AraC/Xyls family of transcriptional regulators

Microbiology and Molecular Biology Reviews

Volumn 61, Issue 4, 1997, Pages 393-410

  Gallegos, María Trinidad ^a,e   Schleif, Robert ^b   Bairoch, Amos ^c   Hofmann, Kay ^d   Ramos, Juan L ^a  

^a CSIC   (Spain)

^b JOHNS HOPKINS UNIVERSITY   (United States)

^c UNIVERSITY OF GENEVA   (Switzerland)

^d SWISS INST FOR EXP CANCER RESEARCH   (Switzerland)

^e IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARABINOSE; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; BINDING SITE; CONSENSUS SEQUENCE; DIMERIZATION; DNA PROTEIN COMPLEX; EVOLUTION; GENE EXPRESSION; GENE EXPRESSION REGULATION; NONHUMAN; PROMOTER REGION; PROTEIN LOCALIZATION; REVIEW; SEQUENCE HOMOLOGY; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION;

CYANOBACTERIA; GAMMAPROTEOBACTERIA; NEGIBACTERIA; POSIBACTERIA; PROKARYOTA; PROTEOBACTERIA;

EID: 0031452318     PISSN: 10922172     EISSN: None     Source Type: Journal    
DOI: 10.1128/.61.4.393-410.1997     Document Type: Review

References (267)

1. Aiba, H., T. Baba, K. Fujita, K. Hayashi, A. Honjo, T. Horiuchi, K. Ikemote, T. Inada, K. Isono, S. Isono, T. Itoh, K. Kanai, H. Kasai, K. Kashimoto, S. Kim, S. Kimura, M. Kitagawa, M. Kitakawa, K. Makino, S. Masuda, T. Miki, K. Mizobuchi, H. Mori, K. Motomura, Y. Nakamura, H. Nashimoto, Y. Nishio, T. Oshima, N. Saito, G. Sampei, Y. Seki, H. Tagami, K. Takemoto, C. Wada, Y. Yamamoto, and M. Yano. 1996. SPTREMBL. Accession no. P77402.
2. Aiba, H., T. Baba, K. Fujita, K. Hayashi, A. Honjo, T. Horiuchi, K. Ikemote, T. Inada, K. Isono, S. Isono, T. Itoh, K. Kanai, H. Kasai, K. Kashimoto, S. Kim, S. Kimura, M. Kitagawa, M. Kitakawa, K. Makino, S. Masuda, T. Miki, K. Mizobuchi, H. Mori, K. Motomura, Y. Nakamura, H. Nashimoto, Y. Nishio, T. Oshima, N. Saito, G. Sampei, Y. Seki, H. Tagami, K. Takemoto, C. Wada, Y. Yamamoto, and M. Yano. 1997. SPTREMBL. Accession no. P77396.
3. Allaoui, A., P. J. Sansonetti, and C. Parsot. 1993. MxiD, an outer membrane protein necessary for the secretion of the Shigella flexneri Ipa invasins. Mol. Microbiol. 7:59-68.
4. Amábile-Cuevas, C. F., and B. Demple. 1991. Molecular characterization of the soxRS genes of Escherichia coli: two genes control a superoxide stress regulon. Nucleic Acids Res. 19:4474-1484.
5. Anderson, W. F., D. H. Ohlendorf, Y. Takeda, and B. W. Matthews. 1981. Structure of the cro repressor from bacteriophage lambda and its interaction with DNA. Nature 290:754-758.
6. Arakawa, E., J. I. Kato, K. I. Ito, and H. Watanabe. 1995. SWISSPROT. Accession no. Q55292.
7. Argos, P., M. Hanei, J. M. Wilson, and W. N. Kelley. 1983. A possible nucleotide-binding domain in the tertiary fold of phosphoribosyltransferases. J. Biol. Chem. 258:6450-6457.
8. Ariza, R. R., S. P. Cohen, N. Bachhawat, S. B. Levy, and B. Demple. 1994. Repressor mutations in the marRAB operon that activate oxidative stress genes and multiple antibiotic resistance in Escherichia coli. J. Bacteriol. 176:143-148.
9. Ariza, R. R., Z. Li, N. Ringstad, and B. Demple. 1995. Activation of multiple antibiotic resistance and binding of stress-inducible promoters by Escherichia coli rob protein. J. Bacteriol. 177:1655-1661.
10. Assinder, S. J., P. de Marco, D. J. Osborne, C. L. Poh, L. E. Shaw, M. K. Winson, and P. A. Williams. 1993. A comparison of multiple alleles of xylS carried by TOL plasmid pWW53 and pDK1 and its implications for their evolutionary relationship. J. Gen. Microbiol. 139:557-568.
11. S and the transcriptional activator AppY on induction of the Escherichia coli and cbdAB-appA operons in response to carbon and phosphate starvation. J. Bacteriol. 179:2141-2146.
12. Atlung, T., A. Nielsen, and F. G. Hansen. 1989. Isolation, characterization and nucleotide sequence of appY, a regulatory gene for growth-phase-dependent gene expression in Escherichia coli. J. Bacteriol. 171:1683-1691.
13. August, P. R., M. C. Flickinger, and D. H. Sherman. 1994. Cloning and analysis of a locus (mcr) involved in mitomycin C resistance in Streptomyces lavendulae. J. Bacteriol. 176:4448-4454.
14. Bairoch, A., and K. E. Rudd. 1995. PROSITE. Accession no. PDOC00884.
15. Bairoch, A., and K. E. Rudd. 1995. PROSITE. Accession no. PDOC00874.
16. Barbeyron, T., B. Henrissat, and B. Kloareg. 1994. The gene encoding the kappacarragenase of Alteromonas carragenovora is related to β-1,3-1,4-glucanases. Gene 139:105-109.
17. Beck von Bodman, S., G. T. Hayman, and S. K. Farrand. 1992. Opine catabolism and conjugal transfer of the nopaline Ti plasmid pTiC58 are coordinately regulated by a single repressor. Proc. Natl. Acad. Sci. USA 89:643-647.
18. Blattner, F. R., V. D. Burland, G. Plunkett III, H. J. Sofia, and D. L. Daniels. 1993. Analysis of the Escherichia coli genome. IV. DNA sequence of the region from 89.2 to 92.8 minutes. Nucleic Acids Res. 21:5408-5417.
19. Blattner, F. R., G. Plunkett III, G. F. Mayhew, N. T. Perna, and F. D. Glasner. 1997. SPTREMBL. Accession no. P76241, P77396, P77634, and Q46855.
20. Bolin, I., and H. Wolf-Watz. 1988. The plasmid-encoded Yop2b protein of Yersinia pseudotuberculosis is a virulence determinant regulated by calcium and temperature at the level of transcription. Mol. Microbiol. 2:237-245.
21. Branden, C., and J. Tooze. 1991. Introduction to protein structure. Garland Publishing Co., New York, N.Y.
22. Braus, G., M. Argast, and C. F. Beck. 1984. Identification of additional genes on transposon Tn10: tetC and tetD. J. Bacteriol. 160:504-509.
23. Brennan, R. G., and B. W. Matthews. 1989. The helix-turn-helix DNA binding motif. J. Biol. Chem. 264:1903-1906.
24. Brøndsted, L., and T. Atlung. 1996. Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appY gene, which encodes a transcriptional activator of Escherichia coli. J. Bacteriol. 178: 1556-1562.
25. Brown, C. E., and R. W. Hogg. 1972. A second transport system of L-arabinose in Escherichia coli controlled by the araC gene. J. Bacteriol. 111: 606-613.
