Calcott, M. | Search bioRxiv

bioRxiv2026

Peptorama: Structure creation and exploratory data analysis for non-ribosomal peptides

Non-ribosomal peptides (NRPs) are a diverse family of compounds with many clinical and biotechnological uses. NRP biodiscovery increasingly focuses on biosynthetic gene clusters (BGCs), and NRP structures can generally be predicted from BGCs. Despite their chemical connection, there is no individual research tool which quickly analyses NRPs and BGCs in combination. Here, we present Peptorama, which simplifies drawing diverse NRP structures and allows rapid comparisons between known and predicted NRPs. We show the utility of peptide comparisons and interactive analysis for biodiscovery, exemplified by retrospective analysis of calcium dependent antibiotics and biodiscovery of novel pyoverdine producing candidate strains. Peptide comparisons are computationally more efficient than BGC comparisons, substantially cutting runtimes without loss of biodiscovery functionality. Peptorama can therefore enhance existing pipelines with a rapid method for comparing peptide-level diversity. It is available online at https://peptorama.com/ and is also available to be run locally.

bioinformatics↗

bioRxiv2020

Efficient rational modification of non-ribosomal peptides by adenylation domain substitution

Non-ribosomal peptide synthetase (NRPS) enzymes form modular assembly-lines, wherein each module typically governs the incorporation of a specific amino acid or related monomer into a short peptide product. Modules are comprised of one or more key domains, including adenylation (A) domains, which recognise and activate the monomer substrate; condensation (C) domains, which catalyse amide bond formation; and thiolation (T) domains, which shuttle reaction intermediates between catalytic domains.1 This arrangement offers prospects for rational peptide modification via substitution of substrate-specifying domains within an assembly line.2,3 For over 20 years, it has been considered that both A domains and C domains play key roles in selecting and "proof-reading" the substrate;4 a presumption that has greatly complicated rational NRPS redesign.2,5 Here we present evidence derived both from natural and directed evolution studies that C domains do not play a substrate-specifying role, and that novel non-ribosomal peptides can be generated by substitution of A domains alone. We identify permissive A domain recombination boundaries and show that these allow us to efficiently generate novel pyoverdine peptides at high yields. We further demonstrate the transferability of our approach in the PheATE-ProCAT model system originally used to infer C domain substrate specificity, generating novel dipeptide products at yields that should not be attainable according to existing dogma.

molecular biology↗