Table 1 Placeholders in ribosome biogenesis

Back to article: Placeholder factors in ribosome biogenesis: please, pave my way

19. Senger B, Lafontaine DL, Graindorge JS, Gadal O, Camasses A, Sanni A, Garnier JM, Breitenbach M, Hurt E, Fasiolo F (2001). The nucle(ol)ar Tif6p and Efl1p are required for a late cytoplasmic step of ribosome synthesis. Mol Cell 8(6): 1363-1373. https://doi.org/10.1016/S1097-2765(01)00403-8

20. Rodríguez-Mateos M, García-Gómez JJ, Francisco-Velilla R, Remacha M, de la Cruz J, Ballesta JPG (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(22): 7519-7532. https://doi.org/10.1093/nar/gkp806

21. Strunk BS, Loucks CR, Su M, Vashisth H, Cheng S, Schilling J, Brooks CL, III., Karbstein K, Skiniotis G (2011). Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates. Science 333(6048): 1449-1453. https://doi.org/10.1126/science.1208245

28. Saveanu C, Namane A, Gleizes PE, Lebreton A, Rousselle JC, Noaillac-Depeyre J, Gas N, Jacquier A, Fromont-Racine M (2003). Sequential protein association with nascent 60S ribosomal particles. Mol Cell Biol 23(13): 4449-4460. https://doi.org/10.1128/MCB.23.13.4449-4460.2003

40. Wu S, Tutuncuoglu B, Yan K, Brown H, Zhang Y, Tan D, Gamalinda M, Yuan Y, Li Z, Jakovljevic J, Ma C, Lei J, Dong MQ, Woolford JL, Jr., Gao N (2016). Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Nature 534(7605): 133-137. https://doi.org/10.1038/nature17942

43 Ma C, Wu S, Li N, Chen Y, Yan K, Li Z, Zheng L, Lei J, Woolford JL, Jr., Gao N (2017). Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1. Nat Struct Mol Biol 24(3): 214-220. https://doi.org/10.1038/nsmb.3364

45. Kemmler S, Occhipinti L, Veisu M, Panse VG (2009). Yvh1 is required for a late maturation step in the 60S biogenesis pathway. J Cell Biol 186(6): 863-880. https://doi.org/10.1083/jcb.200904111

46. Lo KY, Li Z, Wang F, Marcotte EM, Johnson AW (2009). Ribosome stalk assembly requires the dual-specificity phosphatase Yvh1 for the exchange of Mrt4 with P0. J Cell Biol 186(6): 849-862. https://doi.org/10.1083/jcb.200904110

68. Greber BJ, Gerhardy S, Leitner A, Leibundgut M, Salem M, Boehringer D, Leulliot N, Aebersold R, Panse VG, Ban N (2016). Insertion of the biogenesis factor Rei1 probes the ribosomal tunnel during 60S maturation. Cell 164(1-2): 91-102. https://doi.org/10.1016/j.cell.2015.11.027

69. Greber BJ, Boehringer D, Montellese C, Ban N (2012). Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Nat Struct Mol Biol 19(12): 1228-1233. https://doi.org/10.1038/nsmb.2425

70. Bradatsch B, Leidig C, Granneman S, Gnadig M, Tollervey D, Bottcher B, Beckmann R, Hurt E (2012). Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Nat Struct Mol Biol 19(12): 1234-1241. https://doi.org/10.1038/nsmb.2438

95. Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K (2017). Molecular architecture of the 90S small subunit pre-ribosome. eLife 6. https://doi.org/10.7554/eLife.22086

99. Gelperin D, Horton L, Beckman J, Hensold J, Lemmon SK (2001). Bms1p, a novel GTP-binding protein, and the related Tsr1p are required for distinct steps of 40S ribosome biogenesis in yeast. RNA 7(9): 1268-1283. https://doi.org/10.1017.S1355838201013073

102. McCaughan UM, Jayachandran U, Shchepachev V, Chen ZA, Rappsilber J, Tollervey D, Cook AG (2016). Pre-40S ribosome biogenesis factor Tsr1 is an inactive structural mimic of translational GTPases. Nat Commun 7: 11789. https://doi.org/10.1038/ncomms11789

114. Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW (2017). Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. EMBO J 36(7): 854-868. https://doi.org/10.15252/embj.201696012

115. Matsuo Y, Granneman S, Thoms M, Manikas RG, Tollervey D, Hurt E (2014). Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export. Nature 505(7481): 112-116. https://doi.org/10.1038/nature12731

116. Weis F, Giudice E, Churcher M, Jin L, Hilcenko C, Wong CC, Traynor D, Kay RR, Warren AJ (2015). Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat Struct Mol Biol 22(11): 914-919. https://doi.org/10.1038/nsmb.3112

118. Manikas RG, Thomson E, Thoms M, Hurt E (2016). The K+-dependent GTPase Nug1 is implicated in the association of the helicase Dbp10 to the immature peptidyl transferase centre during ribosome maturation. Nucleic Acids Res 44(4): 1800-1812. https://doi.org/10.1093/nar/gkw045

143. Schütz S, Fischer U, Altvater M, Nerurkar P, Pena C, Gerber M, Chang Y, Caesar S, Schubert OT, Schlenstedt G, Panse VG (2014). A RanGTP-independent mechanism allows ribosomal protein nuclear import for ribosome assembly. eLife 3: e03473. https://doi.org/10.7554/eLife.03473

144. Kressler D, Bange G, Ogawa Y, Stjepanovic G, Bradatsch B, Pratte D, Amlacher S, Strauss D, Yoneda Y, Katahira J, Sinning I, Hurt E (2012). Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science 338(6107): 666-671. https://doi.org/10.1126/science.1226960

149. Huber FM, Hoelz A (2017). Molecular basis for protection of ribosomal protein L4 from cellular degradation. Nat Commun 8: 14354. https://doi.org/10.1038/ncomms14354

150. Mitterer V, Gantenbein N, Birner-Gruenberger R, Murat G, Bergler H, Kressler D, Pertschy B (2016). Nuclear import of dimerized ribosomal protein Rps3 in complex with its chaperone Yar1. Sci Rep 6: 36714. https://doi.org/10.1038/srep36714

152. Pausch P, Singh U, Ahmed YL, Pillet B, Murat G, Altegoer F, Stier G, Thoms M, Hurt E, Sinning I, Bange G, Kressler D (2015). Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Nat Commun 6: 7494. https://doi.org/10.1038/ncomms8494

153. Stelter P, Huber FM, Kunze R, Flemming D, Hoelz A, Hurt E (2015). Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension. Mol Cell 58(5): 854-862. https://doi.org/10.1016/j.molcel.2015.03.029

154. Pillet B, García-Gómez JJ, Pausch P, Falquet L, Bange G, de la Cruz J, Kressler D (2015). The dedicated chaperone Acl4 escorts ribosomal protein Rpl4 to its nuclear pre-60S assembly site. PLoS Genet 11(10): e1005565. https://doi.org/10.1371/journal.pgen.1005565

157. Iouk TL, Aitchison JD, Maguire S, Wozniak RW (2001). Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome synthesis. Mol Cell Biol 21(4): 1260-1271. https://doi.org/10.1128/MCB.21.4.1260-1271.2001

158. Schaper S, Fromont-Racine M, Linder P, de la Cruz J, Namade A, Yaniv M (2001). A yeast homolog of chromatin assembly factor 1 is involved in early ribosome assembly. Curr Biol 11(23): 1885-1890. https://doi.org/10.1016/S0960-9822(01)00584-X

162. Frénois F, Legrand P, Fribourg S (2016). Sqt1p is an eight-bladed WD40 protein. Acta Crystallogr F Struct Biol Commun 72 (Pt 1): 59-64. https://doi.org/10.1107/S2053230X15024097

163. Calviño FR, Kharde S, Ori A, Hendricks A, Wild K, Kressler D, Bange G, Hurt E, Beck M, Sinning I (2015). Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site. Nat Commun 6: 6510. https://doi.org/10.1038/ncomms7510

