Genomes and Genes
peptide elongation factors
Summary: Protein factors uniquely required during the elongation phase of protein synthesis.
- Yanagisawa T, Sumida T, Ishii R, Takemoto C, Yokoyama S. A paralog of lysyl-tRNA synthetase aminoacylates a conserved lysine residue in translation elongation factor P. Nat Struct Mol Biol. 2010;17:1136-43 pubmed publisher..In vivo analyses indicate that the EF-P modification by GenX and YjeK is essential for cell survival. ..
- Steiner T, Kaiser J, Marinkovi S, Huber R, Wahl M. Crystal structures of transcription factor NusG in light of its nucleic acid- and protein-binding activities. EMBO J. 2002;21:4641-53 pubmed..The results strongly argue that both protein and nucleic acid contacts are important for NusG's functions and that the factor can act as an adaptor mediating indirect protein-nucleic acid associations...
- Aoki H, Xu J, Emili A, Chosay J, Golshani A, Ganoza M. Interactions of elongation factor EF-P with the Escherichia coli ribosome. FEBS J. 2008;275:671-81 pubmed publisher..We also report that EF-P promotes a ribosome-dependent accommodation of fMet-tRNA into the 70S P-site. ..
- Blaha G, Stanley R, Steitz T. Formation of the first peptide bond: the structure of EF-P bound to the 70S ribosome. Science. 2009;325:966-70 pubmed publisher..EF-P facilitates the proper positioning of the fMet-tRNA(i)(fMet) for the formation of the first peptide bond during translation initiation. ..
- Cohen S, Walker G. The transcription elongation factor NusA is required for stress-induced mutagenesis in Escherichia coli. Curr Biol. 2010;20:80-5 pubmed publisher..Our results are the first to implicate NusA as a crucial participant in the phenomenon of stress-induced mutagenesis. ..
- Beloin C, Michaelis K, Lindner K, Landini P, Hacker J, Ghigo J, et al. The transcriptional antiterminator RfaH represses biofilm formation in Escherichia coli. J Bacteriol. 2006;188:1316-31 pubmed
- Kamikawa R, Inagaki Y, Sako Y. Direct phylogenetic evidence for lateral transfer of elongation factor-like gene. Proc Natl Acad Sci U S A. 2008;105:6965-9 pubmed publisher..Finally, based on a reverse transcriptase quantitative PCR assay and the genome information of Thalassiosira and Phaeodactylum, we propose the loss of elongation factor function in Thalassiosira EF-1alpha...
- Yakhnin A, Babitzke P. NusA-stimulated RNA polymerase pausing and termination participates in the Bacillus subtilis trp operon attenuation mechanism invitro. Proc Natl Acad Sci U S A. 2002;99:11067-72 pubmed..Finally, NusA-stimulated termination is cooperative, suggesting that binding of multiple NusA molecules influences termination. ..
- Cardinale C, Washburn R, Tadigotla V, Brown L, Gottesman M, Nudler E. Termination factor Rho and its cofactors NusA and NusG silence foreign DNA in E. coli. Science. 2008;320:935-8 pubmed publisher..Deletion of the cryptic rac prophage in wild-type E. coli increases bicyclomycin resistance and permits deletion of nusG. Thus, Rho termination, supported by NusA and NusG, is required to suppress the toxic activity of foreign genes...
- Kurata S, Nielsen K, Mitchell S, Lorsch J, Kaji A, Kaji H. Ribosome recycling step in yeast cytoplasmic protein synthesis is catalyzed by eEF3 and ATP. Proc Natl Acad Sci U S A. 2010;107:10854-9 pubmed publisher..No 40S*mRNA complex was observed, indicating that eEF3 action promotes ribosome recycling, not reinitiation. ..
- Kalyani B, Muteeb G, Qayyum M, Sen R. Interaction with the nascent RNA is a prerequisite for the recruitment of Rho to the transcription elongation complex in vitro. J Mol Biol. 2011;413:548-60 pubmed publisher..We concluded that the nascent RNA loading of Rho and its interaction with the rut site are mandatory and prerequisites for its recruitment to the EC under in vitro experimental conditions. ..
