Biology subjects

Roijen, L.-M.

Publications and source records attributed to Roijen, L.-M..

3 recordsLinked to original sources

bioRxiv2026

AI-guided discovery of atypical protein assemblies

Artificial intelligence (AI) systems such as AlphaFold have transformed structural biology by enabling accurate prediction of protein structures. However, their capacity to uncover new classes of macromolecular assemblies remains largely untapped. We developed the Structural Novelty Index (SNI), a quantitative framework for identifying protein complexes that diverge from canonical architectures. As one implementation of SNI, we developed SNINRC-Hexa, to identify unconventional resistosomes formed by nucleotide-binding, leucine-rich repeat immune receptors (NLRs). We used it to analyze AlphaFold 3 models of 637 non-redundant NRC proteins from 346 genomes representing 85 plant species. This analysis identified candidates with predicted architectures distinct from the canonical hexameric resistosomes of NRC proteins. Biochemical purification and negative-stain transmission electron microscopy of NRC7 orthologs from multiple species supported the SNI prediction and revealed an unexpected undecameric (11-mer) assembly. Our results establish SNI as a scalable approach for discovering atypical protein complexes.

bioinformatics↗

bioRxiv2026

Pathogen-induced red pigmentation uncovers a conserved floral defense in Asteraceae

Flower colour is predominantly selected for visual appeal and pollinator-driven evolution, however its role in plant-pathogen interaction remains unclear. Here, we investigated the relationship between anthocyanin accumulation and resistance to the necrotrophic pathogen Botrytis cinerea in Chrysanthemum morifolium. Using a unique set of spontaneous colour mutants sharing a common genetic background, we demonstrate that higher anthocyanin levels are associated with enhanced resistance to B. cinerea. Furthermore, we also observed pathogen induced anthocyanin accumulation at pathogen penetration sites in the white cultivars. Transcriptomics and metabolomics analyses revealed shift in metabolic pathways from flavonols towards flavone and anthocyanin biosynthesis during infections. A broader survey of taxonomically distant flowering species identified pathogen-induced red pigmentation is largely restricted to the members of the Asteraceae family. Notably, we observed divergence between wild and domesticated species, where the wild species retained the inducible pigmentation response and exhibited resistant to B. cinerea, whereas the cultivated species showed loss of this response, correlating with its increased susceptibility. Overall, our findings indicate that breeding for ornamental traits may have inadvertently selected against floral immunity.

plant biology↗

bioRxiv2025

When flowers turn red: Pathogen induced flavonoid and anthocyanin biosynthesis in Chrysanthemum seticuspe confers resistanceto Botrytis cinerea

Botrytis cinerea is a major threat to ornamental crops, yet floral defence responses remain poorly understood. In Chrysanthemum seticuspe, we found that flower petals, unlike leaves, mount a localized resistance response resulting in red spots appearing at fungal penetration sites. We observed an intensification of the coloured response as infections progressed. To investigate the basis of this phenotype, we performed a time-course paired transcriptomic and metabolomic analysis on mock-inoculated vs B. cinerea-inoculated petals and leaves. Infection triggered strong transcriptional reprogramming in petals, with clear induction of phenylpropanoid and flavonoid/anthocyanin pathway genes and candidate regulators, consistent with the visible pigmentation. Metabolite profiles reflected this response, showing time-dependent accumulation of infection induced flavonoids such as quercetin, tilianin, and their derivatives, as well as cyanidin-based anthocyanins in infected petals. Integrating both omics datasets with MEANtools highlighted an anthocyanin-associated transcript-metabolite module, including a module putatively involved in the synthesis of polyyne-type phytoalexins. Antifungal assays demonstrated that selected flavonoids and cyanidin derivatives inhibit B. cinerea in a dose-dependent manner, supporting a direct antifungal role of these compounds. Altogether, our results show that C. seticuspe petals deploy a spatially confined, multi-layered chemical defence in which pathogen-induced flavonoids and anthocyanins operate as active components of resistance against a necrotrophic pathogen. We anticipate that future paired omics analyses in combination with spatial omics and bioactivity assays will yield insights into the role of specialised defence molecules in response to biotic and abiotic stresses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/695701v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@e5dbeborg.highwire.dtl.DTLVardef@c94bd1org.highwire.dtl.DTLVardef@190c030org.highwire.dtl.DTLVardef@39a7b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