Biology subjects

Moore, B.

Publications and source records attributed to Moore, B..

At least 19 recordsLinked to original sources

bioRxiv2026

A phytocannabinoid-sensitive phosphorylation switch converts endocannabinoids into alternative lipid GPCR activators

Abstract: Endocannabinoids (eCBs) like anandamide and 2-arachidonoylglycerol are endogenous lipid ligands for CB1 and CB2 G protein-coupled receptors (GPCRs). Here, we show that phosphorylation of biologically important anandamide generates naturally occurring anandamide phosphate (AEAp), which switches GPCR ligand specificity to lysophosphatidic acid (LPA) receptors (LPARs) and the primate-specific bile acid sensory receptor MRGPRX4. The kinase responsible for anandamide phosphorylation was identified asdiacylglycerol kinase (DGK) theta (DGKq or DGKQ) using activity-guided brain fractionation, inhibitor profiling, recombinant reconstitution, and DGK isozyme screening. DGKQ showed noncanonical biphasic lipid kinetics and was inhibited by phytocannabinoids, most notably tetrahydrocannabinolic acid. Thus, eCBs are not only cannabinoid receptor ligands but also enzymatically adaptable lipid signals activating LPARs and MRGPRX4, thus linking metabolism of the distinct lipid LPA with Cannabis pharmacology.

biochemistry↗

bioRxiv2026

Establishment of the grass lignin metabolic network during monocot evolution

Plants produce a vast diversity of chemical compounds, yet the evolutionary history of the underlying complex metabolic networks remains poorly understood. Grasses (Poaceae family) possess a unique lignin metabolic network that can utilize both phenylalanine and tyrosine as precursors to synthesize canonical lignin as well as non-canonical acylated and tricin-conjugated lignin subunits. This study traces the evolutionary remodeling and establishment of the grass lignin metabolic network by combining phylogenomics with biochemical and chemical analyses across Poaceae, Poales, and other monocot species. These multidisciplinary comparative analyses reveal that the acylated lignin evolved in commelinids, followed by tyrosine-derived lignin biosynthesis in non-grass graminids through fine-tuning of pathway enzymes and transcriptional factors. Later, biosynthesis and incorporation of the flavonoid tricin into the cell wall took place within the core grasses via the evolution of chrysoeriol 5'-hydroxylase (C5'H) activity within the CYP75B enzyme family. These findings illustrate the emergence of different network modules at distinct times during monocot evolution that became integrated into the complex yet coherent metabolic network underlying the unique lignin chemical diversity of grasses.

plant biology↗

bioRxiv2026

Microenvironmental and transcriptional determinants of the robustness of spinal cord regeneration in zebrafish

Unlike mammals, adult zebrafish can regenerate spinal cord tissue after complete transection. We report here that a substantial proportion of zebrafish receiving this injury fail to regain locomotor function, and we analyzed this critically. After stratifying large cohorts of injured animals according to functional recovery, we directly compared recovered and non-recovered individuals at matched post-injury stages. We find that permanently paralyzed animals form a tissue bridge across the lesion yet exhibit impaired axonal invasion and regrowth to downstream targets. Integrative single-nucleus profiling, spatial transcriptomics, and regulatory network analyses revealed that regenerative success is characterized by the coordinated establishment of a permissive multicellular regenerative state rather than major differences in cellular composition. Furthermore, we find that regenerative failure involves persistent non-permissive regulatory programs, including extracellular matrix remodeling, impaired adaptive T-cell activation, and reduced axon growth-associated signaling. Gene regulatory network and cellular trajectory analyses identified candidate transcriptional regulators that could not be resolved through differential expression analysis alone. Functional CRISPR F0 screening of several of these candidates identified hoxb5a as a critical determinant of regenerative outcome. Stable hoxb5a mutants exhibited impaired swimming recovery, disrupted bridge formation, and limited axon bridging after spinal cord injury. Together, our findings reveal key differences between success and failure in a model of elevated regenerative capacity, with hoxb5a acting as a regulator linking multicellular tissue remodeling to axonal regeneration and functional recovery.

