Biology subjects

Osbourn, A.

Publications and source records attributed to Osbourn, A..

8 recordsLinked to original sources

bioRxiv2026

Systematic prediction and functional analysis of amino acid residues determining product specificity in the plant oxidosqualene cyclase superfamily

Oxidosqualene cyclases (OSCs) catalyse one of natures most intricate enzyme reactions, converting the linear precursor 2,3-oxidosqualene into an array of cyclic triterpene scaffolds through sequential carbocation cascades. Predicting OSC function based on sequence is challenging beyond broad family-level classification. Here, we develop a structure-based computational framework to identify amino acid determinants of OSC product specificity. Using 169 functionally characterised OSCs, we deploy a multifaceted approach combining differential conservation along with structural information, physico-chemical properties of amino acids and binding pocket electrostatics in order to understand the determinants of product specificity. Using Arabidopsis thaliana cycloartenol synthase AtCAS as a model, we then validate our predictions through targeted mutagenesis, achieving stepwise reprogramming towards the protosteryl-type products cucurbitadienol and lanosterol, including complete product switches. Molecular dynamics simulations support a mechanism in which subtle pocket remodelling alters active-site volume, water access and proton-elimination chemistry. These findings provide a blueprint for OSC engineering.

plant biology↗

bioRxiv2026

Diverse Diterpenoid Phytoalexins Shape Wheat Chemical Defenses

Cereal crops rely on a wide array of specialized metabolites to defend themselves against microbial pathogens. Here, using a combination of genome-wide analysis, heterologous pathway reconstruction, structural elucidation and in planta validation, we identify two pathogen-induced diterpenoid pathways in wheat that produce diterpenoids: the new glycosylated diterpenes aspisoside A and aspisoside B, and the diterpene alcohols scutenol A and scutenol B. The pathogen-responsive nature of these pathways, together with their antimicrobial activity are consistent with a likely defensive role in wheat. These compounds are produced by two biosynthetic gene clusters, each encoding a discrete pathway, so revealing organizational separation of wheat diterpenoid-based chemical defenses. The aspisoside-producing gene cluster is syntenic with diterpenoid phytoalexin-producing clusters in rice and barley, for momilactone and hordedane biosynthesis, respectively, yet gives rise to structurally distinct phytoalexins in wheat. The scutenol cluster is syntenic with currently uncharacterized predicted biosynthetic gene clusters in barley, oat, and Brachypodium. These findings establish diterpene glycosides as a previously unrecognized component of wheat defense chemistry and provide new insights into the chemical diversification of defense-related biosynthetic gene clusters within the Poaceae.

plant biology↗

bioRxiv2025

plantiSMASH 2.0: improvements to detection, annotation, and prioritization of plant biosynthetic gene clusters

Plants produce bioactive compounds as part of their specialized metabolism, with applications in medicine, agriculture, and nutrition. The biosynthesis of a growing number of these specialized metabolites has been found to be encoded in biosynthetic gene clusters (BGCs), creating increasing demand for genome mining tools to automate their detection. plantiSMASH enables the identification of putative plant BGCs through a rule-based approach, available via both command-line and web interfaces. Here, we present plantiSMASH 2.0 (https://plantismash.bioinformatics.nl/), a major update that expands and improves the original framework with revised and additional BGC detection rules (now supporting 12 BGC types), substrate prediction for selected enzyme families, and regulatory analysis through transcription factor binding site detection. The updated plantiSMASH 2.0 database includes 30,423 putative BGCs across 430 genomes. Together, these improvements make plantiSMASH 2.0 a powerful and comprehensive platform for the detection and characterization of plant biosynthetic pathways, supporting and accelerating research in plant specialized metabolism and plant natural product discovery.

bioinformatics↗

bioRxiv2024

Discovery of lydiamycin A biosynthetic gene cluster in the plant pathogen Rhodococcus fascians guides structural revision and identification of molecular target

The natural products actinonin and matlystatin feature an N-hydroxy-2-pentyl-succinamyl (HPS) chemophore that facilitates metal chelation and confers their metalloproteinase inhibitory activity. Actinonin is the most potent natural inhibitor of peptide deformylase (PDF) and exerts antimicrobial and herbicidal bioactivity by disrupting protein synthesis. Here, we used a genomics-led approach to identify candidate biosynthetic gene clusters (BGCs) hypothesised to produce novel HPS-containing natural products. We show that one of these BGCs is on the pathogenicity megaplasmid of the plant pathogen Rhodococcus fascians and produces lydiamycin A, a macrocyclic pentapeptide. The presence of genes predicted to make a HPS-like chemophore informed the structural recharacterisation of lydiamycin via NMR and crystallography to show it features a rare 2-pentyl-succinyl chemophore. We demonstrate that lydiamycin A inhibits bacterial PDF in vitro and show that a cluster-situated PDF gene confers resistance to lydiamycin A, representing a novel self-immunity mechanism associated with the production of a PDF inhibitor. In planta competition assays showed that lydiamycin enhances the fitness of R. fascians during plant colonisation. This study highlights how a BGC can inform the structure, biochemical target and ecological function of a natural product.

