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Cited by 13RNA and protein synthesis mechanismsNuclear Structure and FunctionRNA Research and Splicing

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Concurrent remodelling of nucleolar 60S subunit precursors by the Rea1 ATPase and Spb4 RNA helicase

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Mitterer, Valentin, Thoms, Matthias, Buschauer, Robert, Berninghausen, Otto, Hurt, Ed, Beckmann, Roland·2023·eLife
DOI 10.7554/elife.84877PMC PMC10154028

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Abstract

Biogenesis intermediates of nucleolar ribosomal 60S precursor particles undergo a number of structural maturation steps before they transit to the nucleoplasm and are finally exported into the cytoplasm. The AAA + -ATPase Rea1 participates in the nucleolar exit by releasing the Ytm1–Erb1 heterodimer from the evolving pre-60S particle. Here, we show that the DEAD-box RNA helicase Spb4 with its interacting partner Rrp17 is further integrated into this maturation event. Spb4 binds to a specific class of late nucleolar pre-60S intermediates, whose cryo-EM structure revealed how its helicase activity facilitates melting and restructuring of 25S rRNA helices H62 and H63/H63a prior to Ytm1–Erb1 release. In vitro maturation of such Spb4-enriched pre-60S particles, incubated with purified Rea1 and its associated pentameric Rix1-complex in the presence of ATP, combined with cryo-EM analysis depicted the details of the Rea1-dependent large-scale pre-ribosomal remodeling. Our structural insights unveil how the Rea1 ATPase and Spb4 helicase remodel late nucleolar pre-60S particles by rRNA restructuring and dismantling of a network of several ribosomal assembly factors.

