Role of guanosine 5'-triphosphate in the initiation of Peptide synthesis, I. Synthesis of formylmethionyl-puromycin

Translation initiation without IF2-dependent GTP hydrolysis

Translation initiation factor IF2 is a guanine nucleotide-binding protein. The free energy change associated with guanosine triphosphate hydrolase (GTPase) activity of these proteins is believed to be the driving force allowing them to perform their functions as molecular switches. We examined role and relevance of IF2 GTPase and demonstrate that an Escherichia coli IF2 mutant bearing a single amino acid substitution (E571K) in its 30S binding domain (IF2-G3) can perform in vitro all individual translation initiation functions of wild type (wt) IF2 and supports faithful messenger RNA translation, despite having a reduced affinity for the 30S subunit and being completely inactive in GTP hydrolysis. Furthermore, the corresponding GTPase-null mutant of Bacillus stearothermophilus (E424K) can replace in vivo wt IF2 allowing an E. coli infB null mutant to grow with almost wt duplication times. Following the E571K (and E424K) mutation, which likely disrupts hydrogen bonding between subdomains G2 and G3, IF2 acquires a guanosine diphosphate (GDP)-like conformation, no longer responsive to GTP binding thereby highlighting the importance of interdomain communication in IF2. Our data underlie the importance of GTP as an IF2 ligand in the early initiation steps and the dispensability of the free energy generated by the IF2 GTPase in the late events of the translation initiation pathway.

Translation Initiation

Selection of correct start codons on messenger RNAs is a key step required for faithful translation of the genetic message. Such a selection occurs in a complex process, during which a translation-competent ribosome assembles, eventually having in its P site a specialized methionyl-tRNAMet base-paired with the start codon on the mRNA. This chapter summarizes recent advances describing at the molecular level the successive steps involved in the process. Special emphasis is put on the roles of the three initiation factors and of the initiator tRNA, which are crucial for the efficiency and the specificity of the process. In particular, structural analyses concerning complexes containing ribosomal subunits, as well as detailed kinetic studies, have shed new light on the sequence of events leading to faithful initiation of protein synthesis in Bacteria.

Initiation of Escherichia coli ribosomes on matrix coupled mRNAs studied by optical biosensor technique

The optical biosensor technique, based on the surface plasmon resonance (SPR) phenomenon, has been used to study the initiation of protein synthesis by E. coli ribosomes on surface coupled mRNA. mRNA was first periodate oxidized and then hydrazide coupled to the surface of a CM5 sensor chip. The formation of initiation complexes on the surface coupled mRNA was monitored in real-time with a BIACORE 2000 instrument. Mature 70S*mRNA*fMet-tRNA(Met) initiation complexes were assembled on mRNA by sequential introduction of the 30S and 50S subunits supplemented with appropriate initiation factors and fMet-tRNA(Met). We show that the formation of 70S*mRNA complexes on the surface coupled mRNA proceeds efficiently only in the presence of tRNA. Moreover, 70S*mRNA*fMet-tRNA(Met) complexes formed with fMet-tRNA(Met) are more stable than similar complexes formed with deacylated tRNAs. The efficient formation and slow dissociation of mature 70S*mRNA*fMet-tRNA(Met) initiation complexes are most easily explained by the stabilization of the interaction of the ribosomal subunits by fMet-tRNA(Met). This work demonstrates the feasibility of the BIACORE technique for studying the initiation of protein synthesis.

Novel roles for classical factors at the interface between translation termination and initiation

The pathway of bacterial ribosome recycling following translation termination has remained obscure. Here, we elucidate two essential steps and describe the roles played by the three translation factors EF-G, RRF, and IF3. Release factor RF3 is known to catalyze the dissociation of RF1 or RF2 from ribosomes after polypeptide release. We show that the next step is dissociation of 50S subunits from the 70S posttermination complex and that it is catalyzed by RRF and EF-G and requires GTP hydrolysis. Removal of deacylated tRNA from the resulting 30S:mRNA:tRNA posttermination complex is then necessary to permit rapid 30S subunit recycling. We show that this step requires initiation factor IF3, whose role was previously thought to be restricted to promoting specific 30S initiation complex formation from free 30S subunits.

