Regulation of phenylacetic acid uptake is θ54 dependent in Pseudomonas putida CA-3

BMC Microbiology

Volumn 11, Issue , 2011, Pages

  O'Leary, Niall D ^a   O'Mahony, Mark M ^a   Dobson, Alan D ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL ENZYME; COENZYME A; PERMEASE; PHENYLACETIC ACID; SIGMA FACTOR RPON; STYRENE; BACTERIAL PROTEIN; CARRIER PROTEIN; PHENYLACETIC ACID DERIVATIVE;

ARTICLE; BACTERIUM MUTANT; BINDING SITE; BIOINFORMATICS; CARBON SOURCE; CATABOLISM; DEGRADATION; GENE ACTIVATION; GENE EXPRESSION; GENE INSERTION; GENETIC COMPLEMENTATION; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN EXPRESSION; PSEUDOMONAS PUTIDA; REGULATORY MECHANISM; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; TRANSCRIPTION INITIATION; TRANSCRIPTION INITIATION SITE; CONSENSUS SEQUENCE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; MOLECULAR GENETICS; PROMOTER REGION; TRANSPORT AT THE CELLULAR LEVEL;

PSEUDOMONAS; PSEUDOMONAS PUTIDA;

BACTERIAL PROTEINS; BASE SEQUENCE; BIOLOGICAL TRANSPORT; CONSENSUS SEQUENCE; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; MEMBRANE TRANSPORT PROTEINS; MOLECULAR SEQUENCE DATA; PHENYLACETATES; PROMOTER REGIONS, GENETIC; PSEUDOMONAS PUTIDA; RNA POLYMERASE SIGMA 54; STYRENE; TRANSCRIPTIONAL ACTIVATION;

EID: 80053930279     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-11-229     Document Type: Article

References (39)

