Promoter upstream bent DNA activates the transcription of the Clostridium perfringens phospholipase C gene in a low temperature-dependent manner

EMBO Journal

Volumn 18, Issue 12, 1999, Pages 3442-3450

  Katayama, Seiichi ^a   Matsushita, Osamu ^a   Jung, Chang Min ^a   Minami, Junzaburo ^a   Okabe, Akinobu ^a  

^a KAGAWA UNIVERSITY   (Japan)

Author keywords

Bent DNA; Clostridium perfingens; Curved DNA; Gene expression; Phospholipase C

Indexed keywords

CURVED DNA; HYDROXYL RADICAL; PHOSPHOLIPASE C; RNA POLYMERASE;

ARTICLE; CLOSTRIDIUM PERFRINGENS; DNA STRUCTURE; ESCHERICHIA COLI; GEL CHROMATOGRAPHY; LOW TEMPERATURE; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; TEMPERATURE DEPENDENCE; TRANSCRIPTION REGULATION;

BINDING, COMPETITIVE; CLOSTRIDIUM PERFRINGENS; DNA; DNA FOOTPRINTING; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; GENE EXPRESSION REGULATION, ENZYMOLOGIC; HYDROXYL RADICAL; NUCLEIC ACID CONFORMATION; PHOSPHOLIPASE C; POLY A; POTASSIUM CHLORIDE; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; RESPONSE ELEMENTS; RRNA OPERON; TEMPERATURE; TRANS-ACTIVATION (GENETICS);

EID: 0033564586     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/18.12.3442     Document Type: Article

References (63)

