Final Pre-40S Maturation Depends on the Functional Integrity of the 60S Subunit Ribosomal Protein L3

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Recent progress has provided us with detailed knowledge of the structure and function of eukaryotic ribosomes. However, our understanding of the intricate processes of pre-ribosome assembly and the transition to translation-competent ribosomal subunits remains incomplete. The early and intermediate steps of ribosome assembly occur successively in the nucleolus and nucleoplasm. The pre-ribosomal subunits are then exported to the cytoplasm where final maturation steps, notably including D site cleavage of the 20S pre-rRNA to mature 18S rRNA, confer subunit joining and translation competence. Recent evidence indicates that pre-40S subunits are subject to a quality control step involving the GTP-dependent translation initiation factor eIF5B/Fun12, in the context of 80S-like ribosomes. Here, we demonstrate the involvement of 60S subunits in promoting 20S pre-rRNA cleavage. In particular, we show that a specific point mutation in the 60S subunit ribosomal protein L3 (rpl3[W255C]) leads to the accumulation of pre-40S particles that contain the 20S pre-rRNA but are translation-competent. Notably, this mutation prevents the stimulation of the GTPase activity of eIF5B/Fun12, which is also required for site D cleavage. We conclude that L3 plays an important role in regulating the function of eIF5B/Fun12 during 3′ end processing of 18S rRNA at site D, in the context of 80S ribosomes that have not yet engaged in translation.

Vyšlo v časopise: Final Pre-40S Maturation Depends on the Functional Integrity of the 60S Subunit Ribosomal Protein L3. PLoS Genet 10(3): e32767. doi:10.1371/journal.pgen.1004205
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1004205

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Zdroje

1. SchmeingTM, RamakrishnanV (2009) What recent ribosome structures have revealed about the mechanism of translation. Nature 461: 1234–1242.

2. MelnikovS, Ben-ShemA, Garreau de LoubresseN, JennerL, YusupovaG, et al. (2012) One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol 19: 560–567.

3. HenrasAK, SoudetJ, GerusM, LebaronS, Caizergues-FerrerM, et al. (2008) The post-transcriptional steps of eukaryotic ribosome biogenesis. Cell Mol Life Sci 65: 2334–2359.

4. KresslerD, HurtE, BasslerJ (2010) Driving ribosome assembly. Biochim Biophys Acta 1803: 673–683.

5. de la Cruz J, Kressler D, Linder P (2004) Ribosomal subunit assembly. In: Olson MOJ, editor. Nucleolus. Georgetown: Kluwer academic. Landes Bioscience/eurekah.com. pp. 258–285.

6. ThomsonE, TollerveyD (2010) The final step in 5.8S rRNA processing is cytoplasmic in Saccharomyces cerevisiae. Mol Cell Biol 30: 976–984.

7. UdemSA, WarnerJR (1973) The cytoplasmic maturation of a ribosomal precursor ribonucleic acid in yeast. J Biol Chem 248: 1412–1416.

8. PanseVG, JohnsonAW (2010) Maturation of eukaryotic ribosomes: acquisition of functionality. Trends Biochem Sci 35: 260–266.

9. KosM, TollerveyD (2010) Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol Cell 37: 809–820.

10. MullineuxST, LafontaineDL (2012) Mapping the cleavage sites on mammalian pre-rRNAs: Where do we stand? Biochimie 94: 1521–1532.

11. DezC, HouseleyJ, TollerveyD (2006) Surveillance of nuclear-restricted pre-ribosomes within a subnucleolar region of Saccharomyces cerevisiae. EMBO J 25: 1534–1546.

12. BabianoR, GamalindaM, WoolfordJLJr, de la CruzJ (2012) Saccharomyces cerevisiae ribosomal protein L26 is not essential for ribosome assembly and function. Mol Cell Biol 32: 3228–3241.

13. WarnerJR (1971) The assembly of ribosomes in yeast. J Biol Chem 246: 447–454.

14. ZempI, KutayU (2007) Nuclear export and cytoplasmic maturation of ribosomal subunits. FEBS Lett 581: 2783–2793.

15. GartmannM, BlauM, ArmacheJP, MielkeT, TopfM, et al. (2010) Mechanism of eIF6-mediated inhibition of ribosomal subunit joining. J Biol Chem 285: 14848–14851.

