Towards a genome-wide mutant library of pseudomonas putida strain KT2440

Pseudomonas

Volumn 5, Issue , 2007, Pages 227-251

  Duque, Estrella ^a   Molina Henares, Antonio J ^a   Torre, Jesús De La ^a   Molina Henares, María A ^a   Castillo, Teresa Del ^a   Lam, Jennifer ^a   Ramos, Juan L ^a  

^a CSIC   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 57049138931     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/978-1-4020-6097-7_8     Document Type: Chapter

References (107)

1. Alaminos, M., and Ramos, J.L., 2001, The methionine biosynthetic pathway from homoserine in Pseudomonas putida involves the metW, metX, metZ, metH and metE gene products. Arch. Microbiol., 176:151-154.
2. Andersen, G.L., Beattie, G.A., and Lindow, S.E., 1998, Molecular characterization and sequence of a methionine biosynthetic locus from Pseudomonas syringae. J. Bacteriol., 180:4497-4507.
3. Aranda-Olmedo, I., Tobes, R., Manzanera, M., Ramos, J.L., and Marques, S., 2002, Species-specific repetitive palindromic (REP) sequences in Pseudomonas putida. Nucleic Acids Res., 30:1826-1833.
4. Auerbach, I.D., Sorensen, C., Hansma, H.G., and Holden, P.A., 2000, Physical morphology and surface properties of unsaturated Pseudomonas putida biofilms. J. Bacteriol., 182:3809-3815.
5. Bagdasarian, M., Lurz, R., Rueckert, B., Franklin, F.C.H., Bagdasarian, M.M., Frey, J., and Timmis, K.N., 1981, Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene, 16:237-247.
6. Bagdasarian, M., and Timmis, K.N., 1982, Host: vector systems for gene cloning in Pseudomonas. Curr. Top Microbiol. Immunol., 96:47-67.
7. Bailey, J., and Manoil, C., 2002, Genome-wide internal tagging of bacterial exported proteins. Nature Biotechnol., 20:839-841.
8. Bork, P., and Rohde, K., 1991, More von Willebrand factor type A domains? Sequence similarities with malaria thrombospondin-related anonymous protein, dihydropyridinesensitive calcium channel and inter-alpha-trypsin inhibitor. Biochem. J., 279:908-910.
9. Caballero, A., and Ramos, J.L., 2006, A double mutant of Pseudomonas putida JLR11 deficient in the synthesis of the nitroreductase PnrA and assimilatory nitrite reductase NasB is impaired from growth on TNT. Environ. Microbiol., 8:1305-1310.
10. Caiazza, N.C., and O'Toole, G.A., 2004, SadB is required for the transition from reversible to irreversible attachment during biofilms formation by Pseudomonas aeruginosa PA14. J. Bacteriol., 186:4476-4485.
11. Cánovas, D., Cases, I., and de Lorenzo, V., 2003, Heavy metal tolerance and metal homeostasis in Pseudomonas putida as revealed by complete genome analysis. Environ. Microbiol., 5:1242-1256.
12. Cao, H., Baldini, R.L., and Rahme, L.G., 2001, Common mechanisms for pathogens of plants and animals. Annu. Rev. Phytopathol., 39:259-84.
13. Chang, W.-S., and Halverson, L.J., 2003, Reduced water availability influences the dynamics, development, and ultrastructural properties of Pseudomonas putida biofilms. J. Bacteriol., 185:6199-6204.
14. Cornelis, P., and Matthijs, S., 2002, Diversity of siderophore-mediated iron uptake systems in fluorescent pseudomonads: not only pyoverdines. Environ. Microbiol., 4:787-798.
15. Cowles, C.E., Nichols, N.N., and Harwood, C.S., 2000, BenR, a XylS homologue, regulates three different pathways of aromatic acid degradation in Pseudomonas putida. J. Bacteriol., 182:6339-6346.
