Activation of the promoter of the fengycin synthetase operon by the UP element

Journal of Bacteriology

Volumn 191, Issue 14, 2009, Pages 4615-4623

  Ke, Wan Ju ^a   Chang, Ban Yang ^b   Lin, Tsuey Pin ^c   Liu, Shih Tung ^a  

^a CHANG GUNG UNIVERSITY   (Taiwan)

^b NATIONAL CHUNG HSING UNIVERSITY   (Taiwan)

^c CHIA NAN UNIVERSITY OF PHARMACY AND SCIENCE   (Taiwan)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIFUNGAL AGENT; COMPLEMENTARY DNA; DNA FRAGMENT; FENGYCIN; FENGYCIN SYNTHETASE; POLYPEPTIDE ANTIBIOTIC AGENT; RNA POLYMERASE; SYNTHETASE; UNCLASSIFIED DRUG; DNA DIRECTED RNA POLYMERASE; PEPTIDE SYNTHASE; RNA POLYMERASE ALPHA SUBUNIT;

ANTIFUNGAL ACTIVITY; ARTICLE; BACILLUS SUBTILIS; BACTERIAL GENE; BACTERIAL SPORE; BIOASSAY; BIOSYNTHESIS; CODON; ENZYME ACTIVITY; ENZYME ASSAY; FENC GENE; GENE MUTATION; GERMINATION; IN VITRO STUDY; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; PAECILOMYCES; PRIORITY JOURNAL; PROMOTER REGION; REAL TIME POLYMERASE CHAIN REACTION; TRANSLATION INITIATION; DNA FOOTPRINTING; ENHANCER REGION; ENZYMOLOGY; GEL MOBILITY SHIFT ASSAY; GENE EXPRESSION; GENETICS; METABOLISM; MOLECULAR GENETICS; PROTEIN BINDING;

BACILLUS SUBTILIS; PAECILOMYCES VARIOTII;

BACILLUS SUBTILIS; BASE SEQUENCE; DNA FOOTPRINTING; DNA-DIRECTED RNA POLYMERASES; ELECTROPHORETIC MOBILITY SHIFT ASSAY; ENHANCER ELEMENTS, GENETIC; GENE EXPRESSION; MOLECULAR SEQUENCE DATA; OPERON; PEPTIDE SYNTHASES; PROMOTER REGIONS, GENETIC; PROTEIN BINDING;

EID: 67650318507     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00255-09     Document Type: Article

References (53)

