Functional characterization of a Trypanosoma brucei TATA-binding protein-related factor points to a universal regulator of transcription in trypanosomes

Molecular and Cellular Biology

Volumn 24, Issue 21, 2004, Pages 9610-9618

  Ruan, Jia Peng ^a   Arhin, George K ^a   Ullu, Elisabetta ^a   Tschudi, Christian ^a  

^a YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; DNA DIRECTED RNA POLYMERASE III; RNA POLYMERASE II; TATA BINDING PROTEIN; TATA BINDING PROTEIN RELATED FACTOR;

ARTICLE; BINDING SITE; CONTROLLED STUDY; IMMUNOPRECIPITATION; NONHUMAN; NUCLEOTIDE SEQUENCE; POSTTRANSCRIPTIONAL GENE SILENCING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN DOMAIN; RNA INTERFERENCE; RNA SPLICING; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TRANSCRIPTION REGULATION; TRYPANOSOMA BRUCEI;

AMINO ACID SEQUENCE; ANIMALS; CELL LINE; DNA, PROTOZOAN; GENE SILENCING; GENES, ESSENTIAL; MOLECULAR SEQUENCE DATA; PHYLOGENY; RNA INTERFERENCE; RNA POLYMERASE I; RNA POLYMERASE II; RNA POLYMERASE III; RNA, SPLICED LEADER; SEQUENCE ALIGNMENT; TATA BOX BINDING PROTEIN-LIKE PROTEINS; TRANSCRIPTION, GENETIC; TRYPANOSOMA BRUCEI BRUCEI;

PROTOZOA; TRYPANOSOMA; TRYPANOSOMA BRUCEI;

EID: 6344251628     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.24.21.9610-9618.2004     Document Type: Article

References (41)