16. Cucarella, C., Solano, C., Valle, J., Amorena, B., Lasa, I., and Penades, J.R., 2001, Bap, a Staphylococcus aureus surface protein involved in biofilm formation. J. Bacteriol., 183:2888-2896.
17. Dagley, S., 1971, Catabolism of aromatic compounds by micro-organisms. Adv. Microb. Physiol., 6:1-46.
18. de Groot, A., Heijnen, I., de Cock, H., Filloux, A., and Tommassen, J., 1994, Characterization of type IV pilus genes in plant growth-promoting Pseudomonas putida WCS358. J. Bacteriol., 176:642-650.
19. de Lorenzo, V., Herrero M., Jakubzik, U., and Timmis K.N., 1990, Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. J. Bacteriol., 172:6568-6572.
20. de Lorenzo, V., and Timmis, K.N., 1994, Analysis and construction of stable phenotypes in gram-negative bacteria with Tn5- And Tn10-derived mini-transposons. Meth. Enzymol., 235:386-405.
21. Djordjevic, M.A., Chen, H.C., Natera, S., Van Noorden, G., Menzel, C., Taylor, S., Renard, C., Geiger, O., and Weiller, G.F., 2003, A global analysis of protein expression profiles in Sinorhizobium meliloti: Discovery of new genes for nodule occupancy and stress adaptation. Mol. Plant-Microbe Interact., 16:508-524.
22. Domínguez-Cuevas, P., González-Pastor, J.E., Marqués, S., Ramos, J.L., and de Lorenzo, V., 2006, Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J. Biol. Chem., 281:11981-11991.
23. Dorr, J., Hurek, T., and Reinhold-Hurek, B., 1998, Type IV pili are involved in plantmicrobe and fungus-microbe interactions. Mol. Microbiol., 30:7-17.
24. Drake, S.L., Sandstedt, S.A., and Koomey, M., 1997, PilP, a pilus biogenesis lipoprotein in Neisseria gonorrhoeae, affects expression of PilQ as a high-molecular-mass multimer. Mol. Microbiol., 23:657-668.
25. Duque, E., Ramos-González, M.I., Delgado, A., Contreras, A., Molin, S., and Ramos, J.L., 1992, Genetically engineered Pseudomonas strains for mineralization of aromatics: Survival, performance, gene transfer, and biological containment, pp. 429-437. In Gaily, E., Silver, S., Withold, B. (eds.), Pseudomonas-91. Molecular Biology and Biotechnology, Chapter 46. American Society for Microbiology, Washington DC.
26. Duque, E., Rodríguez-Herva, J.J., de la Torre, J., Domínguez-Cuevas, P., Muñoz-Rojas, J., and Ramos, J.L., 2007. The RpoT regulon of Pseudomonas putida and its role in endurance against solvents. J. Bacteriol., 189:207-219.
27. Erb, R.W., Eichner, C.A., Wagner-Dobler, I., and Timmis, K.N., 1997, Bioprotection of microbial communities from toxic phenol mixtures by a genetically designed pseudomonad. Nature Biotechnol., 15:378-382.
28. Entner, N., and Doudoroff, M., 1952, Glucose and gluconic acid oxidation of Pseudomonas saccharophila. J. Biol. Chem., 196:853-862.
29. Espinosa-Urgel, M., Salido, A., and Ramos, J.L., 2000, Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. J. Bacteriol., 182:2363-2369.
30. Federal Register, 1982, Appendix E, Certified host-vector systems. 47:17197.
31. Foglino, M., Borne, F., Bally, M., Ball, G., and Patte, J.C., 1995, A direct sulfhydrylation pathway is used for methionine biosynthesis in Pseudomonas aeruginosa. Microbiology, 141:431-439.
32. Fouts, D.E., Abramovitch, R.B., Alfano, J.R., Baldo, A.M., Buell, C.R., Cartinhour, S., et al., 2002, Genome wide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor. Proc. Natl Acad. Sci. U.S.A., 99:2275-2280.