developmental biology↗

bioRxiv2026

Syndecan-4 exerts canonical heparan sulfate-dependent and noncanonical heparan sulfate-independent functions that regulate Aβ amyloid homeostasis

Background Heparan sulfate (HS) and heparan sulfate proteoglycans (HSPGs) are components of the amyloid deposits in Alzheimers disease (AD) and other amyloidoses. HS and HSPGs are canonically thought to facilitate amyloid deposition by accelerating the aggregation of amyloidogenic proteins and impairing their clearance in a HS-dependent manner. Methods Leveraging insights from large-scale proteomic data, we focused on Syndecan-4 (Sdc4), the most increased transmembrane HSPG in the AD brain and in the brain of A{beta} amyloid depositing mice. We used proximity ligation assays (PLA) to evaluate the association of Sdc4 with A{beta} in situ and assessed the impacts of the Sdc4 ectodomain on A{beta} aggregation in vitro. Overexpression studies in cells, hiPSC-derived neurons, and mouse organotypic brain slice cultures (OBSCs) coupled with structure-function studies were used to investigate impacts on A{beta} production and APP processing. Finally, effects of overexpression of Sdc4 in vivo in the CRND8 amyloid deposition model were evaluated. Results Consistent with canonical roles, PLA demonstrated a spatial association of Sdc4 with amyloid deposits, and in vitro, the Sdc4 ectodomain accelerated A{beta} fibril formation in a HS-dependent manner. Unexpectedly, Sdc4 overexpression reduced A{beta} production in CHO cells, hiPSC-derived neurons, and OBSCs. These effects were accompanied by dramatic decreases in the levels of sAPP and C83 and increased immature APP in the cell. Sdc4 promoted altered APP localization into detergent resistant membrane domains and increased APP association with ATG5+/LC3+/Cathepsin D+ vesicles. Structure-function studies revealed that the transmembrane region mediates these effects in a glycosaminoglycan-independent manner. Sdc4 overexpression in the brain of APP mice significantly reduced amyloid deposition at an early age. Conclusions Sdc4 exerts paradoxical and mechanistically distinct effects that could impact AD pathogenesis differentially, potentially promoting A{beta} fibrillization extracellularly while suppressing APP processing and A{beta} production. Such data challenge the prevailing view that increased levels of HSPGs in AD are always pro-amyloidogenic and identify Sdc4 as a previously unrecognized regulator of amyloid homeostasis in AD.

neuroscience↗

bioRxiv2026

Metabarcode and transcriptome datasets of Pinus sylvestris to assess fungal phyllosphere and disease dynamics.

Understanding how host-microbiome interactions influence tree disease is critical for understanding forest resilience. Here, we present foliar microbiome ITS2 metabarcoding transcriptomic datasets from Pinus sylvestris to investigate susceptibility to Dothistroma needle blight (DNB), a globally important foliar disease caused by Dothistroma septosporum. We hypothesised that host genotype shapes foliar microbial communities and their interactions, thereby influencing disease outcomes. Samples were collected from a progeny-provenance field trial in the south of Scotland representing a broad spectrum of disease susceptibilities. The dataset comprises ITS2 metabarcoding samples from 200 genotypes across three timepoints and RNAseq samples from 48 genotypes across two timepoints. Sampling captured key stages of pathogen exposure and disease progression. Both standardised and bespoke protocols were used for nucleotide extraction, sequencing, and quality control, including multiple negative and positive controls. These datasets, available in the European Nucleotide Archive (project accession PRJEB88228), enable analysis of temporal dynamics in foliar fungal communities, host-microbiome transcriptional responses, and genotype-dependent variation in disease susceptibility.

bioinformatics↗

bioRxiv2026

A decade of disease survey data in a progeny-provenance trial: Dothistroma needle blight in Scots pine