microbiology↗

bioRxiv2022

Complex scaffold remodeling in plant triterpene biosynthesis

Triterpenes with complex scaffold modifications are widespread in plants yet little is known regarding biosynthesis. Limonoids are an exemplary family that includes the bitter taste in citrus (e.g., limonin) and the active constituents in neem oil, a widely used bioinsecticide (e.g., azadirachtin). Despite limonoid commercial value, a complete biosynthetic route has not been described. Here, we report the discovery of 22 enzymes that catalyze 12 unique reactions including the 4-carbon scission and furan installation that are a signature of the limonoid family and a pair of sterol isomerases previously unknown in plants. This gene set is then used for the total biosynthesis of kihadalactone A and azadirone in a heterologous plant. These results enable access to valuable limonoids and provide a template for discovery and reconstitution of triterpene biosynthetic pathways in plants that require multiple skeletal rearrangements and oxidations.

biochemistry↗

bioRxiv2021

Genome Mining Uncovers Clustered Biosynthetic Pathways for Defense-Related Molecules in Bread Wheat

Wheat is one of the most widely grown food crops in the world. However, it succumbs to numerous pests and pathogens that cause substantial yield losses. A better understanding of biotic stress responses in wheat is thus of major importance. Here we identify previously unknown pathogen-induced biosynthetic pathways that produce a diverse set of molecules, including flavonoids, diterpenes and triterpenes. These pathways are encoded by six biosynthetic gene clusters and share a common regulatory network. We further identify associations with known or novel phytoalexin clusters in other cereals and grasses. Our results significantly advance the understanding of chemical defenses in wheat and open up new avenues for enhancing disease resistance in this agriculturally important crop.

plant biology↗

bioRxiv2018

Speed breeding in growth chambers and glasshouses for crop breeding and model plant research

1.To meet the challenge of feeding a growing population, breeders and scientists are continuously looking for ways to increase genetic gain in crop breeding. One way this can be achieved is through \"speed breeding\" (SB), which shortens the breeding cycle and accelerates research studies through rapid generation advancement. The SB method can be carried out in a number of ways, one of which involves extending the duration of a plants daily exposure to light (photoperiod) combined with early seed harvest in order to cycle quickly from seed to seed, thereby reducing the generation times for some long-day (LD) or day-neutral crops. Here we present glasshouse and growth chamber-based SB protocols with supporting data from experimentation with several crop species. These protocols describe the growing conditions, including soil media composition, lighting, temperature and spacing, which promote rapid growth of spring and winter bread wheat, durum wheat, barley, oat, various members of the Brassica family, chickpea, pea, grasspea, quinoa and the model grass Brachypodium distachyon. Points of flexibility within the protocols are highlighted, including how plant density can be increased to efficiently scale-up plant numbers for single seed descent (SSD) purposes. Conversely, instructions on how to perform SB on a small-scale by creating a benchtop SB growth cabinet that enables optimization of parameters at a low cost are provided. We also outline the procedure for harvesting and germinating premature wheat, barley and pea seed to reduce generation time. Finally, we provide troubleshooting suggestions to avoid potential pitfalls.

plant biology↗

bioRxiv2016

plantiSMASH: automated identification, annotation and expression analysis of plant biosynthetic gene clusters

Plant specialized metabolites are chemically highly diverse, play key roles in host-microbe interactions, have important nutritional value in crops and are frequently applied as medicines. It has recently become clear that plant biosynthetic pathway-encoding genes are sometimes densely clustered in specific genomic loci: biosynthetic gene clusters (BGCs). Here, we introduce plantiSMASH, a versatile online analysis platform that automates the identification of candidate plant BGCs. Moreover, it allows integration of transcriptomic data to prioritize candidate BGCs based on the coexpression patterns of predicted biosynthetic enzyme-coding genes, and facilitates comparative genomic analysis to study the evolutionary conservation of each cluster. Applied on 48 high-quality plant genomes, plantiSMASH identifies a rich diversity of candidate plant BGCs. These results will guide further experimental exploration of the nature and dynamics of gene clustering in plant metabolism. Moreover, spurred by the continuing decrease in costs of plant genome sequencing, they will allow genome mining technologies to be applied to plant natural product discovery.\n\nThe plantiSMASH web server, precalculated results and source code are freely available from http://plantismash.secondarymetabolites.org.

bioinformatics↗