Genomes and Genes
translational peptide chain elongation
Summary: A process of GENETIC TRANSLATION, when an amino acid is transferred from its cognate TRANSFER RNA to the lengthening chain of PEPTIDES.
- Fluitt A, Pienaar E, Viljoen H. Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis. Comput Biol Chem. 2007;31:335-46 pubmed..06ms and the average delay to process a near-cognate aa-tRNA is 10.45ms and (vii) the model also provides estimates of the vacancy times of the A site of the ribosome - an important factor in frameshifting. ..
- Saini P, Eyler D, Green R, Dever T. Hypusine-containing protein eIF5A promotes translation elongation. Nature. 2009;459:118-21 pubmed publisher..Because eIF5A is a structural homologue of the bacterial protein EF-P, we propose that eIF5A/EF-P is a universally conserved translation elongation factor. ..
- Senamaud Beaufort C, Leforestier E, Saison Behmoaras T. Short pyrimidine stretches containing mixed base PNAs are versatile tools to induce translation elongation arrest and truncated protein synthesis. Oligonucleotides. 2003;13:465-78 pubmed..The remarkable efficacy of the tridecamer PNAs in arresting translation elongation of HIV-1 integrase mRNA is explained by their ability to form stable triplexes at neutral pH with short purine sequences. ..
- Glick B, Ganoza M. Identification of a soluble protein that stimulates peptide bond synthesis. Proc Natl Acad Sci U S A. 1975;72:4257-60 pubmed..We suggest that this extraribosomal factor modulates the intrinsic activity of ribosomes to catalyze peptide-bond synthesis, and regard it as a new factor required for peptide chain elongation, which we call EF-P. ..
- Feinberg J, Joseph S. Identification of molecular interactions between P-site tRNA and the ribosome essential for translocation. Proc Natl Acad Sci U S A. 2001;98:11120-5 pubmed..These results establish a set of functional interactions between P-site tRNA and 23S rRNA that are essential for translocation. ..
- Vanzi F, Vladimirov S, Knudsen C, Goldman Y, Cooperman B. Protein synthesis by single ribosomes. RNA. 2003;9:1174-9 pubmed..This work opens the way for application of biophysical techniques, originally developed for the classical motor proteins, to the understanding of protein biosynthesis. ..
- Kamath A, Chakraburtty K. Role of yeast elongation factor 3 in the elongation cycle. J Biol Chem. 1989;264:15423-8 pubmed..and Kamath, A. (1988) Int. J. Biochem. 20, 581-590). However, we failed to demonstrate the effect of EF-3 in binding aa-tRNA to such a heterologous combination of the ribosomal subunits. ..
- Dick F, Trumpower B. Heterologous complementation reveals that mutant alleles of QSR1 render 60S ribosomal subunits unstable and translationally inactive. Nucleic Acids Res. 1998;26:2442-8 pubmed..Velocity gradient analyses of the hybrid ribosomes after exposure to high concentrations of salt indicate that the decreased activity is due to lability of the hybrid 60S subunits. ..
- Gregio A, Cano V, Avaca J, Valentini S, Zanelli C. eIF5A has a function in the elongation step of translation in yeast. Biochem Biophys Res Commun. 2009;380:785-90 pubmed publisher..Taken together, these results not only reinforce a role for eIF5A in translation but also strongly support a function for eIF5A in the elongation step of protein synthesis. ..
- Zanelli C, Maragno A, Gregio A, Komili S, Pandolfi J, Mestriner C, et al. eIF5A binds to translational machinery components and affects translation in yeast. Biochem Biophys Res Commun. 2006;348:1358-66 pubmed..Our results re-establish a function for eIF5A in translation and suggest a role for this factor in translation elongation instead of translation initiation. ..
- Ruiz Echevarria M, Gonzalez C, Peltz S. Identifying the right stop: determining how the surveillance complex recognizes and degrades an aberrant mRNA. EMBO J. 1998;17:575-89 pubmed..Further, the results indicate that the STE functions in the context of the GCN4 transcript to inactivate the NMD pathway. ..
- Christian B, Haque E, Spremulli L. Ribosome shifting or splitting: it is all up to the EF-G. Mol Cell. 2009;35:400-2 pubmed publisher..Tsuboi et al. (2009) now show that the function of EF-G2(mt) is not in elongation but, rather, in ribosome recycling. ..