33. Galán, B., Díaz, E., and García, J.L., 2000, Enhancing desulphurization by engineering a flavin reductase-encoding gene cassette in recombinant biocatalysts. Environ. Microbiol., 2:687-694.
34. Godoy, P., Ramos-Gonzalez, M.I., and Ramos, J.L., 2001, Involvement of the TonB system in tolerance to solvents and drugs in Pseudomonas putida DOT-T1E. J. Bacteriol., 183:5285-5292.
35. Hallsworth, J.E., Heim S., and Timmis, K.N., 2003, Chaotropic solutes cause water stress in Pseudomonas putida. Environ. Microbiol., 5:1270-1280.
36. Harder, W., and Quayle, J.R., 1971, Aspects of glycine and serine biosynthesis during growth of Pseudomonas AM1 on C compounds. Biochem. J., 121:763-769.
37. Harwood, C.S., and Parales, R.E., 1996, The β-ketoadipate pathway and the biology of self-identity. Annu. Rev. Microbiol., 50:553-590.
38. Harayama, S., and Timmis, K.N., 1989, Catabolism of aromatic hydrocarbons by Pseudomonas, pp. 151-174. In D.A. Hopwood and K.F. Chater (eds.), Genetics of Bacterial Diversity, Academic Press, London.
39. Heim, S., Ferrer, M., Heuer, H., Regenhardt, D., Nimtz, M., and Timmis, K.N., 2003, Proteome reference map of Pseudomonas putida strain KT2440 for genome expression profiling: Distinct responses of KT2440 and Pseudomonas aeruginosa strain PAO1 to iron deprivation and a new form of superoxide dismutase. Environ. Microbiol., 5:1257-1269.
40. Herrero, M., de Lorenzo V., and Timmis K.N., 1990, Transposon vectors containing non-antibiotic resistance selection markers for cloning and stable chromosomal insertion of foreign genes in gram-negative bacteria. J. Bacteriol., 172:6557-6567.
41. Itoh, Y., Wang, X., Hinnebusch, B.J., Preston III, J.F., and Romeo, T., 2005, Depolymerization of β-1, 6-N-acetyl-D-glucosamine disrupts the integrity of diverse bacterial biofilms. J. Bacteriol., 187:382-387.
42. Jacobs, M.A., Alwood, A., Thaipisuttikul, I., Spencer, D., Haugen, E., Ernst, S., Will, O., Kaul, R., Raymond, C., Levy, R., Chun-Rong, L., Guenthner, D., Bovee, D., Olson, M.V., and Manoil, C., 2003, Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc. Natl Acad. Sci. U.S.A., 100:14339-14344.
43. Jiménez, J.I., Miñambres, B., García, J.L., and Díaz, E., 2002, Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol., 4:824-841.
44. Kamilova, F., Validov, S., Azarova, T., Mulders, I., and Lugtenberg, B., 2005, Enrichment for enhanced competitive plant root tip colonizers selects for a new class of biocontrol bacteria. Environ. Microbiol., 7:1809-1817.
45. Lehoux, D.E., Sanschagrin, F., and Levesque, R.C., 1999, Defined oligonucleotide tag pools and PCR screening in signature-tagged mutagenesis of essential genes from bacteria. BioTechniques, 26:473-480.
46. Lessie, T.G., and Phibbs, P.V. Jr., 1984, Alternative pathways of carbohydrate utilization in pseudomonads. Annu. Rev. Microbiol., 38:359-388.
47. Llamas, M.A., Ramos, J.L., and Rodríguez-Herva, J.J., 2003, Transcriptional organization of the Pseudomonas putida tol-oprL Genes. J. Bacteriol., 185:184-195.
