Interaction of guanosine 5'-triphosphate with a supernatant fraction from E. coli and aminoacyl-sRNA

Viruses, IRESs, and a universal translation initiation mechanism

Internal ribosome entry sites (IRESs) are cis-acting RNA elements capable of recruiting ribosomes and initiating translation on an internal portion of an mRNA. This is divergent from canonical eukaryotic translation initiation, where the 5' cap is recognized by initiation factors (IFs) that recruit the ribosome to initiate translation of the encoded peptide. All known IRESs are capable of initiating translation in a cap-independent manner, and are therefore not constrained by the absence or presence of a 5' m⁷G cap. In addition to being cap-independent, IRES-mediated translation often uses only a subset of IFs allowing them to function independently of canonical initiation. The ability to function independently of the canonical translation initiation pathway allows IRESs to mediate gene expression when cap-dependent translation has been inhibited. Recent reports of viral IRESs capable of initiating translation across taxonomic domains (Eukarya and Bacteria) have sparked interest in designing gene expression systems compatible with multiple organisms. The ability to drive translation independent of cellular context using a common mechanism would have a wide range of applications ranging from agriculture biotechnology to the development of antiviral drugs. Here we discuss IRES-mediated translation and critically compare the available mechanistic and structural information. A particular focus will be on IRES-meditated translation across domains of life (viral and cellular IRESs) , IRES bioengineering and the possibility of an evolutionary conserved translation initiation mechanism.

Effect of elongation factor Tu on the conformation of phenylalanyl-tRNAPhe

Structural features of the tRNAPhe molecule upon ternary complex formation with the bacterial elongation factor Tu were investigated. Phosphodiester bonds at positions 18 and 34 were found to be labilized in bound tRNA. Conversely, a higher stability of the phosphodiester links at positions 20, 21 and 36 was detected. Using ethylnitrosourea as a chemical probe a conformational change occurring at phosphate position 53 was observed in complexed tRNA. These results are interpreted by a structural rearrangement of the nucleic acid induced by complex formation.

Recognition of the universally conserved 3'-CCA end of tRNA by elongation factor EF-Tu

Escherichia coli tRNA(Val) with pyrimidine substitutions for the universally conserved 3'-terminal adenine can be readily aminoacylated. It cannot, however, transfer valine into polypeptides. Conversely, despite being a poor substrate for valyl-tRNA synthetase, tRNA(Val) with a 3'-terminal guanine is active in in vitro polypeptide synthesis. To better understand the function of the 3'-CCA sequence of tRNA in protein synthesis, the effects of systematically varying all three bases on formation of the Val-tRNA(Val):EF-Tu:GTP ternary complex were investigated. Substitutions at C74 and C75 have no significant effect, but replacing A76 with pyrimidines decreases the affinity of valyl-tRNA(Val) for EF-Tu:GTP, thus explaining the inability of these tRNA(Val) variants to function in polypeptide synthesis. Valyl-tRNA(Val) terminating in 3'-guanine is readily recognized by EF-TU:GTP. Dissociation constants of the EF-Tu:GTP ternary complexes with valine tRNAs having nucleotide substitutions at the 3' end increase in the order adenine < guanine < uracil; EF-Tu has very little affinity for tRNA terminating in 3' cytosine. Similar observations were made in studies of the interaction of 3' end mutants of E. coli tRNA(Ala) and tRNA(Phe) with EF-Tu:GTP. These results indicate that EF-Tu:GTP preferentially recognizes purines and discriminates against pyrimidines, especially cytosine, at the 3' end of aminoacyl-tRNAs.

Histidine-118 of elongation factor Tu: its role in aminoacyl-tRNA binding and regulation of the GTPase activity

The function of His118 in elongation factor (EF)-Tu from Escherichia coli was investigated by its substitution with glycine. The substitution had a differential effect on individual functions of the protein. The affinity for aminoacyl (aa)-tRNA and the intrinsic GTPase activity of the mutant EF-Tu were decreased whereas the response of its GTPase center to aa-tRNA was strongly increased. These results suggest that the region around His118 is involved in the binding of aa-tRNA and in the transmission of a turn-off signal generated by the interaction with aa-tRNA and directed to the GTPase center of EF-Tu.

Structural features in aminoacyl-tRNAs required for recognition by elongation factor Tu

In bacterial polypeptide synthesis aminoacyl-tRNA (aa-tRNA) bound to elongation factor Tu (EF-Tu) and GTP is part of a crucial intermediate ribonucleoprotein complex involved in the decoding of messenger RNA. The conformation and topology as well as the affinity of the macromolecules in this ternary aa-tRNA X EF-Tu X GTP complex are of fundamental importance for the nature of the interaction of the complex with the ribosome. The structural elements of aa-tRNA required for interaction with EF-Tu and GTP and the resulting functional implications are presented here.

