Archaeal aminoacyl-tRNA synthetases interact with the ribosome to recycle tRNAs

Aminoacyl-tRNA synthetases (aaRS) are essential enzymes catalyzing the formation of aminoacyl-tRNAs, the immediate precursors for encoded peptides in ribosomal protein synthesis. Previous studies have suggested a link between tRNA aminoacylation and high-molecular-weight cellular complexes such as the cytoskeleton or ribosomes. However, the structural basis of these interactions and potential mechanistic implications are not well understood. To biochemically characterize these interactions we have used a system of two interacting archaeal aaRSs: an atypical methanogenic-type seryl-tRNA synthetase and an archaeal ArgRS. More specifically, we have shown by thermophoresis and surface plasmon resonance that these two aaRSs bind to the large ribosomal subunit with micromolar affinities. We have identified the L7/L12 stalk and the proteins located near the stalk base as the main sites for aaRS binding. Finally, we have performed a bioinformatics analysis of synonymous codons in the Methanothermobacter thermautotrophicus genome that supports a mechanism in which the deacylated tRNAs may be recharged by aaRSs bound to the ribosome and reused at the next occurrence of a codon encoding the same amino acid. These results suggest a mechanism of tRNA recycling in which aaRSs associate with the L7/L12 stalk region to recapture the tRNAs released from the preceding ribosome in polysomes.

[1]  M. Deutscher,et al.  An important role for the multienzyme aminoacyl-tRNA synthetase complex in mammalian translation and cell growth. , 2008, Molecular cell.

[2]  Alexey I Nesvizhskii,et al.  Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.

[3]  C. Francklyn,et al.  Methods for kinetic and thermodynamic analysis of aminoacyl-tRNA synthetases. , 2008, Methods.

[4]  N. Ban,et al.  Idiosyncratic Helix-Turn-Helix Motif in Methanosarcina barkeri Seryl-tRNA Synthetase Has a Critical Architectural Role* , 2009, Journal of Biological Chemistry.

[5]  Yuko Yamada,et al.  tRNA1Ser(G34) with the anticodon GGA can recognize not only UCC and UCU codons but also UCA and UCG codons. , 2003, Biochimica et biophysica acta.

[6]  J. Yewdell,et al.  RNA Binding Targets Aminoacyl-tRNA Synthetases to Translating Ribosomes* , 2011, The Journal of Biological Chemistry.

[7]  P. Bork,et al.  Proteome Organization in a Genome-Reduced Bacterium , 2009, Science.

[8]  M. Ibba,et al.  Aminoacyl-tRNA synthesis and translational quality control. , 2009, Annual review of microbiology.

[9]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[10]  Daniel N. Wilson,et al.  The structure and function of the eukaryotic ribosome. , 2012, Cold Spring Harbor perspectives in biology.

[11]  M. Mirande,et al.  The p43 Component of the Mammalian Multi-synthetase Complex Is Likely To Be the Precursor of the Endothelial Monocyte-activating Polypeptide II Cytokine* , 1997, The Journal of Biological Chemistry.

[12]  A. El'skaya,et al.  Novel complexes of mammalian translation elongation factor eEF1A.GDP with uncharged tRNA and aminoacyl-tRNA synthetase. Implications for tRNA channeling. , 2002, European journal of biochemistry.

[13]  Gregor Blaha,et al.  Mutations outside the anisomycin-binding site can make ribosomes drug-resistant. , 2008, Journal of molecular biology.

[14]  H. Beier,et al.  The tRNASer-isoacceptors and their genes in Nicotiana rustica: genome organization, expression in vitro and sequence analyses , 1994, Plant Molecular Biology.

[15]  N. Ban,et al.  Atomic structures of the eukaryotic ribosome. , 2012, Trends in biochemical sciences.

[16]  M. Ibba,et al.  Aminoacyl-tRNA synthetase complexes: molecular multitasking revealed. , 2008, FEMS microbiology reviews.

[17]  Eva Maria Novoa,et al.  Speeding with control: codon usage, tRNAs, and ribosomes. , 2012, Trends in genetics : TIG.

[18]  Yuji Kobayashi,et al.  Interaction among silkworm ribosomal proteins P1, P2 and P0 required for functional protein binding to the GTPase-associated domain of 28S rRNA. , 2002, Nucleic acids research.

[19]  V. Cherkasova,et al.  Analysis of genomic tRNA sets from Bacteria, Archaea, and Eukarya points to anticodon-codon hydrogen bonds as a major determinant of tRNA compositional variations. , 2008, RNA.

[20]  Wolfgang Baumeister,et al.  The three-dimensional organization of polyribosomes in intact human cells. , 2010, Molecular cell.

[21]  M. Deutscher,et al.  A channeled tRNA cycle during mammalian protein synthesis. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[22]  D. Boehringer,et al.  YidC and Oxa1 form dimeric insertion pores on the translating ribosome. , 2009, Molecular cell.

[23]  M. Ibba,et al.  Association of a multi‐synthetase complex with translating ribosomes in the archaeon Thermococcus kodakarensis , 2012, FEBS letters.