Longitudinal data on disease susceptibility in forest trees are rare but essential for understanding host-pathogen dynamics and genetic variation in susceptibility traits. We present a long-term multisite common garden dataset quantifying susceptibility of Scots pine (Pinus sylvestris) to Dothistroma needle blight. The dataset comprises annual disease assessments collected from the same trees across 11 years, spanning 168 families and 21 Scottish provenances. This design enables partitioning of genetic and environmental sources of variation, evaluation of temporal stability in host response, and estimation of variance components and narrow-sense heritability of susceptibility. The data support analyses of phenotypic plasticity, provenance-level responses, and interactions between disease susceptibility and other adaptive traits. This resource will facilitate predictive modelling of host susceptibility under current and future environmental conditions.

ecology↗

bioRxiv2025

Dynamic Retuning of Precursor Supply Before and After the Evolution of the Dual Lignin Pathway in Poales

ABSTRACTPlants produce diverse and abundant natural products, critical for plant adaptation and human society. While tremendous diversification of plant natural product pathways is well documented, how the upstream primary metabolism evolved in coordination with the lineage-specific pathways remain poorly understood. Here we studied the evolution of aromatic amino acid (AAA) biosynthesis during the emergence of tyrosine-derived lignin pathway uniquely found in grasses and closely related Poales. Phylogeny-guided in vitro and in planta functional analyses were conducted on two key regulatory enzymes--3-deoxy-D-arabino-heptulosonate 7-phosphate synthase (DHS) and arogenate dehydrogenase (TyrA)--catalyzing the first and last steps of AAA and tyrosine biosynthesis, respectively. Deregulated TyrAs were broadly present across Poales, with PACMAD grasses exhibiting stronger deregulation, suggesting that the active tyrosine biosynthesis likely emerged before, but were also selected upon, the evolution of tyrosine-lignin pathway. Conversely, DHS deregulation occurred more recently within BOP grasses after the emergence of tyrosine-lignin pathway, via multiple mutations that acted synergistically in the enzymes allosteric regulatory domain. The study highlights how the regulation of upstream primary metabolism is dynamically tuned both before and after the evolution of emerging natural product pathways. These findings underscore the importance of coordinating primary and secondary metabolism for efficient production of natural products in plants.

plant biology↗

bioRxiv2024

Genomes of Poaceae sisters reveal key metabolic innovations preceding the emergence of grasses

The grass family (Poaceae, Poales) holds immense economic and ecological significance, exhibiting unique metabolic traits, including dual starch and lignin biosynthetic pathways. To investigate when and how the metabolic innovations known in grasses evolved, we sequenced the genomes of four Poales species, including Joinvillea ascendens and Ecdeiocolea monostachya representing the sister clade to Poaceae. The rho whole genome duplication ({rho}WGD) in the ancestral lineage for all grasses contributed to the gene family expansions underlying cytosolic starch biosynthesis, whereas an earlier tandem duplication of phenylalanine ammonia lyase (PAL) gave rise to phenylalanine/tyrosine ammonia lyase (PTAL) responsible for the dual lignin biosynthesis. Integrated functional genomic and biochemical analyses of grass relatives further revealed the molecular basis of key metabolic innovations predating the evolution of grasses. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=149 SRC="FIGDIR/small/622220v2_ufig1.gif" ALT="Figure 1"> View larger version (108K): org.highwire.dtl.DTLVardef@117dd71org.highwire.dtl.DTLVardef@1cb5daborg.highwire.dtl.DTLVardef@72a331org.highwire.dtl.DTLVardef@38124e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Attentive graph neural network models for the prediction of blood brain barrier permeability