26. Brunelle, A., W. Hendrickson, and R. Scheif. 1985. Altered DNA contacts made by a mutant AraC protein. Nucleic Acids Res. 13:5019-5026.
27. Brunelle, A., and R. F. Schleif. 1987. Missing contact probing of DNA-protein interactions. Proc. Natl. Acad. Sci. USA 84:673-676.
28. Brunelle, A., and R. F. Schleif. 1989. Determining residue-base interactions between AraC protein and araI DNA. J. Mol. Biol. 209:607-622.
29. Buck, D., and J. R. Guest. 1989. Overexpression and site-directed mutagenesis of the succinyl-CoA synthetase of Escherichia coli and nucleotide sequence of a gene (g30) that is adjacent to the suc operon. Biochem. J. 260:737-747.
30. Burke, K. A., and G. Wilcox. 1987. The araC gene of Citrobacter freundii. Gene 61:243-252.
31. Burland, V., G. Plunkett III, D. L. Daniels, and F. R. Blattner. 1993. DNA sequence and analysis of 136 kilobases of the Escherichia coli genome: organizational symmetry around the origin of replication. Genomics 16: 551-561.
32. Burland, V. D., G. Plunkett III, H. J. Sofia, D. L. Daniels, and F. R. Blattner. 1995. Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes. Nucleic Acids Res 23:2105-2119.
33. Busby, S., and R. H. Ebright. 1994. Promoter structure, promoter recognition and transcription activation in prokaryotes. Cell 79:743-746.
34. Bussey, L. B., and R. L. Switzer. 1993. The degA gene product accelerates degradation of Bacillus subtilis phosphoribosylpyrophosphate amidotransferase in Escherichia coli. J. Bacteriol. 175:6348-6353.
35. Bustos, S. A., and R. F. Schleif. 1993. Functional domains of the AraC protein. Proc. Natl. Acad. Sci. USA 90:5638-5642.
36. Caron, J., L. M. Coffield, and J. R. Scott. 1989. A plasmid-encoded regulatory gene, rns, required for expression of the CS1 and CS2 adhesins of enterotoxigenic Escherichia coli. Proc. Natl. Acad. Sci. USA 86:963-967.
37. Carra, J. H., and R. F. Schleif. 1993. Variation of half-site organization and DNA looping by AraC protein. EMBO J. 12:35-14.
38. Casadaban, M. J. 1976. Regulation of the regulatory gene for the arabinose pathway, araC. J. Mol. Biol. 104:557-566.
39. Cass, L. G., and G. Wilcox. 1986. Mutations in the araC regulatory gene of Escherichia coli B/r that affect repressor and activator functions of AraC protein. J. Bacteriol. 166:892-900.
40. Cass, L. G., and G. Wilcox. 1988. Novel activation of araC expression and DNA site required for araC autoregulation in Escherichia coli B/r. J. Bacteriol. 170:4174-4180.
41. Caswell, R., J. Williams, A. Lyddiatt, and S. Busby. 1992. Overexpression, purification and characterization of the Escherichia coli MelR transcription activator protein. Biochem. J. 287:493-499.
42. Chen, P., D. L. Andersson, and J. R. Roth. 1994. The control region of the pdu/cob regulon in Salmonella typhimurium. J. Bacteriol. 176:5474-5482.
43. Chen, C. W., T. W. Yu, H. M. Chung, and C. F. Chou. 1992. Discovery and characterization of a new transposable element, Tn4811, in Streptomyces lividans 66. J. Bacteriol. 174:7762-7769.
44. Chou, J. H., J. T. Greenberg, and B. Demple. 1993. Posttranscriptional repression of Escherichia coli OmpF protein in response to redox stress: positive control of the micF antisense RNA by the soxRS locus. J. Bacteriol. 175:1026-1031.
45. Chung, E., E. Allen, R. Araujo, A. Aparicio, K. Davis, M. Duncan, N. Federspiel, R. Hyman, S. Kalman, C. Komp, O. Kurdi, H. Lew, D. Lin, A. Namath, P. Oefner, D. Roberts, S. Schramm, and R. W. Davis. 1997. SPTREMBL. Accession no. P77634.
46. Clarke, P., J. H. Lee, K. Burke, and G. Wilcox. 1992. Mutations in the araC gene of Salmonella typhimurium LT2 which affect both activator and autoregulatory functions of the AraC protein. Gene 117:31-37.
47. Cohen, S. P., H. Hachler, and S. B. Levy. 1993. Genetic and functional analysis of the multiple antibiotic resistance (mar) locus in Escherichia coli. J. Bacteriol. 175:1484-1492.
48. Cohen, S. P., L. M. McMurry, and S. B. Levy. 1988. marA locus causes decreased expression of OmpF porin in multiple-antibiotic-resistant (Mar) mutants of Escherichia coli. J. Bacteriol. 170:5416-5422.
49. Collado-Vides, J., B. Magasanik, and J. D. Gralla. 1991. Control site location and transcriptional regulation in Escherichia coli. Microbiol. Rev. 55: 371-394.
50. Compan, I., and D. Touati. 1993. Interaction of six global transcription regulators in expression of manganese superoxide dismutase in Escherichia coli K-12. J. Bacteriol. 175:1686-1696.
51. Cornelis, G. R. 1994. Yersinia pathogenicity factors. Curr. Top. Microbiol. Immunol. 192:243-263.
52. Cornelis, G. R., C. Sluiters, I. Delor, D. Geib, K. Kaniga, C. Lambert de Rouvroit, M. P. Sory, J. C. Vanooteghem, and T. Michiels. 1991. ymoA, a Yersinia enterocolitica chromosomal gene modulating the expression of virulence functions. Mol. Microbiol. 5:1023-1034.
53. Cornelis, G. R., C. Sluiters, C. Lambert de Rouvroit, and T. Michiels. 1989. Homology between VirF, the transcriptional activator of the Yersinia virulence regulon, and AraC, the Escherichia coli arabinose operon regulator. J. Bacteriol. 171:254-262.
54. Cornelis, G. R., M. P. Sory, Y. U. Laroche, and I. Derclaye. 1986. Genetic analysis of the plasmid region controlling virulence in Yersinia enterocolitica O:9 by mini-Mu insertions and lac fusions. Microb. Pathog. 1:349-359.
55. de Haan, L. A. M., G. A. Willshaw, B. A. M. van der Zeijst, and W. Gaastra. 1991. The nucleotide sequence of a regulatory gene present on a plasmid in an enterotoxigenic Escherichia coli strain of serotype O167:H5. FEMS Microbiol. Lett. 67:341-346.
56. Dehoux, P., and P. Cossart. 1995. Homologies between salmolysin and some bacterial regulatory proteins. Mol. Microbiol. 15:591.
57. Demple, B., B. Sedgwick, P. Robins, N. Totty, M. D. Waterfield, and T. Lindahl. 1985. Active sites and complete sequence of the suicidal methyltransferase that counters alkylation mutagenesis. Proc. Natl. Acad. Sci. USA 82:2688-2692.
58. D'Orazio, S. E. F., and C. M. Collins. 1993. The plasmid-encoded urease gene cluster of the family Enterobacteriaceae is positively regulated by UreR, a member of the AraC family of transcriptional activators. J. Bacteriol. 175:3459-3467.
59. D'Orazio, S. E. F., V. Thomas, and C. M. Collins. 1996. Activation of transcription at divergent urea-dependent promoters by the urease gene regulator UreR. Mol. Microbiol. 21:643-655.