- Qin Y, Polacek N, Vesper O, Staub E, Einfeldt E, Wilson D, et al. The highly conserved LepA is a ribosomal elongation factor that back-translocates the ribosome. Cell. 2006;127:721-33 pubmed..We suggest renaming LepA as elongation factor 4 (EF4). ..
- Losón O, Song Z, Chen H, Chan D. Fis1, Mff, MiD49, and MiD51 mediate Drp1 recruitment in mitochondrial fission. Mol Biol Cell. 2013;24:659-67 pubmed publisher..Finally, we find that either MiD49 or MiD51 can mediate Drp1 recruitment and mitochondrial fission in the absence of Fis1 and Mff. These results demonstrate that multiple receptors can recruit Drp1 to mediate mitochondrial fission. ..
- Drögemüller J, Stegmann C, Mandal A, Steiner T, Burmann B, Gottesman M, et al. An autoinhibited state in the structure of Thermotoga maritima NusG. Structure. 2013;21:365-75 pubmed publisher..Wild-type TmNusG and deletion variants could not replace endogenous Escherichia coli NusG, suggesting that the NTD-CTD interaction of TmNusG represents an autoinhibited state. ..
- Pisarev A, Hellen C, Pestova T. Recycling of eukaryotic posttermination ribosomal complexes. Cell. 2007;131:286-99 pubmed..Its activity is enhanced by eIFs 3j, 1, and 1A. eIF1 also mediates release of P site tRNA, whereas eIF3j ensures subsequent dissociation of mRNA. ..
- Chakraburtty K. Translational regulation by ABC systems. Res Microbiol. 2001;152:391-9 pubmed..The reaction requires ATP hydrolysis. EF-3 contains two ATP binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions...
- Eisenmann A, Schwarz S, Prasch S, Schweimer K, Rosch P. The E. coli NusA carboxy-terminal domains are structurally similar and show specific RNAP- and lambdaN interaction. Protein Sci. 2005;14:2018-29 pubmed..NMR titration experiments show clear differences of the interactions of these two domains with alphaCTD and lambdaN, in spite of their structural similarity. ..
- Kamikawa R, Yabuki A, Nakayama T, Ishida K, Hashimoto T, Inagaki Y. Cercozoa comprises both EF-1?-containing and EFL-containing members. Eur J Protistol. 2011;47:24-8 pubmed publisher..Based on the results, we postulate that cercozoan EF-1? genes have been vertically inherited, and the current EFL-containing species may have secondarily lost their EF-1? genes. ..
- Sevostyanova A, Svetlov V, Vassylyev D, Artsimovitch I. The elongation factor RfaH and the initiation factor sigma bind to the same site on the transcription elongation complex. Proc Natl Acad Sci U S A. 2008;105:865-70 pubmed publisher..Our findings highlight the key regulatory role played by the clamp helices during both initiation and elongation stages of transcription. ..
- Santangelo T, Roberts J. RfaH, a bacterial transcription antiterminator. Mol Cell. 2002;9:698-700 pubmed..The bacterial transcription antiterminator RfaH has been shown to act, in a purified biochemical system, by binding both RNA polymerase and the nontemplate strand of DNA at the regulatory site ops. ..
- Zhou Y, Mah T, Greenblatt J, Friedman D. Evidence that the KH RNA-binding domains influence the action of the E. coli NusA protein. J Mol Biol. 2002;318:1175-88 pubmed..These studies provide direct evidence that the both KH as well as the S1 RNA binding domains are important for NusA action in support of bacterial viability as well as transcription antitermination mediated by the lambda N protein. ..
- Carter H, Svetlov V, Artsimovitch I. Highly divergent RfaH orthologs from pathogenic proteobacteria can substitute for Escherichia coli RfaH both in vivo and in vitro. J Bacteriol. 2004;186:2829-40 pubmed..coli gene. Thus, despite the apparently accelerated divergent evolution of the RfaH proteins, the mechanism of their action is conserved well enough to make them transcriptionally active in the E. coli system. ..
