The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site
Ribosomes are the molecular machines that generate proteins from mRNA templates. The biogenesis of eukaryotic ribosomes is an outstandingly complex process, in which around 80 ribosomal proteins and four ribosomal RNAs are accurately pieced together. Actively growing yeast cells must produce more than 160’000 ribosomal proteins per minute in order to meet the cellular demand for new ribosomes. Many ribosomal proteins are prone to aggregation and need therefore to be protected on their path from the cytoplasm to their mostly nuclear incorporation sites within ribosome precursors. Recent evidence has highlighted that specific binding partners, referred to as dedicated chaperones, may ensure the soluble expression, nuclear import and/or correct assembly of ribosomal proteins. Here, we have identified such a dedicated chaperone, termed Acl4, which exclusively interacts with and accompanies the ribosomal protein Rpl4 to its nuclear assembly site. Notably, Acl4 has the capacity to recognize Rpl4 as it is synthesized by the ribosome. Our findings emphasize that co-translational capturing of ribosomal proteins by dedicated chaperones is an advantageous strategy to provide sufficient amounts of assembly-competent ribosomal proteins. A detailed knowledge of eukaryotic ribosome assembly is instrumental to eventually understand and treat ribosomopathies, diseases frequently caused by altered functionalities of ribosomal proteins.
Vyšlo v časopise:
The Dedicated Chaperone Acl4 Escorts Ribosomal Protein Rpl4 to Its Nuclear Pre-60S Assembly Site. PLoS Genet 11(10): e32767. doi:10.1371/journal.pgen.1005565
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Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1005565
Souhrn
Ribosomes are the molecular machines that generate proteins from mRNA templates. The biogenesis of eukaryotic ribosomes is an outstandingly complex process, in which around 80 ribosomal proteins and four ribosomal RNAs are accurately pieced together. Actively growing yeast cells must produce more than 160’000 ribosomal proteins per minute in order to meet the cellular demand for new ribosomes. Many ribosomal proteins are prone to aggregation and need therefore to be protected on their path from the cytoplasm to their mostly nuclear incorporation sites within ribosome precursors. Recent evidence has highlighted that specific binding partners, referred to as dedicated chaperones, may ensure the soluble expression, nuclear import and/or correct assembly of ribosomal proteins. Here, we have identified such a dedicated chaperone, termed Acl4, which exclusively interacts with and accompanies the ribosomal protein Rpl4 to its nuclear assembly site. Notably, Acl4 has the capacity to recognize Rpl4 as it is synthesized by the ribosome. Our findings emphasize that co-translational capturing of ribosomal proteins by dedicated chaperones is an advantageous strategy to provide sufficient amounts of assembly-competent ribosomal proteins. A detailed knowledge of eukaryotic ribosome assembly is instrumental to eventually understand and treat ribosomopathies, diseases frequently caused by altered functionalities of ribosomal proteins.
Zdroje
1. Melnikov S, Ben-Shem A, Garreau de Loubresse N, Jenner L, Yusupova G, et al. (2012) One core, two shells: bacterial and eukaryotic ribosomes. Nat Struct Mol Biol 19: 560–567. doi: 10.1038/nsmb.2313 22664983
2. de la Cruz J, Karbstein K, Woolford JL Jr. (2015) Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo. Annu Rev Biochem 84: 93–129. doi: 10.1146/annurev-biochem-060614-033917 25706898
3. Kressler D, Hurt E, Baßler J (2010) Driving ribosome assembly. Biochim Biophys Acta 1803: 673–683. doi: 10.1016/j.bbamcr.2009.10.009 19879902
4. Woolford JL Jr., Baserga SJ (2013) Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195: 643–681. doi: 10.1534/genetics.113.153197 24190922