- Tapio S, Isaksson L. Base 2661 in Escherichia coli 23S rRNA influences the binding of elongation factor Tu during protein synthesis in vivo. Eur J Biochem. 1991;202:981-4 pubmed..The interaction between this base and EF-Tu is strongly influenced by the structure of ribosomal protein S12. ..
- Erie D. The many conformational states of RNA polymerase elongation complexes and their roles in the regulation of transcription. Biochim Biophys Acta. 2002;1577:224-39 pubmed..The role of each of the conformational states in elongation is then discussed in detail. Finally, an integrated mechanism of elongation is presented, bringing together the panoply of experiments. ..
- Xing C, Bitzer D, Alexander W, Vouk M, Stomp A. Identification of protein-coding sequences using the hybridization of 18S rRNA and mRNA during translation. Nucleic Acids Res. 2009;37:591-601 pubmed publisher..This, in turn, can be utilized for the identification of protein-coding sequences. ..
- Kalies K, Stokes V, Hartmann E. A single Sec61-complex functions as a protein-conducting channel. Biochim Biophys Acta. 2008;1783:2375-83 pubmed publisher..Collectively, our data suggest that the active protein-conducting channel in the ER is formed by a single Sec61-complex. ..
- Zhang L, Aro E. Synthesis, membrane insertion and assembly of the chloroplast-encoded D1 protein into photosystem II. FEBS Lett. 2002;512:13-8 pubmed
- Picking W, Picking W, Ma C, Hardesty B. A synthetic alanyl-initiator tRNA with initiator tRNA properties as determined by fluorescence measurements: comparison to a synthetic alanyl-elongator tRNA. Nucleic Acids Res. 1991;19:5749-54 pubmed..Also, the effect of erythromycin on their fluorescence is quite different, suggesting that the probes and presumably the alanine moiety to which they are covalently linked are in different positions on the ribosomes. ..
- Artsimovitch I, Landick R. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell. 2002;109:193-203 pubmed..This activity predicts a cumulative antitermination model for RfaH's regulation of ops-containing operons in vivo. ..
- Ringquist S, Schneider D, Gibson T, Baron C, Bock A, Gold L. Recognition of the mRNA selenocysteine insertion sequence by the specialized translational elongation factor SELB. Genes Dev. 1994;8:376-85 pubmed..Cis-acting mRNA regulatory elements can tether protein factors to the translation complex during protein synthesis. ..
- Seggerson K, Tang L, Moss E. Two genetic circuits repress the Caenorhabditis elegans heterochronic gene lin-28 after translation initiation. Dev Biol. 2002;243:215-25 pubmed..The role of lin-4 may be to initiate or potentiate the lin-4-independent circuit. We speculate that a parallel lin-4-independent regulatory mechanism regulates the expression of lin-14. ..
- Gershon P, Shi X, Hodel A. Evidence that the RNA methylation and poly(A) polymerase stimulatory activities of vaccinia virus protein VP39 do not impinge upon one another. Virology. 1998;246:253-65 pubmed..Interaction at one of these sites was stabilized by the cap structure. Additional experiments indicated that RNA molecules undergoing poly(A) tail elongation by the VP55-VP39 heterodimer are not favored as cap-methylation substrates. ..
- Grentzmann G, Kelly P, Laalami S, Shuda M, Firpo M, Cenatiempo Y, et al. Release factor RF-3 GTPase activity acts in disassembly of the ribosome termination complex. RNA. 1998;4:973-83 pubmed..Based on our results, we propose a model of how RF3 might function in translational termination and ribosome recycling. ..
- Tork S, Hatin I, Rousset J, Fabret C. The major 5' determinant in stop codon read-through involves two adjacent adenines. Nucleic Acids Res. 2004;32:415-21 pubmed..We propose that the mRNA structure, depending on the nucleotides in the P site, is the main 5' determinant of read-through efficiency. ..
- Nakayama K, Nakanishi Shindo Y, Tanaka A, Haga Toda Y, Jigami Y. Substrate specificity of alpha-1,6-mannosyltransferase that initiates N-linked mannose outer chain elongation in Saccharomyces cerevisiae. FEBS Lett. 1997;412:547-50 pubmed..These results suggest that Och1p is an initiation specific alpha-1,6-mannosyltransferase that requires the intact structure of Man8GlcNAc for efficient mannose outer chain initiation. ..