60. Dudley, E. G., A. C. Husgen, W. He, and J. L. Sttele. 1996. Sequencing, distribution, and inactivation of the dipeptidase A gene (pepDA) from Lactobacillus Helveticus CNRZ32. J. Bacteriol. 178:701-704.
61. Duncan, M., E. Allen, R. Araujo, A. M. Aparicio, E. Chung, K. Davis, N. Federspiel, R. Hyman, S. Kalman, C. Komp, O. Kurdi, H. Lew, D. Lin, A. Namath, P. Oefner, D. Roberts, S. Schramm, and R. W. Davis. 1996. SPTREMBL. Accession no. P77379 and P77601.
62. Dunn, T. M., S. Hahn, S. Ogden, and R. F. 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.
63. Egan, S. M., and R. F. Schleif. 1993. A regulator cascade in the induction of rhaBAD. J. Mol. Biol. 234:87-98.
64. Egan, S. M., and R. F. Schleif. 1994. DNA-dependent renaturation of an insoluble DNA binding protein. J. Mol. Biol. 243:821-829.
65. Englesberg, E., R. L. Anderson, R. Weinberg, N. Lee, P. Hoffee, G. Huttenhauer, and H. Boyer. 1962. L-Arabinose-sensitive, L-ribulose 5-phosphate 4-epimerase-deficient mutants of Escherichia coli. J. Bacteriol. 84:137-146.
66. Englesberg, E., J. Irr, J. Power, and N. Lee. 1965. Positive control of enzyme synthesis by gene C in the L-arabinose system. J. Bacteriol. 90:946-957.
67. Englesberg, E., C. Squires, and F. Meronk. 1969. The L-arabinose operon in Escherichia coli B/r: a genetic demonstration of two functional states of the product of a regulator gene. Proc. Natl. Acad. Sci. USA 62:1100-1107.
68. Entsch, B., L. Squire, and R. E. Wicks. 1994. SPTREMBL. Accession no. Q51543.
69. Eustance, R. J., S. A. Bustos, and R. F. Schleif. 1994. Locating and lengthening the interdomain linker in AraC protein. J. Mol. Biol. 242:330-338.
70. Eustance, R. J., and R. F. Schleif. 1996. The linker region of AraC protein. J. Bacteriol. 178:7025-7030.
71. Fawcett, W. P., and R. E. Wolf, Jr. 1994. Purification of a MalE-SoxS fusion protein and identification of the control sites of Escherichia coli superoxide-inducible genes. Mol. Microbiol. 14:669-679.
72. Fawcett, W. P., and R. E. Wolf, Jr. 1995. Genetic definition of the Escherichia coli zwf "Soxbox," the DNA binding site for SoxS-mediated induction of glucose 6-phosphate dehydrogenase in response to superoxide. J. Bacteriol. 177:1742-1750.
73. Fetherston, J. D., S. W. Bearden, and R. D. Perry. 1996. YbtA, an AraC-type regulator of the Yersinia pestis pesticin/yersiniabactin receptor. Mol. Microbiol. 22:315-325.
74. Fleischmann, R. D., M. D. Adams, O. White, R. A. Clayton, E. F. Kirkness, A. R. Kerlavage, C. J. Bull, J. F. Tomb, B. A. Dougherty, J. M. Merrick, K. McKenney, G. Sutton, W. FitzHugh, C. Fields, J. D. Gocayne, J. Scott, R. Shirley, L. I. Liu, A. Glodek, J. M. Kelley, J. F. Weidman, C. A. Phillips, T. Spriggs, E. Hedblom, M. D. Cotton, T. R. Utterback, M. C. Hanna, D. T. Nguyen, D. M. Saudek, R. C. Brandon, L. D. Fine, J. L. Fritchman, J. L. Fuhrmann, N. S. M. Geoghangen, C. L. Gnehm, L. A. McDonald, K. V. Small, C. M. Fraser, H. O. Smith, and J. C. Venter. 1995. Whole-genome random sequencing and assembly of Haemophilus influenzae. Science 269: 496-512.
75. Forsberg, A., R. Rosqvit, and H. Wolf-Watz. 1994. Regulation and polarized transfer of the Yersinia outer proteins (Yops) involved in antiphagocytosis. Trends Microbiol. 2:14-19.
76. Forsberg, A., and H. Wolf-Watz. 1988. The virulence protein Yop5 of Yersinia pseudotuberculosis is regulated at transcriptional level by plasmid-pIB1-encoded trans-acting elements controlled by temperature and calcium. Mol. Microbiol. 2:121-133.
77. Frank, D. W., and B. H. Iglewski. 1991. Cloning and sequence analysis of a trans-regulatory locus required for exoenzyme S synthesis in Pseadomonas aeruginosa. J. Bacteriol. 173:6460-6468.
78. Franklyn, C. S., and N. Lee. 1988. AraC proteins with altered DNA sequence specificity which activate a mutant promoter in Escherichia coli. J. Biol. Chem. 263:4400-4407.
79. Franklyn, F. C. H., P. R. Lehrbach, R. Lurz, B. Rueckert, M. Bagdasarian, and K. N. Timmis. 1983. Localization and functional analysis of transposon mutations in regulatory genes of the TOL catabolic pathway. J. Bacteriol. 154:676-685.
80. Friedrich, M. J., N. E. Kinsey, J. Vila, and R. J. Kadner. 1993. Nucleotide sequence of a 13.9 kb segment of the 90 kb virulence plasmid of Salmonella typhimurium: the presence of finibrial biosynthetic genes. Mol. Microbiol. 8:543-558.
81. Gallegos, M. T. 1996. Caracterización del regulador transcriptional XylS del plásmido TOL de Pseudomonas putida. Ph.D. dissertation. University of Granada, Granada, Spain.
82. 54-dependent tandem promoters according to the aromatic compound used tor growth. J. Bacteriol. 178:2356-2361.
83. S-dependent Pm promoter of the TOL plasmid is the minimum DNA segment required for transcription stimulation by XylS regulators. J. Bacteriol. 178:6427-6434.
84. Gallegos, M. T., C. Michán, and J. L. Ramos. 1993. The XylS/AraC family of regulators. Nucleic Acids Res. 21:807-810.
85. Galyov, E. E., A. V. Karlishev, T. V. Chernovskaya, D. A. Dolgikh, O. Y. Smirnov, K. L. Volkovoy, V. M. Abramov, and V. P. Zav'yalov. 1991. Expression of the envelope antigen F1 of Yersinia pestis is mediated by the product of caf1M gene having homology with the chaperone protein PapD of Escherichia coli. FEBS Lett. 286:79-82.
86. Gambino, L., S. J. Gracheck, and P. F. Miller. 1993. Overexpression of the MarA positive regulator is sufficient to confer multiple antibiotic resistance in Escherichia coli. J. Bacteriol. 175:2888-2894.
87. Gardner, P. R., and I. Fridovich. 1993. NADPH inhibits transcription of the Escherichia coli mangenese superoxide dismutase gene (sodA) in vitro. J. Biol. Chem. 268:12958-12963.
88. Geelen, D., K. Goethals, M. Van Montagu, and M. Holsters. 1995. The nodD locus from Azorhizobium caulinodans is flanked by two repetitive elements. Gene 164:107-111.
89. Genin, S., C. L. Gough, C. Zischeck, and C. A. Boucher. 1992. Evidence that the hrpB gene encodes a positive regulator of pathogenicity genes from Pseudomonas solanacearum. Mol. Microbiol. 6:3065-3076.
90. George, A. M., R. M. Hall, and H. W. Stokes. 1995. Multidrug resistance in Klebsiella pneumoniae: a novel gene, ramA, confers a multidrug resistance phenotype in Escherichia coli. Microbiology 141:1909-1920.
