Biology subjects

Somani, A.

Publications and source records attributed to Somani, A..

5 recordsLinked to original sources

bioRxiv2026

FoTO1 orchestrates Taxol biosynthesis through catalytic and non-catalytic mechanisms

Taxol is a blockbuster chemotherapeutic derived from the Pacific Yew tree. Recent work in our group has identified a complete pathway to baccatin III, a key intermediate, that hinges on a novel accessory protein, Facilitator of Taxane Oxidation (FoTO1). This protein dramatically improves yield and alters enzyme product profiles when reconstituting the Taxol pathway in N. benthamiana. FoTO1 has been shown to act early in the biosynthetic pathway improving the yields of product generated by the combination of a plastidial diterpene synthase (taxadiene synthase) and an endoplasmic reticulum (ER) localized cytochrome P450 (T5-alpha-hydroxylase). Here, we show that FoTO1 is an enzyme capable of converting taxadiene-(4),5-epoxide, the likely product of T5H oxidation, into taxadien-5-ol. FoTO1 is also functional in yeast, resolving a key bottleneck for development of a bioproduction route to Taxol in this host. Targeted mutagenesis of key catalytic residues in FoTO1 abrogates function in vitro but not in planta, suggesting non-catalytic contributions of FoTO1 to the taxane pathway. A combination of proximity labelling, bimolecular fluorescence complementation assays, and co-immunoprecipitation studies revealed that FoTO1 interacts with and organizes various P450s in the Taxol pathway. These approaches highlight the importance of both FoTO1s catalytic and non-catalytic functions in improving yields in the early Taxol pathway. Beyond Taxol biosynthesis, FoTO1 boosts yields for diverse diterpene pathways from across phylogeny, suggesting a general role of this protein class in mediating metabolism across the plastid and ER in plants.

biochemistry↗

bioRxiv2025

Identification of Scaffold Specific Energy Transfer Networks in the Enthalpic Activation of Orotidine 5'-Monophosphate Decarboxylase

AbstractOrotidine 5-monophosphate decarboxylase (OMPDC) is one of the most efficient enzyme systems studied, enhancing the decarboxylation of OMP to uridine 5-monophosphate (UMP) by ca. 17 orders of magnitude, primarily by reducing the enthalpy of activation by ca. 28 kcal/mol. Despite a substantial reduction in activation enthalpy, OMPDC requires 15 kcal/mol of activation energy post- ES complex formation. This study investigates the physical basis of how thermal energy from solvent collisions is directed into the active site of enzyme to enable efficient thermal activation of the reaction. Comparative study of temperature-dependent hydrogen-deuterium exchange mass spectrometry (TDHDX) for WT and mutant forms of enzymes has recently been shown to uncover site specific protein networks for thermal energy transfer from solvent to enzyme active sites. In this study, we interrogate region-specific changes in the enthalpic barrier for local protein flexibility using a native OMPDC from Methanothermobacter thermautotrophicus (Mt-OMPDC) and a single site variant (Leu123Ala) that alters the activation enthalpy for catalytic turnover. The data obtained implicate four spatially resolved, thermally sensitive networks that originate at different protein/solvent interfaces and terminate at sites surrounding the substrate near the substrate phosphate-binding region (R203), the substrate- ribose binding region (K42), and a reaction enhancing loop5 (S127). These are proposed to act synergistically, transiently optimizing the position and electrostatics of the reactive carboxylate of the substrate to facilitate activated complex formation. The uncovered complexity of thermal activation networks in Mt-OMPDC distinguishes this enzyme from other members of the TIM barrel family previously investigated by TDHDX. The new findings extend the essential role of protein scaffold dynamics in orchestrating enzyme activity, with broad implications for the design of highly efficient biocatalysts.

biochemistry↗

bioRxiv2022

Single-cell Mendelian randomisation identifies cell-type specific genetic effects on human brain disease and behaviour

Translating genome-wide association loci to therapies requires knowledge of the causal genes, their directionality of effect and the cell-types in which they act. To infer these relationships in the human brain, we implemented Mendelian randomisation using single cell-type expression quantitative trait loci (eQTLs) as genetic anchors. Expression QTLs were mapped across 8 major cell-types in brain tissue exclusively ascertained from donors with no history of brain disease. We report evidence for a causal association between the change in expression of 118 genes and one or more of 16 brain phenotypes, revealing candidate targets for risk mitigation and opportunities for shared preventative therapeutic strategies. We highlight key causal genes for neurodegenerative and neuropsychiatric disease and for each, we report its cellular context and the therapeutic directionality required for risk mitigation. Our use of control samples establishes a new resource for the causal interpretation of GWAS risk alleles for human brain phenotypes.

neuroscience↗

bioRxiv2019

Hippocampal morphometry in sudden and unexpected death in epilepsy (SUDEP)

ObjectiveTo determine hippocampal morphometric parameters, including granule cell dispersion and features of malrotation, as potential biomarkers for SUDEP from an archival post-mortem series.\n\nMethodsIn a retrospective study of 187 archival post-mortems from three groups, SUDEP (68; 14 with hippocampal sclerosis (HS)), non-SUDEP epilepsy controls (EP-C =66; 25 with HS) and non-epilepsy controls (NEC= 53), Nissl/H&E stained sections from left and right hippocampus from five coronal levels were digitised. Image analysis was carried out for granule cell layer (GCL) thickness and measurements of hippocampal dimensions (HD) for shape [width (HD1), height (HD2)] and medial hippocampal positioning in relation to the parahippocampal gyrus (PHG) length (HD3). A qualitative evaluation of hippocampal malrotational (HMAL) features, dentate gyrus invaginations (DGI) and subicular/CA1 folds (SCF) was also made.\n\nResultsGCL thickness was increased in HS more than those without (p<0.001). In non-HS cases increased GCL thickness was noted in EP-C compared to NEC (p<0.05) but not between SUDEP and NEC. There was no significant difference in the frequency of DGI, SCF, measurements of hippocampal shape (HD1, HD2 or ratio) or medial positioning between SUDEP, EP-C and NEC groups, when factoring in HS, coronal level and age at death. Comparison between left and right sides within cases showed significantly greater PHG lengths (HD3) on the right side in the SUDEP group only (p=0.018)\n\nConclusionsNo hippocampal morphometric features were identified in support of either excessive granule cell dispersion or features of HMAL as biomarkers for SUDEP. Asymmetries in PHG measurements in SUDEP warrant further investigation as they may indicate abnormal central autonomic networks.

pathology↗

bioRxiv2018

A systems-level analysis highlights microglial activation as a modifying factor in common forms of human epilepsy

The common human epilepsies are associated with distinct patterns of reduced cortical thickness, detectable on neuroimaging, with important clinical consequences. To explore underlying mechanisms, we layered MRI-based cortical structural maps from a large-scale epilepsy neuroimaging study onto highly spatially-resolved human brain gene expression data, identifying >2,500 genes overexpressed in regions of reduced cortical thickness, compared to relatively-protected regions. The resulting set of differentially-expressed genes shows enrichment for microglial markers, and in particular, activated microglial states. Parallel analyses of cell-specific eQTLs show enrichment in human genetic signatures of epilepsy severity, but not epilepsy causation. Post mortem brain tissue from humans with epilepsy shows excess activated microglia. In an experimental model, depletion of activated microglia prevents cortical thinning, but not the development of chronic seizures. These convergent data strongly implicate activated microglia in cortical thinning, representing a new dimension for concern and disease modification in the epilepsies, potentially distinct from seizure control.

neuroscience↗