Biology subjects

Deane, J. E.

Publications and source records attributed to Deane, J. E..

At least 19 recordsLinked to original sources

bioRxiv2026

Development of py-mea-flow for comprehensive analysis of multi-electrode array data and its application to LGI2-deficient neurons

Multi-electrode arrays (MEAs) generate mid- to high-throughput electrophysiological data widely used to characterise neural network activity in vitro. Downstream analysis of recordings from Axion Biosystems instruments, however, has long depended on the manufacturers closed-source pipeline (AxIS Navigator, NeuralMetric Tool, AxIS Metric Plotting Tool), limiting customisation and integration into flexible Python workflows. We present py-mea-flow, an open-source Python package providing end-to-end analysis of Axion Biosystems spk binary files. Our package enables spike extraction, inter-spike interval burst detection, network burst detection and spike synchrony. We also provide tools for preparation of publication-ready visualisations including raster plots with spike-detection-rate histograms, plate-layout heatmaps, time-course trajectories, single timepoint violin plots and statistical comparisons. Outputs reproduce the manufacturers NeuralMetric Tool reference with near perfect accuracy in all benchmarked metrics. A mea-flow command-line interface enables batch processing without writing Python code. As a proof of concept, we applied py-mea-flow to human iPSC-derived cortical neurons with CRISPRi-mediated LGI2 knockdown. This revealed a reproducible network hyperexcitability phenotype in which burst and network burst frequencies were elevated while spike synchrony remained unchanged. Availability and implementation: The package is distributed on PyPI (pip install py-mea-flow), and version-controlled at https://github.com/Molecularbiologyworld/py-mea-flow. User feedback can be provided via the GitHub issues tab.

neuroscience↗

bioRxiv2026

South American Plasmodium falciparum isolates reveal new insights into the role of PfAAT1 in mediating resistance to Chloroquine

Antimalarial drug resistance remains one of the most significant challenges to global malaria control. The emergence of resistance to chloroquine, the first truly globally distributed antimalarial, has been extensively studied but is still not fully understood. While mutations in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) primarily drive resistance, the phenotype is complex and multigenic, with mutations in the putative amino acid transporter PfAAT1 recently confirmed to play a modulatory role. To date studies have focused on PfAAT1 mutations found in African and Southeast Asian P. falciparum lineages, but chloroquine resistance emerged independently in South America, where there may be novel PfAAT1 polymorphisms that are functionally important. We used AlphaFold modelling to reveal high homology between PfAAT1 and the human lysosomal arginine transporter SLC38A9, which allows prediction of membrane orientation and identifies a partially open channel accessible from the cytoplasm. Several PfAAT1 mutations found only in South American isolates sit near the entrance of this pore, most notably V231 where mutation to aspartate is predicted to alter channel conformation and influence transport, while nearby P446A (which is always found in combination with V231D) and I248T are predicted to impact pore flexibility and local structural stability. To functionally validate these insights, we employed CRISPR/Cas9 gene editing across parasite strains with diverse geographic origins. Reverting the regional V231D mutation in the South American 7G8 strain significantly reduced CQ resistance, providing the first functional evidence that this residue modulates drug susceptibility. Furthermore, introducing the apparently Colombia-specific I248T mutation significantly enhanced parasite multiplication rates in 7G8, demonstrating complex fitness and sensitivity trade-offs. Our findings reinforce the distinct evolutionary trajectory for South American CQ resistance and highlight the necessity of including additional pfaat1 mutations in global molecular surveillance strategies. Author SummaryAntimalarial drug resistance is a major threat to global public health. Chloroquine was used widely in the 1950s-60s as part of a global malaria eradication campaign, but resistance emerged in multiple places independently and chloroquine resistant parasites directly led to the death of millions of children. Chloroquine resistance is primarily driven by mutations in the transporter PfCRT which are thought to increase export of chloroquine from the digestive vacuole, where chloroquine acts to prevent the ability of the parasite to digest haemoglobin as a source of energy. However, it is becoming increasingly clear that additional vacuolar transporters can also modulate chloroquine resistance. In this study we focused on mutations in the putative amino acid transporter 1 (PfAAT1) which are specific to South America, where chloroquine resistance emerged independently from Southeast Asia. By integrating AlphaFold structural predictions with CRISPR/Cas9 gene editing across geographically diverse parasite backgrounds we provide the first functional evidence that the region-specific V231D mutation significantly diminishes chloroquine resistance. These findings emphasise that chloroquine resistance in South America followed a unique trajectory and that PfAAT1 is involved in complex fitness and sensitivity trade-offs. This work emphasises the benefits of integrating diverse experimental and modelling approaches with global molecular surveillance.

microbiology↗

bioRxiv2026

FLiPA: A versatile platform for quantitative analysis of protein-glycosphingolipid interactions