91. Gómez-Duarte, O. G., and J. B. Kaper. 1995. A plasmid encoded regulatory region activates chromosomal eaeA expression in enteropathogenic Escherichia coli. Infect. Immun. 63:1767-1776.
92. Gonzalez, M. M. 1997. Personal communication.
93. Greenberg, J. T., and B. Demple. 1989. A global response induced in Escherichia coli by redox-cycling agents overlaps with that induced by peroxide stress. J. Bacteriol. 171:3933-3939.
94. Greenberg, J. T., P. Monach, J. H. Chou, P. D. Josephy, and B. Demple. 1990. Positive control of a global antioxidant defense regulon activated by superoxide-generating agents in Escherichia coli. Proc. Natl. Acad. Sci. USA 87:6181-6185.
95. Greenblatt, J., and R. Schleif. 1971. Arabinose C protein: regulation of the arabinose operon in vitro. Nature (London) New Biol. 233:166-170.
96. Gruer, M. J., and J. R. Guest. 1994. Two genetically-distinct and differentially-regulated aconitases (AcnA and AcnB) in Escherichia coli. Microbiology 140:2531-2541.
97. Gupta, S., and A. K. Tyagi. 1993. Sequence of a newly identified Mycobacterium tuberculosis gene encoding a protein with sequence homology to virulence-regulating proteins. Gene 126:157-158.
98. Haak, B., S. Fetzner, and F. Lingens. 1995. Cloning, nucleotide sequence, and expression of the plasmid-encoded genes for the two-component 2-halobenzoate 1,2-dioxygenase from Pseudomonas cepacia 2CBS. J. Bacteriol. 177:667-675.
99. Hahn, S., T. Dunn, and R. Schleif. 1984. Upstream repression and CRP stimulation of the Escherichia coli L-arabinose operon. J. Mol. Biol. 180: 61-72.
100. Hakura, A., K. Morimoto, T. Sofuni, and T. Nohmi. 1991. Cloning and characterization of the Salmonella typhimurium ada gene, which encodes O-6-methylguanine-DNA methyltransferase. J. Bacteriol. 173:3663-3672.
101. 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.
102. Harrison, S. C. 1991. A structural taxonomy of DNA-binding domains. Nature 353:715-719.
103. Harrison, S. C., and A. K. Aggarwal. 1990. DNA recognition by proteins with the helix-turn-helix motif. Annu. Rev. Biochem. 59:933-969.
104. Haydon, D. J., and J. R. Guest. 1991. A new family of bacterial regulatory proteins. FEMS Microbiol. Lett. 63:291-295.
105. Hebert, M. D., and J. E. Houghton. 1996. SPTREMBL. Accession no. P72171.
106. Heinrichs. D. E., and K. Poole. 1993. Cloning and sequence analysis of a gene (pchR) encoding an AraC family activator of pyochelin and ferripyochelin receptor synthesis in Pseudomonas aeruginosa. J. Bacteriol. 175: 5882-5889.
107. Helmann, J. D., B. T. Ballard, and C. T. Walsh. 1990. The MerR metalloregulatory protein binds mercuric ion as a incoordinate, metal-bridged dimer. Science 247:946-948.
108. Hendrickson, W., C. Flaherty, and L. Molz. 1992. Sequence elements in the Escherichia coli araFGH promoter. J. Bacteriol. 174:6862-6871.
109. Hendrickson, W., and R. Schleif. 1985. A dimer of AraC protein contacts three adjacent major groove regions of the araI DNA site. Proc. Natl. Acad. Sci. USA 82:3129-3133.
110. Hendrickson, W., C. Stoner, and R. Schleif. 1990. Characterization of the araFGH and araJ promoters. J. Mol. Biol. 215:497-510.
111. Henikoff, S., G. W. Haughn, J. M. Calvo, and J. C. Wallace. 1988. A large family of bacterial activator proteins. Proc. Natl. Acad. Sci. USA 85:6602-6606.
112. Henikoff, S., J. C. Wallace, and J. P. Brown. 1990. Finding protein similarities with nucleotide sequence databases. Methods Enzymol. 183:111-132.
113. Higgins, D. E., E. Nazareno, and V. J. Dirita. 1942. The virulence gene activator ToxT from Vibrio cholerae is a member of the AraC family of transcriptional activators. J. Bacteriol. 174:6974-6980.
114. Hirsh, J., and R. Schleif. 1973. On the mechanism of action of L-arabinose C gene activator and lactose repressor. J. Mol. Biol. 80:433-444.
115. Hoe, N. P., and J. D. Goguen. 1993. Temperature sensing in Yersinia pestis: translation of the LcrF activator protein is thermally regulated. J. Bacteriol. 174:7901-7909.
116. Hoe, N. P., F. C. Minion, and J. D. Goguen. 1992. Temperature sensing in Yersinia pestis: regulation of yopE transcription by lcrF. J. Bacteriol. 174: 4275-4286.
117. Huo, L., K. J. Martin, and R. Schleif. 1988. Alternative DNA loops regulate the arabinose operon in Escherichia coli. Proc. Natl. Acad. Sci. USA 85: 5444-5448.
118. Inouye, S., A. Nakazawa, and T. Nakazawa. 1981. Molecular cloning of gene xylS of the TOL plasmid: evidence for positive regulation of the xylDEGF operon by xylS. J. Bacteriol. 148:413-418.
119. Inouye, S., A. Nakazawa, and T. Nakazawa. 1986. Nucleotide sequence of the regulatory gene xylS on the Pseudomonas putida TOL plasmid and identification of the protein product. Gene 44:235-242.
120. Inouye, S., A. Nakazawa, and T. Nakazawa. 1987. Overproduction of the xylS gene product and activation of the xylDLEGF operon on the TOL plasmid. J. Bacteriol. 169:3587-3592.
121. Ishida, H., H. Fujiwara, T. Horiuchi, K. Sato, Y. Osada, and M. Furusawa. 1994. SWISSPROT. Accession no. W52620.
122. Ishihama, A. 1993. Protein-protein communication within the transcription apparatus. J. Bacteriol. 175:2483-2489.
123. Johnson, C., and R. F. Schleif. 1995. In vivo kinetics of the arabinose promoters in Escherichia coli. J. Bacteriol. 177:3438-3442.
124. Jordi, B. J. A. M., B. Dagberg, L. A. M. de Haan, A. M. Hamers, B. A. M. van der Zeijst, W. Gaastra, and B. E. Uhlin. 1992. The positive regulator CfaD overcomes the repression mediated by histone-like protein H-NS (H1) in the CFA/I fimbrial operon of Escherichia coli. EMBO J. 11:2627-2632.
125. Kaldalu, N., T. Mandel, and M. Ustav. 1996. TOL plasmid transcription factor XylS binds specifically to the Pm operator sequence. Mol. Microbiol. 20:569-579.
126. Kaneko, T., S. Sato, H. Kotani, A. Tanaka, E. Asamizu, Y. Nakamura, N. Miyajima, M. Hirosawa, M. Sugiura, S. Sasamoto, T. Kimura, T. Hosouchi, A. Matsuno, A. Muraki, N. Nakazaki, K. Naruo, S. Okumura, S. Shimpo, C. Takeuchi, T. Wada, A. Watanabe, M. Yamada, M. Yasuda, and S. Tabata. 1996. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. Sequence determination of the entire genome and assignment of potential coding regions. DNA Res. 3:109-136.
