Regulation of upp expression in Escherichia coli by UTP-sensitive selection of transcriptional start sites coupled with UTP-dependent reiterative transcription

Journal of Bacteriology

Volumn 179, Issue 21, 1997, Pages 6665-6673

  Tu, Anh Hue Thi ^a   Turnbough Jr , Charles L ^a  

^a UNIVERSITY OF ALABAMA AT BIRMINGHAM   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ELONGATION FACTOR; URIDINE TRIPHOSPHATE;

AMINO ACID SEQUENCE; ARTICLE; DNA FLANKING REGION; GENE CONTROL; GENE EXPRESSION; GENE EXPRESSION REGULATION; GENE SEQUENCE; GENETIC TRANSCRIPTION; PRIORITY JOURNAL; TRANSCRIPTION INITIATION;

ESCHERICHIA COLI;

EID: 0001612470     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/jb.179.21.6665-6673.1997     Document Type: Article

References (45)

1. Alper, M. D., and B. N. Ames. 1978. Transport of antibiotics and metabolite analogs by systems under cyclic AMP control: positive selection of Salmonella typhimurium cya and crp mutants. J. Bacteriol. 133:149-157.
2. Andersen, J. T., K. F. Jensen, and P. Poulsen. 1991. Role of transcription pausing in the control of the pyrE attenuator in Escherichia coli. Mol. Microbiol. 5:327-333.
3. Andersen, P. S., J. M. Smith, and B. Mygind. 1992. Characterization of the upp gene encoding uracil phosphoribosyltransferase of Escherichia coli K12. Eur. J. Biochem. 204:51-56.
4. Barettino, D., M. Feigenbutz, R. Valcárcel, and H. G. Stunnenberg. 1993. Improved method for PCR-mediated site-directed mutagenesis. Nucleic Acids Res. 22:541-542.
5. Burgess, R. R., and J. J. Jendrisak. 1975. A procedure for the rapid, largescale purification of Escherichia coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA-cellulose chromatography. Biochemistry 14:4634-4638.
6. Casadaban, M. J. 1976. Transposition and fusion of the lac genes to selected promoters in Escherichia coli using bacteriophage lambda and Mu. J. Mol. Biol. 104:541-555.
7. Chamberlin, M. J. 1995. New models for the mechanism of transcription elongation and its regulation. Harvey Lect. 88:1-21.
8. Chan, C. L., and R. Landick. 1994. New perspectives on RNA chain elongation and termination by E. coli RNA polymerase, p. 297-321. In R. C. Conaway and J. W. Conaway (ed.), Transcription: mechanisms and regulation. Raven Press, New York, N.Y.
9. Daube, S. S., and P. H. von Hippel. 1992. Functional transcription elongation complexes from synthetic RNA-DNA bubble duplexes. Science 258:1320-1324.
10. Gonzalez, N., J. Wiggs, and M. J. Chamberlin. 1977. A simple procedure for resolution of Escherichia coli RNA polymerase holoenzyme from core polymerase. Arch. Biochem. Biophys. 182:404-408.
11. Guo, H.-C., and J. W. Roberts. 1990. Heterogeneous initiation due to slippage at the bacteriophage 82 late gene promoter in vitro. Biochemistry 29:10702-10709.
12. Han, X., and C. L. Turnbough, Jr. Unpublished data.
13. Hanna, M. M., and C. F. Meares. 1983. Topography of transcription: path of the leading end of nascent RNA through the Escherichia coli transcription complex. Proc. Natl. Acad. Sci. USA 80:4238-4242.
14. Jacques, J. P., and D. Kolakofsky. 1991. Pseudo-templated transcription in prokaryotic and eukaryotic organisms. Genes Dev. 5:707-713.
15. Jeong, S. W., W. H. Lang, and R. H. Reeder. 1996. The yeast transcription terminator for RNA polymerase I is designed to prevent polymerase slippage. J. Biol. Chem. 271:16104-16110.
16. Jin, D. J. 1994. Slippage synthesis at the galP2 promoter of Escherichia coli and its regulation by UTP concentration and cAMP-cAMP receptor protein. J. Biol. Chem. 269:17221-17227.
17. Kainz, M., and J. Roberts. 1992. Structure of transcription elongation complexes in vivo. Science 255:838-841.
18. Komissarova, N., and M. Kashiev. 1997. Transcriptional arrest: Escherichia coli RNA polymerase translocates backward, leaving the 3′ end of the RNA intact and extruded. Proc. Natl. Acad. Sci. USA 94:1755-1760.
19. Lee, D. N., and R. Landick. 1992. Structure of RNA and DNA chains in paused transcription complexes containing Escherichia coli RNA polymerase. J. Mol. Biol. 228:759-777.
20. Linton, M. F., M. Raabe, V. Pierotti, and S. G. Young. 1997. Reading-frame restoration by transcriptional slippage at long stretches of adenine residues in mammalian cells. J. Biol. Chem. 272:14127-14132.
21. Liu, C., L. S. Heath, and C. L. Turnbough, Jr. 1994. Regulation of pyrBI operon expression in Escherichia coli by UTP-sensitive reiterative RNA synthesis during transcriptional initiation. Genes Dev. 8:2904-2912.
