An upp-based markerless gene replacement method for genome reduction and metabolic pathway engineering in Pseudomonas mendocina NK-01 and Pseudomonas putida KT2440

Journal of Microbiological Methods

Volumn 113, Issue , 2015, Pages 27-33

  Wang, Yuanyuan ^a   Zhang, Chi ^a   Gong, Ting ^a   Zuo, Zhenqiang ^a   Zhao, Fengjie ^a   Fan, Xu ^a   Yang, Chao ^a   Song, Cunjiang ^a  

^a NANKAI UNIVERSITY   (China)

Author keywords

5 Fluorouracil; Genome modification; Uracil phosphoribosyltransferase

Indexed keywords

FLUOROURACIL; CARBOXYLESTERASE; GLYCOSYLTRANSFERASE; METHYL PARATHION HYDROLASE, PSEUDOMONAS; PHOSPHATASE; PYRETHROID; URACIL PHOSPHORIBOSYLTRANSFERASE;

ALGA GENE; ARTICLE; BACTERIAL CHROMOSOME; BACTERIAL GENOME; BACTERIUM MUTANT; CONTROLLED STUDY; GENE; GENE CONSTRUCT; GENE DELETION; GENE INSERTION; GENETIC PROCEDURES; MARKERLESS GENE REPLACEMENT; METABOLIC ENGINEERING; MPD GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHAC1 GENE; PHAZ GENE; PLASMID; PRIORITY JOURNAL; PSEUDOMONAS MENDOCINA; PSEUDOMONAS PUTIDA; PYTH GENE; UPP GENE; CHROMOSOME DELETION; GENE VECTOR; GENETICS; METABOLISM; MUTATION; PROCEDURES;

ALGAE; PSEUDOMONAS MENDOCINA; PSEUDOMONAS PUTIDA;

CARBOXYLESTERASE; CHROMOSOME DELETION; FLUOROURACIL; GENETIC VECTORS; GENOME, BACTERIAL; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; MUTATION; PENTOSYLTRANSFERASES; PHOSPHORIC MONOESTER HYDROLASES; PLASMIDS; PSEUDOMONAS MENDOCINA; PSEUDOMONAS PUTIDA; PYRETHRINS;

EID: 84926349399     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2015.03.022     Document Type: Article

References (29)