127. Kaniga, K., J. C. Bossio, and J. E. Galán. 1994. The Salmonella typhimurium invasion genes invF and invG encode homologues of the AraC and PulD family of proteins. Mol. Microbiol. 13:555-568.
128. Karlyshev, A. V., E. E. Galyov, V. M. Abramov, and V. P. Zav'yalov. 1992. caf1R gene and its role in the regulation of capsule formation of Y. pestis. FEBS Lett. 305:37-40.
129. Kato, J. I., K. I. Ito, A. Nakamura, and H. Watanabe. 1989. Cloning of regions required for contact hemolysis and entry into LLC-MK2 cells from Shigella sonnei form I plasmid: virF is a positive regulator gene for these phenotypes. Infect. Immun. 57:1391-1398.
130. Kaufman, M. R., C. E. Shaw, I. D. Jones, and R. K. Taylor. 1993. Biogenesis and regulation of the Vibrio cholerae toxin-coregulated pilus: analogies to other virulence factor secretory systems. Gene 126:43-49.
131. Kemp, E. H., N. P. Minton, and N. H. Mann. 1987. Complete nucleotide sequence and deduced amino acid sequence of the M5 polypeptide gene of Escherichia coli. Nucleic Acids Res. 15:3924.
132. Kessler, B., V. de Lorenzo, and K. N. Timmis. 1993. Identification of a cis-acting sequence within the Pm promoter of the TOL plasmid which confers XylS-mediated responsiveness to substituted benzoates. J. Mol. Biol. 230:699-703.
133. Klaasen, P., and F. K. de Graaf. 1990. Characterization of FapR, a positive regulator of expression of the 987P operon in enterotoxigenic Escherichia coli. Mol. Microbiol. 4:1779-1783.
134. Koh, Y.-S., J. Choih, J. H. Lee, and J. H. Roe. 1996. Regulation of the ribA gene encoding GTP cyclohydrolase II by the soxRS locus in Escherichia coli. Mol. Gen. Genet. 251:591-598.
135. Koh, Y.-S., and J. H. Roe. 1995. Isolation of a novel paraquat-inducible (pqi) gene regulated by the soxRS locus in Escherichia coli. J. Bacteriol. 177:2673-2678.
136. Koh, Y.-S., and J.-H. Roe. 1996. Dual regulation of the paraquat-inducible gene pqi-5 by SoxS and RpoS in Escherichia coli. Mol. Microbiol. 22:53-61.
137. Komeda, H., Y. Hori, M. Kobayashi, and S. Shimizu. 1996. Transcriptional regulation of the Rhodococcus rhodochrous J1 nitA gene encoding nitrilase. Proc. Natl. Acad. Sci. USA 93:10572-10577.
138. Kondo, H., Y. Nakabeppu, H. Kataoka, S. Kuhara, S. Kawabata, and M. Sekiguchi. 1986. Structure and expression of the alkB gene of Escherichia coli related to the repair of alkylated DNA. J. Biol. Chem. 261:15772-15777.
139. Kormanec, J., A. Lempelova, M. Farkasovsky, and D. Homerova. 1995. Cloning, sequencing and expression in Escherichia coli of a Streptomyces aureofaciens gene encoding glyceraldehyde-3-phosphate dehydrogenase. Gene 165:77-80.
140. Kyrpides, N. C., and C. A. Ouzounis. 1995. Nucleic acid-binding metabolic enzymes: living fossils of stereochemical interactions? J. Mol. Evol. 40:564-569.
141. Lambert de Rouvroit, C., C. Sluiters, and G. R. Cornelis. 1992. Rule of the transcriptional activator, VirF, and temperature in the expression of the pYV plasmid genes of Yersinia enterocolitica. Mol. Microbiol. 6:395-409.
142. Landini, P., and M. R. Volkert. 1995. RNA polymerase alfa subunit binding site in positively controlled promoters: a new model for RNA polymerase-promoter interaction and transcriptional activation in the Escherichia coli ada and aidB genes. EMBO J. 14:4329-4335.
143. Lauble, H., Y. Georgalis, and U. Heinemann. 1989. Studies on the domain structure of the Salmonella typhimurium AraC protein. Eur. J. Biochem. 185:319-325.
144. 1. J. Mol. Biol. 224:335-341.
145. Lee, D. H., and R. Schleif. 1989. In vivo DNA loops in araCBAD: size limit and helical repeat. Proc. Natl. Acad. Sci. USA 86:476-480.
146. 2 activates the araBAD operon promoter. Proc. Natl. Acad. Sci. USA 84:8814-8818.
147. Leenhouts, K. K. J., A. A. Bolhuis, J. J. Kok, and G. G. Venema. 1994. SWISSPROT. Accession no. P43465.
148. Lehmann, M., B. Tshisuaka, S. Fetzner, and F. Lingens. 1995. Molecular cloning of the isoquinoline 1-oxidoreductase genes from Pseudomonas diminuta, structural analysis of iorA and iorB, and sequence comparisons with other molybdenum-containing hydroxylases. J. Biol. Chem. 270:14420-14429.
149. Lei, S. P., H. C. Lin, L. Heffernan, and G. Wilcox. 1985. araB gene and nucleotide sequence of araC gene of Erwinia caratovora. J. Bacteriol. 164: 717-722.
150. Lemotte, P. K., and G. C. Walker. 1985. Induction and autoregulation of ada, a positively acting element regulating the response of Escherichia coli K-12 to methylating agents. J. Bacteriol. 161:888-895.
151. Li, Z., and B. Demple. 1994. SoxS, an activator of superoxide stress genes in Escherichia coli: purification and interaction with DNA. J. Biol. Chem. 269:18371-18377.
152. Li, Z., and B. Demple. 1996. Sequence specificity for DNA binding by Escherichia coli SoxS and Rob proteins. Mol. Microbiol. 20:937-945.
153. Lin, J. W., K. Y. Yu, Y. F. Chao, and S. F. Weng. 1995. The lumQ gene is linked to the lumP gene and the lux operon in Photobacterium leiognathi. Biochem. Biophys. Res. Commun. 217:684-695.
154. Liochev, S. I., and I. Fridovich. 1992. Fumarase C, the stable fumarase of Escherichia coli, is controlled by the soxRS regulon. Proc. Natl. Acad. Sci. USA 89:5892-5896.
155. Liochev, S. I., A. Hausladen, W. F. Beyer, and I. Fridovich. 1994. NADPH: ferredoxin oxidoreductase acts as a paraquat diaphorase and is a member of the soxRS regulon. Proc. Natl. Acad. Sci. USA 91:1328-1331.
156. Lobell, R., and R. Schleif. 1990. DNA looping and unlooping by AraC protein. Science 250:528-532.
157. Lobell, R. B., 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.
158. Lu, Y., C. Flaherty, and W. Hendrickson. 1992. AraC protein contacts asymmetric sites in the Escherichia coli araFGH promoter. J. Biol. Chem. 267:24848-24857.
159. Lundrigan, M. D., M. J. Friedrich, and R. J. Kadner. 1989. Nucleotide sequence of the Escherichia coli porin thermoregulatory gene envY. Nucleic Acids Res. 17:800.
160. Lüthy, R., I. Xenarios, and D. Eisenberg. 1994. Profile analysis: detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84:4355-4358.
161. Macinga, D. R., M. M. Parojcic, and P. N. Rather. 1995. Identification and analysis of aarP, a transcriptional activator of the 2′-N-acetyltransferase in Providencia stuartii. J. Bacteriol. 177:3407-3414.
162. Manzanera, M. 1997. Personal communication.
163. Ss in transcription from the positively controlled Pm promoter of the TOL plasmid of Pseudomonas putida. Mol. Microbiol. 18:851-857.
