Biology subjects

Mendonca, C.

Publications and source records attributed to Mendonca, C..

6 recordsLinked to original sources

bioRxiv2026

PRIZM: Combining Low-N Data and Zero-shot Models to Design Enhanced Protein Variants

Machine learning has repeatedly shown the ability to accelerate protein engineering, but many approaches demand large amounts of robust, high-quality training data as well as substantial computational expertise. While large pre-trained models can function as zero-shot proxies for predicting variant effects, selecting the best model for a given protein property is often non-trivial. Here, we introduce Protein Ranking using Informed Zero-shot Modelling (PRIZM), a two-phase workflow that first uses a high-quality low-N dataset to identify the most suitable pre-trained zero-shot model for a target protein property and then applies that model to rank and prioritize an in silico variant library for experimental testing. Across diverse benchmark datasets spanning multiple protein properties, PRIZM reliably separated low- from high-performing models using datasets of [~]20 labelled variants. We further demonstrate PRIZM in enzyme engineering case studies targeting sucrose synthase thermostability and glycosyltransferase activity, where PRIZM-guided selection identified improved variants, including gains of [~]3{degrees}C in apparent melting temperature and [~]20% higher relative activity. PRIZM provides an accessible, data-efficient route to leverage foundation models for protein design while requiring minimal experimental data.

bioinformatics↗

bioRxiv2026

Stability engineering of sucrose synthase for robust UDP-glucose regeneration

Glycosyltransferase-driven glycosylation enables environmentally mild synthesis of high-value chemicals, but industrial implementation is constrained by the cost of UDP-glucose. Sucrose synthase (SuSy) offers an attractive route for UDP-glucose recycling, yet inadequate operational stability has limited its use. Here, we report an integrated engineering workflow that overcomes the longstanding trade-off between efficiency and robustness in glycosyl donor recycling enzymes. We engineered GmSuSy wild-type and obtained variants combining supra-wildtype activity (178%) with enhanced thermostability ({Delta}Tmapp = 13.3 {degrees}C), solvent tolerance (70% retained activity in 25% DMSO) and a 123-fold longer half-life. The variants achieved total turnover numbers of [~]1 million (60 {degrees}C), supporting their industrial relevance. Mechanistic analyses revealed that long-range residue communication networks couple oligomeric interfaces with active sites, shifting conformational populations toward stable, catalytically competent states while increasing hydrophobic packing and reducing solvent accessibility. This enhanced robustness enabled significant process-level gains, including >90% conversion yields in indoxyl and MANT glycosylation. Techno-economic and life-cycle assessments indicate the potential to halve reaction costs and reduce environmental impacts threefold, establishing SuSy robustness as a key lever for sustainable industrial glycosylation.

biochemistry↗

bioRxiv2025

The Staphylococcus aureus LXG-domain toxins EsxX and SAR0287 do not promote virulence in a zebrafish larval infection model

The Staphylococcus aureus type VIIb secretion system (T7SSb) is a multiprotein secretion system that secretes toxins with antibacterial activity, but which is also required for full virulence in animal models of infection. S. aureus strains carry one of four T7SSb locus types, named essC1 to essC4, each of which encodes a characteristic LXG-family substrate at the T7SS locus. In essC2 strains this LXG-domain protein is EsxX, which has a glycine zipper sequence in its C-terminus and has potent antibacterial membrane-depolarising activity. In this work we recognise conserved features of the essC2 and essC3 systems, identifying the LXG protein SAR0287 as structurally and functionally similar to EsxX. Using a zebrafish larval hindbrain ventricle infection model we demonstrate that the T7SSb of essC2 and essC3 representative strains contribute to bacterial replication and zebrafish mortality. However, there is no significant loss of virulence in the model system if EsxX or SAR0287 are absent. These findings indicate there is no discernible role for either toxin in this virulence model.

microbiology↗

bioRxiv2025

Distinct immunity protein families mediate compartment-specificneutralisation of a bacterial toxin

