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Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis


All cells communicate their environmental nutrient status to the gene expression machinery so that transcription occurs in proportion to the nutrients available to support cell growth and proliferation. mTORC1 signaling, which is essential for this process, regulates Pol I-dependent rRNA expression. We provide evidence that the RNA polymerase II regulatory complex, Ccr4-Not, also is a novel Pol I regulator required for mTORC1-dependent control of Pol I activity. Ccr4-Not disruption increases Pol I transcription due to an inability to decrease Pol I interactions with the transcription factor Rrn3 when mTORC1 signaling is reduced. Additionally, genetic and biochemical evidence supports a role for Ccr4-Not as a positive regulator of Pol I transcription elongation as well. Surprisingly, while Ccr4-Not mutations profoundly inhibit growth when mTORC1 activity is reduced, this phenotype is reversed by simultaneously impairing Pol I transcription. Overall, our data demonstrate that the evolutionarily conserved Ccr4-Not complex mediates environmental signaling through mTORC1 to control Pol I transcription initiation and, additionally, to regulate Pol I elongation. These studies further suggest that uncoupling Pol I from upstream mTORC1 activity by targeting Ccr4-Not sensitizes cells to mTORC1 inhibitors which is a concept that could have implications for anti-cancer drug development.


Vyšlo v časopise: Ccr4-Not Regulates RNA Polymerase I Transcription and Couples Nutrient Signaling to the Control of Ribosomal RNA Biogenesis. PLoS Genet 11(3): e32767. doi:10.1371/journal.pgen.1005113
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005113

Souhrn

All cells communicate their environmental nutrient status to the gene expression machinery so that transcription occurs in proportion to the nutrients available to support cell growth and proliferation. mTORC1 signaling, which is essential for this process, regulates Pol I-dependent rRNA expression. We provide evidence that the RNA polymerase II regulatory complex, Ccr4-Not, also is a novel Pol I regulator required for mTORC1-dependent control of Pol I activity. Ccr4-Not disruption increases Pol I transcription due to an inability to decrease Pol I interactions with the transcription factor Rrn3 when mTORC1 signaling is reduced. Additionally, genetic and biochemical evidence supports a role for Ccr4-Not as a positive regulator of Pol I transcription elongation as well. Surprisingly, while Ccr4-Not mutations profoundly inhibit growth when mTORC1 activity is reduced, this phenotype is reversed by simultaneously impairing Pol I transcription. Overall, our data demonstrate that the evolutionarily conserved Ccr4-Not complex mediates environmental signaling through mTORC1 to control Pol I transcription initiation and, additionally, to regulate Pol I elongation. These studies further suggest that uncoupling Pol I from upstream mTORC1 activity by targeting Ccr4-Not sensitizes cells to mTORC1 inhibitors which is a concept that could have implications for anti-cancer drug development.


Zdroje

1. Zaman S, Lippman SI, Zhao X, Broach JR (2008) How Saccharomyces responds to nutrients. Annu Rev Genet 42: 27–81. doi: 10.1146/annurev.genet.41.110306.130206 18303986

2. Warner JR (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24: 437–440. 10542411

3. Woolford JL Jr., Baserga SJ Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195: 643–681. doi: 10.1534/genetics.113.153197 24190922

4. Schneider DA RNA polymerase I activity is regulated at multiple steps in the transcription cycle: recent insights into factors that influence transcription elongation. Gene 493: 176–184. doi: 10.1016/j.gene.2011.08.006 21893173

5. Gallagher JE, Dunbar DA, Granneman S, Mitchell BM, Osheim Y, et al. (2004) RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. Genes Dev 18: 2506–2517. 15489292

6. Osheim YN, French SL, Keck KM, Champion EA, Spasov K, et al. (2004) Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from nascent transcripts in Saccharomyces cerevisiae. Mol Cell 16: 943–954. 15610737

7. Gadal O, Labarre S, Boschiero C, Thuriaux P (2002) Hmo1, an HMG-box protein, belongs to the yeast ribosomal DNA transcription system. EMBO J 21: 5498–5507. 12374750

8. Hall DB, Wade JT, Struhl K (2006) An HMG protein, Hmo1, associates with promoters of many ribosomal protein genes and throughout the rRNA gene locus in Saccharomyces cerevisiae. Mol Cell Biol 26: 3672–3679. 16612005

9. Merz K, Hondele M, Goetze H, Gmelch K, Stoeckl U, et al. (2008) Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules. Genes Dev 22: 1190–1204. doi: 10.1101/gad.466908 18451108

