Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: Implications for transcriptomics studies

Applied Microbiology and Biotechnology

Volumn 75, Issue 5, 2007, Pages 1133-1142

  Ballerstedt, Hendrik ^a   Volkers, Rita J M ^a   Mars, Astrid E ^b   Hallsworth, John E ^c   Santos, Vitor A Martins Dos ^d   Puchalka, Jaçek ^d   Van Duuren, Joost ^b   Eggink, Gerrit ^b   Timmis, Ken N ^d   De Bont, Jan A M ^a,e   Wery, Jan ^a  

^a TNO   (Netherlands)

^b WAGENINGEN UNIVERSITY   (Netherlands)

^c QUEEN'S UNIVERSITY BELFAST   (United Kingdom)

^d HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^e DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

Author keywords

Genomotyping; Pseudomonas putida; Solvent tolerant bacteria; Transcriptomics

Indexed keywords

BACTERIA; GENES; MICROARRAYS; OLIGONUCLEOTIDES; PROTEINS; SOLVENTS;

GENOMOTYPING; MICROARRAY HYBRIDIZATIONS; PSEUDOMONAS PUTIDA; SOLVENT TOLERANT BACTERIA; TRANSCRIPTOMICS;

DNA;

BACTERIAL DNA; BACTERIAL PROTEIN; GENOMIC DNA;

ARRAY; BACTERIUM; CATABOLISM; DNA FINGERPRINTING; GENE; HYBRIDIZATION; METABOLISM; PHYLOGENY; PROTEIN;

ARTICLE; BACTERIAL GENOME; BACTERIAL STRAIN; BACTERIUM CULTURE; CELL FUNCTION; COMPARATIVE STUDY; CONTROLLED STUDY; DNA HYBRIDIZATION; DNA MICROARRAY; GENETIC STRAIN; GENOME ANALYSIS; GENOTYPE; MICROARRAY ANALYSIS; MOLECULAR PHYLOGENY; NONHUMAN; PROTEIN DEGRADATION; PROTEIN METABOLISM; PROTEOMICS; PSEUDOMONAS; PSEUDOMONAS MONTEILII; PSEUDOMONAS PUTIDA; RELIABILITY; TRANSCRIPTOMICS;

PSEUDOMONAS; PSEUDOMONAS MONTEILII; PSEUDOMONAS PUTIDA;

EID: 34250636769     PISSN: 01757598     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00253-007-0914-z     Document Type: Article

References (47)