5. Thomson E, Ferreira-Cerca S, Hurt E (2013) Eukaryotic ribosome biogenesis at a glance. J Cell Sci 126: 4815–4821. doi: 10.1242/jcs.111948 24172536
6. Fernández-Pevida A, Kressler D, de la Cruz J (2015) Processing of preribosomal RNA in Saccharomyces cerevisiae. Wiley Interdiscip Rev RNA 6: 191–209. doi: 10.1002/wrna.1267 25327757
7. Koš M, Tollervey D (2010) Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol Cell 37: 809–820. doi: 10.1016/j.molcel.2010.02.024 20347423
8. 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
9. Karbstein K (2011) Inside the 40S ribosome assembly machinery. Curr Opin Chem Biol 15: 657–663. doi: 10.1016/j.cbpa.2011.07.023 21862385
10. Panse VG, Johnson AW (2010) Maturation of eukaryotic ribosomes: acquisition of functionality. Trends Biochem Sci 35: 260–266. doi: 10.1016/j.tibs.2010.01.001 20137954
11. Gamalinda M, Ohmayer U, Jakovljevic J, Kumcuoglu B, Woolford J, et al. (2014) A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev 28: 198–210. doi: 10.1101/gad.228825.113 24449272
12. Tschochner H, Hurt E (2003) Pre-ribosomes on the road from the nucleolus to the cytoplasm. Trends Cell Biol 13: 255–263. 12742169
13. Matsuo Y, Granneman S, Thoms M, Manikas RG, Tollervey D, et al. (2014) Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export. Nature 505: 112–116. doi: 10.1038/nature12731 24240281
14. Warner JR (1999) The economics of ribosome biosynthesis in yeast. Trends Biochem Sci 24: 437–440. 10542411
15. Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, et al. (2011) The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334: 1524–1529. doi: 10.1126/science.1212642 22096102
16. Klein DJ, Moore PB, Steitz TA (2004) The roles of ribosomal proteins in the structure assembly, and evolution of the large ribosomal subunit. J Mol Biol 340: 141–177. 15184028
17. Klinge S, Voigts-Hoffmann F, Leibundgut M, Ban N (2012) Atomic structures of the eukaryotic ribosome. Trends Biochem Sci 37: 189–198. doi: 10.1016/j.tibs.2012.02.007 22436288
18. Jäkel S, Mingot JM, Schwarzmaier P, Hartmann E, Görlich D (2002) Importins fulfil a dual function as nuclear import receptors and cytoplasmic chaperones for exposed basic domains. EMBO J 21: 377–386. 11823430
19. Bange G, Murat G, Sinning I, Hurt E, Kressler D (2013) New twist to nuclear import: When two travel together. Commun Integr Biol 6: e24792. doi: 10.4161/cib.24792 23940825
20. Hoelz A, Debler EW, Blobel G (2011) The structure of the nuclear pore complex. Annu Rev Biochem 80: 613–643. doi: 10.1146/annurev-biochem-060109-151030 21495847
21. Rout MP, Blobel G, Aitchison JD (1997) A distinct nuclear import pathway used by ribosomal proteins. Cell 89: 715–725. 9182759
22. Koplin A, Preissler S, Ilina Y, Koch M, Scior A, et al. (2010) A dual function for chaperones SSB-RAC and the NAC nascent polypeptide-associated complex on ribosomes. J Cell Biol 189: 57–68. doi: 10.1083/jcb.200910074 20368618
23. Pechmann S, Willmund F, Frydman J (2013) The ribosome as a hub for protein quality control. Mol Cell 49: 411–421. doi: 10.1016/j.molcel.2013.01.020 23395271
24. Abovich N, Gritz L, Tung L, Rosbash M (1985) Effect of RP51 gene dosage alterations on ribosome synthesis in Saccharomyces cerevisiae. Mol Cell Biol 5: 3429–3435. 3915776
25. Tsay YF, Thompson JR, Rotenberg MO, Larkin JC, Woolford JL Jr. (1988) Ribosomal protein synthesis is not regulated at the translational level in Saccharomyces cerevisiae: balanced accumulation of ribosomal proteins L16 and rp59 is mediated by turnover of excess protein. Genes Dev 2: 664–676. 3047007
26. Ecker DJ, Stadel JM, Butt TR, Marsh JA, Monia BP, et al. (1989) Increasing gene expression in yeast by fusion to ubiquitin. J Biol Chem 264: 7715–7719. 2540202
