Academic literature on the topic 'Ribosomally synthesized and post-Translationally modified peptides'

Lasso peptides are ribosomally synthesized and post-translationally modified peptides (RiPPs) characterized by a mechanically interlocked structure in which the C-terminal tail of the peptide is threaded and trapped within an N-terminal macrolactam ring.

Linaridins, defined as linear, dehydrated (arid) peptides, are a small but growing family of natural products belonging to the ribosomally synthesized and post-translationally modified peptide (RiPP) superfamily.

Bromotryptophan is a nonstandard amino acid that is rarely incorporated in ribosomally synthesized and post-translationally modified peptides (ribosomal peptides). Bromotryptophan and its analogs sometimes occur in non-ribosomal peptides. This paper presents an overview of ribosomal and non-ribosomal peptides that are known to contain bromotryptophan and its analogs. This work further covers the biological activities and therapeutic potential of some of these peptides.

Natural peptide products are a valuable source of important therapeutic agents, including antibiotics, antivirals and crop protection agents. Aided by an increased understanding of structure–activity relationships of these complex molecules and the biosynthetic machineries that produce them, it has become possible to re-engineer complete machineries and biosynthetic pathways to create novel products with improved pharmacological properties or modified structures to combat antimicrobial resistance. In this review, we will address the progress that has been made using non-ribosomally produced peptides and ribosomally synthesized and post-translationally modified peptides as scaffolds for designed biosynthetic pathways or combinatorial synthesis for the creation of novel peptide antimicrobials.

Antimicrobial Peptides (AMPs) are short amphipathic biological molecules generally with less than 100 amino acids. AMPs not only present high bioactivities against bacteria, fungi or protists-induced infections, but also play important roles in anticancer activity, immune response and inflammation regulation. AMPs are classified as ribosomally synthesized, non-ribosomally synthesized and post-translationally modified, non-ribosomally synthesized ones and several synthetic or semisynthetic peptides according to their synthesis with or without the involvement of ribosomes. The molecular characterization and bioactivity action mechanisms are summarized for several ribosomally synthesized AMPs and main non-ribosomally synthesized members (cyclopeptides, lipopeptides, glycopeptides, lipoglycopeptides). We also analyze challenges and new strategies to overcome drug resistance and application limitations for AMP discovery. In conclusion, the growing novel small molecular AMPs have huge therapeutic potentials of antibacterial, antiviral, anticancer and immunoregulatory bioactivities through new techniquesdriven drug discovery strategy including bioinformatics prediction, de novo rational design and biosynthesis.

This tutorial review discusses the potential of ribosomally synthesised and post-translationally modified peptides (RiPPs) as antimicrobials and looks at the chemical synthesis of three classes of RiPP: lasso peptides, cyclotides, and lanthipeptides.