- Wen K, Orgel L. The specificity of peptide chain extension by N-carboxyanhydrides. Orig Life Evol Biosph. 2001;31:241-8 pubmed..The homochiral addition was always the more efficient reaction; the enantiospecificity was large in some cases but very small in others. In every case Ala3Glu10 was elongated more efficiently than Glu10. ..
- Stagg S, Valle M, Agrawal R, Frank J, Harvey S. Problems with the transorientation hypothesis. RNA. 2002;8:1093-4 pubmed
- Ganoza M, Kiel M, Aoki H. Evolutionary conservation of reactions in translation. Microbiol Mol Biol Rev. 2002;66:460-85, table of contents pubmed..The possible mechanisms of a new initiation factor and two elongation factors are discussed in this context. ..
- Fulle S, Gohlke H. Statics of the ribosomal exit tunnel: implications for cotranslational peptide folding, elongation regulation, and antibiotics binding. J Mol Biol. 2009;387:502-17 pubmed publisher..In order to explain antibiotics selectivity, action, and resistance, according to these results, differences in the degrees of freedom of the binding regions may need to be considered. ..
- Wang S, Sakai H, Wiedmann M. NAC covers ribosome-associated nascent chains thereby forming a protective environment for regions of nascent chains just emerging from the peptidyl transferase center. J Cell Biol. 1995;130:519-28 pubmed..Since NAC is not a core ribosomal protein, the emergence of nascent chains from the ribosome may be more dynamic than previously thought. ..
- Alekhina O, Vassilenko K, Spirin A. Translation of non-capped mRNAs in a eukaryotic cell-free system: acceleration of initiation rate in the course of polysome formation. Nucleic Acids Res. 2007;35:6547-59 pubmed..The eIF4F-mediated circularization of polysomes may be considered as a possible event that leads to the re-initiation switch and the resultant acceleration effect...
- Lovmar M, Ehrenberg M. Rate, accuracy and cost of ribosomes in bacterial cells. Biochimie. 2006;88:951-61 pubmed..error levels about 1 per million. The future prospect of extensive integration of biochemistry, cell physiology and population genetics is discussed in the light of the maximal fitness theory and other, similar, theoretical approaches. ..
- Rodnina M, Semenkov I, Savelsbergh A, Katunin V, Peske F, Wilden B, et al. [Mechanism of tRNA translocation on the ribosome]. Mol Biol (Mosk). 2001;35:655-65 pubmed
- McGarry K, Walker S, Wang H, Fredrick K. Destabilization of the P site codon-anticodon helix results from movement of tRNA into the P/E hybrid state within the ribosome. Mol Cell. 2005;20:613-22 pubmed..The effects of G2252U are suppressed by C2394A, further implicating the P/E state in mRNA destabilization. This work uncovers a functional attribute of the P/E state crucial for understanding translation. ..
- Salas Marco J, Bedwell D. Discrimination between defects in elongation fidelity and termination efficiency provides mechanistic insights into translational readthrough. J Mol Biol. 2005;348:801-15 pubmed..We used this misincorporation reporter in conjunction with a readthrough reporter system to show that alterations at different regions of the ribosome influence elongation fidelity and termination efficiency to different extents. ..
- Sen R, King R, Weisberg R. Modification of the properties of elongating RNA polymerase by persistent association with nascent antiterminator RNA. Mol Cell. 2001;7:993-1001 pubmed..Some, but not all, complementary oligonucleotides inhibited antitermination. Finally, cleavage of the RNA between putL and the 3'-end released putL RNA from the stalled complex and prevented antitermination. ..
- Guo Z, Shao N. Glycopeptide and glycoprotein synthesis involving unprotected carbohydrate building blocks. Med Res Rev. 2005;25:655-78 pubmed
- Elliott T, Bodmer H, Townsend A. Recognition of out-of-frame major histocompatibility complex class I-restricted epitopes in vivo. Eur J Immunol. 1996;26:1175-9 pubmed..Experiments in which the mutant gene product was processed in the endoplasmic reticulum of target cells suggested that the apparent suppression occurred during polypeptide extension. ..
