burkholderia pseudomallei. Appl. Environ. Microbiol. 74:1064-1075.
24. Tuanyok A, Auerbach RK, Brettin TS, Bruce DC, Munk AC, Detter JC, Pearson T, Hornstra H, Sermswan RW, Wuthiekanun V, Peacock SJ, Currie BJ, Keim P, Wagner DM. 2007. A horizontal gene transfer event defines two distinct groups within Burkholderia pseudomallei that have dissimilar geographic distributions. J. Bacteriol. 189:9044-9049.
25. Crook MB, Lindsay DP, Biggs MB, Bentley JS, Price JC, Clement SC, Clement MJ, Long SR, Griffitts JS. 2012. Rhizobial plasmids that cause impaired symbiotic nitrogen fixation and enhanced host invasion. Mol. Plant Microbe Interact. 25:1026-1033.
26. Joardar V, Lindeberg M, Jackson RW, Selengut J, Dodson R, Brinkac LM, Daugherty SC, Deboy R, Durkin AS, Giglio MG, Madupu R, Nelson WC, Rosovitz MJ, Sullivan S, Crabtree J, Creasy T, Davidsen T, Haft DH, Zafar N, Zhou L, Halpin R, Holley T, Khouri H, Feldblyum T, White O, Fraser CM, Chatterjee AK, Cartinhour S, Schneider DJ, Mansfield J, Collmer A, Buell CR. 2005. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition. J. Bacteriol. 187:6488-6498.
27. Choi K-H, Gaynor JB, White KG, Lopez C, Bosio CM, Karkhoff- Schweizer RR, Schweizer HP. 2005. A Tn7-based broad-range bacterial cloning and expression system. Nat. Methods 2:443-448.
28. Smith AW. 1998. Iron starvation and siderophore-mediated iron transport. Methods Microbiol. 27:331-342.
29. Sokol PA, Lewis CJ, Dennis JJ. 1992. Isolation of a novel siderophore from Pseudomonas cepacia. J. Med. Microbiol. 36:184-189.
30. Trunck LA, Propst KL, Wuthiekanun V, Tuanyok A, Beckstrom-Sternberg SM, Beckstrom-Sternberg JS, Peacock SJ, Keim P, Dow SW, Schweizer HP. 2009. Molecular basis of rare aminoglycoside susceptibility and pathogenesis of Burkholderia pseudomallei clinical isolates from Thailand. PLoS Negl. Trop. Dis. 3:e519. doi:10.1371/journal.pntd.0000519.
31. Kvitko BH, Goodyear A, Propst KL, Dow SW, Schweizer HP. 2012. Burkholderia pseudomallei known siderophores and hemin uptake are dispensable for lethal murine melioidosis. PLoS Negl. Trop. Dis. 6:e1715. doi:10.1371/journal.pntd.0001715.
32. French CT, Toesca IJ, Wu TH, Teslaa T, Beaty SM, Wong W, Liu M, Schroder I, Chiou PY, Teitell MA, Miller JF. 2011. Dissection of the Burkholderia intracellular life cycle using a photothermal nanoblade. Proc. Natl. Acad. Sci. U. S. A. 108:12095-12100.
33. Van Zandt KE, Tuanyok A, Keim P, Warren RL, Carl GH. 2012. An objective approach for Burkholderia pseudomallei strain selection as challenge material for medical countermeasures efficacy testing. Front. Cell. Infect. Microbiol. 2:120.
34. Toukdarian AE, Helinski DR. 1998. TrfA dimers play a role in copynumber control of RK2 replication. Gene 223:205-211.
35. Lopez CM, Rholl DA, Trunck LA, Schweizer HP. 2009. Versatile dualtechnology system for markerless allele replacement in Burkholderia pseudomallei. Appl. Environ. Microbiol. 75:6496-6503.
36. Norris MH, Kang Y, Lu D, Wilcox BA, Hoang TT. 2009. Glyphosate resistance as a novel select-agent-compliant, non-antibiotic-selectable marker in chromosomal mutagenesis of the essential genes asd and dapB of Burkholderia pseudomallei. Appl. Environ. Microbiol. 75: 6062-6075.