1. Bastin, P., Z. Bagherzadeh, K. R. Matthews, and K. Gull. 1996. A novel epitope tag system to study protein targeting and organelle biogenesis in Trypanosoma brucei. Mol. Biochem. Parasitol. 77:235-239.
2. Berk, A. J. 2000. TBP-like factors come into focus. Cell 103:5-8.
3. Burley, S. K., and R. G. Roeder. 1996. Biochemistry and structural biology of transcription factor IID (TFIID). Annu. Rev. Biochem. 65:769-799.
4. Cawley, S., S. Bekiranov, H. H. Ng, P. Kapranov, E. A. Sekinger, D. Kampa, A. Piccolboni, V. Sementchenko, J. Cheng, A. J. Williams, R. Wheeler, B. Wang, J. Drenkaw, M. Yamanaka, S. Patel, S. Brubaker, H. Tammana, G. Helt, K. Struhl, and T. R. Gingeras. 2004. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116:499-509.
5. Clayton, C. E. 2002. Life without transcriptional control? From fly to man and back again. EMBO J. 21:1881-1888.
6. Dantonel, J. C., S. Quintin, L. Lakatos, M. Labouesse, and L. Tora. 2000. TBP-like factor is required for embryonic RNA polymerase II transcription in C. elegans. Mol. Cell 6:715-722.
7. Dantonel, J. C., J. M. Wurtz, O. Poch, D. Moras, and L. Tora. 1999. The TBP-like factor: an alternative transcription factor in metazoa? Trends Biochem. Sci. 24:335-339.
8. Das, A., and V. Bellofatto. 2003. RNA polymerase II-dependent transcription in trypanosomes is associated with a SNAP complex-like transcription factor. Proc. Natl. Acad. Sci. USA 100:80-85.
9. El-Sayed, N. M., E. Ghedin, J. Song, A. MacLeod, F. Bringaud, C. Larkin, D. Wanless, J. Peterson, L. Hou, S. Taylor, A. Tweedie, N. Biteau, H. G. Khalak, X. Lin, T. Mason, L. Hannick, E. Caler, G. Blandin, D. Bartholomeu, A. J. Simpson, S. Kaul, H. Zhao, G. Pai, S. Van Aken, T. Utterback, B. Haas, H. L. Koo, L. Umayam, B. Suh, C. Gerrard, V. Leech, R. Qi, S. Zhou, D. Schwartz, T. Feldblyum, S. Salzberg, A. Tait, C. M. Turner, E. Ullu, O. White, S. Melville, M. D. Adams, C. M. Fraser, and J. E. Donelson. 2003. The sequence and analysis of Trypanosoma brucei chromosome II. Nucleic Acids Res. 31:4856-4863.
10. Fantoni, A., A. O. Dare, and C. Tschudi. 1994. RNA polymerase III-mediated transcription of the trypanosome U2 small nuclear RNA gene is controlled by both intragenic and extragenic regulatory elements. Mol. Cell. Biol. 14:2021-2028.
11. Gilinger, G., and V. Bellofatto. 2001. Trypanosome spliced leader RNA genes contain the first identified RNA polymerase II gene promoter in these organisms. Nucleic Acids Res. 29:1556-1564.
12. Guillebault, D., S. Sasorith, E. Derelle, J. M. Wurtz, J. C. Lozano, S. Bingham, L. Tora, and H. Moreau. 2002. A new class of transcription initiation factors, intermediate between TATA box-binding proteins (TBPs) and TBP-like factors (TLFs), is present in the marine unicellular organism, the dinoflagellate Crypthecodinium cohnii. J. Biol. Chem. 277:40881-40886.
13. Hall, N., M. Berriman, N. J. Lennard, B. R. Harris, C. Hertz-Fowler, E. N. Bart-Delabesse, C. S. Gerrard, R. J. Atkin, A. J. Barron, S. Bowman, S. P. Bray-Allen, F. Bringaud, L. N. Clark, C. H. Corton, A. Cronin, R. Davies, J. Doggett, A. Fraser, E. Gruter, S. Hall, A. D. Harper, M. P. Kay, V. Leech, R. Mayes, C. Price, M. A. Quail, E. Rabbinowitsch, C. Reitter, K. Rutherford, J. Sasse, S. Sharp, R. Shownkeen, A. MacLeod, S. Taylor, A. Tweedie, C. M. Turner, A. Tait, K. Gull, B. Barrell, and S. E. Melville. 2003. The DNA sequence of chromosome I of an African trypanosome: gene content, chromosome organisation, recombination and polymorphism. Nucleic Acids Res. 31:4864-4873.
14. Hernandez, N. 2001. Small nuclear RNA genes: a model system to study fundamental mechanisms of transcription. J. Biol. Chem. 276:26733-26736.
15. Hernandez, N. 1993. TBP, a universal eukaryotic transcription factor? Genes Dev. 7:1291-1308.
16. Hochheimer, A., S. Zhou, S. Zheng, M. C. Holmes, and R. Tjian. 2002. TRF2 associates with DREF and directs promoter-selective gene expression in Drosophila. Nature 420:439-445.
17. Holmes, M. C., and R. Tjian. 2000. Promoter-selective properties of the TBP-related factor TRF1. Science 288:867-870.
18. Kaltenbach, L., M. A. Horner, J. H. Rothman, and S. E. Mango. 2000. The TBP-like factor CeTLF is required to activate RNA polymerase II transcription during C. elegans embryogenesis. Mol. Cell 6:705-713.
19. Kaplan, C. D., L. Laprade, and F. Winston. 2003. Transcription elongation factors repress transcription initiation from cryptic sites. Science 301:1096-1099.