22. Liu, J., and C. L. Turnbough, Jr. 1994. Effects of transcriptional start site sequence and position on nucleotide-sensitive selection of alternative start sites at the pyrC promoter in Escherichia coli. J. Bacteriol. 176:2938-2945.
23. Lowry, O. H., N. J. Rosebrough, A. L. Farr, and R. J. Randall. 1951. Protein measurement with the Folin phenol reagent. J. Biol. Chem. 193:265-275.
24. Macdonald, L. E., Y. Zhou, and W. T. McAllister. 1993. Termination and slippage by bacteriophage T7 RNA polymerase. J. Mol. Biol. 232:1030-1047.
25. McClure, W. R., C. L. Cech, and D. E. Johnston. 1978 A steady state assay for the RNA polymerase initiation reaction. J. Biol. Chem. 253:8941-8948.
26. Miller, J. H. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory, Cold Spring Harbor, N. Y.
27. Neuhard, J., and P. Nygaard. 1987. Purines and pyrimidines, p. 445-473. 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. American Society for Microbiology, Washington, D.C.
28. 1. J. Biol. Chem. 254:7921-7926.
29. Nudler, E., A. Mustaev, E. Lukhtanov, and A. Goldfarb. 1997. The RNA-DNA hybrid maintains the register of transcription by preventing backtracking of RNA polymerase. Cell 89:33-41.
30. Poulsen, P., and K. F. Jensen. 1987. Effect of UTP and GTP pools on attenuation at the pyrE gene of Escherichia coli. Mol. Gen. Genet. 208:152-158.
31. Powell, B. S., D. L. Court, Y. Nakamura, M. P. Rivas, and C. L. Turnbough, Jr. 1994. Rapid confirmation of single copy lambda prophage integration by PCR. Nucleic Acids Res. 22:5765-5766.
32. Qi, F., C. Liu, L. S. Heath, and C. L. Turnbough, Jr. 1996. In vitro assay for reiterative transcription during transcriptional initiation by Escherichia coli RNA polymerase. Methods Enzymol. 273:71-85.
33. Qi, F., and C. L. Turnbough, Jr. Unpublished data.
34. Qi, F., and C. L. Turnbough, Jr. 1995. Regulation of codBA operon expression in Escherichia coli by UTP-dependent reiterative transcription and UTP-sensitive transcriptional start site switching. J. Mol. Biol. 254:552-565.
35. Quinn, C. L., B. T. Stephenson, and R. L. Switzer. 1991. Functional organization and nucleotide sequence of the Bacillus subtilis pyrimidine biosynthetic operon. J. Biol. Chem. 266:9113-9127.
36. Rasmussen, U. B., B. Mygind, and P. Nygaard. 1986. Purification and some properties of uracil phosphoribosyltransferase from Escherichia coli K12. Biochim. Biophys. Acta 881:268-275.
37. Roland, K. L., C. Liu, and C. L. Turnbough, Jr. 1988. Role of the ribosome in suppressing transcriptional termination at the pvrBI attenuator of Escherichia coli K-12. Proc. Natl. Acad. Sci. USA 85:7149-7153.
38. Roland, K. L., F. E. Powell, and C. L. Turnbough, Jr. 1985. Role of translation and attenuation in the control of pyrBI operon expression in Escherichia coli K-12. J. Bacteriol. 163:991-999.
39. Silhavy, T. J., M. L. Berman, and L. W. Enquist. 1984. Experiments with gene fusions. Cold Spring Harbor Laboratory, Cold Spring Harbor, N. Y.
40. Sørensen, K. I., K. E. Baker, R. A. Kelln, and J. Neuhard. 1993. Nucleotide pool-sensitive selection of the transcriptional start site in vivo at the Salmonella typhimurium pyrC and pvrD promoters. J. Bacteriol. 175:4137-4144.
41. Surratt, C. K., S. C. Milan, and M. J. Chamberlin. 1991. Spontaneous cleavage of RNA in ternary complexes of Escherichia coli RNA polymerase and its significance for the mechanism of transcription. Proc. Natl. Acad. Sci. USA 88:7983-7987.
42. Wagner, L. A., R. B. Weiss, R. Driscoll, D. S. Dunn, and R. F. Gesteland. 1990. Transcriptional slippage occurs during elongation at runs of adenine or thymine in Escherichia coli. Nucleic Acids Res. 18:3529-3535.
43. Wilson, H. R., C. D. Archer, J. Liu, and C. L. Turnbough, Jr. 1992. Translational control of pyrC expression mediated by nucleotide-sensitive selection of transcriptional start sites in Escherichia coli. J. Bacteriol. 174:514-524.
44. Yager, T. D., and P. H. von Hippel. 1991. A thermodynamic analysis of RNA transcript elongation and termination in Escherichia coli. Biochemistry 30: 1097-1118.
45. Zaychikov, E., L. Denissova, and H. Heumann. 1995. Translocation of the Escherichia coli transcription complex observed in the registers 11 to 20: "jumping" of RNA polymerase and asymmetric expansion and contraction of the "transcription bubble." Proc. Natl. Acad. Sci. USA 92:1739-1743.