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  1. Adams, 2010, PHENIX: A comprehensive python-based system for macromolecular structure solution, Acta Crystallographica. Section D, Biological Crystallography, 66, 213, 10.1107/S0907444909052925 · DOI · Paper page
  2. Ahmed, 2019, Crystal structures of rea1-MIDAS bound to its ribosome assembly factor ligands resembling integrin-ligand-type complexes, Nature Communications, 10, 10.1038/s41467-019-10922-6 · DOI
  3. Andersen, 2006, Structure of the exon junction core complex with a trapped DEAD-box atpase bound to RNA, Science, 313, 1968, 10.1126/science.1131981 · DOI
  4. Aquino, 2021, The RNA helicase dbp7 promotes domain V/VI compaction and stabilization of inter-domain interactions during early 60S assembly, Nature Communications, 12, 10.1038/s41467-021-26208-9 · DOI
  5. Barrio-Garcia, 2016, Architecture of the rix1-rea1 checkpoint machinery during pre-60S-ribosome remodeling, Nature Structural & Molecular Biology, 23, 37, 10.1038/nsmb.3132 · DOI
  6. Bassler, 2010, The AAA-atpase rea1 drives removal of biogenesis factors during multiple stages of 60S ribosome assembly, Molecular Cell, 38, 712, 10.1016/j.molcel.2010.05.024 · DOI
  7. Baßler, 2019, Eukaryotic ribosome assembly, Annual Review of Biochemistry, 88, 281, 10.1146/annurev-biochem-013118-110817 · DOI
  8. Bonnerot, 2003, Functional redundancy of spb1p and a snr52-dependent mechanism for the 2’-O-ribose methylation of a conserved rrna position in yeast, Molecular Cell, 12, 1309, 10.1016/s1097-2765(03)00435-0 · DOI
  9. Bono, 2006, The crystal structure of the exon junction complex reveals how it maintains a stable grip on mrna, Cell, 126, 713, 10.1016/j.cell.2006.08.006 · DOI
  10. Brüning, 2018, RNA helicases mediate structural transitions and compositional changes in pre-ribosomal complexes, Nature Communications, 9, 10.1038/s41467-018-07783-w · DOI
  11. Burlacu, 2017, High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast, Nature Communications, 8, 10.1038/s41467-017-00761-8 · DOI
  12. Chen, 2018, Structural insights into mdn1, an essential AAA protein required for ribosome biogenesis, Cell, 175, 822, 10.1016/j.cell.2018.09.015 · DOI
  13. Cheng, 2020, 90S pre-ribosome transformation into the primordial 40S subunit, Science, 369, 1470, 10.1126/science.abb4119 · DOI
  14. Choudhury, 2021, The dexd box ATPase DDX55 is recruited to domain IV of the 28S ribosomal RNA by its C-terminal region, RNA Biology, 18, 1124, 10.1080/15476286.2020.1829366 · DOI
  15. Cruz, 2022, Sequence-Specific remodeling of a topologically complex RNP substrate by spb4, Nature Structural & Molecular Biology, 29, 1228, 10.1038/s41594-022-00874-9 · DOI
  16. Cui, 2021, Lead DEAD/H box helicase biomarkers with the therapeutic potential identified by integrated bioinformatic approaches in lung cancer, Computational and Structural Biotechnology Journal, 19, 261, 10.1016/j.csbj.2020.12.007 · DOI
  17. de la Cruz, 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, 10.1017/s1355838298981158 · DOI
  18. de la Cruz, 2015, Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo, Annual Review of Biochemistry, 84, 93, 10.1146/annurev-biochem-060614-033917 · DOI
  19. Dembowski, 2013, Has1 regulates consecutive maturation and processing steps for assembly of 60S ribosomal subunits, Nucleic Acids Research, 41, 7889, 10.1093/nar/gkt545 · DOI
  20. Du, 2020, Cryo-EM structure of 90s small ribosomal subunit precursors in transition states, Science, 369, 1477, 10.1126/science.aba9690 · DOI
  21. Emsley, 2004, Coot: model-building tools for molecular graphics, Acta Crystallographica. Section D, Biological Crystallography, 60, 2126, 10.1107/S0907444904019158 · DOI · Paper page
  22. Emsley, 2010, Features and development of coot, Acta Crystallographica. Section D, Biological Crystallography, 66, 486, 10.1107/S0907444910007493 · DOI · Paper page
  23. García-Gómez, 2011, Dynamics of the putative RNA helicase spb4 during ribosome assembly in Saccharomyces cerevisiae, Molecular and Cellular Biology, 31, 4156, 10.1128/MCB.05436-11 · DOI
  24. Gasse, 2015, Coordinated ribosomal ITS2 RNA processing by the Las1 complex integrating endonuclease, polynucleotide kinase, and exonuclease activities, Molecular Cell, 60, 808, 10.1016/j.molcel.2015.10.021 · DOI
  25. Gnanasundram, 2019, At least two molecules of the RNA helicase HAS1 are simultaneously present in pre-ribosomes during ribosome biogenesis, Nucleic Acids Research, 47, 10852, 10.1093/nar/gkz767 · DOI
  26. Goddard, 2018, UCSF chimerax: meeting modern challenges in visualization and analysis, Protein Science, 27, 14, 10.1002/pro.3235 · DOI · Paper page
  27. Granneman, 2006, Comprehensive mutational analysis of yeast DEXD/H box RNA helicases required for small ribosomal subunit synthesis, Molecular and Cellular Biology, 26, 1183, 10.1128/MCB.26.4.1183-1194.2006 · DOI
  28. Harms, 2014, EIF4B, eif4g and RNA regulate eif4a activity in translation initiation by modulating the eif4a conformational cycle, Nucleic Acids Research, 42, 7911, 10.1093/nar/gku440 · DOI
  29. Jaafar, 2021, Association of snr190 snorna chaperone with early pre-60S particles is regulated by the RNA helicase dbp7 in yeast, Nature Communications, 12, 10.1038/s41467-021-26207-w · DOI
  30. James, 1996, Genomic libraries and a host strain designed for highly efficient two-hybrid selection in yeast, Genetics, 144, 1425, 10.1093/genetics/144.4.1425 · DOI
  31. Janke, 2004, A versatile toolbox for PCR-based tagging of yeast genes: New fluorescent proteins, more markers and promoter substitution cassettes, Yeast, 21, 947, 10.1002/yea.1142 · DOI
  32. Kargas, 2019, Mechanism of completion of peptidyltransferase centre assembly in eukaryotes, eLife, 8, 10.7554/eLife.44904 · DOI
  33. Kater, 2017, Visualizing the assembly pathway of nucleolar pre-60S ribosomes, Cell, 171, 1599, 10.1016/j.cell.2017.11.039 · DOI
  34. Kater, 2020, Construction of the central protuberance and L1 stalk during 60S subunit biogenesis, Molecular Cell, 79, 615, 10.1016/j.molcel.2020.06.032 · DOI
  35. Kerpedjiev, 2015, Forna (force-directed RNA): Simple and effective online RNA secondary structure diagrams, Bioinformatics, 31, 3377, 10.1093/bioinformatics/btv372 · DOI
  36. Klinge, 2019, Ribosome assembly coming into focus, Nature Reviews. Molecular Cell Biology, 20, 116, 10.1038/s41580-018-0078-y · DOI
  37. Kressler, 2010, Driving ribosome assembly, Biochimica et Biophysica Acta, 1803, 673, 10.1016/j.bbamcr.2009.10.009 · DOI
