Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency

Applied and Environmental Microbiology

Volumn 75, Issue 24, 2009, Pages 7682-7691

  Keller, Kimberly L ^a,b   Bender, Kelly S ^a,b,c   Wall, Judy D ^a,b  

^a University of Missouri   (United States)

^b Virtual Institute of Microbial Stress and Survival   (United States)

^c SOUTHERN ILLINOIS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

5-FLUOROURACIL (5-FU); ANTIBIOTIC RESISTANCE; DELETION METHODS; DELETION SYSTEMS; DESULFOVIBRIO VULGARIS; ELECTROPORATION; ENDONUCLEASES; GENE DELETION; GENETIC EXCHANGE; GENETIC MANIPULATIONS; GENETIC TOOLS; KANAMYCINS; MARKERLESS; RESISTANCE GENES; RESTRICTION-MODIFICATION SYSTEMS; SALVAGE ENZYMES; SELECTABLE MARKERS; SULFATE REDUCING BACTERIA; TRANSFORMATION EFFICIENCY; URACIL PHOSPHORIBOSYLTRANSFERASE; VULGARIS; WILD TYPES; WILD-TYPE STRAIN;

GENES;

ANTIBIOTICS;

ANTIBIOTIC RESISTANCE; BACTERIUM; ENZYME ACTIVITY; GENE EXPRESSION; GENETIC ENGINEERING; PLASMID; TOXIC MATERIAL;

DESULFOVIBRIO VULGARIS; GENE DELETION; GENETIC TECHNIQUES; TRANSFORMATION, GENETIC;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO VULGARIS SUBSP. VULGARIS STR. HILDENBOROUGH;

EID: 73249117149     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.01839-09     Document Type: Article

References (35)

