Organization and regulation of the D-xylose operons in Escherichia coli K-12: XylR acts as a transcriptional activator

Journal of Bacteriology

Volumn 179, Issue 22, 1997, Pages 7025-7032

  Song, Sukgil ^a   Park, Chankyu ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

XYLOSE;

ARTICLE; BINDING SITE; ESCHERICHIA COLI; GENE INSERTION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC ORGANIZATION; GENETIC REGULATION; NONHUMAN; OPERON; PRIORITY JOURNAL; PROMOTER REGION; RECEPTOR AFFINITY; TRANSCRIPTION REGULATION; TRANSPOSON;

ESCHERICHIA; ESCHERICHIA COLI K12;

EID: 0030730280     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.179.22.7025-7032.1997     Document Type: Article

References (51)

1. Brennan, R. G., and B. W. Matthews. 1989. The helix-turn-helix DNA binding motif. J. Biol. Chem. 264:1903-1906.
2. Brunelle, A., and R. Schleif. 1989. Determining residue-base interaction between AraC protein and araI DNA. J. Mol. Biol. 209:607-622.
3. Carra, J. H., and R. Schleif. 1993. Variation of half site organization and DNA looping by AraC protein. EMBO J. 12:35-44.
4. Casadaban, M. J. 1976. Regulation of the regulatory gene for the arabinose pathway, araC. J. Mol. Biol. 104:556-557.
5. David, J. D., and H. Wiesmeyer. 1970. Control of xylose metabolism in Escherichia coli. Biochim. Biophys. Acta 201:497-499.
6. Davis, E. O., and P. J. F. Henderson. 1987. The cloning and DNA sequence of the gene xylE for xylose-proton symport in Escherichia coli K-12. J. Biol. Chem. 262:13928-13932.
7. Dunn, T., S. Hahn, and R. Schleif. 1984. An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression. Proc. Natl. Acad. Sci. USA 81:5017-5020.
8. Egan, S. M., and R. F. Schleif. 1994. DNA-dependent renaturation of an insoluble DNA binding protein: identification of the RhaS binding site at rhaBAD. J. Mol. Biol. 243:821-829.
9. Gallegos, M.-T., C. Michan, and J. L. Ramos. 1993. The XylS/AraC family of regulators. Nucleic Acids Res. 21:807-810.
10. Hahn, S., T. Dunn, and R. Schleif. 1984. Upstream repression and CRP stimulation of the Escherichia coli L-arabinose operon. J. Mol. Biol. 180:201-204.
11. Hamilton, E. P., and N. Lee. 1988. Three binding sites for AraC protein are required for autoregulation of araC in Escherichia coli. Proc. Natl. Acad. Sci. USA 85:1749-1753.
12. Horazdovsky, B., and R. Hogg. 1989. Genetic reconstitution of high-affinity L-arabinose operon in Escherichia coli. J. Bacteriol. 171:3053-3059.
13. Hove-Jensen, B. 1985. Cloning and characterization of the prs gene encoding phosphoribosyl pyrophosphate synthetase of Escherichia coli. Mol. Gen. Genet. 201:269-276.
14. Huo, L., K. Martin, and R. Schleif. 1988. Alternative DNA loops regulate the arabinose operon in Escherichia coli. Proc. Natl. Acad. Sci. USA 85: 5444-5448.
15. Johnson, C. M., and R. F. Schleif. 1995. In vivo induction kinetics of the arabinose promoters in Escherichia coli. J. Bacteriol. 177:3438-3442.
16. Jordan, S. R., and C. O. Pabo. 1988. Structure of the lambda complex at 2.5 resolution: details of the repressor-operator interactions. Science 242:893-899.
17. Kraus, A., C. Hueck, D. Gartner, and W. Hillen. 1994. Catabolite repression of the Bacillus subtilis xyl operon involves a cis element functional in the context of an unrelated sequence, and glucose exerts additional xylR-dependent repression. J. Bacteriol. 176:1738-1745.
18. Laemni, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature (London) 227:680-685.
19. Lin, E. C. C. 1987. Dissimilatory pathways for sugars, polyols, and carboxylates, p. 244-284. In F. C. Neidhardt, J. L. Ingraham, K. B. Low, B. Magasanik, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella typhimurium: cellular and molecular biology. American Society for Microbiology, Washington, D.C.
20. Lobell, R., and R. Schleif. 1990. DNA looping and unlooping by AraC protein. Science 250:528-532.
21. Lobell, R., and R. Schleif. 1991. AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein. J. Mol. Biol. 218:45-54.
22. Lowry, O. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall. 1951. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193:265-275.
23. Lo, Y., C. Flaherty, and W. Hendrickson. 1992. AraC protein contacts asymmetric sites in the Escherichia coli araFGH promoter. J. Biol. Chem. 267: 24848-24857.
