Role of protein factor in the functional binding of ribosomes to natural messenger RNA

Dual functions of ribosome recycling factor in protein biosynthesis: disassembling the termination complex and preventing translational errors

We summarize in this communication the data supporting the two functions of ribosome recycling factor (RRF, originally called ribosome releasing factor). The first described role involves the disassembly of the termination complex which consists of mRNA, tRNA and the ribosome bound to the mRNA at the termination codon. This process is catalyzed by two factors, elongation factor G (EF-G) and RRF. RRF stimulated protein synthesis as much as eight-fold in the in vitro lysozyme synthesis system, when ribosomes were limiting. In the absence of RRF, ribosomes remain mRNA-bound at the termination codon and translate downstream codons. In the in vitro system, the site of reinitiation is the triplet codon 3' to the termination codon. RRF is an essential protein for bacterial life. Temperature sensitive (ts) RRF mutants were isolated and in vivo translational reinitiation due to inactivation of ts RRF was demonstrated using the beta-galactosidase reporter gene placed downstream from the termination codon. A second function of RRF involves preventing errors in translation. In polyphenylalanine synthesis programmed by polyuridylic acid, misincorporation of isoleucine, leucine or a mixture of amino acids was stimulated upto 17-fold when RRF was omitted from the in vitro system. RRF did not influence the large error (10-fold increase) induced by streptomycin. This means that RRF participates not only in the disassembly of the termination complex but also in peptide elongation. Extending this concept and its conventional role for releasing ribosomes from mRNA, involvement of RRF in the reinitiation in the 3A' system (a construct using S aureus protein A, a collaborative work with Dr Isaksson), in programmed frame shifting, in trans-translation with 10Sa RNA (collaborative work with Dr Muto), and in the reinitiation downstream from the ORF A of the IS 3 (insertion sequence of a transposon, collaborative work with Dr Sekine) are discussed on the basis of preliminary data to be published elsewhere. Finally, we review the known RRF sequences from various organisms including eukaryotes and discuss the possible mechanism for disassembly of the eukaryotic termination complex.

Translation initiation factor 2 alters transcriptional selectivity of Escherichia coli ribonucleic acid polymerase

Preparations of translation initiation factor IF-2 strongly stimulate the production of rRNA by Escherichia coli RNA polymerase but have little effect on the synthesis of other RNA species. The factor alters the sedimentation characteristics of RNA polymerase holoenzyme. We suggest a mechanism by which IF-2 alters the pattern of transcriptional selectivity of RNA polymerase.

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.

Translation of MS2 RNA in vitro in the absence of initiation factor IF-3

An Escherichia coli cell-free translational system, deprived of initiation factor IF-3, has been used to study the role of the factor in protein synthesis. In this system, 30-S ribosomal subunits are preincubated together with MS2 phage RNA in a small volume in the presence of 10 mM Mg(Ac)2; the missing components required for protein synthesis are then added and assembly of elongating ribosomes is allowed to occur. This stepwise assembly process permits formation of functional complexes which can carry out protein synthesis in the complete absence of IF-3. The translational products, obtained in the absence of IF-3, have been analysed and shown to be similar to those synthesized in the presence of the factor. The main product observed is the phage coat protein.

Differential sensitivity to antibiotics of trp mRNA synthesis originating at the trp promoter and the lambda promoter

Transcription of the Escherichia coli trp operon translocated into the early region of bacteriophage lambda can occur under the control of either of two promoters, the trp promoter on the lambda promoter (OL of N gene). (Imamato, F. and Tani, S. (1972) Nat. New Biol. 240, 172-175 and Ihara S. and Imamoto, F. (1976) Biochim. Biophys. Acta 432, 199-211). Trp mRNA synthesis originating at the trp promoter stopped when translation was blocked by chloramphenicol tetracycline erythromycin or puromycin. In contrast, trp mRNA synthesis originating at the lambda promoter was not affected by antibiotic action. This probably is a reflection of the properties of the "immediate early" class of genes of lambda, whose transcription in initiated at the PL. promoter and is not inhibited by the antibiotic. The inference is strengthened by comparable results with phage lambdatrpE-A (carrying an intact tro operon) and lambdatrpBA (carrying the operator-distal two genes but missing the trp promoter and operator). Thus it seems that either the promoter or other gene(s) located at the beginning of the operon, either at polymerase addition or because of some feature of the transcript, can determine a requirement for "coupling" of RNA polymerase to the translational machinery in vivo.

