Ribosomally synthesized and post-translationally modified peptides (RiPPs), also known as ribosomal natural products, are a diverse class of natural products of ribosomal origin. 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.
As a consequence of the falling cost of genome sequencing and the accompanying rise in available genomic data, scientific interest in RiPPs has increased in the last few decades. 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. This makes RiPPs an attractive target of modern natural product discovery efforts.
Definition.
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. This combination of peptide translation and modification is referred to as "post-ribosomal peptide synthesis" (PRPS) in analogy with nonribosomal peptide synthesis (NRPS).
Historically, the current sub-classes of RiPPs were studied individually, and common practices in nomenclature varied accordingly in the literature. More recently, with the advent of broad genome sequencing, it has been realized that these natural products share a common biosynthetic origin. In 2013, a set of uniform nomenclature guidelines were agreed upon and published by a large group of researchers in the field. Prior to this report, RiPPs were referred to by a variety of designations, including "post-ribosomal peptides", "ribosomal natural products", and "ribosomal peptides".
The acronym "RiPP" stands for "ribosomally synthesized and post-translationally modified peptide".
Prevalence and applications.
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. The advent of next-generation sequencing methods has made genome mining of RiPPs a common strategy. In part due to their increased discovery and hypothesized ease of engineering, the use of RiPPs as drugs is increasing. 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.
The uses and biological activities of RiPPs are diverse.
RiPPs in commercial use include nisin, a food preservative, thiostrepton, a veterinary topical antibiotic, and and duramycin, which are animal feed additives. Phalloidin functionalized with a fluorophore is used in microscopy as a stain due to its high affinity for actin. Anantin is a RiPP used in cell biology as an atrial natriuretic peptide receptor inhibitor.
In 2012-2013, a derivatized RiPP in clinical trials was LFF571. 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. Also recently in clinical trials was the NVB302 (a derivative of the lantibiotic actagardine) which is used for the treatment of "Clostridioides difficile" infection. Duramycin has completed phase II clinical trials for the treatment of cystic fibrosis.
Other bioactive RiPPs include the antibiotics cyclothiazomycin and bottromycin, the ultra-narrow spectrum antibiotic plantazolicin, and the cytotoxin patellamide A. Streptolysin S, the toxic virulence factor of "Streptococcus pyogenes", is also a RiPP. Additionally, human thyroid hormone itself is a RiPP due to its biosynthetic origin as thyroglobulin.
Classifications.
Amatoxins and phallotoxins.
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. 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. α-Amanitin, an amatoxin, has a number of posttranslational modifications in addition to macrocyclization and formation of the tryptathionine bridge: oxidation of the tryptathionine leads to the presence of a sulfoxide, and numerous hydroxylations decorate the natural product. As an amatoxin, α-amanitin is an inhibitor of RNA polymerase II.
Bottromycins.
Bottromycins contain a C-terminal decarboxylated thiazole in addition to a macrocyclic amidine.
There are currently six known bottromycin compounds, which differ in the extent of side chain methylation, an additional characteristic of the bottromycin class. The total synthesis of bottromycin A2 was required to definitively determine the structure of the first bottromycin.
Thus far, gene clusters predicted to produce bottromycins have been identified in the genus "Streptomyces". Bottromycins differ from other RiPPs in that there is no 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.
Cyanobactins.
Cyanobactins are diverse metabolites from cyanobacteria with N-to-C macrocylization of a 6–20 amino acid chain. Cyanobactins are natural products isolated from cyanobacteria, and close to 30% of all cyanobacterial strains are thought to contain cyanobacterial gene clusters. However, while thus far all cyanobactins are credited to cyanobacteria, there exists the possibility that other organisms could produce similar natural products.
The precursor peptide of the cyanobactin family is traditionally designated the "E" gene, whereas precursor peptides are designated gene "A" in most RiPP gene clusters. "A" is a serine protease involved in cleavage of the leader peptide and subsequent macrocyclization of the peptide natural product, in combination with an additional serine protease homologue, the encoded by gene "G". Members of the cyanobactin family may bear thiazolines/oxazolines, thiazoles/oxazoles, and methylations depending on additional modification enzymes. 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.
Lanthipeptides.
 Lanthipeptides are one of the most well-studied families of RiPPs. The family is characterized by the presence of lanthionine (Lan) and 3-methyllanthionine (MeLan) residues in the final natural product. There are four major classes of lanthipeptides, delineated by the enzymes responsible for installation of Lan and MeLan. The dehydratase and cyclase can be two separate proteins or one multifunctional enzyme. Previously, lanthipeptides were known as "lantipeptides" before a consensus was reached in the field.
Lantibiotics are lanthipeptides that have known antimicrobial activity. The founding member of the lanthipeptide family, nisin, is a lantibiotic that has been used to prevent the growth of food-born pathogens for over 40 years.
Lasso peptides.
Lasso peptides are short peptides containing an N-terminal macrolactam macrocycle "ring" through which a linear C-terminal "tail" is threaded. Because of this threaded-loop topology, these peptides resemble lassos, giving rise to their name. They are a member of a larger class of amino-acid-based lasso structures. Additionally, lasso peptides are formally rotaxanes.
The N-terminal "ring" can be from 7 to 9 amino acids long and is formed by an isopeptide bond between the N-terminal amine of the first amino acid of the peptide and the carboxylate side chain of an aspartate or glutamate residue. The C-terminal "tail" ranges from 7 to 15 amino acids in length.
