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    The process of mRNA–tRNA translocation

    In the elongation cycle of translation, translocation is the process that advances the mRNA–tRNA moiety on the ribosome, to allow the next codon to mo...

    Research Article

    Biophysics and Computational Biology

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    The process of mRNA–tRNA translocation

    Joachim Frank [email protected], Haixiao Gao, Jayati Sengupta, +1 , Ning Gao, and Derek J. Taylor -1Authors Info & Affiliations

    December 11, 2007

    104 (50) 19671-19678

    https://doi.org/10.1073/pnas.0708517104

    Profile December 11, 2007 FREE ACCESS

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    Abstract

    In the elongation cycle of translation, translocation is the process that advances the mRNA–tRNA moiety on the ribosome, to allow the next codon to move into the decoding center. New results obtained by cryoelectron microscopy, interpreted in the light of x-ray structures and kinetic data, allow us to develop a model of the molecular events during translocation.

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    Synthesis of proteins from their building blocks, the amino acids, is a fundamental process in the cells of all living organisms, be it animal, plant, or bacteria. The discovery that the macromolecular assembly that facilitates this process, the ribosome, is highly conserved in all essential parts has lent additional credence to the idea of the unity of all life at the molecular level.

    The ribosome is a very large (2.4 MDa in eubacteria) ribonucleic-protein complex composed of two distinct subunits, the small subunit (30S) charged with the task of decoding the genetic message carried by the messenger RNA (mRNA), the large subunit (50S) to the catalysis of peptide bond formation. Instrumental for these fundamental processes is the interaction of the ribosome with transfer RNA (tRNA), a small L-shaped molecule that embodies in its various forms the association of each amino acid with a three-base “word” of the genetic code, the codon. Translation is based on the mutual recognition, by partial Watson–Crick pairing, between the codon on the mRNA and the anticodon of the tRNA carrying the corresponding amino acid. In facilitating tRNA selection, decoding, and the stepwise formation of the polypeptide, ribosomal RNA (rRNA) acts as both a structural framework and a catalyst.

    Despite the success in the elucidation of ribosomal structure by x-ray crystallography, the detailed mechanism by which translation of mRNA code into peptide proceeds is still only scantly understood. One of the obstacles we face is that although the process is complex and dynamic, x-ray crystallography represents the molecule in a static form—packed in a crystal, moreover, whose very stability depends on intermolecular contacts that are largely nonphysiological. Of crucial importance for the understanding of the multistep translation process is the knowledge of how the ribosome interacts with its ligands, notably (apart from the most crucial ligands mRNA and tRNAs) the various factors catalyzing initiation, elongation, termination, and recycling. To date, with the exception of ribosomal complexes containing eubacterial release (RF1 or RF2) (1) or recycling (RRF) (2, 3) factors, there exists no x-ray structure of a factor–ribosome complex. The crystal structures of individual subunits complexed with initiation (4–6) and recycling (7) factors have also been solved; however, crystallographic data of elongation factors bound to the ribosome are currently still not available. Moreover, to date, despite many efforts, no atomic structure is available for a eukaryotic ribosome.

    Increasingly, within the past decade, cryo-electron microscopy (cryo-EM) has filled this gap; in fact, the very first three-dimensional images of the ribosome (8, 9) were obtained by this technique well before the first x-ray structure was solved. In the mean time, cryo-EM has furnished quite detailed information on the interaction of the ribosome with initiation factors (10), elongation factors (11–14), release factors (15–18), and ribosome recycling factor (19, 20). Some of the corresponding complexes have been visualized for the 80S eukaryotic ribosome (21–23).

    As the initially low-resolution maps gave way to density maps in the subnanometer range, evidence of conformational changes both in the ribosome and its ligands was uncovered, and qualitative descriptions were increasingly replaced by quantitative measurements based on fitting and docking of x-ray structures. As a result, we can begin to piece together mechanistic models that explain kinetic, genetic, and other data collected over the five decades of ribosome research in structural terms.

    The Elongation Cycle, and Translocation

    In the course of protein synthesis, tRNA occupies successively the universally conserved A (aminoacyl), P (peptidyl), and E (exit) sites of the mRNA-programmed ribosome. The elongation cycle of translation is a repeating, three-step process catalyzed by the ribosome and two GTPases, EF-Tu and EF-G (eEF1A and eEF2 in eukaryotes). First, in decoding, EF-Tu delivers an aminoacylated-tRNA (aa-tRNA) molecule as part of the ternary complex of aa-tRNA·EF-Tu·GTP to the A/T site. The orientation with which tRNA enters the ribosome is not favorable for codon–anticodon interaction, and the anticodon stem-loop of the tRNA needs to be strongly kinked at the A/T site to allow the anticodon to interact with mRNA (24). If the aa-tRNA is cognate—i.e., when its three-base anticodon forms complementary base pairs with the codon in the messenger RNA—GTP is hydrolyzed, and the aa-tRNA, upon dissociation of EF-Tu·GDP, is accommodated in the ribosomal A site. The second step, the peptidyl-transferase reaction, is catalyzed by the rRNA of the large subunit and occurs immediately following the accommodation of the aa-tRNA. The transfer of the nascent peptide chain, from peptidyl-tRNA in the ribosomal P site to the accommodated aa-tRNA in the A site, results in the “pretranslocational” (PRE) state of the translating ribosome, with the deacylated tRNA in the P site and a peptidyl-tRNA in the A site.

