Cumate-inducible gene expression system for sphingomonads and other Alphaproteobacteria

Applied and Environmental Microbiology

Volumn 79, Issue 21, 2013, Pages 6795-6802

  Kaczmarczyk, Andreas ^a   Vorholt, Julia A ^a   Francez Charlot, Anne ^a  

^a ETH ZURICH   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

DEPLETION ANALYSIS; FLUORESCENT PROTEIN; INDUCIBLE GENE-EXPRESSION SYSTEMS; MAXIMAL INDUCTION; ORDERS OF MAGNITUDE; PARACOCCUS DENITRIFICANS; PSEUDOMONAS PUTIDA F1; TUNABLE PROMOTERS;

BACTERIA; BIOREMEDIATION;

GENE EXPRESSION;

BIOREMEDIATION; GENE EXPRESSION; GENETIC ANALYSIS; INDUSTRIAL DEVELOPMENT; MICROBIAL ACTIVITY; PHYLOGENETICS; PLASMID; PROTEIN;

BENZOIC ACID DERIVATIVE; BETA GALACTOSIDASE; CUMIC ACID;

ARTICLE; DNA SEQUENCE; DRUG EFFECT; ELECTROPORATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENE VECTOR; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLASMID; POLYACRYLAMIDE GEL ELECTROPHORESIS; PROMOTER REGION; SPECIES DIFFERENCE; SPHINGOMONADACEAE; WESTERN BLOTTING;

BASE SEQUENCE; BENZOATES; BETA-GALACTOSIDASE; BLOTTING, WESTERN; ELECTROPHORESIS, POLYACRYLAMIDE GEL; ELECTROPORATION; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENETIC VECTORS; MOLECULAR SEQUENCE DATA; PLASMIDS; PROMOTER REGIONS, GENETIC; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SPHINGOMONADACEAE;

EID: 84886891258     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.02296-13     Document Type: Article

References (42)

