Functional characterization and application of a tightly regulated MekR/P mekA expression system in Escherichia coli and Pseudomonas putida

Applied Microbiology and Biotechnology

Volumn 97, Issue 18, 2013, Pages 8239-8251

  Graf, Nadja ^a   Altenbuchner, Josef ^a  

^a UNIVERSITY OF STUTTGART   (Germany)

Author keywords

AraC XylS family; Broad host range vector; Class II promoter; Expression system; Transcription activation

Indexed keywords

ARAC/XYLS FAMILY; CARBON CATABOLITE REPRESSION; CLASS II; ESCHERICHIA COLI JM109; EXPRESSION SYSTEM; FUNCTIONAL CHARACTERIZATION; MUTATIONAL MODIFICATION; TRANSCRIPTIONAL ACTIVATIONS;

BACTERIA; ESCHERICHIA COLI; GENE EXPRESSION; KETONES;

BIODEGRADATION;

2 BUTANONE; BACTERIAL DNA; BACTERIAL PROTEIN; BETA GALACTOSIDASE; CARBON; CRC PROTEIN; GLUCOSE; MEKA PROTEIN; MEKR PROTEIN; MESSENGER RNA; PLASMID DNA; PTSN PROTIEN; REGULATOR PROTEIN; UNCLASSIFIED DRUG;

BACTERIUM; GENE EXPRESSION; GLUCOSE; KETONE; PLASMID;

ARTICLE; BINDING SITE; CATABOLITE REPRESSION; ENZYME ACTIVITY; ESCHERICHIA COLI; EXPRESSION VECTOR; GENE EXPRESSION REGULATION; GENE EXPRESSION SYSTEM; GENE SEQUENCE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERATOR; PROMOTER REGION; PSEUDOMONAS; PSEUDOMONAS PUTIDA; PSEUDOMONAS VERONII; SEQUENCE ANALYSIS; TANDEM REPEAT; TRANSCRIPTION INITIATION SITE;

ESCHERICHIA COLI; PSEUDOMONAS PUTIDA; PSEUDOMONAS VERONII;

BACTERIAL PROTEINS; BASE SEQUENCE; BUTANONES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; OPERON; PROMOTER REGIONS, GENETIC; PSEUDOMONAS; PSEUDOMONAS PUTIDA; TRANSCRIPTION FACTORS; TRANSCRIPTION INITIATION SITE;

EID: 84883561204     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-5030-7     Document Type: Article

References (80)