164. Marqués, S., and J. L. Ramos. 1993. Transcriptional control of the Pseudomonas putida TOL plasmid catabolic pathways. Mol. Microbiol. 9:923-929.
165. Martin, K., L. Huo, and R. Schleif. 1986. The DNA loop model for ara repression: AraC occupies the proposed loop sites in vivo and repression negative mutations lie in these same sites. Proc. Natl. Acad. Sci. USA 83:3654-3658.
166. Martins, E. A. L., and B. Demple. 1996. SWISSPROT. Accession no. Q56143.
167. McKay, D. B., and T. A. Steitz. 1981. Structure of catabolite gene activator protein at 2.9 Å resolution suggests binding to left-handed B-DNA. Nature 290:744-749.
168. Menon, K. P., and N. L. Lee. 1990. Activation of ara operons by a truncated AraC protein does not require inducer. Proc. Natl. Acad. Sci. USA 87: 3708-3712.
169. Mermod, N., J. L. Ramos, A. Bairoch, and K. N. Timmis. 1987. The XylS gene positive regulator of TOL plasmid pWWO: identification, sequence analysis and overproducing leading to constitutive expression of meta cleavage operon. Mol. Gen. Genet. 207:349-354.
170. Michán, C. M., S. J. W. Busby, and E. I. Hyde. 1995. The Escherichia coli MeIR transcriptional activator: production of a stable fragment containing the DNA-binding domain. Nucleic Acids Res. 23:1518-1523.
171. Michán, C., B. Kessler, V. de Lorenzo, K. N. Timmis, and J. L. Ramos. 1992. XylS domain interactions can be deduced from intraallelic dominance in double mutants. Mol. Gen. Genet. 235:406-412.
172. Michán, C., L. Zhou, M. T. Gallegos, K. N. Timmis, and J. L. Ramos. 1992. Identification of critical amino-terminal regions of XylS. The positive regulator encoded by the TOL plasmid. J. Biol. Chem. 267:22897-22901.
173. Mito, S., Q. M. Zhang, and S. Yonei. 1993. Isolation and characterization of Escherichia coli strains containing new gene fusions (soi::lacZ) inducible by superoxide radicals. J. Bacteriol. 175:2645-2651.
174. Miyada, C. G., A. H. Horwitz, L. G. Cass, J. Timko, and G. Wilcox. 1980. DNA sequence of the araC regulatory gene from Escherichia coli B/n. Nucleic Acids Res. 8:5267-5274.
175. Morby, A. P., J. S. Turner, J. W. Huckle, and N. J. Robinson. 1993. SmtB is a metal-dependent repressor of the cyanobacterial metallothionein gene smtA: identification of a Zn inhibited DNA-protein complex. Nucleic Acids Res. 21:921-925.
176. Moroshi, F., K. Hayashi, and N. Munakata. 1990. Bacillus subtilis ada operon encodes two DNA alkyltransferases. Nucleic Acids Res. 18:5473-5480.
177. Murphy, L., D. Harris, B. G. Barrell, M. A. Rajandream, and S. V. Walsh. 1996. SWISSPROT. Accession no. Q10630.
178. Nagy, Y., G. Schoofs, F. Compernolle, P. Proost, J. Vanderleyden, and R. De Mot. 1995. Degradation of thiocarbamate herbicide EPTC (S-ethyl dipropylcarbamothioate) and biosafening by Rhodococcus sp. strain NI86/21 involve an inducible cytochrome P-450 system and aldehyde dehydrogenase. J. Bacteriol. 177:676-687.
179. Naik, S. M., and H. M. Hassan. 1990. Use of site-directed mutagenesis to identify an upstream regulatory sequence of sodA gene of Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 87:2618-2622.
180. Nakabeppu, Y., H. Kondo, S. Kawabata, S. Iwanaga, and M. Sekiguchi. 1985. Purification and structure of the intact Ada regulatory protein of Escherichia coli K12, O-6-methylguanine-DNA methyltransferase. J. Biol. Chem. 260:7281-7288.
181. Nakajima, H., K. Kobayashi, M. Kobayashi, H. Asako, and R. Aono. 1995. Overexpression of the robA gene increases organic solvent tolerance and multiple antibiotic and heavy metal ion resistance in Escherichia coli. Appl. Environ. Microbiol. 61:2302-2307.
182. Nakayama, S., and H. Watanabe. 1995. Involvement of cpxA, a sensor of a two-component regulatory system in the pH-dependent regulation of expression of the Shigella sonnei virF gene. J. Bacteriol. 177:5062-5069.
183. Nataro, J. P., D. Yikang, D. Yingkang, and K. Walker. 1994. AggR, a transcriptional activator of aggregative adherence fimbria I expression in enteroaggregative Escherichia coli. J. Bacteriol. 176:4691-4699.
184. Neidhardt, F. C. 1987. Multigene systems and regulons, p. 1313-1317. 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, vol. 2. American Society for Microbiology, Washington, D.C.
185. Nicholson, E. B., E. A. Concaugh, P. A. Foxall, M. D. Island, and H. L. T. Mobley. 1993. Proteus mirabilis urease: transcriptional regulation by UreR. J. Bacteriol. 175:465-473.
186. Niland, P., R. Hühne, and B. Müller-Hill. 1996. How AraC interacts specifically with its target DNAs. J. Mol. Biol. 264:667-674.
187. Nishitani, J., and G. Wilcox. 1991. Cloning and characterization of the L-rhamnose regulon in Salmonella typhimurium LT2. Gene 105:37-12.
188. Niu, W., Y. Kim, G. Tan, T. Heyduk, and R. H. Ebright. 1946. Transcription activation at class II CAP-dependent promoters: two interactions between CAP and RNA polymerase. Cell 87:1123-1134.
189. North, A. K., K. E. Klose, K. M. Stedman, and S. Kustu. 1993. Prokaryotic enhancer-binding proteins reflect eukaryote-like modularity: the puzzle of nitrogen regulatory protein C. J. Bacteriol. 175:4267-4273.
190. Nunoshiba, T., E. Hidalgo, C. F. Amábile-Cuevas, and B. Demple. 1992. Two-stage control of an oxidative stress regulon: the Escherichia coli SoxR protein triggers redox-inducible expression of the soxS regulatory gene. J. Bacteriol. 174:6054-6060.
191. Nunoshiba, T., E. Hidalgo, Z. Li, and B. Demple. 1993. Negative autoregulation by the Escherichia coli SoxS protein: a dampening mechanism for the soxRS redox stress response. J. Bacteriol. 175:7492-7494.
192. Ogierman, M. A., and P. A. Manning. 1992. Homology of TcpN, a putative regulatory protein of Vibrio cholerae, to the AraC family of transcriptional activators. Gene 116:93-97.
193. Oku, T., A. M. Alvarez, and C. I. Kado. 1995. Conservation of the hypersensitivity-pathogenicity regulatory gene hrpX of Xanthomonas campestris and oryzae. DNA Seq. 5:245-249.
194. Olsen, G. J., C. R. Woese, and R. Overbeek. 1994. The winds of (evolutionary) change: breathing new life into microbiology. J. Bacteriol. 176:1-6.
195. Pabo, C. O., and M. Lewis. 1992. The operator-binding domain of lambda repressor: structure and DNA recognition. Nature 298:443-447.
196. Pabo, C. O., and R. T. Sauer. 1984. Protein-DNA recognition. Annu. Rev. Biochem. 53:293-321.
197. Pabo, C. O., and R. T. Sauer. 1992. Transcription factors: structural families and principles of DNA recognition. Annu. Rev. Biochem. 61:1053-1095.