- Manchester K. Determination of the kinetics of guanine nucleotide exchange on EF-Tu and EF-Ts: continuing uncertainties. Biochem Biophys Res Commun. 2004;314:1-5 pubmed..Metabolic control analysis has been applied to determine the degree of flux control of the different steps in the pathway. ..
- Shin D, Nguyen H, Jancarik J, Yokota H, Kim R, Kim S. Crystal structure of NusA from Thermotoga maritima and functional implication of the N-terminal domain. Biochemistry. 2003;42:13429-37 pubmed publisher..Structural comparison between TmNusA and Mycobacterium tuberculosis NusA reveals a possible hinge motion between NTD and RBD. In addition, a functional implication of the NTD in its interaction with RNA polymerase is discussed...
- Pestova T, Hellen C. Translation elongation after assembly of ribosomes on the Cricket paralysis virus internal ribosomal entry site without initiation factors or initiator tRNA. Genes Dev. 2003;17:181-6 pubmed..Cycloheximide arrested ribosomes on the IRES only after two cycles of elongation, when the first deacylated tRNA reached the E-site after translocation from the A-site. ..
- Doma M, Parker R. Endonucleolytic cleavage of eukaryotic mRNAs with stalls in translation elongation. Nature. 2006;440:561-4 pubmed..No-go decay provides a mechanism for clearing the cell of stalled translation elongation complexes, which could occur as a result of damaged mRNAs or ribosomes, or as a mechanism of post-transcriptional control. ..
- Gile G, Patron N, Keeling P. EFL GTPase in cryptomonads and the distribution of EFL and EF-1alpha in chromalveolates. Protist. 2006;157:435-44 pubmed..Phylogenetic analysis indicates EFL likely arose early within each subgroup where it is found, but suggests it may have originated multiple times within chromalveolates as a whole. ..
- Zou S, Hersch S, Roy H, Wiggers J, Leung A, Buranyi S, et al. Loss of elongation factor P disrupts bacterial outer membrane integrity. J Bacteriol. 2012;194:413-25 pubmed publisher..Our data support a role for EF-P in the translational regulation of a limited number of proteins that, when perturbed, renders the cell susceptible to stress by the adventitious overexpression of an outer membrane porin. ..
- Richardson J. Rho-dependent termination and ATPases in transcript termination. Biochim Biophys Acta. 2002;1577:251-260 pubmed..Actions of the Rho structure in the channel on the 3' segment that are coupled to ATP hydrolysis pull the RNA from its contacts with the template and RNA polymerase, thus causing termination of its synthesis. ..
- Doerfel L, Wohlgemuth I, Kothe C, Peske F, Urlaub H, Rodnina M. EF-P is essential for rapid synthesis of proteins containing consecutive proline residues. Science. 2013;339:85-8 pubmed publisher..We propose that EF-P and its eukaryotic homolog, eIF5A, are essential for the synthesis of a subset of proteins containing proline stretches in all cells. ..
- Shoji S, Walker S, Fredrick K. Reverse translocation of tRNA in the ribosome. Mol Cell. 2006;24:931-42 pubmed..e., direct movement of the tRNAs from the E and P sites to the P and A sites, respectively). These findings have important implications for the energetics of translocation. ..
- Bailly M, De Crecy Lagard V. Predicting the pathway involved in post-translational modification of elongation factor P in a subset of bacterial species. Biol Direct. 2010;5:3 pubmed publisher..This article was reviewed by Céline Brochier-Armanet, Igor B. Zhulin and Mikhail Gelfand. For the full reviews, please go to the Reviewers' reports section. ..
- Lescure A, Fagegaltier D, Carbon P, Krol A. Protein factors mediating selenoprotein synthesis. Curr Protein Pept Sci. 2002;3:143-51 pubmed..In this review, we will focus on the structural and functional aspects of the SelB and SBP2 factors in selenoprotein synthesis. ..
- Bullwinkle T, Zou S, Rajkovic A, Hersch S, Elgamal S, Robinson N, et al. (R)-?-lysine-modified elongation factor P functions in translation elongation. J Biol Chem. 2013;288:4416-23 pubmed publisher..Taken together, our findings indicate that EF-P functions in translation elongation, a role critically dependent on post-translational ?-lysylation but not hydroxylation...