1. Aranda-Olmedo I, Ramos JL, Marqués S (2005) Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. Appl Environ Microbiol 71:4191-4198 (Pubitemid 41129466)
2. Bakke I, Berg L, Aune TE, Brautaset T, Sletta H, Tondervik A, Valla S (2009) Random mutagenesis of the Pm promoter as a powerful strategy for improvement of recombinant-gene expression. Appl Environ Microbiol 75:2002-2011
3. Bertani G (1951) Studies on lysogenesis. I. The mode of phage liberation by lysogenic Escherichia coli. J Bacteriol 62:293-300
4. 70. J Bacteriol 182:4959-4969 (Pubitemid 30641822)
5. Blatny JM, Brautaset T, Winther-Larsen HC, Haugan K, Valla S (1997a) Construction and use of a versatile set of broad-host-range cloning and expression vectors based on the RK2 replicon. Appl Environ Microbiol 63:370-379 (Pubitemid 27121314)
6. Blatny JM, Brautaset T, Winther-Larsen HC, Karunakaran P, Valla S (1997b) Improved broad-host-range RK2 vectors useful for high and low regulated gene expression levels in gram-negative bacteria. Plasmid 38:35-51 (Pubitemid 27381799)
7. Brautaset T, Lale R, Valla S (2009) Positively regulated bacterial expression systems. Microb Biotechnol 2:15-30
8. Browning DF, Busby SJ (2004) The regulation of bacterial transcription initiation. Nat Rev Microbiol 2:57-65 (Pubitemid 39490048)
9. Ntr) protein of Pseudomonas putida. J Bacteriol 183:1032-1037 (Pubitemid 32095313)
10. Chung CT, Niemela SL, Miller RH (1989) One-step preparation of competent Escherichia coli: transformation and storage of bacterial cells in the same solution. Proc Natl Acad Sci U S A 86:2172-2175 (Pubitemid 19102474)
11. Collier DN, Hager PW, Phibbs PV Jr (1996) Catabolite repression control in the pseudomonads. Res Microbiol 147:551-561 (Pubitemid 26338137)
12. Deana A, Celesnik H, Belasco JG (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature 451:355-358
13. del Castillo T, Ramos JL (2007) Simultaneous catabolite repression between glucose and toluene metabolism in Pseudomonas putida is channeled through different signaling pathways. J Bacteriol 189:6602-6610 (Pubitemid 47397366)
14. Domínguez-Cuevas P, Marin P, Marqués S, Ramos JL (2008) XylS-Pm promoter interactions through two helix-turn-helix motifs: identifying XylS residues important for DNA binding and activation. J Mol Biol 375:59-69 (Pubitemid 350160699)
15. Domínguez-Cuevas P, Ramos JL, Marqués S (2010) Sequential XylS-CTD binding to the Pm promoter induces DNA bending prior to activation. J Bacteriol 192:2682-2690
16. Duetz WA, Marqués S, de Jong C, Ramos JL, van Andel JG (1994) Competition in chemostat culture between Pseudomonas strains that use different pathways for the degradation of toluene. Appl Environ Microbiol 60:2858-2863 (Pubitemid 24242280)
17. Duetz WA, Marqués S, Wind B, Ramos JL, van Andel JG (1996) Catabolite repression of the toluene degradation pathway in Pseudomonas putida harboring pWW0 under various conditions of nutrient limitation in chemostat culture. Appl Environ Microbiol 62:601-606 (Pubitemid 26051574)
18. Egan SM (2002) Growing repertoire of AraC/XylS activators. J Bacteriol 184:5529-5532
19. Egan SM, Schleif RF (1994) DNA-dependent renaturation of an insoluble DNA binding protein. Identification of the RhaS binding site at rhaBAD. J Mol Biol 243:821-829
20. Fetherston JD, Bearden SW, Perry RD (1996) YbtA, an AraC-type regulator of the Yersinia pestis pesticin/yersiniabactin receptor. Mol Microbiol 22:315-325 (Pubitemid 26352696)
21. Gallegos MT, Schleif R, Bairoch A, Hofmann K, Ramos JL (1997) Arac/XylS family of transcriptional regulators. Microbiol Mol Biol Rev 61:393-410 (Pubitemid 28006953)
22. García-González V, Govantes F, Porrua O, Santero E (2005) Regulation of the Pseudomonas sp. strain ADP cyanuric acid degradation operon. J Bacteriol 187:155-167 (Pubitemid 40024191)
23. Geggier S, Vologodskii A (2010) Sequence dependence of DNA bending rigidity. Proc Natl Acad Sci U S A 107:15421-15426
24. González-Pérez MM, Ramos JL, Gallegos MT, Marqués S (1999) Critical nucleotides in the upstream region of the XylS-dependent TOL meta-cleavage pathway operon promoter as deduced from analysis of mutants. J Biol Chem 274:2286-2290 (Pubitemid 29061384)
25. Gruber AR, Lorenz R, Bernhart SH, Neubock R, Hofacker IL (2008) The Vienna RNA websuite. Nucleic Acids Res 36:W70-W74
26. Grunberg-Manago M (1999) Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu Rev Genet 33:193-227 (Pubitemid 30083123)
27. BAD promoter. J Bacteriol 177:4121-4130
28. Hamilton EP, Lee N (1988) Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli. Proc Natl Acad Sci U S A 85:1749-1753 (Pubitemid 24315759)
29. Ho SN, Hunt HD, Horton RM, Pullen JK, Pease LR (1989) Site-directed mutagenesis by overlap extension using the polymerase chain reaction. Gene 77:51-59 (Pubitemid 19125653)