Requirement for ribosome-releasing factor for the release of ribosomes at the termination codon

With the use of 3H-labeled R 17 amB2 phage RNA having an UAG codon at the seventh triplet of the coat cistron, release of the RNA from ribosomes at the termination codon was studied. The ribosome-releasing factor previously described was shown to stimulate the process of mRNA release at the termination factor (RF-1). GTP was required for this process and guanosine 5'-(beta,gamma-methylene)triphosphate could not replace GTP. No apparent change of size of R 17 RNA was observed during the release of the R 17 RNA from the ribosomes. The ribosome-releasing factor is distinct from the known termination codon-specific factor such as RF-1.

The role of IF-3 in the translation of T7- and phi80trp messenger RNA

The DNA dependent synthesis of proteins was studied with a system composed of DNA, washed ribosomes, centrifuged (150,000 X g) bacterial extract from Escherichia coli and purified initiation factors IF-1 and IF-2. Synthesis of active enzymes encoded by the tryptophan (trp)-operon of E. coli was found to depend strongly on the addition of IF-3, with the same IF-3 dependency for all 5 gene-products of this operon, irrespective of the presence of the promotor proximal gene trpE. Synthesis of T7 RNA polymerase with T7 DNA as a template, however, was completely independent of the addition of IF-3. The same difference in IF-3 requirement was found when we compared the overall protein synthesis directed by these templates. This difference could be related to the effect of IF-3 on the formation of initiation complexes with the in vitro prepared mRNA: initiation complexes are readily formed with T7 mRNA also in the absence of IF-3, whereas the formation of these complexes with phi80trp mRNA almost completely depends on the presence of this factor.

Defective 30S ribosomal subunits after infection of Escherichia coli by T2 ghosts

Ribosomes from ghost-treated Escherichia coli can form in vitro initiation complexes but cannot translate added template RNA because of a defect in the 30S subunit; 16S rRNA is degraded.

Interaction of Escherichia coli 30S ribosomal subunits with MS2 phage RNA in the absence of initiation factors

MS2 RNA binds at 0 degrees to 30S subunits from E. coli and, to a smaller extent, to those of a Pseudomonas species, as judged by filtration on nitrocellulose membranes; this mRNA does not bind to 30S subunits from Bacillus brevis or Caulobacter crescentus. Binding does not depend on the presence of initiation factors; it is sensitive to aurintricarboxylic acid but insensitive to edeine and is competitive with such synthetic polynucleotides as poly(U) and poly(AUG). Complex formation can also be detected by electrophoresis on polyacrylamide-agarose gels. By this procedure, E. coli 30S subunits are separated into two major components. Only the more slowly moving component, which contains the ribosomal protein S1, interacts with the RNA.

Messenger selection by bacterial ribosomes

The counterpart of Escherichia coli initiation factor 3(IF-3) was isolated from Caulobacter crescentus, purified to homogeneity, and used in comparative studies on in vitro translation of RNA from the C. crescentus RNA phage Cb5 and of coliphage MS2 RNA. The two phage RNAs are similar in physical properties and analogous in genetic content. The factor, C-IF-3, substitutes for E. coli IF-3 and promotes correct translation of MS2 RNA by E. coli ribosomes. Conversely, E. coli IF-3 substitutes for C-IF-3 in translation of Cb5 RNA by C. crescentus ribosomes. However, each phage RNA could be translated only by host ribosomes or by mixed ribosomes containing the host 30S subunit. C-IF-3 dissociates C. crescentus and E. coli 70S ribosomes into subunits. It binds phage, ribosomal, and, less efficiently, transfer RNA.

Effect of elevated temperatures on protein synthesis in Escherichia coli

Upon a temperature shift from 30 C to 42 to 44 C, Escherichia coli experiences a transient slowdown in rate of optical density increase, uridine incorporation, and amino acid incorporation. The data show that the primary target for thermal inactivation is a molecule(s) required for the initiation of protein synthesis. The effect on ribonucleic acid synthesis is a secondary effect.

Control of single ribosome formation by an initiation factor for protein synthesis

30 and 50S ribosomal subunits, released from polysomes upon polypeptide chain termination, possess a high affinity for each other and readily form single ribosomes. Highly purified initiation factor F3(B), acting stoichiometrically, prevents the formation of single ribosomes without promoting their dissociation. These findings are interpreted in terms of a ribosome cycle in which a limiting amount of factor F3(B) controls the number of ribosomes active in protein synthesis, in response to metabolic changes in the cell, by regulating the flow of ribosomal subunits into polysomes or into a sidetrack pool of synthetically inactive single ribosomes. The reported apparent ribosome dissociation activity of F3(B) is explained.

Stimulation of DNA-dependent RNA synthesis by a protein associated with ribosomes

A protein factor partially purified from ribosomes of Escherichia coli RC(rel) cells starved for an amino acid markedly stimulates DNA-dependent RNA synthesis by core and whole RNA polymerase. This protein factor appears to differ from the sigma factor and the M factor. The properties of this new factor and its mechanism of action have been explored.