10. Moorefield B, Greene EA, Reeder RH (2000) RNA polymerase I transcription factor Rrn3 is functionally conserved between yeast and human. Proc Natl Acad Sci U S A 97: 4724–4729. 10758157

11. Yamamoto RT, Nogi Y, Dodd JA, Nomura M (1996) RRN3 gene of Saccharomyces cerevisiae encodes an essential RNA polymerase I transcription factor which interacts with the polymerase independently of DNA template. EMBO J 15: 3964–3973. 8670901

12. Fath S, Milkereit P, Peyroche G, Riva M, Carles C, et al. (2001) Differential roles of phosphorylation in the formation of transcriptional active RNA polymerase I. Proc Natl Acad Sci U S A 98: 14334–14339. 11717393

13. Milkereit P, Tschochner H (1998) A specialized form of RNA polymerase I, essential for initiation and growth-dependent regulation of rRNA synthesis, is disrupted during transcription. EMBO J 17: 3692–3703. 9649439

14. Peyroche G, Milkereit P, Bischler N, Tschochner H, Schultz P, et al. (2000) The recruitment of RNA polymerase I on rDNA is mediated by the interaction of the A43 subunit with Rrn3. EMBO J 19: 5473–5482. 11032814

15. Bier M, Fath S, Tschochner H (2004) The composition of the RNA polymerase I transcription machinery switches from initiation to elongation mode. FEBS Lett 564: 41–46. 15094040

16. Philippi A, Steinbauer R, Reiter A, Fath S, Leger-Silvestre I, et al. TOR-dependent reduction in the expression level of Rrn3p lowers the activity of the yeast RNA Pol I machinery, but does not account for the strong inhibition of rRNA production. Nucleic Acids Res 38: 5315–5326. doi: 10.1093/nar/gkq264 20421203

17. Claypool JA, French SL, Johzuka K, Eliason K, Vu L, et al. (2004) Tor pathway regulates Rrn3p-dependent recruitment of yeast RNA polymerase I to the promoter but does not participate in alteration of the number of active genes. Mol Biol Cell 15: 946–956. 14595104

18. Mayer C, Zhao J, Yuan X, Grummt I (2004) mTOR-dependent activation of the transcription factor TIF-IA links rRNA synthesis to nutrient availability. Genes Dev 18: 423–434. 15004009

19. Blattner C, Jennebach S, Herzog F, Mayer A, Cheung AC, et al. Molecular basis of Rrn3-regulated RNA polymerase I initiation and cell growth. Genes Dev 25: 2093–2105. doi: 10.1101/gad.17363311 21940764

20. Laferte A, Favry E, Sentenac A, Riva M, Carles C, et al. (2006) The transcriptional activity of RNA polymerase I is a key determinant for the level of all ribosome components. Genes Dev 20: 2030–2040. 16882981

21. Chedin S, Laferte A, Hoang T, Lafontaine DL, Riva M, et al. (2007) Is ribosome synthesis controlled by pol I transcription? Cell Cycle 6: 11–15. 17245116

22. Kuhn CD, Geiger SR, Baumli S, Gartmann M, Gerber J, et al. (2007) Functional architecture of RNA polymerase I. Cell 131: 1260–1272. 18160037

23. Geiger SR, Lorenzen K, Schreieck A, Hanecker P, Kostrewa D, et al. RNA polymerase I contains a TFIIF-related DNA-binding subcomplex. Mol Cell 39: 583–594. doi: 10.1016/j.molcel.2010.07.028 20797630

24. Van Mullem V, Landrieux E, Vandenhaute J, Thuriaux P (2002) Rpa12p, a conserved RNA polymerase I subunit with two functional domains. Mol Microbiol 43: 1105–1113. 11918799

25. Beckouet F, Labarre-Mariotte S, Albert B, Imazawa Y, Werner M, et al. (2008) Two RNA polymerase I subunits control the binding and release of Rrn3 during transcription. Mol Cell Biol 28: 1596–1605. 18086878

26. Schneider DA, Michel A, Sikes ML, Vu L, Dodd JA, et al. (2007) Transcription elongation by RNA polymerase I is linked to efficient rRNA processing and ribosome assembly. Mol Cell 26: 217–229. 17466624

27. Kos M, Tollervey D Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol Cell 37: 809–820. doi: 10.1016/j.molcel.2010.02.024 20347423

28. Venters BJ, Pugh BF (2009) How eukaryotic genes are transcribed. Crit Rev Biochem Mol Biol 44: 117–141. doi: 10.1080/10409230902858785 19514890