1. Biochemistry, genetics and physiology of microbial styrene degradation. O' Leary ND, O' Connor KE, Dobson ADW, FEMS Microbiol Rev 2002 26 403 417 12413667 (Pubitemid 35284470)
2. The phenylacetyl-CoA catabolon: a complex catabolic unit with broad biotechnological applications. Luengo JM, Garcia JL, Olivera ER, Mol Microbiol 2001 39 1434 1442 10.1046/j.1365-2958.2001.02344.x 11260461 (Pubitemid 32269741)
3. Recurring cluster and operon assembly for phenylacetate degradation genes. Martin F, McInerney J, BMC Evol Biol 2009 9 1 9 10.1186/1471-2148-9-1 19121213
4. Bacterial phenylalanine and phenylacetate catabolic pathways revealed. Tuefel R, Mascaraque V, Ismail W, Vossa M, Perera J, Eisenreich W, Haehnel W, Fuchs G, PNAS 2010 107, 32 14390 14395
5. Genetic and functional analysis of the styrene catabolic cluster of Pseudomonas sp. strain Y2. Velasco A, Alonso S, Garcia JL, Perera J, Diaz E, J Bacteriol 1998 180 1063 1071 9495743 (Pubitemid 28119462)
6. Transcriptional regulation of styrene degradation in Pseudmonas putida CA-3. O' Leary ND, O' Connor KE, Deutz W, Dobson ADW, Microbiology 2001 147 973 979 11283293 (Pubitemid 32401337)
7. Physiological analysis of the expression of the styrene degradation gene cluster in Pseudomonas fluorescens ST. Santos PM, Blatny JM, Di Bartolo I, Valla S, Zennaro E, Appl Environ Microbiol 2000 66 1305 1310 10.1128/AEM.66.4.1305- 1310.2000 10742204 (Pubitemid 30185594)
8. Functional genomics by NMR spectroscopy; phenylacetate catabolism in Escherichia coli. Ismail W, Mohamed ME, Wanner BL, Datsenko KA, Eisenreich W, Rohdich F, Bacher F, Fuchs G, Eur J Biochem 2003 270 3047 3054 10.1046/j.1432-1033.2003.03683.x 12846838 (Pubitemid 36876273)
9. Genetic characterization of accumulation of polyhydroxyalkanoate from styrene in Pseudomonas putida CA-3. O' Leary ND, O'Connor KE, Ward P, Goff M, Dobson ADW, Appl Environ Microbiol 2005 71 4380 4387 10.1128/AEM.71.8.4380-4387. 2005 16085828 (Pubitemid 41129491)
10. Aerobic catabolism of phenylacetic acid in Pseudomonas putida U: Biochemical characterisation of a specific phenylacetic acid transport system and formal demonstration that phenylacetyl-Coenzyme A is a catabolic intermediate. Schleissner C, Olivera E, Fernandez-Valverde M, Luengo JM, J Bacteriol 1994 176 7667 7676 8002592 (Pubitemid 24382047)
11. Catabolism of phenylacetic acid in Escherichia coli. Ferrandez A, Minambres B, Garcia B, Olivera ER, Luengo JM, Garcia JL, Diaz E, J Biol Chem 1998 273 25974 25986 10.1074/jbc.273.40.25974 9748275 (Pubitemid 28475830)
12. Characterisation of a second functional gene cluster for the catabolism of phenylacetic acid in Pseudomonas sp. strain Y2. Bartolome-Martin D, Martinez-Garcia E, Mascaraque V, Rubio J, Perera J, Alonso S, Gene 2004 341 167 179 15474299 (Pubitemid 39341176)
13. The effect of nutrient limitation on styrene metabolism in Pseudomonas putida CA-3. O' Connor KE, Duetz W, Wind B, Dobson ADW, Appl Environ Microbiol 1996 64 3594 3599 (Pubitemid 26329582)
14. Possible regulatory role for non aromatic carbon sources in styrene degradation by Pseudomonas putida CA-3. O' Connor KE, Buckley CM, Hartmans S, Dobson ADW, Appl Environ Microbiol 1995 61 544 548 7574594
15. Analysis of the Pseudomonas putida CA-3 proteome during growth on styrene under nitrogen-limiting and non-limiting conditions. Nikodinovic-Runic J, Flanagan M, Hume A, Cagney G, O' Connor KE, Microbiology 2009 155 3348 3361 10.1099/mic.0.031153-0 19608612
16. Microbial degradation of styrene: biochemistry, molecular genetics, and perspectives for biotechnological applications. Mooney A, Ward P, O' Connor KE, Appl Microbiol Biotechnol 2006 72 1 10 10.1007/s00253-006-0443-1 16823552 (Pubitemid 44222417)
17. Molecular mechanisms of genetic adaptation to xenobiotic compounds. van der Meer JR, de Vos WM, Harayama S, Zehnder AJB, Microbiol Rev 1992 56 677 694 1480115
18. Accumulation of polyhydroxyalkanoate from styrene and phenylacetic acid by Pseudomonas putida CA-3. Ward PG, de Roo G, O' Connor KE, Appl Environ Microbiol 2005 71 2046 2052 10.1128/AEM.71.4.2046-2052.2005 15812037 (Pubitemid 40546129)
19. The sigma 54 regulon (sigmulon) of Pseudomonas putida. Cases I, Ussery DW, de Lorenzo V, Environ Microbiol 2003 5 1281 1293 10.1111/j.1462-2920.2003. 00528.x 14641574 (Pubitemid 38038940)
