Structural basis for transcription reactivation by RapA

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

Volumn 112, Issue 7, 2015, Pages 2006-2010

  Liu, Bin ^a   Zuo, Yuhong ^a   Steitz, Thomas A ^a,b,c   Yang, Wei ^d  

^a Department of Molecular Biophysics and Biochemistry ^*  (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c YALE UNIVERSITY   (United States)

^d NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Backtranslocation; DNA translocase; RapA; RNA polymerase; Transcription

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ADENOSINE TRIPHOSPHATE; CARRIER PROTEIN; DNA A; DOUBLE STRANDED DNA; POLYDEOXYRIBONUCLEOTIDE SYNTHASE; RAPA PROTEIN; RNA POLYMERASE; SINGLE STRANDED DNA; SNF2 TRANSLOCASE; SWI2 TRANSLOCASE; UNCLASSIFIED DRUG; DNA DIRECTED RNA POLYMERASE; ESCHERICHIA COLI PROTEIN; RAPA PROTEIN, E COLI;

ALPHA HELIX; ARTICLE; BINDING SITE; CARBOXY TERMINAL SEQUENCE; CELLULAR ORGANISM; CONFORMATIONAL TRANSITION; CRYSTAL STRUCTURE; DNA BINDING; DNA DAMAGE; DNA REPAIR; DNA RNA HYBRIDIZATION; DNA TEMPLATE; ENZYME CONFORMATION; ENZYME REACTIVATION; ESCHERICHIA COLI; GENE PRODUCT; GENETIC TRANSCRIPTION; GENOMIC INSTABILITY; HYDROLYSIS; MUTATION RATE; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA CLEAVAGE; RNA STRUCTURE; RNA SYNTHESIS; SULFOLOBUS SOLFATARICUS; TRANSCRIPTION ELONGATION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; TRANSCRIPTION TERMINATION; ULTRAVIOLET RADIATION; CHEMICAL STRUCTURE; CHEMISTRY; ENZYMOLOGY; METABOLISM; PHYSIOLOGY; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA COLI;

CRYSTALLOGRAPHY, X-RAY; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; MODELS, MOLECULAR; TRANSCRIPTION, GENETIC;

EID: 84923281143     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1417152112     Document Type: Article

References (37)

