Assembly of ribosomes and spliceosomes: complex ribonucleoprotein machines.

Ribosomes and spliceosomes are ribonucleoprotein nanomachines that catalyze translation of mRNA to synthesize proteins and splicing of introns from pre-mRNAs, respectively. Assembly of ribosomes involves more than 300 proteins and RNAs, and that of spliceosomes over 100 proteins and RNAs. Construction of these enormous ribonucleoprotein particles (RNPs) is a dynamic process, in which the nascent RNPs undergo numerous ordered rearrangements of RNA-RNA, RNA-protein, and protein-protein interactions. Here we outline similar principles that have emerged from studies of ribosome and spliceosome assembly. Constituents of both RNPs form subassembly complexes, which can simplify the task of assembly and segregate functions of assembly factors. Reorganization of RNP topology, and proofreading of proper assembly, are catalyzed by protein- or RNA-dependent ATPases or GTPases. Dynamics of intermolecular interactions may be facilitated or regulated by cycles of post-translational modifications. Despite this repertoire of tools, mistakes occur in RNP assembly or in processing of RNA substrates. Quality control mechanisms recognize and turnover misassembled RNPs and reject improper substrates.

[1]  E. Hurt,et al.  The AAA ATPase Rix7 powers progression of ribosome biogenesis by stripping Nsa1 from pre-60S particles , 2008, The Journal of cell biology.

[2]  V. G. Panse,et al.  Formation and Nuclear Export of Preribosomes Are Functionally Linked to the Small‐Ubiquitin‐Related Modifier Pathway , 2006, Traffic.

[3]  B. Schwer.  A conformational rearrangement in the spliceosome sets the stage for Prp22-dependent mRNA release. , 2008, Molecular cell.

[4]  D. Tollervey,et al.  Identification of a Regulated Pathway for Nuclear Pre-mRNA Turnover , 2000, Cell.

[5]  David Tollervey,et al.  60S pre‐ribosome formation viewed from assembly in the nucleolus until export to the cytoplasm , 2002, The EMBO journal.

[6]  Maurille J. Fournier,et al.  RNA-guided Nucleotide Modification of Ribosomal and Other RNAs* , 2003, The Journal of Biological Chemistry.

[7]  Arlen W. Johnson,et al.  Arx1 is a nuclear export receptor for the 60S ribosomal subunit in yeast. , 2007, Molecular biology of the cell.

[8]  J. Lauber,et al.  An evolutionarily conserved U5 snRNP‐specific protein is a GTP‐binding factor closely related to the ribosomal translocase EF‐2 , 1997, EMBO Journal.

[9]  J. Doudna,et al.  An essential GTPase promotes assembly of preribosomal RNA processing complexes. , 2005, Molecular cell.

[10]  D. Tollervey,et al.  Nuclear Export of 60S Ribosomal Subunits Depends on Xpo1p and Requires a Nuclear Export Sequence-Containing Factor, Nmd3p, That Associates with the Large Subunit Protein Rpl10p , 2001, Molecular and Cellular Biology.

[11]  Anna Marie Pyle,et al.  Crystal Structure of a Self-Spliced Group II Intron , 2008, Science.

[12]  J. Beggs,et al.  Yeast Ntr1/Spp382 Mediates Prp43 Function in Postspliceosomes , 2006, Molecular and Cellular Biology.

[13]  Soo-Chen Cheng,et al.  Both Catalytic Steps of Nuclear Pre-mRNA Splicing Are Reversible , 2008, Science.

[14]  E. C. Small,et al.  The EF-G-like GTPase Snu114p regulates spliceosome dynamics mediated by Brr2p, a DExD/H box ATPase. , 2006, Molecular cell.

[15]  K. Karbstein.  Role of GTPases in ribosome assembly. , 2007, Biopolymers.

[16]  J. Manley,et al.  PP1/PP2A phosphatases are required for the second step of Pre-mRNA splicing and target specific snRNP proteins. , 2006, Molecular cell.

[17]  D. Tollervey,et al.  Surveillance of nuclear‐restricted pre‐ribosomes within a subnucleolar region of Saccharomyces cerevisiae , 2006, The EMBO journal.

[18]  Roger E. Moore,et al.  Composition and functional characterization of the yeast spliceosomal penta-snRNP. , 2002, Molecular cell.

