Swi2/Snf2 remodelers: Hybrid views on hybrid molecular machines

Current Opinion in Structural Biology

Volumn 22, Issue 2, 2012, Pages 225-233

  Hopfner, Karl Peter ^a   Gerhold, Christian Benedikt ^a   Lakomek, Kristina ^a   Wollmann, Petra ^a  

^a UNIVERSITY OF MUNICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; CHAPERONE; HELICASE; HYBRID PROTEIN; PROTEIN; PROTEIN MOT1; PROTEIN SWI; PROTEIN SWI2; TATA BINDING PROTEIN RELATED FACTOR; TRANSCRIPTION FACTOR SNF; TRANSCRIPTION FACTOR SNF2; UNCLASSIFIED DRUG;

DNA HISTONE INTERACTION; ENZYME LOCALIZATION; ENZYME REGULATION; ENZYME SPECIFICITY; EPIGENETICS; MOLECULAR MECHANICS; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN CROSS LINKING; PROTEIN DNA BINDING; PROTEIN DOMAIN; PROTEIN HYDROLYSIS; PROTEIN PROTEIN INTERACTION; REVIEW; TATA BOX; TRANSCRIPTION INITIATION;

ADENOSINE TRIPHOSPHATASES; ANIMALS; HUMANS; MOLECULAR CHAPERONES; NUCLEIC ACIDS; NUCLEOSOMES; PROTEIN BINDING; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION FACTORS;

EID: 84861762301     PISSN: 0959440X     EISSN: 1879033X     Source Type: Journal    
DOI: 10.1016/j.sbi.2012.02.007     Document Type: Review

References (52)

