Structural Basis of Core Promoter Recognition in a Primitive Eukaryote

Cell

Volumn 115, Issue 4, 2003, Pages 413-424

  Schumacher, Maria A ^a   Lau, Audrey O T ^b   Johnson, Patricia J ^b  

^a OREGON HEALTH AND SCIENCE UNIVERSITY   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; PROTEIN SUBUNIT; RNA POLYMERASE II;

ARTICLE; CRYSTAL STRUCTURE; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FAMILY; PROTEIN MOTIF; PROTEIN RNA BINDING; PROTEIN STRUCTURE; TRANSCRIPTION INITIATION SITE; TRANSCRIPTION REGULATION; TRICHOMONAS VAGINALIS;

EUKARYOTA; MASTIGOPHORA (FLAGELLATES); PARABASALIDEA; PROKARYOTA; TRICHOMONAS VAGINALIS;

EID: 0345690206     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(03)00887-0     Document Type: Article

References (56)

1. Arkhipova I.R. Promoter elements in Drosophila melanogaster revealed by sequence analysis. Genetics. 139:1995;1359-1369.
2. Barron-Casella E., Corden J.L. Conservation of the mammalian RNA polymerase II largest-subunit C-terminal domain. J. Mol. Evol. 35:1992;405-410.
3. Brünger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Crosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography and NMR System. A new software suite for macromolecular structure determination Acta Crystallogr. D Biol. Crystallogr. 54:1998;905-921.
4. Burke T.W., Kadonaga J.T. Drosophila TFIID binds to a conserved downstream basal promoter element that is present in many TATA-box-deficient promoters. Genes Dev. 11:1996;3020-3031.
5. Chalkley G.E., Verrijzer C.P. DNA binding site selection by RNA polymerase II TAFs. A TAF(II)250-TAF(II)150 complex recognizes the initiator EMBO J. 18:1999;4835-4845.
6. Chapman A.B., Agabian N. Trypanosoma brucei RNA polymerase II is phosphorylated in the absence of carboxyl-terminal domain heptapeptide repeats. J. Biol. Chem. 269:1994;4754-4760.
7. Cho E.J., Takagi T., Moore C.R., Buratowski S. mRNA capping enzyme is recruited to the transcription complex by phosphorylation of the RNA polymerase II carboxy-terminal domain. Genes Dev. 11:1997;3319-3326.
8. Corden J.L., Cadena D.L., Ahearn J.M., Dahmus M.E. A unique structure at the carboxyl terminus of the largest subunit of eukaryotic RNA polymerase II. Proc. Natl. Acad. Sci. USA. 82:1985;7934-7938.
9. Cramer P. Multisubunit RNA polymerases. Curr. Opin. Struct. Biol. 12:2002;89-97.
10. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase at 2.8 Ångstrom resolution Science. 292:2001;1863-1876.
11. Dahmus M.E. Reversible phosphorylation of the C-terminal domain of RNA polymerase II. J. Biol. Chem. 271:1996;19009-19012.
12. Donaldson L.W., Petersen J.M., Graves B.J., McIntosh L.P. Solution structure of the ETS domain from murine Ets-1. a winged helix-turn-helix DNA binding motif EMBO J. 15:1996;125-134.
13. Evers R., Hammer A., Cornelissen A.W. Unusual C-terminal domain of the largest subunit of RNA polymerase II of Crithidia fasciculata. Nucleic Acids Res. 17:1989;3403-3413. a.
14. Evers R., Hammer A., Kock J., Jess W., Borst P., Memet S., Cornelissen A.W. Trypanosoma brucei contains two RNA polymerase II largest subunit genes with an altered C-terminal domain. Cell. 56:1989;585-597. b.
15. Fabrega C., Shen V., Schuman S., Lima C.D. Structure of an mRNA capping enzyme bound to the phosphorylated carboxy-terminal domain of RNA polymerase II. Mol. Cell. 11:2003;1549-1561.
16. Fujii Y., Shimizu T., Kusumoto M., Kyogoku Y., Taniguchi T., Hakoshima T. Crystal structure of an IRF-DNA complex reveals novel DNA recognition and cooperative binding to a tandem repeat of core sequences. EMBO J. 18:1999;5028-5041.
17. Guex N., Peitsch M.C. SWISS-MODEL and the Swiss-PdbViewer. an environment for comparative protein modeling Electrophoresis. 18:1997;2714-2723.
18. Hansen S., Tijan R. TAFs and TFIIA mediate differential utilization of the tandem Adh promoters. Cell. 82:1995;565-575.
19. Heyduk T., Ma Y., Tang H., Ebright R.H. Fluorescence anisotropy. Rapid, quantitative assay for protein-DNA and protein-protein interaction Methods Enzymol. 274:1996;492-503.
20. Hirose Y., Manley J.L. RNA polymerase II is an essential mRNA polyadenylation factor. Nature. 395:1998;93-96.
21. Hirose Y., Tacke R., Manley J.L. Phosphorylated RNA polymerase II stimulates pre-mRNA splicing. Genes Dev. 13:1999;1234-1239.
22. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233:1993;123-138.
23. Jones T.A., Zou J.-Y., Cowan S.W., Kjeldgaard M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119.
24. Kadonaga J.T. The DPE, a core promoter element for transcription by RNA polymerase II. Exp. Mol. Med. 34:2002;259-264.
25. Kaufmann J., Ahrens K., Koop R., Smale S.T., Müller R. CIF150, a human cofactor for TFIID-dependent initiator function. Mol. Cell. Biol. 18:1998;233-239.
26. Kim Y., Geiger J.H., Hahn S., Sigler P.B. Crystal structure of a yeast TBP/TATA-box complex. Nature. 365:1993;512-520. a.
27. Kim J.L., Nikolov D.B., Burley S.K. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature. 365:1993;520-527. b.