1. Aiba, H., S. Adhya, and B. de Crombrugghe. 1981. Evidence for two functional gal promoters in intact Escherichia coli cells. J. Biol. Chem. 256: 11905-11910.
2. Aiyar, S. E., R. L. Gourse, and W. Ross. 1998. Upstream A-tracts increase bacterial promoter activity through interactions with the RNA polymerase alpha subunit. Proc. Natl. Acad. Sci. USA 95:14652-14657.
3. Asanuma, K., N. Tsuji, T. Endoh, A. Yagihashi, and N. Watanabe. 2004. Survivin enhances Fas ligand expression via up-regulation of specificity protein 1-mediated gene transcription in colon cancer cells. J. Immunol. 172: 3922-3929.
4. Banner, C. D., C. P. Moran, Jr., and R. Losick. 1983. Deletion analysis of a complex promoter for a developmentally regulated gene from Bacillus subtilis. J. Mol. Biol. 168:351-365.
5. Caramori, T., and A. Galizzi. 1998. The UP element of the promoter for the flagellin gene, hag, stimulates transcription from both SigD- and SigA-dependent promoters in Bacillus subtilis. Mol. Gen. Genet. 258:385-388.
6. Chang, B. Y., K. Y. Chen, Y. D. Wen, and C. T. Liao. 1994. The response of a Bacillus subtilis temperature-sensitive sigA mutant to heat stress. J. Bacteriol. 176:3102-3110.
7. Chang, L. K., C. L. Chen, Y. S. Chang, J. S. Tschen, Y. M. Chen, and S. T. Liu. 1994. Construction of Tn917ac1, a transposon useful for mutagenesis and cloning of Bacillus subtilis genes. Gene 150:129-134.
8. Chen, C. L., L. K. Chang, Y. S. Chang, S. T. Liu, and J. S. Tschen. 1995. Transposon mutagenesis and cloning of the genes encoding the enzymes of fengycin biosynthesis in Bacillus subtilis. Mol. Gen. Genet. 248:121-125.
9. Clugston, S. L., S. A. Sieber, M. A. Marahiel, and C. T. Walsh. 2003. Chirality of peptide bond-forming condensation domains in nonribosomal peptide synthetases: the C5 domain of tyrocidine synthetase is a (D)C(L) catalyst. Biochemistry 42:12095-12104.
10. Conti, E., T. Stachelhaus, M. A. Marahiel, and P. Brick. 1997. Structural basis for the activation of phenylalanine in the non-ribosomal biosynthesis of gramicidin S. EMBO J. 16:4174-4183.
11. Estrem, S. T., T. Gaal, W. Ross, and R. L. Gourse. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. USA 95:9761-9766.
12. Estrem, S. T., W. Ross, T. Gaal, Z. W. Chen, W. Niu, R. H. Ebright, and R. L. Gourse. 1999. Bacterial promoter architecture: subsite structure of UP elements and interactions with the carboxy-terminal domain of the RNA polymerase alpha subunit. Genes Dev. 13:2134-2147.
13. Finking, R., and M. A. Marahiel. 2004. Biosynthesis of nonribosomal peptides. Annu. Rev. Microbiol. 58:453-488.
14. Fleige, S., V. Walf, S. Huch, C. Prgomet, J. Sehm, and M. W. Pfaffl. 2006. Comparison of relative mRNA quantification models and the impact of RNA integrity in quantitative real-time RT-PCR. Biotechnol. Lett. 28:1601-1613.
15. Fredrick, K., T. Caramori, Y. F. Chen, A. Galizzi, and J. D. Helmann. 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.
16. Gaal, T., L. Rao, S. T. Estrem, J. Yang, R. M. Wartell, and R. L. Gourse. 1994. Localization of the intrinsically bent DNA region upstream of the E. coli rrnB P1 promoter. Nucleic Acids Res. 22:2344-2350.
17. Gaal, T., W. Ross, E. E. Blatter, H. Tang, X. Jia, V. V. Krishnan, N. Assa-Munt, R. H. Ebright, and R. L. Gourse. 1996. DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture. Genes Dev. 10:16-26.
18. Gourse, R. L., W. Ross, and T. Gaal. 2000. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37:687-695.
19. Helmann, J. D. 1995. Compilation and analysis of Bacillus subtilis sigma A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 23: 2351-2360.
20. Hilden, I., B. N. Krath, and B. Hove-Jensen. 1995. Tricistronic operon expression of the genes gcaD (tms), which encodes N-acetylglucosamine 1-phosphate uridyltransferase, prs, which encodes phosphoribosyl diphosphate synthetase, and ctc in vegetative cells of Bacillus subtilis. J. Bacteriol. 177:7280-7284.
21. Hsu, H. H., W. C. Huang, J. P. Chen, L. Y. Huang, C. F. Wu, and B. Y. Chang. 2004. Properties of Bacillus subtilis sigma A factors with region 1.1 and the conserved Arg-103 at the N terminus of region 1.2 deleted. J. Bacteriol. 186:2366-2375.
22. Jeon, Y. H., T. Negishi, M. Shirakawa, T. Yamazaki, N. Fujita, A. Ishihama, and Y. Kyogoku. 1995. Solution structure of the activator contact domain of the RNA polymerase alpha subunit. Science 270:1495-1497.
23. Kim, S. I., Y. S. Nam, and S. Y. Lee. 1997. Improvement of the production of foreign proteins using a heterologous secretion vector system in Bacillus subtilis: effects of resistance to glucose-mediated catabolite repression. Mol. Cells 7:788-794.
24. Koglin, A., F. Lohr, F. Bernhard, V. V. Rogov, D. P. Frueh, E. R. Strieter, M. R. Mofid, P. Guntert, G. Wagner, C. T. Walsh, M. A. Marahiel, and V. Dotsch. 2008. Structural basis for the selectivity of the external thioesterase of the surfactin synthetase. Nature 454:907-911.
25. Kolb, A., K. Igarashi, A. Ishihama, M. Lavigne, M. Buckle, and H. Buc. 1993. E. coli RNA polymerase, deleted in the C-terminal part of its alpha-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter. Nucleic Acids Res. 21:319-326.