[19]  Ed Hurt,et al.  Nuclear export of ribosomal 60S subunits by the general mRNA export receptor Mex67-Mtr2. , 2007, Molecular cell.

[20]  K. Neugebauer,et al.  Cotranscriptional spliceosome assembly occurs in a stepwise fashion and requires the cap binding complex. , 2005, Molecular cell.

[21]  Ueli Aebi,et al.  A pre-ribosome with a tadpole-like structure functions in ATP-dependent maturation of 60S subunits. , 2004, Molecular cell.

[22]  J. Butler,et al.  5-Fluorouracil Enhances Exosome-Dependent Accumulation of Polyadenylated rRNAs , 2004, Molecular and Cellular Biology.

[23]  T. Hughes,et al.  Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. , 2007, Genes & development.

[24]  E. Koonin,et al.  G-patch: a new conserved domain in eukaryotic RNA-processing proteins and type D retroviral polyproteins. , 1999, Trends in biochemical sciences.

[25]  S. Baserga,et al.  The long unwinding road of RNA helicases. , 2007, Molecular cell.

[26]  Javier De Las Rivas,et al.  The 90S Preribosome Is a Multimodular Structure That Is Assembled through a Hierarchical Mechanism , 2007, Molecular and Cellular Biology.

[27]  M. Konarska,et al.  Splicing fidelity revisited , 2006, Nature Structural &Molecular Biology.

[28]  Melissa A. Mefford,et al.  U2 toggles iteratively between the stem IIa and stem IIc conformations to promote pre-mRNA splicing. , 2007, Genes & development.

[29]  C. Guthrie,et al.  A mechanism to enhance mRNA splicing fidelity: The RNA-dependent ATPase Prp16 governs usage of a discard pathway for aberrant lariat intermediates , 1993, Cell.

[30]  J. Beggs,et al.  Prp8 protein: at the heart of the spliceosome. , 2005, RNA.

[31]  J. Beggs,et al.  Functional contacts with a range of splicing proteins suggest a central role for Brr2p in the dynamic control of the order of events in spliceosomes of Saccharomyces cerevisiae. , 2001, Genetics.

[32]  I. J. van der Klei,et al.  Cytoplasmic Recycling of 60S Preribosomal Factors Depends on the AAA Protein Drg1 , 2007, Molecular and Cellular Biology.

[33]  E. Sontheimer,et al.  A role for ubiquitin in the spliceosome assembly pathway , 2008, Nature Structural &Molecular Biology.

[34]  Ping Li,et al.  Binding of the Human Prp31 Nop Domain to a Composite RNA-Protein Platform in U4 snRNP , 2007, Science.

[35]  J. Woolford,et al.  Interactions among Ytm1, Erb1, and Nop7 required for assembly of the Nop7-subcomplex in yeast preribosomes. , 2008, Molecular biology of the cell.

[36]  Xiang-Dong Fu,et al.  Functional integration of transcriptional and RNA processing machineries. , 2008, Current opinion in cell biology.

[37]  Letian Kuai,et al.  Polyadenylation of rRNA in Saccharomyces cerevisiae. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[38]  J. Doudna,et al.  GTP-dependent formation of a ribonucleoprotein subcomplex required for ribosome biogenesis. , 2006, Journal of molecular biology.

[39]  M. Ares,et al.  Rearrangement of competing U2 RNA helices within the spliceosome promotes multiple steps in splicing. , 2007, Genes & development.

[40]  C. Guthrie,et al.  Mechanical Devices of the Spliceosome: Motors, Clocks, Springs, and Things , 1998, Cell.

[41]  H. Urlaub,et al.  Isolation of an active step I spliceosome and composition of its RNP core , 2008, Nature.

[42]  S. Baserga,et al.  Crosstalk in gene expression: coupling and co-regulation of rDNA transcription, pre-ribosome assembly and pre-rRNA processing. , 2005, Current opinion in cell biology.

[43]  C. Will,et al.  Functional spliceosomal A complexes can be assembled in vitro in the absence of a penta-snRNP. , 2006, RNA.

[44]  Pei-Jung Lee,et al.  Dynamic Interactions of Ntr1-Ntr2 with Prp43 and with U5 Govern the Recruitment of Prp43 To Mediate Spliceosome Disassembly , 2007, Molecular and Cellular Biology.

