Biology subjects

Cahill, J. F.

Publications and source records attributed to Cahill, J. F..

6 recordsLinked to original sources

bioRxiv2026

Integrated phytohormone quantification and metabolomics analysis enables new insights into the soil phytohormonome

The contribution of soil chemistry to plant growth and resilience, including presence of phytohormones, is increasingly recognized, yet characterization is limited by chemical complexity of soil matrices, diversity and low-abundance of metabolites. To enable further discoveries, we developed and characterized performance of a liquid chromatography-mass spectrometry method with solid phase extraction, integrating targeted and untargeted hormonomic approaches for comprehensive soil phytohormone profiling. Method performance was evaluated for fifteen plant growth-regulating compounds and precursors, including abscisic, gibberellic, jasmonic, and salicylic acids, auxins, cytokinins, karrikins, melatonin, and tryptophan, showing strong linearity (R{superscript 2} = 0.989-0.999), sensitivity (limits of detection and quantification 0.1-50.2 and 1.4-167.3 pg on-column, respectively), and precision (1.3-9.6% intraday; 3.4-34.8% interday). Soil composition impacted recovery; however, for most phytohormones rates were within 20% of matrix-adjusted spiked value, showing robustness across sandy, peat-rich, and clay-rich textures and suitable for use. We used the method to quantify analytes in research-relevant, active soils. Integration of untargeted analysis expanded coverage to 250 additional putative phytohormones and related metabolites, revealing chemical signatures potentially associated with plant community composition. This approach provides a versatile framework for investigating belowground phytohormone dynamics and their roles in plant physiology, resilience, and soil-plant feedbacks.

plant biology↗

bioRxiv2026

Structural and Oligomeric Characterization of Substrate- and Product-selective Nylon Hydrolases

Enzymatic degradation of synthetic polymers has attracted broad interest because it offers environmental and manufacturing advantages compared to traditional mechanical and chemical breakdown approaches. Enzymes are highly specific and reaction conditions are generally aqueous and require low pressure and temperature, resulting in lower energy consumption and lower chemical waste production. Here we report the biochemical and structural characterization of three newly discovered enzymes capable of nylon hydrolysis: Nyl10, Nyl12 and Nyl50. Using solution characterization techniques, we found that the enzymes adopt a single oligomeric state consistent with a tetramer over a wide range of concentrations. X-ray crystallographic structures of all three enzymes support the association into tetramers. Comparison of ligand-bound X-ray crystal structures of Nyl10 and Nyl12 with the previously determined structure of Nyl50 identified key structural determinants involved in ligand binding. Noticeably, a flexible loop found in several polyamide degrading enzymes is observed to flip towards (closed conformation) and away (open conformation) from the active site upon ligand binding. Analysis of adduct and surrogate substrate-bound enzyme complex structures provide a model for substrate binding directionality. Finally, activity assays showed that both Nyl10 and Nyl12 can hydrolyze ester bonds, and that Nyl12 has the highest activity toward PA66, identifying it as the best candidate for protein engineering for efficient nylon hydrolysis.

biochemistry↗

bioRxiv2025

Process optimization for enhanced enzymatic nylon deconstruction

Plastics such as polyamides (PAs) possess unique physicochemical properties that make them indispensable in modern society. However, their energy-intensive production and challenging end-of-life management highlight the urgent need for efficient recycling or remanufacturing solutions. Enzymatic depolymerization offers a promising route toward circular recycling, yet remains constrained by limited enzyme characterization, lack of validation under industrially relevant conditions, and overall performance. Here we optimized the reaction conditions for three recently discovered nylon-degrading enzymes. One of them, Nyl12, achieved product titers with PA6 and PA66 that exceed previously reported values, without enzyme engineering or substrate pretreatment. We further demonstrated the scalability of the process and its application to complex PA-based materials used in microelectronic components. Analysis of substrate features, including surface area and particle size, revealed key parameters governing enzymatic activity and provided a framework for future pretreatment and process optimization efforts. In combination, these efforts provide a new benchmark for enzymatic nylon recycling.

