Dividing a supercoiled DNA molecule into two independent topological domains

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 50, 2011, Pages 19973-19978

  Leng, Fenfei ^a   Chen, Bo ^a   Dunlap, David D ^b  

^a FLORIDA INTERNATIONAL UNIVERSITY   (United States)

^b EMORY UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; DNA BINDING PROTEIN; HISTONE; NUCLEAR PROTEIN;

ARTICLE; ATOMIC FORCE MICROSCOPY; CONTROLLED STUDY; DNA SEQUENCE; DNA SUPERCOILING; ESCHERICHIA COLI; IN VITRO STUDY; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN;

BINDING SITES; DIFFUSION; DNA, SUPERHELICAL; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; LAC REPRESSORS; MICROSCOPY, ATOMIC FORCE; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; PLASMIDS; REPRESSOR PROTEINS;

EID: 84055179007     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1109854108     Document Type: Article

References (40)

1. Worcel A, Burgi E (1972) On the structure of the folded chromosome of Escherichia coli. J Mol Biol 71:127-147.
2. Sinden RR, Pettijohn DE (1981) Chromosomes in living Escherichia coli cells are segregated into domains of supercoiling. Proc Natl Acad Sci USA 78:224-228. (Pubitemid 11131269)
3. Postow L, Hardy CD, Arsuaga J, Cozzarelli NR (2004) Topological domain structure of the Escherichia coli chromosome. Genes Dev 18:1766-1779. (Pubitemid 38938191)
4. Valens M, et al. (2004) Macrodomain organization of the Escherichia coli chromosome. EMBO J 23:4330-4341. (Pubitemid 39546170)
5. Travers A, Muskhelishvili G (2005) Bacterial chromatin. Curr Opin Genet Dev 15:507-514. (Pubitemid 41262406)
6. Thanbichler M, Viollier PH, Shapiro L (2005) The structure and function of the bacterial chromosome. Curr Opin Genet Dev 15:153-162. (Pubitemid 40410663)
7. Liu LF, Wang JC (1987) Supercoiling of the DNA template during transcription. Proc Natl Acad Sci USA 84:7024-7027.
8. Deng S, Stein RA, Higgins NP (2004) Transcription-induced barriers to supercoil diffusion in the Salmonella typhimurium chromosome. Proc Natl Acad Sci USA 101:3398-3403. (Pubitemid 38338206)
9. Deng S, Stein RA, Higgins NP (2005) Organization of supercoil domains and their reorganization by transcription. Mol Microbiol 57:1511-1521. (Pubitemid 41337382)
10. Wu HY, Liu LF (1991) DNA looping alters local DNA conformation during transcription. J Mol Biol 219:615-622.
11. Saldanha R, Flanagan P, Fennewald M (1987) Recombination by resolvase is inhibited by lac repressor simultaneously binding operators between res sites. J Mol Biol 196:505-516.
12. Leng F, McMacken R (2002) Potent stimulation of transcription-coupled DNA supercoiling by sequence-specific DNA-binding proteins. Proc Natl Acad Sci USA 99:9139-9144. (Pubitemid 34764580)
13. Leng F, Amado L, McMacken R (2004) Coupling DNA supercoiling to transcription in defined protein systems. J Biol Chem 279:47564-47571. (Pubitemid 39540901)
14. Matthews KS, Nichols JC (1998) Lactose repressor protein: functional properties and structure. Prog Nucleic Acid Res Mol Biol 58:127-164.
15. Oehler S, Eismann ER, Kramer H, Muller-Hill B (1990) The three operators of the lac operon cooperate in repression. EMBO J 9:973-979.
16. Dodson M, et al. (1986) Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: localized unwinding of duplex DNA by a six- protein reaction. Proc Natl Acad Sci USA 83:7638-7642. (Pubitemid 17183903)
17. Lia G, et al. (2003) Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping. Proc Natl Acad Sci USA 100:11373-11377. (Pubitemid 37205942)
