Paradigm in biodegradation using Pseudomonas putida-A review of proteomics studies

Enzyme and Microbial Technology

Volumn 43, Issue 1, 2008, Pages 1-12

  Loh, Kai Chee ^a   Cao, Bin ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biodegradation; Catabolic pathway; Physiological response; Proteomics; Pseudomonas putida

Indexed keywords

AROMATIC COMPOUNDS; BIODEGRADATION; ENVIRONMENTAL IMPACT; METABOLISM; PROTEINS;

CATABOLIC PATHWAY; PHYSIOLOGICAL RESPONSE; PROTEOMICS; PSEUDOMONAS PUTIDA;

BACTERIA;

PROTEOME;

BIODEGRADATION; BIOREMEDIATION; CATABOLISM; ENVIRONMENT; GEL; MEDICAL RESEARCH; METHODOLOGY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYSIOLOGY; PROTEOMICS; PSEUDOMONAS PUTIDA; REVIEW; TECHNOLOGY;

BACTERIA (MICROORGANISMS); PSEUDOMONAS PUTIDA;

EID: 43949102015     PISSN: 01410229     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.enzmictec.2008.03.004     Document Type: Review

References (81)

1. O'Farrell P.H. High resolution two-dimensional electrophoresis of proteins. J Biol Chem 250 (1975) 4007-4021
2. Norbeck J., and Blomberg A. Two-dimensional electrophoretic separation of yeast proteins using a non-linear wide range (pH 3-10) immobilized pH gradient in the first dimension; reproducibility and evidence for isoelectric focusing of alkaline (pI > 7) proteins. Yeast 13 (1997) 1519-1534
3. Blomberg A., Blomberg L., Norbeck J., Fey S.J., Larsen P.M., Larsen M., et al. Interlaboratory reproducibility of yeast protein-patterns analyzed by immobilized pH gradient 2-dimensional gel-electrophoresis. Electrophoresis 16 (1995) 1935-1945
4. Tonella L., Hoogland C., Binz P.A., Appel R.D., Hochstrasser D.F., and Sanchez J.C. New perspectives in the Escherichia coli proteome investigation. Proteomics 1 (2001) 409-423
5. Molloy M.P., Herbert B.R., Walsh B.J., Tyler M.I., Traini M., Sanchez J.C., et al. Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19 (1998) 837-844
6. Berkelman T. Sensitivity and protein-to-protein consistency of Flamingo fluorescent gel stain compared to other fluorescent stains. Mol Cell Proteom 5 (2006) S47-S147
7. Lanne B., and Panfilov O. Protein staining influences the quality of mass spectra obtained by peptide mass fingerprinting after separation on 2D gels. A comparison of staining with Coomassie Brilliant Blue and SYPRO Ruby. J Proteome Res 4 (2005) 175-179
8. White I.R., Pickford R., Wood J., Skehel J.M., Gangadharan B., and Cutler P. A statistical comparison of silver and SYPRO Ruby staining for proteomic analysis. Electrophoresis 25 (2004) 3048-3054
9. Lopez M.F., Berggren K., Chernokalskaya E., Lazarev A., Robinson M., and Patton W.F. A comparison of silver stain and SYPRO Ruby protein gel stain with respect to protein detection in two-dimensional gels and identification by peptide mass profiling. Electrophoresis 21 (2000) 3673-3683
10. Wolters D.A., Washburn M.P., and Yates J.R. An automated multidimensional protein identification technology for shotgun proteomics. Anal Chem 73 (2001) 5683-5690
11. Washburn M.P., Wolters D., and Yates J.R. Large-scale analysis of the yeast proteome by multidimensional protein identification technology. Nat Biotechnol 19 (2001) 242-247
12. Ross P.L., Huang Y.L.N., Marchese J.N., Williamson B., Parker K., Hattan S., et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteom 3 (2004) 1154-1169