biochemistry↗

bioRxiv2025

Enzymatic synthesis of diverse oligoamide polymer precursors

Nylons, a major class of synthetic polyamides, are widely used due to their excellent mechanical strength, thermal stability, and chemical resistance. Conventional nylon production relies on the polymerization of lactams or stoichiometric nylon salts. However, applying these approaches to unconventional precursors such as bio-derived glutaric acid produces polymers with low molecular weight and limited applications. To address these challenges, we demonstrated that chemically-synthesized nylon diads enable the production of higher-molecular-weight polyamides compared with traditional salts. We then identified a biosynthetic approach using amide synthetases to convert unprotected bifunctional substrates into nylon-relevant diads. Using a cofactor regeneration system, enzymatic diad synthesis was scaled to produce sufficient material for laboratory-scale characterization and solid-state polymerization. Amide synthetases demonstrated broad substrate scope, catalyzing the regioselective assembly of diverse nylon-relevant diacids, diamines, and {omega}-amino acids. This strategy offers a novel route to synthesize challenging nylon monomers and advances production of bioderived nylons.

biochemistry↗

bioRxiv2024

Identification and characterization of substrate- and product-selective nylon hydrolases

Enzymes have evolved to rapidly and selectively hydrolyze diverse natural and anthropogenic polymers, but only a limited group of related enzymes have been shown to hydrolyze synthetic polyamides. In this work, we synthesized and characterized a panel of 95 diverse enzymes from the N-terminal nucleophile hydrolase superfamily with 30-50% pairwise amino acid identity. We found that nearly 40% of the enzymes had substantial nylon hydrolase activity, in many cases comparable to that of the best-characterized nylon hydrolase, NylC. There was no relationship between phylogeny and activity, nor any evidence of prior selection for nylon hydrolase activity. Several newly-identified hydrolases showed significant substrate selectivity, generating up to 20-fold higher product titers with Nylon 6,6 versus Nylon 6. Finally, we determined the crystal structure and oligomerization state of a Nylon 6,6-selective hydrolase to elucidate structural factors that could affect activity and selectivity. These new enzymes provide insights into the widespread potential for nylon hydrolase evolution and opportunities for analysis and engineering of improved hydrolases. SignificanceNylons are common industrial polyamides with few recycling options. As an alternative to mechanical or chemical recycling, enzymes may provide a selective and energy-efficient route to deconstruct nylons from mixed waste. Several nylon hydrolases have been identified, most notably NylC, but these enzymes are all closely related and demonstrated similar activity and substrate range. In this work, we investigated a diverse set of enzymes and showed that nylon hydrolase activity is common, providing new insights into the evolution of microbial nylon hydrolysis. Unlike NylC, several enzymes demonstrated unprecedented substrate selectivity, preferentially hydrolyzing Nylon 6,6 compared to Nylon 6. These enzymes can be used to understand substrate selectivity in nylon hydrolysis and to engineer enzymes for nylon recycling from mixed waste.

biochemistry↗

bioRxiv2019

The maize Hairy Sheath Frayed1 (Hsf1) mutant alters leaf patterning through increased cytokinin signaling

Leaf morphogenesis requires growth polarized along three axes - proximal-distal, medial-lateral and abaxial-adaxial. Grass leaves display a prominent proximal-distal (P-D) polarity consisting of a proximal sheath separated from the distal blade by the auricle and ligule. Although proper specification of the four segments is essential for normal morphology, our knowledge is incomplete regarding the mechanisms which influence P-D specification in monocots like maize (Zea mays). Here we report the identification of the gene underlying the semi-dominant, leaf patterning, maize mutant Hairy Sheath Frayed1 (Hsf1). Hsf1 plants produce leaves with outgrowths consisting of proximal segments - sheath, auricle and ligule - emanating from the distal blade margin. Analysis of three independent Hsf1 alleles revealed gain-of-function missense mutations in the ligand binding domain of the maize cytokinin (CK) receptor Zea mays Histidine Kinase1 (ZmHK1) gene. Biochemical analysis and structural modeling suggest the mutated residues near the CK binding pocket affect CK binding affinity. Treatment of wild type seedlings with exogenous CK phenocopied the Hsf1 leaf phenotypes. Results from expression and epistatic analyses indicated the Hsf1 mutant receptor appears to be hypersignaling. Our results demonstrate that hypersignaling of CK in incipient leaf primordia can reprogram developmental patterns in maize.\n\nSummaryIncreased cytokinin signaling in the maize Hairy Sheath Frayed1 mutant modifies leaf development leading to changes in pattering, growth and cell identity.

plant biology↗