Biology subjects

Brown, S.

Publications and source records attributed to Brown, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Necroptotic Signalling Diverts Keratinocyte Fate to Promote Differentiation and Slow Wound Healing

Necroptosis is best known as a lytic, proinflammatory cell-death pathway mediated by RIPK3 and MLKL. Effective wound repair requires the rapid resolution of inflammation, and ongoing necroptotic activity would only exacerbate tissue damage, delaying healing. However, damaged skin presents a trigger-rich environment for necroptotic signalling, an apparent paradox that remains unresolved. Using genetic ablation and pharmacological inhibition across multiple wound models, we show that inhibiting necroptosis accelerates wound closure, revealing that necroptotic signalling normally restrains repair. Surprisingly, we found that MLKL activation in wild-type keratinocytes induces differentiation and membrane repair rather than cell lysis. This adaptive, non-lethal mode of necroptotic signalling preserves barrier integrity but slows re-epithelialisation. Our findings redefine epidermal necroptotic signalling as a stress-responsive program that modulates keratinocyte fate in a trigger-rich environment. Temporarily dampening this pathway may enhance regeneration after barrier loss without compromising immune defence, revealing necroptosis as a tunable mechanism balancing tissue repair and inflammation.

cell biology↗

bioRxiv2026

MOLA: a novel topological data analysis framework for analyzing multiomic loops in precision medicine

Multiomic datasets contain complex nonlinear relationships that are often missed by conventional analysis methods. Topological data analysis (TDA) can detect some such patterns (i.e., loops), and here we extend previous TDA approaches with MOLA (MultiOmic Loop Analysis), a framework for multiomic loop visualization, filtering, association with sample-level characteristics and functional characterization. In an Influenza A virus dataset, MOLA better captured anticipated characteristic-dependent epigenetic alterations compared to standard approaches. In a breast cancer cohort, higher loop participation in five genes was associated with increased hazard of progression. MOLA provides an interpretable framework for discovering biologically meaningful multiomic patterns and potential biomarkers.

genomics↗

bioRxiv2026

First genetic detection and ongoing eDNA monitoring of the golden mussel (Limnoperna fortunei) in California

Here, we report the first genetic confirmation of golden mussels (Limnoperna fortunei) in North America, and the subsequent development, optimization, and deployment of golden mussel eDNA monitoring procedures. Aquatic species invasions are economically costly, disrupt ecosystem functionality, and impact native aquatic communities. Early detection of new invasive species enables rapid response via implementation of effective eradication or control measures and is key for reducing harmful outcomes. Initial species detection and taxonomic identification can be aided by genetic methods that have high detection sensitivity and accuracy. Genetic methods such as environmental DNA (eDNA) sampling can be used to detect invasive species before they become established in new systems, providing an early alert system to inform resource managers. Golden mussels were first detected in North America in October 2024 near the Port of Stockton in the San Francisco Estuary (SFE). The SFE is particularly vulnerable to invasion due to the access and connectivity provided by the presence of engineering infrastructure and shipping lanes. Collaborative efforts between public agencies and academic institutions are underway to develop a coordinated detection and response plan. Early detection followed by a rapid response is the best defense against prolific invasive species, such as the golden mussel.

genetics↗

bioRxiv2026

Multi-locus metabarcoding and intensive sampling reveal extraordinary diversity carried in the ballast water of a single vessel

Understanding risks of biological invasions associated with ballast water (BW) requires full understanding of the biodiversity transported in ballast tanks. Here we characterize the remarkable level of diversity that can be carried in the BW of a single vessel. To maximize our ability to capture BW diversity we: 1) utilized DNA-based methods to describe biodiversity, including both native and non-native taxa; 2) exploited multiple primer sets targeting multiple genomic loci with different expectations for taxonomic coverage; 3) assessed multiple tanks on a single vessel to capture different communities present in different tanks; and 4) sampled those tanks with far higher-than-usual replication both to improve representation of the diversity present and to enable statistical estimation of total richness. Using this approach, we found extraordinarily high diversity associated with a single vessel. Across all loci, we estimate a total of 272 taxa that can be assigned species names; looking more broadly at unnamed molecular operational taxonomic units, our estimates are between 425 and 742 individual taxa, depending on the locus. We confirm that only a fraction of this diversity would be captured with typical sampling efforts. We found that different loci capture different snapshots of biodiversity and that our ability to detect taxa of interest (e.g., non-native species) depends on sampling effort and genomic locus. Our results expand upon previous studies describing highly diverse BW communities and add to a growing literature that demonstrates the value of molecular methods for characterizing those communities and assessing the associated risk of non-native species introduction.

ecology↗

bioRxiv2026

HF-125, a first-in-class computer-modeled novel inhibitor of Tribbles 2, for therapy of enzalutamide resistant, neuroendocrine prostate cancer.