Interactions between proteins and glycosphingolipids (GSLs) regulate various cellular processes and altered GSL metabolism contributes to numerous diseases. The diverse glycan headgroups and ceramide backbones of GSLs shape membrane organisation, fluidity, curvature, and tension. As protein recognition frequently depends on both glycan specificity and the organisation of GSLs within the membrane, these interactions remain challenging to characterise in vitro. Here, we introduce FLiPA (Fluorescent Liposome Plate Assay), a versatile method that utilises fluorescent agarose-embedded giant liposomes for the quantitative analysis of protein-GSL interactions. By enabling systematic control of membrane and buffer composition, FLiPA provides an accessible and robust platform for dissecting the molecular determinants of protein-GSL interactions, including the roles of cholesterol, membrane order, protein oligomerisation and ionic strength.

molecular biology↗

bioRxiv2026

Herpes simplex virus pUL56 abolishes neuronal activity by removing voltage-gated ion channels from the plasma membrane

Herpes simplex virus 1 (HSV-1) infections of the central nervous system cause encephalitis and are associated with increased risk of neurodegeneration, yet the molecular consequences of lytic infection in human neurones remain incompletely defined. We map the transcriptomic, proteomic and surface-proteome changes induced by HSV-1 across the lytic infection cycle in human iPSC-derived cortical glutamatergic neurones. HSV-1 drives extensive plasma-membrane remodelling, including the removal of voltage-gated sodium, potassium and calcium channels, resulting in a profound loss of synchronous calcium signalling. We identify the viral ubiquitin-ligase adaptor pUL56 as the principal effector of this process: pUL56-dependent depletion of ion channels abolishes coordinated calcium signalling, whereas deletion or mutation of its E3-ligase binding motifs preserves synchrony. Furthermore, expression of pUL56 alone is sufficient to abolish neuronal electrical activity. These findings establish pUL56 as a potent viral suppressor of neuronal excitability and provide potential mechanistic links between HSV-1 infection and neurodegenerative pathology.

microbiology↗

bioRxiv2026

Human iPSC Models of Ganglioside Deficiency Reveal a Sialylated Lipid Requirement for Plasma-Membrane Organization and Neuronal Activity

Gangliosides are abundant neuronal glycosphingolipids, yet their roles in organizing the plasma membrane and supporting neuronal function remain poorly defined. Mutations in the biosynthetic enzymes ST3GAL5 or B4GALNT1 cause severe neurodevelopmental disorders, yet their cellular consequences are unclear. Using isogenic human iPSC-derived cortical neurons, we show that loss of these enzymes eliminates major neuronal gangliosides but produces strikingly divergent outcomes. ST3GAL5 deficiency reprograms the glycosphingolipid repertoire toward non-neuronal species and abolishes network-level electrical activity. In contrast, B4GALNT1-deficient neurons retain near-normal excitability, supported by accumulation of simple sialylated precursors (GM3/GD3). Quantitative proteomics reveals a profound loss of plasma membrane proteins, including ion channels and synaptic organizers, only in ST3GAL5-deficient neurons. These findings identify sialylated glycosphingolipids as essential scaffolds for plasma membrane organization and neuronal excitability, providing a mechanistic basis for the severe phenotype caused by loss of GM3 synthase in humans. TEASERHuman neuronal models reveal why loss of GM3 synthase causes severe neurodevelopmental disease

cell biology↗

bioRxiv2026

Ensemble Machine Learning Approaches Predict Survival in Lower-Grade Glioma Based on Glycosphingolipid Gene Expression and Metabolic Modelling

Glycosphingolipids (GSLs) are essential components of biological membranes with important roles in cell signalling. Disrupted GSL metabolism is associated with malignancy across a range of cancers, with different GSLs implicated in distinct tumours. GSLs have potential mechanistic roles in cancer; however, their functions in Lower Grade Gliomas (LGGs) remain poorly understood. We present ensemble machine learning approaches using transcriptomic data from LGG, combined with GSL-specific metabolic simulations, to predict survival outcomes. The ensemble approach demonstrates effective risk stratification for LGG patients based on GSL gene expression. Pathway analysis of model-derived risk groups highlighted potential association of GSLs with cell motility, division and Wnt signalling in LGG pathology. Given the strong performance of machine learning approaches to predict outcomes and that GSLs are shed into the tumour microenvironment, GSL-based diagnostics and prognostics may prove clinically beneficial. A Python package enabling GSL-specific metabolic modelling and risk prediction from RNA-seq data is provided.

bioinformatics↗

bioRxiv2025

Optimisation of lytic herpes simplex virus infection in human induced pluripotent stem cell derived cortical neurones