The first amino acid of lasso peptides is almost invariably glycine or cysteine, with mutations at this site not being tolerated by known enzymes. Thus, bioinformatics-based approaches to lasso peptide discovery have thus used this as a constraint. However, some lasso peptides were recently discovered that also contain serine or alanine as their first residue.
The threading of the lasso tail is trapped either by disulfide bonds between ring and tail cysteine residues (class I lasso peptides), by steric effects due to bulky residues on the tail (class II lasso peptides), or both (class III lasso peptides). The compact structure makes lasso peptides frequently resistant to proteases or thermal unfolding.
Linear azol(in)e-containing peptides.
Linear azole(in)e-containing peptides (LAPs) contain thiazoles and oxazoles, or their reduced thiazoline and oxazoline forms. Thiazol(in)es are the result of cyclization of Cys residues in the precursor peptide, while (methyl)oxazol(in)es are formed from Thr and Ser. Azole and azoline formation also modifies the residue in the -1 position, or directly "C"-terminal to the Cys, Ser, or Thr. A dehydrogenase in the LAP gene cluster is required for oxidation of azolines to azoles.
Plantazolicin is a LAP with extensive cyclization. Two sets of five heterocycles endow the natural product with structural rigidity and unusually selective antibacterial activity. Streptolysin S (SLS) is perhaps the most well-studied and most famous LAP, in part because the structure is still unknown since the discovery of SLS in 1901. Thus, while the biosynthetic gene cluster suggests SLS is a LAP, structural confirmation is lacking.
Microcins.
Microcins are all RiPPs produced by Enterobacteriaceae with a molecular weight ;10 kDa. Many members of other RiPP families, such as microcin E492, microcin B17 (LAP) and microcin J25 (Lasso peptide) are also considered microcins. Instead of being classified based on posttranslational modifications or modifying enzymes, microcins are instead identified by molecular weight, native producer, and antibacterial activity. Microcins are either plasmid- or chromosome-encoded, but specifically have activity against Enerobacteriaceae. Because these organisms are also often producers of microcins, the gene cluster contains not only a precursor peptide and modification enzymes, but also a self-immunity gene to protect the producing strain, and genes encoding export of the natural product.
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.
Thiopeptides.
Most of the characterized thiopeptides have been isolated from Actinobacteria. General structural features of thiopeptide macrocycles, are dehydrated amino acids and thiazole rings formed from dehydrated serine/threonine and cyclized cysteine residues, respectively
The thiopeptide macrocycle is closed with a six-membered nitrogen-bearing ring. Oxidation state and substitution pattern of the nitrogenous ring determines the series of the thiopeptide natural product. While the mechanism of macrocyclization is not known, the nitrogenous ring can exist in thiopeptides as a piperidine, dehydropiperidine, or a fully oxidized pyridine. Additionally, some thiopeptides bear a second macrocycle, which bears a quinaldic acid or indolic acid residue derived from tryptophan. Perhaps the most well-characterized thiopeptide, thiostrepton A, contains a dehydropiperidine ring and a second, quinaldic acid-containing macrocycle. Four residues are dehydrated during posttranslational modification, and the final natural product also bears four thiazoles and one azoline.
Other RiPPs.
"Autoinducing Peptides" (AIPs) and quorum sensing peptides are used as signaling molecules in the process called quorum sensing. AIPs are characterized by the presence of a cyclic ester or thioester, unlike other regulatory peptides that are linear. In pathogens, exported AIPs bind to extracellular receptors that trigger the production of virulence factors. In "Staphylococcus aureus", AIPs are biosynthesized from a precursor peptide composed of a C-terminal leader region, the core region, and negatively charged tail region that is, along with the leader peptide, cleaved before AIP export.
"Bacterial Head-to-Tail Cyclized Peptides" refers exclusively to ribosomally synthesized peptides with 35-70 residues and a peptide bond between the N- and C-termini, sometimes referred to as bacteriocins, although this term is used more broadly. The distinctive nature of this class is not only the relatively large size of the natural products but also the modifying enzymes responsible for macrocyclization. Other N-to-C cyclized RiPPs, such as the cyanobactins and orbitides, have specialized biosynthetic machinery for macrocylization of much smaller core peptides. Thus far, these bacteriocins have been identified only in Gram-positive bacteria. 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. Based on solution structures and sequence alignments, bacteriocins appear to take on similar 3D structures despite little sequence homology, contributing to stability and resistance to degradation.
"Conopeptides" and other toxoglossan peptides are the components of the venom of predatory marine snails, such as the cone snails or "Conus". Venom peptides from cone snails are generally smaller than those found in other animal venoms (10-30 amino acids vs. 30-90 amino acids) and have more disulfide crosslinks. A single species may have 50-200 conopeptides encoded in its genome, recognizable by a well-conserved signal sequence.
"Cyclotides" are RiPPs with a head-to-tail cyclization and three conserved disulfide bonds that form a knotted structure called a cyclic cysteine knot motif. No other posttranslational modifications have been observed on the characterized cyclotides, which are between 28 - 37 amino acids in size. Cyclotides are plant natural products and the different cyclotides appear to be species-specific. While many activities have been reported for cyclotides, it has been hypothesized that all are united by a common mechanism of binding to and disrupting the cell membrane.
"Glycocins" are RiPPs that are glycosylated antimicrobial peptides. Only two members have been fully characterized, making this a small RiPP class. Sublancin 168 and glycocin F are both Cys-glycosylated and, in addition, have disulfide bonds between non-glycosylated