48. Llamas, M.A., Rodríguez-Herva, J.J., Hancock, R.E.W., Bitter, W., Tommasen, J., and Ramos, J.L., 2003, Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane. J. Bacteriol., 185:4707-4716.
49. Lugtenberg, B.J.J., and Dekkers, L.C., 1999, What makes Pseudomonas bacteria rhizosphere competent? Environ. Microbiol., 1:9-13.
50. Lugtenberg, B.J.J., Kravchenko, L.V., and Simon, M., 1999, Tomato seed and root exudates sugars: composition, utilization by Pseudomonas biocontrol strains and role in rhizosphere colonization. Environ. Microbiol., 1:439-446.
51. Ma, J.-F., Hager, P.W., Howell, M.L., Phibbs, P.V., and Hassett, D.J., 1998, Cloning and characterization of the Pseudomonas aeruginosa zwf gene encoding glucose-6-phosphate dehydrogenase, an enzyme important in resistance to methyl viologen (paraquat). J. Bacteriol., 180:1741-1749.
52. Madan Babu, M.M., Teichmann, S.A., and Aravind, L., 2006, Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol., 358:614-633.
53. Martin dos Santos, V., Timmis, K., Tümmler, B., and Weinel, C., 2004, Genomic features of Pseudomonas Strain KT2440, pp. 77-112. In J.L. Ramos (ed.), Pseudomonas, Vol. 1. Kluwer Academic/Plenum Publishers, New York.
54. Martínez-Bueno, M.A., Tobes, R., Rey, M., and Ramos, J.L., 2002, Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01. Environ. Microbiol., 4:842-855.
55. Martin dos Santos, V.A.P., Heim, S., Moore, E.R.B., Strätz, M., and Timmis, K.N., 2004, Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ. Microbiol., 6:1264-1286.
56. Maxam, A.M., and Gilbert, W., 1977, A new method for sequencing DNA. Proc. Natl Acad. Sci. U.S.A., 74:560-564.
57. McClure, N.C., Fry, J.C., and Weightman, A.J., 1991, Survival and catabolic activity of natural and genetically engineered bacteria in a laboratory-scale activated-sludge unit. Appl. Environ. Microbiol., 57:366-373.
58. McClure, N.C., Weightman, A.J., and Fry, J.C., 1989, Survival of Pseudomonas putida UWC1 containing cloned catabolic genes in a model activated-sludge unit. Appl. Environ. Microbiol., 55:2627-2634.
59. Mermod, N., Lehrbach, P.R., Reineke, W., and Timmis, K.N., 1984, Transcription of the TOL plasmid toluate catabolic pathway operon of Pseudomonas putida is determined by a pair of co-ordinately and positively regulated overlapping promoters. EMBO J., 3:2461-2466.
60. Molina, L., Ramos, C., Ronchel, M.C., Molin, S., and Ramos, J.L., 1998, Construction of an efficient biologically contained Pseudomonas putida strain and its survival in outdoor assays. Appl. Environ. Microbiol., 64:2072-2078.
61. Molina, L., Ramos, C., Duque, E., Ronchel, M.C., García, J.M., Wyke, L., and Ramos, J.L., 2000, Survival of Pseudomonas putida KT2440 in soil and in the rhizosphere of plants under greenhouse and environmental conditions. Soil Biol. Biochem., 32:315-321.
62. Molina, L., Ramos, C., Ronchel, M.C., Molin, S., and Ramos, J.L., 2000, Construction of an efficient biologically contained Pseudomonas putida strain and its survival in outdoor assays. pp. 170-177. In: Biotechnology of soil: Monitoring, conservation and remediation, EC-COST, Brussels.
63. Muñoz-Rojas, J., Bernal, P., Duque, E., Godoy, P., Segura, A., and Ramos, J.L., 2006, Involvement of Cyclopropane fatty acids in the response of Pseudomonas putida KT2440 to freeze-drying. Appl. Environ. Microbiol., 72:472-477.