1. Anzai Y, Kim H, Park J-Y, Wakabayashi H, Oyaizu H (2000) Phylogenetic affiliation of the pseudomonads based on 16S rRNA sequence. Int J Syst Evol Microbiol 50:1563-1589
2. Brosch R, Lefevre M, Grimont F, Grimont PAD (1996) Taxonomic diversity of pseudomonads revealed by computer interpretation of ribotyping data. Syst Appl Microbiol 19:541-555
3. Dabboussi F, Hamze M, Singer E, Geoffroy V, Meyer JM, Izard D (2002) Pseudomonas mosselii sp. nov., a novel species isolated from clinical specimens. Int J Syst Evol Microbiol 52:363-376
4. De Bont JAM (1998) Solvent-tolerant bacteria in biocatalysis. Trends Biotechnol 16:493-499
5. Dominguez-Cuevas P, Gonzalez-Pastor JE, Marques S, Ramos JL, 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
6. Duque E, Rodriguez-Herva JJ, de la Torre J, Dominguez-Cuevas P, Munoz-Rojas J, Ramos JL (2007) The RpoT regulon of Pseudomonas putida DOT-T1E and its role in stress endurance against solvents. J Bacteriol 189(1):207-219
7. Elomari M, Coroler L, Verhille S, Izard D, Leclerc H (1997) Pseudomonas monteilii sp. nov., isolated from clinical specimens. Int J Syst Bacteriol 47:846-852
8. Grimont PAD, Vancanneyt M, Lefevre M, Vandemeulebroecke K, Vauterin L, Brosch R, Kersters K, Grimont F (1996) Ability of Biolog and Biotype-100 systems to reveal the taxonomic diversity of the pseudomonads. System Appl Microbiol 19:510-527
9. Hallsworth JE, Heim S, Timmis KN (2003) Chaotropic solutes cause water stress in Pseudomonas putida. Environ Microbiol 5:1270-1280
10. Hartmans S, Van der Werf MJ, De Bont JAM (1990) Bacterial degradation of styrene involving a novel flavine adenine dinucleotide-dependent styrene monooxygenase. Appl Environ Microbiol 56:1347-1351
11. Janssen P, Coopman R, Huys G, Swings J, Bleeker M, Vos P, Zabeau M, Kersters K (1996) Evaluation of the DNA fingerprinting method AFLP as a new tool in bacterial taxonomy. Microbiology 142:1881-1893
12. Jimenez JI, Minambres B, Garcia JL, Diaz E (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4:824-841
13. Kieboom J, De Bont JAM (2000) Mechanisms of organic solvent tolerance in bacteria. In: Storz G, Hengge-Aronis R (eds) Bacterial stress responses. ASM press, Washington, pp 393-402
14. Martins dos Santos VAP, Heim S, Moore ERB, Strätz M, Timmis KN (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6:1264-1286
15. Morales G, Ugidos A, Rojo F (2006) Inactivation of the Pseudomonas putida cytochrome o ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environ Microbiol 8:1764-1774
16. Nakazawa T (2002) Travels of a Pseudomonas, from Japan around the world. Environ Microbiol 4:782-786
17. Nelson KE, Paulsen IT, Weinel C, Dodson RJ, Hilbert H, Fouts DE, Gill SR, Pop M, Martins dos Santos VAP, Holmes M, Brinkac L, Beanan M, DeBoy RT, 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 JA, Timmis KN, Dusterhoft A, Tümmler B, Fraser CM (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4:799-808
18. Nijkamp K, Van Luijk N, De Bont JAM, Wery J (2005) The solvent-tolerant Pseudomonas putida S12 as host for the production of cinnamic acid from glucose. Appl Microbiol Biotechnol 69:170-177
19. Nijkamp K, Westerhof RGM, Ballerstedt H, de Bont JAM, Wery J (2006) Optimization of the solvent-tolerant Pseudomonas putida S12 as host for the production of p-coumarate from glucose Appl Microbiol Biotechnol DOI 10.1007/s00253-006-0703-0
20. Ochsner UA, Wilderman PJ, Vasil AI, Vasil ML (2002) GeneChip expression analysis of the iron starvation response in Pseudomonas aeruginosa: identification of novel pyoverdine biosynthesis genes. Mol Microbiol 45:1277-1287
21. Ramos-Gonzalez MI, Ben-Bassat A, Campos MJ, Ramos JL (2003) Genetic engineering of a highly solvent-tolerant Pseudomonas putida strain for biotransformation of toluene to p-hydroxybenzoate. Appl Environ Microbiol 69:5120-5127
22. Ramos JL, Duque E, Gallegos MT, Godoy P, Ramos-Gonzalez MI, Rojas A, Teran W, Segura A (2002) Mechanisms of solvent tolerance in gram-negative bacteria. Annu Rev Microbiol 56:743-768
23. Regenhardt D, Heuer H, Heim S, Fernandez DU, Strömpl C, Moore ERB, Timmis KN (2002) Pedigree and taxonomic credentials of Pseudomonas putida strain KT2440. Environ Microbiol 4:912-915
