Crystal structure of the human transcription elongation factor DSIF hSpt4 subunit in complex with the hSpt5 dimerization interface

Biochemical Journal

Volumn 425, Issue 2, 2010, Pages 373-380

  Wenzel, Sabine ^a   Martins, Berta M ^a   Rösch, Paul ^a   Wöhrl, Birgitta M ^a  

^a UNIVERSITY OF BAYREUTH   (Germany)

Author keywords

Crystal structure; Eukaryotic transcription; hSpt4 hSpt5; Human DRB (5.6 dichloro 1 D ribofuranosyl benzimidazole) sensitivity inducing factor (DSIP); NusG; NusG N terminal homology doman (NGN)

Indexed keywords

ARCHAEAL TRANSCRIPTION; BACTERIAL TRANSCRIPTION; BENZIMIDAZOLES; E. COLI; ELONGATION FACTOR; HETERODIMERS; N-TERMINAL DOMAINS; N-TERMINALS; NMR TITRATION; PROCESSIVITY; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE; STRUCTURAL SIMILARITY; THREE-DIMENSIONAL STRUCTURE; TRANSCRIPTIONAL ACTIVATIONS;

AMINO ACIDS; BACTERIOLOGY; COMPLEXATION; DIMERIZATION; ELONGATION; ESCHERICHIA COLI; ORGANIC ACIDS; RNA; SEMICONDUCTOR DOPING; TITRATION; TRANSCRIPTION; TRANSCRIPTION FACTORS; YEAST;

CRYSTAL STRUCTURE;

5,6 DICHLOROBENZIMIDAZOLE RIBOSIDE; GLUTAMIC ACID; GLUTAMINE; HETERODIMER; TRANSCRIPTION ELONGATION FACTOR; TRANSCRIPTION FACTOR NUSG; TRANSCRIPTION FACTOR RPOE; TRANSCRIPTION FACTOR SPT4; TRANSCRIPTION FACTOR SPT5; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; COMPLEX FORMATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DIMERIZATION; ESCHERICHIA COLI; HUMAN; NUCLEAR MAGNETIC RESONANCE; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SEQUENCE ALIGNMENT;

CRYSTALLOGRAPHY, X-RAY; GLUTAMINE; HUMANS; MAGNETIC RESONANCE SPECTROSCOPY; NUCLEAR PROTEINS; PROTEIN CONFORMATION; PROTEIN MULTIMERIZATION; REPRESSOR PROTEINS; STRUCTURAL HOMOLOGY, PROTEIN; TRANSCRIPTION FACTORS; TRANSCRIPTIONAL ELONGATION FACTORS;

ARCHAEA; BACTERIA (MICROORGANISMS); ESCHERICHIA COLI; EUKARYOTA; SACCHAROMYCES CEREVISIAE;

EID: 73849136441     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20091422     Document Type: Article

References (49)