Second generation antiandrogens, such as enzalutamide, are commonly prescribed to treat advanced prostate cancer. However, enzalutamide resistant prostate cancer (ERPC) invariably develops with more aggressive features. Management of ERPC is extremely difficult not only because available therapies cannot effectively eliminate ERPC cells but also due to enhanced growth and highly metastatic features in ERPC cells to invade distant organs. This problem is amplified by the lack of proper knowledge about suitable molecular targets in ERPC cells. Recently, we reported that Tribbles 2 (TRIB2), is overexpressed in ERPC cells and tumors and inhibition of TRIB2 kills ERPC cells via apoptosis. TRIB2 enhances cancer cell growth and invasion and confers resistance to enzalutamide, while inhibition of TRIB2 resensitizes the resistant cells. Interestingly, TRIB2 induces neuroendocrine (NE) features in ERPC cells and both the de novo and treatment-emergent NEPC cells consistently overexpress TRIB2. Though TRIB2 has emerged as a promising target, suitable inhibitors are not commercially available for clinical use. We used artificial intelligence (AI)-based molecular modeling to design a series of small chemical entities with potentially high specificity to bind with TRIB2. Extensive virtual screening and molecular editing yielded few highly selective and potent agents to inhibit TRIB2 and kill ERPC-NE/NEPC cells. One such compound (HF-125) directly binds to destabilize and degrade TRIB2 proteins involving proteasomes and is effective both in vitro and in vivo. Based on these findings, HF-125 emerges as a promising novel agent for development of a new therapeutic strategy for ERPC-NE/NEPC types of aggressive prostate cancer.

cancer biology↗

bioRxiv2026

NPP-21/TPR is required for developmental control of spindle checkpoint strength in C. elegans

The spindle checkpoint ensures accurate chromosome segregation by monitoring whether chromosomes, via kinetochores, are properly attached to the spindle. If chromosomes fail to establish bipolar attachment, the checkpoint delays the cell cycle to enable error correction. In C. elegans early embryos, activation of the spindle checkpoint produces a longer mitotic delay in primordial germ cells than somatic cells. We show that the conserved nucleoporin and spindle matrix component, NPP-21/TPR, is required for the stronger spindle checkpoint in germline cells. A checkpoint-proficient NPP-21::GFP transgene localizes to a spindle-like structure during mitosis and is enriched in germline cells, consistent with a cell-fate specific function for this protein. Finally, NPP-21 controls spindle checkpoint strength in germline cells via two, potentially linked, mechanisms: concentrating PCH-2 around mitotic chromosomes and promoting the localization of the checkpoint effector, Mad2, to unattached kinetochores. These experiments demonstrate a developmental role for NPP-21, and the spindle matrix, in controlling spindle checkpoint strength in immortal germline cells in C. elegans.

cell biology↗

bioRxiv2026

Decoding epitope immunodominance in HIV Env using cryoEM and machine learning

Viral surface glycoproteins, such as the HIV envelope protein (Env), present numerous antibody (Ab) epitopes, yet immune responses consistently focus on only a subset, a phenomenon known as immunodominance. Although structural studies have provided insights into Env antigenicity, our understanding of the molecular features that govern efficient Ab engagement remains incomplete, thereby limiting the predictive and rational design of vaccines. Here, we characterized the structural determinants of epitope immunodominance in HIV Env by integrating high-resolution cryoEM-based polyclonal epitope mapping (cryoEMPEM) across different clades with quantitative analyses of epitope topology, accessibility, and physicochemical properties. More than 70 new structures were resolved to assemble a library of >100 Env-antibody complexes. These data informed the development of a surface-centric, machine-learning model to predict relative Antigen Surface Immunodominance (ASI model). Comparison of ASI-predicted epitope sites with the specificities of Env-induced antibodies showed that the model accurately identifies immunodominant regions and highlights the structural features driving immune bias. Notably, immunogens redesigned based on model predictions successfully redirected Ab responses toward a normally subdominant epitope, demonstrating the potential of strategies coupling targeted assembly of focused structural libraries with machine learning to uncover complex molecular patterns and enable design of more effective vaccine antigens.