64. Muramatsu, H., Mihara, H., Kakutani, R., Yasuda, M., Ueda, M., Kurihara, T., and Esaci, N., 2005, The putative malate/lactate dehydrogenase from Pseudomonas putida is an NADPH-dependent 1-piperideine-2-carboxylate/1-pyrroline-2-carboxylate reductase involved in the catabolism of D-lysine and D-Proline. J. Biol. Chem., 280:5329-5335.
65. Nakazawa, T., 2002, Travels of a Pseudomonas, from Japan around the world. Environ. Microbiol., 4:782-786.
66. Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martin dos Santos, V.A., Fouts, D.E., Gill, S.R., Pop, M., Holmes, M., Brinkac, L., Beanan, M., DeBoy, R.T., Daugherty, S., Kolonay, J., Madupu, R., Nelson, W., White, O., Peterson, J., Khouri, H., Hance, I., Chris Lee, P., Holtzapple, E., Scanlan, D., Tran, K., Moazzez, A., Utterback, T., Rizzo, M., Lee, K., Kosack, D., Moestl, D., Wedler, H., Lauber, J., Stjepandic, D., Hoheisel, J., Straetz, M., Heim, S., Kiewitz, C., Eisen, J.A., Timmis, K.N., Dusterhoft, A., Tummler, B., and Fraser, C.M., 2002, Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol., 4:799-808.
67. Nichols, N.N., and Harwood, C.S., 1997, PcaK, a high-affinity permease for the aromatic compounds 4-hydroxybenzoate and protocatechuate from Pseudomonas putida. J. Bacteriol., 179:5056-5061.
68. Nozaki, M., Kagamiyama, H., and Hayaishi, O., 1963, Metapyrocatechase. I. Purification, crystallization and some properties. Biochem Z., 338:582-590.
69. Nüsslein, K., Maris, D., Timmis, K.N., and Dwyer, D.F., 1992, Expression and transfer of engineered catabolic pathways harbored by Pseudomonas spp. introduced into activated sludge microcosms. Environ. Microbiol., 58:3380-3386.
70. Olivera, E.R., Minambres, B., Garcia, B., Muniz, C., Moreno, M.A., Ferrández, A., Díaz, E., García, J.L., and Luengo, J.M., 1998, Molecular characterization of the phenylacetic acid catabolic pathway in Pseudomonas putida U: The phenylacetyl-CoA catabolon. Proc. Natl Acad. Sci. U.S.A., 95:6419-6424.
71. Paulsen, I.T., Press, C.M., Ravel, J., Kobayashi, D.Y., Myers, G.S.A., Mavrodi, D.V., DeBoy, R.T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R.J., Durkin, A.S., Brinkac, L.M., Daugherty, S.C., Sullivan, S.A., Rosovitz, M.J., Gwinn, M.L., Zhou, L., Schneider, D.J., Cartinhour, S.W., Nelson, W.C., Weidman, J., Watkins, K., Tran, K., Khouri, H., Pierson, E.A., Pierson III, L.S., Thomashow, L.S., and Loper, J.E., 2005, Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnol., 23:873-878.
72. Phillips, A.T., 1986, Biosynthetic and catabolic features of amino acid metabolism in Pseudomonas. In J.R. Sokatch (ed.), The Bacteria, Vol. X. Academic Press, New York.
73. Pipke, R., Wagner-Döbler, I., Timmis, K.N., and Dwyer, D.F., 1992, Survival and function of a genetically engineered Pseudomonad in aquatic sediment microcosms. Appl. Environ. Microbiol., 58:1259-1265.
74. Ramos, J.L., Díaz, E., Dowling, D., de Lorenzo, V., Molin, S., O'Gara, F., Ramos, C., and Timmis, K.N., 1994, The behavior of bacteria designed for biodegradation. Bio/Technol., 12:1349-1356.
