Mechanism of translational coupling between coat protein and replicase genes of RNA bacteriophage MS2

We have analyzed the molecular mechanism that makes translation of the MS2 replicase cistron dependent on the translation of the upstream coat cistron. Deletion mapping on cloned cDNA of the phage shows that the ribosomal binding site of the replicase cistron is masked by a long distance basepairing to an internal coat cistron region. Removal of the internal coat cistron region leads to uncoupled replicase synthesis. Our results confirm the model as originally proposed by Min Jou et al. (1). Activation of the replicase start is sensitive to the frequency of upstream translation, but never reaches the level of uncoupled replicase synthesis.

Translational interference at overlapping reading frames in prokaryotic messenger RNA

In overlapping reading frames of prokaryotic mRNA, the ribosome-binding site (RBS) of the downstream cistron is part of the coding sequence of the upstream message. We have examined whether the rate of translation in Escherichia coli can be sufficiently high to preclude the use of an RBS in initiation of protein synthesis when it is part of an actively decoded reading frame. The two sets of gene overlap present in the RNA phage MS2 are used as a model system. We find that translation of an upstream cistron can fully block initiation of protein synthesis at the overlapping RBS of the downstream cistron. Nonsense mutations in the upstream gene restore the translation of the downstream gene.

Effect of the sequences upstream from the ribosome-binding site on the yield of protein from the cloned gene for phage MS2 coat protein

The translational efficiency of the coat protein gene of phage MS2 has been examined in vivo with respect to neighbouring sequences. The cloned MS2 DNA has been gradually shortened starting at the 5' or 3' terminus, and its effect on coat protein synthesis monitored. Removal of the 3'-terminal sequences had little influence. In contrast, the gradual removal of the 5'-terminal region profoundly reduces translation. Long before the ribosomal binding site (RBS) of the coat protein (CP) gene is reached, the yield of CP has dropped by one order of magnitude. Functional half-lives of the various messengers were found not to be significantly different. Available evidence indicates that the secondary structure of the RBS in native and shortened MS2 RNA is identical. We infer that important determinants for ribosome recognition lie 5' to the RBS region of the MS2 RNA coat gene.

Lysis gene expression of RNA phage MS2 depends on a frameshift during translation of the overlapping coat protein gene

Translation of the lysis cistron of MS2 RNA requires a frameshift of ribosomes reading the upstream coat protein mRNA. The out-of-phase fraction of ribosomes terminates at either one of two nonsense codons just preceding the lysis cistron. Termination is followed by initiation at the start codon of the lysis protein message.

Translational fidelity and specificity of ribosomes cleaved by cloacin DF13

The effect of cloacin DF13 cleavage on several functional properties of the ribosome has been studied in a translational system in vitro. Cleaved ribosomes synthesize relatively shorter polypeptide chains on synthetic and natural templates. Their translational specificity is, however, unchanged as judged by the read-out of MS2 RNA. Here, cleaved as well as control ribosomes start translation only on the coat cistron of the phage RNA. Cloacin cleavage of ribosomes increases their fidelity of translation. Differential inhibition of translation of synthetic and natural template was not observed.

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.

Involvement of ribosomal protein S1 in the assembly of the initiation complex

Antibodies against ribosomal protein S1 (anti-S1) have been used to determine the function of S1 in the partial reactions involved in the translation of MS2 RNA in vitro. Vacant ribosomes are fully sensitive to the antibodies, whereas elongating ribosomes are resistant. We have determined at which stage of translation the resistance to anti-S1 is acquired. We find that insensitivity to anti-S1 already arises upon mixing 30-S subunits with MS2 RNA. Apparently the two particles form a complex in which S1 is functionally protected against its antibody. Complex formation depends on elevated temperature, a suitable ionic environment and it is stimulated by the initiation factor IF-3. It does not depend on IF-1, IF-2 or fMet-tRNA. Thus ribosomes have the potential to recognize the messenger in the absence of fMet-tRNA. Protein S1 appears directly involved in this primary recognition reaction.

Exchange of individual ribosomal proteins between ribosomes as studied by heavy isotope-transfer experiments

Whether the individual ribosomal proteins undergo exchange between robosomes in vivo during cell growth was examined using heavy isotope transfer methodology. E. coli was grown first in a heavy isotope medium in the presence of [3H] leucine and then transferred to normal medium and allowed to grow for one generation in the presence of [14C] leucine. The "heavy" and "light" ribosomes that were present in such cells were separated by sedimentation and the ribosomal proteins resolved by two-dimensional gel electrophoresis. The individual proteins were burnt in O2 and their contents of [3H] and [14C] labels determined. From the analysis of the data we find that the great majority of the ribosomal proteins of E. coli does not undergo exchange during cell growth. Proteins which were found to exchange to varying levels in different transfer experiments were S1, S2, L7/L12, L9, L10 and L33. All of them except L9 exchanged to the same levels in control experiments in which separately grown heavy and light cells were mixed and processed. These proteins therefore undergo exchange during cell breakage and ribosome isolation. Protein L9 consistently showed appreciably greater exchange in transfer experiments as compared to the controls suggesting that it may exchange in vivo.

The effect of the ribosomal protein S1 from Escherichia coli on the synthesis in vitro of bacterial-, DNA phage- and RNA phage proteins

Using an in vitro preparation for protein synthesis, we have studied the effect of the ribosomal protein S1 from Escherichia coli on the synthesis of the coat protein of the RNA-containing phages Qbeta and MS2, on that of an "early" and a "late" enzyme encoded by the DNA containing phage T7, and on that of anthranilate synthetase, an enzyme encoded by the bacterial tryptophan operon. Our results indicate that for the synthesis of these five proteins the presence of S1 is required. From these results we conclude that S1 is an essential protein for the translation of bacterial and bacteriophage messenger RNA.

The specific role of ribosomal protein S1 in the recognition of native phage RNA

The previously reported requirement of ribosomal protein S1 for translation of phage RNA is now shown to be related to the involvement of the protein in initiation complex formation. The structure of the messenger RNA appears to be uniquely related to S1 function, since translation and initiation and midly unfolded phage RNA (by modification with formaldehyde) are independent of S1. It is proposed that S1 functions in conjunction with initiation factor IF-3 by recognizing and unfolding elements of the tertiary structure of phage RNA. A model is suggested for S1 function in both initiation of protein synthesis and initiation of phage RNA replication.