18. Lewis DE, Adhya S (2002) In vitro repression of the gal promoters by GalR and HU depends on the proper helical phasing of the two operators. J Biol Chem 277:2498-2504. (Pubitemid 34953272)
19. Chen B, et al. (2010) DNA linking number change induced by sequence-specific DNA-binding proteins. Nucleic Acids Res 38:3643-3654.
20. Finzi L, Dunlap DD (2010) Single-molecule approaches to probe the structure, kinetics, and thermodynamics of nucleoprotein complexes that regulate transcription. J Biol Chem 285:18973-18978.
21. Virnik K, et al. (2003) "Antiparallel" DNA loop in gal repressosome visualized by atomic force microscopy. J Mol Biol 334:53-63. (Pubitemid 37330099)
22. Gaczynska M, et al. (2004) Atomic force microscopic analysis of the binding of the Schizosaccharomyces pombe origin recognition complex and the spOrc4 protein with origin DNA. Proc Natl Acad Sci USA 101:17952-17957. (Pubitemid 40054056)
23. Heddle JG, Mitelheiser S, Maxwell A, Thomson NH (2004) Nucleotide binding to DNA gyrase causes loss of DNA wrap. J Mol Biol 337:597-610. (Pubitemid 38326880)
24. Lyubchenko YL (2011) Preparation of DNA and nucleoprotein samples for AFM imaging. Micron 42:196-206.
25. Wang H, Finzi L, Lewis DE, Dunlap D (2009) AFM studies of lambda repressor oligomers securing DNA loops. Curr Pharm Biotechno 10:494-501.
26. Dodson M, Roberts J, McMacken R, Echols H (1985) Specialized nucleoprotein structures at the origin of replication of bacteriophage lambda: complexes with lambda O protein and with lambda O, lambda P, and Escherichia coli DnaB proteins. Proc Natl Acad Sci USA 82:4678-4682. (Pubitemid 16239626)
27. Scheirer KE, Higgins NP (2001) Transcription induces a supercoil domain barrier in bacteriophage Mu. Biochimie 83:155-159. (Pubitemid 32243559)
28. Gamper HB, Hearst JE (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. (Pubitemid 12027674)
29. Hase T, Nakai M, Masamune Y (1989) Transcription of a region downstream from lambda ori is required for replication of plasmids derived from coliphage lambda. Mol Gen Genet 216:120-125.
30. Sei-Hoon Chung (1996) Transcriptional activation of bacteriophage lambda DNA replication. Ph.D. Dissertation (Johns Hopkins University, Baltimore, MD), pp 1-185.
31. Baker TA, Kornberg A (1988) Transcriptional activation of initiation of replication from the E. coli chromosomal origin: an RNA-DNA hybrid near oriC. Cell 55:113-123.
32. Pettijohn DE (1988) Histone-like proteins and bacterial chromosome structure. J Biol Chem 263:12793-12796.
33. Schmid MB (1990) More than just "histone-like" proteins. Cell 63:451-453.
34. Stonington OG, Pettijohn DE (1971) The folded genome of Escherichia coli isolated in a protein-DNA-RNA complex. Proc Natl Acad Sci USA 68:6-9.
35. Rouviere-Yaniv J, Yaniv M, Germond JE (1979) E. coli DNA binding protein HU forms nucleosomelike structure with circular double-stranded DNA. Cell 17:265-274. (Pubitemid 9230307)
36. Swinger KK, Lemberg KM, Zhang Y, Rice PA (2003) Flexible DNA bending in HU-DNA cocrystal structures. EMBO J 22:3749-3760. (Pubitemid 36898351)
37. Tupper AE, et al. (1994) The chromatin-associated protein H-NS alters DNA topology in vitro. EMBO J 13:258-268.
38. Mojica FJ, Higgins CF (1997) In vivo supercoiling of plasmid and chromosomal DNA in an Escherichia coli hns mutant. J Bacteriol 179:3528-3533. (Pubitemid 27232989)
39. Higgins NP, Yang X, Fu Q, Roth JR (1996) Surveying a supercoil domain by using the gamma delta resolution system in Salmonella typhimurium. J Bacteriol 178:2825-2835. (Pubitemid 26144039)
40. Luger K, et al. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389:251-260. (Pubitemid 27406632)