[45]  M. Ares,et al.  Prp43p Is a DEAH-Box Spliceosome Disassembly Factor Essential for Ribosome Biogenesis , 2006, Molecular and Cellular Biology.

[46]  J. Soudet,et al.  The post-transcriptional steps of eukaryotic ribosome biogenesis , 2008, Cellular and Molecular Life Sciences.

[47]  J. Rain,et al.  The Splicing ATPase Prp43p Is a Component of Multiple Preribosomal Particles , 2005, Molecular and Cellular Biology.

[48]  Jonathan P Staley,et al.  Exon ligation is proofread by the DExD/H-box ATPase Prp22p , 2006, Nature Structural &Molecular Biology.

[49]  R. Wickner,et al.  Linking the 3′ Poly(A) Tail to the Subunit Joining Step of Translation Initiation: Relations of Pab1p, Eukaryotic Translation Initiation Factor 5B (Fun12p), and Ski2p-Slh1p , 2001, Molecular and Cellular Biology.

[50]  Uttiya Basu,et al.  The Saccharomyces cerevisiae 60 S Ribosome Biogenesis Factor Tif6p Is Regulated by Hrr25p-mediated Phosphorylation* , 2008, Journal of Biological Chemistry.

[51]  E. Petfalski,et al.  RNA Degradation by the Exosome Is Promoted by a Nuclear Polyadenylation Complex , 2005, Cell.

[52]  B. Schwer,et al.  Ntr1 activates the Prp43 helicase to trigger release of lariat-intron from the spliceosome. , 2007, Genes & development.

[53]  P. Mitchell,et al.  Degradation of ribosomal RNA precursors by the exosome. , 2000, Nucleic acids research.

[54]  M. Fournier,et al.  The Helicase Has1p Is Required for snoRNA Release from Pre-rRNA , 2006, Molecular and Cellular Biology.

[55]  David Tollervey,et al.  A pre-ribosome-associated HEAT-repeat protein is required for export of both ribosomal subunits. , 2004, Genes & development.

[56]  J. Gallagher,et al.  RNA polymerase I transcription and pre-rRNA processing are linked by specific SSU processome components. , 2004, Genes & development.

[57]  C. Query,et al.  Competition between the ATPase Prp5 and branch region-U2 snRNA pairing modulates the fidelity of spliceosome assembly. , 2007, Molecular cell.

[58]  R. Parker,et al.  Cytoplasmic degradation of splice-defective pre-mRNAs and intermediates. , 2003, Molecular cell.

[59]  T. Hughes,et al.  The Splicing Factor Prp43p, a DEAH Box ATPase, Functions in Ribosome Biogenesis , 2006, Molecular and Cellular Biology.

[60]  C. Guthrie,et al.  Genetic Analysis Reveals a Role for the C Terminus of the Saccharomyces cerevisiae GTPase Snu114 During Spliceosome Activation , 2005, Genetics.

[61]  M. Konarska,et al.  Suppression of multiple substrate mutations by spliceosomal prp8 alleles suggests functional correlations with ribosomal ambiguity mutants. , 2004, Molecular cell.

[62]  Duncan J. Smith,et al.  "Nought may endure but mutability": spliceosome dynamics and the regulation of splicing. , 2008, Molecular cell.

[63]  David Tollervey,et al.  Depletion of the Yeast Nuclear Exosome Subunit Rrp6 Results in Accumulation of Polyadenylated RNAs in a Discrete Domain within the Nucleolus , 2007, Molecular and Cellular Biology.

[64]  E. Hurt,et al.  Arx1 functions as an unorthodox nuclear export receptor for the 60S preribosomal subunit. , 2007, Molecular cell.

[65]  Daniel F Tardiff,et al.  Arrested yeast splicing complexes indicate stepwise snRNP recruitment during in vivo spliceosome assembly. , 2006, RNA.

[66]  E. Petfalski,et al.  Hrr25-dependent phosphorylation state regulates organization of the pre-40S subunit , 2006, Nature.

[67]  D. Tollervey,et al.  The Putative RNA Helicase Dbp4p Is Required for Release of the U14 snoRNA from Preribosomes in Saccharomyces cerevisiae. , 2005, Molecular cell.