Ribosomally synthesized and post-translationally modified peptides
[1] Consisting of more than 20 sub-classes, RiPPs are produced by a variety of organisms, including prokaryotes, eukaryotes, and archaea, and they possess a wide range of biological functions.
Because the chemical structures of RiPPs are more closely predictable from genomic data than are other natural products (e.g. alkaloids, terpenoids), their presence in sequenced organisms can, in theory, be identified rapidly.
RiPPs consist of any peptides (i.e. molecular weight below 10 kDa) that are ribosomally-produced and undergo some degree of enzymatic post-translational modification.
More recently, with the advent of broad genome sequencing, it has been realized that these natural products share a common biosynthetic origin.
RiPPs constitute one of the major superfamilies of natural products, like alkaloids, terpenoids, and nonribosomal peptides, although they tend to be large, with molecular weights commonly in excess of 1000 Da.
Although they are ribosomal peptides in origin, RiPPs are typically categorized as small molecules rather than biologics due to their chemical properties, such as moderate molecular weight and relatively high hydrophobicity.
RiPPs in commercial use include nisin, a food preservative, thiostrepton, a veterinary topical antibiotic, and nosiheptide and duramycin, which are animal feed additives.
Phase II clinical trials of LFF571, a derivative of the thiopeptide GE2270-A, for the treatment of Clostridioides difficile infections, with comparable safety and efficacy to vancomycin, was terminated early as the results were unfavorable.
Amatoxins and phallotoxins are 8- and 7-membered natural products, respectively, characterized by N-to-C cyclization in addition to a tryptathionine motif derived from the crosslinking of Cys and Trp.
[8][9] The amatoxins and phallotoxins also differ from other RiPPs based on the presence of a C-terminal recognition sequence in addition to the N-terminal leader peptide.
Rather, the precursor peptide has a C-terminal extension of 35-37 amino acids, hypothesized to act as a recognition sequence for posttranslational machinery.
For example, perhaps the most famous cyanobactin is patellamide A, which contains two thiazoles, a methyloxazoline, and an oxazoline in its final state, a macrocycle derived from 8 amino acids.
Two sets of five heterocycles endow the natural product with structural rigidity and unusually selective antibacterial activity.
Instead of being classified based on posttranslational modifications or modifying enzymes, microcins are instead identified by molecular weight, native producer, and antibacterial activity.
Microcins have bioactivity against Gram-negative bacteria but usually display narrow-spectrum activity due to hijacking of specific receptors involved in the transport of essential nutrients.
Oxidation state and substitution pattern of the nitrogenous ring determines the series of the thiopeptide natural product.
Other N-to-C cyclized RiPPs, such as the cyanobactins and orbitides, have specialized biosynthetic machinery for macrocylization of much smaller core peptides.
Enterocin AS-48 was isolated from Enterococcus and, like other bacteriocins, is relatively resistant to high temperature, pH changes, and many proteases as a result of macrocyclization.
Polytheonamides are exceptionally large, as a single molecule is able to span a cell membrane and form an ion channel.
In 2003, the first RiPP with a sulfur-to-α-carbon linkage was reported when the structure of subtilosin A was determined using isotopically enriched media and NMR spectroscopy.
The biosynthetic enzymes responsible for Lan and MeLan installation first dehydrate Ser and Thr to dehydroalanine (Dha) and dehydrobutyrine (Dhb), respectively.
However, class II, III, and IV lanthipeptides have bifunctional lanthionine synthetases in their gene clusters, meaning a single enzyme carries out both dehydration and cyclization steps.
[1][45] Many cyanobactins also undergo heterocyclization by a heterocyclase (referred to as the D protein), installing oxazoline or thiazoline moieties from Ser/Thr/Cys residues prior to the action of the A and G proteases.
[1] The heterocyclase is an ATP-dependent YcaO homologue that behaves biochemically in the same manner as YcaO-domain cyclodehydratases in thiopeptide and linear azol(in)e-containing peptide (LAP) biosynthesis (described above).
Unusual for ribosomal peptides, cyanobactins can include D-amino acids; these can occur adjacent to azole or azoline residues.
Indeed, due to the highly complex structures of thiopeptides, it was commonly thought that these natural products were nonribosomal peptides.
These include lanthipeptide-like dehydratases, designated the B and C proteins, which install dehydroalanine and dehydrobutyrine moieties by dehydrating Ser/Thr precursor residues.
The nitrogen-containing heterocycle is installed by the D protein cyclase via a putative [4+2] cycloaddition of dehydroalanine moieties to form the characteristic macrocycle.
The C protein displays homology to asparagine synthetase and is thought to activate the carboxylic acid side chain of a glutamate or aspartate residue via adenylylation.
The exact steps and reaction intermediates in lasso peptide biosynthesis remain unknown due to experimental difficulties associated with the proteins.
