Biology subjects

Davies, B. W.

Publications and source records attributed to Davies, B. W..

7 recordsLinked to original sources

bioRxiv2025

Structural Insights into Cir-mediated Killing by the Antimicrobial Protein Microcin V

Drug-resistant bacterial infections have become a high-priority concern in the global healthcare landscape. Novel treatments for such infections are needed, but can be especially difficult to develop for Gram-negative species owing to the need to traverse the outer membrane to reach targets beneath. A promising solution is found in natural antibiotics such as albomycin, which can bind outer membrane siderophore receptors and co-opt them for import into the periplasm. Exploring this and similar mechanisms may open avenues for antibiotic development. An underappreciated class of natural antibiotics are the microcins, which are small antimicrobial proteins secreted by certain bacterial species as a means of inter-species competition. Once secreted, the microcins bind specific outer-membrane receptors of prey species and cross into the periplasm. Microcins have potent activity, bind specific targets, and have been shown to control pathobiont expansion and pathogen colonization in animal models. One such microcin, MccV, has previously been shown to utilize the E. coli colicin Ia receptor, Cir, for periplasmic import. Here, we report the first high-resolution structure of the Cir/MccV complex by Cryo-EM, revealing an interaction centered on an electropositive cavity within a usually occluded binding pocket in Cir. We also report the calculated affinity of MccV for Cir. We mutagenized putative interacting residues at this interface and identified key contacts that are critical to MccV binding and Cir-mediated import and bacteriolysis. Future efforts in this project will help us better understand the mechanisms of microcin killing, and will assess relationships between other microcins and their respective importers with the aim of understanding the potential for microcins to be used as treatment for drug-resistant pathogens.

molecular biology↗

bioRxiv2023

Semantic search using protein large language models detects class II microcins in bacterial genomes

Class II microcins are antimicrobial peptides that have shown some potential as novel antibiotics. However, to date only ten class II microcins have been described, and discovery of novel microcins has been hampered by their short length and high sequence divergence. Here, we ask if we can use numerical embeddings generated by protein large language models to detect microcins in bacterial genome assemblies and whether this method can outperform sequence-based methods such as BLAST. We find that embeddings detect known class II microcins much more reliably than does BLAST and that any two microcins tend to have a small distance in embedding space even though they typically are highly diverged at the sequence level. In datasets of Escherichia coli, Klebsiella spp., and Enterobacter spp. genomes, we further find novel putative microcins that were previously missed by sequence-based search methods.

microbiology↗

bioRxiv2023

Deep mutational scanning and machine learning uncover antimicrobial peptide features driving membrane selectivity

Antimicrobial peptides commonly act by disrupting bacterial membranes, but also frequently damage mammalian membranes. Deciphering the rules governing membrane selectivity is critical to understanding their function and enabling their therapeutic use. Past attempts to decipher these rules have failed because they cannot interrogate adequate peptide sequence variation. To overcome this problem, we develop deep mutational surface localized antimicrobial display (dmSLAY), which reveals comprehensive positional residue importance and flexibility across an antimicrobial peptide sequence. We apply dmSLAY to Protegrin-1, a potent yet toxic antimicrobial peptide, and identify thousands of sequence variants that positively or negatively influence its antibacterial activity. Further analysis reveals that avoiding large aromatic residues and eliminating disulfide bound cysteine pairs while maintaining membrane bound secondary structure greatly improves Protegrin-1 bacterial specificity. Moreover, dmSLAY datasets enable machine learning to expand our analysis to include over 5.7 million sequence variants and reveal full Protegrin-1 mutational profiles driving either bacterial or mammalian membrane specificity. Our results describe an innovative, high-throughput approach for elucidating antimicrobial peptide sequence-structure-function relationships which can inform synthetic peptide-based drug design.

biochemistry↗

bioRxiv2023

Export of diverse and bioactive peptides through a type I secretion system.

