HU protein induces incoherent DNA persistence length

Biophysical Journal

Volumn 100, Issue 3, 2011, Pages 784-790

  Nir, Guy ^a   Lindner, Moshe ^a   Dietrich, Heidelinde R C ^b   Girshevitz, Olga ^a   Vorgias, Constantinos E ^c   Garini, Yuval ^a  

^a BAR ILAN UNIVERSITY   (Israel)

^b DELFT UNIVERSITY OF TECHNOLOGY   (Netherlands)

^c UNIVERSITY OF ATHENS   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA (MICROORGANISMS);

EID: 79551667960     PISSN: 00063495     EISSN: 15420086     Source Type: Journal    
DOI: 10.1016/j.bpj.2010.12.3687     Document Type: Article

References (44)

1. Thanbichler, M., S. C. Wang, and L. Shapiro. 2005. The bacterial nucleoid: a highly organized and dynamic structure. J. Cell. Biochem. 96:506-521.
2. Johnson, R. C., L. M. Johnson, J. F. Gardner. 2005. Major nucleoid proteins in the structure and function of the Escherichia coli chromosome. In The Bacterial Chromosome. N. P. Higgins, editor. ASM Press, Washington, DC. 65-132.
3. Stavans, J., and A. Oppenheim. 2006. DNA-protein interactions and bacterial chromosome architecture. Phys. Biol. 3: R1-R10.
4. Luijsterburg, M. S., M. C. Noom, R. T. Dame. 2006. The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective. J. Struct. Biol. 156:262-272.
5. Krawiec, S., and M. Riley. 1990. Organization of the bacterial chromosome. Microbiol. Rev. 54:502-539.
6. Kamashev, D., and J. Rouviere-Yaniv. 2000. The histone-like protein HU binds specifically to DNA recombination and repair intermediates. EMBO J. 19:6527-6535.
7. Pinson, V., M. Takahashi, and J. Rouviere-Yaniv. 1999. Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J. Mol. Biol. 287:485-497.
8. Swinger, K. K., and P. A. Rice. 2007. Structure-based analysis of HU-DNA binding. J. Mol. Biol. 365:1005-1016.
9. Manna, D., and J. Gowrishankar. 1994. Evidence for involvement of proteins HU and RpoS in transcription of the osmoresponsive proU operon in Escherichia coli. J. Bacteriol. 176:5378-5384.
10. Oberto, J., S. Nabti, J. Rouviere-Yaniv. 2009. The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction. PLoS ONE. 4: e4367.
11. Dixon, N. E., and A. Kornberg. 1984. Protein HU in the enzymatic replication of the chromosomal origin of Escherichia coli. Proc. Natl. Acad. Sci. USA. 81:424-428. (Pubitemid 14185742)
12. Grove, A., A. Galeone, E. P. Geiduschek. 1996. Localized DNA flexibility contributes to target site selection by DNA-bending proteins. J. Mol. Biol. 260:120-125.
13. Boubrik, F., and J. Rouviere-Yaniv. 1995. Increased sensitivity to γ irradiation in bacteria lacking protein HU. Proc. Natl. Acad. Sci. USA. 92:3958-3962.
14. van Noort, J., S. Verbrugge, R. T. Dame. 2004. Dual architectural roles of HU: formation of flexible hinges and rigid filaments. Proc. Natl. Acad. Sci. USA. 101:6969-6974.
15. Skoko, D., B. Wong, J. F. Marko. 2004. Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes. Biochemistry. 43:13867-13874.
16. Schnurr, B., C. Vorgias, and J. Stavans. 2006. Compaction and supercoiling of single, long DNA molecules by HU protein. Biophys. Rev. Lett. 1:29-44.
17. Sagi, D., N. Friedman, J. Stavans. 2004. Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes. J. Mol. Biol. 341:419-428.
18. Xiao, B., R. C. Johnson, and J. F. Marko. 2010. Modulation of HU-DNA interactions by salt concentration and applied force. Nucleic Acids Res. 38:6176-6185.
19. Neuman, K. C., and A. Nagy. 2008. Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat. Methods. 5:491-505.
20. Gore, J., Z. Bryant, C. Bustamante. 2006. DNA overwinds when stretched. Nature. 442:836-839.