29. Schneider DA, French SL, Osheim YN, Bailey AO, Vu L, et al. (2006) RNA polymerase II elongation factors Spt4p and Spt5p play roles in transcription elongation by RNA polymerase I and rRNA processing. Proc Natl Acad Sci U S A 103: 12707–12712. 16908835

30. Zhang Y, Sikes ML, Beyer AL, Schneider DA (2009) The Paf1 complex is required for efficient transcription elongation by RNA polymerase I. Proc Natl Acad Sci U S A 106: 2153–2158. doi: 10.1073/pnas.0812939106 19164765

31. Zhang Y, Anderson SJ, French SL, Sikes ML, Viktorovskaya OV, et al. The SWI/SNF chromatin remodeling complex influences transcription by RNA polymerase I in Saccharomyces cerevisiae. PLoS One 8: e56793. doi: 10.1371/journal.pone.0056793 23437238

32. Birch JL, Tan BC, Panov KI, Panova TB, Andersen JS, et al. (2009) FACT facilitates chromatin transcription by RNA polymerases I and III. EMBO J 28: 854–865. doi: 10.1038/emboj.2009.33 19214185

33. Fatyol K, Grummt I (2008) Proteasomal ATPases are associated with rDNA: the ubiquitin proteasome system plays a direct role in RNA polymerase I transcription. Biochim Biophys Acta 1779: 850–859. doi: 10.1016/j.bbagrm.2008.08.010 18804559

34. Hontz RD, Niederer RO, Johnson JM, Smith JS (2009) Genetic identification of factors that modulate ribosomal DNA transcription in Saccharomyces cerevisiae. Genetics 182: 105–119. doi: 10.1534/genetics.108.100313 19270272

35. Miller JE, Reese JC (2012) Ccr4-Not complex: the control freak of eukaryotic cells. Crit Rev Biochem Mol Biol 47: 315–333. doi: 10.3109/10409238.2012.667214 22416820

36. Panasenko O, Landrieux E, Feuermann M, Finka A, Paquet N, et al. (2006) The yeast Ccr4-Not complex controls ubiquitination of the nascent-associated polypeptide (NAC-EGD) complex. J Biol Chem 281: 31389–31398. 16926149

37. Panasenko OO, David FP, Collart MA (2009) Ribosome association and stability of the nascent polypeptide-associated complex is dependent upon its own ubiquitination. Genetics 181: 447–460. doi: 10.1534/genetics.108.095422 19087962

38. Panasenko OO, Collart MA Not4 E3 ligase contributes to proteasome assembly and functional integrity in part through Ecm29. Mol Cell Biol 31: 1610–1623. doi: 10.1128/MCB.01210-10 21321079

39. Halter D, Collart MA, Panasenko OO The Not4 E3 ligase and CCR4 deadenylase play distinct roles in protein quality control. PLoS One 9: e86218. doi: 10.1371/journal.pone.0086218 24465968

40. Kruk JA, Dutta A, Fu J, Gilmour DS, Reese JC The multifunctional Ccr4-Not complex directly promotes transcription elongation. Genes Dev 25: 581–593. doi: 10.1101/gad.2020911 21406554

41. Gaillard H, Tous C, Botet J, Gonzalez-Aguilera C, Quintero MJ, et al. (2009) Genome-wide analysis of factors affecting transcription elongation and DNA repair: a new role for PAF and Ccr4-not in transcription-coupled repair. PLoS Genet 5: e1000364. doi: 10.1371/journal.pgen.1000364 19197357

42. Denis CL, Chiang YC, Cui Y, Chen J (2001) Genetic evidence supports a role for the yeast CCR4-NOT complex in transcriptional elongation. Genetics 158: 627–634. 11404327

43. Swanson MJ, Qiu H, Sumibcay L, Krueger A, Kim SJ, et al. (2003) A multiplicity of coactivators is required by Gcn4p at individual promoters in vivo. Mol Cell Biol 23: 2800–2820. 12665580

44. French SL, Osheim YN, Cioci F, Nomura M, Beyer AL (2003) In exponentially growing Saccharomyces cerevisiae cells, rRNA synthesis is determined by the summed RNA polymerase I loading rate rather than by the number of active genes. Mol Cell Biol 23: 1558–1568. 12588976

45. Lenssen E, Oberholzer U, Labarre J, De Virgilio C, Collart MA (2002) Saccharomyces cerevisiae Ccr4-not complex contributes to the control of Msn2p-dependent transcription by the Ras/cAMP pathway. Mol Microbiol 43: 1023–1037. 11929548