13. DeSouza L., Diehl G., Rodrigues M.J., Guo J.Z., Romaschin A.D., Colgan T.J., et al. Search for cancer markers from endometrial tissues using differentially labeled tags iTRAQ and clCAT with multidimensional liquid chromatography and tandem mass spectrometry. J Proteome Res 4 (2005) 377-386
14. Unwin R.D., Pierce A., Watson R.B., Sternberg D.W., and Whetton A.D. Quantitative proteomic analysis using isobaric protein tags enables rapid comparison of changes in transcript and protein levels in transformed cells. Mol Cell Proteom 4 (2005) 924-935
15. Hardt M., Witkowska H.E., Webb S., Thomas L.R., Dixon S.E., Hall S.C., et al. Assessing the effects of diurnal variation on the composition of human parotid saliva: quantitative analysis of native peptides using iTRAQ reagents. Anal Chem 77 (2005) 4947-4954
16. Shadforth I., Crowther D., and Bessant C. Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines. Proteomics 5 (2005) 4082-4095
17. Babnigg G., and Giometti C.S. ProteomeWeb: a web-based interface for the display and interrogation of proteomes. Proteomics 3 (2003) 584-600
18. Pleissner K.P., Eifert T., Buettner S., Schmidt F., Boehme M., Meyer T.F., et al. Web-accessible proteome databases for microbial research. Proteomics 4 (2004) 1305-1313
19. Drews O., and Gorg A. DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels. Nucleic Acids Res 33 (2005) D583-D587
20. Elliott S.T., Crider D.G., Garham C.P., Boheler K.R., and Van Eyk J.E. Two-dimensional gel electrophoresis database of cultured murine R1 embryonic stem cells. Proteomics 4 (2004) 3813-3832
21. Laukens K., Deckers P., Esmans E., Van Onckelen H., and Witters E. Construction of a two-dimensional gel electrophoresis protein database for the Nicotiana tabacum cv. Bright Yellow-2 cell suspension culture. Proteomics 4 (2004) 720-727
22. Pruess M., Fleischmann W., Kanapin A., Karavidopoulou Y., Kersey P., Kriventseva E., et al. The proteome analysis database: a tool for the in silico analysis of whole proteomes. Nucleic Acids Res 31 (2003) 414-417
23. Haoudi A., and Bensmail H. Bioinformatics and data mining in proteomics. Exp. Rev. Proteomics 3 (2006) 333-343
24. Englbrecht C.C., and Facius A. Bioinformatics challenges in proteomics. Comb. Chem. High Throughput Screen. 8 (2005) 705-715
25. Cristoni S., and Bernordi L.R. Bioinformatics in mass spectrometry data analysis for proteomics studies. Expert Rev. Proteomics 1 (2004) 469-483
26. Stover C.K., Pham X.Q., Erwin A.L., Mizoguchi S.D., Warrener P., Hickey M.J., et al. Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406 (2000) 959-964
27. Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., dos Santos V., et al. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4 (2002) 799-808
28. Heim S., Ferrer M., Heuer H., Regenhardt D., Nimtz M., and Timmis K.N. 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 (2003) 1257-1269
29. Kurbatov L., Albrecht D., Herrmann H., and Petruschka L. Analysis of the proteome of Pseudomonas putida KT2440 grown on different sources of carbon and energy. Environ Microbiol 8 (2006) 466-478
30. Volkers R.J.M., de Jong A.L., Hulst A.G., van Baar B.L.M., de Bont J.A.M., and Wery J. Chemostat-based proteomic analysis of toluene-affected Pseudomonas putida S12. Environ Microbiol 8 (2006) 1674-1679
31. Kim Y.H., Cho K., Yun S.-H., Kim J.Y., Kwon K.-H., Yoo J.S., et al. Analysis of aromatic catabolic pathways in Pseudomonas putida KT2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. Proteomics 6 (2006) 1301-1318