    Source : www.pnas.org

    Bio 99 Pre Lec Quiz 9 Flashcards

    Start studying Bio 99 Pre Lec Quiz 9. Learn vocabulary, terms, and more with flashcards, games, and other study tools.

    Bio 99 Pre Lec Quiz 9

    29 studiers in the last hour

    The phosphorylation of eIF2 inhibits translation initiation by:

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    preventing the exchange of GTP for GDP.

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    Which of the following is not true of the process of nonsense-mediated mRNA decay?

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    The participation of the ribosome is not required.

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    Terms in this set (13)

    The phosphorylation of eIF2 inhibits translation initiation by:

    preventing the exchange of GTP for GDP.

    Which of the following is not true of the process of nonsense-mediated mRNA decay?

    The participation of the ribosome is not required.

    Which of the following events occur during translation initiation?

    Proteins bound to the 5' cap associate with ribosome associated proteins.

    The ribosome finds the start codon on the mRNA.

    fMet-tRNA binds to the P site of the ribosome.

    A helicase eliminates secondary structure in the 5' UTR of the mRNA.

    Which of the following is true of the process of eukaryotic mRNA degradation?

    The 5' cap is removed.

    The exosome degrades the mRNA to individual nucleotides.

    Degradation is at least partially carried out in processing bodies.

    Which of the following best describes the translational elongation process?

    The polypeptide chain is lengthened by synthesizing peptide bonds between amino acids.

    Which of the following statements explains how N-formylmethionine (fMet) is only associated with the 5' AUG initiation codon and not with internal AUG codons, given that methionine in both cases in encoded by an AUG in the mRNA.

    The N-formyl group attached to methionine prevents fMet from entering interior positions in a polypeptide.

    There are more than one tRNA with the 5' CAU 3' anticodon.

    Only Met-tRNA(Met) can bind first to the P site in the ribosome.

    Viral genomes can consist of:

    Double stranded DNA Single stranded DNA Double stranded RNA Single stranded RNA

    Which of the following is a function of the release factors in bacterial translation termination?

    Mediating the hydrolysis of the terminal peptidyl-tRNA bond.

    Releasing the last uncharged tRNA from the P site.

    Recognition of a stop codon.

    Which of the following is not true of the translocation step of translation elongation in bacteria?

    The tRNA associated with the polypeptide moves from the P site to the A site upon peptide bond formation.

    The Shine-Dalgarno mRNA sequence is:

    the ribosomal binding site on the mRNA.

    Which of the following is not true with regard to compacting nucleic acids?

    DNA viruses do not need to compact their genomes significantly because their genome is found as chromatin.

    Which of the following mRNA described would tend to have the longest half-life?

    An mRNA molecule containing one or more hairpin structures.

    Which of the following eukaryotic RNA processing events does not occur in the nucleus?

    Degradation of mRNA

    miRNA binding of mRNA.

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    Verified questions

    BIOLOGY

    Which term describes the boundary where two air masses meet? (a) anticyclone (b) cyclone (c) front (d) jet stream

    Verified answer BIOLOGY

    Support the argument that a forest fire impacts a population of birds that nest in the trees.

    Verified answer BIOLOGY

    You are given two strains of E. coli. The Hfr strain is

    \text { arg}^{+} a l a ^ { + } g l u ^ { + } p r o ^ { + } l e u ^ { + } T ^ { s } ; \text { the } F ^ { - } \text { strain is } a r g ^ { - } a l a ^ { - } g l u ^ { - } p r o ^ { - } l e u ^ { - } T ^ { r }

    arg + ala + glu + pro + leu + T s ; the F − strain is arg − ala − glu − pro − leu − T r

    All the markers are nutritional except T, which determines sensitivity or resistance to phage T1. The order of entry is as given, with arg + entering the recipient first and

    T^s T s

    last. You find that the

    F^- F −

    strain dies when exposed to penicillin

    (pen^s), (pen s ),

    but the Hfr strain does not

    (pen^r). (pen r ).

    How would you locate the locus for pen on the bacterial chromosome with respect to arg, ala, glu, pro, and leu? Formulate your answer in logical, well-explained steps, and draw explicit diagrams where possible.

    Source : quizlet.com

    Translation Elongation

    Translation Elongation

    During translation elongation, the peptidyltransferase reaction (the reaction by which amino acid residues are attached to each other to form proteins) is catalyzed by the rRNA itself.

