Generation of a catR deficient mutant of P. putida KT2440 that produces cis, cis-muconate from benzoate at high rate and yield

Journal of Biotechnology

Volumn 156, Issue 3, 2011, Pages 163-172

  Van Duuren, J B J H ^a,b,d   Wijte, D ^c   Leprince, A ^b   Karge, B ^b   Puchalka J ^b,d   Wery, J ^c,d   Dos Santos, V A P Martins ^b,d   Eggink, G ^a,d   Mars, A E ^a,c  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^c TNO   (Netherlands)

^d KLUYVER CENTRE FOR GENOMICS OF INDUSTRIAL FERMENTATION   (Netherlands)

Author keywords

3 Fluorobenzoate; Benzoate; Catechol 1,2 dioxygenase; Cis, cis muconate; NTG mutagenesis; P. putida KT2440

Indexed keywords

3-FLUOROBENZOATE; BENZOATE; CATECHOL 1 ,2-DIOXYGENASE; CIS, CIS-MUCONATE; NTG MUTAGENESIS; P. PUTIDA KT2440;

GLUCOSE; MUTAGENESIS;

PHENOLS;

BENZOIC ACID; CARBON; CATECHOL 1,2 DIOXYGENASE; MUCONIC ACID; TRANSCRIPTOME;

ARTICLE; DNA BINDING; NONHUMAN; OPERON; PRIORITY JOURNAL; PSEUDOMONAS PUTIDA; TRANSCRIPTION REGULATION;

BACTERIAL PROTEINS; BENZOATES; BENZOIC ACIDS; BIOTECHNOLOGY; DNA-BINDING PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; MUTATION; OPERON; PSEUDOMONAS PUTIDA; REGULATORY ELEMENTS, TRANSCRIPTIONAL; SORBIC ACID; TRANSCRIPTION FACTORS; UP-REGULATION;

PSEUDOMONAS PUTIDA;

EID: 80054104927     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2011.08.030     Document Type: Article

References (52)