198. Pan, W., and B. G. Spratt. 1994. Regulation of the permeability of the gonococcal cell envelope by the mtr system. Mol. Microbiol. 11:769-775.
199. Parker, L. L., and B. G. Hall. 1990. Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12. Genetics 124:455-471.
200. Philipp, W. J., S. Poulet, K. Eiglmeier, L. Pascopella, V. Balasubramanian, B. Heym, S. Bergh, B. R. Bloom, W. R. Jacobs Jr., and S. T. Cole. 1996. An integrated map of the genome of the tubercle bacillus, Mycobacterium tuberculosis H37Rv, and comparison with Mycobacterium leprae. Proc. Natl. Acad. Sci. USA 93:3132-3137.
201. Plunkett, G., III, V. D. Burland, D. L. Daniels, and F. R. Blattner. 1993. Analysis of the Escherichia coli genome. III. DNA sequence of the region from 87.2 to 89.2 minutes. Nucleic Acids Res. 21:3391-3398.
202. Porter, M. E., and C. J. Dorman. 1994. A role of H-NS in the thermoosmotic regulation of virulence gene expression in Shigella flexneri. J. Bacteriol. 176:4187-4191.
203. Price, S. T., K. Y. Leung, S. S. Barve, and S. C. Straley. 1989. Molecular analysis of LcrGVH, the V antigen operon of Yersinia pestis. J. Bacteriol. 171:5646-5653.
204. Prieto, M. A., and J. L. García. 1994. Molecular characterization of 4-hydroxyphenylacetate 3-hydroxylase of Escherichia coli. J. Biol. Chem. 269: 22823-22829.
205. Quirk, P. G., A. A. Guffanti, S. Clejan, J. Cheng, and T. A. Krulwich. 1994. Isolation of Tn917 insertion mutants of Bacillus subtilis that are resistant to the protonophore carbonyl cyanide m-chlorophenylhydrazone. Biochim. Biophys. Acta 1186:27-34.
206. Ramos, J. L., S. Marqués, and K. N. Timmis. Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid encoded regulators. Annu. Rev. Microbiol., in press.
207. Ramos, J. L., N. Mermod, and K. N. Timmis. 1987. Regulatory circuits controlling transcription of TOL plasmid encoding meta-cleavage pathway for degradation of alkylbenzoates by Pseudomonas. Mol. Microbiol. 1:293-300.
208. Ramos, J. L., C. Michán, F. Rojo, D. Dwyer, and K. N. Timmis. 1990. Signal-regulator interactions: genetic analysis of the effector binding site of xylS, the benzoate-activated positive regulator of Pseudomonas TOL plasmid meta-cleavage pathway operon. J. Mol. Biol. 211:373-382.
209. Ramos, J. L., F. Rojo, L. Zhou, and K. N. Timmis. 1990. A family of positive regulators related to the Pseudomonas putida plasmid XylS and the Escherichia coli AraC activators. Nucleic Acids Res. 18:2149-2152.
210. Ramos, J. L., A. Stolz, W. Reineke, and K. N. Timmis. 1986. Altered effector specificities in regulators of gene expression: TOL plasmid xylS mutants and their use to engineer expansion of the range of aromatics degraded by bacteria. Proc. Natl. Acad. Sci. USA 83:8467-8471.
211. Ramos, J. L., A. Wasserfallen, K. Rose, and K. N. Timmis. 1987. Redesigning metabolic routes: manipulation of TOL plasmid pathway for catabolism of alkylbenzoates. Science 235:593-596.
212. 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.
213. Reizer, A., J. Deutscher, M. H. Saier, and J. Reizer. 1991 Analysis of the gluconate (gnt) operon of Bacillus subtilis. Mol. Microbiol. 5:1081-1089.
214. Reverchon, S., W. Nasser, and J. Robert-Baudouy. 1991. Characterization of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation. Mol. Microbiol. 5:2203-2216.
215. Rohde, J. R., J. M. Fox, and S. A. Minnich. 1994. Thermoregulation in Yersinia enterocolitica is coincident with changes in DNA supercoiling. Mol. Microbiol. 12:187-199.
216. Rosner, J. L., and J. L. Slonczewski. 1994. Dual regulation of inaA by the multiple antibiotic resistance (Mar) and superoxide (SoxRS) stress response systems in Escherichia coli. J. Bacteriol. 176:6262-6269.
217. Rost, B., and C. Sander. 1993. Improved prediction of protein secondary structure by use of sequence profiles and neural networks. Proc. Natl. Acad. Sci. USA 90:7558-7562.
218. 12) biosynthetic genes of Salmonella typhimurium. J. Bacteriol. 175:3303-3316.
219. Russell, R. R. B., J. Aduse-Opoku, I. C. Sutcliffe, L. Tao, and J. J. Ferretti. 1992. A binding protein-dependent transport system in Streptococcus mutans responsible for multiple sugar metabolism. J. Biol. Chem. 267:4631-4637.
220. Sakai, T., C. Sasakawa, S. Makino, and M. Yoshikawa. 1986. DNA sequence and product analysis of the virF locus responsible for Congo red binding and cell invasion in Shigella flexneri 2a. Infect. Immun. 54:395-402.
221. Sander, C., and R. Schneider. 1991. Database homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68.
222. Savelkoul, P. H. M., G. A. Willshaw, M. M. McConnell, H. R. Smith, A. M. Hamers, B. A. M. van der Zeijst, and W. Gaastra. 1990. Expression of CFA/I fimbriae is positively regulated. Microb. Pathog. 8:91-99.
223. Schleif, R. 1969. An L-arabinose binding protein and arabinose permeation in Escherichia coli. J. Mol. Biol. 46:185-196.
224. Schleif, R. 1987. The L-arabinose operon, p. 1473-1481. In F. C. Ncidhardt, 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.
225. Schleif, R. 1992. Regulation of the L-arabinose catabolic operon araBAD, p. 643-665. In S. L. McKnight and K. R. Yamamoto (ed.), Transcriptional regulation, vol. 2. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
226. Schleif, R., and M. Favreau. 1982. Hyperproduction of AraC protein from Escherichia coli. Biochemistry 21:778-782.
227. Schollmeier, K., and W. Hillen. 1984. Transposon Tn10 contains two structural genes with opposite polarity between tetA and IS10R. J. Bacteriol. 160:499-503.
228. Schwecke, T., J. F. Aparicio, I. Molnar, A. Koening, L. E. Khaw, S. F. Haydock, M. Oliynyk, P. Caffrey, J. Cortes, J. B. Lester, G. A. Boehm, J. Staunton, and P. F. Leadlay. 1995. The biosynthetic gene cluster for the polyketide immunosuppressant rapamycin. Proc. Natl. Acad. Sci. USA 92: 7839-7843.
229. Skarstad, K., B. Thöny, D. S. Hwang, and A. Kornberg. 1993. A novel binding protein of the origin of the Escherichia coli chromosome. J. Biol. Chem. 268:5365-5370.
230. Skurnik, M., and P. Toivanen. 1992. LcrF is the temperature-regulated activator of the yadA gene of Yersinia enterocolitica and Yersinia pseudotuberculosis. J. Bacteriol. 174:2047-2051.
231. Sofia, H. J., V. Burland, D. L. Daniels, G. Plunkett III, and F. R. Blattner. 1994. Analysis of the Escherichia coli genome. V. DNA sequence of the region from 76.0 to 81.5 minutes. Nucleic Acids Res. 22:2576-2586.