The blood brain barriers (BBB) unique endothelial cells and tight junctions selectively regulate passage of molecules to the central nervous system (CNS) to prevent pathogen entry and maintain neural homeostasis. Various neurological conditions and neurodegenerative diseases benefit from small molecules capable of BBB penetration (BBBP) to elicit a therapeutic effect. Predicting BBBP often involves in silico assessment of molecular properties such as lipophilicity (logP) and polar surface area (PSA) using the CNS multiparameter optimization (MPO) method. This study curated an open-source dataset to benchmark rigorously machine learning (ML) and neural network (NN) models with each other and with MPO for predicting BBBP. Our analysis demonstrated that AI models, especially attentive NNs using stereochemical features, significantly outperform MPO in predicting BBBP. An attentive graph neural network (GNN), we refer to as CANDID-CNS, achieved a 0.23-0.26 higher AUROC score than MPO on full test sets, and a 0.17-0.19 higher score on stereoisomers filtered subsets. Regarding stereoisomers that differ in BBBP, which MPO cannot distinguish, attentive GNNs correctly classify these with AUROC and MCC metrics comparable to or better than MPOs AUROC and MCC on less difficult test molecules. These findings suggest that integrating attentive GNN models into pharmaceutical drug discovery processes can substantially improve prediction rates, and thereby reduce the timeline, cost, and increase probability of success of designing brain penetrant therapeutics for the treatment of a wide variety of neurological and neurodegenerative diseases.

pharmacology and toxicology↗

bioRxiv2024

Chromosome-level genome assembly and annotation of Corallium rubrum: a Mediterranean coral threatened by overharvesting and climate change.

Reference genomes are key resources in biodiversity conservation. Yet, sequencing efforts are not evenly distributed in the tree of life questioning our true ability to enlighten conservation with genomic data. Good quality reference genomes remain scarce in octocorals while these species are highly relevant target for conservation. Here, we present the first annotated reference genome in the red coral, Corallium rubrum (Linnaeus, 1758), a habitat-forming octocoral from the Mediterranean and neighboring Atlantic, impacted by overharvesting and anthropogenic warming-induced mass mortality events. Combining long reads from Oxford Nanopore Technologies (ONT), Illumina paired-end reads for improving the base accuracy of the ONT-based genome assembly and Arima Hi-C contact data to place the sequences into chromosomes, we assembled a genome of 475 Mb (21 chromosomes, 326 scaffolds) with contig and scaffold N50 of 1.6 Mb and 16.2 Mb, respectively. Fifty percent of the sequence (L50) was contained in eight superscaffolds. The consensus quality (QV) of the final assembly was 42 and the gene completeness reported by BUSCO was 74% (metazoa_odb10 database). We annotated 39,114 protein-coding genes and 32,678 non-coding transcripts. This annotated chromosome-level genome assembly, one of the first in octocorals, is currently used in a project based on whole genome re-sequencing dedicated to the conservation and management of C. rubrum. Significance StatementThe Mediterranean red coral, Corallium rubrum, is critically impacted by overharvesting and by mass mortality events linked to marine heat waves. Accordingly, C. rubrum is increasingly receiving conservation efforts. Previous population genetics studies based on microsatellites contributed to improving our knowledge of the species ecology. Yet, crucial questions regarding, admixture among lineages, demographic history, effective population sizes and local adaptation, are still open owing to a lack of genomic resources. Here, we present the first chromosome-level genome assembly for the species with high contiguity, good completeness and protein-coding genes and repeat sequence annotations. This genome, one of the first in octocorals, will pave the way for the integration of population genomics data into ongoing interdisciplinary conservation efforts dedicated to C. rubrum.