- Kim H, Puglisi J, Chu S. Fluctuations of transfer RNAs between classical and hybrid states. Biophys J. 2007;93:3575-82 pubmed..The antibiotic viomycin, a translocation inhibitor, suppresses tRNA dynamics, suggesting that the enhanced fluctuations of tRNAs after peptide-bond formation drive spontaneous attempts at translocation by the ribosome. ..
- Tan G, DeBlasio A, Mankin A. Mutations in the peptidyl transferase center of 23 S rRNA reveal the site of action of sparsomycin, a universal inhibitor of translation. J Mol Biol. 1996;261:222-30 pubmed..Our findings provide further support for the idea that rRNA may be directly involved in interaction with antibiotics and the catalysis of the peptide bond formation. ..
- Ichetovkin I, Abramochkin G, Shrader T. Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain. J Biol Chem. 1997;272:33009-14 pubmed..Overall, our results identified an essential core of an L/F-transferase and revealed that a peptidyltransferase catalyst may be constructed from approximately 120 amino acids...
- Ismail N, Crawshaw S, High S. Active and passive displacement of transmembrane domains both occur during opsin biogenesis at the Sec61 translocon. J Cell Sci. 2006;119:2826-36 pubmed
- Frøsig C, Sajan M, Maarbjerg S, Brandt N, Roepstorff C, Wojtaszewski J, et al. Exercise improves phosphatidylinositol-3,4,5-trisphosphate responsiveness of atypical protein kinase C and interacts with insulin signalling to peptide elongation in human skeletal muscle. J Physiol. 2007;582:1289-301 pubmed..Furthermore, endurance exercise increased the responsiveness of aPKC to PIP3 providing a possible link to improved insulin-stimulated glucose uptake after exercise. ..
- Talens A, Boon K, Kraal B, Bosch L. Translational activities of EF-Tu [G222D] which cannot be reconciled with the classical scheme of the polypeptide chain elongation cycle. Biochem Biophys Res Commun. 1996;225:961-7 pubmed..Vijgenboom, E., & Zeef, L.A.H., 1996, Biochemistry 36). ..
- Hou Y, Yaskowiak E, March P. Carboxyl-terminal amino acid residues in elongation factor G essential for ribosome association and translocation. J Bacteriol. 1994;176:7038-44 pubmed..We propose that all of these mutations are present in a domain that is essential for ribosome association and that GTP hydrolysis was deficient as a secondary consequence of impaired binding to 70S ribosomes. ..
- Kootstra N, Schuitemaker H. Phenotype of HIV-1 lacking a functional nuclear localization signal in matrix protein of gag and Vpr is comparable to wild-type HIV-1 in primary macrophages. Virology. 1999;253:170-80 pubmed..In conclusion, our results confirm the dependency of the process of HIV-1 reverse transcriptase on cell proliferation in primary macrophages and exclude an important role of MA-NLS and Vpr in macrophage infection. ..
- Shiba K, Ito K, Yura T. Suppressors of the secY24 mutation: identification and characterization of additional ssy genes in Escherichia coli. J Bacteriol. 1986;166:849-56 pubmed..A delicate balance may exist between the systems for synthesizing and exporting proteins. ..
- Van Dyke N, Pickering B, Van Dyke M. Stm1p alters the ribosome association of eukaryotic elongation factor 3 and affects translation elongation. Nucleic Acids Res. 2009;37:6116-25 pubmed publisher..In addition, ribosomes with increased levels of Stm1p exhibit decreased association with eEF3. Taken together, our data indicate that Stm1p plays a complementary role to eEF3 in translation...
- Pal M, McKean D, Luse D. Promoter clearance by RNA polymerase II is an extended, multistep process strongly affected by sequence. Mol Cell Biol. 2001;21:5815-25 pubmed..Polymerases halted during the clearance phase translocate upstream to the preclearance location and arrest in at least one sequence context. ..
- Ganoza M, Cunningham C, Chung D, Neilson T. A proposed role for IF-3 and EF-T in maintaining the specificity of prokaryotic initiation complex formation. Mol Biol Rep. 1991;15:33-8 pubmed..We propose that one function of EF-T may be to prevent the entry of aminoacyl-tRNAs into the 30S particle during initiation. The possibility that a special site for fMet-tRNA resides on 16S rRNA is also discussed. ..