46. Tsang CK, Bertram PG, Ai W, Drenan R, Zheng XF (2003) Chromatin-mediated regulation of nucleolar structure and RNA Pol I localization by TOR. EMBO J 22: 6045–6056. 14609951

47. Clemente-Blanco A, Mayan-Santos M, Schneider DA, Machin F, Jarmuz A, et al. (2009) Cdc14 inhibits transcription by RNA polymerase I during anaphase. Nature 458: 219–222. doi: 10.1038/nature07652 19158678

48. Bywater MJ, Poortinga G, Sanij E, Hein N, Peck A, et al. Inhibition of RNA polymerase I as a therapeutic strategy to promote cancer-specific activation of p53. Cancer Cell 22: 51–65. doi: 10.1016/j.ccr.2012.05.019 22789538

49. El Hage A, French SL, Beyer AL, Tollervey D (2010) Loss of Topoisomerase I leads to R-loop-mediated transcriptional blocks during ribosomal RNA synthesis. Genes Dev 24: 1546–1558. doi: 10.1101/gad.573310 20634320

50. Azzouz N, Panasenko OO, Colau G, Collart MA (2009) The CCR4-NOT complex physically and functionally interacts with TRAMP and the nuclear exosome. PLoS One 4: e6760. doi: 10.1371/journal.pone.0006760 19707589

51. Parker R RNA degradation in Saccharomyces cerevisae. Genetics 191: 671–702. doi: 10.1534/genetics.111.137265 22785621

52. Meier A, Thoma F (2005) RNA polymerase I transcription factors in active yeast rRNA gene promoters enhance UV damage formation and inhibit repair. Mol Cell Biol 25: 1586–1595. 15713619

53. Bedwell GJ, Appling FD, Anderson SJ, Schneider DA (2012) Efficient transcription by RNA polymerase I using recombinant core factor. Gene 492: 94–99. doi: 10.1016/j.gene.2011.10.049 22093875

54. Chen J, Chiang YC, Denis CL (2002) CCR4, a 3'-5' poly(A) RNA and ssDNA exonuclease, is the catalytic component of the cytoplasmic deadenylase. Embo J 21: 1414–1426. 11889047

55. Chan TF, Carvalho J, Riles L, Zheng XF (2000) A chemical genomics approach toward understanding the global functions of the target of rapamycin protein (TOR). Proc Natl Acad Sci U S A 97: 13227–13232. 11078525

56. Hyle JW, Shaw RJ, Reines D (2003) Functional distinctions between IMP dehydrogenase genes in providing mycophenolate resistance and guanine prototrophy to yeast. J Biol Chem 278: 28470–28478. 12746440

57. Chang M, French-Cornay D, Fan HY, Klein H, Denis CL, et al. (1999) A complex containing RNA polymerase II, Paf1p, Cdc73p, Hpr1p, and Ccr4p plays a role in protein kinase C signaling. Mol Cell Biol 19: 1056–1067. 9891041

58. Pan X, Ye P, Yuan DS, Wang X, Bader JS, et al. (2006) A DNA integrity network in the yeast Saccharomyces cerevisiae. Cell 124: 1069–1081. 16487579

59. Wilmes GM, Bergkessel M, Bandyopadhyay S, Shales M, Braberg H, et al. (2008) A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing. Mol Cell 32: 735–746. doi: 10.1016/j.molcel.2008.11.012 19061648

60. Phipps KR, Charette JM, Baserga SJ The small subunit processome in ribosome biogenesis-progress and prospects. Wiley Interdiscip Rev RNA 2: 1–21. doi: 10.1002/wrna.57 21318072

61. Babbarwal V, Fu J, Reese JC (2014) The Rpb4/7 module of RNA polymerase II is required for carbon catabolite repressor protein 4-negative on TATA (Ccr4-not) complex to promote elongation. J Biol Chem 289: 33125–33130. doi: 10.1074/jbc.C114.601088 25315781

62. Chen H, Fan M, Pfeffer LM, Laribee RN (2012) The histone H3 lysine 56 acetylation pathway is regulated by target of rapamycin (TOR) signaling and functions directly in ribosomal RNA biogenesis. Nucleic Acids Res 40: 6534–6546. doi: 10.1093/nar/gks345 22553361

63. Mumberg D, Muller R, Funk M (1995) Yeast vectors for the controlled expression of heterologous proteins in different genetic backgrounds. Gene 156: 119–122. 7737504

64. Janke C, Magiera MM, Rathfelder N, Taxis C, Reber S, et al. (2004) A versatile toolbox for PCR-based tagging of yeast genes: new fluorescent proteins, more markers and promoter substitution cassettes. Yeast 21: 947–962. 15334558

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