The yeast prefoldin-like URI-orthologue Bud27 associates with the RSC nucleosome remodeler and modulates transcription

Nucleic Acids Research

Volumn 42, Issue 15, 2014, Pages 9666-9676

  Miron García, María Carmen ^a   Garrido Godino, Ana Isabel ^a   Martínez Fernandez, Veronica ^a   Fernandez Pevida, Antonio ^b,c   Cuevas Bermúdez, Abel ^a   Martín Expósito, Manuel ^a   Chavez, Sebastian ^b,c   De La Cruz, Jesus ^b,c   Navarro, Francisco ^a  

^a UNIVERSITY OF JAÉN   (Spain)

^b HOSPITAL UNIVERSITARIO VIRGEN DEL ROCÍO   (Spain)

^c UNIVERSITY OF SEVILLE   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

BUD27 PROTEIN; FUNGAL PROTEIN; RNA POLYMERASE II; RPB5 PROTEIN; UNCLASSIFIED DRUG; CELL CYCLE PROTEIN; CHROMATIN; INITIATION FACTOR; NUCLEAR PROTEIN; RPB1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN; STH1 PROTEIN, S CEREVISIAE; URI1 PROTEIN, S CEREVISIAE;

ARTICLE; CHROMATIN ASSEMBLY AND DISASSEMBLY; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME PHOSPHORYLATION; GENE EXPRESSION; GENE INTERACTION; GENETIC TRANSCRIPTION; IN VIVO STUDY; NONHUMAN; NUCLEOSOME; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN FUNCTION; TRANSCRIPTION ELONGATION; TRANSCRIPTION REGULATION; CHROMATIN; GENETICS; METABOLISM; MUTATION;

CELL CYCLE PROTEINS; CHROMATIN; MUTATION; NUCLEAR PROTEINS; PEPTIDE INITIATION FACTORS; RNA POLYMERASE II; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION ELONGATION, GENETIC;

EID: 84929518562     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku685     Document Type: Article

References (46)