- Carlomagno M, Nappo A. NusA modulates intragenic termination by different pathways. Gene. 2003;308:115-28 pubmed..Our data support the hypothesis that NusA may program a fraction of the RNA polymerase to terminate transcription upon interactions with specific sites on the nascent mRNA and either other Nuses or ribosomes. ..
- Torres M, Balada J, Zellars M, Squires C, Squires C. In vivo effect of NusB and NusG on rRNA transcription antitermination. J Bacteriol. 2004;186:1304-10 pubmed
- Antonicka H, Ostergaard E, Sasarman F, Weraarpachai W, Wibrand F, Pedersen A, et al. Mutations in C12orf65 in patients with encephalomyopathy and a mitochondrial translation defect. Am J Hum Genet. 2010;87:115-22 pubmed publisher..We suggest that it might play a role in recycling abortive peptidyl-tRNA species, released from the ribosome during the elongation phase of translation. ..
- Anand M, Balar B, Ulloque R, Gross S, Kinzy T. Domain and nucleotide dependence of the interaction between Saccharomyces cerevisiae translation elongation factors 3 and 1A. J Biol Chem. 2006;281:32318-26 pubmed..The dynamics of when eEF3 interacts with eEF1A may be part of the signal for transition of the post to pre-translocational ribosomal state in yeast. ..
- Jeppesen M, Navratil T, Spremulli L, Nyborg J. Crystal structure of the bovine mitochondrial elongation factor Tu.Ts complex. J Biol Chem. 2005;280:5071-81 pubmed..The structure of the EF-Tumt.Tsmt complex provides new insights into the nucleotide exchange mechanism and provides a framework for explaining much of the mutational data obtained for this complex. ..
- Priya P, Venkatachalam P, Thulaseedharan A. Differential expression pattern of rubber elongation factor (REF) mRNA transcripts from high and low yielding clones of rubber tree (Hevea brasiliensis Muell. Arg.). Plant Cell Rep. 2007;26:1833-8 pubmed..It is evident from the results that both tapping and ethephon treatment had a direct effect on induction of REF gene expression. Results demonstrate a positive correlation between REF gene expression pattern and latex yield...
- Ishitani Y, Kamikawa R, Yabuki A, Tsuchiya M, Inagaki Y, Takishita K. Evolution of elongation factor-like (EFL) protein in Rhizaria is revised by radiolarian EFL gene sequences. J Eukaryot Microbiol. 2012;59:367-73 pubmed publisher..We propose an updated model for EF-1?/EFL evolution in Rhizaria by incorporating new EFL data obtained in this study. ..
- Leibundgut M, Frick C, Thanbichler M, B ck A, Ban N. Selenocysteine tRNA-specific elongation factor SelB is a structural chimaera of elongation and initiation factors. EMBO J. 2005;24:11-22 pubmed publisher..In our model of SelB bound to the ribosome, domain IV points towards the 3' mRNA entrance cleft ready to interact with the downstream secondary structure element...
- Svetlov V, Belogurov G, Shabrova E, Vassylyev D, Artsimovitch I. Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res. 2007;35:5694-705 pubmed
- Nagy G, Dobrindt U, Schneider G, Khan A, Hacker J, Emody L. Loss of regulatory protein RfaH attenuates virulence of uropathogenic Escherichia coli. Infect Immun. 2002;70:4406-13 pubmed..trans complementation of the mutant strain with the rfaH gene restores wild-type levels of the affected virulence factors and consequently restitutes virulence in the mouse model of ascending urinary tract infection. ..
- Burmann B, Knauer S, Sevostyanova A, Schweimer K, Mooney R, Landick R, et al. An ? helix to ? barrel domain switch transforms the transcription factor RfaH into a translation factor. Cell. 2012;150:291-303 pubmed publisher..As a consequence, RfaH-CTD binding to S10 is enabled and translation of RfaH-controlled operons is strongly potentiated. PAPERFLICK: ..