75. Ramos, J.L., Duque, E., Godoy, P., and Segura, A., 1998, Efflux pumps involved in toluene tolerance in Pseudomonas putida DOT-T1E. J. Bacteriol., 180:3323-3329.
76. Ramos, J.L., Duque, E., and Ramos-González, M.I., 1991, Survival in soils of an herbicide- resistant Pseudomonas putida bearing a recombinant TOL plasmid. Appl. Environ. Microbiol., 57:260-266.
77. Ramos, J.L., Wasserfallen, A., Rose, K., and Timmis, K.N., 1987, Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science, 235:593-596.
78. Ramos-Díaz, M.A., and Ramos, J.L., 1998, Combined physical and genetic map of the Pseudomonas putida KT2440 Chromosome. J. Bacteriol., 180: 6352-6363.
79. Ramos-González, M.I., Campos, M.J., Ramos, J.L., and Espinosa-Urgel, M., 2006, Characterization of the Pseudomonas putida mobile genetic element ISPpu10: An occupant of repetitive extragenic palindromic sequences. J. Bacteriol., 188:37-44.
80. Regenhardt, D., Heuer, H., Heim, S., Fernandez, U.D., Strömpl, C., Moore, E.R.B., and Timmis, K.N., 2002, Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ. Microbiol., 4:912-915.
81. Reva, O.N., Weinel, C., Weinel, M., Böhm, K., Stjepandic, D., Hoheisel, J.D., and Tümmler, B., 2006, Functional genomics of stress response in Pseudomonas putida KT2440. J. Bacteriol., 188:4079-4092.
82. Revelles, O., Espinosa-Urgel, M., Fuhrer, T., Sauer, U., and Ramos, J.L., 2005, Multiple and interconnected pathways for L-Lysine catabolism in Pseudomonas putida KT2440. J. Bacteriol., 187:7500-7510.
83. Ronchel, M.C., Ramos, C., Jensen, L.B., Molin, S., and Ramos, J.L., 1995, Construction and behavior of biologically contained bacteria for environmental applications in bioremediation. Appl. Environ. Microbiol., 61:2990-2994.
84. Rodríguez-Herva, J.J., Ramos-González, M.I., and Ramos, J.L., 1996, The Pseudomonas putida peptidoglycan-associated outer membrane lipoprotein is involved in maintenance of the integrity of the cell envelope. J. Bacteriol., 178:1699-1706.
85. Sánchez-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.
86. Sanger, F., Nicklen, S., and Coulson, A.R., 1977, DNA Sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci. U.S.A., 74:5463-5467.
87. Santiago, M.F., and West, T.P., 2002, Control of pyrimidine formation in Pseudomonas putida ATCC 17536. Can. J. Microbiol., 48:1076-1081.
88. Sauer, K., and Camper, A.K., 2001, Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J. Bacteriol., 183:6579-6589.
89. Sawyer, M.H., Baumann, L., Berman, S.M., Canovas, J.L., and Berman, R.H., 1977, Pathways of D-fructose catabolism in species of Pseudomonas. Arch. Microbiol., 112:49-55.
90. Schleissner, C., Reglero, A., and Luengo, J.M., 1997, Catabolism of D-glucose by Pseudomonas putida U occurs via extracellular transformation into D-gluconic acid and induction of a specific gluconate transport system. Microbiology, 143:1595-1603.
91. Schnider-Keel, U., Seematter, A., Maurhofer, M., Blumer, C., Duffy, B., Gigot-Bonnefoy, C., Reimmann, C., Notz, R., Defago, G., Haas, D., and Keel, C., 2000, Autoinduction of 2, 4-diacetylphloroglucinol biosynthesis in the biocontrol agent Pseudomonas fluorescens CHA0 and repression by the bacterial metabolites salicylate and pyoluteorin. J. Bacteriol., 182:1215-1225.