1. Forget, D., Lacombe, A.A., Cloutier, P., Al-Khoury, R., Bouchard, A., Lavallee-Adam, M., Faubert, D., Jeronimo, C., Blanchette, M. and Coulombe, B. (2010) The protein interaction network of the human transcription machinery reveals a role for the conserved GTPase RPAP4/GPN1 and microtubule assembly in nuclear import and biogenesis of RNA polymerase II. Mol. Cell. Proteomics, 9, 2827-2839.
2. Cloutier, P. and Coulombe, B. (2010) New insights into the biogenesis of nuclear RNA polymerases? Biochem. Cell. Biol., 88, 211-221.
3. Miron-Garcia, M.C., Garrido-Godino, A.I., Garcia-Molinero, V., Hernandez-Torres, F., Rodriguez-Navarro, S. and Navarro, F. (2013) The prefoldin bud27 mediates the assembly of the eukaryotic RNA polymerases in an rpb5-dependent manner. PLoS Genet., 9, e1003297.
4. Millán-Zambrano, G. and Chávez, S. (2014) Nuclear functions of prefoldin. Open Biol., 4, 140085.
5. Dorjsuren, D., Lin, Y., Wei, W., Yamashita, T., Nomura, T., Hayashi, N. and Murakami, S. (1998) RMP, a novel RNA polymerase II subunit 5-interacting protein, counteracts transactivation by hepatitis B virus X protein. Mol. Cell. Biol., 18, 7546-7555.
6. Mockli, N., Deplazes, A., Hassa, P.O., Zhang, Z., Peter, M., Hottiger, M.O., Stagljar, I. and Auerbach, D. (2007) Yeast split-ubiquitin-based cytosolic screening system to detect interactions between transcriptionally active proteins. Biotechniques, 42, 725-730.
7. Gstaiger, M., Luke, B., Hess, D., Oakeley, E.J., Wirbelauer, C., Blondel, M., Vigneron, M., Peter, M. and Krek, W. (2003) Control of nutrient-sensitive transcription programs by the unconventional prefoldin URI. Science, 302, 1208-1212.
8. Deplazes, A., Mockli, N., Luke, B., Auerbach, D. and Peter, M. (2009) Yeast Uri1p promotes translation initiation and may provide a link to cotranslational quality control. EMBO J., 28, 1429-1441.
9. Parusel, C.T., Kritikou, E.A., Hengartner, M.O., Krek, W. and Gotta, M. (2006) URI-1 is required for DNA stability in C. elegans. Development, 133, 621-629.
10. Mita, P., Savas, J.N., Djouder, N., Yates, J.R. 3rd, Ha, S., Ruoff, R., Schafler, E.D., Nwachukwu, J.C., Tanese, N., Cowan, N.J. et al. (2011) Regulation of androgen receptor mediated transcription by Rpb5 binding protein URI/RMP. Mol. Cell. Biol., 31, 3639-3652.
11. 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. (Tokyo), 138, 215-224.
12. Wei, W., Gu, J.X., Zhu, C.Q., Sun, F.Y., Dorjsuren, D., Lin, Y. and Murakami, S. (2003) Interaction with general transcription factor IIF (TFIIF) is required for the suppression of activated transcription by RPB5-mediating protein (RMP). Cell Res., 13, 111-120.
13. Huen, J., Kakihara, Y., Ugwu, F., Cheung, K.L., Ortega, J. and Houry, W.A. (2010) Rvb1-Rvb2: essential ATP-dependent helicases for critical complexes. Biochem. Cell. Biol., 88, 29-40.
14. Cvackova, Z., Albring, K.F., Koberna, K., Ligasova, A., Huber, O., Raska, I. and Stanek, D. (2008) Pontin is localized in nucleolar fibrillar centers. Chromosoma, 117, 487-497.
15. Yart, A., Gstaiger, M., Wirbelauer, C., Pecnik, M., Anastasiou, D., Hess, D. and Krek, W. (2005) The HRPT2 tumor suppressor gene product parafibromin associates with human PAF1 and RNA polymerase II. Mol. Cell. Biol., 25, 5052-5060.
16. Garcia-Lopez, M.C., Pelechano, V., Miron-Garcia, M.C., Garrido-Godino, A.I., Garcia, A., Calvo, O., Werner, M., Perez-Ortin, J.E. and Navarro, F. (2011) The conserved foot domain of RNA pol II associates with proteins involved in transcriptional initiation and/or early elongation. Genetics, 189, 1235-1248.
17. Flores, A., Briand, J.F., Gadal, O., Andrau, J.C., Rubbi, L., Van Mullem, V., Boschiero, C., Goussot, M., Marck, C., Carles, C. et al. (1999) A protein-protein interaction map of yeast RNA polymerase III. Proc. Natl. Acad. Sci. U.S.A., 96, 7815-7820.
18. Soutourina, J., Bordas-Le Floch, V., Gendrel, G., Flores, A., Ducrot, C., Dumay-Odelot, H., Soularue, P., Navarro, F., Cairns, B.R., Lefebvre, O. et al. (2006) Rsc4 connects the chromatin remodeler RSC to RNA polymerases. Mol. Cell. Biol., 26, 4920-4933.
19. Liang, C. and Stillman, B. (1997) Persistent initiation of DNA replication and chromatin-bound MCM proteins during the cell cycle in cdc6 mutants. Genes Dev., 11, 3375-3386.
20. Rodriguez-Gil, A., Garcia-Martinez, J., Pelechano, V., Munoz-Centeno Mde, L., Geli, V., Perez-Ortin, J.E. and Chavez, S. (2010) The distribution of active RNA polymerase II along the transcribed region is gene-specific and controlled by elongation factors. Nucleic Acids Res., 38, 4651-4664.
21. Nonet, M., Scafe, C., Sexton, J. and Young, R. (1987) Eucaryotic RNA polymerase conditional mutant that rapidly ceases mRNA synthesis. Mol. Cell. Biol., 7, 1602-1611.
22. Morillo-Huesca, M., Vanti, M. and Chavez, S. (2006) A simple in vivo assay for measuring the efficiency of gene length-dependent processes in yeast mRNA biogenesis. FEBS J., 273, 756-769.
