Studies on translocation of F-MET-tRNA and peptidyl-tRNA with antibiotics

Mechanism of Action of Ribosomally Synthesized and Post-Translationally Modified Peptides

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a natural product class that has undergone significant expansion due to the rapid growth in genome sequencing data and recognition that they are made by biosynthetic pathways that share many characteristic features. Their mode of actions cover a wide range of biological processes and include binding to membranes, receptors, enzymes, lipids, RNA, and metals as well as use as cofactors and signaling molecules. This review covers the currently known modes of action (MOA) of RiPPs. In turn, the mechanisms by which these molecules interact with their natural targets provide a rich set of molecular paradigms that can be used for the design or evolution of new or improved activities given the relative ease of engineering RiPPs. In this review, coverage is limited to RiPPs originating from bacteria.

Bottromycins - biosynthesis, synthesis and activity

Covering: 1950s up to the end of 2020Bottromycins are a class of macrocyclic peptide natural products that are produced by several Streptomyces species and possess promising antibacterial activity against clinically relevant multidrug-resistant pathogens. They belong to the ribosomally synthesised and post-translationally modified peptide (RiPP) superfamily of natural products. The structure contains a unique four-amino acid macrocycle formed via a rare amidine linkage, C-methylation and a d-amino acid. This review covers all aspects of bottromycin research with a focus on recent years (2009-2020), in which major advances in total synthesis and understanding of bottromycin biosynthesis were achieved.

New aspects of the ribosomal elongation cycle

The ribosomal elongation cycle represents a series of reactions during which the polypeptide is prolonged by one amino acid and after which the prolonged polypeptidyl residue is again ready to accept the next aminoacyl residue. It is generally believed that the ribosome carries two tRNA binding sites, the A site for aminoacyl-tRNA and the P site for peptidyl-tRNA, leading to the classical two-site model of the ribosome as a description for the elongation cycle. However, evidence is accumulating which is in conflict with the classical two-site model. These conflicts are resolved in a new three-site model which is discussed in detail in this paper.

Testing an alternative model for the ribosomal peptide elongation cycle

A kinetic analysis of poly(U)-dependent poly(Phe) synthesis with [14C]tRNAPhe and [3H]phenylalanine demonstrated that, in the course of efficient poly(Phe) synthesis, two tRNAs are present per 70S ribosome at all times, although at least 70% of the poly(Phe)-tRNAPhe is found at the peptidyl-tRNA (P) site. Together with our recent observation of a third tRNA-binding site on Escherichia coli ribosomes, these findings suggest a model for the peptide elongation cycle in which two tRNA molecules are present on the ribosome at both the pre- and the post-translocational state. This model predicts that deacylated tRNA is not released from the P site but translocated to the exit (E) site before release occurs. A series of translocation experiments with deacylated [14C]tRNAPhe at the P site and oligo [( 3H]Phe)-tRNA at the aminoacyl-tRNA (A) site proved that efficient elongation factor G-dependent translocation is not accompanied by a corresponding [14C]tRNAPhe release. However, significant [14C]tRNAPhe release was observed after translocation when an aminoacyl-tRNA was bound to the A site. Thus, deacylated tRNA is not released from the P site but is translocated to the E site, which therefore must be located "upstream" adjacent to the P site. Furthermore, the trigger for the release of deacylated tRNA from the E site is the binding of aminoacyl-tRNA to the A site.

Ribosomal function and its inhibition by antibiotics in prokaryotes

Most of the known antibiotics act at the level of protein biosynthesis probably due to the extraordinary complexity of the translation machinery which can be interfered with at many points. At first a survey is given of our present knowledge covering the structure and function of the prokaryotic ribosome. The most important antibiotics acting at the translational level are integrated into this network of data. The binding sites and the inhibition mechanisms of the drugs, together with the ribosomal components altered in resistant mutants are described. Finally, the points of interference with the translational machinery are indicated in an extended scheme of ribosomal functions.