26. Kopp, F., U. Linne, M. Oberthur, and M. A. Marahiel. 2008. Harnessing the chemical activation inherent to carrier protein-bound thioesters for the characterization of lipopeptide fatty acid tailoring enzymes. J. Am. Chem. Soc. 130:2656-2666.
27. Lambalot, R. H., A. M. Gehring, R. S. Flugel, P. Zuber, M. LaCelle, M. A. Marahiel, R. Reid, C. Khosla, and C. T. Walsh. 1996. A new enzyme superfamily-the phosphopantetheinyl transferases. Chem. Biol. 3:923-936.
28. Lin, G. H., C. L. Chen, J. S. Tschen, S. S. Tsay, Y. S. Chang, and S. T. Liu. 1998. Molecular cloning and characterization of fengycin synthetase gene fenB from Bacillus subtilis. J. Bacteriol. 180:1338-1341.
29. Lin, T. P., C. L. Chen, L. K. Chang, J. S. Tschen, and S. T. Liu. 1999. Functional and transcriptional analyses of a fengycin synthetase gene, fenC, from Bacillus subtilis. J. Bacteriol. 181:5060-5067.
30. Lin, T. P., C. L. Chen, H. C. Fu, C. Y. Wu, G. H. Lin, S. H. Huang, L. K. Chang, and S. T. Liu. 2005. Functional analysis of fengycin synthetase FenD. Biochim. Biophys. Acta 1730:159-164.
31. Luo, L., R. M. Kohli, M. Onishi, U. Linne, M. A. Marahiel, and C. T. Walsh. 2002. Timing of epimerization and condensation reactions in nonribosomal peptide assembly lines: kinetic analysis of phenylalanine activating elongation modules of tyrocidine synthetase B. Biochemistry 41:9184-9196.
32. Meijer, W. J., and M. Salas. 2004. Relevance of UP elements for three strong Bacillus subtilis phage phi29 promoters. Nucleic Acids Res. 32:1166-1176.
33. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY.
34. Nelson, R. M., and G. L. Long. 1989. A general method of site-specific mutagenesis using a modification of the Thermus aquaticus polymerase chain reaction. Anal. Biochem. 180:147-151.
35. Newlands, J. T., C. A. Josaitis, W. Ross, and R. L. Gourse. 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.
36. Noel, R. J., Jr., and W. S. Reznikoff. 1998. CAP, the -45 region, and RNA polymerase: three partners in transcription initiation at lacP1 in Escherichia coli. J. Mol. Biol. 282:495-504.
37. Pan, S. H., and B. A. Malcolm. 2000. Reduced background expression and improved plasmid stability with pET vectors in BL21(DE3). BioTechniques 29:1234-1238.
38. Rao, L., W. Ross, J. A. Appleman, T. Gaal, S. Leirmo, P. J. Schlax, M. T. Record, Jr., and R. L. Gourse. 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.
39. Ross, W., K. K. Gosink, J. Salomon, K. Igarashi, C. Zou, A. Ishihama, K. Severinov, and R. L. Gourse. 1993. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407-1413.
40. Schlumbohm, W., T. Stein, C. Ullrich, J. Vater, M. Krause, M. A. Marahiel, V. Kruft, and B. Wittmann-Liebold. 1991. An active serine is involved in covalent substrate amino acid binding at each reaction center of gramicidin S synthetase. J. Biol. Chem. 266:23135-23141.
41. Shu, H. Y., G. H. Lin, Y. C. Wu, J. S. Tschen, and S. T. Liu. 2002. Amino acids activated by fengycin synthetase FenE. Biochem. Biophys. Res. Commun. 292:789-793.
42. Sieber, S. A., and M. A. Marahiel. 2003. Learning from nature's drug factories: nonribosomal synthesis of macrocyclic peptides. J. Bacteriol. 185: 7036-7043.
43. Stachelhaus, T., A. Huser, and M. A. Marahiel. 1996. Biochemical characterization of peptidyl carrier protein (PCP), the thiolation domain of multifunctional peptide synthetases. Chem. Biol. 3:913-921.
44. Stachelhaus, T., and M. A. Marahiel. 1995. Modular structure of genes encoding multifunctional peptide synthetases required for non-ribosomal peptide synthesis. FEMS Microbiol. Lett. 125:3-14.
45. Stein, T., J. Vater, V. Kruft, A. Otto, B. Wittmann-Liebold, P. Franke, M. Panico, R. McDowell, and H. R. Morris. 1996. The multiple carrier model of nonribosomal peptide biosynthesis at modular multienzymatic templates. J. Biol. Chem. 271:15428-15435.
46. Tanovic, A., S. A. Samel, L. O. Essen, and M. A. Marahiel. 2008. Crystal structure of the termination module of a nonribosomal peptide synthetase. Science 321:659-663.
47. Vanittanakom, N., W. Loeffler, U. Koch, and G. Jung. 1986. Fengycin-a novel antifungal lipopeptide antibiotic produced by Bacillus subtilis F-29-3. J. Antibiot. (Tokyo) 39:888-901.
48. Wu, C. Y., C. L. Chen, Y. H. Lee, Y. C. Cheng, Y. C. Wu, H. Y. Shu, F. Gotz, and S. T. Liu. 2007. Nonribosomal synthesis of fengycin on an enzyme complex formed by fengycin synthetases. J. Biol. Chem. 282:5608-5616.
49. Yamanaka, K., J. Araki, M. Takano, and J. Sekiguchi. 1997. Characterization of Bacillus subtilis mutants resistant to cold shock-induced autolysis. FEMS Microbiol. Lett. 150:269-275.
50. Yokoyama, E., Y. Matsuzaki, K. Doi, and S. Ogata. 1998. Gene encoding a replication initiator protein and replication origin of conjugative plasmid pSA1.1 of Streptomyces cyaneus ATCC 14921. FEMS Microbiol. Lett. 169: 103-109.
51. Yonus, H., P. Neumann, S. Zimmermann, J. J. May, M. A. Marahiel, and M. T. Stubbs. 2008. Crystal structure of DltA: implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains. J. Biol. Chem. 47:32484-32491.
52. Zähner, H., and W. K. Maas. 1972. Biology of antibiotics. Springer, New York, NY.
53. Zhang, Y., S. Nakano, S. Y. Choi, and P. Zuber. 2006. Mutational analysis of the Bacillus subtilis RNA polymerase alpha C-terminal domain supports the interference model of Spx-dependent repression. J. Bacteriol. 188:4300-4311.