Biology subjects

Alam, R. M.

Publications and source records attributed to Alam, R. M..

4 recordsLinked to original sources

bioRxiv2026

The floral illusion: A parasitic beetle mimics the scent of flowers to attract bees

Animals are not known to biosynthesize floral signals to manipulate pollinators, although such mimicry could profoundly shape plant-pollinator interactions. Larvae of the poisonous European blister beetle Meloe proscarabaeus parasitize multiple solitary bee species, yet the mechanism enabling host attraction has remained unresolved. Here we show that these larvae lure bees by emitting a bouquet of volatile compounds that closely resembles floral scent. Chemical analyses reveal a complex blend of monoterpenoids derived from (S)-linalool, a ubiquitous floral volatile. Behavioral assays demonstrate that these compounds function as floral cues, eliciting attraction in bees. Transcriptomic and functional analyses identify cytochrome P450 enzymes that oxidize (S)-linalool, demonstrating that larvae biosynthesize these plant-like volatiles de novo. Together, these findings broaden the scope of interkingdom chemical mimicry and uncover a striking form of sensory deception in which an insect chemically assumes the signal identity of a flower, revealing that animals can evolve biosynthetic pathways to exploit plant-pollinator communication.

ecology↗

bioRxiv2025

Fine-tuned Protein Language Model Identifies Antigen-specific B Cell Receptors from Immune Repertoires

Scalable identification of antigen-specific antibodies from whole immune repertoire V(D)J sequences is a central challenge in biomedical engineering. We show that protein language models (PLMs) fine-tuned on antibody heavy-chain sequences can directly predict antigen specificity from unselected immune repertoires. We assessed our model, Antigen Specificity Predictor (ASPred), against SARS-CoV-2, influenza, and HIV-AIDS antigens, observing comparable predictive performance. In the whole immune repertoire V(D)J sequences of mice immunized with the SARS-CoV-2 spike proteins receptor-binding domain (RBD), ASPred identified antibody sequences specific to RBD. Several candidate sequences were validated, including one as a heavy chain-only nanobody with 20.7 nM dissociation constant. Molecular dynamics simulations supported the predicted interactions at coarse-grained and atomic levels. Benchmarking against Barcode-Enabled Antigen Mapping (BEAM) of B cell receptor sequence data had highly significant overlaps with ASPred predictions, suggesting scalability. The predicted SARS-CoV-2 binders differed substantially from training sequences, demonstrating generalization beyond sequence memorization. Together, we establish that heavy chain antibody sequences encode sufficient information for PLMs to infer specificity, offering a scalable framework for antibody discovery with broad applications.

bioinformatics↗

bioRxiv2025

Discovery of iridoid cyclase completes the iridoid pathway in asterids

Iridoids are specialized monoterpenes ancestral to asterid flowering plants (Albach et al, 2001; Stull et al, 2018). Iridoids play key roles in plant defense and are also essential precursors for pharmacologically important alkaloids (Dobler et al, 2011; Eisner, 1964). The biosynthesis of all iridoids involves the cyclization of a reactive enol intermediate. While this cyclization occurs spontaneously at low yields, it has long been hypothesized that a dedicated enzyme is involved in this process (Geu-Flores et al, 2012; Lichman et al, 2019b). Here, we report the discovery of asterid iridoid cyclases (ICYC). We show that these enzymes catalyze cyclization of the reactive intermediate to form the two major iridoid stereoisomers found in plants. Our work uncovers the last missing key step in the otherwise well-characterized iridoid biosynthesis pathway in asterids. This discovery unlocks the possibility to generate previously inaccessible iridoid stereoisomers, which will enable metabolic engineering for the sustainable production of valuable iridoid and iridoid-derived compounds.

plant biology↗

bioRxiv2025

It runs in the family: Discovery of enzymes in the oleuropein pathway in Olive (Olea europaea) by comparative transcriptomics

Olive (Olea europaea L.) is one of the most important crop trees, with olive oil being a key ingredient of the Mediterranean diet. Oleuropein, an oleoside-type secoiridoid, is the major determinant of flavor and quality of olive oil. Iridoid biosynthesis has been elucidated in Catharanthus roseus, which produces secologanin-type secoiridoids, but iridoid biosynthesis in other species remains unresolved. In this work, we sequenced RNA from olive fruit mesocarp of six commercial olive cultivars with varying oleuropein content, during maturation and ripening. Using this data we discovered three polyphenol oxidases with oleuropein synthase (OS) activity, a novel oleoside-11-methyl ester glucosyl transferase (OMEGT) synthesizing a potential intermediate in the route, and a 7-epi-loganic acid O-methyltransferase (7eLAMT). Interestingly, integrating transcriptomics data from 15 plant species from three iridoid-producing plant orders (Lamiales, Gentianales, and Cornales), and tissue expression panels from Jasminum sambac and Fraxinus excelsior, we discovered two 2-oxoglutarate dependent dioxygenases (named 7eLAS) that synthesize 7-epi-loganic acid; in contrast C. roseus 7-deoxy-loganic acid hydroxylase (7DLH), a known bottleneck in MIA production, is a cytochrome p450. This comparative co-expression method, which combines guilt by association and comparative transcriptomics approaches, can successfully leverage big datasets for untargeted discovery of enzymes. Key FindingsO_LIExpression of genes involved in iridoid biosynthesis, from the early MEP pathway to the last step of oleuropein biosynthesis, decreases during olive fruit maturation. C_LIO_LIWe discovered an oxoglutarate dependent dioxygenase, 7-epi-loganic acid synthase (7eLAS), catalyzing the stereoselective oxidation of 7-deoxy-loganic acid to 7-epi-loganic acid, in a reaction analogous to C. roseus 7-deoxy-loganic acid hydroxylase (7DLH), a cytochrome p450. C_LIO_LIWe report a 7-epi-loganic acid O-methyltransferase (7eLAMT) orthologous to Catharanthus roseus loganic acid O-methyltransferase and found a novel oleoside-11-methyl ester glucosyl transferase (OMEGT) synthesizing 7-{beta}-1-D-glucopyranosyl-oleoside-11-methyl ester, a potential intermediate in the oleuropein biosynthesis route. C_LIO_LIWe discovered three olive polyphenol oxidases that have oleuropein synthase (OS) activity, catalyzing the conversion of ligstroside to oleuropein. C_LI

biochemistry↗