Random and cyclical deletion of large DNA segments in the genome of Pseudomonas putida

Environmental Microbiology

Volumn 14, Issue 6, 2012, Pages 1444-1453

  Leprince, Audrey ^a,b   de Lorenzo, Víctor ^c   Völler, Petra ^a   van Passel, Mark W J ^b   Martins dos Santos, Vitor A P ^a,b  

^a HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; DNA POLYMERASE;

ARTICLE; BACTERIAL GENOME; GENE DELETION; GENETIC ENGINEERING; GENETICS; METHODOLOGY; PSEUDOMONAS PUTIDA;

DNA; DNA NUCLEOTIDYLTRANSFERASES; GENETIC ENGINEERING; GENOME, BACTERIAL; PSEUDOMONAS PUTIDA; SEQUENCE DELETION;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

EID: 84861943059     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/j.1462-2920.2012.02730.x     Document Type: Article

References (37)

1. Dammeyer, T., Steinwand, M., Kruger, S.C., Dubel, S., Hust, M., and Timmis, K.N. (2011) Efficient production of soluble recombinant single chain Fv fragments by a Pseudomonas putida strain KT2440 cell factory. Microb Cell Fact 10: 11.
2. Danchin, A. (2009) Natural selection and immortality. Biogerontology 10: 503-516.
3. De las Heras, A., Carreno, C.A., and De Lorenzo, V. (2008) Stable implantation of orthogonal sensor circuits in Gram-negative bacteria for environmental release. Environ Microbiol 10: 3305-3316.
4. De Lorenzo, V., and Timmis, K.N. (1994) Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- and Tn10-derived minitransposons. Methods Enzymol 235: 386-405.
5. Dos Santos, V.A., Heim, S., Moore, E.R., Stratz, M., and Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6: 1264-1286.
6. Fang, G., Rocha, E., and Danchin, A. (2005) How essential are nonessential genes? Mol Biol Evol 22: 2147-2156.
7. Galvao, T.C., and de Lorenzo, V. (2005) Adaptation of the yeast URA3 selection system to gram-negative bacteria and generation of a {delta}betCDE Pseudomonas putida strain. Appl Environ Microbiol 71: 883-892.
8. Giddens, S.R., Jackson, R.W., Moon, C.D., Jacobs, M.A., Zhang, X.-X., Gehrig, S.M., and Rainey, P.B. (2007) Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment. PNAS 104: 18247-18252.
9. Gilbert, E.S., Walker, A.W., and Keasling, J.D. (2003) A constructed microbial consortium for biodegradation of the organophosphorus insecticide parathion. Appl Microbiol Biotechnol 61: 77-81.
10. Goryshin, I.Y., Naumann, T.A., Apodaca, J., and Reznikoff, W.S. (2003) Chromosomal deletion formation system based on Tn5 double transposition: use for making minimal genomes and essential gene analysis. Genome Res 13: 644-653.
11. Grant, J.R., Stothard, P. (2008) The CGView Server: a comparative genomics tool for circular genomes. Nucleic Acids Res 36: W181-W184.
12. Hervas, A.B., Canosa, I., and Santero, E. (2008) Transcriptome analysis of Pseudomonas putida in response to nitrogen availability. J Bacteriol 190: 416-420.
13. Jimenez, J.I., Minambres, B., Garcia, J.L., and Diaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4: 824-841.
14. Kurbatov, L., Albrecht, D., Herrmann, H., and Petruschka, L. (2006) Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy. Environ Microbiol 8: 466-478.
15. Leprince, A., Janus, D., de Lorenzo, V., and Santos, V.M. (2012) Streamlining of a Pseudomonas putida genome using a combinatorial deletion method based on minitransposon insertion and the Flp-FRT recombination system. Methods Mol Biol 813: 249-266.
16. de Lorenzo, V. (2008) Systems biology approaches to bioremediation. Curr Opin Biotechnol 19: 579-589.
17. Martinez-Garcia, E., and de Lorenzo, V. (2011) Engineering multiple genomic deletions in Gram-negative bacteria: analysis of the multi-resistant antibiotic profile of Pseudomonas putida KT2440. Environ Microbiol 13: 2702-2716.
