Diversification of function by different isoforms of conventionally shared RNA polymerase subunits

Molecular Biology of the Cell

Volumn 18, Issue 4, 2007, Pages 1293-1301

  Devaux, Sara ^a   Kelly, Steven ^b   Lecordier, Laurence ^a   Wickstead, Bill ^b   Perez Morga, David ^a   Pays, Etienne ^a   Vanhamme, Luc ^a   Gull, Keith ^b  

^a UNIVERSITÉ LIBRE DE BRUXELLES   (Belgium)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

DNA DIRECTED RNA POLYMERASE; ISOENZYME; PROTEIN RPB10; PROTEIN RPB12; PROTEIN RPB5; PROTEIN RPB6; PROTEIN RPB8; PROTEIN SUBUNIT; RNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; BIOINFORMATICS; CELL NUCLEUS; CELLULAR DISTRIBUTION; COMPLEX FORMATION; CONTROLLED STUDY; ENZYME LOCALIZATION; ENZYME SUBUNIT; HUMAN; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DEPLETION; PROTEIN FUNCTION; RNA INTERFERENCE; TRANSCRIPTION REGULATION; TRYPANOSOMA BRUCEI; UNINDEXED SEQUENCE;

ANIMALS; CELL NUCLEOLUS; CELL NUCLEUS STRUCTURES; DATABASES, PROTEIN; DNA-DIRECTED RNA POLYMERASES; EUKARYOTIC CELLS; EVOLUTION, MOLECULAR; MUTATION; PROTEIN CONFORMATION; PROTEIN SUBUNITS; TRANSCRIPTION, GENETIC; TRYPANOSOMA BRUCEI BRUCEI;

EMBRYOPHYTA; EUKARYOTA; PROTISTA; PROTOZOA; TRYPANOSOMA BRUCEI;

EID: 34247188093     PISSN: 10591524     EISSN: None     Source Type: Journal    
DOI: 10.1091/mbc.E06-09-0841     Document Type: Article

References (51)

1. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
2. Arnaiz, O., Cain, S., Cohen, J., and Sperling, L. (2007). ParameciumDB: a community resource that integrates the Paramecium tetraurelia genome sequence with genetic data. Nucleic Acids Res. 35, D439-D444.
3. Best, A. A., Morrison, H. G., McArthur, A. G., Sogin, M. L., and Olsen, G. J. (2004). Evolution of eukaryotic transcription: insights from the genome of Giardia lamblia. Genome Res. 14, 1537-1547.
4. Boucher, N., McNicoll, F., Dumas, C., and Papadopoulou, B. (2002). RNA polymerase I-mediated transcription of a reporter gene integrated into different loci of Leishmania. Mol. Biochem. Parasitol. 119, 153-158,
5. Brun, R., and Jenni, L. (1977). A new semi-defined medium for Trypanosoma brucei sspp. Acta Trop. 34, 21-33.
6. Buhler, J. M., Huet, J., Davies, K. E., Sentenac, A., and Fromageot, P. (1980). Immunological studies of yeast nuclear RNA polymerases at the subunit level. J. Biol. Chem. 255, 9949-9954.
7. Carruthers, V. B., and Cross, G. A. (1992). High-efficiency clonal growth of bloodstream- and insect-form Trypanosoma brucei on agarose plates. Proc. Natl. Acad. Sci. USA 89, 8818-8821.
8. Clayton, C. E. (2002). Life without transcriptional control? From fly to man and back again. EMBO J. 21, 1881-1888.
9. Cramer, P., Bushnell, D. A., Fu, J., Gnatt, A. L., Maier-Davis, B., Thompson, N. E., Burgess, R. R., Edwards, A. M., David, P. R., and Kornberg, R. D. (2000). Architecture of RNA polymerase II and implications for the transcription mechanism. Science 288, 640-649.
10. Devaux, S., Lecordier, L., Uzureau, P., Walgraffe, D., Dierick, J. F., Poelvoorde, P., Pays, E., and Vanhamme, L. (2006). Characterization of RNA polymerase II subunits of Trypanosoma brucei. Mol. Biochem. Parasitol. 148, 60-68.
11. dos Santos, W. G., and Buck, G. A. (2000). Simultaneous stable expression of neomycin phosphotransferase and green fluorescence protein genes in Trypanosoma cruzi. J. Parasitol. 86, 1281-1288.
12. Eddy, S. R. (1998). Profile hidden Markov models. Bioinformatics 14, 755-763.
13. Gay, L. S., Wilson, M. E., and Donelson, J. E. (1996). The promoter for the ribosomal RNA genes of Leishmania chagasi. Mol. Biochem. Parasitol. 77, 193-200.
14. Gunzl, A., Bruderer, T., Laufer, G., Schimanski, B., Tu, L. C., Chung, H. M., Lee, P. T., and Lee, M. G. (2003). RNA polymerase I transcribes procyclin genes and variant surface glycoprotein gene expression sites in Trypanosoma brucei. Eukaryot. Cell 2, 542-551.
15. Hayashi, K., Watanabe, T., Tanaka, A., Furumoto, T., Sato-Tsuchiya, C., Kimura, M., Yokoi, M., Ishihama, A., Hanaoka, F., and Ohkuma, Y. (2005). Studies of Schizosaccharomyces pombe TFIIE indicate conformational and functional changes in RNA polymerase II at transcription initiation. Genes Cells 10, 207-224.
16. Hirumi, H., and Hirumi, K. (1989). Continuous cultivation of Trypanosoma brucei blood stream forms in a medium containing a low concentration of serum protein without feeder cell layers. J. Parasitol. 75, 985-989.
17. Huelsenbeck, J. P., and Ronquist, F. (2001). MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics 17, 754-755.
18. Ivens, A. C., et al. (2005). The genome of the kinetoplastid parasite, Leishmania major. Science 309, 436-442.
19. Kelly, S., Wickstead, B., and Gull, K. (2005). An in silico analysis of trypanosomatid RNA polymerases: insights into their unusual transcription. Biochem. Soc. Trans. 33, 1435-1437.
20. Kettenberger, H., Armache, K. J., and Cramer, P. (2004). Complete RNA polymerase II elongation complex structure and its interactions with NTP and TFIIS. Mol. Cell 16, 955-965.
21. Lanzendorfer, M., Smid, A., Klinger, C., Schultz, P., Sentenac, A., Carles, C., and Riva, M. (1997). A shared subunit belongs to the eukaryotic core RNA polymerase. Genes Dev. 11, 1037-1047.
22. Larkin, R. M., Hagen, G., and Guilfoyle, T. J. (1999). Arabidopsis thaliana RNA polymerase II subunits related to yeast and human RPB5. Gene 231, 41-47.
23. Le, T. T., Zhang, S., Hayashi, N., Yasukawa, M., Delgermaa, L., and Murakami, S. (2005). Mutational analysis of human RNA polymerase II subunit 5 (RPB5): the residues critical for interactions with TFIIF subunit RAP30 and hepatitis B virus X protein. J. Biochem. 138, 215-224.
24. LeBowitz, J. H., Smith, H. Q., Rusche, L., and Beverley, S. M. (1993). Coupling of poly(A) site selection and trans-splicing in Leishmania. Genes Dev. 7, 996-1007.
25. Lin, Y., Nomura, T., Cheong, J., Dorjsuren, D., Iida, K., and Murakami, S. (1997). Hepatitis B virus X protein is a transcriptional modulator that communicates with transcription factor IIB and the RNA polymerase II subunit 5. J. Biol. Chem. 272, 7132-7139.