immunology↗

bioRxiv2025

An Evaluation of the Efficacy of Single-Echo and Multi-Echo fMRI Denoising Strategies

Resting-state functional magnetic resonance imaging (rsfMRI) is commonly used to study brain-wide patterns of inter-regional functional coupling (FC). However, the resulting signals are vulnerable to multiple sources of noise, such as those related to non-neuronal physiological fluctuations and head motion, which can alter FC estimates and influence their associations with behavioral outcomes. The best strategy for acquiring and processing rsfMRI data to mitigate noise remains an open question. In this study of 358 healthy individuals, we compared the denoising efficacy of 60 multi-echo (ME) and 30 single-echo (SE) rsfMRI preprocessing pipelines across six distinct measures of data quality. We also evaluated how each pipeline influences the effect sizes of FC-based predictive models of personality and cognitive measures estimated via cross-validated kernel ridge regression. We found that ME pipelines generally showed superior denoising efficacy to SE pipelines, but that no single pipeline was associated with both superior denoising efficacy and behavioural prediction. Using a heuristic scheme to rank pipelines across benchmark evaluations, we found that an ME acquisition combined with Automatic Removal of Motion Artifacts Independent Component Analysis (ICA-AROMA) and Regressor Interpolation at Progressive Time Delays (RIPTiDe) offered a reasonable compromise between denoising efficacy and brain-behavior predictions for both ME and SE data. In general, ME pipelines ranked more highly than SE pipelines. These findings support the use of ME acquisitions in future work but suggest that no single denoising pipeline should be considered optimal for all purposes.

neuroscience↗

bioRxiv2025

Optimal TELSAM-Target Protein Linker Character is TargetProtein-Dependent

Fusing a variant of the sterile alpha motif domain of the human translocation ETS leukaemia protein (TELSAM) to a protein of interest has been shown to significantly enhance crystallization propensity. TELSAM is a pH-dependent, polymer-forming protein crystallization chaperone which, when covalently fused to a protein of interest, forms a stable, well-ordered crystal lattice. However, despite its success, a challenge persists in that crystal quality and diffraction limits appear to be heavily dependent on the choice of linker between TELSAM and the protein of interest, with identification of a functional linker relying on trial-and-error methods. Likewise, previous studies revealed that the 10xHis tag at the TELSAM N-terminus can either facilitate or hinder the ordered crystallization of target proteins attached via flexible or semi-flexible linkers. To address these challenges, we designed multiple constructs with several types of linkers--rigid (helical fusion), semi-flexible (Pro-Alan), and flexible (poly-Gly)--of varying lengths to fuse a designed ankyrin repeat protein (DARPin) to the TELSAM C-terminus. Semi-flexible and flexible linker constructs were made with and without the 10xHis tag. Our findings indicate that short semi-flexible and rigid linkers consistently yield large crystals within 24 hours with a DARPin target protein, but that flexible linkers perform best with a TNK1 UBA domain target protein. Removing the 10xHis tag enhanced crystallization rates, improved crystal morphology, and increased the crystallization propensity of semi-flexible and flexible linker constructs. While removing the His tag did not have a significant effect on crystal size, it improved the diffraction limits and crystal quality of the 1TEL-PA-DARPin construct. These results suggest that the ideal linker selection primarily depends on the properties of the target protein. Our data support the recommendation to use a short yet flexible or semi-flexible linker between TELSAM and the target protein to facilitate protein crystallization and high-resolution structure determination. SynopsisIn this study, we examine the effect of short to medium-length flexible, semi-flexible, and rigid linkers on the crystallization of a DARPin fused to the 1TEL protein crystallization chaperone, demonstrating that while rigid linkers impair crystallization and reduce diffraction quality, the ideal linker character remain target-protein dependent. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=91 SRC="FIGDIR/small/672704v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@b90d1org.highwire.dtl.DTLVardef@1508e7dorg.highwire.dtl.DTLVardef@1baf0d1org.highwire.dtl.DTLVardef@1843df_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

MALDI Deamidation Score (MDS): A Fast and Flexible Method for Assessing Deamidation in ZooMS Data and Its Application to the Denisova Cave Bone Assemblage