Transfer ribonucleic acid deprived of the C-C-A 3'-extremity can interact with elongation factor Tu

In this work we describe that uncharged tRNAs or modified tRNAs lacking all or part of the C-C-A end (i.e., tRNA minus pCpCpA, tRNA minus pA, and tRNA minus A) can still influence the GTPase activity of the elongation factor Tu (EF-Tu), thus showing that, besides the aminoacylated 3'-end, other regions of the aa-tRNA interact with EF-Tu. The existence of an interaction between EF-Tu and truncated tRNAs was also confirmed by examining the dissociation of the EF-Tu-GTP complex: the rate of this reaction is decreased upon addition of tRNAVal1 minus pCpCpA. The effect on the EF-Tu GTPase activity of tRNAs deprived of the C-C-A 3'-end is still evident in the presence of C-C-A-aa. The stimulatory pattern obtained with C-C-A-Val at 5 mM MgCl2 is decreased upon addition of tRNAVal1 minus pCpCpA, tRNAVal1 minus pA, or tRNAVal1 minus A. This shows that the effect of the aminoacylated C-C-A 3'-end can be influenced via EF-Tu by the remaining regions of the tRNA, after cleavage of a bond in the 3'-extremity. However, also with an excess of tRNAVal1 minus pCpCpA over C-C-A-Val, no "aa-tRNA-like" effect, i.e., no inhibition of the EF-Tu GTPase, was obtained, suggesting that, upon binding with EF-Tu, a specific conformational change in the aa-tRNA molecule also takes place, regulating the expression of the GTPase activity. Our results unequivocally show that different regions of the aa-tRNA are needed for a coordinated interaction with EF-Tu.

Interaction between the different domains of aminoacyl-tRNA and the elongation-factor-Tu x kirromycin complex

In this work, we have studied the effect of aa-tRNA and derived 3' aminoacylated fragments on the EF-Tu GTPase in the presence of kirromycin, using two systems: without and with ribosomes. The aa-tRNA fragments were obtained by enzymatic digestion. Procedures for the enzymatic preparation of C-A-Val and Val-tRNA Val1 3' half molecule, as well as a purification method for short 3' aminoacylated fragments based on the amino group charge, were newly developed for this work. Aminoacyl-adenosine was found to be able to stimulate the EF-Tu x kirromycin GTPase, but only to a very small extent. Increasing the length of the aminoacylated fragments increased the stimulatory effect as follow: A-Val much less than C-A-Val less than C-C-A-Val less than 3' valyladenosine dodecanucleotide much less than Val-tRNA Val1 3' half molecule less than Val-tRNA Val1. The presence of ribosomes did not affect the order of effectiveness, but increased the basic GTPase activity of EF-Tu x kirromycin and the stimulation by aa-tRNA, its 3' half molecule and even more by its 3' short fragments. The effect of aa-tRNA and derived 3' fragments in the absence of ribosomes was not influenced by MgCl2 concentrations of 5-30 mM whereas, in the presence of ribosomes, low concentrations of MgCl2 (5 mM) greatly reduced the stimulation of aa-tRNA and, to a lesser extent, also the effect of the C-C-A-aa as well as the basic activity of the EF-Tu x kirromycin GTPase. The extent of the stimulation by aa-tRNA, and even more by C-C-A-aa, depends on the nature of the amino acid. Among the aminoacyl side chains tested (Arg-, Phe-, Val-, Met-, Leu-, Lys-) arginine was found to be the most active and leucine the least. Our results show that (a) the 3' aminoacylated extremity is of prime importance for the stimulation of the EF-Tu GTPase, (b) in the 3' extremity there are critical sequences for the interaction with EF-Tu and (c) other domains of the aa-tRNA molecule are capable of influencing this reaction: one of the most important is the region including the T psi C loop and stem.

Properties and regulation of the GTPase activities of elongation factors Tu and G, and of initiation factor 2

During protein synthesis the interaction with ribosomes of elongation factors Tu (EF-Tu), G (EF-G) and initiation factor 2 (IF-2) is associated with the hydrolysis of GTP which is directly related to the functions of the factors. In this article we review systematically the properties of these GTPase activities in the presence and absence of protein synthesis, and by examining the characteristics of the different minimal systems for the expression of these activities we point to the role of the various effectors and to the enzymological aspects of the systems. For EF-Tu, it has been possible to eliminate any requirement for macromolecular effectors, showing that the factor itself is a GTPase. For EF-G, the presence of at least the 50S ribosomal subunit has remained a requirement, whereas IF-2 needs both the 50S and 30S subunits to exhibit GTPase activity. Between the GTPase activities of the three factors there are some striking similarities, but important differences prevail as a consequence of the specificity of the different functions. This can also be seen by examining the respective ribosomal regions implicated in these reactions. When coupled with protein synthesis, the three GTPase activities reveal characteristics differing from those observed in partial systems.