20. Keogh, M. C., and S. Buratowski. 2004. Using chromatin immunoprecipitation to map cotranscriptional mRNA processing in Saccharomyces cerevisiae. Methods Mol. Biol. 257:1-16.
21. Kim, J. L., D. B. Nikolov, and S. K. Burley. 1993. Co-crystal structure of TBP recognizing the minor groove of a TATA element. Nature 365:520-527.
22. Laufer, G., and A. Günzl. 2001. In-vitro competition analysis of procyclin gene and variant surface glycoprotein gene expression site transcription in Trypanosoma brucei. Mol. Biochem. Parasitol., 113:55-65.
23. Laufer, G., G. Schaaf, S. Bollgonn, and A. Günzl. 1999. In vitro analysis of alpha-amanitin-resistant transcription from the rRNA, procyclic acidic repetitive protein, and variant surface glycoprotein gene promoters in Trypanosoma brucei. Mol. Cell. Biol. 19:5466-5473.
24. Lee, M. G., and L. H. Van der Ploeg. 1997. Transcription of protein-coding genes in trypanosomes by RNA polymerase I. Annu. Rev. Microbiol. 51:463-489.
25. Martianov, I., G. M. Fimia, A. Dierich, M. Parvinen, P. Sassone-Corsi, and I. Davidson. 2001. Late arrest of spermiogenesis and germ cell apoptosis in mice lacking the TBP-like TLF/TRF2 gene. Mol. Cell 7:509-515.
26. Martinez-Calvillo, S., S. Yan, D. Nguyen, M. Fox, K. Stuart, and P. J. Myler. 2003. Transcription of Leishmania major Friedlin chromosome 1 initiates in both directions within a single region. Mol. Cell 11:1291-1299.
27. Mason, P. B., and K. Struhl. 2003. The FACT complex travels with elongating RNA polymerase II and is important for the fidelity of transcriptional initiation in vivo. Mol. Cell. Biol. 23:8323-8333.
28. Myler, P. J., L. Audleman, T. deVos, G. Hixson, P. Kiser, C. Lemley, C. Magness, E. Rickel, E. Sisk, S. Sunkin, S. Swartzell, T. Westlake, P. Bastien, G. Fu, A. Ivens, and K. Stuart. 1999. Leishmania major Friedlin chromosome 1 has an unusual distribution of protein-coding genes. Proc. Natl. Acad. Sci. USA 96:2902-2906.
29. Nakaar, V., A. O. Dare, D. Hong, E. Ullu, and C. Tschudi. 1994. Upstream tRNA genes are essential for expression of small nuclear and cytoplasmic RNA genes in trypanosomes. Mol. Cell. Biol. 14:6736-6742.
30. Ngo, H., C. Tschudi, K. Gull, and E. Ullu. 1998. Double-stranded RNA induces mRNA degradation in Trypanosoma brucei. Proc. Natl. Acad. Sci. USA 95:14687-14692.
31. Schultz, M. C., R. H. Reeder, and S. Hahn. 1992. Variants of the TATA-binding protein can distinguish subsets of RNA polymerase I, II, and III promoters. Cell 69:697-702.
32. Shen, S., G. K. Arhin, E. Ullu, and C. Tschudi. 2001. In vivo epitope tagging of Trypanosoma brucei genes using a one step PCR-based strategy. Mol. Biochem. Parasitol. 113:171-173.
33. 2 checkpoint. Mol. Cell. Biol. 23:4107-4120.
34. Takada, S., J. T. Lis, S. Zhou, and R Tjian. 2000. A TRF1:BRF complex directs Drosophila RNA polymerase III transcription. Cell 101:459-469.
35. Tschudi, C., and E. Ullu. 2002. Unconventional rules of small nuclear RNA transcription and cap modification in trypanosomatids. Gene Expr. 10:3-16.
36. Ullu, E., and C. Tschudi. 1990. Permeable trypanosome cells as a model system for transcription and trans-splicing. Nucleic Acids Res. 18:3319-3326.
37. Veenstra, G. J., D. L. Weeks, and A. P. Wolffe. 2000. Distinct roles for TBP and TBP-like factor in early embryonic gene transcription in Xenopus. Science 290:2312-2315.
38. Weinmann, A. S., S. M. Bartley, T. Zhang, M. Q. Zhang, and P. J. Farnham. 2001. Use of chromatin immunoprecipitation to clone novel E2F target promoters. Mol. Cell. Biol. 21:6820-6832.
39. Wirtz, E., S. Leal, C. Ochatt, and G. A. Cross. 1999. A tightly regulated inducible expression system for conditional gene knock-outs and dominant-negative genetics in Trypanosoma brucei. Mol. Biochem. Parasitol. 99:89-101.
40. Worthey, E. A., S. Martinez-Calvillo, A. Schnaufer, G. Aggarwal, J. Cawthra, G. Fazelinia, C. Fong, G. Fu, M. Hassebrock, G. Hixson, A. C. Ivens, P. Kiser, F. Marsolini, E. Rickell, R. Salavati, E. Sisk, S. M. Sunkin, K. D. Stuart, and P. J. Myler. 2003. Leishmania major chromosome 3 contains two long convergent polycistronic gene clusters separated by a tRNA gene. Nucleic Acids Res. 31:4201-4210.
41. Zhang, D., T. L. Penttila, P. L. Morris, M. Teichmann, and R. G. Roeder. 2001. Spermiogenesis deficiency in mice lacking the Trf2 gene. Science 292:1153-1155.