20. Genetic characterization of the styrene lower catabolic pathway of Pseudomonas sp. strain Y2. Alonso S, Bartolome-Martn D, del Alamoa M, Daz E, Garca JL, Perera J, Gene 2003 319 71 83 14597173 (Pubitemid 37346202)
21. Induction and repression of the sty operon in Pseudomonas putida CA-3 during growth on phenylacetic acid under organic and inorganic nutrient-limiting continuous culture conditions. O'Leary ND, Duetz WA, Dobson AD, O'Connor KE, FEMS Microbiol Lett 2002 208 263 268 10.1111/j.1574-6968.2002.tb11092.x 11959447 (Pubitemid 34310606)
22. Styrene lower catabolic pathway in Pseudomonas fluorescens ST: identification and characterization of genes for phenylacetic acid degradation. Di Gennaro P, Ferrara S, Ronco I, Galli E, Sello G, Papacchini M, Bestetti G, Arch Microbiol 2007 188 117 125 10.1007/s00203-007-0226-9 17377771 (Pubitemid 47101326)
23. Performance of a styrene degrading biofilter inoculated with Pseudomonas sp. SR-5. Jang JH, Hirai M, Shoda M, J Biosci Bioeng 2005 100 297 302 10.1263/jbb.100.297 16243280 (Pubitemid 41755295)
24. Cloning and functional characterization of the styE gene involved in styrene transport in Pseudomonas putida CA-3. Mooney A, O' Leary ND, Dobson ADW, Appl Environ Microbiol 2006 72 1302 1309 10.1128/AEM.72.2.1302-1309.2006 16461680 (Pubitemid 43271240)
25. Compilation and analysis of sigma54-dependent promoter sequences. Barrios H, Valderrama B, Morett E, Nucleic Acids Res 1999 27 4305 4313 10.1093/nar/27.22.4305 10536136 (Pubitemid 29533168)
26. The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. Studholme DJ, Buck M, FEMS Microbiol Lett 2000 186 1 9 10.1111/j.1574-6968.2000.tb09074.x 10779705 (Pubitemid 30211734)
27. Bacterial transcriptional regulators for degradation pathways of aromatic compounds. Tropel D, van der Meer JR, Microbiol Mol Biol Rev 2004 68 474 500 10.1128/MMBR.68.3.474-500.2004 15353566 (Pubitemid 39238279)
28. Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. Rappas M, Bose D, Zhang X, Curr Opin Struct Biol 2007 17 110 116 10.1016/j.sbi.2006.11.002 17157497 (Pubitemid 46240806)
29. Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Bailey TL, Elkan C, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology AAAI Press, Menlo Park, California 1994
30. Quantifying similarity between motifs. Gupta S, Stamatoyannopolous JA, Bailey T, Noble WS, Genome Biol 2007 8 24 10.1186/gb-2007-8-2-r24 (Pubitemid 351851032)
31. Indigo formation by microorganisms expressing styrene monooxygenase activity. O' Connor KE, Dobson ADW, Hartmans S, Appl Environ Microbiol 1997 63 4287 4291 9361415 (Pubitemid 27485752)
32. Virtual Footprint and PRODORIC: an integrative framework for regulon prediction in prokaryotes. Münch R, Hiller K, Grote A, Scheer M, Klein J, Schobert M, Jahn D, Bioinformatics 2005 21 4187 4189 10.1093/bioinformatics/ bti635 16109747 (Pubitemid 41672111)
33. The black cat/white cat principle of signal integration in bacterial promoters. Cases I, de Lorenzo V, EMBO J 2001 20 1 11 10.1093/emboj/20.1.1 11226149 (Pubitemid 32099096)
34. Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria. de Lorenzo V, Herrero M, Jakubzik U, Timmis K, J Bacteriol 1990 172 6568 6572 2172217 (Pubitemid 20372802)
35. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K, Current protocols in Molecular Biology New York, Greene Publishing Associates & Wiley Interscience 1987
36. Indigo formation by microorganisms expressing styrene monooxygenase activity. O' Connor KE, Dobson ADW, Hartmans S, Appl Environ Microbiol 1997 63 4287 4291 9361415 (Pubitemid 27485752)
37. Purification and biochemical characterization of phenylacetyl-CoA ligase from Pseudomonas putida. A specific enzyme for the catabolism of phenylacetic acid. Martinez-Blanco H, Reglero A, Rodriguez-Aparicio L, Luengo JM, J Biol Chem 1990 265 7084 7090 2324116
38. Genetic analysis of functions involved in adhesion of Pseudomonas putida to seeds. Espinosa-Urgel M, Salido A, Ramos JL, J Bacteriol 2000 182 2363 2369 10.1128/JB.182.9.2363-2369.2000 10762233 (Pubitemid 30212890)
39. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Kovach M, Elzer P, Hill D, Robertson G, Farris M, Roop R, Peterson K, Gene 1995 166 175 179