1. Yamaguchi, Y., Takagi, T., Wada, T., Yano, K., Furuya, A., Sugimoto, S., Hasegawa, J. and Handa, H. (1999) NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97, 41-51
2. Narita, T., Yamaguchi, Y., Yano, K., Sugimoto, S., Chanarat, S., Wada, T., Kim, D. K., Hasegawa, J., Omori, M., Inukai, N. et al. (2003) Human transcription elongation factor NELF: identification of novel subunits and reconstitution of the functionally active complex. Mol. Cell. Biol. 23, 1863-1873
3. Ivanov, D., Kwak, Y. T., Guo, J. and Gaynor, R. B. (2000) Domains in the SPT5 protein that modulate its transcriptional regulatory properties. Mol. Cell. Biol. 20, 2970-2983
4. Yamaguchi, Y., Takagi, T., Wada, T., Yano, K., Furuya, A., Sugimoto, S., Hasegawa, J. and Handa, H. (1999) NELF, a multisubunit complex containing RD, cooperates with DSIF to repress RNA polymerase II elongation. Cell 97, 41-51
5. Yamaguchi, Y., Inukai, N., Narita, T., Wada, T. and Handa, H. (2002) Evidence that negative elongation factor represses transcription elongation through binding to a DRB sensitivity-inducing factor/RNA polymerase II complex and RNA. Mol. Cell. Biol. 22, 2918-2927
6. Fujinaga, K., Irwin, D., Huang, Y., Taube, R., Kurosu, T. and Peterlin, B. M. (2004) Dynamics of human immunodeficiency virus transcription: P-TEFb phosphorylates RD and dissociates negative effectors from the transactivation response element. Mol. Cell. Biol. 24, 787-795
7. Ping, Y. H. and Rana, T. M. (2001) DSIF and NELF interact with RNA polymerase II elongation complex and HIV-1 tat stimulates P-TEFb-mediated phosphorylation of RNA polymerase II and DSIF during transcription elongation. J. Biol. Chem. 276, 12951-12958
8. Yamada, T., Yamaguchi, Y., Inukai, N., Okamoto, S., Mura, T. and Handa, H. (2006) P-TEFb-mediated phosphorylation of hSpt5 C-terminal repeats is critical for processive transcription elongation. Mol. Cell 21, 227-237
9. Lis, J. T., Mason, P., Peng, J., Price, D. H. and Werner, J. (2000) P-TEFb kinase recruitment and function at heat shock loci. Genes Dev. 14, 792-803
10. Andrulis, E. D., Guzman, E., Doring, P., Werner, J. and Lis, J. T. (2000) High-resolution localization of Drosophila Spt5 and Spt6 at heat shock genes in vivo: roles in promoter proximal pausing and transcription elongation. Genes Dev. 14, 2635-2649
11. Wu, C. H., Yamaguchi, Y., Benjamin, L. R., Horvat-Gordon, M., Washinsky, J., Enerly, E., Larsson, J., Lambertsson, A., Handa, H. and Gilmour, D. (2003) NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev. 17, 1402-1414.
12. Lindstrom, D. L., Squazzo, S. L., Muster, N., Burckin, T. A., Wachter, K. C., Emigh, C. A., McCleery, J. A., Yates, 3rd, J.R., Hartzog and, G.A. (2003) Dual roles for Spt5 in pre-mRNA processing and transcription elongation revealed by identification of Spt5-associated proteins. Mol. Cell. Biol. 23, 1368-1378
13. Mandal, S. S., Chu, C., Wada, T., Handa, H., Shatkin, A. J. and Reinberg, D. (2004) Functional interactions of RNA-capping enzyme with factors that positively and negatively regulate promoter escape by RNA polymerase II. Proc. Natl. Acad. Sci. U.S.A. 101, 7572-7577
14. Sims, III, R. J., Belotserkovskaya, R. and Reinberg, D. (2004) Elongation by RNA polymerase II: the short and long of it. Genes Dev. 18, 2437-2468
15. Krogan, N. J., Kim, M., Ahn, S. H., Zhong, G., Kobor, M. S., Cagney, G., Emili, A., Shilatifard, A., Buratowski, S. and Greenblatt, J. F. (2002) RNA polymerase II elongation factors of Saccharomyces cerevisiae: a targeted proteomics approach. Mol. Cell. Biol. 22, 6979-6992
16. Wada, T., Takagi, T., Yamaguchi, Y., Ferdous, A., Imai, T., Hirose, S., Sugimoto, S., Yano, K., Hartzog, G. A., Winston, F. et al. (1998) DSIF, a novel transcription elongation factor that regulates RNA polymerase II processivity, is composed of human Spt4 and Spt5 homologs. Genes Dev. 12, 343-356
17. Sullivan, S. L. and Gottesman, M. E. (1992) Requirement for. E. coli NusG protein in factor-dependent transcription termination. Cell 68, 989-994
18. Cardinale, C. J., Washburn, R. S., Tadigotla, V. R., Brown, L. M., Gottesman, M. E. and Nudler, E. (2008) Termination factor rho and its cofactors NusA and NusG silence foreign DNA in. E coli. Science 320, 935-938.
19. DeVito, J. and Das, A. (1994) Control of transcription processivity in phage lambda: Nus factors strengthen the termination-resistant state of RNA polymerase induced by N antiterminator. Proc. Natl. Acad. Sci. U.S.A. 91, 8660-8664
20. Torres, M., Balada, J. M., Zellars, M., Squires, C. and Squires, C. L. (2004) In vivo effect of NusB and NusG on rRNA transcription antitermination. J. Bacteriol. 186, 1304-1310