30. Holcroft CC, Egan SM (2000) Roles of cyclic AMP receptor protein and the carboxyl-terminal domain of the α subunit in transcription activation of the Escherichia coli rhaBAD operon. J Bacteriol 182:3529-3535 (Pubitemid 30341617)
31. Holtel A, Marqués S, Möhler I, Jakubzik U, Timmis KN (1994) Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid. J Bacteriol 176:1773-1776 (Pubitemid 24100232)
32. BAD promoter for tightly regulated display of proteins on bacteriophage. Gene 251:187-197 (Pubitemid 30394265)
33. Ibarra JA, Pérez-Rueda E, Segovia L, Puente JL (2008) The DNA-binding domain as a functional indicator: the case of the AraC/XylS family of transcription factors. Genetica 133:65-76 (Pubitemid 351464227)
34. Jair KW, Martin RG, Rosner JL, Fujita N, Ishihama A, Wolf RE Jr (1995) Purification and regulatory properties of MarA protein, a transcriptional activator of Escherichia coli multiple antibiotic and superoxide resistance promoters. J Bacteriol 177:7100-7104
35. Jair KW, Fawcett WP, Fujita N, Ishihama A, Wolf RE Jr (1996a) Ambidextrous transcriptional activation by SoxS: requirement for the C-terminal domain of the RNA polymerase α subunit in a subset of Escherichia coli superoxide-inducible genes. Mol Microbiol 19:307-317
36. Jair KW, Yu X, Skarstad K, Thony B, Fujita N, Ishihama A, Wolf RE Jr (1996b) Transcriptional activation of promoters of the superoxide and multiple antibiotic resistance regulons by Rob, a binding protein of the Escherichia coli origin of chromosomal replication. J Bacteriol 178:2507-2513 (Pubitemid 26134472)
37. Kaldalu N, Mandel T, Ustav M (1996) TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence. Mol Microbiol 20:569-579 (Pubitemid 26151898)
38. Kovach ME, Phillips RW, Elzer PH, Roop RM, Peterson KM (1994) pBBR1MCS: a broad-host-range cloning vector. Biotechniques 16:800-802 (Pubitemid 2103380)
39. Kwon HJ, Bennik MH, Demple B, Ellenberger T (2000) Crystal structure of the Escherichia coli Rob transcription factor in complex with DNA. Nat Struct Biol 7:424-430 (Pubitemid 30250008)
40. 70 subunit of RNA polymerase according to promoter architecture: identification of the target of Ada activation at the alkA promoter. J Bacteriol 181:1524-1529 (Pubitemid 29110812)
41. Landini P, Gaal T, Ross W, Volkert MR (1997) The RNA polymerase σ subunit carboxyl-terminal domain is required for both basal and activated transcription from the alkA promoter. J Biol Chem 272:15914-15919 (Pubitemid 27265571)
42. Landini P, Bown JA, Volkert MR, Busby SJ (1998) Ada protein-RNA polymerase σ subunit interaction and σ subunit-promoter DNA interaction are necessary at different steps in transcription initiation at the Escherichia coli ada and aidB promoters. J Biol Chem 273:13307-13312 (Pubitemid 28246904)
43. Li Z, Demple B (1994) SoxS, an activator of superoxide stress genes in Escherichia coli. Purification and interaction with DNA. J Biol Chem 269:18371-18377
44. Li Z, Demple B (1996) Sequence specificity for DNA binding by Escherichia coli SoxS and Rob proteins. Mol Microbiol 20:937-945 (Pubitemid 26198267)
45. Lim HK, Jung KH, Park DH, Chung SI (2000) Production characteristics of interferon-alpha using an l-arabinose promoter system in a high-cell-density culture. Appl Microbiol Biotechnol 53:201-208
46. Loessner H, Endmann A, Leschner S, Westphal K, Rohde M, Miloud T, Hammerling G, Neuhaus K, Weiss S (2007) Remote control of tumour-targeted Salmonella enterica serovar Typhimurium by the use of l-arabinose as inducer of bacterial gene expression in vivo. Cell Microbiol 9:1529-1537 (Pubitemid 46774023)
47. 70 subunit. J Mol Biol 284:1353-1365 (Pubitemid 28566072)
48. Magnet S, Blanchard JS (2005) Molecular insights into aminoglycoside action and resistance. Chem Rev 105:477-498 (Pubitemid 40351630)
49. Martin RG, Rosner JL (2001) The AraC transcriptional activators. Curr Opin Microbiol 4:132-137 (Pubitemid 32294413)
50. Martin K, Huo L, Schleif RF (1986) The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in these same sites. Proc Natl Acad Sci U S A 83:3654-3658 (Pubitemid 16062343)
51. Mathews DH, Disney MD, Childs JL, Schroeder SJ, Zuker M, Turner DH (2004) Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure. Proc Natl Acad Sci U S A 101:7287-7292 (Pubitemid 38638025)
52. Mermod N, Ramos JL, Lehrbach PR, Timmis KN (1986) Vector for regulated expression of cloned genes in a wide range of gram-negative bacteria. J Bacteriol 167:447-454 (Pubitemid 16049954)
53. Michan CM, Busby SJ, Hyde EI (1995) The Escherichia coli MelR transcription activator: production of a stable fragment containing the DNA-binding domain. Nucleic Acids Res 23:1518-1523
