Biology subjects

Crown, M.

Publications and source records attributed to Crown, M..

7 recordsLinked to original sources

bioRxiv2024

Comprehensive Analysis of SARS-CoV-2 Spike Evolution: Epitope Classification and Immune Escape Prediction

The evolution of SARS-CoV-2, the virus responsible for the COVID-19 pandemic, has produced unprece-dented numbers of structures of the Spike protein. This study presents a comprehensive analysis of 1,560 published Spike protein structures, capturing most variants that emerged throughout the pandemic and covering diverse heteromerization and interacting complexes. We employ an interaction-energy informed geometric clustering to identify 14 epitopes characterized by their conformational specificity, shared interface with ACE2 binding, and glycosylation patterns. Our per-residue interaction evaluations accurately predict each residues role in antibody recognition and as well as experimental measurements of immune escape, showing strong correlations with DMS data, thus making it possible to predict the behaviour of future variants. We integrate the structural analysis with a longitudinal analysis of nearly 3 million viral sequences. This broad-ranging structural and longitudinal analysis provides insight into the effect of specific mutations on the energetics of interactions and dynamics of the SARS-CoV-2 Spike protein during the course of the pandemic. Specifically, with the emergence of widespread immunity, we observe an enthalpic trade-off in which mutations in the receptor binding motif (RBM) that promote immune escape also weaken the interaction with ACE2. Additionally, we also observe a second mechanism, that we call entropic trade-off, in which mutations outside of the RBM contribute to decrease the occupancy of the open state of SARS-CoV-2 Spike, thus also contributing to immune escape at the expense of ACE2 binding but without changes on the ACE2 binding interface. This work not only highlights the role of mutations across SARS-CoV-2 Spike variants but also reveals the complex interplay of evolutionary forces shaping the evolution of the SARS-CoV-2 Spike protein over the course of the pandemic.

biophysics↗

bioRxiv2024

ProCogGraph: A Graph-Based Mapping of Cognate Ligand Domain Interactions

MotivationMappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docking and protein design. Since the last available cognate-ligand domain database was released, the PDB has grown significantly and new tools are available for measuring similarity and determining contacts. ResultsWe present ProCogGraph, a graph database of cognate-ligand domain mappings in PDB structures. Building upon the work of the predecessor database, PROCOGNATE, we use data-driven approaches to develop thresholds and interaction modes. We explore new aspects of domain-cognate ligand interactions, including the chemical similarity of bound cognate ligands and how domain combinations influence cognate ligand binding. Finally, we use the graph to add specificity to partial EC IDs, showing that ProCogGraph can complete partial annotations systematically through assigned cognate ligands. Availability and ImplementationThe ProCogGraph pipeline, database and flat files are available at https://github.com/bashton-lab/ProCogGraph and https://doi.org/10.5281/zenodo.13165851. Contactmatthew.bashton@northumbria.ac.uk Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2024

TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication

SARS-CoV-2 is a highly transmissible virus that causes COVID-19 disease. Mechanisms of viral pathogenesis include excessive inflammation and viral-induced cell death, resulting in tissue damage. We identified the host E3-ubiquitin ligase TRIM7 as an inhibitor of apoptosis and SARS-CoV-2 replication via ubiquitination of the viral membrane (M) protein. Trim7-/- mice exhibited increased pathology and virus titers associated with epithelial apoptosis and dysregulated immune responses. Mechanistically, TRIM7 ubiquitinates M on K14, which protects cells from cell death. Longitudinal SARS-CoV-2 sequence analysis from infected patients revealed that mutations on M-K14 appeared in circulating variants during the pandemic. The relevance of these mutations was tested in a mouse model. A recombinant M- K14/K15R virus showed reduced viral replication, consistent with the role of K15 in virus assembly, and increased levels of apoptosis associated with the loss of ubiquitination on K14. TRIM7 antiviral activity requires caspase-6 inhibition, linking apoptosis with viral replication and pathology.

microbiology↗

bioRxiv2023

OMEinfo: Global Geographic Metadata for -omics Experiments

Microbiome studies increasingly associate geographical features like rurality and climate types with microbiomes. However, microbiologists/bioinformaticians often struggle to access and integrate rich geographical metadata from sources such as GeoTIFFs; and inconsistent definitions of rurality, for example, can hinder cross-study comparisons. To address this, we present OMEinfo, a Python-based tool for automated retrieval of consistent geographical metadata from user-provided location data. OMEinfo leverages open data sources such as the Global Human Settlement Layer, Koppen-Geiger climate classification models, and Open-Data Inventory for Anthropogenic Carbon dioxide, to ensure metadata accuracy and provenance. OMEinfos Dash application enables users to visualise their sample metadata on an interactive map and to investigate the spatial distribution of metadata features, which is complemented by data visualisation to analyse patterns and trends in the geographical data before further analysis. The tool is available as a Docker container, providing a portable, lightweight solution for researchers. Through its standardised metadata retrieval approach and incorporation of FAIR and Open data principles, OMEinfo promotes reproducibility and consistency in microbiome metadata. To demonstrate its utility, OMEinfo is utilised to replicate the results of a previous study linking population density to soil sample alpha diversity. As the field continues to explore the relationship between microbiomes and geographical features, tools like OMEinfo will prove vital in developing a robust, accurate, and interconnected understanding of these interactions, whilst having applicability beyond this field to any studies utilising location-based metadata. Finally, we release the OMEinfo annotation dataset, a collection of 5.3 million OMEinfo annotated samples from the ENA, for use in a retrospective analysis of sequencing samples, and highlight a number of ways researchers and sequencing read repositories can improve the quality of underlying metadata submitted to these public stores. AvailabilityOMEinfo is freely available and released under an MIT licence. OMEinfo source code is available at https://github.com/m-crown/OMEinfo/ Contactmatthew.crown@northumbria.ac.uk, matthew.bashton@northumbria.ac.uk

bioinformatics↗

bioRxiv2023

Lycopene Production in Dedicated Novel Chasses for Lignocellulosic Waste Material Utilisation Capable of Sustained Coculture