Initiation factors IF1 and IF2 synergistically remove peptidyl-tRNAs with short polypeptides from the P-site of translating Escherichia coli ribosomes

A novel function of initiation factors IF1 and IF2 in Escherichia coli translation has been identified. It is shown that these factors efficiently catalyse dissociation of peptidyl-tRNAs with polypeptides of different length from the P-site of E. coli ribosomes, and that the simultaneous presence of both factors is required for induction of drop-off. The factor-induced drop-off occurs with both sense and stop codons in the A-site and competes with peptide elongation or termination. The efficiency with which IF1 and IF2 catalyse drop-off decreases with increasing length of the nascent polypeptide, but is quite significant for hepta-peptidyl-tRNAs, the longest polypeptide chains studied. In the absence of IF1 and IF2 the rate of drop-off varies considerably for different peptidyl-tRNAs, and depends both on the length and sequence of the nascent peptide. Efficient factor-catalysed drop-off requires GTP but not GTP hydrolysis, as shown in experiments without guanine nucleotides, with GDP or with the non-cleavable analogue GMP-PNP.Simultaneous overexpression of IF1 and IF2 in vivo inhibits cell growth specifically in some peptidyl-tRNA hydrolase deficient mutants, suggesting that initiation factor-catalysed drop-off of peptidyl-tRNA can occur on a significant scale in the bacterial cell. Consequences for the bacterial physiology of this previously unknown function of IF1 and IF2 are discussed.

On the target of a novel class of antibiotics, oxazolidinones, active against multidrug-resistant Gram-positive bacteria

Oxazolidinones are a promising new class of synthetic antibiotics active against multidrug-resistant Gram-positive bacteria. To elucidate their mode of action, the effect of DuP 721 on individual steps of protein translation was studied. The drug does not interfere with translation initiation at the stage of mRNA binding or formation of 30S pre-initiation complexes. However, it inhibits the puromycin-mediated release of [35S]formyl-methionine from 70S initiation complexes in a dose-dependent manner. Inhibition involves binding of the oxazolidinone to the large ribosomal subunit and is twice as high with 50S subunits from Gram-positive as with those from Gram-negative bacteria.

Dissociation rates of peptidyl-tRNA from the P-site of E.coli ribosomes

We studied the dissociation rates of peptidyl-tRNA from the P-site of poly(U)-programmed wild-type Escherichia coli ribosomes, hyperaccurate variants altered in S12 (SmD, SmP) and error-prone variants (Ram) altered in S4 or S5. The experiments were carried out in the presence and absence of streptomycin, and the effects of neomycin were tested in the wild-type ribosomes. Binding of peptidyl-tRNA to the P-site of wild-type ribosomes is much stronger than to their A-site. Addition of streptomycin dramatically reduces its affinity for the P-site. The S12 alternations make the P-site binding of peptidyl-tRNA much tighter, and the S4, S5 alterations make it weaker than in the case of the wild-type. We find that when binding of peptidyl-tRNA to the A-site is weak, then the affinity for the P-site is stronger, and vice versa. From these results, we formulate a hypothesis for the actions of streptomycin and neomycin based on deformations of the 16S rRNA tertiary structure. The results are also used to interpret some in vivo experiments on translational processivity.

Binding of S21 to the 50S subunit and the effect of the 50S subunit on nonradiative energy transfer between the 3' end of 16S RNA and S21

Escherichia coli ribosomal protein S21 was labeled at its single cysteine group with a fluorescent probe. Labeled S21 showed full activity in supporting MS2 RNA-dependent binding of formylmethionyl-tRNAf to 30S ribosomal subunits. Fluorescence anisotropy measurements and direct analysis on glycerol gradients demonstrate conclusively that labeled S21 binds to 50S ribosomal subunits as well as to 30S and 70S particles. The relative binding affinities are in the order 70S greater than 30S greater than 50S. Other results presented appear to indicate that S21 is bound in the same position on either 50S subunits or 30S subunits as in 70S ribosomes, suggesting that the protein is bound simultaneously to both subunits in the latter. Addition of 50S subunits to 30S particles containing probes on S21 and at the 3' end of 16S RNA caused a decrease in the energy transfer between these points. The results correspond to an apparent change in distance from 51 to 61 A.

