A novel type of DNA curvature present in a Clostridium perfringens ferredoxin gene: characterization and role in gene expression

References

1. Azam T. A., Ishihama A. 1999; Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity. J Biol Chem 274:33105–33113
   [Google Scholar]
2. Barne K. A., Bown J. A., Busby S. J., Minchin S. D. 1997; Region 2.5 of the Escherichia coli RNA polymerase σ⁷⁰ subunit is responsible for the recognition of the ‘extended −10’ motif at promoters. EMBO J 16:4034–4040
   [Google Scholar]
3. Bolshoy A., Nevo E. 2000; Ecologic genomics of DNA: upstream bending in prokaryotic promoters. Genome Res 10:1185–1193
   [Google Scholar]
4. Bullifent H. L., Moir A., Titball R. W. 1995; The construction of a reporter system and use for the investigation of Clostridium perfringens gene expression. FEMS Microbiol Lett 131:99–105
   [Google Scholar]
5. Fujinaga K., Taniguchi Y., Sun Y., Katayama S., Minami J., Matsushita O., Okabe A. 1999; Analysis of genes involved in nitrate reduction in Clostridium perfringens. Microbiology 145:3377–3387
   [Google Scholar]
6. Gabrielian A. E., Landsman D., Bolshoy A. 1999–2000; Curved DNA in promoter sequences. In Silico Biol 1:183–196
   [Google Scholar]
7. Graves M. C., 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
   [Google Scholar]
8. Graves M. C., Mullenbach G. T., Rabinowitz J. C. 1985; Cloning and nucleotide sequence determination of the Clostridium pasteurianum ferredoxin gene. Proc Natl Acad Sci U S A 82:1653–1657
   [Google Scholar]
9. Hatheway C. L. 1990; Toxigenic clostridia. Clin Microbiol Rev 3:66–98
   [Google Scholar]
10. Kaji M., Taniguchi Y., Matsushita O., Katayama S., Miyata S., Morita S., Okabe A. 1999; The hydA gene encoding the H₂-evolving hydrogenase of Clostridium perfringens: molecular characterization and expression of the gene. FEMS Microbiol Lett 181:329–336
    [Google Scholar]
11. Katayama S., Matsushita O., Jung C.-M., Minami J., Okabe A. 1999; Promoter upstream bent DNA activates the transcription of the Clostridium perfringens phospholipase C gene in a low temperature-dependent manner. EMBO J 18:3442–3450
    [Google Scholar]
12. Katayama S., Matsushita O., Tamai E., Miyata S., Okabe A. 2001; Phased A-tracts bind to the alpha subunit of RNA polymerase with increased affinity at low temperature. FEBS Lett 509:235–238
    [Google Scholar]
13. Kiyama R., Trifonov E. N. 2002; What positions nucleosomes? – A model. FEBS Lett 523:7–11
    [Google Scholar]
14. Knight E. J., Hardy R. W. 1966; Isolation and characteristics of flavodoxin from nitrogen-fixing Clostridium pasteurianum. J Biol Chem 241:2752–2756
    [Google Scholar]
15. Lovenberg W., Buchanan B. B., Rabinowitz J. C. 1963; Studies on the chemical nature of clostridial ferredoxin. J Biol Chem 238:3899–3913
    [Google Scholar]
16. Mahony D. E., Moore T. J. 1976; Stable L-forms of Clostridium perfringens and their growth on glass surfaces. Can J Microbiol 22:953–959
    [Google Scholar]
17. Marczak R., Ballongue J., Petitdemange H., Gay R. 1985; Differential levels of ferredoxin and rubredoxin in Clostridium acetobutylicum. Biochimie 67:241–248
    [Google Scholar]
18. Matsushita C., Matsushita O., Koyama M., Okabe A. 1994; A Clostridium perfringens vector for the selection of promoters. Plasmid 31:317–319
    [Google Scholar]
19. Matsushita C., Matsushita O., Katayama S., Minami J., Takai K., Okabe A. 1996; An upstream activating sequence containing curved DNA involved in activation of the Clostridium perfringens plc promoter. Microbiology 142:2561–2566
    [Google Scholar]
20. Matsushita O., Jung C.-M., Minami J., Katayama S., Nishi N., Okabe A. 1998; A study of the collagen-binding domain of a 116-kDa Clostridium histolyticum collagenase. J Biol Chem 273:3643–3648
    [Google Scholar]
21. Mazin A., Milot E., Devoret R., Chartrand P. 1994; KIN17, a mouse nuclear protein, binds to bent DNA fragments that are found at illegitimate recombination junctions in mammalian cells. Mol Gen Genet 244:435–438