1. Guajardo R, Sousa R (1997) A model for the mechanism of polymerase translocation. J Mol Biol 265(1):8-19.
2. Martinez-Rucobo FW, Cramer P (2013) Structural basis of transcription elongation. Biochim Biophys Acta 1829(1):9-19.
3. Landick R (2006) The regulatory roles and mechanism of transcriptional pausing. Biochem Soc Trans 34(Pt 6):1062-1066.
4. Neuman KC, Abbondanzieri EA, Landick R, Gelles J, Block SM (2003) Ubiquitous transcriptional pausing is independent of RNA polymerase backtracking. Cell 115(4): 437-447.
5. Adelman K, et al. (2002) Single molecule analysis of RNA polymerase elongation reveals uniform kinetic behavior. Proc Natl Acad Sci USA 99(21):13538-13543.
6. Artsimovitch I, Landick R (2000) Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc Natl Acad Sci USA 97(13):7090-7095.
7. Roberts J, Park JS (2004) Mfd, the bacterial transcription repair coupling factor: Translocation, repair and termination. Curr Opin Microbiol 7(2):120-125.
8. Peters JM, Vangeloff AD, Landick R (2011) Bacterial transcription terminators: The RNA 3'-end chronicles. J Mol Biol 412(5):793-813.
9. Sydow JF, Cramer P (2009) RNA polymerase fidelity and transcriptional proofreading. Curr Opin Struct Biol 19(6):732-739.
10. Nudler E (2012) RNA polymerase backtracking in gene regulation and genome instability. Cell 149(7):1438-1445.
11. Epshtein V, et al. (2014) UvrD facilitates DNA repair by pulling RNA polymerase backwards. Nature 505(7483):372-377.
12. Sukhodolets MV, Jin DJ (1998) RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of SWI2/SNF2. J Biol Chem 273(12):7018-7023.
13. Shaw G, et al. (2008) Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure 16(9):1417-1427.
14. Muzzin O, et al. (1998) Disruption of Escherichia coli hepA, an RNA polymeraseassociated protein, causes UV sensitivity. J Biol Chem 273(24):15157-15161.
15. Sukhodolets MV, Cabrera JE, Zhi H, Jin DJ (2001) RapA, a bacterial homolog of SWI2/ SNF2, stimulates RNA polymerase recycling in transcription. Genes Dev 15(24): 3330-3341.
16. Vassylyev DG, Vassylyeva MN, Perederina A, Tahirov TH, Artsimovitch I (2007) Structural basis for transcription elongation by bacterial RNA polymerase. Nature 448(7150):157-162.
17. Bork P, Koonin EV (1993) An expanding family of helicases within the 'DEAD/H' superfamily. Nucleic Acids Res 21(3):751-752.
18. Flaus A, Martin DM, Barton GJ, Owen-Hughes T (2006) Identification of multiple distinct Snf2 subfamilies with conserved structural motifs. Nucleic Acids Res 34(10): 2887-2905.
19. Murakami KS, Masuda S, Darst SA (2002) Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296(5571):1280-1284.
20. Vassylyev DG, et al. (2002) Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417(6890):712-719.
21. Zuo Y, Wang Y, Steitz TA (2013) The mechanism of E. coli RNA polymerase regulation by ppGpp is suggested by the structure of their complex. Mol Cell 50(3):430-436.
22. Yawn B, Zhang L, Mura C, Sukhodolets MV (2009) RapA, the SWI/SNF subunit of Escherichia coli RNA polymerase, promotes the release of nascent RNA from transcription complexes. Biochemistry 48(33):7794-7806.
23. Dürr H, Körner C, Müller M, Hickmann V, Hopfner KP (2005) X-ray structures of the Sulfolobus solfataricus SWI2/SNF2 ATPase core and its complex with DNA. Cell 121(3):363-373.
24. Lee JY, Yang W (2006) UvrD helicase unwinds DNA one base pair at a time by a twopart power stroke. Cell 127(7):1349-1360.
25. Hudson BP, et al. (2009) Three-dimensional EM structure of an intact activatordependent transcription initiation complex. Proc Natl Acad Sci USA 106(47): 19830-19835.
26. Park JS, Marr MT, Roberts JW (2002) E. coli Transcription repair coupling factor (Mfd protein) rescues arrested complexes by promoting forward translocation. Cell 109(6): 757-767.
27. Deaconescu AM, et al. (2006) Structural basis for bacterial transcription-coupled DNA repair. Cell 124(3):507-520.
28. Bar-Nahum G, et al. (2005) A ratchet mechanism of transcription elongation and its control. Cell 120(2):183-193.
29. Sukhodolets MV, Jin DJ (2000) Interaction between RNA polymerase and RapA, a bacterial homolog of the SWI/SNF protein family. J Biol Chem 275(29):22090-22097.
30. Leslie AG (1999) Integration of macromolecular diffraction data. Acta Crystallogr D Biol Crystallogr 55(Pt 10):1696-1702.
31. Evans P (2006) Scaling and assessment of data quality. Acta Crystallogr D Biol Crystallogr 62(Pt 1):72-82.
32. McCoy AJ, et al. (2007) Phaser crystallographic software. J Appl Cryst 40(Pt 4):658-674.
33. Cowtan K (1999) Error estimation and bias correction in phase-improvement calculations. Acta Crystallogr D Biol Crystallogr 55(Pt 9):1555-1567.
34. Winn MD, et al. (2011) Overview of the CCP4 suite and current developments. Acta Crystallogr D Biol Crystallogr 67(Pt 4):235-242.
35. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60(Pt 12 Pt 1):2126-2132.
36. Murshudov GN, et al. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr 67(Pt 4):355-367.
37. DeLano WL (2002) The PyMOL Molecular Graphics System (DeLano Scientific, San Carlos, CA).