Localization of the 3' end of 16S rRNA in Escherichia coli 30S ribosomal subunits by immuno electron microscopy

The location of the 3' end of 16S rRNA in E. coli 30S ribosomal subunits has been determined by immuno electron microscopy. The 3' terminal adenosine of isolated 16S rRNA was oxidized with sodium periodate and reacted with N-gamma-(2,4-dinitrophenyl) aminobutyric acid hydrazide. Functionally active 30S subunits were reconstituted from DNP-16S rRNA and total 30S ribosomal proteins. DNP-30S subunits were complexed with DNP-specific IgG-antibody and examined in the electron microscope. The 3' end of the 16S rRNA was mapped at a single region located at the inner side of the large lobe of the 30S subunit. The location of the 3' end also provides information as to the topography of the binding domain of natural mRNA on 30S subunits, since a pyrimidine-rich sequence at the 3' terminal region of 16S rRNA participates in the correct alignment of natural mRNAs during initiation complex formation.

Dinucleotide codon-anticodon interaction as a minimum requirement for ribosomal aa-tRNA binding: stabilisation by viomycin of aa-tRNA in the A site

The requirements for the decoding process at the ribosomal A site have been investigated in the presence of viomycin. For these studies natural mRNA was replaced either by the synthetic oligonucleotide A-U-G(-U)n, with 0 less than or equal to n less than or equal to 4, or by a physical mixture of the oligonucleotides A-U-G and various oligo(U) sequences. Thus the effect of the "removal" of selected covalent bonds from the sequence A-U-G(U)n could be studied. When the ribosomal P site contains tRNAMetf, then normally the full hexanucleotide "messenger" A-U-G-U-U-U is needed for the EF-Tu-mediated binding of Phe-tRNA into the A site. However in presence of viomycin the pentanucleotide A-U-G-U-U suffices for this. It is also possible in the presence of viomycin to replace A-U-G-U and U-U. In all the above systems the binding of Phe-tRNA required the presence of EF-Tu and GTP. The results suggest that viomycin reinforces interactions between aa-tRNA and the A site after the codon-anticodon recognition step.

Tetranucleotides as effectors for the binding of initiator tRNA to Escherichia coli ribosomes

Oligonucleotides such as G-A-G-G, which are complementary to the C-U-C-C region at the 3' end of 16-S RNA, inhibit the R17-RNA-dependent binding of the initiator tRNA (fMet-rRNA) to 30-S ribosomal subunits. However, if phage RNA is replaced by A-U-G, the same oligonucleotides stimulate the binding of fMet-tRNA to the 30-S subunits. This indicates that the formation of the RNA x RNA hybrid acts as a positive control signal for the selection of the initiator tRNA by the 30-S-subunit x mRNA complex. Tetranucleotides of the type A-U-G-N (where N = A, G, C or U) stimulated the IF-2-dependent binding of fMet-tRNA to the 30-S subunit more effectively than A-U-G, with A-U-G-R better than A-U-G-Y (where R is a purine nucleoside and Y is a pyrimidine nucleoside). Since the 3'-terminal adenosine in A-U-G-A can be replaced by 6-deamino-adenosine, a stacking type of interaction between U-33 of tRNA and N of A-U-G-N should additionally stabilize the codon-anticodon complex. The situation is strictly reversed for 70-S ribosomes where A-U-G is the best codon followed by A-U-G-U, A-U-G-C, A-U-G-G and A-U-G-A. Replacement of GTP by guanosine 5'-[beta, gamma-methylene]triphosphate (GuoPP[CH2]P] results in A-U-G-A becoming more efficient than A-U-G as the codon for the binding of fMet-tRNA to 70-S ribosomes. This indicates that IF-2 and GTP hold the anticodon of the fMet-tRNA in a conformation capable of binding to a tetranucleotide codon. GTP hydrolysis and release of IF-2 from the 70-S ribosome results in a change of the tertiary structure of fMet-tRNA as a consequence of which the initiator tRNA reassumes the conformation which preferentially binds to A-U-G.