  38. Kressler, 2017, A puzzle of life: crafting ribosomal subunits, Trends in Biochemical Sciences, 42, 640, 10.1016/j.tibs.2017.05.005 · DOI
  39. Lapeyre, 2004, Spb1p-directed formation of gm2922 in the ribosome catalytic center occurs at a late processing stage, Molecular Cell, 16, 663, 10.1016/j.molcel.2004.10.022 · DOI
  40. Lau, 2021, Structure of the maturing 90S pre-ribosome in association with the RNA exosome, Molecular Cell, 81, 293, 10.1016/j.molcel.2020.11.009 · DOI
  41. Leidig, 2014, 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle, Nature Communications, 5, 10.1038/ncomms4491 · DOI
  42. Liang, 2006, The helicase Has1p is required for snoRNA release from pre-rRNA, Molecular and Cellular Biology, 26, 7437, 10.1128/MCB.00664-06 · DOI
  43. Liebschner, 2019, Macromolecular structure determination using x-rays, neutrons and electrons: recent developments in phenix, Acta Crystallographica. Section D, Structural Biology, 75, 861, 10.1107/S2059798319011471 · DOI · Paper page
  44. Longtine, 1998, Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae, Yeast, 14, 953, 10.1002/(SICI)1097-0061(199807)14:10<953::AID-YEA293>3.0.CO;2-U · DOI
  45. Ma, 2017, Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by NMD3, lsg1, TIF6 and Reh1, Nature Structural & Molecular Biology, 24, 214, 10.1038/nsmb.3364 · DOI
  46. Mallam, 2012, Structural basis for RNA-duplex recognition and unwinding by the DEAD-box helicase Mss116p, Nature, 490, 121, 10.1038/nature11402 · DOI
  47. Malyutin, 2017, Nmd3 is a structural mimic of eIF5A, and activates the cpgtpase lsg1 during 60S ribosome biogenesis, The EMBO Journal, 36, 854, 10.15252/embj.201696012 · DOI
  48. Matsuo, 2014, Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export, Nature, 505, 112, 10.1038/nature12731 · DOI
  49. Mickolajczyk, 2022, The Midas domain of AAA mechanoenzyme mdn1 forms catch bonds with two different substrates, eLife, 11, 10.7554/eLife.73534 · DOI
  50. Mitterer, 2022, Rna folding and functions of RNA helicases in ribosome biogenesis, RNA Biology, 19, 781, 10.1080/15476286.2022.2079890 · DOI
  51. Oeffinger, 2009, Rrp17p is a eukaryotic exonuclease required for 5’ end processing of pre-60S ribosomal RNA, Molecular Cell, 36, 768, 10.1016/j.molcel.2009.11.011 · DOI
  52. Pettersen, 2021, UCSF chimerax: structure visualization for researchers, educators, and developers, Protein Science, 30, 70, 10.1002/pro.3943 · DOI
  53. Punjani, 2017, CryoSPARC: Algorithms for rapid unsupervised cryo-EM structure determination, Nature Methods, 14, 290, 10.1038/nmeth.4169 · DOI · Paper page
  54. Rocak, 2005, Characterization of the ATPase and unwinding activities of the yeast DEAD-box protein Has1p and the analysis of the roles of the conserved motifs, Nucleic Acids Research, 33, 999, 10.1093/nar/gki244 · DOI
  55. Rodríguez-Galán, 2013, Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives, Biochimica et Biophysica Acta, 1829, 775, 10.1016/j.bbagrm.2013.01.007 · DOI
  56. Rohou, 2015, CTFFIND4: Fast and accurate defocus estimation from electron micrographs, Journal of Structural Biology, 192, 216, 10.1016/j.jsb.2015.08.008 · DOI
  57. Sanghai, 2018, Modular assembly of the nucleolar pre-60S ribosomal subunit, Nature, 556, 126, 10.1038/nature26156 · DOI
  58. Schuller, 2018, Structure of the nuclear exosome captured on a maturing preribosome, Science, 360, 219, 10.1126/science.aar5428 · DOI
  59. Sengoku, 2006, Structural basis for RNA unwinding by the DEAD-box protein Drosophila vasa, Cell, 125, 287, 10.1016/j.cell.2006.01.054 · DOI
  60. Singh, 2021, Nucleolar maturation of the human small subunit processome, Science, 373, 10.1126/science.abj5338 · DOI
  61. Sosnowski, 2018, The cryoEM structure of the Saccharomyces cerevisiae ribosome maturation factor rea1, eLife, 7, 10.7554/eLife.39163 · DOI
  62. Talkish, 2012, Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae, Nucleic Acids Research, 40, 8646, 10.1093/nar/gks609 · DOI
  63. Theissen, 2008, Cooperative binding of ATP and RNA induces a closed conformation in a DEAD box RNA helicase, PNAS, 105, 548, 10.1073/pnas.0705488105 · DOI
  64. Thomas, 1989, Elevated recombination rates in transcriptionally active DNA, Cell, 56, 619, 10.1016/0092-8674(89)90584-9 · DOI
  65. Thoms, 2015, The exosome is recruited to RNA substrates through specific adaptor proteins, Cell, 162, 1029, 10.1016/j.cell.2015.07.060 · DOI
  66. Thoms, 2016, Concerted removal of the erb1-ytm1 complex in ribosome biogenesis relies on an elaborate interface, Nucleic Acids Research, 44, 926, 10.1093/nar/gkv1365 · DOI
  67. Ulbrich, 2009, Mechanochemical removal of ribosome biogenesis factors from nascent 60S ribosomal subunits, Cell, 138, 911, 10.1016/j.cell.2009.06.045 · DOI
  68. Waterhouse, 2018, SWISS-MODEL: Homology modelling of protein structures and complexes, Nucleic Acids Research, 46, W296, 10.1093/nar/gky427 · DOI
  69. Wegrecki, 2015, The structure of erb1-ytm1 complex reveals the functional importance of a high-affinity binding between two β-propellers during the assembly of large ribosomal subunits in eukaryotes, Nucleic Acids Research, 43, 11017, 10.1093/nar/gkv1043 · DOI
  70. Wu, 2016, Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes, Nature, 534, 133, 10.1038/nature17942 · DOI
  71. Yelland, 2023, A single 2’-O-methylation of ribosomal RNA gates assembly of a functional ribosome, Nature Structural & Molecular Biology, 30, 91, 10.1038/s41594-022-00891-8 · DOI
  72. Yu, 2022, DDX55 promotes hepatocellular carcinoma progression by interacting with BRD4 and participating in exosome-mediated cell-cell communication, Cancer Science, 113, 3002, 10.1111/cas.15393 · DOI
  73. Zhang, 2016, Gctf: real-time CTF determination and correction, Journal of Structural Biology, 193, 1, 10.1016/j.jsb.2015.11.003 · DOI
  74. Zheng, 2017, MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy, Nature Methods, 14, 331, 10.1038/nmeth.4193 · DOI
  75. Zhou, 2019, Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome, Nature Communications, 10, 10.1038/s41467-019-08880-0 · DOI
  76. Zhou, 2019, Cryo-em structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate, Protein & Cell, 10, 120, 10.1007/s13238-018-0526-7 · DOI
  77. Zivanov, 2018, New tools for automated high-resolution cryo-EM structure determination in RELION-3, eLife, 7, 10.7554/eLife.42166 · DOI
  78. Zivanov, 2020, Estimation of high-order aberrations and anisotropic magnification from cryo-EM data sets in RELION-3.1, IUCrJ, 7, 253, 10.1107/S2052252520000081 · DOI