27. Fernández-Pevida A, Rodríguez-Galán O, Díaz-Quintana A, Kressler D, de la Cruz J (2012) Yeast ribosomal protein L40 assembles late into precursor 60S ribosomes and is required for their cytoplasmic maturation. J Biol Chem 287: 38390–38407. doi: 10.1074/jbc.M112.400564 22995916
28. Finley D, Bartel B, Varshavsky A (1989) The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis. Nature 338: 394–401. 2538753
29. Lacombe T, García-Gómez JJ, de la Cruz J, Roser D, Hurt E, 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. doi: 10.1111/j.1365-2958.2009.06622.x 19210616
30. Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, et al. (2014) A new system for naming ribosomal proteins. Curr Opin Struct Biol 24: 165–169. doi: 10.1016/j.sbi.2014.01.002 24524803
31. 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: 4154–4160. doi: 10.1016/j.jmb.2013.08.022 24021814
32. Koch B, Mitterer V, Niederhauser J, Stanborough T, Murat G, et al. (2012) Yar1 protects the ribosomal protein Rps3 from aggregation. J Biol Chem 287: 21806–21815. doi: 10.1074/jbc.M112.365791 22570489
33. Schütz S, Fischer U, Altvater M, Nerurkar P, Peña C, et al. (2014) A RanGTP-independent mechanism allows ribosomal protein nuclear import for ribosome assembly. Elife 3: e03473. doi: 10.7554/eLife.03473 25144938
34. Calviño FR, Kharde S, Ori A, Hendricks A, Wild K, et al. (2015) Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site. Nat Commun 6: 6510. doi: 10.1038/ncomms7510 25849277
35. Kressler D, Bange G, Ogawa Y, Stjepanovic G, Bradatsch B, et al. (2012) Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science 338: 666–671. doi: 10.1126/science.1226960 23118189
36. Eisinger DP, Dick FA, Denke E, Trumpower BL (1997) SQT1, which encodes an essential WD domain protein of Saccharomyces cerevisiae, suppresses dominant-negative mutations of the ribosomal protein gene QSR1. Mol Cell Biol 17: 5146–5155. 9271392
37. Iouk TL, Aitchison JD, Maguire S, Wozniak RW (2001) Rrb1p, a yeast nuclear WD-repeat protein involved in the regulation of ribosome biosynthesis. Mol Cell Biol 21: 1260–1271. 11158312
38. Pausch P, Singh U, Ahmed YL, Pillet B, Murat G, et al. (2015) Co-translational capturing of nascent ribosomal proteins by their dedicated chaperones. Nat Commun 6: 7494. doi: 10.1038/ncomms8494 26112308
39. Schaper S, Fromont-Racine M, Linder P, de la Cruz J, Namane A, et al. (2001) A yeast homolog of chromatin assembly factor 1 is involved in early ribosome assembly. Curr Biol 11: 1885–1890. 11728313
40. West M, Hedges JB, Chen A, Johnson AW (2005) Defining the order in which Nmd3p and Rpl10p load onto nascent 60S ribosomal subunits. Mol Cell Biol 25: 3802–3813. 15831484
41. Klinge S, Voigts-Hoffmann F, Leibundgut M, Arpagaus S, Ban N (2011) Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science 334: 941–948. doi: 10.1126/science.1211204 22052974
42. Kruiswijk T, Planta RJ, Krop JM (1978) The course of the assembly of ribosomal subunits in yeast. Biochim Biophys Acta 517: 378–389. 626744
43. Pöll G, Braun T, Jakovljevic J, Neueder A, Jakob S, et al. (2009) rRNA maturation in yeast cells depleted of large ribosomal subunit proteins. PLoS One 4: e8249. doi: 10.1371/journal.pone.0008249 20011513
44. Chook YM, Süel KE (2011) Nuclear import by karyopherin-βs: recognition and inhibition. Biochim Biophys Acta 1813: 1593–1606. doi: 10.1016/j.bbamcr.2010.10.014 21029754
45. Stelter P, Huber FM, Kunze R, Flemming D, Hoelz A, et al. (2015) Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension. Mol Cell 58: 854–862. doi: 10.1016/j.molcel.2015.03.029 25936803
46. D'Andrea LD, Regan L (2003) TPR proteins: the versatile helix. Trends Biochem Sci 28: 655–662. 14659697
47. Zeytuni N, Zarivach R (2012) Structural and functional discussion of the tetra-trico-peptide repeat, a protein interaction module. Structure 20: 397–405. doi: 10.1016/j.str.2012.01.006 22404999
48. Gamalinda M, Woolford JL Jr. (2014) Deletion of L4 domains reveals insights into the importance of ribosomal protein extensions in eukaryotic ribosome assembly. RNA 20: 1725–1731. doi: 10.1261/rna.046649.114 25246649