32. Harwood C.S., and Parales R.E. The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50 (1996) 553-590
33. Jimenez J.I., Minambres B., Garcia J.L., and Diaz E. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4 (2002) 824-841
34. Moody J.D., Doerge D.R., Freeman J.P., and Cerniglia C.E. Degradation of biphenyl by Mycobacterium sp. strain PYR-1. Appl Microbiol Biotechnol 58 (2002) 364-369
35. Loh K.C., and Chua S.S. Ortho pathway of benzoate degradation in Pseudomonas putida: induction of meta pathway at high substrate concentrations. Enzyme Microbial Technol 30 (2002) 620-626
36. Ward P.G., and O'Connor K.E. Induction and quantification of phenylacyl-CoA ligase enzyme activities in Pseudomonas putida CA-3 grown on aromatic carboxylic acids. FEMS Microbiol Lett 251 (2005) 227-232
37. Nogales J., Macchi R., Franchi F., Barzaghi D., Fernandez C., Garcia J.L., et al. Characterization of the last step of the aerobic phenylacetic acid degradation pathway. Microbiology 153 (2007) 357-365
38. Kiesel B., and Muller R.H. The meta pathway as a potential energy-generating sequence and its effects on the growth rate during the utilisation of aromatics. Acta Biotechnol 22 (2002) 221-234
39. Yang Y.J., Chen R.F., and Shiaris M.P. Metabolism of naphthalene, fluorene, and phenanthrene-preliminary characterization of a cloned gene-cluster from Pseudomonas putida NCIB-9816. J Bacteriol 176 (1994) 2158-2164
40. Mooney A., O'Leary N.D., and Dobson A.D.W. Cloning and functional characterization of the styE gene, involved in styrene transport in Pseudomonas putida CA-3. Appl Environ Microbiol 72 (2006) 1302-1309
41. Tsirogianni I., Aivaliotis M., Karas M., and Tsiotis G. Mass spectrometric mapping of the enzymes involved in the phenol degradation of an indigenous soil pseudomonad. Biochim Biophys Acta: Proteins Proteom 1700 (2004) 117-123
42. Tsirogianni E., Aivaliotis M., Papasotiriou D.G., Karas M., and Tsiotis G. Identification of inducible protein complexes in the phenol degrader Pseudomonas sp. strain phDV1 by blue native gel electrophoresis and mass spectrometry. Amino Acids 30 (2006) 63-72
43. Madhusudhan K.T., McLaughlin R., Komori N., and Matsumoto H. Identification of a major protein upon phosphate starvation of Pseudomonas aeruginosa PAO1. J Basic Microbiol 43 (2003) 36-46
44. Lee Y., Pena-Llopis S., Kang Y.S., Shin H.D., Demple B., Madsen E.L., et al. Expression analysis of the fpr (ferredoxin-NADP(+) reductase) gene in Pseudomonas putida KT2440. Biochem Biophys Res Commun 339 (2006) 1246-1254
45. Kertesz M.A., Leisinger T., and Cook A.M. Proteins induced by sulfate limitation in Escherichia coli, Pseudomonas putida, or Staphylococcus aureus. J Bacteriol 175 (1993) 1187-1190
46. Givskov M., Eberl L., and Molin S. Responses to nutrient starvation in Pseudomonas putida KT2442-2-dimensional electrophoretic analysis of starvation-induced and stress-induced proteins. J Bacteriol 176 (1994) 4816-4824
47. Lupi C.G., Colangelo T., and Mason C.A. 2-Dimensional gel-electrophoresis analysis of the response of Pseudomonas putida KT2442 to 2-chlorophenol. Appl Environ Microbiol 61 (1995) 2863-2872
48. Reardon K.F., and Kim K.H. Two-dimensional electrophoresis analysis of protein production during growth of Pseudomonas putida F1 on toluene, phenol, and their mixture. Electrophoresis 23 (2002) 2233-2241