Microcins are peptide antibiotics secreted by Gram-negative bacteria that inhibit the growth of neighboring microbes. They are exported from the cytosol to the environment in a one-step process through a specific type I secretion system (T1SS). While the rules governing export of natural or non-native substrates have been resolved for T1SSs that secrete large proteins, relatively little is known about substrate requirements for peptides exported through T1SSs that secrete microcins. Here, we investigate the prototypic microcin V T1SS from Escherichia coli and show it can export a remarkably wide range of natural and synthetic peptides. We demonstrate that secretion through this system is not affected by peptide charge or hydrophobicity and appears only constrained by peptide length. A varied range of bioactive peptides, including an antibacterial peptide, a microbial signaling factor, a protease inhibitor, and a human hormone, can all be secreted and elicit their intended biological effect. Secretion through this system is not limited to E. coli, and we demonstrate its function in additional Gram-negative species that can inhabit the gastrointestinal tract. Our findings uncover the highly promiscuous nature of peptide export thorough the microcin V T1SS, which has implications for native cargo capacity and use of Gram-negative bacteria for peptide research and delivery. ImportanceMicrocin type I secretion systems in Gram-negative bacteria transport antibacterial peptides from the cytoplasm to the extracellular environment in single step. In nature, each microcin secretion system is generally paired with a specific peptide. We know little about the export capacity of these transporters and how peptide sequence influences secretion. Here, we investigate the microcin V type I secretion system. Remarkably, our studies show this system can export diverse peptides and is only limited by peptide length. Furthermore, we demonstrate that various bioactive peptides can be secreted, and this system can be used in Gram-negative species that colonize the gastrointestinal tract. These finding expand our understanding of secretion through type I systems and their potential uses in peptide applications.

microbiology↗

bioRxiv2022

Designing β-hairpin peptide macrocycles for antibiotic potential

Peptide macrocycles are a rapidly emerging new class of therapeutic, yet the design of their structure and activity remains challenging. This is especially true for those with {beta}-hairpin structure due to weak folding properties and a propensity for aggregation. Here we use proteomic analysis and common antimicrobial features to design a large peptide library with macrocyclic {beta}-hairpin structure. Using an activity-driven high-throughput screen we identify dozens of peptides killing bacteria through selective membrane disruption and analyze their biochemical features via machine learning. Active peptides contain a unique constrained structure and are highly enriched for cationic charge with arginine in their turn region. Our results provide a synthetic strategy for structured macrocyclic peptide design and discovery, while also elucidating characteristics important for {beta}-hairpin antimicrobial peptide activity. Brief SummaryWe design, screen, and computationally analyze a synthetic macrocyclic {beta}-hairpin peptide library for antibiotic potential.

biochemistry↗

bioRxiv2020

A systematic analysis of the beta hairpin motif in the Protein Data Bank

The beta hairpin motif is a ubiquitous protein structural motif that can be found in molecules across the tree of life. This motif, which is also popular in synthetically designed proteins and peptides, is known for its stability and adaptability to broad functions. Here we systematically probe all 49,000 unique beta hairpin substructures contained within the Protein Data Bank (PDB) to uncover key characteristics correlated with stable beta hairpin structure, including amino acid biases and enriched inter-strand contacts. We also establish a set of broad design principles that can be applied to the generation of libraries encoding proteins or peptides containing beta hairpin structures. ImportanceThe beta hairpin motif is a common protein structural motif that is known for its stability and varied activity in diverse proteins. Here we use nearly fifty thousand beta hairpin substructures from the Protein Data Bank to systematically analyze and identify key characteristics of the beta hairpin motif. Ultimately, we provide a set of design principles for the generation of synthetic libraries encoding proteins containing beta hairpin structures.

bioinformatics↗

bioRxiv2020

A comprehensive co-expression network analysis in Vibrio cholerae

Research into the evolution and pathogenesis of Vibrio cholerae has benefited greatly from the generation of high throughput sequencing data to drive molecular analyses. The steady accumulation of these datasets now provides a unique opportunity for in silico hypothesis generation via co-expression analysis. Here we leverage all published V. cholerae RNA-sequencing data, in combination with select data from other platforms, to generate a gene co-expression network that validates known gene interactions and identifies novel genetic partners across the entire V. cholerae genome. This network provides direct insights into genes influencing pathogenicity, metabolism, and transcriptional regulation, further clarifies results from previous sequencing experiments in V. cholerae (e.g. Tn-seq and ChIP-seq), and expands upon micro-array based findings in related gram-negative bacteria. ImportanceCholera is a devastating illness that kills tens of thousands of people annually. Vibrio cholerae, the causative agent of cholera, is an important model organism to investigate both bacterial pathogenesis and the impact of horizontal gene transfer on the emergence and dissemination of new virulent strains. Despite this importance, roughly one third of V. cholerae genes are functionally un-annotated, leaving large gaps in our understanding of this microbe. Through co-expression network analysis of existing RNA-sequencing data, this work develops an approach to uncover novel gene-gene relationships and contextualize genes with no known function, which will advance our understanding of V. cholerae virulence and evolution.

microbiology↗