26. Matsuzaki, M., et al. (2004). Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature 428, 653-657.
27. Navarro, M., and Gull, K. (2001). A pol I transcriptional body associated with VSG mono-allelic expression in Trypanosoma brucei. Nature 414, 759-763.
28. Nguyen, T. N., Schimanski, B., Zahn, A., Klumpp, B., and Gunzl, A. (2006). Purification of an eight subunit RNA polymerase I complex in Trypanosoma brucei. Mol. Biochem. Parasitol. 149, 27-37.
29. Ogbadoyi, E., Ersfeld, K., Robinson, D., Sherwin, T., and Gull, K. (2000). Architecture of the Trypanosoma brucei nucleus during interphase and mitosis. Chromosoma 108, 501-513.
30. Palenchar, J. B., and Bellofatto, V. (2006). Gene transcription in trypanosomes. Mol. Biochem. Parasitol. 146, 135-141.
31. Puig, O., Caspary, F., Rigaut, G., Rutz, B., Bouveret, E., Bragado-Nilsson, E., Wilm, M., and Seraphin, B. (2001). The tandem affinity purification (TAP) method: a general procedure of protein complex purification. Methods 24, 218-229.
32. Roeder, R. G., and Rutter, W. J. (1969). Multiple forms of DNA-dependent RNA polymerase in eukaryotic organisms. Nature 224, 234-237.
33. Roeder, R. G., Schwartz, L. B., and Sklar, V. E. (1976). Function, structure, and regulation of eukaryotic nuclear RNA polymerases. Symp. Soc. Dev. Biol., 29-52.
34. Sampath, V., and Sadhale, P. (2005). Rpb4 and Rpb 7, a sub-complex integral to multi-subunit RNA polymerases performs a multitude of functions. IUBMB Life 57, 93-102.
35. Schwede, T., Kopp, J., Guex, N., and Peitsch, M. C. (2003). SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res. 31, 3381-3385.
36. Sentenac, A. (1985). Eukaryotic RNA polymerases. CRC Crit. Rev. Biochem. 18, 31-90.
37. Shpakovski, G. V., Acker, J., Wintzerith, M., Lacroix, J. F., Thuriaux, P., and Vigneron, M. (1995). Four subunits that are shared by the three classes of RNA polymerase are functionally interchangeable between Homo sapiens and Saccharomyces cerevisiae. Mol. Cell Biol. 15, 4702-4710.
38. Swofford, D. L. (1998). Phylogenetic Analysis by Parsimony (*and Other Methods), Sunderland, MA: Sinauer.
39. Tan, Q., Prysak, M. H., and Woychik, N. A. (2003). Loss of the Rpb4/Rpb7 subcomplex in a mutant form of the Rpb6 subunit shared by RNA polymerases I, II, and III. Mol. Cell Biol. 23, 3329-3338.
40. Teixeira, S. M., and daRocha, W. D. (2003). Control of gene expression and genetic manipulation in the Trypanosomatidae. Genet. Mol. Res. 2, 148-158,
41. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22, 4673-4680.
42. Todone, F., Weinzierl, R. O., Brick, P., and Onesti, S. (2000). Crystal structure of RPB5, a universal eukaryotic RNA polymerase subunit and transcription factor interaction target. Proc. Natl. Acad. Sci. USA 97, 6306-6310.
43. Tyler-Cross, R. E., Short, S. L., Floeter-Winter, L. M., and Buck, G. A. (1995). Transient expression mediated by the Trypanosoma cruzi rRNA promoter. Mol. Biochem. Parasitol. 72, 23-31.
44. Ullu, E., Matthews, K. R., and Tschudi, C. (1993). Temporal order of RNA-processing reactions in trypanosomes: rapid trans splicing precedes polyadenylation of newly synthesized tubulin transcripts. Mol. Cell. Biol. 13, 720-725.
45. Ullu, E., and Tschudi, C. (1990). Permeable trypanosome cells as a model system for transcription and trans-splicing. Nucleic Acids Res. 18, 3319-3326.
46. Vanhamme, L., and Pays, E. (1995). Control of gene expression in trypanosomes. Microbiol. Rev. 59, 223-240.
47. Walgraffe, D., Devaux, S., Lecordier, L., Dierick, J. F., Dieu, M., Van den Abbeele, J., Pays, E., and Vanhamme, L. (2005). Characterization of subunits of the RNA polymerase I complex in Trypanosoma brucei. Mol. Biochem. Parasitol. 139, 249-260.
48. Wang, Z., Morris, J. C., Drew, M. E., and Englund, P. T. (2000). Inhibition of Trypanosoma brucei gene expression by RNA interference using an integratable vector with opposing T7 promoters. J. Biol. Chem. 275, 40174-40179.
49. Wei, W., Dorjsuren, D., Lin, Y., Qin, W., Nomura, T., Hayashi, N., and Murakami, S. (2001). Direct interaction between the subunit RAP30 of transcription factor IIF (TFIIF) and RNA polymerase subunit 5, which contributes to the association between TFIIF and RNA polymerase II. J. Biol. Chem. 276, 12266-12273.
50. Wickstead, B., Ersfeld, K., and Gull, K. (2002). Targeting of a tetracycline-inducible expression system to the transcriptionally silent minichromosomes of Trypanosoma brucei. Mol. Biochem. Parasitol. 125, 211-216.
51. Wirtz, E., Leal, S., Ochatt, C., and Cross, G. A. (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.