A novel form of initiation factors from escherichia coli which binds formyl methionyl tRNA and GTP: "F2-F3 complex"

Generation of potential structures for the G-domain of chloroplast EF-Tu using comparative molecular modeling

Comparative molecular modeling has been used to generate several possible structures for the G-domain of chloroplast elongation factor Tu (EF-Tu(chl)) based on the crystallographic data of the homologous E. coli protein. EF-Tu(chl) contains a 10 amino acid insertion not present in the E. coli protein and this region has been modeled based on its predicted secondary structure. The insertion appears to lie on the surface of the protein. Its orientation could not be determined unequivocally but several likely structures for the nucleotide binding domain of EF-Tu(chl) have been developed. The effects of the presence of water in the Mg2+ coordination sphere and of the protonation state of the GDP ligand on the conformation of the guanine nucleotide binding site have been examined. Relative binding constants of several guanine nucleotide analogs for EF-Tu(chl) have been obtained. The interactions between EF-Tu(chl) and GDP predicted to be important by the models that have been developed are discussed in relation to the nucleotide binding properties of this factor and to the interactions proposed to be important in the binding of guanine nucleotides to related proteins.

A circular dichroism study of Escherichia coli Initiation Factor-1 binding to polynucleotides

Binding of Escherichia coli Initiation Factor-1 protein to the nucleic acid lattice induces alterations in the secondary structures of a variety of purine and pyrimidine containing polynucleotides in both the single and double stranded conformations, as assessed by circular dichroism spectroscopy. The helical hairpin form of poly(U), the single-stranded stacked form of poly(C), and the duplex poly(A) x poly(U) (in the presence of Mg2+) are stoichiometrically converted by Initiation Factor-1 (IF-1) to structures spectrally indistinguishable from their partially or completely thermally denatured forms. By contrast, the binding of IF-1 to double stranded poly(C), single- and double-stranded poly(A) elicited spectral responses which were interpreted in terms of diminished base-base interaction, not equivalent to that induced by thermal means. Stoichiometric endpoints of 3-5 nucleotide residues/IF-1 were determined for polynucleotide structures in those cases where light scattering artifacts at low nucleotide residue to protein ratios were absent. In the absence of Mg2+ IF-1 was unable to elicit a conformation alteration effect in poly(A) x poly(U), while for poly(U) much less of an effect was observed than in the presence of this divalent ion. The functional significance of these results is briefly considered.

Initiation factor IF-3 and the binary complex between initiation factor IF-2 and formylmethionyl-tRNA are mutually exclusive on the 30-S ribosomal subunit

The formation of 30-S initiation complexes depends strongly on initiation factor IF-3; at molar ratios of IF-3 to 30-S ribosomes up to one a stimulation is observed, whereas at ratios higher than one, initiation complex formation declines strongly. The target of the observed inhibition of fMet-tRNA binding at high concentrations of IF-3 is the 30-S initiation complex itself. On the one hand addition of IF-3 to preformed 30-S initiation complexes leads to a release of bound fMet-tRNA which is linear with the amount of factor added, whereas no effect on isolated 70-S initiation complexes is seen. The release of fMet-tRNA from preformed 30-S initiation complexes is accompanied by a release of IF-2 in a one-to-one molar ratio which is in agreement with our previous findings showing that binding of fMet-tRNA takes place via a binary complex: IF-2 . fMet-tRNA (Eur. J. Biochem. 66, 181--192 and 77, 69--75). On the other hand increasing amounts of both IF-2 and fMet-tRNA relieve the IF-3-induced inhibition of 30-S initiation complex formation. From these findings it is concluded that IF-3 and the IF-2 . fMet-tRNA complex are mutually exclusive on the 30-S ribosome. This implies that under our experimental conditions MS2 RNA binding precedes fMet-tRNA binding if one accepts that the presence of IF-3 on the 30-S subunit is obligatory for messenger binding.

Derivatives of guanosine triphosphate with ribose 2'-hydroxyl substituents. Interactions with the protein synthetic enzymes of Escherichia coli

This report describes the preparation of four methylated and phosphorylated derivatives of GTP, 2'-O-methylguanosine 5'-triphosphate (PPP-Me2' Guo), and guanosine 2'-monophosphate 5'-triphosphate (PPP-Guo-2'P), 3'-O-methylguanosine 5'-triphosphate (PPP-Me3'Guo), and guanosine 3'-monophosphate 5'-triphosphate (PPP-Guo-3'P). These compounds were compared to GTP in their ability to support reactions catalyzed by Escherichia coli initiation factor 2(IF-2), elongation factor Tu (EF-Tu), and elongation factor G )EF-G). As with previously studied GTP analogues, the nucleotide specificities of IF-2-dependent N-formylmethionylpuromycin formation and EF-Tu-dependent Ac-Phe2-tRNA formation were similar. There was little difference between the reactions supported by GTP, PPP-Me2' Guo, PPP-Me3' Guo, and PPP-Guo-3'P, but PPP-Guo-2'P was a poor substrate with both enzymes. A spectrum of activity was observed in EF-G-dependent formation of N-acetylphenylalanylphenylalanylpuromycin. While PPP-Me2' Guo was almost as effective as GTP in supporting translocation, PPP-Guo-2'P was a very poor substrate, having even less activity than guanosine 3'-diphosphate 5'-triphosphate. Intermediate activities were observed with PPP-Me3' Guo and PPP-Guo-3'P, the former nucleotide being more active than the latter.