1. Bloor A.E., Cranenburgh R.M. An efficient method of selectable marker gene excision by Xer recombination for gene replacement in bacterial chromosomes. Appl. Environ. Microbiol. 2006, 72:2520-2525.
2. Dennis J.J., Sokol P.A. Electrotransformation of pseudomonas. Methods. Mol. Biol. 1995, 47:125-133.
3. Dhillon B.K., Chiu T.A., Laird M.R., Langille M.G., Brinkman F.S. IslandViewer update: improved genomic island discovery and visualization. Nucleic Acids Res. 2013, 41:W129-W132.
4. Fabret C., Ehrlich S.D., Noirot P. A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol. Microbiol. 2002, 46:25-36.
5. Friedrich B., Hogrefe C., Schlegel H.G. Naturally occurring genetic transfer of hydrogen-oxidizing ability between strains of Alcaligenes eutrophus. J. Bacteriol. 1981, 147:198-205.
6. Goh Y.J., Azcarate-Peril M.A., O'Flaherty S., et al. 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. 2009, 75:3093-3105.
7. Graf N., Altenbuchner J. Development of a method for markerless gene deletion in Pseudomonas putida. Appl. Environ. Microbiol. 2011, 77:5549-5552.
8. Guo W., Song C., Kong M., Geng W., Wang Y., Wang S. Simultaneous production and characterization of medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides by Pseudomonas mendocina NK-01. Appl. Microbiol. Biotechnol. 2011, 92:791-801.
9. Guo W., Wang Y., Song C., et al. Complete genome of Pseudomonas mendocina NK-01, which synthesizes medium-chain-length polyhydroxyalkanoates and alginate oligosaccharides. J. Bacteriol. 2011, 193:3413-3414.
10. Hay I.D., Ur Rehman Z., Moradali M.F., Wang Y., Rehm B.H. Microbial alginate production, modification and its applications. Microb. Biotechnol. 2013, 6:637-650.
11. Jendrossek D., Pfeiffer D. New insights in the formation of polyhydroxyalkanoate granules (carbonosomes) and novel functions of poly(3-hydroxybutyrate). Environ. Microbiol. 2014, 16:2357-2373.
12. Jiang J., Zhang R., Li R., Gu J.D., Li S. Simultaneous biodegradation of methyl parathion and carbofuran by a genetically engineered microorganism constructed by mini-Tn5 transposon. Biodegradation 2007, 18:403-412.
13. Keller K.L., Bender K.S., Wall J.D. Development of a markerless genetic exchange system for Desulfovibrio vulgaris Hildenborough and its use in generating a strain with increased transformation efficiency. Appl. Environ. Microbiol. 2009, 75:7682-7691.
14. Kristich C.J., Manias D.A., Dunny G.M. Development of a method for markerless genetic exchange in Enterococcus faecalis and its use in construction of a srtA mutant. Appl. Environ. Microbiol. 2005, 71:5837-5849.
15. Langille M.G., Brinkman F.S. IslandViewer: an integrated interface for computational identification and visualization of genomic islands. Bioinformatics 2009, 25:664-665.
16. Madyagol M., Al-Alami H., Levarski Z., Drahovska H., Turna J., Stuchlik S. Gene replacement techniques for Escherichia coli genome modification. Folia Microbiol. (Praha) 2011, 56:253-263.
17. Nelson K.E., Weinel C., Paulsen I.T., et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 2002, 4:799-808.
18. Onaca C., Kieninger M., Engesser K.H., Altenbuchner J. Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J. Bacteriol. 2007, 189:3759-3767.
19. Ramos J.L., Wasserfallen A., Rose K., Timmis K.N. Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science 1987, 235:593-596.
20. Rehm B.H., Steinbuchel A. Biochemical and genetic analysis of PHA synthases and other proteins required for PHA synthesis. Int. J. Biol. Macromol. 1999, 25:3-19.
21. Remminghorst U., Rehm B.H. Bacterial alginates: from biosynthesis to applications. Biotechnol. Lett. 2006, 28:1701-1712.
22. Reyrat J.M., Pelicic V., Gicquel B., Rappuoli R. Counterselectable markers: untapped tools for bacterial genetics and pathogenesis. Infect. Immun. 1998, 66:4011-4017.
23. Sayler G.S., Hooper S.W., Layton A.C., King J.M. Catabolic plasmids of environmental and ecological significance. Microb. Ecol. 1990, 19:1-20.
24. Schafer A., Tauch A., Jager W., Kalinowski J., Thierbach G., Puhler A. Small mobilizable multi-purpose cloning vectors derived from the Escherichia coli plasmids pK18 and pK19: selection of defined deletions in the chromosome of Corynebacterium glutamicum. Gene 1994, 145:69-73.
25. Shetty R.P., Endy D., Knight T.F. Engineering BioBrick vectors from BioBrick parts. J. Biol. Eng. 2008, 2:5.
26. Wang B.Z., Guo P., Hang B.J., Li L., He J., Li S.P. Cloning of a novel pyrethroid-hydrolyzing carboxylesterase gene from Sphingobium sp. strain JZ-1 and characterization of the gene product. Appl. Environ. Microbiol. 2009, 75:5496-5500.
27. Zhang Z., Hong Q., Xu J., Zhang X., Li S. Isolation of fenitrothion-degrading strain Burkholderia sp. FDS-1 and cloning of mpd gene. Biodegradation 2006, 17:275-283.
28. Zhang W., Gao W., Feng J., et al. A markerless gene replacement method for B. amyloliquefaciens LL3 and its use in genome reduction and improvement of poly-gamma-glutamic acid production. Appl. Microbiol. Biotechnol. 2014, 98:8963-8973.
29. Zhongli C., Shunpeng L., Guoping F. Isolation of methyl parathion-degrading strain M6 and cloning of the methyl parathion hydrolase gene. Appl. Environ. Microbiol. 2001, 67:4922-4925.