21. Yamaguchi, Y., Wada, T., Watanabe, D., Takagi, T., Hasegawa, J. and Handa, H. (1999) Structure and function of the human transcription elongation factor DSIF. J. Biol. Chem. 274, 8085-8092
22. Ponting, C. P. (2002) Novel domains and orthologues of eukaryotic transcription elongation factors. Nucleic Acids Res. 30, 3643-3652
23. Reference deleted
24. Schwer, B., Schneider, S., Pei, Y., Aronova, A. and Shuman, S. (2009) Characterization of the Schizosaccharomyces pombe Spt5-Spt4 complex. RNA 15, 1241-1250
25. Hartzog, G. A., Wada, T., Handa, H. and Winston, F. (1998) Evidence that Spt4, Spt5, and Spt6 control transcription elongation by RNA polymerase II in Saccharomyces cerevisiae. Genes Dev. 12, 357-369
26. Kyrpides, N. C., Woese, C. R. and Ouzounis, C. A. (1996) KOW: a novel motif linking a bacterial transcription factor with ribosomal proteins. Trends Biochem. Sci. 21, 425-426
27. Kwak, Y. T., Guo, J., Prajapati, S., Park, K. J., Surabhi, R. M., Miller, B., Gehrig, P. and Gaynor, R. B. (2003) Methylation of SPT5 regulates its interaction with RNA polymerase II and transcriptional elongation properties. Mol. Cell 11, 1055-1066
28. Chiang, P. W., Wang, S. Q., Smithivas, P., Song, W. J., Crombez, E., Akhtar, A., Im, R., Greenfield, J., Ramamoorthy, S., Van Keuren, M. et al. (1996) Isolation and characterization of the human and mouse homologues (SUPT4H and Supt4h) of the yeast SPT4 gene. Genomics 34, 368-375
29. Wenzel, S., Schweimer, K., Rösch, P. and Wöhrl, B. M. (2008) The small hSpt4 subunit of the human transcription elongation factor DSIF is a Zn-finger protein with α/β type topology. Biochem. Biophys. Res. Commun. 370, 414-418
30. Werner, F. (2007) Structure and function of archaeal RNA polymerases. Mol. Microbiol. 65, 1395-1404
31. Guo, M., Xu, F., Yamada, J., Egelhofer, T., Gao, Y., Hartzog, G. A., Teng, M. and Niu, L. (2008) Core structure of the yeast Spt4-Spt5 complex: A conserved module for regulation of transcription elongation. Structure 16, 1649-1658
32. Mori, S., Abeygunawardana, C., Johnson, M. O. and van Zijl, P. C. (1995) Improved sensitivity of HSQC spectra of exchanging protons at short interscan delays using a new fast HSQC (FHSQC) detection scheme that avoids water saturation. J. Magn. Reson. B 108, 94-98
33. Johnson, B. A. and Blevins, R. A. (1994) NMRview: A computer program for the visualization and analysis of NMR data. J. Biomol. NMR 4, 603-614
34. Kabsch, W. (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J. Appl. Chrystallogr. 26, 795-800
35. Sheldrick, G. M. (2008) A short history of SHELX. Acta Crystallogr. A 64, 112-122
36. Morris, R. J., Perrakis, A. and Lamzin, V. S. (2003) ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol. 374, 229-244
37. Emsley, P. and Cowtan, K. (2004) COOT: Model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr. 60, 2126-2132
38. Murshudov, G. N., Vagin, A. A. and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240-255
39. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr. D Biol. Crystallogr. 50, 760-763
40. Reference deleted
41. Baker, N. A., Sept, D., Joseph, S., Holst, M. J. and McCammon, J. A. (2001) Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. U.S.A. 98, 10037-10041
42. Laskowski, R. A., MacArthur, M. W., Moss, D. S. and Thornton, J. M. (1993) PROCHECK: A program to check the stereochemical quality of protein structures. J. Appl. Cryst. 26, 283-291
43. Larkin, M. A., Blackshields, G., Brown, N. P., Chenna, R., McGettigan, P. A., McWilliam, H., Valentin, F., Wallace, I. M., Wilm, A., Lopez, R. et al. (2007) Clustal W and clustal X version 2.0. Bioinformatics 23, 2947-2948
44. Wallace, A. C., Laskowski, R. A. and Thornton, J. M. (1995) LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8, 127-134
45. Krissinel, E. and Henrick, K. (2007) Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774-797
46. Mooney, R. A., Schweimer, K., Rosch, P., Gottesman, M. E. and Landick, R. (2009) Two structurally independent domains of. E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. J. Mol. Biol. 391, 341-358
47. Belogurov, G. A., Vassylyeva, M. N., Svetlov, V., Klyuyev, S., Grishin, N. V., Vassylyev, D. G. and Artsimovitch, I. (2007) Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol. Cell. 26, 117-129
48. Nickels, B. E. (2009) Genetic assays to define and characterize protein-protein interactions involved in gene regulation. Methods 47, 53-62
49. Zhou, H., Liu, Q., Gao, Y., Teng, M. and Niu, L. (2009) Crystal structure of NusG N-terminal (NGN) domain from Methanocaldococcus jannaschii and its interaction with RpoE". Proteins 76, 787-793