A ribosome-catalyzed reaction between N-formylmethionyl-trna and puromycin

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.

Recent studies implicate the nucleolus as the major site of nuclear translation

The nucleolus is the most prominent morphological feature within the nucleus of eukaryotic cells and is best known for its role in ribosome biogenesis. It forms around highly transcribed ribosomal RNA gene repeats which yield precursor rRNAs that are co-transcriptionally processed, folded and, while still within the nucleolus, associate with most of the ribosomal proteins. The nucleolus is therefore often thought of as a factory for making ribosomal subunits, which are exported as inactive precursors to the cytoplasm where late maturation makes them capable of mRNA binding and translation initiation. However, recent studies have shown substantial evidence for the presence of functional, translation competent ribosomal subunits within the nucleus, particularly in the nucleolus. These observations raise the intriguing possibility that the nucleolus, as well as being a ribosome factory, is also an important nuclear protein-synthesis plant.

Specific bonding of puromycin to full-length protein at the C-terminus

Puromycin, an analog of the 3' end of aminoacyl-tRNA, causes premature termination of translation by being linked non-specifically to growing polypeptide chains. Here we report the interesting phenomenon that puromycin acting as a non-inhibitor at very low concentration (e.g. 0.04 microM) can bond only to full-length protein at the C-terminus. This was proved by using a carboxypeptidase digestion assay of the products obtained by Escherichia coli cell-free translation of human tau 4 repeat (tau4R) mRNA in the presence of low concentrations of puromycin or its derivatives. The tau4R mRNA was modified to code for three C-terminal methionines, which were radioactively labeled, followed by a stop codon. The translation products could not be digested by carboxy-peptidase if puromycin or a derivative was present at the C-terminus of full-length tau4R. Puromycin and its derivatives at 0. 04-1.0 microM bonded to 7-21% of full-length tau4R, depending on the ability to act as acceptor substrates. Furthermore, the bonding efficiency of a puromycin derivative to tau4R was decreased by addition of release factors. These results suggest that puromycin and its derivatives at concentrations lower than those able to compete effectively with aminoacyl-tRNA can bond specifically to full-length protein at a stop codon. This specific bonding of puromycin to full-length protein should be useful for in vitro selection of proteins and for in vitro and in vivo C-terminal end protein labeling.

Translocation in Bacillus subtilis: characterization of elongation factor G by peptidyl-[3H]puromycin synthesis

This communication describes the characterization of elongation factor G from Bacillus subtilis by the translocation of "native" peptide donors. Translocation was followed by elongation factor G-dependent increase in the synthesis of peptidyl-[3H]puromycin using "washed" ribosomes carrying in vivo-bound peptidyl-transfer ribonucleic acid ("native" peptidyl-transfer ribonucleic acid) molecules as peptide donors. Such ribosomes were obtained from cell extracts by washing at a high salt concentration. The use of "native" peptide donors facilitated the study of translocation under conditions that are closer to the in vivo state than those in the methods previously employed.

Growth and initiation of protein synthesis in Escherichia coli in the presence of trimethoprim

Escherichia coli grew exponentially at a reduced rate in the presence of 50 or 100 mug of trimethoprim/ml if the low-molecular-weight products of folate metabolism or their precursors (thymidine, purines, methionine, glycine, and pantothenate) were supplied in the medium. Folate metabolism was inhibited 99.9% by these concentrations of trimethoprim, but a low level of formylation of methionyl transfer ribonucleic acid (met-tRNA(F)) could be detected. However, in a medium containing all major amino acids, nucleosides, and vitamins, formylation of met-tRNA(F) was undetectable in the presence of trimethoprim. No other amino-masked amino acids were detected, and methionine remained a major amino-terminal amino acid of mature proteins. met-tRNA(F) was rapidly labeled with exogenous methionine and was associated with 30s ribosomal subunits and 70s ribosomes. It was concluded that initiation of protein synthesis can occur with unformylated met-tRNA(F) in E. coli. Changes in macromolecular composition were associated with the lack of formylation, in particular a fourfold increase in both met-tRNA(F) and ribosomal subunits. These changes would tend to compensate for the low specific rate of initiation with unformylated met-tRNA(F).

Peptidyl puromycin synthesis; effect of several antibiotics which act on 50 S ribosomal subunits

The effects of several antibiotics which are know to bind with 50 S ribosomal subunits, on the formation of several di- and tri-peptidyl puromycins have been examined. Tylosin and spiramycin inhibited the formation of phenylalanyl-(14)C-phenylalanyl-puromycin, glycyl-(14)C-phenyllalanyl-puromycin, leucyl-(14)C-phenylalanyl-puromycin, N(epsilon)-carbobenzoxylysyl-(14)C-phenylalanyl-puromycin, and valyl-glycyl-(14)C-phenylalanyl-puromycin as well as N-acetyl-(14)C-phenylalanyl-puromycin. Of these compounds, erythromycin and oleandomycin selectively inhibited the formation of phenylalanyl-(14)C-phenylalanyl-puromycin. Although chloramphenicol and lincomycin inhibited the formation of most of these peptidyl puromycins, the formation of phenylalanyl-(14)C-phenylalanyl-puromycin and leucyl-(14)C-phenylalanyl-puromycin was found to be resistant to these antibiotics. So far, no significant effect of siomycin has been observed on pepetidyl puromycin formation in the absence of G factor.

Studies on the formation of transfer ribonucleic acid-ribosome complexes. XI. Antibiotic effects on phenylalanyl-oligonucleotide binding to ribosomes

The effect of antibiotics on the binding of phenylalanyl-oligonucleotide to ribosomes has been examined. The results show that many classes of antibiotics can interfere with binding of the aminoacyl-oligonucleotide terminus of tRNA to ribosomes: chloramphenicol, sparsomycin, D-WIN-5094, vernamycin A, PA114A, streptogramin, amicetin, gougerotin, tylosin, and spiramycin III. The results are consistent with the hypothesis that these antibiotics inhibit protein synthesis by interfering with the binding of the aminoacyl-end of aminoacyl-tRNA to ribosomes.

Ribosomal proteins of Escherichia coli. I. Demonstration of different primary structures

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