[24]  S. Yokoyama,et al.  The Escherichia coli argU10(Ts) Phenotype Is Caused by a Reduction in the Cellular Level of the argU tRNA for the Rare Codons AGA and AGG , 2004, Journal of bacteriology.

[25]  M. Mirande,et al.  Caenorhabditis elegans Evolves a New Architecture for the Multi-aminoacyl-tRNA Synthetase Complex* , 2011, The Journal of Biological Chemistry.

[26]  Jian-Qun Chen,et al.  Synonymous Codon Ordering: A Subtle but Prevalent Strategy of Bacteria to Improve Translational Efficiency , 2012, PloS one.

[27]  C. L. Harris.  An aminoacyl-tRNA synthetase complex in Escherichia coli , 1987, Journal of bacteriology.

[28]  I. Tanaka,et al.  Structural Basis for Translation Factor Recruitment to the Eukaryotic/Archaeal Ribosomes* , 2009, The Journal of Biological Chemistry.

[29]  Z. Kelman,et al.  Association between Archaeal Prolyl- and Leucyl-tRNA Synthetases Enhances tRNAPro Aminoacylation* , 2005, Journal of Biological Chemistry.

[30]  M. Prætorius-Ibba,et al.  An aminoacyl-tRNA synthetase:elongation factor complex for substrate channeling in archaeal translation , 2007, Nucleic acids research.

[31]  Nicol N. Schraudolph,et al.  A Role for Codon Order in Translation Dynamics , 2010, Cell.

[32]  M. Mirande.  Processivity of translation in the eukaryote cell: Role of aminoacyl‐tRNA synthetases , 2010, FEBS letters.

[33]  Paul F Agris,et al.  tRNA's modifications bring order to gene expression. , 2008, Current opinion in microbiology.

[34]  V. Ramakrishnan,et al.  What recent ribosome structures have revealed about the mechanism of translation , 2009, Nature.

[35]  G. Bec,et al.  Reconstitution in vitro of the valyl-tRNA synthetase-elongation factor (EF) 1 beta gamma delta complex. Essential roles of the NH2-terminal extension of valyl-tRNA synthetase and of the EF-1 delta subunit in complex formation. , 1994, The Journal of biological chemistry.

[36]  M. Yusupov,et al.  One core, two shells: bacterial and eukaryotic ribosomes , 2012, Nature Structural &Molecular Biology.

[37]  Sergey Steinberg,et al.  Compilation of tRNA sequences and sequences of tRNA genes , 2004, Nucleic Acids Res..

[38]  J. Ballesta,et al.  The large ribosomal subunit stalk as a regulatory element of the eukaryotic translational machinery. , 1996, Progress in nucleic acid research and molecular biology.

[39]  Dieter Braun,et al.  Protein-binding assays in biological liquids using microscale thermophoresis. , 2010, Nature communications.

[40]  M. Ibba,et al.  An Archaeal tRNA-Synthetase Complex that Enhances Aminoacylation under Extreme Conditions* , 2010, The Journal of Biological Chemistry.

[41]  M. Prætorius-Ibba,et al.  Functional Association between Three Archaeal Aminoacyl-tRNA Synthetases* , 2006, Journal of Biological Chemistry.

[42]  Daniel Boehringer,et al.  Cryo-EM structure of the archaeal 50S ribosomal subunit in complex with initiation factor 6 and implications for ribosome evolution. , 2012, Journal of molecular biology.

[43]  Julio O. Ortiz,et al.  The Native 3D Organization of Bacterial Polysomes , 2009, Cell.

[44]  Dieter Braun,et al.  Molecular interaction studies using microscale thermophoresis. , 2011, Assay and drug development technologies.

[45]  Y. Goldgur,et al.  Aminoacyl-tRNA synthetases from Haloarcula marismortui: an evidence for a multienzyme complex in a procaryotic system. , 1994, Biochemistry and molecular biology international.

[46]  M. Deutscher,et al.  Channeling of aminoacyl-tRNA for protein synthesis in vivo. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[47]  D. Söll,et al.  Structure of the unusual seryl‐tRNA synthetase reveals a distinct zinc‐dependent mode of substrate recognition , 2006, The EMBO journal.

[48]  M. Ibba,et al.  Structural and functional mapping of the archaeal multi‐aminoacyl‐tRNA synthetase complex , 2008, FEBS letters.

[49]  M. Mirande,et al.  Dynamic Organization of Aminoacyl-tRNA Synthetase Complexes in the Cytoplasm of Human Cells* , 2009, Journal of Biological Chemistry.

[50]  Y. Bessho,et al.  Life without tRNAArg–adenosine deaminase TadA: evolutionary consequences of decoding the four CGN codons as arginine in Mycoplasmas and other Mollicutes , 2013, Nucleic acids research.

[51]  D. Svergun,et al.  Structural Relationships Among the Ribosomal Stalk Proteins from the Three Domains of Life , 2008, Journal of Molecular Evolution.

[52]  G. Hong,et al.  Nucleic Acids Research , 2015, Nucleic Acids Research.

[53]  Marina V. Rodnina,et al.  Structural Basis for the Function of the Ribosomal L7/12 Stalk in Factor Binding and GTPase Activation , 2005, Cell.