Municipal solid waste (MSW) represents tonnes of material that, for the most part, is relegated to landfill. Synthetic biology proposes solutions to many of the challenges faced by humanity today, but many approaches are confined to use in classical chassis organisms. In MSW there are a variety of potentially toxic materials such as glues, dyes, and preservatives that could pose a challenge to its capitalisation when using these commonplace chassis. We have isolated a bank of strains that utilise paper and cardboard waste from a relevant waste environment. From these we have identified three strains that are capable of utilising cellulose as a sole carbon source. We have analysed how they utilise cellulose and hemicelluloses, both alone and in coculture. This revealed insights to how they might be used in synthetic consortia which were then produced under laboratory conditions. Production of complete genome sequences of these strains provides genetic insight to how these processes may be occurring at the metabolic level, and how they could be augmented using synthetic biology. To this end, we have produced protocols for transforming plasmids into these strains and have produced high value metabolites from this material. HighlightsO_LIFully annotated genomes were produced from novel mesophilic aerobic strains isolated from lignocellulosic solid waste C_LIO_LILycopene was produced directly from relevant solid waste substrates by genetically modified variants of these strains C_LIO_LIOptimised carbon source blends influence coculture compositions of specific strains C_LI

synthetic biology↗

bioRxiv2022

Viral burdens are associated with age and viral variant in a population-representative study of SARS-CoV-2 that accounts for time-since-infection related sampling bias.

In this study, we evaluated the impact of viral variant, in addition to other variables, on within-host viral burdens, by analysing cycle threshold (Ct) values derived from nose and throat swabs, collected as part of the UK COVID-19 Infection Survey. Because viral burden distributions determined from community survey data can be biased due to the impact of variant epidemiology on the time-since-infection of samples, we developed a method to explicitly adjust observed Ct value distributions to account for the expected bias. Analysing the adjusted Ct values using partial least squares regression, we found that among unvaccinated individuals with no known prior infection, the average Ct value was 0.94 lower among Alpha variant infections, compared those with the predecessor strain, B.1.177. However, among vaccinated individuals, it was 0.34 lower among Delta variant infections, compared to those with the Alpha variant. In addition, the average Ct value decreased by 0.20 for every 10 year age increment of the infected individual. In summary, within-host viral burdens are associated with age, in addition to the interplay of vaccination status and viral variant.

genetics↗

bioRxiv2021

Computational analysis of the effect of SARS-CoV-2 variant Omicron Spike protein mutations on dynamics, ACE2 binding and propensity for immune escape

The recently reported Omicron (B.1.1.529) SARS-CoV-2 variant has a large number of mutations in the Spike (S) protein compared to previous variants. Here we evaluate the potential effect of Omicron S mutations on S protein dynamics and ACE2 binding as contributing factors to infectivity as well as propensity for immune escape. We define a consensus set of mutations from 77 sequences assigned as Omicron in GISAID as of November 25. We create structural models of the Omicron S protein in the open and closed states, as part of a complex with ACE2 and for each of 77 complexes of S bound to different antibodies with known structures. We have previously utilized Dynamical Signatures (DS) and the Vibrational Entropy Score (VDS) to evaluate the propensity of S variants to favour the open state. Here, we introduce the Binding Influence Score (BIS) to evaluate the influence of mutations on binding affinity based on the net gain or loss of interactions within the protein-protein interface. BIS shows excellent correlation with experimental data (Pearson correlation coefficient of 0.87) on individual mutations in the ACE2 interface for the Alpha, Beta, Gamma, Delta and Omicron variants combined. On the one hand, the DS of Omicron highly favours a more rigid open state and a more flexible closed state with the largest VDS of all variants to date, suggesting a large increase in the chances to interact with ACE2. On the other hand, the BIS shows that apart from N501Y, all other mutations in the interface reduce ACE2 binding affinity. VDS and BIS show opposing effects on the overall effectiveness of Omicron mutations to promote binding to ACE2 and therefore initiate infection. To evaluate the propensity for immune escape we calculated the net change of favourable and unfavourable interactions within each S-antibody interface. The net change of interactions shows a positive score (a net increase of favourable interactions and decrease of unfavourable ones) for 41 out of 77 antibodies, a nil score for 15 and a negative score for 21 antibodies. Therefore, in only 28% of S-antibody complexes (21/77) we predict some level of immune escape due to a weakening of the interactions with Omicron S. Considering that most antibody epitopes and the mutations are within the S-ACE2 interface our results suggest that mutations within the RBD of Omicron may give rise to only partial immune escape, which comes at the expense of reduced ACE2 binding affinity. However, this reduced ACE2 affinity appears to have been offset by increasing the occupancy of the open state of the Spike protein.

biophysics↗