Spatial distribution and diffusive motion of rna polymerase in live Escherichia coli

Journal of Bacteriology

Volumn 193, Issue 19, 2011, Pages 5138-5146

  Bratton, Benjamin P ^a   Mooney, Rachel A ^a   Weisshaar, James C ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA POLYMERASE;

ARTICLE; BACTERIAL CELL; CELL HETEROGENEITY; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DIFFUSION; DNA BINDING; DNA STRAND; ENZYME BINDING; ENZYME LOCALIZATION; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROTEIN EXPRESSION; PROTEIN TRANSPORT;

DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; MICROSCOPY, FLUORESCENCE;

ESCHERICHIA COLI;

EID: 80053602167     PISSN: 00219193     EISSN: 10985530     Source Type: Journal    
DOI: 10.1128/JB.00198-11     Document Type: Article

References (34)

1. Bremer, H., and P. P. Dennis. 1996. Modulation of chemical composition and other parameters of the cell by growth rate, p. 1553-1569. In F. C. Neidhardt et al. (ed.), Escherichia coli and Salmonella: cellular and molecular biology, 2nd ed. ASM Press, Washington, DC.
2. Bremer, H., and D. Yuan. 1968. RNA chain growth-rate in Escherichia coli. J. Mol. Biol. 38:163-180.
3. Cabrera, J. E., C. Cagliero, S. Quan, C. L. Squires, and D. J. Jin. 2009. Active transcription of rRNA operons condenses the nucleoid in Escherichia coli: examining the effect of transcription on nucleoid structure in the absence of transertion. J. Bacteriol. 191:4180-4185.
4. Cabrera, J. E., and D. J. Jin. 2003. The distribution of RNA polymerase in Escherichia coli is dynamic and sensitive to environmental cues. Mol. Microbiol. 50:1493-1505.
5. Elf, J., G.-W. Li, and X. S. Xie. 2007. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 316:1191-1194.
6. Elowitz, M. B., M. G. Surette, P. E. Wolf, J. B. Stock, and S. Leibler. 1999. Protein mobility in the cytoplasm of Escherichia coli. J. Bacteriol. 181:197- 203.
7. Espeli, O., R. Mercier, and F. Boccard. 2008. DNA dynamics vary according to macrodomain topography in the E. coli chromosome. Mol. Microbiol. 68:1418-1427.
8. Grainger, D. C., D. Hurd, M. Harrison, J. Holdstock, and S. J. W. Busby. 2005. Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome. Proc. Natl. Acad. Sci. U. S. A. 102:17693-17698.
9. Herring, C. D., et al. 2005. Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays. J. Bacteriol. 187:6166-6174.
10. Kim, J. H., and R. G. Larson. 2007. Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules. Nucleic Acids Res. 35:3848-3858.
11. Klumpp, S., and T. Hwa. 2008. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc. Natl. Acad. Sci. U. S. A. 105:20245-20250.
12. Konopka, M. C., I. A. Shkel, S. Cayley, M. T. Record, and J. C. Weisshaar. 2006. Crowding and confinement effects on protein diffusion in vivo. J. Bacteriol. 188:6115-6123.
13. Konopka, M. C., et al. 2009. Cytoplasmic protein mobility in osmotically stressed Escherichia coli. J. Bacteriol. 191:231-237.
14. Kumar, M., M. S. Mommer, and V. Sourjik. 2010. Mobility of cytoplasmic, membrane, and DNA-binding proteins in Escherichia coli. Biophys. J. 98: 552-559.
15. Lewis, P. J., S. D. Thaker, and J. Errington. 2000. Compartmentalization of transcription and translation in Bacillus subtilis. EMBO J. 19:710-718.
16. Manor, H., D. Goodman, and G. S. Stent. 1969. RNA chain growth rates in Escherichia coli. J. Mol. Biol. 39:1-27.
17. Marenduzzo, D., C. Micheletti, and P. R. Cook. 2006. Entropy-driven genome organization. Biophys. J. 90:3712-3721.
18. McClure, W. R. 1985. Mechanism and control of transcription initiation in prokaryotes. Annu. Rev. Biochem. 54:171-204.
19. Mika, J. T., G. v. d. Bogaart, L. Veenhoff, V. Krasnikov, and B. Poolman. 2010. Molecular sieving properties of the cytoplasm of Escherichia coli and consequences of osmotic stress. Mol. Microbiol. 77:200-207.
20. Mondal, J., B. P. Bratton, Y. Li, A. Yethiraj, and J. C. Weisshaar. 2011. Entropy-based mechanism of ribosome-nucleoid segregation in E. coli cells. Biophys. J. 100:2605-2613.
21. Mooney, R. A., and R. Landick. 2003. Tethering σ70 to RNA polymerase reveals high in vivo activity of σ factors and σ70-dependent pausing at promoter-distal locations. Genes Dev. 17:2839-2851.
22. Mullineaux, C. W., A. Nenninger, N. Ray, and C. Robinson. 2006. Diffusion of green fluorescent protein in three cell environments in Escherichia coli. J. Bacteriol. 188:3442-3448.
23. Neidhardt, F. C., P. L. Bloch, and D. F. Smith. 1974. Culture medium for enterobacteria. J. Bacteriol. 119:736-747.
24. Nenninger, A., G. Mastroianni, and C. W. Mullineaux. 2010. Size dependence of protein diffusion in the cytoplasm of Escherichia coli. J. Bacteriol. 192:4535-4540.
25. Oden, K. L., L. C. DeVeaux, C. R. T. Vibat, and J. E. Croman. 1990. Genomic replacement in Escherichia coli K-12 using covalently closed circular plasmid DNA. Gene 96:29-36.
26. Ricchetti, M., W. Metzger, and H. Heumann. 1988. One-dimensional diffusion of Escherichia coli DNA-dependent RNA polymerase: a mechanism to facilitate promoter location. Proc. Natl. Acad. Sci. U. S. A. 85:4610-4614.
27. Robinow, C., and E. Kellenberger. 1994. The bacterial nucleoid revisited. Microbiol. Mol. Biol. Rev. 58:211-232.
28. Saitoh, T., and A. Ishihama. 1977. Biosynthesis of RNA polymerase in Escherichia coli. VI. Distribution of RNA polymerase subunits between nucleoid and cytoplasm. J. Mol. Biol. 115:403-416.
29. Shepherd, N., P. Dennis, and H. Bremer. 2001. Cytoplasmic RNA polymerase in Escherichia coli. J. Bacteriol. 183:2527-2534.
30. Singer, P., and C. W. Wu. 1987. Promoter search by Escherichia coli RNA polymerase on a circular DNA template. J. Biol. Chem. 262:14178-14189.
31. Sniegowski, J. A., J. W. Lappe, H. N. Patel, H. A. Huffman, and R. M. Wachter. 2005. Base catalysis of chromophore formation in Arg96 and Glu222 variants of green fluorescent protein. J. Biol. Chem. 280:26248- 26255.
32. Sochacki, K. A., I. A. Shkel, M. T. Record, and J. C. Weisshaar. 2011. Protein diffusion in the periplasm of E. coli under osmotic stress. Biophys. J. 100: 22-31.
33. Valkenburg, J. A., and C. L. Woldringh. 1984. Phase separation between nucleoid and cytoplasm in Escherichia coli as defined by immersive refractometry. J. Bacteriol. 160:1151-1157.
34. van den Bogaart, G., N. Hermans, V. Krasnikov, and B. Poolman. 2007. Protein mobility and diffusive barriers in Escherichia coli: consequences of osmotic stress. Mol. Microbiol. 64:858-871.