Activities of guanosine triphosphate analogues in reactions catalyzed by elongation factor Tu and initiation factor 2 of Escherichia coli

In earlier studies two natural analogues of GTP, guanosine 3'-diphosphate 5'-triphosphate (pppGpp) and dGTP, were found to substitute for GTP in reactions catalyzed by initiation factor 2 (IF-2) and elongation factor Tu (EF-Tu), while only dGTP could replace GTP with elongation factor G. These observations with IF-2 and EF-Tu have been extended to two analogues of GTP modified at the 3' ribose hydroxyl position, 3'-deoxyguanosine 5'-triphosphate (3'dGTP) and 3'-deoxy-3'-aminoguanosine 5'-triphosphate (3'dNH2GTP). These compounds were found to be similar to GTP, dGTP, and pppGpp in IF-2-dependent formation of N-formylmethionyl-puromycin and EF-Tu-dependent formation of N-acetyl-Phe-Phe-tRNA. The apparent Km values for the five guanosine nucleotides were 2 - 10(-6)-4 - 10(-6)M in the former reaction and 2-10(-7)--6-10(-7) M in the latter. These reactions did not have an absolute requirement for either an intact pentose ring or for the guanine base in the nucleotide. Although substantially less active than the guanine nucleotides, ITP and the dialcohol derived from GTP by periodate oxidation and borohydride reduction (ox-redGTP) were partially active in both the IF-2 and EF-Tu-dependent reactions, with apparent Km values about 40-100 times those of GTP.

The effect of tRNA derivatives bound with natural or synthetic mRNA on the interaction of Escherichia coli ribosomes with colicin E3

Ribosomal binding complexes directed by poly(U) or T4 mRNA were formed with aminoacyl-tRNA or its derivatives bound to predominantly the P or A binding site. The defined binding complexes were reacted with colicin E3 and the reaction was assessed by the ability of the complexes to proceed with polypeptide synthesis. The results indicated that only one of the four complexes tested was completely resistant to colicin E3-induced inactivation: that of Phe-tRNA bound in the presence of poly(U) to the A-site. The poly(U) directed complex of AcPhe-tRNA and the T4-mRNA-directed complex at the A-site appeared slightly resistant, while the T4 mRNA initiation complex was inactivated by colicin E3 in a manner similar to non-complexed ribosomes. Colicin E3 added to ribosomes after protein synthesis had been initiated affected the subsequent polymerization in a manner corresponding to the response of the binding complexes. Thus, poly(U)-translating ribosomes were less affected than ribosomes translating the viral mRNA. The vulnerability of natural-mRNA-directed binding complexes to inactivation by colicin E3 is in accord with the mode of inactivation by the colicin in vivo.

Blocks in elongation and initiation of protein synthesis induced by interferon treatment in mouse L cells

Synthesis of polypeptide chains coded by exogenous messenger RNAs is inhibited in cell-free extracts from interferon-treated mouse L cells, due to a "deficiency" in some specific tRNA species. A detailed analysis shows that polypeptide chain elongation is blocked and incomplete chains are formed. After a few minutes, however, initiation of new polypeptide chains is also blocked. Messenger RNA still binds to ribosomes but initiator Met-tRNA(FMET) binding is inhibited. The block in initiation appears to be secondary to the block in elongation.

Interaction of poly(A) and mRNA with eukaryotic initiator met-tRNA-f binding factor: identification of this activity on reticulocyte ribonucleic acid protein particles

Messenger ribonucleoprotein particles (mRNPs) have been isolated from rabbit reticulocyte polysomes. One of the proteins of the mRNP complex has many properties of a specific eukaryotic initiation factor, the soluble Met-tRNA-f binding protein. A purified preparation of this factor, in addition to binding Met-tRNA-f, binds poly(A) and globin mRNA. The binding of these substrates is greater than that obtained with other natural or artificial polyribonucleotides. The mRNP fraction also binds poly(A) and Met-tRNA-f. Since the factor which binds initiator tRNA also binds poly(A) and mRNA, and this activity can be found on mRNPs, there may be a relationship between initiator tRNA binding and messenger binding in early events of eukaryotic initiation.

Factor-promoted dissociation of free ribosomes in a rabbit reticulocyte lysate system: inhibition and requirement for an energy source

A factor that promoted the dissociation of ribosomes into ribosomal subunits in a complete globin-synthesizing system was isolated from rabbit reticulocyte ribosomes. The factor stimulated both globin synthesis and the association of the small ribosomal subunit with polyribosomes. The dissociation of free ribosomes by the factor could be followed as an independent reaction in the presence of a high concentration of cycloheximide, which inhibited translation and the resulting accumulation of runoff subunits. This reaction required an energy source and was inhibited by P-(5'-guanylyl)-methylenebisphosphonate. These data suggest that energy generated by hydrolysis of GTP may be a requirement for the dissociation reaction. Aurintricarboxylic acid inhibited the factor-mediated dissociation of free ribosomes but not the factor-mediated preservation of subunits formed on peptide-chain termination.

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.