genomics↗

bioRxiv2023

MICROGLIAL CELL EXPRESSION OF THE TYPE 2 CANNABINOID RECEPTOR REGULATES IMMUNE-MEDIATED NEUROINFLAMMATION

Neuroinflammation is a recognized complication of immunotherapeutic approaches such as immune checkpoint inhibitor treatment, chimeric antigen receptor therapy, and graft versus host disease (GVHD) occurring after allogeneic hematopoietic stem cell transplantation. While T cells and inflammatory cytokines play a role in this process, the precise interplay between the adaptive and innate arms of the immune system that propagates inflammation in the central nervous system remains incompletely understood. Using a murine model of GVHD, we demonstrate that type 2 cannabinoid receptor (CB2R) signaling plays a critical role in the pathophysiology of neuroinflammation. In these studies, we identify that CB2R expression on microglial cells induces an activated inflammatory phenotype which potentiates the accumulation of donor-derived proinflammatory T cells, regulates chemokine gene regulatory networks, and promotes neuronal cell death. Pharmacological targeting of this receptor with a brain penetrant CB2R inverse agonist/antagonist selectively reduces neuroinflammation without deleteriously affecting systemic GVHD severity. Thus, these findings delineate a therapeutically targetable neuroinflammatory pathway and has implications for the attenuation of neurotoxicity after GVHD and potentially other T cell-based immunotherapeutic approaches.

immunology↗

bioRxiv2023

Longitudinal characterization of the captive adult and tadpole Wyoming toad (Anaxyrus baxteri) microbiome

At one time thought to be extinct in the wild, the Wyoming toad (Anaxyrus baxteri) is one of the most critically endangered North American amphibian species. Despite approximately 20 years of ex situ breeding and reintroduction programs, these animals remain functionally extinct in the wild. There is concern among those working in these programs that individuals bred in captivity fail to develop the proper microbiome to withstand the stressors of their native habitat following release. In related species, the skin microbiome has been shown to have a defensive function against common pathogens affecting these animals. However, the early-life microbiome of developing tadpoles in this species remains unknown and therefore this defensive function is unexplored in the Wyoming toad. This study employed 16S rRNA amplicon sequencing to document the baseline microbiome of tadpoles bred for release and captive adult breeder populations. To characterize microbiome development, multiple rounds of skin mucosal and cloacal swabs were obtained concurrently from adult Wyoming toads bred at Omahas Henry Doorly Zoo and Aquarium. Our results revealed significant differences between tadpole and adult microbiomes, as well as significant sex-dependent differences within the adult Wyoming toads, in terms of richness and composition. Thus, these findings have identified the baseline microbiome of this endangered species, and variables significantly influencing its composition. Ongoing studies of the only extant wild population are expected to identify taxa not present in captive toads, and potentially help design husbandry modifications to maximize survivability following reintroduction to the wild.

microbiology↗

bioRxiv2023

Linking bacterial tetrabromopyrrole biosynthesis to coral metamorphosis

An important factor dictating coral fitness is the quality of bacteria associated with corals and coral reefs. One way that bacteria benefit corals is by stimulating the larval to juvenile life cycle transition of settlement and metamorphosis. Tetrabromopyrrole (TBP) is a small molecule produced by bacteria that stimulates metamorphosis in a range of coral species. A standing debate remains, however, about whether TBP biosynthesis from live Pseudoalteromonas bacteria is the primary stimulant of coral metamorphosis. In this study, we create a Pseudoalteromonas sp. PS5 mutant lacking the TBP brominase gene, bmp2. Using this mutant, we confirm that the bmp2 gene is critical for TBP biosynthesis in Pseudoalteromonas sp. PS5. Mutation of this gene ablates the bacteriums ability in live cultures to stimulate the metamorphosis of the stony coral Porites astreoides. We further demonstrate that expression of TBP biosynthesis genes is strongest in stationary and biofilm modes of growth, where Pseudoalteromonas sp. PS5 might exist within surface-attached biofilms on the sea floor. Finally, we create a modular transposon plasmid for genomic integration and fluorescent labeling of Pseudoalteromonas sp. PS5 cells. Our results functionally link a TBP biosynthesis gene from live bacteria to a morphogenic effect in corals. The genetic techniques established here provide new tools to explore coral-bacteria interactions and could help to inform future decisions about utilizing marine bacteria or their products for restoring degraded coral reefs.

microbiology↗

bioRxiv2023

Nutrient niche partitioning between tropical legumes and grasses strengthens under elevated CO2

