Transcription-coupled DNA supercoiling in defined protein systems and in E. coli topA mutant strains

IUBMB Life

Volumn 65, Issue 7, 2013, Pages 615-622

  Fulcrand, Geraldine ^a   Zhi, Xiaoduo ^a   Leng, Fenfei ^a  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

Author keywords

DNA topological barriers; E. coli topA mutants; the leu 500 promoter; transcription coupled DNA supercoiling; twin supercoiled domain model of transcription

Indexed keywords

DNA BINDING PROTEIN; NUCLEOPROTEIN; RNA POLYMERASE;

BACTERIAL MUTATION; BACTERIAL STRAIN; CHROMOSOME STRUCTURE; DNA REPLICATION ORIGIN; DNA SUPERCOILING; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PROMOTER REGION; PROTEIN LOCALIZATION; REVIEW; SALMONELLA TYPHIMURIUM; TRANSCRIPTION INITIATION;

DNA, BACTERIAL; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; GENE EXPRESSION REGULATION, BACTERIAL; NUCLEIC ACID CONFORMATION; PROMOTER REGIONS, GENETIC; SALMONELLA TYPHIMURIUM; TRANSCRIPTION, GENETIC;

ESCHERICHIA COLI; SALMONELLA TYPHIMURIUM;

EID: 84879421049     PISSN: 15216543     EISSN: 15216551     Source Type: Journal    
DOI: 10.1002/iub.1179     Document Type: Review

References (50)