- Bonin I, Mühlberger R, Bourenkov G, Huber R, Bacher A, Richter G, et al. Structural basis for the interaction of Escherichia coli NusA with protein N of phage lambda. Proc Natl Acad Sci U S A. 2004;101:13762-7 pubmed..Contrary to the RNA polymerase alpha subunit, lambdaN binding does not stimulate RNA interaction of NusA. The results demonstrate that lambdaN serves as a scaffold to closely oppose NusA and the mRNA in antitermination complexes. ..
- Hersch S, Wang M, Zou S, Moon K, Foster L, Ibba M, et al. Divergent protein motifs direct elongation factor P-mediated translational regulation in Salmonella enterica and Escherichia coli. MBio. 2013;4:e00180-13 pubmed publisher..This work expands the known repertoire of EF-P target motifs and implicates factors beyond polyproline motifs that are required for EF-P-mediated regulation...
- Kalarickal N, Ranjan A, Kalyani B, Wal M, Sen R. A bacterial transcription terminator with inefficient molecular motor action but with a robust transcription termination function. J Mol Biol. 2010;395:966-82 pubmed publisher..tb. (Rv0639) or E. coli. These results strongly suggest that the ATPase activity of M. tb. Rho is uncoupled from its transcription termination function and this function may not be dependent on its helicase/translocase activity. ..
- Belogurov G, Vassylyeva M, Svetlov V, Klyuyev S, Grishin N, Vassylyev D, et al. Structural basis for converting a general transcription factor into an operon-specific virulence regulator. Mol Cell. 2007;26:117-29 pubmed..Finally, we argue that RfaH binds to the beta' subunit coiled coil, the major target site for the initiation sigma factors. ..
- Zhou Y, Filter J, Court D, Gottesman M, Friedman D. Requirement for NusG for transcription antitermination in vivo by the lambda N protein. J Bacteriol. 2002;184:3416-8 pubmed..Earlier work suggested that NusG was not required for N activity in vivo. Here we present evidence that NusG also stimulates N-mediated transcription antitermination in intact cells. ..
- Pittman Y, Valente L, Jeppesen M, Andersen G, Patel S, Kinzy T. Mg2+ and a key lysine modulate exchange activity of eukaryotic translation elongation factor 1B alpha. J Biol Chem. 2006;281:19457-68 pubmed..These results indicate the significant role of Mg2+ in the nucleotide exchange reaction by eEF1B alpha and establish the catalytic function of Lys-205 in displacing Mg2+ from its binding site. ..
- Zhao J, Liu T, Jin S, Wang X, Qu M, Uhlen P, et al. Human MIEF1 recruits Drp1 to mitochondrial outer membranes and promotes mitochondrial fusion rather than fission. EMBO J. 2011;30:2762-78 pubmed publisher..As MIEF1 is vertebrate-specific, these data also reveal important differences between yeast and vertebrates in the regulation of mitochondrial dynamics. ..
- Zhang L, Ging N, Komoda T, Hanada T, Suzuki T, Watanabe K. Antibiotic susceptibility of mammalian mitochondrial translation. FEBS Lett. 2005;579:6423-7 pubmed..coli system. The present results, taken together with atomic structure of the ribosome, may provide useful information for the rational design of new antibiotics having less adverse effects in humans and animals. ..
- Rahn A, Whitfield C. Transcriptional organization and regulation of the Escherichia coli K30 group 1 capsule biosynthesis (cps) gene cluster. Mol Microbiol. 2003;47:1045-60 pubmed..However, the Rcs system can potentially influence levels of capsular polysaccharide production by increasing galF transcription and influencing the available pool of biosynthetic precursors. ..
- Prasch S, Jurk M, Washburn R, Gottesman M, Wohrl B, Rosch P. RNA-binding specificity of E. coli NusA. Nucleic Acids Res. 2009;37:4736-42 pubmed publisher..These differences may explain why lambda requires an additional protein, lambda N, to suppress termination. Knowledge of the different affinities now describes the assembly of the anti-termination complex in quantitative terms...