54. Miller JH (1972) Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor
55. Moreno R, Marzi S, Romby P, Rojo (2009) The Crc global regulator binds to an unpaired A-rich motif at the Pseudomonas putida alkS mRNA coding sequence and inhibits translation initiation. Nucleic Acids Res 37:7678-7690
56. Moreno R, Fonseca P, Rojo F (2010) The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes. J Biol Chem 285:24412-24419
57. Munson GP, Scott JR (2000) Rns, a virulence regulator within the AraC family, requires binding sites upstream and downstream of its own promoter to function as an activator. Mol Microbiol 36:1391-1402 (Pubitemid 30449974)
58. Nunoshiba T, Hidalgo E, Li Z, Demple B (1993) Negative autoregulation by the Escherichia coli SoxS protein: a dampening mechanism for the soxRS redox stress response. J Bacteriol 175:7492-7494 (Pubitemid 23339333)
59. Olsen DB, Carroll SS, Culberson JC, Shafer JA, Kuo LC (1994) Effect of template secondary structure on the inhibition of HIV-1 reverse transcriptase by a pyridinone non-nucleoside inhibitor. Nucleic Acids Res 22:1437-1443 (Pubitemid 24166844)
60. Onaca C, Kieninger M, Engesser KH, Altenbuchner J (2007) Degradation of alkyl methyl ketones by Pseudomonas veronii MEK700. J Bacteriol 189:3759-3767 (Pubitemid 46740173)
61. BAD -based shuttle vectors for functional analysis of toxic and highly regulated genes in Pseudomonas and Burkholderia spp. and other bacteria. Appl Environ Microbiol 74:7422-7426 (Pubitemid 352773595)
62. Rhee S, Martin RG, Rosner JL, Davies DR (1998) A novel DNA-binding motif in MarA: the first structure for an AraC family transcriptional activator. Proc Natl Acad Sci U S A 95:10413-10418 (Pubitemid 28413081)
63. Rojo F (2010) Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34:658-684
64. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Laboratory, Cold Spring Harbor
65. Sanger F, Nicklen S, Coulson AR (1977) DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A 74:5463-5467
66. Schüller A, Slater AW, Norambuena T, Cifuentes JJ, Almonacid LI, Melo F (2012) Computer-based annotation of putative AraC/XylS-family transcription factors of known structure but unknown function. J Biomed Biotechnol 2012:103132
67. Silva-Rocha R, de Lorenzo V (2012) Broadening the signal specificity of prokaryotic promoters by modifying cis-regulatory elements associated with a single transcription factor. Mol Biosyst 8:1950-1957
68. Sletta H, Nedal A, Aune TE, Hellebust H, Hakvag S, Aune R, Ellingsen TE, Valla S, Brautaset T (2004) Broad-host-range plasmid pJB658 can be used for industrial-level production of a secreted host-toxic single-chain antibody fragment in Escherichia coli. Appl Environ Microbiol 70:7033-7039 (Pubitemid 39643765)
69. Sonnleitner E, Abdou L, Haas D (2009) Small RNA as global regulator of carbon catabolite repression in Pseudomonas aeruginosa. Proc NatI Acad Sci U S A 106:21866-21871
70. Sukchawalit R, Vattanaviboon P, Sallabhan R, Mongkolsuk S (1999) Construction and characterization of regulated l-arabinose-inducible broad host range expression vectors in Xanthomonas. FEMS Microbiol Lett 181:217-223
71. Sun T, Altenbuchner J (2010) Characterization of a mannose utilization system in Bacillus subtilis. J Bacteriol 192:2128-2139
72. 70 subunit of RNA polymerase. J Mol Biol 419:139-157
73. Timmes A, Rodgers M, Schleif R (2004) Biochemical and physiological properties of the DNA binding domain of AraC protein. J Mol Biol 340:731-738 (Pubitemid 38829634)
74. Tobes R, Ramos JL (2002) AraC-XylS database: a family of positive transcriptional regulators in bacteria. Nucleic Acids Res 30:318-321 (Pubitemid 34679574)
75. Varani G (1995) Exceptionally stable nucleic acid hairpins. Annu Rev Biophys Biomol Struct 24:379-404
76. Völker A, Kirschner A, Bornscheuer UT, Altenbuchner J (2008) Functional expression, purification, and characterization of the recombinant Baeyer-Villiger monooxygenase MekA from Pseudomonas veronii MEK700. Appl Microbiol Biotechnol 77:1251-1260
77. Warth L, Altenbuchner J (2013) A new site-specific recombinase-mediated system for targeted multiple genomic deletions employing chimeric loxP and mrpS sites. Appl Microbiol Biotechnol. doi: 10.1007/s0025301348278
78. Winther-Larsen HC, Blatny JM, Valand B, Brautaset T, Valla S (2000a) Pm promoter expression mutants and their use in broad-host-range RK2 plasmid vectors. Metab Eng 2:92-103 (Pubitemid 30416582)
79. Winther-Larsen HC, Josefsen KD, Brautaset T, Valla S (2000b) Parameters affecting gene expression from the Pm promoter in gram-negative bacteria. Metab Eng 2:79-91 (Pubitemid 30416581)
80. Yanisch-Perron C, Vieira J, Messing J (1985) Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103-119 (Pubitemid 15122816)