O_LIPlant community biodiversity can be maintained, at least partially, by shifts in species interactions between facilitation and competition for resources as environmental conditions change. These interactions also drive ecosystem functioning, including productivity, and can promote over-yielding-an ecosystem service prioritized in agro-ecosystems, such as pastures, that occurs when multiple species together are more productive than the component species alone. Importantly, species interactions that can result in over-yielding may shift in response to rising CO2 concentrations and changes in resource availability, and the consequences these shifts have on production is uncertain especially in the context of tropical mixed-species grasslands. C_LIO_LIWe examined the relative performance of two species pairs of tropical pasture grasses and legumes growing in monoculture and mixtures in a glasshouse experiment manipulating CO2. We investigated how over-yielding can arise from nitrogen (N) niche partitioning and biotic facilitation using stable isotopes to differentiate soil N from biological N fixation (BNF) within N acquisition into aboveground biomass for these two-species mixtures. C_LIO_LIWe found that N niche partitioning in species-level use of soil N vs. BNF drove species interactions in mixtures. Importantly partitioning and overyielding were generally reduced under elevated CO2. However, this finding was mixture-dependent based on biomass of dominant species in mixtures and the strength of selection effects for the dominant species. C_LIO_LIThis study demonstrates that rising atmospheric CO2 may alter niche partitioning between co-occurring species, with negative implications for the over-yielding benefits predicted for legume-grass mixtures in working landscapes with tropical species. Furthermore, these changes in inter-species interactions may have consequences for grassland composition that are not yet considered in larger-scale projections for impacts of climate change and species distributions. C_LI Graphical abstract(Image by H. Zhang): Among our tropical pasture species we found that grasses (dotted lines) grown in monoculture rely fully on soil nitrogen (N), while legumes (solid lines) grown in monoculture relied approximately equally on soil N and biological nitrogen fixation (BNF) to meet N requirements. When grown with tropical grasses, however, legumes shifted to rely more strongly on BNF, indicative of niche partitioning and decreased competition for soil nutrients with grasses. This separation of niche space was weakened under elevated CO2 conditions, ultimately reducing legume production. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/524162v3_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@70de5corg.highwire.dtl.DTLVardef@1685f0org.highwire.dtl.DTLVardef@b3662corg.highwire.dtl.DTLVardef@1f911a3_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2022

The chromosome-scale genome assembly of the yellowtail clownfish Amphiprion clarkii provides insights into melanic pigmentation of anemonefish

Anemonefish are an emerging group of model organisms for studying genetic, ecological, evolutionary, and developmental traits of coral reef fish. The yellowtail clownfish Amphiprion clarkii possesses species-specific characteristics such as inter-species co-habitation, high intra-species color variation, no anemone specificity, and a broad geographic distribution, that can increase our understanding of anemonefish evolutionary history, behavioral strategies, fish-anemone symbiosis, and color pattern evolution. Despite its position as an emerging model species, the genome of A. clarkii is yet to be published. Using PacBio long-read sequencing and Hi-C chromatin capture technology, we generated a high-quality chromosome-scale genome assembly initially comprised of 1,840 contigs with an N50 of 1,203,211 bp. These contigs were successfully anchored into 24 chromosomes of 843,582,782 bp and annotated with 25,050 protein-coding genes encompassing 97.0 % of conserved actinopterygian genes, making the quality and completeness of this genome the highest amongst all published anemonefish genomes to date. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further analyses revealed higher copy numbers of erbb3b (a gene involved in melanophore development) in A. clarkii compared to other anemonefish, thus suggesting a possible link between erbb3b and the natural melanism polymorphism observed in A. clarkii. The publication of this high-quality genome, along with A. clarkiis many unique traits, position this species as an ideal model organism for addressing scientific questions across a range of disciplines.