Inhibition of the initiation of translation by a factor isolated from Escherichia coli cells

A low molecular weight factor isolated from Escherichia coli cells was found to inhibit protein synthesis in vitro directed by RNA of bacteriophage R-17. The factor also inhibited poly(U)-directed translation, but higher concentrations were required. When the factor was added after R-17 RNA-directed translation was initiated, the onset of inhibition was delayed. Initiation-independent translation of polysomes was not inhibited. The factor inhibited the binding of N-formylmethionyl-tRNAfMet to 70S ribosomes to form the 70S initiation complex, and it released the N-flrmylmethionyl-tRNAfMet from preformed complexes. The factor did not prevent the formation of N-formylmethionylpuromycin. It was concluded that the factor inhibits specifically the initiation of translation.

Identification of cysteine-10 of protein S18 as part of the mRNA-binding site of Escherichia coli ribosomes by affinity-labeling studies with a chemically reactive A-U-G analog

The reaction of a bromoacetamidophenyl derivative of the initiation codon A-U-G (A-U-G) with tight couples of Escherichia coli ribosomes leads to an exclusive crosslinking of label to protein S18. This crosslinking inhibits A-U-G-directed fMet-tRNAfMet binding into the puromycin-sensitive site of ribosomes and stimulates elongation-factor-dependent binding of Met-tRNAmMet. It is, therefore, concluded that protein S18 is located at or near the aminoacyl-tRNA binding site of E. coli ribosomes. Peptide as well as amino acid analysis shows that the reaction between A-U-G and ribosomes took place at cysteine-10 of protein S18. A-U-G could not be crosslinked to ribosomal proteins of the temperature-sensitive E. coli strain 258ts, where arginine-11 of protein S18 is replaced by a cysteine residue.

Location of protein S1 of Escherichia coli ribosomes at the 'A'-site of the codon binding site. Affinity labeling studies with a 3'-modified A-U-G analog

An affinity analog with a 5-bromoacetamido uridine 5'-phosphate moiety bonded to the 3' end of A-U-G has been prepared with the aid of polynucleotide phosphorylase. This 3'-modified, chemically reactive A-U-G analog was used to probe the ribosomal codon binding site. The yield of the reaction depended strongly on the ribosomal source and was sensitive to salt-washing ribosomes. The major crosslinking product was identified to be protein S1. Since the reaction of this 3'-modified A-U-G programmed ribosomes for Met-tRNA-Met-M binding, it is concluded that protein S1 is located at or near the 3'-side of the ribosomal codon binding site.

Affinity labeling of the ribosomal decoding site with an AUG-substrate analog

The trinucleotide AUG was condensed at the 5'-end with N-bromoacetyl-p-aminophenylphosphate. This bromoactylated AUG analog reacted irreversibly with the mRNA binding site of Escherichia coli 70S ribosomes. After reaction of 70S ribosomes with the AUG analog, labeled 30S subunits could be isolated that were programmed for initiation-factor-dependent binding of fMet-tRNAfMet. This shows that this AUG-affinity label reacted in the decoding site for fMet-tRNAfMet. By combination of sodium dodecyl sulfate-, Sarkosyl-, and ureapolyacrylamide gel electrophoresis the AUG-affinity label was found to be irreversibly bound to ribosomal proteins S4, the ram gene product, and S18.