1. Bates, A. D., and, Maxwell, A., (2005) DNA Topology. Oxford University Press, Oxford, UK.
2. James C. Wang, (2009) Untangling the Double Helix: DNA Entanglement and the Action of the DNA Topoisomerases. Cold Spring Harbor Laboratory Press, New York.
3. Champoux, J. J., (2001) DNA topoisomerases: structure, function, and mechanism. Annu. Rev. Biochem., 70, 369-413.
4. Snoep, J. L., van der Weijden, C. C., Andersen, H. W., Westerhoff, H. V., and, Jensen, P. R., (2002) DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. Eur. J. Biochem. 269, 1662-1669.
5. Lockshon, D., and, Morris, D. R., (1983) Positively supercoiled plasmid DNA is produced by treatment of Escherichia coli with DNA gyrase inhibitors. Nucleic Acids Res. 11, 2999-3017.
6. Pruss, G. J., (1985) DNA topoisomerase I mutants. Increased heterogeneity in linking number and other replicon-dependent changes in DNA supercoiling. J. Mol. Biol. 185, 51-63.
7. Liu, L. F., and, Wang, J. C., (1987) Supercoiling of the DNA template during transcription. Proc. Natl. Acad. Sci. USA 84, 7024-7027.
8. Cook, D. N., Ma, D., Pon, N. G., and, Hearst, J. E., (1992) Dynamics of DNA supercoiling by transcription in Escherichia coli. Proc. Natl. Acad. Sci. USA 89, 10603-10607.
9. Leng, F., and, McMacken, R., (2002) Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins. Proc. Natl. Acad. Sci. USA 99, 9139-9144.
10. Leng, F., Amado, L., and, McMacken, R., (2004) Coupling DNA supercoiling to transcription in defined protein systems. J. Biol. Chem. 279, 47564-47571.
11. Lodge, J. K., Kazic, T., and, Berg, D. E., (1989) Formation of supercoiling domains in plasmid pBR322. J. Bacteriol. 171, 2181-2187.
12. Lynch, A. S., and, Wang, J. C., (1993) Anchoring of DNA to the bacterial cytoplasmic membrane through cotranscriptional synthesis of polypeptides encoding membrane proteins or proteins for export: a mechanism of plasmid hypernegative supercoiling in mutants deficient in DNA topoisomerase I. J. Bacteriol. 175, 1645-1655.
13. Samul, R., and, Leng, F., (2007) Transcription-coupled hypernegative supercoiling of plasmid DNA by T7 RNA polymerase in Escherichia coli topoisomerase I-deficient strains. J. Mol. Biol., 374, 925-935.
14. Stupina, V. A., and, Wang, J. C., (2005) Viability of Escherichia coli topA mutants lacking DNA topoisomerase I. J. Biol. Chem. 280, 355-360.
15. Kuimova, M. K., Yahioglu, G., Levitt, J. A., and, Suhling, K., (2008) Molecular rotor measures viscosity of live cells via fluorescence lifetime imaging. J. Am. Chem. Soc. 130, 6672-6673.
16. Zimmerman, S. B., and, Minton, A. P., (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu. Rev. Biophys. Biomol. Struct. 22, 27-65.
17. Nelson, P., (1999) Transport of torsional stress in DNA. Proc. Natl. Acad. Sci. USA 96, 14342-14347.
18. Mielke, S. P., Fink, W. H., Krishnan, V. V., Gronbech-Jensen, N., and, Benham, C. J., (2004) Transcription-driven twin supercoiling of a DNA loop: a Brownian dynamics study. J. Chem. Phys. 121, 8104-8112.
19. Tsao, Y. P., Wu, H. Y., and, Liu, L. F., (1989) Transcription-driven supercoiling of DNA: direct biochemical evidence from in vitro studies. Cell 56, 111-118.
20. Drolet, M., Bi, X., and, Liu, L. F., (1994) Hypernegative supercoiling of the DNA template during transcription elongation in vitro. J. Biol. Chem. 269, 2068-2074.
21. Leng, F., Chen, B., and, Dunlap, D. D., (2011) Dividing a supercoiled DNA molecule into two independent topological domains. Proc. Natl. Acad. Sci. USA 108, 19973-19978.
22. Chen, B., Xiao, Y., Liu, C., Li, C., and, Leng, F., (2010) DNA linking number change induced by sequence-specific DNA-binding proteins. Nucleic Acids Res. 38, 3643-3654.
23. Liu, Y., Bondarenko, V., Ninfa, A., and, Studitsky, V. M., (2001) DNA supercoiling allows enhancer action over a large distance. Proc. Natl. Acad. Sci. USA 98, 14883-14888.
24. Dodson, M., McMacken, R., and, Echols, H., (1989) Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda. Protein association and disassociation reactions responsible for localized initiation of replication. J. Biol. Chem. 264, 10719-10725.
25. Postow, L., Hardy, C. D., Arsuaga, J., and, Cozzarelli, N. R., (2004) Topological domain structure of the Escherichia coli chromosome. Genes Dev. 18, 1766-1779.
26. Deng, S., Stein, R. A., and, Higgins, N. P., (2004) Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium chromosome. Proc. Natl. Acad. Sci. USA 101, 3398-3403.
27. Rouviere-Yaniv, J., Yaniv, M., and, Germond, J. E., (1979) E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA. Cell 17, 265-274.
28. Tupper, A. E., Owen-Hughes, T. A., Ussery, D. W., Santos, D. S., Ferguson, D. J., et al. (1994) The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J. 13, 258-268.
29. Dame, R. T., (2005) The role of nucleoid-associated proteins in the organization and compaction of bacterial chromatin. Mol. Microbiol. 56, 858-870.
30. Wang, W., Li, G. W., Chen, C., Xie, X. S., and, Zhuang, X., (2011) Chromosome organization by a nucleoid-associated protein in live bacteria. Science 333, 1445-1449.
31. Whitson, P. A., Hsieh, W. T., Wells, R. D., and, Matthews, K. S., (1987) Supercoiling facilitates lac operator-repressor-pseudooperator interactions. J. Biol. Chem. 262, 4943-4946.
32. Gamper, H. B., and, Hearst, J. E., (1982) A topological model for transcription based on unwinding angle analysis of E. coli RNA polymerase binary, initiation and ternary complexes. Cell 29, 81-90.
33. Luger, K., Mader, A. W., Richmond, R. K., Sargent, D. F., and, Richmond, T. J., (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389, 251-260.
34. Heng, H. H., Goetze, S., Ye, C. J., Liu, G., Stevens, J. B., et al. (2004) Chromatin loops are selectively anchored using scaffold/matrix-attachment regions. J. Cell Sci. 117, 999-1008.
35. Pruss, G. J., and, Drlica, K., (1986) Topoisomerase I mutants: the gene on pBR322 that encodes resistance to tetracycline affects plasmid DNA supercoiling. Proc. Natl. Acad. Sci. USA 83, 8952-8956.
36. Stuber, D., and, Bujard, H., (1981) Organization of transcriptional signals in plasmids pBR322 and pACYC184. Proc. Natl. Acad. Sci. USA 78, 167-171.
37. Zhi, X., and, Leng, F., (2013) Dependence of transcription-coupled DNA supercoiling on promoter strength in Escherichia coli topoisomerase I deficient strains. Gene 514, 82-90.
38. Yamada, M., Kabir, M. S., and, Tsunedomi, R., (2003) Divergent promoter organization may be a preferred structure for gene control in Escherichia coli. J. Mol. Microbiol. Biotechnol. 6, 206-210.
39. Rhee, K. Y., Opel, M., Ito, E., Hung, S., Arfin, S. M., et al. (1999) Transcriptional coupling between the divergent promoters of a prototypic LysR-type regulatory system, the ilvYC operon of Escherichia coli. Proc. Natl. Acad. Sci. USA 96, 14294-14299.
40. Dubnau, E., and, Margolin, P., (1972) Suppression of promoter mutations by the pleiotropic supx mutations. Mol. Gen. Genet. 117, 91-112.
41. Margolin, P., Zumstein, L., Sternglanz, R., and, Wang, J. C., (1985) The Escherichia coli supX locus is topA, the structural gene for DNA topoisomerase I. Proc. Natl. Acad. Sci. USA 82, 5437-5441.
42. Wang, J. C., and, Becherer, K., (1983) Cloning of the gene topA encoding for DNA topoisomerase I and the physical mapping of the cysB-topA-trp region of Escherichia coli. Nucleic Acids Res. 11, 1773-1790.
43. Lilley, D. M., and, Higgins, C. F., (1991) Local DNA topology and gene expression: the case of the leu-500 promoter. Mol. Microbiol. 5, 779-783.
44. Chen, D., Bowater, R., Dorman, C. J., and, Lilley, D. M., (1992) Activity of a plasmid-borne leu-500 promoter depends on the transcription and translation of an adjacent gene. Proc. Natl. Acad. Sci. USA 89, 8784-8788.
45. Tan, J., Shu, L., and, Wu, H. Y., (1994) Activation of the leu-500 promoter by adjacent transcription. J. Bacteriol. 176, 1077-1086.
46. Wu, H. Y., Tan, J., and, Fang, M., (1995) Long-range interaction between two promoters: activation of the leu-500 promoter by a distant upstream promoter. Cell 82, 445-451.
47. Fang, M., and, Wu, H. Y., (1998) A promoter relay mechanism for sequential gene activation. J. Bacteriol. 180, 626-633.
48. El, H. D., and, Bossi, L., (2000) Activation and silencing of leu-500 promoter by transcription-induced DNA supercoiling in the Salmonella chromosome. Mol. Microbiol. 37, 583-594.
49. Chen, C. C., and, Wu, H. Y., (2003) Transcription-driven DNA supercoiling and gene expression control. Front Biosci. 8, d430-d439.
50. van Loenhout, M. T., de Grunt, M. V., and, Dekker, C., (2012) Dynamics of DNA supercoils. Science 338, 94-97.