49. Hallsworth J.E., Heim S., and Timmis K.N. Chaotropic solutes cause water stress in Pseudomonas putida. Environ Microbiol 5 (2003) 1270-1280
50. Santos P.M., Benndorf D., and Sa-Correia I. Insights into Pseudomonas putida KT2440 response to phenol-induced stress by quantitative proteomics. Proteomics 4 (2004) 2640-2652
51. Krayl M., Benndorf D., Loffhagen N., and Babel W. Use of proteomics and physiological characteristics to elucidate ecotoxic effects of methyl tert-butyl ether in Pseudomonas putida KT2440. Proteomics 3 (2003) 1544-1552
52. Benndorf D., Thiersch M., Loffhagen N., Kunath C., and Harms H. Pseudomonas putida KT2440 responds specifically to chlorophenoxy herbicides and their initial metabolites. Proteomics 6 (2006) 3319-3329
53. Segura A., Godoy P., van Dillewijn P., Hurtado A., Arroyo N., Santacruz S., et al. Proteomic analysis reveals the participation of energy- and stress-related proteins in the response of Pseudomonas putida DOT-T1E to toluene. J Bacteriol 187 (2005) 5937-5945
54. Yun S.-H., Kim Y.H., Joo E.J., Choi J.-S., Sohn J.-H., and Kim S.I. Proteome analysis of cellular response of Pseudomonas putida KT2440 to tetracycline stress. Curr Microbiol 53 (2006) 95-101
55. Leonhäuser J., Wang W., Deckwer W., and Wagner-Döbler I. Functioning of the mercury resistance operon at extremely high Hg(II) loads in a chemostat: a proteome analysis. J Biotechnol 132 (2007) 469-480
56. Waite R.D., Papakonstantinopoulou A., Littler E., and Curtis M.A. Transcriptome analysis of Pseudomonas aeruginosa growth: comparison of gene expression in planktonic cultures and developing and mature biofilms. J Bacteriol 187 (2005) 6571-6576
57. Schuster M., Lostroh C.P., Ogi T., and Greenberg E.P. Identification, timing, and signal specificity of Pseudomonas aeruginosa quorum-controlled genes: a transcriptome analysis. J Bacteriol 185 (2003) 2066-2079
58. Sauer K., Camper A.K., Ehrlich G.D., Costerton J.W., and Davies D.G. Pseudomonas aeruginosa displays multiple phenotypes during development as a biofilm. J Bacteriol 184 (2002) 1140-1154
59. Whiteley M., Bangera M.G., Bumgarner R.E., Parsek M.R., Teitzel G.M., Lory S., et al. Gene expression in Pseudomonas aeruginosa biofilms. Nature 413 (2001) 860-864
60. Fagerlind M.G., Rice S.A., Nilsson P., Harlen M., James S., Charlton T., et al. The role of regulators in the expression of quorum-sensing signals in Pseudomonas aeruginosa. J Mol Microbiol Biotechnol 6 (2003) 88-100
61. Sauer K., and Camper A.K. Characterization of phenotypic changes in Pseudomonas putida in response to surface-associated growth. J Bacteriol 183 (2001) 6579-6589
62. Arevalo-Ferro C., Reil G., Gorg A., Eberl L., and Riedel K. Biofilm formation of Pseudomonas putida IsoF: the role of quorum sensing as assessed by proteomics. Syst Appl Microbiol 28 (2005) 87-114
63. Kjelleberg S., and Molin S. Is there a role for quorum sensing signals in bacterial biofilms?. Curr Opin Microbiol 5 (2002) 254-258
64. Shen Y.F., Zhao R., Belov M.E., Conrads T.P., Anderson G.A., Tang K.Q., et al. Packed capillary reversed-phase liquid chromatography with high-performance electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry for proteomics. Anal Chem 73 (2001) 1766-1775