232. Soisson, S. M., B. MacDougall-Shackleton, R. Schleif, and C. Wolberger. 1997. Structural basis for ligand-regulated oligomerization of AraC. Science 276:421-425.
233. Spiro, S., and J. R. Guest. 1990. FNR and its role in oxygen-regulated gene expression in Escherichia coli. FEMS Microbiol. Rev. 6:399-428.
234. Spooner, R. A., M. Bagdasarian, and F. C. H. Franklin. 1987. Activation of the xylDLEGF promoter of the TOL toluene-xylene degradation pathway by overproduction of the xylS regulatory gene product. J. Bacteriol 169: 3581-3586.
235. Spooner, R. A., K. Lindsay, and F. C. H. Franklyn. 1986. Genetic, functional and sequence analysis of the xylR and xylS regulatory genes of the TOL plasmid pWW0. J. Gen. Microbiol. 132:1347-1358.
236. Steele, M. I., D. Lorenz, K. Hatter, A. Park, and J. R. Sokatch. 1992. Characterization of the mmsAB operon of Pseudomonas aeruginosa PAO encoding methylmalonate-semialdehyde dehydrogenase and 3-hydroxybutyrate dehydrogenase. J. Biol. Chem. 267:13585-13592.
237. Stim-Herndon, K. P., T. M. Flores, and G. N. Bennett. 1996. Molecular characterization of adiY, a regulatory gene which affects expression of the biodegradative acid-induced arginine decarboxylase gene (adiA) of Escherichia coli. Microbiology 142:1311-1320.
238. Stoner, C. M., and R. Schleif. 1982. Is the amino acid but not the nucleotide sequence of the Escherichia coli araC gene conserved? J. Mol. Biol. 154: 649-652.
239. Stoner, C. M., and R. Schleif. 1983. The araE low affinity L-arabinose transport promoter. J. Mol. Biol. 170:1049-1053.
240. Sulavik, M. C., M. Dazer, and P. F. Miller. 1996. SWISSPROT. Accession no. Q56070.
241. + transport protein in Salmonella typhimurium and Escherichia coli. J. Biol. Chem. 267:6923-6932.
242. Tobe, T., M. Yoshikawa, T. Mizuno, and C. Sasakawa. 1993. Transcriptional control of the invasion regulatory gene of Shigella flexneri: activation by VirF and repression by H-NS. J. Bacteriol. 175:6142-6149.
243. Tobin, J. F., and R. F. Schleif. 1987. Positive regulation of the Escherichia coli L-rhamnose operon is mediated by products of tandemly repeated regulatory genes. J. Mol. Biol. 196:789-799.
244. Tohin, J. F., and R. F. Schleif. 1990. Purification and properties of RhaR, the positive regulator of the L-rhamnose operons of Escherichia coli. J Mol. Biol. 211:75-89.
245. Troup, B., M. Jahn, C. Hungerer, and D. Jahn. 1994. Isolation of the hemF operon containing the gene for the Escherichia coli aerobic coproporphyrinogen III oxidase by in vivo complementation of a yeast HEM13 mutant. J. Bacteriol. 176:673-680.
246. Tsaneva, I. R., and B. Weiss. 1990. soxR, a locus governing a superoxide response regulon in Escherichia coli K-12. J. Bacteriol. 172:4197-4205.
247. Volkert, M. R., L. I. Hajec, Z. Matijasevic, F. C. Fang, and R. Prince. 1994. Induction of the Escherichia coli aidB gene under oxygen-limiting conditions requires a functional rpoS (katF) gene. J. Bacteriol. 176:7638-7645.
248. Wallace, R. G., N. Lee, and A. V. Fowler. 1980. The araC gene of Escherichia coli: transcriptional and translational start-points and complete nucleotide sequence. Gene 12:179-190.
249. Wattiau, P., B. Bernier, P. Deslee, T. Michiels, and G. R. Cornelis. 1994. Individual chaperones required for Yop secretion by Yersinia. Proc. Natl. Acad. Sci. USA 91:1074-1078.
250. Wattiau, P., and G. R. Cornelis. 1994. Identification of DNA sequences recognized by VirF, the transcriptional activator of the Yersinia yop regulon. J. Bacteriol. 176:3878-3884.
251. Webster, C., K. Kempsell, I. Booth, and S. Busby. 1987. Organisation of the regulatory region of the Escherichia coli melibiose operon. Gene 59:253-263.
252. Webster, C., L. Gardner, and S. Busby. 1989. The Escherichia coli melR gene encodes a DNA-binding protein with affinity for specific sequences located in the melibiose-operon regulatory region. Gene 83:207-213.
253. Weickert, M. J., and S. Adhya. 1992. A family of bacterial regulators homologous to Gal and Lac repressors. J. Biol. Chem. 267:15869-15874.
254. Wengelnik, K., and U. Bonas. 1996. HrpXv, and AraC-type regulator, activates expression of five of the six loci in the hrp cluster of Xanthomonas campestris pv. resicatoria. J. Bacteriol. 178:3462-3469.
255. Wilcox, G., and P. Meuris. 1976. Stabilization and size of AraC protein. Mol. Gen. Genet. 145:97-100.
256. Wilcox, G., P. Meuris, R. Bass, and E. Englesberg. 1974. Regulation of the L-arabinose operon BAD in vitro. J. Biol. Chem. 249:2946-2952.
257. Wintjens, R., and M. Rooman. 1996. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. J. Mol. Biol. 262: 294-313.
258. Wolf, M. K., and E. C. Boedeker. 1990. Cloning of the genes for AF/R1 pili from rabbit enteroadherence Escherichia coli RDEC-1 and DNA sequence of the major structural subunit. Infect. Immun. 58:1124-1128.
259. Wong, C. M., M. J. Dilworth, and A. R. Glenn. 1995. SPTREMBL. Accession no. Q52799.
260. Wu, J., and B. Weiss. 1991. Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli. J. Bacteriol. 173:2864-2871.
261. Yahr, T. L., and D. W. Frank. 1994. Transcriptional organization of the trans-regulatory locus which controls exoenzyme S synthesis in Pseudomonas aeruginosa. J. Bacteriol. 176:3832-3838.
262. Yamamoto, H., S. Uchiyama, A. N. Fajar, N. Ogasawara, and J. Sekiguchi. 1996. Determination of a 12 kb nucleotide sequence around the 76 degrees region of the Bacillus subtilis chromosome. Microbiology 142:1417-1421.
263. Yamashita, M., H. Azakami, N. Yokoro, J. H. Roh, H. Suzuki, H. Kumagai, and Y. Murooka. 1996. maoB, a gene that encodes a positive regulator of the monoamine oxidase gene (maoA) in Escherichia coli. J. Bacteriol. 178: 2941-2947.
264. Yao, R., L. V. Reddy, and S. Palchaudhuri. 1991. SWISSPROT. Accession no. Q04248.
265. Yu, T. W., and C. W. Chen. 1993. The unstable melC operon of Streptomyces antibioticus is codeleted with a Tn4811-homologous locus. J. Bacteriol. 175:1847-1852.
266. Yura, T., H. Mori, H. Nagai, T. Nagata, A. Ashihama, N. Fujita, K. Isono, K. Mizobuchi, and A. Nakata. 1992. Systematic sequencing of the Escherichia coli genome: analysis of the 0-2.4 min region. Nucleic Acids Res. 20:3305-3308.
267. Zhou, L., K. N. Timmis, and J. L. Ramos. 1990. Mutations leading to constitutive expression from the TOL plasmid meta-cleavage pathway operon are located at the C-terminal end of the positive regulator XylS protein. J. Bacteriol. 172:3707-3710.