24. Reva ON, Weinel C, Weinel M, Bohm K, Stjepandic D, Hoheisel JD, Tümmler B (2006) Functional genomics of stress response in Pseudomonas putida KT2440. J Bacteriol 188:4079-4092
25. Rojas A, Duque E, Schmid A, Hurtado A, Ramos J-L, Segura A (2004) Biotransformation in double-phase systems: physiological responses of Pseudomonas putida DOT-T1E to a double phase made of aliphatic alcohols and biosynthesis of substituted catechols. Appl Environ Microbiol 70:3637-3643
26. Sambrook J, Fritsch EF, Maniatis T (1982). Molecular cloning: a laboratory manual. Cold Spring Harbour Laboratory Press, Cold Spring Harbor, NY
27. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463-5467
28. Santos PM, Benndorf D, Sa-Correia I (2004) Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4:2640-2652
29. Savelkoul PHM, Aarts HJM, De Haas J, Dijkshoorn L, Duim B, Otsen M, Rademaker JLW, Schouls L, Lenstra JL (1999) Amplified-fragment length polymorphism analysis: the state of the art. J Clin Microbiol 37:3083-3091
30. Segura A, Godoy P, Van Dillewijn P, Hurtado A, Arroyo N, Santacruz S, Ramos JL (2005) Proteomic analysis reveals the participation of energy- and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J Bacteriol 187:5937-5945
31. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Evol Microbiol 44:846-849
32. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637
33. Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA (2003) The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41-55
34. Timmis KN (2002) Pseudomonas putida: a cosmopolitan opportunist par excellence. Environ Microbiol 4:779-781
35. Vacanneyt M, Torck U, de Wettinck D, Vaerewijck M, Kersters K (1996) Grouping of pseudomonads by SDS-PAGE of whole-cell proteins. System Appl Microbiol 19:556-568
36. Van den Braak N, Simons G, Gorkink R, Reijans M, Eadie K, Kremers K, Van Soolingen D, Savelkoul P, Verbrugh H, Van Belkum, A (2004) A new high-throughput AFLP approach for identification of new genetic polymorphism in the genome of the clonal microorganismen Mycobacterium tuberculosis. J Microbiol Methods 56:4-62
37. Volkers RJM, De Jong AL, Hulst AG, Van Baar BLM, De Bont JAM, Wery J (2006) Chemostat-based proteomic analysis of toluene-affected Pseudomonas putida S12. Environ Microbiol 8:1674-1679
38. Vos P, Hogers R, Bleeker M, Reijans M, Van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper J, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407-4414
39. Wackett LP (2003) Pseudomonas putida-a versatile biocatalyst. Nat Biotechnol 21:136-138
40. Wagner VE, Bushnell D, Passador L, Brooks AI, Iglewski BH (2003) Microarray analysis of Pseudomonas aeruginosa quorum-sensing regulons: effects of growth phase and environment. J Bacteriol 185:2080-2095
41. Wery J, De Bont JAM (2004) Solvent-tolerance of pseudomonads: a new degree of freedom in biocatalysis. In: Ramos JL (ed) Pseudomonas Vol 3: Biosynthesis of macromolecules and molecular metabolism, Kluwer Academic/Plenum Publishers, New York, pp 609-634
42. Wery J, Mendes da Silva DI, De Bont JAM (2000) A genetically modified solvent-tolerant bacterium for optimized production of a toxic fine chemical. Appl Microbiol Biotechnol 54:180-185
43. Whiteley M, Bangera MG, Baumgarner RE, Parsek MR, Teitzel GM, Lory S, Greenberg EP (2001) Gene expression in Pseudomonas aeruginosa biofilms. Nature 413:860-864
44. Wierckx JPN, Ballerstedt H, De Bont JAM, Wery J (2005) Bioproduction of phenol from glucose by Pseudomonas putida S12. Appl Environ Microbiol 71:8221-8227
45. Wolfgang MC, Lee VT, Gilmore ME, Lory S (2003) Coordinate regulation of bacterial virulence genes by a novel adenylate cyclase-dependent signaling pathway. Dev Cell 4:253-263
46. Woo Y, Affourtit J, Daigle S, Viale A, Johnson K, Naggert J, Churchill G (2004) A comparison of cDNA, oligonucleotide, and Affymetrix GeneChip gene expression microarray platforms. J Biomol Tech 15:276-284
47. Yuste L, Hervás AB, Canosa I, Tobes R, Jiménez JI, Nogales J, Pérez-Pérez MM, Santero E, E. D, Ramos J-L, De Lorenzo V, 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