1. Alm, E. J., K. H. Huang, M. N. Price, R. P. Koche, K. Keller, I. L. Dubchak, and A. P. Arkin. 2005. The MicrobesOnline Web site for comparative genomics. Genome Res. 15:1015-1022.
2. Bender, K. S., H.-C. B. Yen, C. L. Hemme, Z. Yang, Z. He, Q. He, J. Zhou, K. H. Huang, E. J. Alm, T. C. Hazen, A. P. Arkin, and J. D. Wall. 2007. Analysis of a ferric uptake regulator (fur) mutant of Desulfovibrio vulgaris Hildenborough. Appl. Environ. Microbiol. 73:5389-5400.
3. Bender, K. S., H.-C. Yen, and J. D. Wall. 2006. Analysing the metabolic capabilities of Desulfovibrio species through genetic manipulation. Biotechnol. Genet. Eng. Rev. 23:157-174.
4. Bitan-Banin, G., R. Ortenberg, and M. Mevarech. 2003. Development of a gene knockout system for the halophilic archaeon Haloferax volcanii by use of the pyrE gene. J. Bacteriol. 185:772-778.
5. Boeke, J. D., F. LaCroute, and G. R. Fink. 1984. A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoroorotic acid resistance. Mol. Gen. Genet. 197:345-346.
6. Brandis, A., and R. K. Thauer. 1981. Growth of Desulfovibrio species on hydrogen and sulfate as sole energy source. J. Gen. Microbiol. 126:249-252.
7. Coppi, M. V., C. Leang, S. J. Sandler, and D. R. Lovely. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl. Environ. Microbiol. 67:3180-3187.
8. Dolla, A., B. K. J. Pohorelic, J. K. Voordouw, and G. Voordouw. 2000. Deletion of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough hampers hydrogen metabolism and low-redox-potential niche establishment. Arch. Microbiol. 174:143-151.
9. Fabret, C., S. D. Ehrlich, and P. Noirot. 2002. A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol. Microbiol. 46:25-36.
10. Fu, R., and G. Voordouw. 1997. Targeted gene-replacement mutagenesis of dcrA, encoding an oxygen sensor of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough. Microbiology 143:1815-1826.
11. Fu, R., and G. Voordouw. 1998. ISDI, an insertion element from the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough: structure, transposition, and distribution. Appl. Environ. Microbiol. 64:53-61.
12. Fukagawa, T., N. Hayward, J. Yang, C. Azzalin, D. Griffin, A. F. Stewart, and W. Brown. 1999. The chicken HPRT gene: a counter selectable marker for the DT40 cell line. Nucleic Acids Res. 27:1966-1969.
13. Gay, P., D. Le Coq, M. Steinmetz, E. Ferrari, and J. A. Hoch. 1983. Cloning structural gene sacB, which codes for exoenzyme levansucrase of Bacillus subtilis: expression of the gene in Escherichia coli. J. Bacteriol. 153:1424-1431.
14. Giaever, G., and C. Nislow. 2009. Knocking sense into regulatory pathways. Nat. Biotechnol. 27:149-150.
15. Goenka, A., J. K. Voordouw, W. Lubitz, W. Gaertner, and G. Voordouw. 2005. Construction of a [NiFe]-hydrogenase deletion mutant of Desulfovibrio vulgaris Hildenborough. Biochem. Soc. Trans. 33:59-60.
16. Goh, Y. J., M. A. Azcaŕate-Peril, S. O'Flaherty, E. Durmaz, F. Valence, J. Jardin, S. Lortal, and T. R. Klaenhammer. 2009. Development and application of a upp-based counterselective gene replacement system for the study of the S-layer protein SlpX of Lactobacillus acidophilus NCFM. Appl. Environ. Microbiol. 75:3093-3105.
17. Hanahan, D. 1983. Studies on transformation of Escherichia coli with plasmids. J. Mol. Biol. 166:557-580.
18. Haveman, S. A., V. Brunelle, J. K. Voordouw, G. Voordouw, J. F. Heidelberg, and R. Rabus. 2003. Gene expression analysis of energy metabolism mutants of Desulfovibrio vulgaris Hildenborough indicates an important role for alcohol dehydrogenase. J. Bacteriol. 185:4345-4353.
19. Haveman, S. A., E. A. Greene, C. P. Stilwell, J. K. Voordouw, and G. Voordouw. 2004. Physiological and gene expression analysis of inhibition of Desulfovibrio vulgaris Hildenborough by nitrite. J. Bacteriol. 186:7944-7950.
20. Horton, R. M., Z. Cai, S. N. Ho, and L. R. Pease. 1990. Gene splicing by overlap extension: tailor-made genes using the polymerase chain reaction. BioTechniques 8:528-8535.
21. Keon, R. G., F. Rongdian, and G. Voordouw. 1997. Deletion of two downstream genes alters expression of the hmc operon of Desulfovibrio vulgaris subsp. vulgaris Hildenborough. Arch. Microbiol. 167:376-383.
22. Kristich, C. J., D. A. Manias, and G. M. Dunny. 2005. Development of a method for markerless genetic exchange in Enterococcus faecalis and its use in construction of a srtA mutant. Appl. Environ. Microbiol. 71:5837-5849.
23. Michel, C., M. Brugna, C. Aubert, A. Bernadac, and M. Bruschi. 2001. Enzymatic reduction of chromate: comparative studies using sulfate-reducing bacteria. Key role of polyheme cytochromes c and hydrogenases. Appl. Microbiol. Biotechnol. 55:95-100.
24. Moore, B. C., and J. A. Leigh. 2005. Markerless mutagenesis in Methanococcus maripaludis demonstrates roles for alanine dehydrogenase, alanine racemase, and alanine permease. J. Bacteriol. 187:972-979.
25. Mukhopadhyay, A., Z. He, E. J. Alm, A. P. Arkin, E. E. Baidoo, S. C. Borglin, W. Chen, T. C. Hazen, Q. He, H.-Y. Holman, K. Huang, R. Huang, D. C. Joyner, N. Katz, M. Keller, P. Oeller, A. Redding, J. Sun, J. Wall, J. Wei, Z. Yang, H.-C. Yen, J. Zhou, and J. D. Keasling. 2006. Salt stress in Desulfovibrio vulgaris Hildenborough: an integrated genomics approach. J. Bacteriol. 188:4068-4078.
26. Payne, R. B., D. M. Gentry, B. J. Rapp-Giles, L. Casalot, and J. D. Wall. 2002. Uranium reduction by Desulfovibrio desulfuricans strain G20 and a cytochrome c3 mutant. Appl. Environ. Microbiol. 68:3129-3132.
27. Peck, R. F., S. Dassarma, and M. P. Krebs. 2000. Homologous gene knockout in the archaeon Halobacterium salinarum with ura3 as a counterselectable marker. Mol. Microbiol. 35:667-676.
28. Postgate, J. R. 1984. The sulphate-reducing bacteria. Cambridge University Press, London, United Kingdom.
29. Pritchett, M. A., J. K. Zhang, and W. W. Metcalf. 2004. Development of a markerless genetic exchange method for Methanosarcina acetivorans C2A and its use in construction of new genetic tools for methanogenic archaea. Appl. Environ. Microbiol. 70:1425-1433.
30. Rother, M., and W. W. Metcalf. 2005. Genetic technologies for Archaea. Curr. Opin. Microbiol. 8:745-751.
31. Rousset, M., L. Casalot, B. J. Rapp-Giles, Z. Dermoun, P. de Philip, J. P. Bélaich, and J. D. Wall. 1998. New shuttle vectors for the introduction of cloned DNA in Desulfovibrio. Plasmid 39:114-122.
32. Steyert, S. R., and S. A. Pineiro. 2007. Development of a novel genetic system to create markerless deletion mutants of Bdellovibrio bacteriovorus. Appl. Environ. Microbiol. 73:4717-4724.
33. Wall, J. D., B. J. Rapp-Giles, and M. Rousset. 1993. Characterization of a small plasmid from Desulfovibrio desulfuricans and its use for shuttle vector construction. J. Bacteriol. 175:4121-4128.
34. Wang, G., S. P. Kennedy, S. Fasiludeen, C. Rensing, and S. DasSarma. 2004. Arsenic resistance in Halobacterium sp. strain NRC-1 examined by using an improved gene knockout system. J. Bacteriol. 186:3187-3194.
35. Wu, S. S., and D. Kaiser. 1996. Markerless deletions of pil genes in Myxococcus xanthus generated by counterselection with the Bacillus subtilis sacB gene. J. Bacteriol. 178:5817-5821.