- Kamikawa R, Brown M, Nishimura Y, Sako Y, Heiss A, Yubuki N, et al. Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol Biol. 2013;13:131 pubmed publisher..As the dual-EF-containing species are distantly related to each other, we propose that independent re-modelling of EF-1α function took place in multiple branches in the tree of eukaryotes. ..
- Wolff E, Kang K, Kim Y, Park M. Posttranslational synthesis of hypusine: evolutionary progression and specificity of the hypusine modification. Amino Acids. 2007;33:341-50 pubmed
- 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...
- Hirosawa Takamori M, Chung H, Jackle H. Conserved selenoprotein synthesis is not critical for oxidative stress defence and the lifespan of Drosophila. EMBO Rep. 2004;5:317-22 pubmed..Protecting cells from oxidative stress can therefore not account for the selection pressure that conserves selenoprotein biosynthesis during the course of evolution. ..
- Beuth B, Pennell S, Arnvig K, Martin S, Taylor I. Structure of a Mycobacterium tuberculosis NusA-RNA complex. EMBO J. 2005;24:3576-87 pubmed
- Ardehali M, Yao J, Adelman K, Fuda N, Petesch S, Webb W, et al. Spt6 enhances the elongation rate of RNA polymerase II in vivo. EMBO J. 2009;28:1067-77 pubmed publisher..Furthermore, RNAi depletion of Spt6 reveals its broad requirement during different stages of development. ..
- Shankar S, Hatoum A, Roberts J. A transcription antiterminator constructs a NusA-dependent shield to the emerging transcript. Mol Cell. 2007;27:914-27 pubmed..Furthermore, as NusA is not required for the antipausing activity of Q(82) in vitro, we distinguish two distinct activities of antiterminators, namely antipausing and RNA occlusion, and discuss their roles in Q(82) function. ..
- Zou S, Roy H, Ibba M, Navarre W. Elongation factor P mediates a novel post-transcriptional regulatory pathway critical for bacterial virulence. Virulence. 2011;2:147-51 pubmed..Other observations suggest that the eukaryotic homolog of EF-P, eIF5A, may illicit similar changes in the translation machinery during stress adaptation, indicating that the role of these factors in physiology may be broadly conserved. ..
- Belogurov G, Sevostyanova A, Svetlov V, Artsimovitch I. Functional regions of the N-terminal domain of the antiterminator RfaH. Mol Microbiol. 2010;76:286-301 pubmed publisher..The third region is apparently dispensable for RfaH binding to the transcription complex but is required for the antitermination modification of RNAP. ..
- Andersen C, Becker T, Blau M, Anand M, Halic M, Balar B, et al. Structure of eEF3 and the mechanism of transfer RNA release from the E-site. Nature. 2006;443:663-8 pubmed..eEF3 uses an entirely new factor binding site near the ribosomal E-site, with the chromodomain likely to stabilize the ribosomal L1 stalk in an open conformation, thus allowing tRNA release. ..
- Arnvig K, Pennell S, Gopal B, Colston M. A high-affinity interaction between NusA and the rrn nut site in Mycobacterium tuberculosis. Proc Natl Acad Sci U S A. 2004;101:8325-30 pubmed..Finally, we present evidence that this NusA-RNA interaction affects transcriptional events further downstream. ..
- Ghazi A, Henis Korenblit S, Kenyon C. A transcription elongation factor that links signals from the reproductive system to lifespan extension in Caenorhabditis elegans. PLoS Genet. 2009;5:e1000639 pubmed publisher..Thus, TCER-1 specifically links the activity of a broadly deployed transcription factor, DAF-16/FOXO, to longevity signals from reproductive tissues. ..
- Burmann B, Scheckenhofer U, Schweimer K, Rosch P. Domain interactions of the transcription-translation coupling factor Escherichia coli NusG are intermolecular and transient. Biochem J. 2011;435:783-9 pubmed publisher..This notion of two virtually independent domains in a monomeric protein was supported by 15N-relaxation measurements. Thus we suggest that a regulatory role of NusG interdomain interactions is highly unlikely. ..