23. Mottarella, S.E., Rosa, M., Bangura, A., Bernstein, H.J. and Craig, P.A. (2010) Conscript: RasMol to PyMOL script converter. Biochem. Mol. Biol. Educ., 38, 419-422.
24. Kirchner, J., Vissi, E., Gross, S., Szoor, B., Rudenko, A., Alphey, L. and White-Cooper, H. (2008) Drosophila Uri, a PP1alpha binding protein, is essential for viability, maintenance of DNA integrity and normal transcriptional activity. BMC Mol. Biol., 9, 36.
25. Zaros, C., Briand, J.F., Boulard, Y., Labarre-Mariotte, S., Garcia-Lopez, M.C., Thuriaux, P. and Navarro, F. (2007) Functional organization of the Rpb5 subunit shared by the three yeast RNA polymerases. Nucleic Acids Res., 35, 634-647.
26. Cramer, P., Bushnell, D.A. and Kornberg, R.D. (2001) Structural basis of transcription: RNA polymerase II at 2.8 angstrom resolution. Science, 292, 1863-1876.
27. Shaw, R.J., Wilson, J.L., Smith, K.T. and Reines, D. (2001) Regulation of an IMP dehydrogenase gene and its overexpression in drug-sensitive transcription elongation mutants of yeast. J. Biol. Chem., 276, 32905-32916.
28. Garcia-Lopez, M.C., Miron-Garcia, M.C., Garrido-Godino, A.I., Mingorance, C. and Navarro, F. (2010) Overexpression of SNG1 causes 6-azauracil resistance in Saccharomyces cerevisiae. Curr. Genet., 56, 251-263.
29. Gari, E., Piedrafita, L., Aldea, M. and Herrero, E. (1997) A set of vectors with a tetracycline-regulatable promoter system for modulated gene expression in Saccharomyces cerevisiae. Yeast, 13, 837-848.
30. Garcia, A., Rosonina, E., Manley, J.L. and Calvo, O. (2010) Sub1 globally regulates RNA polymerase II CTD phosphorylation. Mol. Cell. Biol., 30, 5180-5193.
31. Mason, P.B. and Struhl, K. (2005) Distinction and relationship between elongation rate and processivity of RNA polymerase II in vivo. Mol. Cell, 17, 831-840.
32. Kuryan, B.G., Kim, J., Tran, N.N., Lombardo, S.R., Venkatesh, S., Workman, J.L. and Carey, M. (2012) Histone density is maintained during transcription mediated by the chromatin remodeler RSC and histone chaperone NAP1 in vitro. Proc. Natl. Acad. Sci. U.S.A., 109, 1931-1936.
33. Spain, M.M. and Govind, C.K. (2011) A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamics. Transcription, 2, 78-81.
34. Collins, S.R., Miller, K.M., Maas, N.L., Roguev, A., Fillingham, J., Chu, C.S., Schuldiner, M., Gebbia, M., Recht, J., Shales, M. et al. (2007) Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map. Nature, 446, 806-810.
35. Costanzo, M., Baryshnikova, A., Bellay, J., Kim, Y., Spear, E.D., Sevier, C.S., Ding, H., Koh, J.L., Toufighi, K., Mostafavi, S. et al. (2010) The genetic landscape of a cell. Science, 327, 425-431.
36. Wang, Y., Zhang, X., Zhang, H., Lu, Y., Huang, H., Dong, X., Chen, J., Dong, J., Yang, X., Hang, H. et al. (2012) Coiled-coil networking shapes cell molecular machinery. Mol. Biol. Cell., 23, 3911-3922.
37. Tronnersjo, S., Hanefalk, C., Balciunas, D., Hu, G.Z., Nordberg, N., Muren, E. and Ronne, H. (2007) The jmjN and jmjC domains of the yeast zinc finger protein Gis1 interact with 19 proteins involved in transcription, sumoylation and DNA repair. Mol. Genet. Genom., 277, 57-70.
38. Ng, H.H., Robert, F., Young, R.A. and Struhl, K. (2002) Genome-wide location and regulated recruitment of the RSC nucleosome-remodeling complex. Genes Dev., 16, 806-819.
39. Boulon, S., Pradet-Balade, B., Verheggen, C., Molle, D., Boireau, S., Georgieva, M., Azzag, K., Robert, M.C., Ahmad, Y., Neel, H. et al. (2010) HSP90 and its R2TP/Prefoldin-like cochaperone are involved in the cytoplasmic assembly of RNA polymerase II. Mol. Cell, 39, 912-924.
40. Mita, P., Savas, J.N., Ha, S., Djouder, N., Yates, J.R. 3rd and Logan, S.K. (2013) Analysis of URI nuclear interaction with RPB5 and components of the R2TP/prefoldin-like complex. PLoS One, 8, e63879.
41. Delgermaa, L., Hayashi, N., Dorjsuren, D., Nomura, T., Thuy l.e., T.T. and Murakami, S. (2004) Subcellular localization of RPB5-mediating protein and its putative functional partner. Mol. Cell. Biol., 24, 8556-8566.
42. Millan-Zambrano, G., Rodriguez-Gil, A., Penate, X., de Miguel-Jimenez, L., Morillo-Huesca, M., Krogan, N. and Chavez, S. (2013) The prefoldin complex regulates chromatin dynamics during transcription elongation. PLoS Genet., 9, e1003776.
43. Garrido-Godino, A.I., Garcia-Lopez, M.C. and Navarro, F. (2013) Correct assembly of RNA polymerase II depends on the foot domain and is required for multiple steps of transcription in Saccharomyces cerevisiae. Mol. Cell. Biol., 33, 3611-3626.
44. García-López, M.C. and Navarro, F. (2011) RNA polymerase II conserved protein domains as platforms for protein-protein interactions. Transcription, 2, 193-197.
45. Imbeault, D., Gamar, L., Rufiange, A., Paquet, E. and Nourani, A. (2008) The Rtt106 histone chaperone is functionally linked to transcription elongation and is involved in the regulation of spurious transcription from cryptic promoters in yeast. J. Biol. Chem., 283, 27350-27354.
46. Sawarkar, R. and Paro, R. (2013) Hsp90@chromatin.nucleus: an emerging hub of a networker. Trends Cell. Biol., 23, 193-201.