AbstractThe emergence and re-emergence of viral epidemics and the risks of antiviral drug resistance are a serious threat to global public health. New options to supplement or replace currently used drugs for antiviral therapy are urgently needed. The research in the field of ribosomally synthesized and post-translationally modified peptides (RiPPs) has been booming in the last few decades, in particular in view of their strong antimicrobial activities and high stability. The RiPPs with antiviral activity, especially those against enveloped viruses, are now also gaining more interest. RiPPs have a number of advantages over small molecule drugs in terms of specificity and affinity for targets, and over protein-based drugs in terms of cellular penetrability, stability and size. Moreover, the great engineering potential of RiPPs provides an efficient way to optimize them as potent antiviral drugs candidates. These intrinsic advantages underscore the good therapeutic prospects of RiPPs in viral treatment. With the aim to highlight the underrated antiviral potential of RiPPs and explore their development as antiviral drugs, we review the current literature describing the antiviral activities and mechanisms of action of RiPPs, discussing the ongoing efforts to improve their antiviral potential and demonstrate their suitability as antiviral therapeutics. We propose that antiviral RiPPs may overcome the limits of peptide-based antiviral therapy, providing an innovative option for the treatment of viral disease.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) represent a significant potential for novel therapeutic applications because of their bioactive properties, stability, and specificity. RiPPs are synthesized on ribosomes, followed by intricate post-translational modifications (PTMs), crucial for their diverse structures and functions. PTMs, such as cyclization, methylation, and proteolysis, play crucial roles in enhancing RiPP stability and bioactivity. Advances in synthetic biology and bioinformatics have significantly advanced the field, introducing new methods for RiPP production and engineering. These methods encompass strategies for heterologous expression, genetic refactoring, and exploiting the substrate tolerance of tailoring enzymes to create novel RiPP analogs with improved or entirely new functions. Furthermore, the introduction and implementation of cutting-edge screening methods, including mRNA display, surface display, and two-hybrid systems, have expedited the identification of RiPPs with significant pharmaceutical potential. This comprehensive review not only discusses the current advancements in RiPP research but also the promising opportunities that leveraging these bioactive peptides for therapeutic applications presents, illustrating the synergy between traditional biochemistry and contemporary synthetic biology and genetic engineering approaches.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a growing class of natural products biosynthesized from a genetically encoded precursor peptide. The enzymes that install the post-translational modifications on these peptides have the potential to be useful catalysts in the production of natural-product-like compounds and can install non-proteogenic amino acids in peptides and proteins. However, engineering these enzymes has been somewhat limited, due in part to limited structural information on enzymes in the same families that nonetheless exhibit different substrate selectivities. Despite AlphaFold2’s superior performance in single-chain protein structure prediction, its multimer version lacks accuracy and requires high-end GPUs, which are not typically available to most research groups. Additionally, the default parameters of AlphaFold2 may not be optimal for predicting complex structures like RiPP biosynthetic enzymes, due to their dynamic binding and substrate-modifying mechanisms. This study assessed the efficacy of the structure prediction program ColabFold (a variant of AlphaFold2) in modeling RiPP biosynthetic enzymes in both monomeric and dimeric forms. After extensive benchmarking, it was found that there were no statistically significant differences in the accuracy of the predicted structures, regardless of the various possible prediction parameters that were examined, and that with the default parameters, ColabFold was able to produce accurate models. We then generated additional structural predictions for select RiPP biosynthetic enzymes from multiple protein families and biosynthetic pathways. Our findings can serve as a reference for future enzyme engineering complemented by AlphaFold-related tools.

Peptides are small proteins that are crucial in many biological pathways such as antimicrobial defense, hormone signaling, and virulence. They often exhibit tight specificity for their targets and therefore have great therapeutic potential. Many peptide-based therapeutics are currently available, and the demand for this type of drug is expected to continue to increase. In order to satisfy the growing demand for peptide-based therapeutics, new engineering approaches to generate novel peptides should be developed. Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a group of peptides that have the potential to be effective scaffolds for in vivo peptide engineering projects. These natural RiPP peptides are enzymatically endowed with post-translational modifications (PTMs) that result in increased stability and greater target specificity. Many RiPPs, such as microcin J25 and micrococcin, can tolerate considerable amino acid sequence randomization while still being capable of receiving unique post-translational modifications. This thesis describes how we successfully engineered E. coli to produce the lasso peptide microcin J25 using a two-plasmid inducible expression system. In addition, we characterized the protein-protein interactions between PTM enzymes in the synthesis of micrococcin. The first step in micrococcin synthesis is the alteration of cysteines to thiazoles on the precursor peptide TclE. This step is accomplished by three proteins: TclI, TclJ, and TclN. We found that a 4-membered protein complex is formed consisting of TclI, TclJ, TclN, and TclE. Furthermore, the TclI protein functions as a central adaptor joining two other enzymes in the Tcl pathway with the substrate peptide.