1. Fairman-Williams M.E., Guenther U.P., Jankowsky E. SF1 and SF2 helicases: family matters. Curr Opin Struct Biol 2010, 20:313-324.
2. Pyle A.M. Translocation and unwinding mechanisms of RNA and DNA helicases. Annu Rev Biophys 2008, 37:317-336.
3. Dürr H., Korner C., Müller M., Hickmann V., Hopfner K.P. X-ray structures of the Sulfolobus solfataricus Swi2/Snf2 ATPase core and its complex with DNA. Cell 2005, 121:363-373.
4. Zhang Y., Smith C.L., Saha A., Grill S.W., Mihardja S., Smith S.B., Cairns B.R., Peterson C.L., Bustamante C. DNA translocation and loop formation mechanism of chromatin remodeling by SWI/SNF and RSC. Mol Cell 2006, 24:559-568.
5. Saha A., Wittmeyer J., Cairns B.R. Chromatin remodeling by RSC involves ATP-dependent DNA translocation. Genes Dev 2002, 16:2120-2134.
6. Amitani I., Baskin R.J., Kowalczykowski S.C. Visualization of Rad54, a chromatin remodeling protein, translocating on single DNA molecules. Mol Cell 2006, 23:143-148.
7. Sirinakis G., Clapier C.R., Gao Y., Viswanathan R., Cairns B.R., Zhang Y. The RSC chromatin remodelling ATPase translocates DNA with high force and small step size. EMBO J 2011, 30:2364-2372.
8. Thoma N.H., Czyzewski B.K., Alexeev A.A., Mazin A.V., Kowalczykowski S.C., Pavletich N.P. Structure of the Swi2/Snf2 chromatin-remodeling domain of eukaryotic Rad54. Nat Struct Mol Biol 2005, 12:350-356.
9. Hauk G., McKnight J.N., Nodelman I.M., Bowman G.D. The chromodomains of the Chd1 chromatin remodeler regulate DNA access to the ATPase motor. Mol Cell 2010, 39:711-723.
10. Shaw G., Gan J., Zhou Y.N., Zhi H., Subburaman P., Zhang R., Joachimiak A., Jin D.J., Ji X. Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure 2008, 16:1417-1427.
11. Myong S., Bruno M.M., Pyle A.M., Ha T. Spring-loaded mechanism of DNA unwinding by hepatitis C virus NS3 helicase. Science 2007, 317:513-516.
12. Liu N., Balliano A., Hayes J.J. Mechanism(s) of Swi/Snf-induced nucleosome mobilization. Chembiochem 2011, 12:196-204.
13. Rowe C.E., Narlikar G.J. The ATP-dependent remodeler RSC transfers histone dimers and octamers through the rapid formation of an unstable encounter intermediate. Biochemistry 2010, 49:9882-9890.
14. Mizuguchi G., Shen X., Landry J., Wu W.H., Sen S., Wu C. ATP-driven exchange of histone H2AZ variant catalyzed by Swr1 chromatin remodeling complex. Science 2004, 303:343-348.
15. Papamichos-Chronakis M., Watanabe S., Rando O.J., Peterson C.L. Global regulation of H2A.Z localization by the INO80 chromatin-remodeling enzyme is essential for genome integrity. Cell 2011, 144:200-213.
16. Racki L.R., Yang J.G., Naber N., Partensky P.D., Acevedo A., Purcell T.J., Cooke R., Cheng Y., Narlikar G.J. The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 2009, 462:1016-1021.
17. Strohner R., Wachsmuth M., Dachauer K., Mazurkiewicz J., Hochstatter J., Rippe K., Langst G. A 'loop recapture' mechanism for ACF-dependent nucleosome remodeling. Nat Struct Mol Biol 2005, 12:683-690.
18. Wippo C.J., Israel L., Watanabe S., Hochheimer A., Peterson C.L., Korber P. The RSC chromatin remodelling enzyme has a unique role in directing the accurate positioning of nucleosomes. EMBO J 2011, 30:1277-1288.
19. Bao Y., Shen X. Chromatin remodeling in DNA double-strand break repair. Curr Opin Genet Dev 2007, 17:126-131.
20. Viswanathan R., Auble D.T. One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes?. Biochim Biophys Acta 2011, 1809:488-496.
21. Yusufzai T., Kadonaga J.T. HARP is an ATP-driven annealing helicase. Science 2008, 322:748-750.
22. Grüne T., Brzeski J., Eberharter A., Clapier C.R., Corona D.F., Becker P.B., Müller C.W. Crystal structure and functional analysis of a nucleosome recognition module of the remodeling factor ISWI. Mol Cell 2003, 12:449-460.
23. Erdel F., Schubert T., Marth C., Langst G., Rippe K. Human ISWI chromatin-remodeling complexes sample nucleosomes via transient binding reactions and become immobilized at active sites. Proc Natl Acad Sci U S A 2010, 107:19873-19878.
24. Erdel F., Rippe K. Binding kinetics of human ISWI chromatin-remodelers to DNA repair sites elucidate their target location mechanism. Nucleus 2011, 2:105-112.
25. Ruthenburg A.J., Li H., Milne T.A., Dewell S., McGinty R.K., Yuen M., Ueberheide B., Dou Y., Muir T.W., Patel D.J., Allis C.D. Recognition of a mononucleosomal histone modification pattern by BPTF via multivalent interactions. Cell 2011, 145:692-706.
26. Shen X., Ranallo R., Choi E., Wu C. Involvement of actin-related proteins in ATP-dependent chromatin remodeling. Mol Cell 2003, 12:147-155.
27. Harata M., Oma Y., Mizuno S., Jiang Y.W., Stillman D.J., Wintersberger U. The nuclear actin-related protein of Saccharomyces cerevisiae, Act3p/Arp4, interacts with core histones. Mol Biol Cell 1999, 10:2595-2605.
28. Kashiwaba S., Kitahashi K., Watanabe T., Onoda F., Ohtsu M., Murakami Y. The mammalian INO80 complex is recruited to DNA damage sites in an Arp8 dependent manner. Biochem Biophys Res Commun 2010, 402:619-625.