Estimating deamidation from MALDI-TOF MS spectra of bones has most frequently been achieved using the q2e method due to its high-throughput capacity and ease of use. Despite this accessibility, q2e is only capable of estimating deamidation at the peptide level on a fixed peptide list and does not generate a sample-wide summary. The introduction of the Parchment Glutamine Index (PQI) presented an alternative method for deamidation estimation. Initially designed for a large ZooMS dataset of parchment, it utilises weighted least squares and a linear mixed-effects model (LME) to generate deamidation estimation on both the peptide and sample level. To address the limitations of q2e and expand the applicability of PQI to a wider range of archaeological tissues and MALDI-derived data (such as ZooMS data on bone collagen), we developed the MALDI Deamidation Score (MDS), an iteration of the PQI method optimized for handling large-scale datasets. Compared to PQI, MDS is more streamlined for the analysis of multi-species data with customisable peptide lists, offering a dramatically decreased processing time while being able to normalise the peak intensity for higher accuracy. Through a case study on the published Denisova Cave ZooMS assemblage, we demonstrate that different peptides exhibit varying deamidation patterns over time, making the use of a single peptide to represent overall deamidation potentially biased. Such information is invaluable for investigating key questions such as protein preservation and site formation processes, especially when contextualized with other lines of archaeological evidence.

bioinformatics↗

bioRxiv2025

Sphingomonas nivalis sp. nov., a novel psychrophilic bacteria isolated from a permanent snowfield in Glacier Peaks Wilderness Area, Washington State, USA

A novel chemoheterotrophic psychrophilic bacterium, designated as strain I4T was isolated form a permanent snowfield in Washington State, USA. Growth is extremely slow, regardless of temperate (tested between 4{degrees}-25{degrees} C) but was had marginal optimal growth at 8.5{degrees} C. I4T was determined to be able to utilize 102 of the 190 tested carbon sources, 70 or the 95 tested nitrogen sources, 34 or the 59 tested phosphorous sources, and 10 of the 35 tested sulfur sources. I4T was seen to grow from pH 5.0-5.5 but could grow as low as 4.5 pH and as high as 9.5 pH with specific amendments. The genome of I4T was sequenced and it is approximate 4.0 Mb and has a G + C content of 66.2 mol%. Phylogenomic analyses using two independent methods places I4T within the genus Sphingomonas with S. sanguinis being its closest relative. On the basis of its genomic, physiological, and morphological properties, I4T (=ATCC TSD-357T= NCIMB 15472T) is proposed as the type strain of a novel species, Sphingomonas nivalis sp. nov.

microbiology↗

bioRxiv2025

Comprehensive Functional Self-Antigen Screening to Assess Cross-Reactivity in a Promiscuous Engineered T-cell Receptor

T cell receptor therapeutics are an emerging modality of biologic and cell-based medicines with the unique ability to target intracellular antigens and finely discriminate between healthy and infected or mutated cells. An obstacle to the development of new T cell receptor therapeutics is the difficulty in engineering these proteins for enhanced therapeutic efficacy while avoiding introduction of unexpected off-target autoreactivity. In this study, we apply a functional high-throughput screening assay, Tope-seq, to detecting cross-reactive epitopes in libraries of >5 x 105 unique peptide-coding sequences. We retrospectively analyze an affinity-enhanced engineered T cell receptor, which previously failed clinical trials due to severe off-target toxicity caused by epitope cross-reactivity, by comprehensive functional testing against all genome-coded self-antigens. Using the Tope-seq methodology, we were able to identify the epitope mediating off-target reactivity at a significance threshold of p < 0.01 in first-pass bulk screening. We also identified other potential cross-reactive epitopes of the engineered TCR of-interest, suggesting that the need for assessing promiscuity in TCR based therapeutics is larger than previously appreciated.

immunology↗

bioRxiv2025

3D Printed Nerve Guidance Conduit for Biologics-Free Nerve Regeneration and Vascular Integration