16. SenguptaJ, BussiereC, PallesenJ, WestM, JohnsonAW, et al. (2010) Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit. J Cell Biol 189: 1079–1086.

17. Ben-ShemA, Garreau de LoubresseN, MelnikovS, JennerL, YusupovaG, et al. (2011) The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334: 1524–1529.

18. LafontaineDLJ, PreissT, TollerveyD (1998) Yeast 18S rRNA dimethylase Dim1p: a quality control mechanism in ribosome synthesis? Mol Cell Biol 18: 2360–2370.

19. PertschyB, SchneiderC, GnadigM, SchaferT, TollerveyD, et al. (2009) RNA helicase Prp43 and its co-factor Pfa1 promote 20 to 18 S rRNA processing catalyzed by the endonuclease Nob1. J Biol Chem 284: 35079–35091.

20. StrunkBS, LoucksCR, SuM, VashisthH, ChengS, et al. (2011) Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science 333: 1449–1453.

21. KarbsteinK (2011) Inside the 40S ribosome assembly machinery. Curr Opin Chem Biol 15: 657–663.

22. MeskauskasA, DinmanJD (2010) A molecular clamp ensures allosteric coordination of peptidyltransfer and ligand binding to the ribosomal A-site. Nucleic Acids Res 38: 7800–7813.

23. MeskauskasA, DinmanJD (2007) Ribosomal protein L3: gatekeeper to the A site. Mol Cell 25: 877–888.

24. RosadoIV, KresslerD, de la CruzJ (2007) Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis. Nucleic Acids Res 35: 4203–4213.

25. StrunkBS, NovakMN, YoungCL, KarbsteinK (2012) A translation-like cycle is a quality control checkpoint for maturing 40S ribosome subunits. Cell 150: 111–121.

26. LebaronS, SchneiderC, van NuesRW, SwiatkowskaA, WalshD, et al. (2012) Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits. Nat Struct Mol Biol 19: 744–753.

27. PetrovA, MeskauskasA, DinmanJD (2004) Ribosomal protein L3: influence on ribosome structure and function. RNA Biol 1: 59–65.

28. RosadoIV, DezC, LebaronS, Caizergues-FerrerM, HenryY, et al. (2007) Characterization of Saccharomyces cerevisiae Npa2p (Urb2p) reveals a low-molecular-mass complex containing Dbp6p, Npa1p (Urb1p), Nop8p, and Rsa3p involved in early steps of 60S ribosomal subunit biogenesis. Mol Cell Biol 27: 1207–1221.

29. de la CruzJ, LacombeT, DelocheO, LinderP, KresslerD (2004) The putative RNA helicase Dbp6p functionally interacts with Rpl3p, Nop8p and the novel trans-acting factor Rsa3p during biogenesis of 60S ribosomal subunits in Saccharomyces cerevisiae. Genetics 166: 1687–1699.

30. MeskauskasA, HargerJW, JacobsKL, DinmanJD (2003) Decreased peptidyltransferase activity correlates with increased programmed −1 ribosomal frameshifting and viral maintenance defects in the yeast Saccharomyces cerevisiae. RNA 9: 982–992.

31. OhtakeY, WicknerRB (1995) Yeast virus propagation depends critically on free 60S ribosomal subunit concentration. Mol Cell Biol 15: 2772–2781.

32. JakovljevicJ, de MayoloPA, MilesTD, NguyenTM, Léger-SilvestreI, et al. (2004) The carboxy-terminal extension of yeast ribosomal protein S14 is necessary for maturation of 43S preribosomes. Mol Cell 14: 331–342.

33. BrandRC, KlootwijkJ, van SteenbergenTJM, de KokAJ, PlantaRJ (1977) Secondary methylation of yeast ribosomal precursor RNA. Eur J Biochem 75: 311–318.

34. LacombeT, García-GómezJJ, de la CruzJ, RoserD, HurtE, et al. (2009) Linear ubiquitin fusion to Rps31 and its subsequent cleavage are required for the efficient production and functional integrity of 40S ribosomal subunits. Mol Microbiol 72: 69–84.

35. FordCL, Randal-WhitisL, EllisSR (1999) Yeast proteins related to the p40/laminin receptor precursor are required for 20S ribosomal RNA processing and the maturation of 40S ribosomal subunits. Cancer Res 59: 704–710.

