1887

Abstract

This study has revealed that a ferredoxin gene (per-) possesses a novel type of DNA curvature, which is formed by five phased A-tracts extending from upstream to downstream of the −35 region. The three A-tracts upstream of the promoter and the two within the promoter are located at the positions corresponding to A-tracts present in a phospholipase C gene () and a ferredoxin gene (pas-), respectively. DNA fragments of the per-, pas- and genes (nucleotide positions −69 to +1 relative to the transcription initiation site) were fused to a chloramphenicol acetyltransferase reporter gene on a plasmid, pPSV, and their promoter activities were examined by assaying the chloramphenicol acetyltransferase activity of each transformant. Comparison of the three constructs showed that the order of promoter activity is, in descending order, per-, pas- and . Deletion of the three upstream A-tracts of the per- gene drastically decreased the promoter activity, as demonstrated previously for the promoter. Substitution of the most downstream A-tract decreased the promoter activities of the per- and pas- genes. These results indicate that not only the phased A-tracts upstream of the promoter but also those within the promoter stimulate the promoter activity, and suggest that the high activity of the per- promoter is due to the combined effects of these two types of A-tracts.

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2003-11-01
2019-10-16
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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.[CrossRef]
    [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 σ 70 subunit is responsible for the recognition of the ‘extended −10’ motif at promoters. EMBO J 16, 4034–4040.[CrossRef]
    [Google Scholar]
  3. Bolshoy, A. & Nevo, E. ( 2000; ). Ecologic genomics of DNA: upstream bending in prokaryotic promoters. Genome Res 10, 1185–1193.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [Google Scholar]
  13. Kiyama, R. & Trifonov, E. N. ( 2002; ). What positions nucleosomes? – A model. FEBS Lett 523, 7–11.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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 B. I. Duerden & B. S. Drasar. London: Edward Arnold.
  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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [Google Scholar]
  28. Ohyama, T. ( 2001; ). Intrinsic DNA bends: an organizer of local chromatin structure for transcription. Bioessays 23, 708–715.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [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.[CrossRef]
    [Google Scholar]
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