There is a clinical need for an effective nerve guidance conduit to treat peripheral nerve injuries. Many studies have explored different materials and active cues to guide neural regeneration, with some success. However, none have demonstrated a comparable or better functional recovery than the clinical standard autograft. Autografts are often insufficient for reconstruction of an injury to long nerves such as the sciatic or brachial plexus. Synthetic nerve guidance conduits (NGCs) have been investigated for these injuries to guide axonal regeneration and lead to functional recovery. We have designed a biologics-free hydrogel-based multi-channel conduit with defined microscale features to guide axonal outgrowth. To investigate extraneural vascular infiltration and its effects on functional recovery, we also designed a multi-microchannel conduit with defined regularly spaced micropores, orthogonal to the axon guidance channels. Using our custom-built Rapid Projection, Image-guided, Dynamic (RaPID) bioprinting system, we are able to fabricate each hydrogel conduit within minutes from a milliliter-volume prepolymer vat. With our state-of-the-art printing platform, we have achieved NGCs with a consistent channel wall width of 10 microns. We implanted the NGCs for 17 weeks in a murine sciatic nerve transection injury model. We assessed the functional recovery by dynamic gait analysis throughout the recovery period and by compound muscle action potential (CMAP) electrophysiology before NGC harvesting. Both the non-porous and micro-porous conduit groups led to functional nerve regeneration on par with the autograft group. Further, both conduit groups resulted in restoration of bulk motor function to pre-injury performance. Translational Impact StatementWe have developed a synthetic therapeutic that can be implanted to aid nerve regeneration after a debilitating injury that performs similarly to the current clinical standard treatment. One major hurdle to clinically translating an implantable therapeutic is needing to include biologics such as cells or active biomolecules, which increases the regulatory burden. With this in mind, we systematically developed a biologics-free synthetic hydrogel nerve guidance conduit, composed of polymer backbones that have been used in many FDA-approved applications, capable of restoring motor function.

bioengineering↗

bioRxiv2025

Viral Infection Depends on Host's Metabolism

Viral infection begins with attachment to host surface structures such as receptors, pili, or porins. While prior research has focused on structural compatibility and recognition, the role of host physiology, particularly metabolic state, on viral commitment to infection remains underexplored. Here, we measured the adsorption rates () of five Escherichia coli phages representing various life cycles and entry pathways under controlled metabolic conditions. Four phages showed significantly reduced adsorption under energy-limited states, with weaker-binding phages being more sensitive. Using E. coli and its phages allowed us to institute a number of control infections that would be difficult with other organisms. Our findings support a two-step infection model where bound phages may disengage under unfavorable conditions, reducing commitment to non-productive infections. We observed a correlation between adsorption rates under energy-competent conditions and sensitivity to host metabolic state. Our results highlight host physiology as a key factor in virus-host interactions under energy-limited conditions.

microbiology↗

bioRxiv2025

The inflammatory skin disease map (ISD map): an interactive computational resource focused on psoriasis and atopic dermatitis molecular mechanisms

BackgroundInflammatory skin diseases (ISD), including atopic dermatitis (AD) and psoriasis (PsO), emerge from a complex network of inter- and intracellular biochemical interactions under the influence of genetic and environmental factors. The complexity of ISD mechanisms hinders translation of research findings into effective treatments and may explain the low remission rates despite the availability of modern targeted therapies. ObjectiveTo model AD- and PsO-associated mechanisms as networks of context-specific molecular interactions, the so-called ISD map, and to check the usefulness of this map as a graphically guided review of AD and PsO mechanisms and as a mechanistic hypothesis-generating platform. MethodsThe ISD map was built by assembling mechanistically resolved causal interactions obtained from relevant biomedical literature via manual curation. ResultsWe demonstrate that the ISD map (https://imi-biomap.elixir-luxembourg.org/) serves as an interactive, graphical review of AD and PsO molecular mechanisms and as a mechanistic hypothesis-generating platform. By analysing the map structure itself or the map integrated with genetics and functional genomics data, we could generate the following mechanistic hypotheses: (i) AD poor response to dupilumab is associated with a potential upregulation of IFNG, IL22, TSLP, IL-17A and IL25 signalling pathways in keratinocytes and/or single nucleotide polymorphisms (SNPs) in genes encoding regulators of IFNG expression in Th1 cells and (ii) PsO resistance to cytokine-induced apoptosis is associated with SNPs in IFNG signalling genes regulating SOCS1 in keratinocytes. Finally, the IL4/IL13 pathway in the AD submap of the ISD map was converted into a probabilistic Boolean model to simulate the effects of IFNG in sensory perception of itching after treatment with dupilumab. Our findings suggest that inhibiting both IFNG and IL4R may improve the therapeutic management of itching. ConclusionThe ISD map provides a significant interactive, computationally accessible resource of molecular knowledge on AD and PsO that can be used to graphically review known AD and PsO mechanisms and generate mechanistic hypotheses.

bioinformatics↗

bioRxiv2025

Development of a floxed Gabbr2 gene allows for widespread conditional disruption of GABBR2 and recapitulates the phenotype of germline Gabbr2 knockout mice

