5190 Nucleic Acids Research, 2010, Vol. 38, No. 15 28. Scha¨ fer,T., Maco,B., Petfalski,E., Tollervey,D., Bottcher,B., Aebi,U. and Hurt,E. (2006) Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit. Nature, 441, 651–655. 29. Lebreton,A., Rousselle,J.C., Lenormand,P., Namane,A., Jacquier,A., Fromont-Racine,M. and Saveanu,C. (2008) 60S ribosomal subunit assembly dynamics deﬁned by semi-quantitative mass spectrometry of puriﬁed complexes. Nucleic Acids Res., 36, 4988–4999. 30. Saveanu,C., Namane,A., Gleizes,P.E., Lebreton,A., Rousselle,J.C., Noaillac-Depeyre,J., Gas,N., Jacquier,A. and Fromont-Racine,M. (2003) Sequential protein association with nascent 60S ribosomal particles. Mol. Cell. Biol., 23, 4449–4460. 31. van Nues,R.W., Venema,J., Rientjes,J.M., Dirks-Mulder,A. and Raue´ ,H.A. (1995) Processing of eukaryotic pre-rRNA: the role of the transcribed spacers. Biochem Cell Biol, 73, 789–801. 32. Coˆ t e´,C.A., Greer,C.L. and Peculis,B.A. (2002) Dynamic conformational model for the role of ITS2 in pre-rRNA processing in yeast. RNA, 8, 786–797. 33. Woolford,J.L. Jr and Warner,J.R. (1991) The ribosome and its synthesis. In Broach,J.R., Pringle,J.R. and Jones,E.W. (eds), The Molecular and Cellular Biology of the yeast Saccharomyces: Genome Dynamics, Protein Synthesis, and Energetics, Vol. 1. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp. 587–626. 34. Ferreira-Cerca,S., Poll,G., Gleizes,P.E., Tschochner,H. and Milkereit,P. (2005) Roles of eukaryotic ribosomal proteins in maturation and transport of pre-18S rRNA and ribosome function. Mol. Cell, 20, 263–275. 35. Po¨ ll,G., Braun,T., Jakovljevic,J., Neueder,A., Jakob,S., Woolford,J.L. Jr, Tschochner,H. and Milkereit,P. (2009) rRNA maturation in yeast cells depleted of large ribosomal subunit proteins. PLoS ONE, 4, e8249. 36. Deshmukh,M., Tsay,Y.-F., Paulovich,A.G. and Woolford,J.L. Jr (1993) Yeast ribosomal protein L1 is required for the stability of newly synthesized 5S rRNA and the assembly of 60S ribosomal subunits. Mol. Cell. Biol., 13, 2835–2845. 37. Deshmukh,M., Stark,J., Yeh,L.C., Lee,J.C. and Woolford,J.L. Jr (1995) Multiple regions of yeast ribosomal protein L1 are important for its interaction with 5 S rRNA and assembly into ribosomes. J. Biol. Chem., 270, 30148–30156. 38. Rodrı´ guez-Mateos,M., Garcı´ a-Go´ mez,J.J., Francisco-Velilla,R., Remacha,M., de la Cruz,J. and Ballesta,J.P.G. (2009) Role and dynamics of the ribosomal protein P0 and its related trans-acting factor Mrt4 during ribosome assembly in Saccharomyces cerevisiae. Nucleic Acids Res., 37, 7519–7532. 39. Martı´ n-Marcos,P., Hinnebusch,A.G. and Tamame,M. (2007) Ribosomal protein L33 is required for ribosome biogenesis, subunit joining, and repression of GCN4 translation. Mol. Cell. Biol., 27, 5968–5985. 40. van Beekvelt,C.A., de Graaﬀ-Vincent,M., Faber,A.W., van0t Riet,J., Venema,J. and Raue´ ,H.A. (2001) All three functional domains of the large ribosomal subunit protein L25 are required for both early and late pre-rRNA processing steps in Saccharomyces cerevisiae. Nucleic Acids Res., 29, 5001–5008. 41. Rosado,I.V., Kressler,D. and de la Cruz,J. (2007) Functional analysis of Saccharomyces cerevisiae ribosomal protein Rpl3p in ribosome synthesis. Nucleic Acids Res., 35, 4203–4213. 42. Krogan,N.J., Cagney,G., Yu,H., Zhong,G., Guo,X., Ignatchenko,A., Li,J., Pu,S., Datta,N., Tikuisis,A.P. et al. (2006) Global landscape of protein complexes in the yeast Saccharomyces cerevisiae. Nature, 440, 637–643. 43. Gavin,A.C., Bosche,M., Krause,R., Grandi,P., Marzioch,M., Bauer,A., Schultz,J., Rick,J.M., Michon,A.M., Cruciat,C.M. et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature, 415, 141–147. 