1. Adelberg E.A., Mandel M., Chen G.C.C. Optimal conditions for mutagenesis by N-methyl-N'-nitro-N-nitrosoguanidine in Escherichia coli K12. Biochem. Biophys. Res. Commun. 1965, 18:788-795.
2. Ballerstedt H., Volkers R.J.M., Mars A.E., Hallsworth J.E., dos Santos V.A., Puchalka J., van Duuren J., Eggink G., Timmis K.N., de Bont J.A.M., Wery J. Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays, implications for transcriptomics studies. Appl. Microbiol. Biotechnol. 2007, 75:1133-1142.
3. Bang S.G., Choi C.Y. DO-stat fed-batch production of cis, cis-muconic acid from benzoic-acid by Pseudomonas putida BM014. J. Ferment. Bioeng. 1995, 79:381-383.
4. Bang S.G., Choi W.J., Choi C.Y., Cho M.H. Production of cis, cis-muconic acid from benzoic acid via microbial transformation. Biotechnol. Bioprocess Bioeng. 1996, 1:36-40.
5. Breitling R., Armengaud P., Amtmann A., Herzyk P. Rank products: a simple, yet powerful, new method to detect differentially regulated genes in replicated microarray experiments. FEBS Lett. 2004, 573:83-92.
6. Cao B., Geng A., Loh K.C. Induction of ortho- and meta-cleavage pathways in Pseudomonas in biodegradation of high benzoate concentration: MS identification of catabolic enzymes. Appl. Microbiol. Biotechnol. 2008, 81:99-107.
7. Cao B., Loh K.C. Catabolic pathways and cellular responses of Pseudomonas putida P8 during growth on benzoate with a proteomics approach. Biotechnol. Bioeng. 2008, 101:1297-1312.
8. Cheng Y., Prusoff W.H. Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. Biochem. Pharmacol. 1973, 22:3099-3108.
9. Choi W.J., Lee E.Y., Cho M.H., Choi C.Y. Enhanced production of cis,cis-muconate in a cell-recycle bioreactor. J. Ferment. Bioeng. 1997, 84:70-76.
10. de Groot M.J.L., Daran-Lapujade P., van Breukelen B., Knijnenburg T.A., de Hulster E.A.F., Reinders M.J.T., Pronk J.T., Heck A.J.R., Slijper M. Quantitative proteomics and transcriptomics of anaerobic and aerobic yeast cultures reveals post-transcriptional regulation of key cellular processes. Microbiology 2007, 153:3864-3878.
11. Domínguez-Cuevas P., González-Pastor J.E., Marqués S., Ramos J.L., de Lorenzo V. Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J. Biol. Chem. 2006, 281:11981-11991.
12. Duetz W.A., van Beilen J.B., Witholt B. Using proteins in their natural environment: potential and limitations of microbial whole-cell hydroxylations in applied biocatalysis. Curr. Opin. Biotechnol. 2001, 12:419-425.
13. Dudoit S., Popper Shaffer J., Boldrick J.C. Multiple hypothesis testing in microarray experiments. Stat. Sci. 2003, 18:71-103.
14. Earhart C.A., Vetting M.W., Gosu R., Michaud-Soret I., Que L., Ohlendorf D.H. Structure of catechol 1,2-dioxygenase from Pseudomonas arvilla. Biochem. Biophys. Res. Commun. 2005, 338:198-205.
15. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D: Biol. Crystallogr. 2004, 60:2126-2132.
16. Federal Register, 1982. Certified Host-Vector Systems, 17197.
17. Gentleman R.C., Carey V.J., Bates D.M., Bolstad B., Dettling M., Dudoit S., Ellis B., Gautier L., Ge Y., Gentry J., Hornik K., Hothorn T., Huber W., Iacus S., Irizarry R., Leisch F., Li C., Maechler M., Rossini A.J., Sawitzki G., Smith C., Smyth G., Tierney L., Yang J.Y.H., Zhang J. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 2004, 5:R80.
18. Göbel M., Kassel-Cati K., Schmidt E., Reineke W. Degradation of aromatics and chloroaromatics by Pseudomonas sp. strain B13: cloning, characterization, and analysis of sequences encoding 3-oxoadipate: succinyl-coenzyme A (CoA) transferase and 3-oxoadipyl-CoA thiolase. J. Bacteriol. 2002, 184:216-223.
19. Hartmans S., Smits J.P., van der Werf M.J., Volkering F., de Bont J.A.M. Metabolism of styrene oxide and 2-phenylethanol in the styrene-degrading Xanthobacter Strain 124X. Appl. Environ. Microbiol. 1989, 55:2850-2855.
20. Havlis J., Thomas H., Sebela M., Shevchenko A. Fast-response proteomics by accelerated in-gel digestion of proteins. Anal. Chem. 2003, 75:1300-1306.
21. Holtwick R., von Wallbrunn A., Keweloh H., Meinhardt F. A novel rolling-circle-replicating plasmid from Pseudomonas putida P8: molecular characterization and use as vector. Microbiology 2001, 147:337-344.
22. Houghton J.E., Brown T.M., Appel A.J., Hughes E.J., Ornston L.N. Discontinuities in the evolution of Pseudomonas putida cat genes. J. Bacteriol. 1995, 177:401-412.
23. Jeffrey W.H., Cuskey S.M., Chapman P.J., Resnick S., Olsen R.H. Characterization of Pseudomonas putida mutants unable to catabolize benzoate: cloning and characterization of Pseudomonas genes involved in benzoate catabolism and isolation of a chromosomal DNA fragment able to substitute for xylS in activation of the TOL lower-pathway promoter. J. Bacteriol. 1992, 174:4986-4996.
24. Jiménez J.I., Miñambres B., García J.L., Díaz E. Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ. Microbiol. 2002, 4:824-841.
25. Kiefer F., Arnold K., Künzli M., Bordoli L., Schwede T. The SWISS-MODEL repository and associated resources. Nucleic Acids Res. 2009, 37:D387-D392.
26. Kim B.J., Choi W.J., Lee E.Y., Choi C.Y. Enhancement of cis, cis-muconate productivity by overexpressing of catechol 1.2-dioxygenase in Pseudomonas putida BCM114. Biotechnol. Bioprocess Eng. 1988, 3:112-114.