Pulvomycin, an inhibitor of protein biosynthesis preventing ternary complex formation between elongation factor Tu, GTP, and aminoacyl-tRNA

Pulvomycin and the synonymous antibiotics labilomycin and 1063-Z are shown to inhibit prokaryotic protein synthesis by acting on elongation factor Tu (EF-Tu): in the presence of the antibiotic, the affinity of EF-Tu for guanine nucleotides is altered, the EF-Tu.GDP/GTP exchange is catalyzed, and the formation of the EF-Tu.GTP complex is stimulated. Hydrolysis of GTP by EF-Tu, induced by aminoacyl-tRNA, ribosomes, and mRNA or by kirromycin, is inhibited by pulvomycin. As shown by Millipore filtration, chromatographic analysis, and hydrolysis protection experiments, pulvomycin prevents interaction between aminoacyl-tRNA and EF-Tu.GTP to yield the ternary complex aminoacyl-tRNA.EF-Tu.GTP. Thus, enzymatic binding of aminoacyl-tRNA to ribosomes is blocked.

Interaction of elongation factor 1 with aminoacylated brome mosaic virus and tRNA's

Tyrosylated Brome mosaic virus RNA was found to interact with a binary complex of wheat germ, elongation factor 1 and [3H]GTP. Increasing amounts of the aminoacylated viral RNA proportionately reduced radioactivity bound to a nitrocellulose filter, as has previously been noted by others for the charged forms of tobacco mosaic virus, turnip yellow mosaic virus, and tRNA's. However, Sephadex chromatography of the products showed that instead of forming the ternary complex elongation factor-GTP-aminoacyl RNA, the viral RNA caused release of GTP from its complex with elongation factor. Acetylated tyrosyl Brome mosaic virus RNA did not react with the binary complex,and only a slight degree, if any, of stabilization of tyrosine bound to viral RNA was observed after interaction with elongation factor 1. Although such interactions are similar to the reaction of elongation factor with aminoacyl-tRNA , the release of GTP is different and accentuates the possible role for aminoacylation in transcription rather than in translation events.

Enzymatic binding of aminoacyl transfer ribonucleic acid to ribosomes: the study of binding sites of 2' and 3' isomers of aminoacyl transfer ribonucleic acid

The mechanism of enzymatic binding of AAtRNA to the acceptor site Escherichia coli ribosomes has been studied using the following aminoacyl oligonucleotides as models of the 3' terminus of AA-tRNA: C-A-Phe, C-A-(2'-Phe)H, and C-A(2'H)Phe. T-psi-C-Gp was used as a model of loop IV of tRNA. The EF-T dependent binding of Phe-tRNA to ribosomes (in the presence of either GTP or GMPPCP) and the GTPase activity associated with EF-T dependent binding of the Phe-tRNA were inhibited by C-A-Phe,C-A(2'Phe)H, and C-A(2'H)Phe. These aminoacyl oligonucleotides inhibit both the formation of ternary complex EF-Tu-GTP-AA-tRNA and the interaction of this complex with the ribosomal A site. The uncoupled EF-Tu dependent GTPase (in the absence of AA-tRNA) was also inhibited by C-A-Phe, C-A(2'Phe)H, and C-A(2'H)Phe, while nonenzymatic binding of Phe-tRNA to the ribosomal A site was inhibited by C-A-Phe and C-A(2'-Phe)H, but not by C-A(2'H)Phe. The tetranucleotide T-psi-C-Gp inhibited both enzyme binding of Phe-tRNA and EF-T dependent GTP hydrolysis. However, inhibition of the latter reaction occured at a lower concentration of T-psi-C-Gp suggesting a specific role of T-psi-C-Gp loop of AA-tRNA in the GTPase reaction. The role of the 2' and 3' isomers of AA-tRNA during enzymatic binding to ribosomes is discussed and it is suggested that 2' leads to 3' transacylation in AA-tRNA is a step which follows GTP hydrolysis but precedes peptide bond formation.