92. Schweizer, H., and de Lorenzo, V., 2004, Molecular tools for genetic analysis of Pseudomonads, pp. 317-350. In J.L. Ramos (ed.), Pseudomonas, Vol. I. Kluwer Academic/Plenum Publishers, New York.
93. Segura, A., Godoy, P., van Dillewijn, P., Hurtado, A., Arroyo, N., Santacruz, S., and Ramos, J.L., 2005, Proteomic analysis reveals the participation of energy- And stressrelated proteins in the response of Pseudomonas putida DOT-T1E to toluene. J. Bacteriol., 187:5937-5945.
94. Stover, C.K., et al., 2000, Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature, 406:959-964.
95. Swanson, B.L., Hager, P., Phibbs, P. Jr., Ochsner, U., Vasil, M.L., and Hamood, A.N., 2000, Characterization of the 2-ketogluconate utilization operon in Pseudomonas aeruginosa PAO1. Mol. Microbiol., 37:561-573.
96. Timmis, K.N., 2002, Pseudomonas putida: A cosmopolitan opportunist par excellence. Environ. Microbiol., 4:779-781.
97. Velázquez, F., di Bartolo, I., and de Lorenzo, V., 2004, Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma-54 Pu promoter of Pseudomonas putida. J. Bacteriol., 186:8267-8275.
98. Vicente, M., and Canovas, J.L., 1973, Glucolysis in Pseudomonas putida: Physiological role of alternative routes from the analysis of defective mutants. J. Bacteriol., 116:908-914.
99. Vicente, M., and Canovas, J.L., 1973, Regulation of the glucolytic enzymes in Pseudomonas putida. Arch. Mikrobiol., 93:53-64.
100. Venturi, V., Zennaro, F., Degrassi, G., Okeke, B.C., and Bruschi, C.V., 1998, Genetics of ferulic acid bioconversion to protocatechuic acid in plant-growth-promoting Pseudomonas putida WCS358. Microbiology, 144:965-73.
101. Visca, P., Leoni, L., Wilson, M.J., and Lamont, I.L., 2002, Iron transport and regulation, cell signalling and genomics: lessons from Escherichia coli and Pseudomonas. Mol. Microbiol., 45:1177-90.
102. Vodovar, N., Vallenet, D., Cruveiller, S., Rouy, Z., Barbe, V., Acosta, C., Cattolico, L., Jubin, C., Lajus, A., Segurens, B., Vacherie, B., Wincker, P., Weissenbach, J., Lemaitre, B., Medigue, C., and Boccard, F., 2006, Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila. Nature Biotechnol., 24:673-679.
103. Wagner-Döbler, I., Pipke, R., Timmis, K.N., and Dwyer, D.F., 1992, Evaluation of aquatic sediment microcosms and their use in assessing possible effects of introduced microorganisms on ecosystem parameters. Appl. Environ. Microbiol., 58:1249-1258.
104. Watson, J.D., and Crick, F.H.C., 1953, Genetical implications of the structure of deoxyribonucleic acid. Nature, 171:964-967.
105. Weinel, C., Nelson, K.E., and Tummler, B., 2002, Global features of the Pseudomonas putida KT2440 genome sequence. Environ. Microbiol., 4:809-818.
106. Wubbolts, M.G., and Timmis, K.N., 1990, Biotransformation of substituted benzoates to the corresponding cis-diols by an engineered strain of Pseudomonas oleovorans producing the TOL plasmid-specified enzyme toluate-1, 2-dioxygenase. Appl. Environ. Microbiol., 56:569-71.
107. Yuste, L., Hervás, A.B., Canosa, I., Tobes, R., Jiménez, J.I., Nogales, J., Pérez-Pérez, M.M., Santero, E., Díaz, E., Ramos, J.-L., de Lorenzo, V., and Rojo, F., 2006, Growth phase-dependent expression of the Pseudomonas putida KT2440 transcriptional machinery analysed with a genome-wide DNA microarray. Environ. Microbiol., 8:165-177.