28. Keeling P.J., Palmer J.D. Parabasalian flagellates are ancient eukaryotes. Nature. 405:2000;635-637.
29. Kodandapani R., Pio F., Ni C.Z., Piccialli G., Klemsz M., McKercher S., Maki R.A., Ely K.R. A new pattern for helix-turn-helix recognition revealed by the PU.1 ETS-domain-DNA complex. Nature. 380:1996;456-460.
30. Kowestra D., Granzin J., Koch C., Choe H.W., Raghunathan S., Wolf W., Labahn J., Kahmann R., Saenger W. Three-dimensional structure of the E. coli DNA-binding protein FIS. Nature. 349:1991;178-180.
31. Lagrande T., Kapanidis A.N., Tang H., Reinberg D., Ebright R.H. New core promoter element in RNA polymerase II-dependent transcription. Sequence-specific DNA binding by transcription factor IIB Genes Dev. 12:1998;34-44.
32. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck. A program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
33. Levine M., Tijan R. Transcription regulation and animal diversity. Nature. 424:2003;147-151.
34. Liston D.R., Johnson P.J. Analysis of a ubiquitous promoter element in a primitive eukaryote. early evolution of the initiator element Mol. Cell. Biol. 19:1999;2380-2388.
35. Liston D.R., Lau A.O., Ortiz D., Smale S.T., Johnson P.J. Initiator recognition in a primitive eukaryote. IBP39, an initiator-binding protein from Trichomonas vaginalis Mol. Cell. Biol. 21:2001;7872-7882.
36. Litingtung Y., Lawler A.M., Sebald S.M., Lee E., Gearhart D., Westphal H., Corden J.L. Growth retardation and neonatal lethality in mice with a homozygous deletion in the C-terminal domain of RNA polymerase II. Mol. Gen. Genet. 261:1999;100-105.
37. Lo K., Smale S.T. Generality of a functional initiator consensus sequence. Gene. 182:1996;13-22.
38. Lu H., Flores O., Weinmann R., Reinberg D. The nonphosphorylated form of RNA polymerase II preferentially associates with the preinitation complex. Proc. Natl. Acad. Sci. USA. 88:1991;10004-10008.
39. Mo Y., Vaessen B., Johnston K., Marmorstein R. Structure of SAP-1 bound to DNA targets from the E74 and c-fos promoters. Insights into DNA sequence discrimination by Ets proteins Mol. Cell. 2:1998;201-212.
40. Mo Y., Vaessen B., Johnston K., Marmorstein R. Structure of the elk-1-DNA complex reveals how DNA-distal residues affect ETS domain recognition of DNA. Nat. Struct. Biol. 7:2000;292-297.
41. Myers J.K., Morris D.P., Greenleaf A.L., Oas T.G. Phosphorylation of RNA polymerase II CTD fragments results in tight binding to the WW domain from the yeast prolyl isomerase Ess1. Biochemistry. 40:2001;8479-8486.
42. Murakami K.S., Masuda S., Campbell E.A., Muzzin O., Darst S.A. Structural basis of transcription initiation. an RNA polymerase holoenzyme-DNA complex Science. 296:2002;1285-1290.
43. Nicholls A., Sharp K.A., Honig B. Protein folding and association. insights from the interfacial and thermodynamic properties of hydrocarbons Proteins. 11:1991;281-296.
44. Quon D.V., Delgadillo M.G., Khachi A., Smale S.T., Johnson P.J. Similarity between a ubiquitous promoter element in an ancient eukaryote and mammalian elements. Proc. Natl. Acad. Sci. USA. 91:1994;4579-4583.
45. Quon D.V.K., Delgadillo M.G., Johnson P.J. Transcription in the early diverging eukaryote Trichomonas vaginalis. An unusual RNA polymerase II and α-amanitin-resistant transcription of protein-coding genes J. Mol. Evol. 43:1996;253-262.
46. Ravishanker G., Swaminathan S., Beveridge D.L., Lavery R., Sklenar H. Conformational and helicoidal analysis of 30 PS of molecular dynamics on the d(CGCGAATTCGCG) double helix. "Curves", dials and windows J. Biomol. Struct. Dyn. 6:1989;669-699.
47. Roeder R.G. The role of general initiation factors in transcription by RNA polymerase II. Trends Biochem. Sci. 21:1996;327-335.
48. Smale S.T., Baltimore D. The "initiator" as a transcription control element. Cell. 57:1989;103-113.
49. Smale S.T., Kadonaga J.T. The RNA polymerase II core promoter. Annu. Rev. Biochem. 72:2003;449-479.
50. Smale S.T., Jain A., Kaufmann J., Emami K.H., Lo K., Garraway I.P. The initiator element. A paradigm for core promoter heterogeneity within metazoan protein-coding genes Cold Spring Harb. Symp. Quant. Biol. 63:1998;21-31.
51. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D Biol. Crystallogr. 55:1999;849-861.
52. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature. 417:2002;712-719.
53. Verger A., Duterque-Coquilliaud M. When Ets transcription factors meet their partners. Bioessays. 24:2002;362-370.
54. Werner M.H., Clore G.M., Fisher C.L., Fisher R.J., Trinh L., Shiloach J., Gronenborn A.M. Correction of the NMR structure of the ETS1/DNA complex. J. Biomol. NMR. 10:1997;317-328.
55. West M.L., Corden J.L. Construction and analysis of yeast RNA polymerase II CTD deletion and substitution mutations. Genetics. 140:1995;1223-1233.
56. Wintjens R., Rooman M. Structural classification of HTH DNA-binding domains and protein-DNA interaction modes. J. Mol. Biol. 262:1996;294-313.