The irreversible step in formation of initiation complexes of Escherichia coli

At some stage during initiation the ribosomal subunits of Escherichia coli must become irreversibly coupled, since polysomal ribosomes, in contrast to free ribosomes, are not dissociated by initiation factor IF-3. To determine when irreversibility develops we have compared the response to IF-3 of mature, puromycin-reactive initiation complexes, made with GTP, and of intermediate, puromycin-unreactive complexes, made with GMPPCP. The latter complexes initially appeared to be dissociated by the factor but this effect was found to be due to artificial loss of the ligands at the Mg2+ concentration customary in the test for dissociation. At a slightly higher Mg2+ concentration (4 mM), sufficient to retain the ligands, the GMPPCP complexes were not significantly dissociated by IF-3, at concentrations that caused complex dissociation of free ribosomes. It thus appears that the intermediate 70S initiation complex, though less stable to ionic dissociation than the mature complex, is in effect irreversible under physiological conditions.

Selective inhibition of initiating ribosomes by spectinomycin

Spectinomycin at low concentrations inhibits initiating ribosomes but not ribosomes already engaged in chain elongation. The initiating ribosomes are blocked in some step after formation of the initiation complex, probably the first translocation. Cells inhibited by spectinomycin accumulate polysomes, and these have proved to be unstable polyinitiation complexes: they can be pulse-labeled with methionine but not with valine, and they disappear after addition of rifampicin. Hence, the blocked ribosomes evidently are released and then reinitiate. In heterozygotes this cyclic reinitiation by the sensitive ribosomes, each blocking an initiation site for an average of 10-15 min, can explain (just as with streptomycin) the dominance of sensitivity over resistance.

Translocation of messenger RNA and "accommodation" of fMet-tRNA

Messenger RNA is moved a distance of approximately three nucleotides in the 5' direction relative to the ribosome during the translocation of peptidyl-tRNA from the A to the P site. This movement is catalyzed by G factor and is dependent on the hydrolysis of GTP. In contrast, mRNA is not moved during the f(2)-catalyzed hydrolysis of GTP that is involved in the activation of ribosome-bound fMet-tRNA. This second type of GTP-dependent reaction has been named "Accommodation".

Breakdown by streptomycin of initiation complexes formed on ribosomes of Escherichia coli

Streptomycin induces breakdown of the completed 70S initiation complex on ribosomes of Escherichia coli, but it does not interfere with any step in the formation of the complex. Moreover, it does not appear to interact with the ribosome in any special way during initiation, since the kinetics of breakdown are the same whether streptomycin is added before formation of the initiation complex, or after its completion, or (as previously observed) after formation of a polypeptide. fMet-tRNA is released as such, without chain elongation; it is released from a puromycin-reactive ("P") site. Streptomycin thus appears to distort not only the A site of the ribosome (as suggested earlier) but also the P site.

A new protein synthesis factor from Escherichia coli

A new factor that effects protein synthesis by Escherichia coli extracts was partially purified from the 1 M NH(4)Cl wash of E. coli ribosomes. This factor stimulates the binding of aminoacyl-tRNA to 30S ribosomes, and it increases the rate of synthesis of polyphenylalanine in the presence of 30S and 50S subunits.

Peptide chain termination. VII. The ribosomal and release factor requirements for peptide release

Release factors participate in release of fMet from fMet-tRNA . AUG . ribosome intermediates upon binding to ribosomes. This release requires R factor and occurs in the absence of terminator codon in reactions containing 20 per cent ethanol. Release occurs only when both 30S and 50S ribosomal subunits are present and when fMet-tRNA is located in the ribosomal P site. Release factor-dependent deacylation of fMet-tRNA is inhibited by sparsomycin, amicetin, lincocin, and chloramphenicol, antibiotics which have little effect on binding of R factor to ribosomes. The possible role of peptidyl transferase in the release reaction is discussed.

Deacylated tRNA-phe binding to a reticulocyte ribosomal site for the initiation of polyphenylalanine synthesis

The initiation of polyphenylalanine synthesis at low MgCl(2) concentration in the reticulocyte transfer system has been found to have a stringent requirement for deacylated tRNA(Phe). An initial poly-U-directed complex between deacylated tRNA(Phe) and ribosomes is formed. The onset of polyphenylalanine synthesis causes the rapid release of tRNA(Phe) from the complex. Thermal dissociation studies indicate that deacylated tRNA(Phe) and phenylalanyl-tRNA are bound to the same ribosomes. A total of three ribosomal tRNA binding sites is indicated.