Translation Mechanisms
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Edited By:Jacques LapointeUniversite Laval Léa Brakier-Gingras University of Montreal ISBN: 978-0-306-47839-0 Published: 2003-06-26 |
Chapters available from this book
Translational Elongation
Poul Nissen, Jens Nyborg and Brian F.C. Clark
The elongation phase of protein biosynthesis adds one amino acid at a time to the growing polypeptide according to the sequence information contained in the mRNA. The process is catalyzed by elongation factors of which two are GTP/GDP binding proteins (G-proteins). Several crystal structures illu...
Crystal Structures of the Ribosome and Ribosomal Subunits
Brian T. Wimberly
Efforts to understand the structural basis for translational mechanisms have long been hampered by the low resolution of ribosome structures. This impasse suddenly and dramatically changed in 2000 as a result of the determination of crystal structures of entire ribosomes and of ribosomal subun...
Transfer RNA Structure and Identity
Richard Giegé and Magali Frugier
The structure of tRNA and its relationship with the biological necessity of specific tRNA aminoacylation reactions, in other words with identity, is reviewed. New structural data show the typical L-shaped tRNA architecture in great detail and highlight how adequate rigidity and plasticit...
Translational Termination, Ribosome Recycling and tmRNA Function
R.H. Buckingham and M. Ehrenberg
The function of peptide release factors has been greatly clarified in recent years by experiments using improved in vitro systems, analysis of mutant factors and new structural information. In class I release factors, which carry stop codon specificity, important domains have been identi...
Mitochondrial tRNA Aminoacylation and Human Diseases
Catherine Florentz and Marie Sissler
The human mitochondrial (mt) genome encodes for only 13 proteins which are all subunits of transmembranar respiratory chain complexes. These complexes contribute to a major mt functions namely the synthesis of energy in the way of ATP. Translation of the mRNAs is performed by a set of 22...
Control of Stable RNA Synthesis
Melanie M. Barker and Richard L. Gourse
Transcription of rRNA is the ratelimiting step in ribosome production. In rapidly dividing Escherichia coli, ribosome synthesis represents the single largest expenditure of biosynthetic energy. At the fastest growth rates, over 70% of all transcription derives from the s...
Antibiotics as Indicators of the Functional Components of the Ribosome
D. Fourmy, S. Yoshizawa and S. Douthwaite
The inhibitory action of many antibiotics is to block directly the synthesis of proteins on the bacterial ribosome. How these antibiotics interact with their targets on the bacerial ribosome has been the focus of considerable scrutiny over the last four decades. It was envisaged that elucidation of ...
Inhibitors of Aminoacyl-tRNA Synthetases as Antibiotics and Tools for Structural and Mechanistic Studies
Robert Chênevert, Stéphane Bernier and Jacques Lap
Aminoacyl-tRNA synthetases (aaRS) catalyze the esterification of a particular tRNA with its corresponding amino acid. In the first reaction step, the appropriate amino acid is recognized by the enzyme and reacts with ATP to form an enzyme-bound mixed anhydride; in the second step, thi...
The Role of the Exosome and Ski Complexes in mRNA Turnover
Philip Mitchell
The amount of protein synthesized from an individual mRNA reflects both its translation efficiency and stability. The translation and turnover of eukaryotic mRNAs are closely linked; alterations in translation can influence decay and vice versa, and the cap and poly(A) tail structures of...
Ribosomes on Standby: A Prelude to Translational (Re)Initiation
Maarten H. de Smit and Jan van Duin
Prokaryotic ribosomes, in landing at internal ribosome binding sites, have to deal with the secondary structure that is present in every RNA molecule. In previous work, we have described how the binding of ribosomes competes with the spontaneous folding of the mRNA. The strength of the m...
Mechanism of Translation Initiation in Eukaryotes
Francis Poulin and Nahum Sonenberg
The initiation of protein synthesis consists in the recruitment of a ribosome·initiator tRNA complex to the initiation codon of a messenger RNA. In prokaryotes, this process involves the direct interaction of the ribosomal RNA with the mRNA. In contrast, eukaryotes have evolved a sophist...
Recoding: Site or mRNA-Specific Alteration of Genetic Readout Utilized for Gene Expression
Ivaylo P. Ivanov, Olga L. Gurvich, Raymond F. Gesteland and John F. Atkins
A minority of genes in probably all organisms rely on "recoding" for translation of their mRNAs. Recoding can involve a proportion of ribosomes changing frame at a specific site in response to signals in mRNA, or some ribosomes reading through a stop codon to insert a standa...
The End in Sight: Poly(A), Translation and mRNA Stability in Eukaryotes
Thomas Preiss
All nuclear-encoded eukaryotic messenger RNAs possess a 5' cap structure (m7GpppN) and, with a few exceptions, also a 3' poly(A) tail. These modifications are added as part of the mRNA processing pathway during or immediately after transcription in the nucleus. Subsequently, t...