genomics↗

bioRxiv2022

A chromosome-scale genome assembly of the false clownfish, Amphiprion ocellaris

BackgroundThe false clownfish Amphiprion ocellaris is a popular fish species and an emerging model organism for studying the ecology, evolution, adaptation, and developmental biology of reef fishes. Despite this, high-quality genomic resources for this species are scarce, hindering advanced genomic analyses. Leveraging the power of PacBio long-read sequencing and Hi-C chromosome conformation capture techniques, we constructed a high-quality chromosome-scale genome assembly for the clownfish A. ocellaris. ResultsThe initial genome assembly comprised of 1,551 contigs of 861.42 Mb, with an N50 of 863.85 kb. Hi-C scaffolding of the genome resulted in 24 chromosomes containing 856.61 Mb. The genome was annotated with 26,797 protein-coding genes and had 96.62 % completeness of conserved actinopterygian genes, making this genome the most complete and high quality among published anemonefish genomes. Transcriptomic analysis identified tissue-specific gene expression patterns, with the brain and optic lobe having the largest number of expressed genes. Further, comparative genomic analysis revealed 91 genome elements conserved only in A. ocellaris and its sister species Amphiprion percula, and not in other anemonefish species. These elements are close to genes that are involved in various nervous system functions and exhibited distinct expression patterns in brain tissue, potentially highlighting the genetic toolkits involved in lineage-specific divergence and behaviors of the clownfish branch. ConclusionsOverall, our study provides the highest quality A. ocellaris genome assembly and annotation to date, whilst also providing a valuable resource for understanding the ecology and evolution of reef fishes.

genomics↗

bioRxiv2020

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The COVID-19 pandemic has seen unprecedented use of SARS-CoV-2 genome sequencing for epidemiological tracking and identification of emerging variants. Understanding the potential impact of these variants on the infectivity of the virus and the efficacy of emerging therapeutics and vaccines has become a cornerstone of the fight against the disease. To support the maximal use of genomic information for SARS-CoV-2 research, we launched the Ensembl COVID-19 browser, incorporating a new Ensembl gene set, multiple variant sets (including novel variation calls), and annotation from several relevant resources integrated into the reference SARS-CoV-2 assembly. This work included key adaptations of existing Ensembl genome annotation methods to model ribosomal slippage, stringent filters to elucidate the highest confidence variants and utilisation of our comparative genomics pipelines on viruses for the first time. Since May 2020, the content has been regularly updated and tools such as the Ensembl Variant Effect Predictor have been integrated. The Ensembl COVID-19 browser is freely available at https://covid-19.ensembl.org.

bioinformatics↗

bioRxiv2020

The Phaeodactylum tricornutum Diaminopimelate Decarboxylase was Acquired via Horizontal Gene Transfer from Bacteria and Displays Substrate Promiscuity

Diatoms are predicted to synthesize certain amino acids within the chloroplast, including L-lysine via a diaminopimelate-dependent pathway. Herein, we report that the model diatom, Phaeodactylum tricornutum, possesses a chimeric lysine biosynthetic pathway, which coalesces bacterial and plant genes, and is terminated by a chloroplast-localized diaminopimelate decarboxylase (DAPDC, PtLYSA). We show that while RNAi ablation of PtLYSA is either synthetically lethal or concomitant with a slower growth rate, Cas9-mediated mutagenesis of PtLYSA results in recovery of heterozygous cells lines, suggesting that PtLYSA is an essential gene. Previously characterized DAPDCs are unique within the PLP-dependent decarboxylases where catalysis occurs at the D-stereocenter of the substrate and display a strict stereochemical preference for a (D,L)- or meso-substrate and not the D,D- or L,L-isomers of diaminopimelate (DAP) to synthesize L-lysine. Using decarboxylation assays and differential scanning calorimetry analyses, we validate that PtLYSA is a bona fide DAPDC and uncover its unexpected stereopromiscuous behavior in substrate specificity. The crystal structure of PtLYSA confirms the enzyme is an obligate homodimer in which both protomers reciprocally participate in the active site. The structure underscores features unique to the PtLYSA clan of DAPDC and provides structural insight into the determinants responsible for the substrate-promiscuity observed in PtLYSA.

biochemistry↗