    From: Cell Biology (Third Edition), 2017

    Related terms:

    Elongation FactorProtein BiosynthesisNested GeneMutationTranslation InitiationCodon

    View all Topics

    Elongation Factors: Translation☆

    D. Hughes, in Reference Module in Life Sciences, 2017

    Abstract

    Translation elongation factors perform critical functions in protein synthesis in all domains of life, including the delivery of aminoacyl-tRNAs into the ribosome, and the translocation of peptidyl-tRNA from the ribosomal A-site to the ribosomal P-site. Elongation factor Tu (EF-Tu, EF1-alpha) is a GTP-binding protein that is responsible for carrying each aminoacyl-tRNA to the ribosome, a process that involves hydrolysis of GTP and dissociation of the complex. EF-Ts is responsible for exchanging GDP for GTP on EF-Tu, ensuring that EF-Tu is reactivated for aminoacyl-tRNA binding after interacting with the ribosome. A third factor, EF-G (EF2 in eukaryotes), is responsible for catalyzing the translocation of peptidyl-tRNA from the A-site to the P-site. The elongation factors EF-Tu and EF-G are targets for several natural antibiotics, including fusidic acid (targets EF-G) which is used clinically to treat infections by Staphylococcus aureus.

    View chapter Purchase book

    Improved analyses of regulatory genome, transcriptome and gene function, mutation penetrance, and clinical applications

    Moyra Smith, in Progress in Genomic Medicine, 2022

    7.15 Translation of mRNA to proteins and associated defects leading to disease

    Steps in translation of mRNA to proteins were reviewed by Gabut et al. (2020). Early steps include passage and coupling of the 5′ mRNA regions to the 40s ribosome through action of the eif4 complex that merges with a bound preinitiation complex (PIC). The PIC includes GTP (Guanosine triphosphate), EIF3, EIF5, EIF1 subunits, and EIF1A that together with methionyl initiator TRNA bind to the 40s ribosome unit. The PIC complex was noted to scan the mRNA to identify the AUG initiation codon. Subsequent release of GTP (guanosine triphosphate) and bound initiation factors allow for recruitment and binding of EIF3B and the 80s ribosome unit. The aminoacyl TRNA binding site is exposed, and translation can begin.

    7.15.1 Aminoacyl tRNA synthases

    Translation elongation requires specific aminoacyl TRNAs being escorted to the ribosome by GTP-coupled elongation factor. Elongation requires movement along the ribosome-coupled mRNA, three nucleotides at a time to add aminoacids that have been bound to TRNAs. A specific aminoacyl tRNA synthetase must select the correct amino acid, and it must select the correct tRNA from the TRNA pool. Fuchs et al. (2019) reviewed aminoacyl tRNA synthetase defects noting that they were particularly encountered in children with psychomotor retardation and seizures.

    7.15.2 Noncanonical functions of aminoacyl tRNA synthetases

    Musier-Forsyth (2019) reported that the canonical function of aminoacyl tRNA synthetases is well-known and is attachment of cognate tRNAs to specific aminoacids. Additional noncanonical functions have been discovered. Those include regulation or splicing, stimulation of MTOR activity, and DNA repair.

    Rubio Gomez and Ibba (2020) reviewed aminoacyl tRNA synthetases and noted that they are not only essential for accurate translation of the genetic code, but they had roles in other processes.

    In their primary function, aminoacyl tRNA synthetases were noted to catalyze a two-step reaction. This involved esterification of aminoacid and hydrolysis of ATP to generate aminoacyl tRNA.

    Aminoacyl tRNA synthetase defects have been particularly associated with nervous system disorders.

    View chapter Purchase book

    Translation Elongation in Eukaryotes

    William C. Merrick, Anton A. Komar, in Encyclopedia of Biological Chemistry, 2004

    The Other Elongation Factor, eEF3

    A translation elongation factor unique to yeast and fungi is eEF3. This protein, which contains two-nucleotide-binding sites, appears to be required for the nucleotide-dependent release of the nonacylated tRNA from the ribosomal E site. As this protein is an essential gene product in yeast, it is surprising that an equivalent activity has not been identified in other eukaryotes. However, it has been noted in vitro that only elongation reactions using yeast ribosomes demonstrate the eEF3 requirement, and thus this requirement for eEF3 would appear to reflect unusual properties of the yeast ribosome compared to other eukaryotic ribosomes.

    View chapter Purchase book

    Non-Conventional Yeast Species for Recombinant Protein and Metabolite Production

    Hoang D. Do, ... Chrispian W. Theron, in Reference Module in Life Sciences, 2019

    3.2.3 The expression cassette: Emphasis on promoters

    3.2.3.1 Constitutive promoters

    The promoter of the translation elongation factor-1α (TEF1) gene (Müller et al., 1998), is the most widely used constitutive promoter in Y. lipolytica (Madzak and Beckerich, 2013). It is regarded as the strongest identified natural promoter for this yeast and hence serves a reference promoter for comparison of strength to other promoters. Another constitutive promoter described for this yeast is the promoter for ribosomal protein S7 (RPS7), which provides more moderate expression levels (Müller et al., 1998).

    Source : www.sciencedirect.com

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