170. Peng WT, Robinson MD, Mnaimneh S, Krogan NJ, Cagney G, Morris Q, Davierwala AP, Grigull J, Yang X, Zhang W, Mitsakakis N, Ryan OW, Datta N, Jojic V, Pal C, Canadien V, Richards D, Beattie B, Wu LF, Altschuler SJ, Roweis S, Frey BJ, Emili A, Greenblatt JF, Hughes TR (2003). A panoramic view of yeast noncoding RNA processing. Cell 113(7): 919-933. https://doi.org/10.1016/S0092-8674(03)00466-5

171. Peña C, Schütz S, Fischer U, Chang Y, Panse VG (2016). Prefabrication of a ribosomal protein subcomplex essential for eukaryotic ribosome formation. eLife 5: e21755. https://doi.org/10.7554/eLife.21755

173. Ting YH, Lu TJ, Johnson AW, Shie JT, Chen BR, Kumar SS, Lo KY (2017). Bcp1 is the Nuclear Chaperone of the 60S ribosomal protein Rpl23 in Saccharomyces cerevisiae. J Biol Chem 292(2): 585-596. https://doi.org/10.1074/jbc.M116.747634

174. Loar JW, Seiser RM, Sundberg AE, Sagerson HJ, Ilias N, Zobel-Thropp P, Craig EA, Lycan DE (2004). Genetic and biochemical interactions among Yar1, Ltv1 and Rps3 define novel links between environmental stress and ribosome biogenesis in Saccharomyces cerevisiae. Genetics 168(4): 1877-1889. https://doi.org/10.1534/genetics.104.032656

178. Holzer S, Ban N, Klinge S (2013). Crystal structure of the yeast ribosomal protein rpS3 in complex with its chaperone Yar1. J Mol Biol 425(22): 4154-4160. https://doi.org/10.1016/j.jmb.2013.08.022

179. Mitterer V, Murat G, Rety S, Blaud M, Delbos L, Stanborough T, Bergler H, Leulliot N, Kressler D, Pertschy B (2016). Sequential domain assembly of ribosomal protein S3 drives 40S subunit maturation. Nat Commun 7: 10336. https://doi.org/10.1038/ncomms10336

184. Hellmich UA, Weis BL, Lioutikov A, Wurm JP, Kaiser M, Christ NA, Hantke K, Kotter P, Entian KD, Schleiff E, Wohnert J (2013). Essential ribosome assembly factor Fap7 regulates a hierarchy of RNA-protein interactions during small ribosomal subunit biogenesis. Proc Natl Acad Sci USA 110(38): 15253-15258. https://doi.org/10.1073/pnas.1306389110

185. Loc’h J, Blaud M, Rety S, Lebaron S, Deschamps P, Bareille J, Jombart J, Robert-Paganin J, Delbos L, Chardon F, Zhang E, Charenton C, Tollervey D, Leulliot N (2014). RNA mimicry by the fap7 adenylate kinase in ribosome biogenesis. PLoS Biol 12(5): e1001860. https://doi.org/10.1371/journal.pbio.1001860

186. Li S, Duan J, Li D, Ma S, Ye K (2011). Structure of the Shq1-Cbf5-Nop10-Gar1 complex and implications for H/ACA RNP biogenesis and dyskeratosis congenita. EMBO J 30(24): 5010-5020. https://doi.org/10.1038/emboj.2011.427

187. Walbott H, Machado-Pinilla R, Liger D, Blaud M, Réty S, Grozdanov PN, Godin K, van Tilbeurgh H, Varani G, Meier UT, Leulliot N (2011). The H/ACA RNP assembly factor SHQ1 functions as an RNA mimic. Genes Dev 25(22): 2398-2408. https://doi.org/10.1101/gad.176834.111

188. Leulliot N, Godin KS, Hoareau-Aveilla C, Quevillon-Cheruel S, Varani G, Henry Y, Van Tilbeurgh H (2007). The box H/ACA RNP assembly factor Naf1p contains a domain homologous to Gar1p mediating its interaction with Cbf5p. J Mol Biol 371(5): 1338-1353. https://doi.org/10.1016/j.jmb.2007.06.031

189. Vanrobays E, Gelugne JP, Caizergues-Ferrer M, Lafontaine DL (2004). Dim2p, a KH-domain protein required for small ribosomal subunit synthesis. RNA 10(4): 645-656. https://doi.org/10.1261/rna.5162204