1. Guzman LM, Belin D, Carson MJ, Beckwith J. 1995. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol. 177:4121-4130.
2. Iniesta AA, Garcia-Heras F, Abellon-Ruiz J, Gallego-Garcia A, Elias-Arnanz M. 2012. Two systems for conditional gene expression in Myxococcus xanthus inducible by isopropyl-beta-D-thiogalactopyranoside or vanillate. J. Bacteriol. 194:5875-5885.
3. Meisenzahl AC, Shapiro L, Jenal U. 1997. Isolation and characterization of a xylose-dependent promoter from Caulobacter crescentus. J. Bacteriol. 179:592-600.
4. Quisel JD, Burkholder WF, Grossman AD. 2001. In vivo effects of sporulation kinases on mutant Spo0A proteins in Bacillus subtilis. J. Bacteriol. 183:6573-6578.
5. Stephens C, Christen B, Watanabe K, Fuchs T, Jenal U. 2007. Regulation of D-xylose metabolism in Caulobacter crescentus by a LacI-type repressor. J. Bacteriol. 189:8828-8834.
6. Thanbichler M, Iniesta AA, Shapiro L. 2007. A comprehensive set of plasmids for vanillate-and xylose-inducible gene expression in Caulobacter crescentus. Nucleic Acids Res. 35:e137. doi:10.1093/nar/gkm818.
7. Yansura DG, Henner DJ. 1984. Use of the Escherichia coli lac repressor and operator to control gene expression in Bacillus subtilis. Proc. Natl. Acad. Sci. U.S.A. 81:439-443.
8. Browning DF, Busby SJ. 2004. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2:57-65.
9. mxaF) of Methylobacterium extorquens by a applying regulatory elements of Pseudomonas putida F1. Appl. Environ. Microbiol. 72:7723-7729.
10. Choi YJ, Morel L, Le Francois T, Bourque D, Bourget L, Groleau D, Massie B, Miguez CB. 2010. Novel, versatile, and tightly regulated expression system for Escherichia coli strains. Appl. Environ. Microbiol. 76: 5058-5066.
11. Takeuchi M, Hamana K, Hiraishi A. 2001. Proposal of the genus Sphingomonas sensu stricto and three new genera, Sphingobium, Novosphingobium and Sphingopyxis, on the basis of phylogenetic and chemotaxonomic analyses. Int. J. Syst. Evol. Microbiol. 51:1405-1417.
12. Balkwill DL, Fredrickson JK, Romine MF. 2006. Sphingomonas and related genera, p 605-629. In Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E, (ed), The prokaryotes: a handbook on the biology of bacteria, vol 7, proteobacteria, delta and epsilon subclasses. Deeply rooting bacteria. Springer-SBM, New York, NY.
13. Fialho AM, Moreira LM, Granja AT, Popescu AO, Hoffmann K, Sa-Correia I. 2008. Occurrence, production, and applications of gellan: current state and perspectives. Appl. Microbiol. Biotechnol. 79:889-900.
14. Innerebner G, Knief C, Vorholt JA. 2011. Protection of Arabidopsis thaliana against leaf-pathogenic Pseudomonas syringae by Sphingomonas strains in a controlled model system. Appl. Environ. Microbiol. 77:3202-3210.
15. White DC, Sutton SD, Ringelberg DB. 1996. The genus Sphingomonas: physiology and ecology. Curr. Opin. Biotechnol. 7:301-306.
16. Eaton RW. 1996. p-Cumate catabolic pathway in Pseudomonas putida Fl: cloning and characterization ofDNAcarrying the cmt operon. J. Bacteriol. 178:1351-1362.
17. Eaton RW. 1997. p-Cymene catabolic pathway in Pseudomonas putida F1: cloning and characterization ofDNAencoding conversion of p-cymene to p-cumate. J. Bacteriol. 179:3171-3180.
18. EcfG cascade in general stress response and identification of a negative regulator of PhyR. J. Bacteriol. 193:6629-6638.
19. Nunn DN, Lidstrom ME. 1986. Isolation and complementation analysis of 10 methanol oxidation mutant classes and identification of the methanol dehydrogenase structural gene of Methylobacterium sp. strain AM1. J. Bacteriol. 166:581-590.
20. Poindexter JS. 1964. Biological properties and classification of the Caulobacter group. Bacteriol. Rev. 28:231-295.
21. Smith EF, Townsend CO. 1907. A plant-tumor of bacterial origin. Science 25:671-673.
22. Jin DJ, Gross CA. 1988. Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J. Mol. Biol. 202:45-58.
23. Peyraud R, Kiefer P, Christen P, Massou S, Portais JC, Vorholt JA. 2009. Demonstration of the ethylmalonyl-CoA pathway by using 13C metabolomics. Proc. Natl. Acad. Sci. U.S.A. 106:4846-4851.
24. Kaczmarczyk A, Vorholt JA, Francez-Charlot A. 2012. Markerless gene deletion system for sphingomonads. Appl. Environ. Microbiol. 78:3774-3777.
25. Simon R, Priefer U, Pühler A. 1983. A broad-host range mobilization system for in vivo genetic engineering: transposon mutagenesis in gramnegative bacteria. Nat. Biotechnol. 1:784-791.
26. Miller JH. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
27. Metzger LC, Francez-Charlot A, Vorholt JA. 2013. Single-domain response regulator involved in the general stress response of Methylobacterium extorquens. Microbiology 159:1067-1076.
28. Laemmli UK. 1970. Cleavage of structural proteins during assembly of head of bacteriophage T4. Nature 227:680-685.
29. Sambrook J, Russel D. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
30. Vick JE, Johnson ET, Choudhary S, Bloch SE, Lopez-Gallego F, Srivastava P, Tikh IB, Wawrzyn GT, Schmidt-Dannert C. 2011. Optimized compatible set of BioBrick vectors for metabolic pathway engineering. Appl. Microbiol. Biotechnol. 92:1275-1286.
31. Bloemberg GV, Wijfjes AH, Lamers GE, Stuurman N, Lugtenberg BJ. 2000. Simultaneous imaging of Pseudomonas fluorescens WCS365 populations expressing three different autofluorescent proteins in the rhizosphere: new perspectives for studying microbial communities. Mol. Plant Microbe Interact. 13:1170-1176.
32. Kovach ME, Elzer PH, Hill DS, Robertson GT, Farris MA, Roop RM, II, PetersonKM.1995. Four new derivatives of the broad-host-range cloning vector pBBR1MCS,carrying different antibiotic-resistance cassettes. Gene 166:175-176.
33. Marx CJ, Lidstrom ME. 2001. Development of improved versatile broadhost-range vectors for use in methylotrophs and other Gram-negative bacteria. Microbiology 147:2065-2075.
34. Heeb S, Itoh Y, Nishijyo T, Schnider U, Keel C, Wade J, Walsh U, O'Gara F, Haas D. 2000. Small, stable shuttle vectors based on the minimal pVS1 replicon for use in gram-negative, plant-associated bacteria. Mol. Plant Microbe Interact. 13:232-237.
35. Markowitz VM, Chen IMA, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang JH, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC. 2012. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 40:D115-D122.
36. Bailey TL, Elkan C. 1994. Fitting a mixture model by expectation maximization to discover motifs in biopolymers, p 28-36. In Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA.
37. Corpet F. 1988. Multiple sequence alignment with hierarchical clustering. Nucleic Acids Res. 16:10881-10890.
38. Lanzer M, Bujard H. 1988. Promoters largely determine the efficiency of repressor action. Proc. Natl. Acad. Sci. U.S.A. 85:8973-8977.
39. Francez-Charlot A, Frunzke J, Reichen C, Ebneter JZ, Gourion B, Vorholt JA. 2009. Sigma factor mimicry involved in regulation of general stress response. Proc. Natl. Acad. Sci. U.S.A. 106:3467-3472.
40. Chubiz LM, Purswani J, Carroll SM, Marx CJ. 2013. A novel pair of inducible expression vectors for use in Methylobacterium extorquens.BMC Res. Notes 6:183. doi:10.1186/1756-0500-6-183.
41. Ind AC, Porter SL, Brown MT, Byles ED, de Beyer JA, Godfrey SA, Armitage JP. 2009. Inducible-expression plasmid for Rhodobacter sphaeroides and Paracoccus denitrificans. Appl. Environ. Microbiol. 75:6613-6615.
42. Tett AJ, Rudder SJ, Bourdes A, Karunakaran R, Poole PS. 2012. Regulatable vectors for environmental gene expression in Alphaproteobacteria. Appl. Environ. Microbiol. 78:7137-7140.