1. Abe, A., Kenny, B., Stein, M. and Finlay, B.B. (1997) Characterization of two virulence proteins secreted by rabbit enteropathogenic Escherichia coli, EspA and EspB, whose maximal expression is sensitive to host body temperature. Infect. Immun., 65, 3547-3555.
2. Aiyar, S.E., Gourse, R.L. and Ross, W. (1998) Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase α subunit. Proc. Natl Acad. Sci. USA, 95, 14652-14657.
3. Banner, C.D., Moran, C.P.J. and Losick, R. (1983) Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis. J. Mol. Biol., 168, 351-365.
4. 70 subunit is responsible for the recognition of the 'extended -10' motif at promoters. EMBO J., 16, 4034-4040.
5. Blatter, E.E., Ross, W., Tang, H., Gourse, R.L. and Ebright, R.H. (1994) Domain organization of RNA polymerase α subunit: C-terminal 85 amino acids constitute a domain capable of dimerization and DNA binding. Cell, 78, 889-896.
6. Bolshoy, A., McNamara, P., Harrington, R.E. and Trifonov, E.N. (1991) Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles. Proc. Natl Acad. Sci. USA, 88, 2312-2316.
7. Bowater, R.P., Aboul-ela, F. and Lilley, D.M. (1994) Large-scale opening of A + T rich regions within supercoiled DNA molecules is suppressed by salt. Nucleic Acids Res., 22, 2042-2050.
8. Bradford, M.M. (1976) A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem., 72, 248-254.
9. Brahms, G., Brahms, S. and Magasanik, B. (1995) A sequence-induced superhelical DNA segment serves as transcriptional enhancer. J. Mol. Biol., 246, 35-42.
10. Brandi, A., Pietroni, P., Gualerzi, C.O. and Pon, C.L. (1996) Post-transcriptional regulation of CspA expression in Escherichia coli. Mol. Microbiol., 19, 231-240.
11. Brosius, J., Dull, T.J., Sleeter, D.D. and Noller, H.F. (1981) Gene organization and primary structure of a ribosomal RNA operon from Escherichia coli. J. Mol. Biol., 148, 107-127.
12. Brukner, J., Susic, S., Dlakic, M., Savic, A. and Pongor, S. (1994) Physiological concentration of magnesium ions induces a strong macroscopic curvature in GGGCCC-containing DNA. J. Mol. Biol., 236, 26-32.
13. Burns, H.D., Belyaeva, T.A., Busby, S.J. and Minchin, S.D. (1996) Temperature-dependence of open-complex formation at two Escherichia coli promoters with extended -10 sequences. Biochem. J., 317, 305-311.
14. Busby, S. and Ebright, R.H. (1994) Promoter structure, promoter recognition and transcription activation in prokaryotes. Cell, 79, 743-746.
15. 5 tracts. Biochemistry, 32, 11776-11784.
16. Crothers, D.M., Haran, T.E. and Nadeau, J.G. (1990) Intrinsically bent DNA, J. Biol. Chem., 265, 7093-7096.
17. Deuschle, U., Kammerer, W., Gentz, R. and Bujard, H. (1986) Promoters of Escherichia coli: a hierarchy of in vivo strength indicates alternate structures. EMBO J., 5, 2987-2994.
18. Diekmann, S. (1987) Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res., 15, 247-265.
19. Economides, A.N., Everdeen, D. and Panayotatos, N. (1996) A shared, non-canonical DNA conformation detected at DNA/protein contact sites and bent DNA in the absence of supercoiling or cognate protein binding. J. Biol. Chem., 271, 24836-24841.
20. Ellinger, T., Behnke, D., Knaus, R., Bujard, H. and Gralla, J.D. (1994) Context-dependent effects of upstream A-tracts. Stimulation or inhibition of Escherichia coli promoter function. J. Mol. Biol., 239, 466-475.
21. Estrem, S.T., Gaal, T., Ross, W. and Gourse, R.L. (1998) Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl Acad. Sci. USA, 95, 9761-9766.
22. Fredrick, K., Caramori, T., Chen, Y.F., Galizzi, A. and Helmann, J.D. (1995) Promoter architecture in the flagellar regulon of Bacillus subtilis: high-level expression of flagellin by the sigma D RNA polymerase requires an upstream promoter element. Proc. Natl Acad. Sci. USA, 92, 2582-2586.
23. Frisby, D. and Zuber, P. (1991) Analysis of the upstream activating sequence and site of carbon and nitrogen source repression in the promoter of an early-induced sporulation gene of Bacillus subtilis. J. Bacteriol., 173, 7557-7564.
24. Gaal, T., Rao, L., Estrem, S.T., Yang, J., Wartell, R.M. and Gourse, R.L. (1994) Localization of the intrinsically bent DNA region upstream of the E.coli rrnB P1 promoter. Nucleic Acids Res., 22, 2344-2350.
25. Galas, D.J., Eggert, M. and Waterman, M.S. (1985) Rigorous pattern-recognition methods for DNA sequences. Analysis of promoter sequences from Escherichia coli. J. Mol. Biol., 186, 117-128.
26. Garnier, T. and Cole, S.T. (1988) Studies of UV-inducible promoters from Clostridium perfringens in vivo and in vitro. Mol. Microbiol., 2, 607-614.
27. L promoter at low temperature. Proc. Natl Acad. Sci. USA, 92, 2184-2188.
28. Goldenberg, D., Azar, I. and Oppenheim, A.B. (1996) Differential mRNA stability of the cspA gene in the cold-shock response of Escherichia coli. Mol. Microbiol., 19, 241-248.
29. Graves, M.C. and Rabinowitz, J.C. (1986) In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for 'extended' promoter elements in Gram-positive organisms. J. Biol. Chem., 261, 11409-11415.
30. Grimes, E., Busby, S. and Minchin, S. (1991) Different thermal energy requirement for open complex formation by Escherichia coli RNA polymerase at two related promoters. Nucleic Acids Res., 19, 6113-6118.
31. Grosschedl, R., Giese, K. and Pagel, J. (1994) HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet., 10, 94-100.
32. A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res., 23, 2351-2360.
33. Jeon, Y.H., Negishi, T., Shirakawa, M., Yamazaki, T., Fujita, N., Ishihama, A. and Kyogoku, Y. (1995) Solution structure of the activator contact domain of the RNA polymerase α subunit. Science, 270, 1495-1497.