    [Google Scholar]
22. Meyer J. 2000; Clostridial iron–sulphur proteins. J Mol Microbiol Biotechnol 2:9–14
    [Google Scholar]
23. Morris J. G. 1991; Characteristics of anaerobic metabolism. In Anaerobes in Human Disease pp  16–37 Edited by Duerden B. I., Drasar B. S. London: Edward Arnold;
    [Google Scholar]
24. Mortenson L. E., Valentine R. C., Camahan J. E. 1962; An electron transport factor from Clostridium pasteurianum. Biochem Biophys Res Commun 7:448–452
    [Google Scholar]
25. Moulis J.-M., Davasse V. 1995; Probing the role of electrostatic forces in the interaction of Clostridium pasteurianum ferredoxin with its redox partners. Biochemistry 34:16781–16788
    [Google Scholar]
26. Murakami K. S., Masuda S., Campbell E. A., Muzzin O., Darst S. A. 2002; Structural basis of transcription initiation: an RNA polymerase holoenzyme–DNA complex. Science 296:1285–1290
    [Google Scholar]
27. Nair T. M., Madhusudan K., Nagaraja V., Kulkarni B. D., Majumdar H. K., Singh R. 1994; On the mobility behavior of a curved DNA fragment located in circular permutation. FEBS Lett 351:321–324
    [Google Scholar]
28. Ohyama T. 2001; Intrinsic DNA bends: an organizer of local chromatin structure for transcription. Bioessays 23:708–715
    [Google Scholar]
29. Pedersen A. G., Jensen L. J., Brunak S., Staerfeldt H. H., Ussery D. W. 2000; A DNA structural atlas for Escherichia coli. J Mol Biol 299:907–930
    [Google Scholar]
30. Pérez-Martín J., Rojo F., de Lorenzo V. 1994; Promoters responsive to DNA bending: a common theme in prokaryotic gene expression. Microbiol Rev 58:268–290
    [Google Scholar]
31. Rabinowitz J. 1972; Preparation and properties of clostridial ferredoxins. Methods Enzymol 24:431–446
    [Google Scholar]
32. Ragsdale S. W., Ljungdahl L. G. 1984; Characterization of ferredoxin, flavodoxin, and rubredoxin from Clostridium formicoaceticum grown in media with high and low iron contents. J Bacteriol 157:1–6
    [Google Scholar]
33. Rimsky S., Zuber F., Buckle M., Buc H. 2001; A molecular mechanism for the repression of transcription by the H-NS protein. Mol Microbiol 42:1311–1323
    [Google Scholar]
34. Saint-Amans S., Girbal L., Andrade J., Ahrens K., Soucaille P. 2001; Regulation of carbon and electron flow in Clostridium butyricum VPI 3266 grown on glucose-glycerol mixtures. J Bacteriol 183:1748–1754
    [Google Scholar]
35. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning: a Laboratory Manual, 2nd edn. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
36. Shaw W. V. 1975; Chloramphenicol acetyltransferase from chloramphenicol-resistant bacteria. Methods Enzymol 43:737–755
    [Google Scholar]
37. Shimizu T., Ohtani K., Hirakawa H. 7 other authors 2002; Complete genome sequence of Clostridium perfringens, an anaerobic flesh-eater. Proc Natl Acad Sci U S A 99:996–1001
    [Google Scholar]
38. Shpigelman E. S., Trifonov E. N., Bolshoy A. 1993; curvature: software for the analysis of curved DNA. Comput Appl Biosci 9:435–440
    [Google Scholar]
39. Songer J. G. 1996; Clostridial enteric diseases of domestic animals. Clin Microbiol Rev 9:216–234
    [Google Scholar]
40. Toyonaga T., Matsushita O., Katayama S., Minami J., Okabe A. 1992; Role of the upstream region containing an intrinsic DNA curvature in the negative regulation of the phospholipase C gene of Clostridium perfringens. Microbiol Immunol 36:603–613
    [Google Scholar]
41. Ueguchi C., Kakeda M., Yamada H., Mizuno T. 1994; An analogue of the DnaJ molecular chaperone in Escherichia coli. Proc Natl Acad Sci U S A 91:1054–1058
    [Google Scholar]
42. Yasuno K., Yamazaki T., Tanaka Y., Kodama T. S., Matsugami A., Katahira M., Ishihama A., Kyogoku Y. 2001; Interaction of the C-terminal domain of the E. coli RNA polymerase alpha subunit with the UP element: recognizing the backbone structure in the minor groove surface. J Mol Biol 306:213–225
    [Google Scholar]