18. Martinez-Garcia, E., Calles, B., Arevalo-Rodriguez, M., and de Lorenzo, V. (2011) pBAM1: an all-synthetic genetic tool for analysis and construction of complex bacterial phenotypes. BMC Microbiol 11: 38.
19. Milne, I., Bayer, M., Cardle, L., Shaw, P., Stephen, G., Wright, F., and Marshall, D. (2010) Tablet-next generation sequence assembly visualization. Bioinformatics 26: 401-402.
20. Molina-Henares, M.A., Garcia-Salamanca, A., Molina-Henares, A.J., de la Torre, J., Herrera, M.C., Ramos, J.L., and Duque, E. (2009) Functional analysis of aromatic biosynthetic pathways in Pseudomonas putida KT2440. Microb Biotechnol 2: 91-100.
21. Molina-Henares, M.A., de la Torre, J., Garcia-Salamanca, A., Molina-Henares, A.J., Herrera, M.C., Ramos, J.L., and Duque, E. (2010) Identification of conditionally essential genes for growth of Pseudomonas putida KT2440 on minimal medium through the screening of a genome-wide mutant library. Environ Microbiol 12: 1468-1485.
22. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A., etal. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4: 799-808.
23. Nogales, J., Palsson, B.O., and Thiele, I. (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2: 79.
24. O'Toole, G.A., Pratt, L.A., Watnick, P.I., Newman, D.K., Weaver, V.B., and Kolter, R. (1999) Genetic approaches to study of biofilms. Methods Enzymol 310: 91-109.
25. Pieper, D.H., Martins dos Santos, V.A., and Golyshin, P.N. (2004) Genomic and mechanistic insights into the biodegradation of organic pollutants. Curr Opin Biotechnol 15: 215-224.
26. Pósfai, G., Plunkett Iii, G., Fehér, T., Frisch, D., Keil, G.M., Umenhoffer, K., etal. (2006) Emergent properties of reduced-genome Escherichia coli. Science 312: 1044-1046.
27. Puchalka, J., Oberhardt, M.A., Godinho, M., Bielecka, A., Regenhardt, D., Timmis, K.N., etal. (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4: e1000210.
28. Quénée, L., Lamotte, D., and Polack, B. (2005) Combined sacB-based negative selection and cre-lox antibiotic marker recycling for efficient gene deletion in Pseudomonas aeruginosa. Biotechniques 38: 63-67.
29. Rozen, S., and Skaletsky, H. (2000) Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132: 365-386.
30. Sanchez-Romero, J.M., Diaz-Orejas, R., and De Lorenzo, V. (1998) Resistance to tellurite as a selection marker for genetic manipulations of Pseudomonas strains. Appl Environ Microbiol 64: 4040-4046.
31. Schweizer, H.P. (2003) Applications of the Saccharomyces cerevisiae Flp-FRT system in bacterial genetics. J Mol Microbiol Biotechnol 5: 67-77.
32. Wang, H.H., Isaacs, F.J., Carr, P.A., Sun, Z.Z., Xu, G., Forest, C.R., and Church, G.M. (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460: 894-898.
33. Warner, J.R., Reeder, P.J., Karimpour-Fard, A., Woodruff, L.B., and Gill, R.T. (2010) Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nat Biotechnol 28: 856-862.
34. Weinel, C., Nelson, K.E., and Tummler, B. (2002) Global features of the Pseudomonas putida KT2440 genome sequence. Environ Microbiol 4: 809-818.
35. Woodruff, L.B., and Gill, R.T. (2011) Engineering genomes in multiplex. Curr Opin Biotechnol 22: 576-583.
36. Yu, B.J., Sung, B.H., Koob, M.D., Lee, C.H., Lee, J.H., Lee, W.S., etal. (2002) Minimization of the Escherichia coli genome using a Tn5-targeted Cre/loxP excision system. Nat Biotechnol 20: 1018-1023.
37. Yu, B.J., Kang, K.H., Lee, J.H., Sung, B.H., Kim, M.S., and Kim, S.C. (2008) Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res 36: e84.