Metadata

Authors
Mitterer, V., Thoms, M., Buschauer, R., Berninghausen, O., Hurt, E., & Beckmann, R.
Affiliations
  • Heidelberg University (DE)
  • Ludwig-Maximilians-Universität München (DE)
Corresponding author
  • Mitterer, Valentin
  • Hurt, Ed
  • Beckmann, Roland
ORCID
Venue
eLife
Publisher
eLife Sciences Publications, Ltd
Published
2023-03-17
Volume
12
ISSN
2050-084X (ISSN-L)
DOI
10.7554/elife.84877
PMC
PMC10154028
OpenAlex
W4327679299
Cited by
13
References
1
Citations by year
2026: 3 · 2025: 2 · 2024: 6 · 2023: 2
FWCI
1.15
Type
journal article
Language
en
Open access
Licence
Locations
  • eLife (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • European Research Council (885711-Human-Ribogenesis, ADG 741781 GLOWSOME)
  • Deutsche Forschungsgemeinschaft (HU363/15-2)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
cryo-EM structure
MeSH terms
Adenosine Triphosphatases, Ribosomal Proteins, Ribosomes, RNA Precursors, RNA, Ribosomal, Saccharomyces cerevisiae, RNA Helicases, Saccharomyces cerevisiae Proteins

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