GABBR1 and GABBR2 are widely expressed in the brain and genetic inhibition of their function leads to widespread neurologic dysfunction and premature death in mice. Given that GABBR1 and GABBR2 heterodimerize to form a functional receptor, global knockout of GABBR1 or GABBR2 results in a similar phenotype, characterized by spontaneous epileptiform activity, hyperlocomotor activity, hyperalgesia, impaired memory and premature death. It is now known that both GABBR1 and GABBR2 are expressed in a variety of tissues outside the nervous system and that GABA-B receptors can heterodimerize with other class C GPCRs, including the extracellular calcium-sensing receptor (CaSR). Studies in vitro have demonstrated that interactions with GABBR1 and GABBR2 can alter CaSR signaling in human embryonic kidney cells and breast cancer cells. The neurologic consequences of global loss of function of GABBR1 or GABBR2 has made it difficult to study the effects of loss of GABBR function in other organs. While a conditional knockout for GABBR1 is available, the GABBR2 gene had not been "floxed". We have used CRISPR to insert loxP sites into the GABBR2 locus in mice. These mice are normal at baseline but when bred with mice expressing Cre-recombinase under the control of the ubiquitously expressed Actin gene promoter, they recapitulate the phenotype of global GABBR2 knockout mice. Phenotypic changes through the brain, including the cortex, hippocampus and cerebellum. Evidence of abnormal neuronal function, increase cell death, and changes in neuronal architecture are seen throughout the brain of CRISPR knockout mice. These mice should be useful tools to study cell type-specific loss of GABBR2 function in the brain and other organs.

neuroscience↗

bioRxiv2024

Giving it a fair shake: A simple, fast, & efficient method to extract amatoxins from the death cap mushroom, Amanita phalloides

1.1.The death cap mushroom, Amanita phalloides, is well known for containing amatoxins such as alpha- and beta-amanitin, which inhibit eukaryotic RNA polymerase II. While these toxins have been used in research for almost a century, they have recently garnered attention for their role in drug-antibody conjugates. The amatoxins are still largely extracted from wild mushrooms, which cannot be made to fruit in the lab. We propose simplified extraction methods that could reduce hazardous exposures to dust and expedite sample analysis without sacrificing accuracy. We recently developed a Lateral Flow Immunoassay (LFIA), for which we identified that sample maceration was not needed to extract the amatoxins and that the incubation time for extraction could be accomplished in 1 minute. In this current work, we hypothesized that these same extraction adjustments-minimal tissue maceration and reduced incubation time-could be transferable to instrumental detection methods. To test the need for sample maceration, we utilized three different techniques: 1) traditional mortar and pestle, 2) a similarly disruptive method of bead beating, and 3) no grinding, but rather hand shaking dried mushroom tissue in extraction buffer. In addition, we performed the solvent extraction step at varying times to observe if more time allows for more toxin to be removed from the tissue. Lastly, we utilized two comparable solvent evaporation methods (rotovap or speedvac) to establish if multiple samples could be processed simultaneously, thus improving sample throughput. We adjusted aspects of the typical extraction protocol, which resulted in a rapid (1 min) incubation step, along with minimal sample handling (no grinding) of the dried mushroom tissue. We present an extraction protocol that saves time, reduces equipment contamination, and minimizes risk to the researcher. The impact of this faster, safer method may help produce these important toxins faster, for both research and medical use.

microbiology↗

bioRxiv2024

Degradation of PET plastic with engineered environmental bacteria

Polyethylene terephthalate (PET) is one of the most widely used plastic materials in the food and textile industry. Consequently, post-consumer PET waste is a common environmental pollutant that leaks into the environment in the form of macro and microplastics with concerning health impacts. There is a pressing need to identify novel and sustainable solutions to process the abundance of PET waste contributing to this pollution. While there is extensive research into enzymes able to hydrolyse PET in vitro, a similar solution for discarded or difficult-to-collect PET based on whole-cell microbial catalysts is missing. In this work we report the engineering of environmental bacteria to use PET as a growth substrate. This was achieved by isolating a strain of Pseudomonas umsongensis able to use the PET monomer terephthalate as carbon source, engineering the strain to effectively secrete the high-activity PET hydrolase PHL7 through the addition of a recombinant TAT secretion leader sequence, and enhancing the bioavailability of PET by transforming it into an amorphous and macroporous structure by pre-treatment with an organic solvent. Our findings demonstrate the direct microbial consumption of PET, which could lead to improved and more sustainable upcycling strategies for this plastic.

synthetic biology↗