65. Chong B.E., Yan F., Lubman D.M., and Miller F.R. Chromatofocusing nonporous reversed-phase high-performance liquid chromatography/electrospray ionization time-of-flight mass spectrometry of proteins from human breast cancer whole cell lysates: a novel two-dimensional liquid chromatography/mass spectrometry method. Rapid Commun Mass Spectrom 15 (2001) 291-296
66. Breci L., Hattrup E., Keeler M., Letarte J., Johnson R., and Haynes P.A. Comprehensive proteomics in yeast using chromatographic fractionation, gas phase fractionation, protein gel electrophoresis, and isoelectric focusing. Proteomics 5 (2005) 2018-2028
67. Wei J., Sun J., Yu W., Jones A., Oeller P., Keller M., et al. Global proteome discovery using an online three-dimensional LC-MS/MS. J Proteome Res 4 (2005) 801-808
68. Oda Y., Huang K., Cross F.R., Cowburn D., and Chait B.T. Accurate quantitation of protein expression and site-specific phosphorylation. Proc Natl Acad Sci USA 96 (1999) 6591-6596
69. Gygi S.P., Rist B., Gerber S.A., Turecek F., Gelb M.H., and Aebersold R. Quantitative analysis of complex protein mixtures using isotope-coded affinity tags. Nat Biotechnol 17 (1999) 994-999
70. Yao X.D., Freas A., Ramirez J., Demirev P.A., and Fenselau C. Proteolytic O-18 labeling for comparative proteomics: model studies with two serotypes of adenovirus. Anal Chem 73 (2001) 2836-2842
71. Sonawane A., Kloppner U., Hovel S., Volker U., and Rohm K.-H. Identification of Pseudomonas proteins coordinately induced by acidic amino acids and their amides: a two-dimensional electrophoresis study. Microbiology 149 (2003) 2909-2918
72. Sonawane A.M., Singh B., and Rohm K.-H. The AauR-AauS two-component system regulates uptake and metabolism of acidic amino acids in Pseudomonas putida. Appl Environ Microbiol 72 (2006) 6569-6577
73. Cases I., Lopez J.A., Albar J.P., and De Lorenzo V. Evidence of multiple regulatory functions for the PtsN (IIA(Ntr)) protein of Pseudomonas putida. J Bacteriol 183 (2001) 1032-1037
74. Morales G., Linares J.F., Beloso A., Albar J.P., Martinez J.L., and Rojo F. The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds. J Bacteriol 186 (2004) 1337-1344
75. Denef V.J., Patrauchan M.A., Florizone C., Park J., Tsoi T.V., Verstraete W., et al. Growth substrate- and phase-specific expression of biphenyl, benzoate, and C-1 metabolic pathways in Burkholderia xenovorans LB400. J Bacteriol 187 (2005) 7996-8005
76. Patrauchan M.A., Florizone C., Dosanjh M., Molm W.W., Davies J., and Eltis L.D. Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence. J Bacteriol 187 (2005) 4050-4063
77. Kim S.I., Kim J.Y., Yun S.-H., Kim J.H., Leem S.H., and Lee C. Proteome analysis of Pseudomonas sp. K82 biodegradation pathways. Proteomics 4 (2004) 3610-3621
78. Kim S.I., Song S.Y., Kim K.W., Ho E.M., and Oh K.H. Proteomic analysis of the benzoate degradation pathway in Acinetobacter sp. KS-1. Res Microbiol 154 (2003) 697-703
79. Kim S.I., Kim S.J., Nam M.H., Kim S.H., Ha K.S., Oh K.H., et al. Proteome analysis of aniline-induced proteins in Acinetobacter lwoffii K24. Curr Microbiol 44 (2002) 61-66
80. Denef V.J., Park J., Tsoi T.V., Rouillard J.M., Zhang H., Wibbenmeyer J.A., et al. Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70 (2004) 4961-4970
81. Tomas-Gallardo L., Ganosa I., Santero E., Camafeita E., Calvo E., Lopez J.A., et al. Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodoccocus sp. strain TFB. Proteomics 6 (2006) S119-S132