Biology subjects

Smith, M. W.

Publications and source records attributed to Smith, M. W..

3 recordsLinked to original sources

bioRxiv2026

Orally available designed miniproteins inhibit enterotoxigenic Bacteroides fragilis pathology by blocking toxin receptor binding

Toxigenic bacterial infections in the gut are a significant contributor to the global burden of disease. Advanced tools for protein and live biotherapeutic engineering offer potentially transformative strategies for treating such diseases, while avoiding the collateral effects of traditional antibacterials. Here we used de novo protein design to identify inhibitors of the metzincin family protease Bacteroides fragilis toxin (BFT). These inhibitors, which bind distal to the active site, interfere with toxin-mediated E-cadherin cleavage and downstream proinflammatory signaling by blocking claudin-4 receptor binding. We tested the inhibitors as disulfide-stabilized variants administered directly to the cecum or in drinking water, as well as through in situ secretion by an engineered live biotherapeutic. Across these delivery modalities, the inhibitors successfully neutralized the toxin and effectively prevented BFT-associated gut pathology, including tumor formation. These results highlight the potential of de novo designed proteins as precise, non-antibiotic interventions to mitigate bacterial toxin-driven disease in the gut.

microbiology↗

bioRxiv2026

Proximity labeling of the Listeria monocytogenes surface reveals pathogen control of a host deubiquitinase

Intracellular pathogens must navigate the crowded cellular environment to establish infection. Listeria monocytogenes achieves this by recruiting host factors to its surface to hijack the host actin cytoskeleton for motility, form membrane protrusions, and spread from cell to cell. Although these types of Listeria-host interactions are critical for infection, systematic characterization of this interface has been limited. Here, we implement surface display of the promiscuous biotin ligase split-TurboID to profile host proteins recruited to the surface of L. monocytogenes during intracellular infection. This approach identified the host deubiquitinase CYLD as a protein selectively enriched at the pathogen surface. While CYLD promotes infection by suppressing autophagy and innate immunity in macrophages, how L. monocytogenes recruits and appropriates CYLD function in other cell types has remained unclear. We demonstrate that the E3 ligase RNF213 decorates bacterial poles with M1-linked linear ubiquitin, thereby redirecting CYLD to the bacterial surface. We further show ubiquitin is not sufficient to recruit CYLD but requires the L. monocytogenes secreted effector internalin C (InlC). Despite its presence at the bacterial surface, CYLD does not deubiquitinate bacteria or regulate autophagic bacterial clearance in infected epithelial cells. Instead, CYLD and InlC protect L. monocytogenes from IFN-{gamma}- and RNF213-dependent restriction of cell-to-cell spread. Overall, our work profiling the bacterial surface-host interactome has identified a new mechanism by which InlC spatially reprograms CYLD activity, uncoupling its canonical immune functions to promote cell-to-cell spread in epithelial cells. These findings highlight how L. monocytogenes exploits, a host deubiquitinase, to perform cell-type-specific functions during infection.

microbiology↗

bioRxiv2022

Haplotype resolved chromosome level genome assembly of Citrus australis reveals disease resistance and other citrus specific genes

Recent advances in genome sequencing and assembly techniques have made it possible to achieve chromosome level reference genomes for citrus. Relatively few genomes have been anchored at the chromosome level and/or are haplotype phased, with the available genomes of varying accuracy and completeness. We now report a phased high-quality chromosome level genome assembly for an Australian native citrus species; Citrus australis (round lime) using highly accurate PacBio HiFi long reads, complemented with Hi-C scaffolding. Hifiasm with Hi-C integrated assembly resulted in a 331 Mb genome of C. australis with two haplotypes of nine pseudochromosomes with an N50 of 36.3 Mb and 98.8% genome assembly completeness (BUSCO). Repeat analysis showed that more than 50% of the genome contained interspersed repeats. Among them, LTR elements were the predominant type (21.0%), of which LTR Gypsy (9.8 %) and LTR copia (7.7 %) elements were the most abundant repeats. A total of 29,464 genes and 32,009 transcripts were identified in the genome. Of these, 28,222 CDS (25,753 genes) had BLAST hits and 21,401 CDS (75.8%) were annotated with at least one GO term. Citrus specific genes for antimicrobial peptides, defense, volatile compounds and acidity regulation were identified. This chromosome scale, and haplotype resolved C. australis genome will facilitate the study of important genes for citrus breeding and will also allow the enhanced definition of the evolutionary relationships between wild and domesticated citrus species.

plant biology↗