The Directed Evolution of Organismal Chemistry: Unnatural Amino Acid Incorporation
Jamie M. Bacher and Andrew D. Ellington
Life on earth is tremendously diverse. Organisms that have adapted to extreme environments are surprisingly ubiquitous. However, all known extremophiles have adapted to unusual physicochemical environments using the same underlying biochemistry. Although small perturbations in the geneti...
In vitro Tools and in vivo Engineering: Incorporation of Unnatural Amino Acids into Proteins
Thomas J. Magliery, Miro Pastrnak, J. Christopher Anderson, Stephen W. Santoro, Brad Herberich, Eric Meggers, Lei Wang and Peter G. Schultz
Unnatural protein mutagenesis has dramatically enhanced our ability to probe the basis of structure and function in protein biochemistry and has enabled us to create proteins with entirely novel properties. Recent advances in in vitro unnatural amino acid incorporation have expanded the ...
Aminoacyl-Transfer RNA Maturation
Sylvain Blanquet, Yves Mechulam, Emmanuelle Schmitt and Lionel Vial
Some aminoacylated tRNAs are subject to specific maturation. These maturations can be necessary either to produce the correct aminoacylated species for the ribosome or to regenerate toxic or nonproductive tRNAs produced after errors of the translational machinery. This chapter will first...
Tests of a Stereochemical Genetic Code
Rob Knight, Laura Landweber and Michael Yarus
Does the genetic code assign similar codons to similar amino acids because of chemical interactions between them? Unlike adaptive explanations, which can only explain the relative positions of amino acids in the code, stereochemical explanations could tie codon assignments to absolute, v...
Aminoacyl-tRNA Synthetase Structure and Evolution
Dieter Söll and Michael Ibba
The pairing of codons in mRNA with tRNA anticodons determines the order of amino acids in a protein. It is therefore imperative for accurate translation that tRNAs are only coupled to amino acids corresponding to the RNA anticodon. This is mostly, but not exclusively, achieved by the dir...
Probing the Role of Ribosomal RNA in Protein Synthesis Through Mutagenesis
L. Brakier-Gingras, F. Bélanger and M. O'Connor
This review presents a survey of the classic and novel approaches developed for the study of the effects of mutations in ribosomal RNA of Escherichia coli on ribosome structure and function. It analyzes representative examples of these mutations at the peptidyl transferase ...
Conformational Dynamics within the Ribosome
J. Stephen Lodmell and Scott P. Hennelly
The ribosome is a dynamic particle that undergoes an iterative series of conformational changes during translation. Individual structural changes in the ribosome in response to tRNA or mRNA binding, initiation or elongation factor binding, buffer conditions, and antibiotic effects have b...
Transfer RNA-Dependent Amino Acid Discrimination by Aminoacyl-tRNA Synthetases
Tamara L. Hendrickson and Paul Schimmel
Aminoacyl-tRNA synthetases (AARSs) form a direct connection between the trinucleotide codons of the genetic code and their corresponding amino acids. Each AARS catalyzes the biosynthesis of a specific, cognate set of AA-tRNAAA isoacceptors. In some cases, the cognate amino aci...
Regulation of the Expression of Aminoacyl-tRNA Synthetases and Translation Factors
Harald Putzer and Soumaya Laalami
Aminoacyl-tRNA synthetases and translation factors are key enzymes required for protein biosynthesis. Escherichia coli and Bacillus subtilis often use different strategies to regulate the expression of the genes encoding these enzymes. Synthesis of several E. coli Am...
Polyadenylation and Degradation of RNA in Prokaryotes
Philippe Régnier, Paulo E. Marujo
Polyadenylation is a postranscriptional modification of RNA found in all cells and in organelles. In bacteria, a small fraction of RNA harbors oligo(A) tails which are mostly shorter than 20 As. Poly(A) polymerase I of Escherichia coli can adenylate mRNAs, and small RNA regulators...
The Interplay Between Translation and mRNA Decay in Procaryotes: A Discussion on Current Paradigms
Marc Dreyfus and Susan Joyce
We discuss here the different aspects of the translation-mRNA degradation relationship in bacteria. Whereas mRNAs are usually protected against endonucleases by the presence of ribosomes, protection does not invariably require direct shielding of the cleavage sites. Possible mechanisms u...
Nonsense-Mediated mRNA Decay in Mammalian Cells: From pre-mRNA Processing to mRNA Translation and Degradation
Lynne E. Maquat
Studies of nonsense-mediated messenger RNA decay (NMD) in mammalian cells have lent great insight into splicing-dependent modifications of mRNA and how these modifications recruit factors that are required for NMD. In demonstrating that NMD takes place on cap binding protein (CBP)80-boun...