34. Jin, F., Matsushita, O., Katayama, S., Jin, S., Matsushita, C., Minami, J. and Okabe, A. (1996) Purification, characterization and primary structure of Clostridium perfringens λ-toxin, a thermolysin-like metalloprotease. Infect. Immun., 64, 230-237.
35. Katahira, M., Sugeta, H. and Kyogoku, Y. (1990) A new model for the bending of DNAs containing the oligo(dA) tracts based on NMR observations. Nucleic Acids Res., 18, 613-618.
36. Kim, J., Klooster, S. and Shapiro, D.J. (1995) Intrinsically bent DNA in a eukaryotic transcription factor recognition sequence potentiates transcription activation. J. Biol. Chem., 270, 1282-1288.
37. Koo, H.-S. and Crothers, D.M. (1988) Calibration of DNA curvature and a unified description of sequence-directed bending. Proc. Natl Acad. Sci. USA, 85, 1763-1767.
38. Koo, H.-S., Wu, H.-M. and Crothers, D.M. (1986) DNA bending at adenine-thymine tracts. Nature, 320, 501-506.
39. Lowe, P.A., Hager, D.A. and Burgess, R.R. (1979) Purification and properties of the σ subunit of Escherichia coli DNA-dependent RNA polymerase. Biochemistry, 18, 1344-1352.
40. Matsushita, C., Matsushita, O., Katayama, S., Minami, J., Takai, K. and Okabe, A. (1996) An upstream activating sequence containing curved DNA involved in activation of the Clostridium perfringens plc promoter. Microbiology, 142, 2561-2566.
41. Matsushita, O., Jung, C.-M., Minami, J., Katayama, S., Nishi, N. and Okabe, A. (1998) A study of the collagen-binding domain of a 116-kDa Clostridium histolyticum collagenase. J. Biol. Chem., 273, 3643-3648.
42. McAllister, C.F. and Achberger, E.C. (1988) Effect of polyadenine-containing curved DNA on promoter utilization in Bacillus subtilis. J. Biol. Chem., 263, 11743-11749.
43. McAllister, C.F. and Achberger, E.C. (1989) Rotational orientation of upstream curved DNA affects promoter function in Bacillus subtilis. J. Biol. Chem., 264, 10451-10456.
44. Mekalanos, J.J. (1992) Environmental signals controlling expression of virulence determinants in bacteria. J. Bacteriol., 174, 1-7.
45. Miao, Y.J. and Wang, J.Y.J. (1996) Binding of A/T-rich DNA by three high mobility group-like domains in c-Abl tyrosine kinase. J. Biol. Chem., 271, 22823-22830.
46. Négre, D., Bonod-Bidaud, C., Oudot, C., Prost, J.F., Kolb, A., Ishihama, A., Cozzone, A.J. and Cortay, J.C. (1997) DNA flexibility of the UP element is a major determinant for transcriptional activation at the Escherichia coli acetate promoter. Nucleic Acids Res., 25, 713-718.
47. Newlands, J.T., Josaitis, C.A., Ross, W. and Gourse, R.L. (1992) Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent. Nucleic Acids Res., 20, 719-726.
48. Nickerson, C.A. and Achberger, E.C. (1995) Role of curved DNA in binding of Escherichia coli RNA polymerase to promoters. J. Bacteriol., 177, 5756-5761.
49. Ohlsen, K., Koller, K.P. and Hacker, J. (1997) Analysis of expression of the α-toxin gene (hla) of Staphylococcus aureus by using a chromosomally encoded hla::lacZ gene fusion. Infect. Immun., 65, 3606-3614.
50. Pérez-Martín, J., Rojo, F. and de Lorenzo, V. (1994) Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol. Rev., 58, 268-290.
51. Pich, A. and Bahl, H. (1991) Purification and characterization of the DNA-dependent RNA polymerase from Clostridium acetobutylicum. J. Bacteriol., 173, 2120-2124.
52. Plaskon, R.R. and Wartell, R.M. (1987) Sequence distributions associated with DNA curvatures are found upstream of strong E.coli promoters. Nucleic Acids Res., 15, 785-796.
53. Rao, L., Ross, W., Appleman, J., Gaal, T., Leirmo, S., Schlax, P., Record, T. and Gourse, R.L. (1994) Factor-independent activation of rrnB P1: an extended promoter with an upstream element that dramatically increases promoter strength. J. Mol. Biol., 235, 1421-1435.
54. Ross, W., Gosink, K., Salomon, J., Igarashi, K., Zhou, C., Ishiharna, A., Severinov, K. and Gourse, R.L. (1993) A third recognition element in bacterial promoters: DNA binding by the α subunit of RNA polymerase. Science, 262, 1407-1413.
55. Sambrook, J., Fritsch, E.F. and Maniatis, T. (1989) Molecular Cloning: A Laboratory Manual. 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
56. Schickor, P. and Heumann, H. (1994) Hydroxyl radical footprinting. In Kneale, G.G. (ed.), DNA-Protein Interactions. Humana Press Inc., Totowa, NJ, pp. 21-32.
57. Shimizu, M., Miyake, M., Kanke, F., Matsumoto, U. and Shindo, H. (1995) Characterization of the binding of HU and IHF, homologous histone-like proteins of Escherichia coli, to curved and uncurved DNA. Biochim. Biophys. Acta, 1264, 330-336.
58. Shpigelman, E.S., Trifonov, E.N. and Bolshoy, A. (1993) CURVATURE: software for the analysis of curved DNA. Comput. Appl. Biosci., 9, 435-440.
59. Stockinger, E.J., Gilmour, S.J. and Thomashow, M.F. (1997) Arabidopsis thaliana CBF1 encodes an AP2 domain-containing transcriptional activator that binds to the C-repeat/DRE, a cis-acting DNA regulatory element that stimulates transcription in response to low temperature and water deficit. Proc. Natl Acad. Sci. USA, 94, 1035-1040.
60. Tanaka, K., Muramatsu, S., Yamada, H. and Mizuno, T. (1991) Systematic characterization of curved DNA segments randomly cloned from Escherichia coli and their functional significance. Mol. Gen. Genet., 226, 367-376.
61. Tsen, H. and Levene, S.D. (1997) Supercoiling-dependent flexibility of adenosine-tract-containing DNA detected by a topological method. Proc. Natl Acad. Sci. USA, 94, 2817-2882.
62. Tsutsui, K., Minami, J., Matsushita, O., Katayama, S., Taniguchi, Y., Nakamura, S., Nishioka, M. and Okabe, A. (1995) Phylogenetic analysis of phospholipase C genes from Clostridium perfringens types A to E and Clostridium novyi. J. Bacteriol., 177, 7164-7170.
63. Wu, H.-M. and Crothers, D.M. (1984) The locus of sequence-directed and protein induced DNA bending. Nature, 308, 509-513.