27. Kim Y.H., Cho K., Yun S.H., Kim J.Y., Kwon K.H., Yoo J.S., Kim S.I. Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. Proteomics 2006, 6:1301-1318.
28. Kolkman A., Daran-Lapujade P., Fullaondo A., Olsthoorn M.M., Pronk J.T., Slijper M., Heck A.J. Proteome analysis of yeast response to various nutrient limitations. Mol. Syst. Biol. 2006, 0026.
29. Kopp J., Schwede T. The SWISS-MODEL repository: new features and functionalities. Nucleic Acids Res. 2006, 34:D315-D318.
30. Kovach M.E., Elzer P.H., Hill D.S., Robertson G.T., Farris M.A., Roop R.M., Peterson K.M. Four new derivatives of the broad-host-range cloning vector pBBR1MCS, carrying different antibiotic-resistance cassettes. Gene 1995, 166:175-176.
31. Krieg R.C., Paweletz C.P., Liotta L.A., Petricoin E.F. Dilution of protein gel stain results in retention of staining capacity. Biotechniques 2003, 35:376-378.
32. Martins dos Santos V.A.P., Heim S., Strätz M., Timmis K.N. Insights into the genomic basis of niche specificity of Pseudomonas putida strain KT2440. Environ. Microbiol. 2004, 6:1264-1286.
33. Mizuno S., Yoshikawa N., Schi M., Mikawa T., Imada Y. Microbial-production of cis, cis-muconic acid from benzoic-acid. Appl. Microbiol. Biotechnol. 1988, 28:20-25.
34. Muraoka S., Okumura R., Ogawa N., Nonaka T., Miyashita K., Senda T. Crystal structure of a full-length LysR-type transcriptional regulator, CbnR: unusual combination of two subunit forms and molecular bases for causing and changing DNA bend. J. Mol. Biol. 2003, 328:555-566.
35. Myers A.G., Siegel D.R., Buzard D.J., Charest M.G. Synthesis of a broad array of highly functionalized, enantiomerically pure cyclohexanecarboxylic acid derivatives by microbial dihydroxylation of benzoic acid and subsequent oxidative and rearrangement reactions. Org. Lett. 2001, 3:2923-2926.
36. Nakai C., Uyeyama H., Kagamiyama H., Nakazawa T., Inouye S., Kishi F., Nakazawa A., Nozaki M. Cloning, DNA sequencing, and amino acid sequencing of catechol 1,2-dioxygenases (pyrocatechase) from Pseudomonas putida mt-2 and Pseudomonasarvilla C-1. Arch. Biochem. Biophys. 1995, 321:353-362.
37. Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H., Martins dos Santos V.A.P., 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., Düsterhöft A., Tümmler B., Fraser C.M. Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ. Microbiol. 2002, 4:799-808.
38. Parke D. Supraoperonic clustering of pca genes for catabolism of the phenolic compound protocatechuate in Agrobacterium tumefaciens. J. Bacteriol. 1995, 177:3808-3817.
39. Parsek M.R., Shinabarger D.L., Rothmel R.K., Chakrabarty A.M. Roles of CatR and cis, cis-muconate in activation of the catBC operon, which is involved in benzoate degradation in Pseudomonas putida. J. Bacteriol. 1992, 174:7798-7806.
40. Pieper D.H., Martins dos Santos V.A.P., Golyshin P.N. Genomic and mechanistic insights into the biodegradation of organic pollutants. Curr. Opin. Biotechnol. 2004, 6:4-13.
41. Ramos J.L., Wasserfallen A., Rose K., Timmis K.N. Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science 1987, 235:593-596.
42. Romero-Steiner S., Parales R.E., Harwood C.S., Houghton J.E. Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate. J. Bacteriol. 1994, 176:5771-5779.
43. Rosen R., Ron E.Z. Proteome analysis in the study of the bacterial heat-shock response. Mass. Spectrom. Rev. 2002, 21:244-265.
44. Schmidt E., Knackmuss H.J. Production of cis,cis-Muconate from benzoate and 2-fluoro-cis,cis-muconate from 3-fluorobenzoate by 3-chlorobenzoate degrading bacteria. Appl. Microbiol. Biotechnol. 1984, 20:351-355.
45. Schreiber A., Hellwig M., Dorn E., Reineke W., Knackmuss H.J. Critical reactions in fluorobenzoic acid degradation by Pseudomonas sp. B13. Appl. Environ. Microbiol. 1980, 39:58-67.
46. Thompson J.D., Gibson T.J., Higgins D.G. Multiple sequence alignment using ClustalW and ClustalX. Curr. Protoc. Bioinformatics 2002, Chapter 2, Unit 2.3.
47. VanBogelen R.A., Neidhardt F.C. Preparation of Escherichia coli samples for 2-D gel analysis. Methods Mol. Biol. 1999, 112:21-29.
48. van Duuren J.B., Brehmer B., Mars A.E., Eggink G., Dos Santos V.A., Sanders J.P. A limited LCA of bio-adipic acid: manufacturing the nylon-6,6 precursor adipic acid using the benzoic acid degradation pathway from different feedstocks. Biotechnol. Bioeng. 2011, 108:1298-1306.
49. Wackett L.P. P. putida - a versatile biocatalyst. Nat. Biotechnol. 2003, 21:136-138.
50. Wijte D., de Jong A.L., Mol M.A.E., van Baar B.L.M., Heck A.J.R. ProteomIQ blue, a potent post-stain for the visualization and subsequent mass spectrometry based identification of fluorescent stained proteins on 2D-gels. J. Proteome Res. 2006, 5:2033-2038.
51. Wu C.M., Lee T.H., Lee S.N., Lee Y.A., Wu J.Y. Microbial synthesis of cis, cis-muconic acid from benzoate by Sphingobacterium sp. GCG generated from effluent of a styrene monomer (SM) production plant. Biochem. Eng. J. 2006, 29:35-40.
52. Wu Z., Irizarry R.A., Gentleman R., Murillo F.M., Spencer F. A model-based background adjustment for oligonucleotide expression arrays. J. Am. Stat. Assoc. 2004, 99:909-917.