Interaction of elongation factor Tu with 2'(3')-O-aminoacyloligonucleotides derived from the 3' terminus of aminoacyl-tRNA

The interaction between Escherichia coli elongation factor-Tu-GTP complex and chemically synthesized 2'(3')-O-aminoacyldinucleoside phosphates with the nucleotide sequence of the 3' terminus of aminoacyl-tRNA (AA-tRNA) has been studied. It was found that C-A-Phe, C-A-Pro, and C-A-Asp interact with EF-Tu-GTP, causing the release of GTP bound to the enzyme. The specificity of this interaction closely resembles that of AA-tRNA since C-A and C-A(Ac-Phe) as well as the corresponding tRNAs are inactive. The 3'-O-aminoacyl derivative C-2'-dA-Phe does not interact with EF-Tu-GTP, whereas the 2'-O-aminoacyl derivative C-3'-dA-Phe is almost as active as the 2'(3')-O-aminoacyl derivative, C-A-Phe. C-A-Phe also interacts with the EF-Tu-GDP complex in a manner similar to its interaction with EF-Tu-GTP. It is concluded that interaction of 2'(3')-O-aminoacyloligonucleotides possessing the sequence of the 3' terminus of AA-tRNA is analogous to the interaction of that terminus with EF-Tu and it is suggested that EF-Tu is specific for 2'-O-AA-tRNA.

Protein initiation in eukaryotes: formation and function of a ternary complex composed of a partially purified ribosomal factor, methionyl transfer RNA, and guanosine triphosphate

A protein factor contained in a 1 M KCl extract of L-cell ribosomes and partially purified by chromatography on DEAE-cellulose forms a specific ternary complex with rat-liver Met-tRNA(f) and GTP. The complex is measured by its quantitative retention on nitrocellulose membranes. Complex assembly is optimal at 100 mM KCl and 0.2 mM MgCl(2), and is independent of mRNA and of ribosomes. The GTP requirement can be replaced over 65% by its methylene analogue GDPCH(2)P, indicating that GTP hydrolysis is not involved. Complex formation is inhibited by 10 muM aurintricarboxylic acid, but is unaffected by 100 muM pactamycin, 100 muM fusidic acid, or by excess uncharged methionine tRNA(f). The ternary complex is relatively stable and appears at the void volume during filtration on Sephadex G-100. At 1-3 mM MgCl(2) and in the presence of other factors, the ternary complex is implicated in protein initiation by (i) its capacity to bind to the 40S ribosomal subunit to form a 48S complex; and (ii) the subsequent association of the 48S complex with a 60S subunit to form a functional "80S complex."

A complex between initiation factor IF2, guanosine triphosphate, and fMet-tRNA: an intermediate in initiation complex formation

Evidence is presented that suggests the formation of a complex between polypeptide chain-initiation factor IF 2, GTP, and fMet-tRNA(f). This complex transfers both fMet-tRNA(f) and GTP to 30S ribosomal subunits in the presence of ApUpG and initiation factor IF 1. The resultant 30S initiation complex reacts with 50S subunits to form a 70S initiation complex. fMet-tRNA(f) in this 70S complex reacts with puromycin to form fMet-puromycin. These results suggest that [IF 2, GTP, fMet-tRNA(f)] is an intermediate in the initiation of protein synthesis in Escherichia coli.

Polypeptide chain initiation in E. coli: sulfhydryl groups and the function of initiation factor F2

The activity of the chain initiation factor F(2) in promoting the messenger-dependent binding of formylmethionyl-transfer RNA (fMet approximately tRNA(f)) to purified E. coli ribosomes is inhibited by sulfhydryl-binding reagents, such as N-ethylmaleimide or p-hydroxymercuribenzoate, but prior incubation with guanosine triphosphate (GTP) or with ribosomes largely prevents this inhibition. The effect of GTP suggests that it forms a complex with F(2) whereby "active" sulfhydryl groups become sheltered. Experiments on the time course of the binding reaction, with and without preincubation of F(2) with GTP, and gel filtration experiments with (3)H-labeled GTP lend support to this suggestion.

Polypeptide chain initiation in E. coli: isolation of homogeneous initiation factor E2 and its relation to ribosomal proteins

Previous work has shown that F(2), one of several ribosomal factors involved in polypeptide chain initiation, functions in the binding of formylmethionyl-transfer RNA (fMet approximately tRNA(f)) to a messenger RNA-ribosome complex. F(2) was isolated from 1.0 M ammonium chloride washes of E. coli Q13 ribosomes as a protein homogeneous on polyacrylamide gel electrophoresis at both pH 4.5 and 7.8. Its molecular weight is approximately 80,000. Comparison of electrophoretic patterns of ribosomal proteins from NH(4)Cl-washed and unwashed ribosomes and F(2), at pH 4.5, shows that F(2) corresponds to the slowest-moving component of the proteins derived from unwashed ribosomes. This component is missing from the NH(4)Cl-washed ribosomes. The activity of F(2) is stimulated by two additional factors, initiation factor F(1) and a factor(s) present in a narrow ammonium sulfate fraction of the ribosomal NH(4)Cl wash. The nature of the latter is unknown.