49. Amlacher S, Sarges P, Flemming D, van Noort V, Kunze R, et al. (2011) Insight into structure and assembly of the nuclear pore complex by utilizing the genome of a eukaryotic thermophile. Cell 146: 277–289. doi: 10.1016/j.cell.2011.06.039 21784248
50. Stelter P, Kunze R, Radwan M, Thomson E, Thierbach K, et al. (2012) Monitoring spatiotemporal biogenesis of macromolecular assemblies by pulse-chase epitope labeling. Mol Cell 47: 788–796. doi: 10.1016/j.molcel.2012.06.015 22819325
51. Thomas BJ, Rothstein R (1989) Elevated recombination rates in transcriptionally active DNA. Cell 56: 619–630. 2645056
52. James P, Halladay J, Craig EA (1996) Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast. Genetics 144: 1425–1436. 8978031
53. 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
54. Longtine MS, McKenzie A 3rd, Demarini DJ, Shah NG, Wach A, et al. (1998) Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast 14: 953–961. 9717241
55. Pratte D, Singh U, Murat G, Kressler D (2013) Mak5 and Ebp2 act together on early pre-60S particles and their reduced functionality bypasses the requirement for the essential pre-60S factor Nsa1. PLoS One 8: e82741. doi: 10.1371/journal.pone.0082741 24312670
56. Kressler D, de la Cruz J, Rojo M, Linder P (1997) Fal1p is an essential DEAD-box protein involved in 40S-ribosomal-subunit biogenesis in Saccharomyces cerevisiae. Mol Cell Biol 17: 7283–7294. 9372960
57. Kressler D, Doère M, Rojo M, Linder P (1999) Synthetic lethality with conditional dbp6 alleles identifies Rsa1p, a nucleoplasmic protein involved in the assembly of 60S ribosomal subunits. Mol Cell Biol 19: 8633–8645. 10567587
58. Yaffe MP, Schatz G (1984) Two nuclear mutations that block mitochondrial protein import in yeast. Proc Natl Acad Sci U S A 81: 4819–4823. 6235522
59. de la Cruz J, Kressler D, Tollervey D, Linder P (1998) Dob1p (Mtr4p) is a putative ATP-dependent RNA helicase required for the 3' end formation of 5.8S rRNA in Saccharomyces cerevisiae. EMBO J 17: 1128–1140. 9463390
60. Dez C, Froment C, Noaillac-Depeyre J, Monsarrat B, Caizergues-Ferrer M, et al. (2004) Npa1p, a component of very early pre-60S ribosomal particles, associates with a subset of small nucleolar RNPs required for peptidyl transferase center modification. Mol Cell Biol 24: 6324–6337. 15226434
61. Notredame C, Higgins DG, Heringa J (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205–217. 10964570
62. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292: 195–202. 10493868
63. Karpenahalli MR, Lupas AN, Soding J (2007) TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences. BMC Bioinformatics 8: 2. 17199898
64. Altenhoff AM, Skunca N, Glover N, Train CM, Sueki A, et al. (2015) The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. Nucleic Acids Res 43: D240–249. doi: 10.1093/nar/gku1158 25399418
65. Katoh K, Standley DM (2013) MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 30: 772–780. doi: 10.1093/molbev/mst010 23329690
66. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ (2009) Jalview Version 2—a multiple sequence alignment editor and analysis workbench. Bioinformatics 25: 1189–1191. doi: 10.1093/bioinformatics/btp033 19151095
67. Letunic I, Bork P (2011) Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res 39: W475–478. doi: 10.1093/nar/gkr201 21470960
68. Ban N, Nissen P, Hansen J, Moore PB, Steitz TA (2000) The complete atomic structure of the large ribosomal subunit at 2.4 A resolution. Science 289: 905–920. 10937989
69. Gabdulkhakov A, Nikonov S, Garber M (2013) Revisiting the Haloarcula marismortui 50S ribosomal subunit model. Acta Crystallogr D Biol Crystallogr 69: 997–1004. doi: 10.1107/S0907444913004745 23695244
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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