24. Maleszka, R., P. Y. Wang, and H. Schneider. 1982. A ColEI hybrid plasmid containing Escherichia coli genes complementing D-xylose negative mutants of Escherichia coli and Salmonella typhimurium. Can. J. Biochem. 60:144-151.
25. Martin, K., and R. F. Schleif. 1986. The DNA loop model for ara repression: AraC protein occupies the proposed loop sites in vivo and repression-negative mutations lie in the same sites. Proc. Natl. Acad. Sci. USA 83:3654-3658.
26. Maxam, A., and W. Gilbert. 1977. A new method for sequencing DNA. Proc. Natl. Acad. Sci. USA 74:560-564.
27. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
28. Novotny, C., and E. Englesberg. 1966. The L-arabinose permease system in Escherichia coli B/r. Biochim. Biophys. Acta 117:217-230.
29. Ogden, S., D. Haggerty, C. M. Stoner, D. Kolodrubetz, and R, Schleif. 1980. The Escherichia coli L-arabinose operon: binding sites of the regulatory protein and a mechanism of positive and negative regulation. Proc. Natl. Acad. Sci. USA 77:3346-3350.
30. Park, C., and G. L. Hazelbauer. 1986. Mutations specifically affecting ligund interaction of Trg chemosensory transducer. J. Bacteriol. 167:101-109
31. Powell, B. S., D. L. Court, Y. Nakamura, M. P. Rivas, and C. L. Turnbough. 1994. Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res. 22:5765-5766.
32. Reeder, T., and R. Schleif. 1991. Mapping, sequence, and apparent lack of function of araJ, a gene of the Escherichia coli arabinose regulon. J. Bacteriol. 173:7765-7771.
33. Reeder, T., and R. Schleif. 1993. AraC protein can activate transcription from only one position and when pointed in only one direction. J. Mol. Biol. 231:205-218.
34. Rosenfeld, S. A., P. E. Steve, and N. W. Y. Ho. 1984. Cloning and characterization of the xyl genes from Escherichia coli. Mol. Gen. Genet. 194:410-415.
35. Rygus, T., and W. Hillen. 1992. Catabolite repression of the xyl operon in Bacillus megaterium. J. Bacteriol. 174:3049-3055.
36. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory, Cold Spring Harbor, N.Y.
37. Scheler, A., and W. Hillen. 1994. Regulation of xylose utilization in Bacillus licheniformis; Xyl-repressor-xyl-operator interaction studied by DNA modification protection and interference. Mol. Microbiol. 13:505-512.
38. Scripture, J. B., C. Voelker, S. Miller, R. T. O'Donnell, L. Polgar, J. Rade, B. F. Horazdovsky, and R. W. Hogg. 1987. High-affinity L-arabinose transport operon. Nucleotide sequence and analysis of gene products. J. Mol. Biol. 197:37-46.
39. Shamanna, D. K., and K. E. Sanderson. 1979. Uptake and catabolism of xylose in Salmonella typhimurium LT2. J. Bacteriol. 139:64-70.
40. Shamanna, D. K., and K. E. Sanderson. 1979. Genetics and regulation of D-xylose utilization in Salmonella typhimurium LT2. J. Bacteriol. 139:71-79.
41. Simons, R. W., F. Houman, and N. Kleckner. 1987. Improved single and multicopy lac-based vectors for protein and operon fusion. Gene 53:85-96.
42. Sizemore, C., B. Wieland, F. Gotz, and W. Hillen. 1992. Regulation of Staphylococcus xylosus xylose utilization genes at the molecular level. J. Bacteriol. 174:3042-3048.
43. Sofia, H. J., V. Burland, D. L. Daniels, G. Plunkett III, and F. Blattner. 1994. Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res. 22:2576-2584.
44. Song, S., and C. Park. Unpublished data.
45. Tobin, J. F., and R. F. Schleif. 1990. Purification and properties of RhaR, the positive regulator of the L-rhamnose operons of E. coli. J. Mol. Biol. 211: 75-89.
46. Tsung, K., R. E. Brissette, and M. Inouye. 1989. Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting. J. Biol. Chem. 264:10104-10109.
47. Wilcox, G., et al. 1974. Regulation of the L-arabinose operon BAD in vitro. J. Biol. Chem. 249:2946-2952.
48. Wilmes-Riesenberg, M. R., and B. L. Wanner. 1992. TnphoA and TnphoA′ elements for making and switching fusions for study of transcription, translation, and cell surface localization. J. Bacteriol. 174:4558-4575.
49. Wolberger, C., Y. Dong, M. Ptashne, and S. C. Harrison. 1988. Structure of a phage 434 Cro/DNA complex. Nature (London) 335:789-795.
50. Xu, J., and R. C. Johnson. 1995. Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli. J. Bacteriol. 177:938-947.
51. Xu, J., and R. C. Johnson. 1995. Fis activates the RpoS-dependent stationary-phase expression of proP in Escherichia coli. J. Bacteriol. 177:5222-5231.