29. Cai Y., Jin J., Yao T., Gottschalk A.J., Swanson S.K., Wu S., Shi Y., Washburn M.P., Florens L., Conaway R.C., Conaway J.W. YY1 functions with INO80 to activate transcription. Nat Struct Mol Biol 2007, 14:872-874.
30. Hogan C.J., Aligianni S., Durand-Dubief M., Persson J., Will W.R., Webster J., Wheeler L., Mathews C.K., Elderkin S., Oxley D., Ekwall K., et al. Fission yeast Iec1-Ino80-mediated nucleosome eviction regulates nucleotide and phosphate metabolism. Mol Cell Biol 2010, 30:657-674.
31. Gottschalk A.J., Timinszky G., Kong S.E., Jin J., Cai Y., Swanson S.K., Washburn M.P., Florens L., Ladurner A.G., Conaway J.W., Conaway R.C. Poly(ADP-ribosyl)ation directs recruitment and activation of an ATP-dependent chromatin remodeler. Proc Natl Acad Sci U S A 2009, 106:13770-13774.
32. Ahel D., Horejsi Z., Wiechens N., Polo S.E., Garcia-Wilson E., Ahel I., Flynn H., Skehel M., West S.C., Jackson S.P., Owen-Hughes T., et al. Poly(ADP-ribose)-dependent regulation of DNA repair by the chromatin remodeling enzyme Alc1. Science 2009, 325:1240-1243.
33. Prasad P., Bartholomew B. Control of nucleosome movement: to space or not to space nucleosomes?. Epigenetics 2010, 5:282-286.
34. Fischer C.J., Yamada K., Fitzgerald D.J. Kinetic mechanism for single-stranded DNA binding and translocation by Saccharomyces cerevisiae Isw2. Biochemistry 2009, 48:2960-2968.
35. Gangaraju V.K., Prasad P., Srour A., Kagalwala M.N., Bartholomew B. Conformational changes associated with template commitment in ATP-dependent chromatin remodeling by Isw2. Mol Cell 2009, 35:58-69.
36. Blosser T.R., Yang J.G., Stone M.D., Narlikar G.J., Zhuang X. Dynamics of nucleosome remodelling by individual ACF complexes. Nature 2009, 462:1022-1027.
37. Yamada K., Frouws T.D., Angst B., Fitzgerald D.J., DeLuca C., Schimmele K., Sargent D.F., Richmond T.J. Structure and mechanism of the chromatin remodelling factor Isw1a. Nature 2011, 472:448-453.
38. Ryan D.P., Sundaramoorthy R., Martin D., Singh V., Owen-Hughes T. The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. EMBO J 2011, 30:2596-2609.
39. Sharma A., Jenkins K.R., Heroux A., Bowman G.D. Crystal structure of the chromo-helicase-DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA. J Biol Chem 2011, 286:42099-42104.
40. Flanagan J.F., Mi L.Z., Chruszcz M., Cymborowski M., Clines K.L., Kim Y., Minor W., Rastinejad F., Khorasanizadeh S. Double chromodomains cooperate to recognize the methylated histone H3 tail. Nature 2005, 438:1181-1185.
41. Morettini S., Tribus M., Zeilner A., Sebald J., Campo-Fernandez B., Scheran G., Worle H., Podhraski V., Fyodorov D.V., Lusser A. The chromodomains of Chd1 are critical for enzymatic activity but less important for chromatin localization. Nucleic Acids Res 2010, 39:3103-3115.
42. Sen P., Ghosh S., Pugh B.F., Bartholomew B. A new, highly conserved domain in Swi2/Snf2 is required for SWI/SNF remodeling. Nucleic Acids Res 2011, 39:9155-9166.
43. Dasgupta A., Darst R.P., Martin K.J., Afshari C.A., Auble D.T. Mot1 activates and represses transcription by direct, ATPase-dependent mechanisms. Proc Natl Acad Sci U S A 2002, 99:2666-2671.
44. Hsu J.Y., Juven-Gershon T., Marr M.T., Wright K.J., Tjian R., Kadonaga J.T. TBP, Mot1, and NC2 establish a regulatory circuit that controls DPE-dependent versus TATA-dependent transcription. Genes Dev 2008, 22:2353-2358.
45. van Werven F.J., van Bakel H., van Teeffelen H.A., Altelaar A.F., Koerkamp M.G., Heck A.J., Holstege F.C., Timmers H.T. Cooperative action of NC2 and Mot1p to regulate TATA-binding protein function across the genome. Genes Dev 2008, 22:2359-2369.
46. Sprouse R.O., Karpova T.S., Mueller F., Dasgupta A., McNally J.G., Auble D.T. Regulation of TATA-binding protein dynamics in living yeast cells. Proc Natl Acad Sci U S A 2008, 105:13304-13308.
47. de Graaf P., Mousson F., Geverts B., Scheer E., Tora L., Houtsmuller A.B., Timmers H.T. Chromatin interaction of TATA-binding protein is dynamically regulated in human cells. J Cell Sci 2010, 123(Pt 15):2663-2671.
48. Wollmann P., Cui S., Viswanathan R., Berninghausen O., Wells M.N., Moldt M., Witte G., Butryn A., Wendler P., Beckmann R., Auble D.T., et al. Structure and mechanism of the Swi2/Snf2 remodeller Mot1 in complex with its substrate TBP. Nature 2011, 475:403-407.
49. Sprouse R.O., Brenowitz M., Auble D.T. Snf2/Swi2-related ATPase Mot1 drives displacement of TATA-binding protein by gripping DNA. EMBO J 2006, 25:1492-1504.
50. Avvakumov N., Nourani A., Cote J. Histone chaperones: modulators of chromatin marks. Mol Cell 2011, 41:502-514.
51. Leschziner A.E. Electron microscopy studies of nucleosome remodelers. Curr Opin Struct Biol 2011, 21:1-10.
52. Leitner A., Walzthoeni T., Kahraman A., Herzog F., Rinner O., Beck M., Aebersold R. Probing native protein structures by chemical cross-linking, mass spectrometry, and bioinformatics. Mol Cell Proteomics: MCP 2010, 9:1634-1649.