Staphylococcus aureus utilises a type VII secretion system (T7SS) to secrete antibacterial toxins that target competitor bacteria. EsxX is a T7SS substrate protein secreted by ST398 strains that has an LXG domain at its N-terminus. Here we show that the EsxX C-terminus is a membrane-depolarising toxin with a glycine zipper motif. EsxX is profoundly toxic to bacteria, displaying toxicity from both cytoplasmic and extracellular compartments. A pair of polytopic membrane proteins, ExiCD, protect cells from intoxication by extracellular EsxX. By contrast, a distinct soluble heterodimer, ExiAB, neutralises cytoplasmic EsxX by sequestration of its glycine zipper motif in a binding groove on ExiB. The exiA-exiB gene pair co-occur in staphylococcal genomes with esxX, invoking a model whereby ExiAB protects EsxX-producing cells from self-toxicity prior to EsxX secretion. By contrast ExiCD is encoded by both EsxX producers and in antitoxin islands of competitor strains that do not encode EsxX, consistent with providing immunity against the secreted form of the toxin. This work defines a new class of antibacterial toxin requiring two distinct types of immunity protein which follow different phylogenetic distributions.

microbiology↗

bioRxiv2020

Predator morphology affects prey consumption: evidence from an anuran population in subtropical wetlands

Morphology and diet are key factors in the ecology of organisms, determining aspects of natural history and evolution of the species. In this work, we evaluated the diet-morphology relationship in an anuran population, measuring the influence of morphological traits on the variation in the diet of individuals of Leptodactylus latrans. For this purpose, we collected individuals from a natural grassland habitat in southern Brazil. We analyzed the stomach content of individuals and consumed food items were classified up to the level of order. We also measured four morphological traits per individual of L. latrans: snout-vent length, relative limb length, distance between eyes and relative mouth width. We applied Linear Mixed Effect Models to evaluate the relationship of anuran morphological traits, number of prey taxa and volume of consumed prey. We tested the hypothesis that the configuration of predator morphological traits determines both the number of taxa and the volume of consumed prey. Our results indicate that individuals of L. latrans with larger body size consume a larger volume of prey and mouth width is directly and positively associated with the number of consumed taxa. In the same way that body size seems to define the capacity to ingest a large number of prey items, mouth width could be a limiting factor in prey selection. The capacity to consume a large prey volume could be an advantage in unpredictable environments, especially those with great daily thermal amplitudes such as the subtropical Brazilian grasslands.

ecology↗

bioRxiv2018

A membrane-depolarising toxin substrate of the Staphylococcus aureus Type VII protein secretion system targets eukaryotes and bacteria

The type VII protein secretion system (T7SS) is conserved across Staphylococcus aureus strains and plays important roles in virulence and interbacterial competition. To date only one T7SS substrate protein, encoded in a subset of S. aureus genomes, has been functionally characterized. Here, using an unbiased proteomic approach, we identify TspA as a further T7SS substrate. TspA is encoded distantly from the T7SS gene cluster and is found across all S. aureus strains as well as in Listeria and Enterococci. Heterologous expression of TspA from S. aureus strain RN6390 indicates its C-terminal domain is toxic when targeted to the Escherichia coli periplasm and that it depolarizes the cytoplasmic membrane. The membrane depolarizing activity is alleviated by co-production of the membrane-bound TsaI immunity protein, which is encoded adjacent to tspA on the S. aureus chromosome. Using a zebrafish hindbrain ventricle infection model, we demonstrate that the T7SS of strain RN6390 promotes bacterial replication in vivo, and deletion of tspA leads to increased bacterial clearance. The toxin domain of TspA is highly polymorphic and S. aureus strains encode multiple tsaI homologues at the tspA locus, suggestive of additional roles in intra-species competition. In agreement, we demonstrate TspA-dependent growth inhibition of RN6390 by strain COL in the zebrafish infection model that is alleviated by the presence of TsaI homologues. Significance statementStaphylococcus aureus, a human commensal organism that asymptomatically colonizes the nares, is capable of causing serious disease following breach of the mucosal barrier. S. aureus strains encode a Type VII secretion system (T7SS) that is required for virulence in mouse infection models, and some strains also secrete a nuclease toxin by this route that has antibacterial activity. Here we identify TspA, widely found in Staphylococci and other pathogenic bacteria, as a T7 substrate. We show that TspA has membrane-depolarizing activity and that S. aureus uses TspA to inhibit the growth of a bacterial competitor in vivo.

microbiology↗