36. GrannemanS, NandineniMR, BasergaSJ (2005) The putative NTPase Fap7 mediates cytoplasmic 20S pre-rRNA processing through a direct interaction with Rps14. Mol Cell Biol 25: 10352–10364.

37. SoudetJ, GelugneJP, Belhabich-BaumasK, Caizergues-FerrerM, MouginA (2010) Immature small ribosomal subunits can engage in translation initiation in Saccharomyces cerevisiae. EMBO J 29: 80–92.

38. AltmannM, SonenbergN, TrachselH (1989) Translation in Saccharomyces cerevisiae: initiation factor 4E-dependent cell-free system. Mol Cell Biol 9: 4467–4472.

39. WaldronC, JundR, LacrouteF (1977) Evidence for a high proportion of inactive ribosomes in slow-growing yeast cells. Biochem J 168: 409–415.

40. PestovaTV, LomakinIB, LeeJH, ChoiSK, DeverTE, et al. (2000) The joining of ribosomal subunits in eukaryotes requires eIF5B. Nature 403: 332–335.

41. LiZ, LeeI, MoradiE, HungNJ, JohnsonAW, et al. (2009) Rational extension of the ribosome biogenesis pathway using network-guided genetics. PLoS Biol 7: e1000213.

42. DengY, SingerRH, GuW (2008) Translation of ASH1 mRNA is repressed by Puf6p-Fun12p/eIF5B interaction and released by CK2 phosphorylation. Genes Dev 22: 1037–1050.

43. DeverTE, GreenR (2012) The elongation, termination, and recycling phases of translation in eukaryotes. Cold Spring Harbor Perspect Biol 4: a013706.

44. Roll-MecakA, CaoC, DeverTE, BurleySK (2000) X-Ray structures of the universal translation initiation factor IF2/eIF5B: conformational changes on GDP and GTP binding. Cell 103: 781–792.

45. ClementiN, PolacekN (2010) Ribosome-associated GTPases: the role of RNA for GTPase activation. RNA Biol 7: 521–527.

46. UnbehaunA, MarintchevA, LomakinIB, DidenkoT, WagnerG, et al. (2007) Position of eukaryotic initiation factor eIF5B on the 80S ribosome mapped by directed hydroxyl radical probing. EMBO J 26: 3109–3123.

47. GrannemanS, PetfalskiE, SwiatkowskaA, TollerveyD (2010) Cracking pre-40S ribosomal subunit structure by systematic analyses of RNA-protein cross-linking. EMBO J 29: 2026–2036.

48. MangiarottiG, ChiabergeS, BulfoneS (1997) rRNA maturation as a “quality” control step in ribosomal subunit assembly in Dictyostelium discoideum. J Biol Chem 272: 27818–27822.

49. BécamAM, NasrF, RackiWJ, ZagulskiM, HerbertCJ (2001) Ria1p (Ynl163c), a protein similar to elongation factors 2, is involved in the biogenesis of the 60S subunit of the ribosome in Saccharomyces cerevisiae. Mol Genet Genomics 266: 454–462.

50. SengerB, LafontaineDL, GraindorgeJS, GadalO, CamassesA, et al. (2001) The nucle(ol)ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis. Mol Cell 8: 1363–1373.

51. GraindorgeJS, RousselleJC, SengerB, LenormandP, NamaneA, et al. (2005) Deletion of EFL1 results in heterogeneity of the 60 S GTPase-associated rRNA conformation. J Mol Biol 352: 355–369.

52. SiK, MaitraU (1999) The Saccharomyces cerevisiae homologue of mammalian translation initiation factor 6 does not function as a translation initiation factor. Mol Cell Biol 19: 1416–1426.

53. KlingeS, Voigts-HoffmannF, LeibundgutM, ArpagausS, BanN (2011) Crystal Structure of the Eukaryotic 60S Ribosomal Subunit in Complex with Initiation Factor 6. Science 334: 941–948.

54. BussiereC, HashemY, AroraS, FrankJ, JohnsonAW (2012) Integrity of the P-site is probed during maturation of the 60S ribosomal subunit. J Cell Biol 197: 747–759.

55. MenneTF, GoyenecheaB, Sanchez-PuigN, WongCC, TonkinLM, et al. (2007) The Shwachman-Bodian-Diamond syndrome protein mediates translational activation of ribosomes in yeast. Nature Genet 39: 486–495.