44. Lastick,S.M. (1980) The assembly of ribosomes in HeLa cell nucleoli. Eur . J. Biochem., 113, 175–182. 45. Kruiswijk,T., Planta,R.J. and Krop,J.M. (1978) The course of the assembly of ribosomal subunits in yeast. Biochim. Biophys. Acta, 517, 378–389. 46. Ferreira-Cerca,S., Poll,G., Kuhn,H., Neueder,A., Jakob,S., Tschochner,H. and Milkereit,P. (2007) Analysis of the in vivo assembly pathway of eukaryotic 40S ribosomal proteins. Mol. Cell, 28, 446–457. 47. Klein,D.J., Moore,P.B. and Steitz,T.A. (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J. Mol. Biol., 340, 141–177. 48. Kramer,G., Boehringer,D., Ban,N. and Bukau,B. (2009) The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nature Struct. Mol. Biol., 16, 589–597. 49. Becker,T., Bhushan,S., Jarasch,A., Armache,J.P., Funes,S., Jossinet,F., Gumbart,J., Mielke,T., Berninghausen,O., Schulten,K. et al. (2009) Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome. Science, 326, 1369–1373. 50. Zhong,T. and Arndt,K.T. (1993) The yeast SIS1 protein, a DnaJ homolog, is required for the initiation of translation. Cell, 73, 1175–1186. 51. Amsterdam,A., Sadler,K.C., Lai,K., Farrington,S., Bronson,R.T., Lees,J.A. and Hopkins,N. (2004) Many ribosomal protein genes are cancer genes in zebraﬁsh. PLoS Biol., 2, E139. 52. Brachmann,C.B., Davies,A., Cost,G.J., Caputo,E., Li,J., Hieter,P. and Boeke,J.D. (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. 53. Ausubel,F.M., Brent,R., Kingston,R.E., Moore,D.D., Seidman,J.G., Smith,J.A. and Struhl,K. (1994) Saccharomyces cerevisiae. Current Protocols in Molecular Biology, Vol. 2. John Wiley & Sons, Inc., New York, NY, pp. 13.10.11–13.14.17. 54. Kaiser,C., Michaelis,S. and Mitchell,A. (1994) Methods in Yeast Genetics: A Cold Spring Harbor Laboratory Course Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 55. Sambrook,J., Fritsch,E.F. and Maniatis,T. (1989) Molecular Cloning: A Laboratory Manual, 2nd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 56. Kressler,D., de la Cruz,J., Rojo,M. and Linder,P. (1998) Dbp6p is an essential putative ATP-dependent RNA helicase required for 60S-ribosomal-subunit assembly in Saccharomyces cerevisiae. Mol. Cell. Biol., 18, 1855–1865. 57. Frey,S., Pool,M. and Seedorf,M. (2001) Scp160p, an RNA-binding, polysome-associated protein, localizes to the endoplasmic reticulum of Saccharomyces cerevisiae in a microtubule-dependent manner. J. Biol. Chem., 276, 15905–15912. 58. Petitjean,A., Bonneaud,N. and Lacroute,F. (1995) The duplicated Saccharomyces cerevisiae gene SSM1 encodes a eucaryotic homolog of the eubacterial and archeabacterial L1 ribsomal protein. Mol. Cell. Biol., 15, 5071–5081. 59. Milkereit,P., Strauss,D., Bassler,J., Gadal,O., Kuhn,H., Schutz,S., Gas,N., Lechner,J., Hurt,E. and Tschochner,H. (2003) A Noc-complex speciﬁcally involved in the formation and nuclear export of ribosomal 40S subunits. J. Biol. Chem., 278, 4072–4081. 60. Venema,J., Planta,R.J. and Raue´ ,H.A. (1998) In vivo mutational analysis of ribosomal RNA in Saccharomyces cerevisiae. In Martin,R. (ed.), Protein Synthesis: Methods and Protocols, Vol. 77. Humana Press, Totowa, NJ, pp. 257–270. 61. Rosado,I.V., Dez,C., Lebaron,S., Caizergues-Ferrer,M., Henry,Y. and de la Cruz,J. (2006) 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. 62. Gadal,O., Strauss,D., Kessl,J., Trumpower,B., Tollervey,D. and Hurt,E. (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. 63. Belk,J.P., he,F. and Jacobson,A. (1999) Overexpression of truncated Nmd3p inhibits protein synthesis in yeast. RNA, 5, 1055–1070. 64. Hedges,J., West,M. and Johnson,A.W. (2005) Release of the export adapter, Nmd3p, from the 60S ribosomal subunit requires