21. Woodside, M. T., C. García-García, and S. M. Block. 2008. Folding and unfolding single RNA molecules under tension. Curr. Opin. Chem. Biol. 12:640-646.
22. Bryant, Z., M. D. Stone, C. Bustamante. 2003. Structural transitions and elasticity from torque measurements on DNA. Nature. 424:338-341.
23. Zhuang, X. 2004. Molecular biology. Unraveling DNA condensation with optical tweezers. Science. 305:188-190.
24. Lia, G., D. Bensimon, L. Finzi. 2003. Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc. Natl. Acad. Sci. USA. 100:11373-11377.
25. Marko, J. F., and E. D. Siggia. 1997. Driving proteins off DNA using applied tension. Biophys. J. 73:2173-2178.
26. Rappaport, S. M., and Y. Rabin. 2008. Model of DNA bending by cooperative binding of proteins. Phys. Rev. Lett. 101:038101.
27. Koh, J., R. M. Saecker, and M. T. Record, Jr. 2008. DNA binding mode transitions of Escherichia coli HU (αβ): evidence for formation of a bent DNA-protein complex on intact, linear duplex DNA. J. Mol. Biol. 383:324-346.
28. Czapla, L., D. Swigon, and W. K. Olson. 2008. Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations. J. Mol. Biol. 382:353-370.
29. Schafer, D. A., J. Gelles, R. Landick. 1991. Transcription by single molecules of RNA polymerase observed by light microscopy. Nature. 352:444-448.
30. Lindner, M., G. Nir, Y. Garini. 2009. Studies of single molecules in their natural form. Isr. J. Chem. 49:283-291.
31. Zurla, C., A. Franzini, L. Finzi. 2006. Novel tethered particle motion analysis of CI protein-mediated DNA looping in the regulation of bacteriophage-λ. J. Phys. Condens. Matter. 18: S225-S234.
32. Zurla, C., C. Manzo, L. Finzi. 2009. Direct demonstration and quantification of long-range DNA looping by the λ bacteriophage repressor. Nucleic Acids Res. 37:2789-2795.
33. Nelson, P. C., C. Zurla, D. Dunlap. 2006. Tethered particle motion as a diagnostic of DNA tether length. J. Phys. Chem. B. 110:17260-17267.
34. Beausang, J. F., C. Zurla, P. C. Nelson. 2007. Elementary simulation of tethered Brownian motion. Am. J. Phys. 75:520-523.
35. Pouget, N., C. Turlan, M. Chandler. 2006. IS911 transpososome assembly as analyzed by tethered particle motion. Nucleic Acids Res. 34:4313-4323.
36. Vanzi, F., L. Sacconi, and F. S. Pavone. 2007. Analysis of kinetics in noisy systems: application to single molecule tethered particle motion. Biophys. J. 93:21-36.
37. Lyubchenko, Y. L., and L. S. Shlyakhtenko. 1997. Visualization of supercoiled DNA with atomic force microscopy in situ. Proc. Natl. Acad. Sci. USA. 94:496-501.
38. Rivetti, C., M. Guthold, and C. Bustamante. 1996. Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J. Mol. Biol. 264:919-932.
39. Rubinstein, M., and R. H. Colby. 2003. Polymer Physics. Oxford University Press, Oxford, UK.
40. Segall, D. E., P. C. Nelson, and R. Phillips. 2006. Volume-exclusion effects in tethered-particle experiments: bead size matters. Phys. Rev. Lett. 96:088306.
41. Wong, W. P., and K. Halvorsen. 2006. The effect of integration time on fluctuation measurements: calibrating an optical trap in the presence of motion blur. Opt. Express. 14:12517-12531.
42. Destainville, N., and L. Salomé. 2006. Quantification and correction of systematic errors due to detector time-averaging in single-molecule tracking experiments. Biophys. J. 90: L17-L19.
43. Padas, P. M., K. S. Wilson, and C. E. Vorgias. 1992. The DNA-binding protein HU from mesophilic and thermophilic bacilli: gene cloning, overproduction and purification. Gene. 117:39-44.
44. Grove, A. 2010. Functional evolution of bacterial histone-like HU proteins. Curr. Issues Mol. Biol. 13:1-12.