56. LoKY, LiZ, BussiereC, BressonS, MarcotteEM, et al. (2010) Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol Cell 39: 196–208.

57. LebretonA, SaveanuC, DecourtyL, RainJC, JacquierA, et al. (2006) A functional network involved in the recycling of nucleocytoplasmic pre-60S factors. J Cell Biol 173: 349–360.

58. DemoinetE, JacquierA, LutfallaG, Fromont-RacineM (2007) The Hsp40 chaperone Jjj1 is required for the nucleo-cytoplasmic recycling of preribosomal factors in Saccharomyces cerevisiae. RNA 13: 1570–1581.

59. PertschyB, SaveanuC, ZisserG, LebretonA, TenggM, et al. (2007) Cytoplasmic recycling of 60S preribosomal factors depends on the AAA protein Drg1. Mol Cell Biol 27: 6581–6592.

60. KarbsteinK (2013) Quality control mechanisms during ribosome maturation. Trends Cell Biol

61. ThomasBJ, RothsteinR (1989) Elevated recombination rates in transcriptionally active DNA. Cell 56: 619–630.

62. BrachmannCB, DaviesA, CostGJ, CaputoE, LiJ, et al. (1998) Designer deletion strains derived from Saccharomyces cerevisiae S288C: a useful set of strains and plasmids for PCR-mediated gene disruption and other applications. Yeast 14: 115–132.

63. de la CruzJ, IostI, KresslerD, LinderP (1997) The p20 and Ded1 proteins have antagonistic roles in eIF4E-dependent translation in Saccharomyces cerevisiae. Proc Natl Acad Sci USA 94: 5201–5206.

64. Kaiser C, Michaelis S, Mitchell A (1994) Methods in yeast genetics: a Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor, N. Y.: Cold Spring Harbor Laboratory Press.

65. GietzRD, SuginoA (1988) New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74: 527–534.

66. GadalO, StraussD, KesslJ, TrumpowerB, TollerveyD, et al. (2001) Nuclear export of 60S ribosomal subunit depends on Xpo1p and requires a nuclear export sequence-containing factor, Nmd3p, that associates with the large subunit protein Rpl10p. Mol Cell Biol 21: 3405–3415.

67. MilkereitP, StraussD, BasslerJ, GadalO, KuhnH, et al. (2003) A Noc-complex specifically involved in the formation and nuclear export of ribosomal 40S subunits. J Biol Chem 278: 4072–4081.

68. BasslerJ, GrandiP, GadalO, LessmannT, PetfalskiE, et al. (2001) Identification of a 60S preribosomal particle that is closely linked to nuclear export. Mol Cell 8: 517–529.

69. KresslerD, de la CruzJ, RojoM, LinderP (1997) Fal1p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 17: 7283–7294.

70. de la CruzJ, KresslerD, RojoM, TollerveyD, LinderP (1998) Spb4p, an essential putative RNA helicase, is required for a late step in the assembly of 60S ribosomal subunits in Saccharomyces cerevisiae. RNA 4: 1268–1281.

71. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, et al. (1994) Saccharomyces cerevisiae. Current Protocols in Molecular Biology. New York, N. Y.: John Wiley & Sons, Inc. pp. 13.10.11–13.14.17.

72. Venema J, Planta RJ, Raué HA (1998) In vivo mutational analysis of ribosomal RNA in Saccharomyces cerevisiae. In: Martin R, editor. Protein synthesis: Methods and protocols. Totowa, N. J.: Humana Press. pp. 257–270.

73. BabianoR, de la CruzJ (2010) Ribosomal protein L35 is required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res 38: 5177–5192.

74. GrosshansH, HurtE, SimosG (2000) An aminoacylation-dependent nuclear tRNA export pathway in yeast. Genes Dev 14: 830–840.

75. LebaronS, FromentC, Fromont-RacineM, RainJC, MonsarratB, et al. (2005) The splicing ATPase Prp43p is a component of multiple preribosomal particles. Mol Cell Biol 25: 9269–9282.

76. PettersenEF, GoddardTD, HuangCC, CouchGS, GreenblattDM, et al. (2004) UCSF Chimera-a visualization system for exploratory research and analysis. J Comput Chem 25: 1605–1612.