Diversity of nature's assembly lines – recent discoveries in non-ribosomal peptide synthesis

Abstract

The biosynthesis of complex natural products by non-ribosomal peptide synthetases (NRPSs) and the related polyketide synthases (PKSs) represents a major source of important bioactive compounds. These large, multi-domain machineries are able to produce a fascinating range of molecules due to the nature of their modular architectures, which allows natural products to be assembled and tailored in a modular, step-wise fashion. In recent years there has been significant progress in characterising the important domains and underlying mechanisms of non-ribosomal peptide synthesis. More significantly, several studies have uncovered important examples of novel activity in many NRPS domains. These discoveries not only greatly increase the structural diversity of the possible products of NRPS machineries but - possibly more importantly - they improve our understanding of what is a highly important, yet complex, biosynthetic apparatus. In this review, several recent examples of novel NRPS function will be introduced, which highlight the range of previously uncharacterised activities that have now been detected in the biosynthesis of important natural products by these mega-enzyme synthetases.

A route to diastereomerically pure phenylglycine thioester peptides: crucial intermediates for investigating glycopeptide antibiotic biosynthesis

“…1), with vancomycin and teicoplanin as representative members -there is a need to characterise NRPS biosynthesis in order to explore the possibilities for compound development through redesigning the corresponding biosynthetic machinery. [1][2][3][4] In this regard, GPAs are perfect examples: total synthesis is highly challenging, meaning that all GPAs in clinical use stem from bacterial production in vivo and modified GPAs generated via total synthesis are not always accessible for the use in clinics. 4,5 The main reasons for this synthetic complexity are the high content of racemisation-prone phenylglycine residues as well as the highly crosslinked structure of GPAs (vancomycin:…”

“…6 In all these cases, however, the assessment of enzymatic activity is complicated by the necessity of peptide intermediates to be bound to peptidyl carrier protein (PCP)-domains, which serve as an attachment point for all amino acid and peptide intermediates during NRPS biosynthesis. 1,2,8 The ability to enzymatically load coenzyme A (CoA) substrates onto PCP domains using the promiscuous phosphopantetheinyl transferase Sfp has made a vital contribution to overcome this problem, as it allows biosynthetic steps to be interrogated without complete reconstitution of the NRPS. 1,8 It does, however, require effective methods for the generation of peptide thioester CoA substrates to be able to undertake these experiments.…”

“…[1][2][3][4] Due to the modular structure of nonribosomal peptide synthetases (NRPSs) -comprising repeating domains performing specific catalytic functions -and their non-dependence on the ribosome, NRPS assembly lines are able to synthesise peptides from a wide range of amino acids.…”

“…1,3 This feature, combined with the extensive incorporation of (D)-amino acids and large range of further structural modifications, contribute to the extensive diversity of natural NRPS-peptides. 1,2 Given the complexity of many of these compounds that are of medical interest -such as the glycopeptide antibiotics ( Fig. 1), with vancomycin and teicoplanin as representative members -there is a need to characterise NRPS biosynthesis in order to explore the possibilities for compound development through redesigning the corresponding biosynthetic machinery.…”

“…1,2 To achieve redesign, a comprehensive understanding of the NRPS assembly line is required in order to generate modified NRPS enzymes that retain efficiency and productivity for modified peptides. In this regard, the characterisation of the rates and specificities of individual domains -such as adenylation (A)-domains, responsible for amino acid selection and activation, condensation (C)-domains, responsible for peptide bond formation, epimerisation (E)-domains, responsible for peptide epimerisation, and thioesterase (TE)-domains, ultimately responsible for peptide cleavage from the NRPS -is key to ensuring that modified assembly lines will be functional.…”