Plus de 40 familles de RiPPs, des produits naturels peptidiques synthétisés par voie ribosomale et modifiés post-traductionnellement, ont été identifiées à ce jour. En particulier, les RiPPs bactériens impliquant des enzymes MNIO (multinuclear non-heme iron-dependent oxidative enzymes) constituent un groupe en pleine expansion. Les enzymes MNIO sont impliquées dans la biosynthèse de divers types de RiPPs où ils catalysent des modifications chimiques très inhabituelles et diverses, fréquemment sur des résidus cystéine. Une nouvelle classe de RiPPs impliquant une sous-famille d’enzymes MNIO, que nous avons appelée « bufferines », a fait l’objet de ces travaux de thèse. Les bufferines possèdent des cystéines conservées. Elles présentent aussi des propriétés originales, notamment la grande taille de leurs précurseurs et la présence de peptides signaux N-terminaux Sec-dépendants, qui sont inhabituelles parmi les RiPPs bactériens.Nous avons caractérisé deux bufferines modèles chez la bactérie environnementale Caulobacter vibrioides. Nous avons découvert que ces bufferines font partie des deux plus grandes familles de RiPPs modifiées par des enzymes MNIO, largement répandues dans différents phyla bactériens. Des travaux antérieurs rapportés dans la littérature avaient montré une régulation par le cuivre des opérons de biosynthèse des bufferines chez C. vibrioides. Le cuivre est un métal essentiel utilisé pour ses propriétés d’oxydo-réduction dans divers processus biologiques dont la respiration. Il est également toxique en excès car il cause indirectement du stress oxydant, inactive certaines protéines et joue ainsi un rôle dans les interactions hôte-pathogène. Les bactéries ont donc développé des mécanismes très bien régulés d’homéostasie du cuivre. Nos travaux ont permis d’identifier le rôle des deux bufferines produites par C. vibrioides pour la protection contre un excès de cuivre, ce qui représente une stratégie d’homéostasie originale. Nous avons montré que les bufferines chélatent le cuivre dans ses deux états d’oxydation. Nos travaux ont aussi permis de mettre en évidence une nouvelle modification catalysée par les enzymes MNIO. Les cystéines conservées des bufferines sont modifiées en hétérocycles thiooxazole, une modification rare dans les produits naturels et essentielle pour la fonction des membres de cette nouvelle famille de RiPPs. Enfin, nous avons commencé à caractériser la biogenèse des deux bufferines de C. vibrioides. La présence de peptides-signaux N-terminaux conditionne nécessairement la biogenèse des bufferines, qui sont modifiées dans le cytoplasme avant leur export. Nos premiers résultats indiquent que la reconnaissance du précurseur de bufferine par l’enzyme MNIO et son partenaire implique plusieurs régions du précurseur, dont le peptide signal, ce qui pourrait retarder l’export pour permettre la mise en place des modifications post-traductionnelles.De façon intrigante, nous n’avons pas pu mettre en évidence un rôle de la bufferine produite par Bordetella pertussis, un pathogène respiratoire humain, dans la protection contre le cuivre. Ceci suggère que les bufferines pourraient exercer différentes fonctions selon le style de vie des bactéries productrices. Son rôle chez B. pertussis reste à élucider
More than 40 families of RiPPs, ribosomally synthesized and post-translationally modified peptides, have been identified. In particular, bacterial RiPPs involving MNIO enzymes (multinuclear non-heme iron-dependent oxidative enzymes) constitute a fast-expanding group. MNIO enzymes are involved in the biosynthesis of various types of RiPPs, where they catalyze unusual and chemically diverse modifications, generally on cysteine residues. A new class of RiPPs involving a subfamily of MNIO enzymes, which we have called «bufferins», has been the subject of this thesis. Bufferins harbour conserved Cys residues. In addition, they have original features, notably the large size of their precursors and the presence of Sec-dependent N-terminal signal peptides, which are unusual among bacterial RiPPs.We have characterized two model bufferins in the environmental bacterium Caulobacter vibrioides. We discovered that these bufferins belong to the largest two families of RiPPs modified by MNIO enzymes, and that they are prevalent in several bacterial phyla. It has been reported in the literature that the C. vibrioides bufferin operons are regulated by copper. Copper is an essential metal used for its redox properties in various biological processes including respiration. It is also toxic in excess because it causes oxidative stress, inactivates some proteins, and thus it plays a role in host-pathogen interactions. Bacteria have therefore developed finely regulated mechanisms of copper homeostasis. Our work allowed to identify a role in the protection against copper for the bufferins of C. vibrioides, which represents an original strategy of adaptation to excess copper. We showed that the bufferins chelate copper in both oxidation states. This work has also revealed a new modification catalyzed by MNIO enzymes. The conserved cysteines of bufferins are modified into thiooxazole heterocycles, a rare modification in natural products and essential for the function of the members of this new family of RiPPs. Finally, we have initiated the characterization of the biogenesis of the bufferins in C. vibrioides. The presence of a signal-peptide necessarily impacts their biogenesis, as bufferins are modified in the cytoplasm before their export. Our preliminary results indicate that recognition of the bufferin precursor by the MNIO enzyme and its partner involves several regions of the precursor including the signal peptide, which may delay export to allow installation of the post-translational modifications.Intriguingly, we could not establish that the bufferin produced by Bordetella pertussis, a human respiratory pathogen, is involved in protection against copper. This suggests that the functions of bufferins might depend on the lifestyles of the producing bacteria. Its role in B. pertussis remains to be elucidated