Herpes simplex virus (HSV)-1 infection of cortical neurones is a leading cause of encephalitis. While we have substantial knowledge about the molecular virology of HSV-1 lytic infection in cells of the periphery, like keratinocytes or fibroblasts, we know much less about infection of human neurones owing to the challenges of working with neuronal cell-based models. Here we demonstrate the use of a human induced pluripotent stem cell (iPSC)-derived cortical neurone model (i3Neurones) for HSV-1 infection. i3Neurones are highly scalable and can be rapidly and efficiently differentiated into an isogenic population of cortical glutamatergic neurones. We show that i3Neurones support the full HSV-1 lytic replication cycle. We present an optimised protocol for the infection of i3Neurones with HSV-1 that allows their synchronous infection at near-100% efficiency, and optimised fixation methods that preserves organelle and neurite structure for immunocytochemistry analysis. Our study highlights i3Neurones as a robust, scalable platform for microscopy and biochemical studies of HSV-1 and other neurotropic pathogens. Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

microbiology↗

bioRxiv2025

Alphaherpesvirus pUL21 homologues use non-canonical motifs to compete with cellular adaptors for protein phosphatase 1 binding

Protein phosphatase 1 (PP1) is a key regulator of cellular phosphorylation and its activity is regulated via binding to cellular regulatory proteins via conserved short linear motifs (SLiMs). The herpes simplex virus (HSV)-1 protein pUL21 binds PP1 via the TROPPO motif, which lacks sequence similarity to canonical PP1-binding SLiMs. Here, we combine structure prediction, mutagenesis, and biophysical assays to elucidate the molecular basis of this interaction. AlphaFold2-Multimer structural models suggest that the TROPPO motifs of pUL21 and of pORF38, the varicella-zoster virus homologue of pUL21, bind the same hydrophobic groove on PP1 as RVxF and {phi}{phi}[xF] motifs, forming an extended {beta}-sheet that bridges PP1 and the N-terminal domain of pUL21 or pORF38. Site-directed mutagenesis of both pUL21 and PP1 confirms key predicted interactions. Competition fluorescence polarisation confirms that pUL21 competes directly with cellular PP1 RvXF motifs for PP1 binding, albeit with lower affinity. Substituting key residues of the pUL21 TROPPO motif to resemble a canonical RVxF sequence increases PP1 binding, suggesting that alphaherpesviruses have evolved suboptimal motifs to fine-tune phosphatase recruitment that may balance viral kinase and phosphatase activities during infection. Our findings reveal a novel mechanism of PP1 recruitment by viral proteins and suggest that many other PP1 regulators may possess non-canonical binding motifs and thus remain undiscovered.

biochemistry↗

bioRxiv2025

Flexibility and modulation of translation initiation in enterovirus genomes

Enteroviruses comprise a large group of mammalian pathogens that often utilize two open reading frames (ORFs) to encode their proteins: the upstream protein (UP) and the main polyprotein. In some enteroviruses, in addition to the canonical upstream AUG (uAUG), there is another AUG that may represent an alternative upstream initiation site. An analysis of enterovirus sequences containing additional upstream AUGs identified several clusters, including strains of pathogenic Enterovirus alphacoxsackie and E. coxsackiepol. Using ribosome profiling on coxsackievirus CVA-13 (E. coxsackiepol), we demonstrate that both upstream AUG codons can be used for translation initiation in infected cells. Moreover, we confirm translation from both upstream AUGs using a reporter system. Mutating the additional upstream AUG in the context of CVA-13 did not result in phenotypic changes in immortalized cell lines. However, the wild-type virus outcompeted this mutant in human intestinal organoids and differentiated neuronal systems, representing an advantage in physiologically relevant infection sites. Mutation of the stop codon of the shorter upstream ORF led to dysregulated translation of the other ORFs in the reporter system, suggesting a potential role for the additional uORF in modulating the expression level of the other ORFs. These findings demonstrate the remarkable plasticity of enterovirus IRES-mediated initiation and the competitive advantage of double-upstream-AUG-containing viruses in terminally differentiated intestinal organoids and neuronal systems.

microbiology↗

bioRxiv2025

Patching up the nucleus: a novel role for PMLII in nuclear envelope rupture repair

The nuclear envelope (NE) is important for cellular health as it protects and organizes the genome. NE dynamics is important for various cellular processes including cell growth, migration and removal of defective NE components. In extreme cases, the NE can rupture leading to exchange of material between the nuclear interior and the cytoplasm. Rapid repair of the NE is initiated to minimize the effect on the genome. While our understanding of the machinery involved in this repair process is increasing, a lot is still unknown about this process including events leading up to NE rupture. Interestingly, biomolecular condensates have recently been found to play important roles in membrane repair and remodelling in cells. Here, we found that promyelocytic leukemia protein isoform II (PMLII), a protein involved in nuclear PML body formation, forms condensates at the NE. These condensates specifically form at sites where the lamina is disrupted. We show that NE rupture often occurs at these sites and that PMLII stays present until rupture repair is initiated suggesting a role in stabilization of the site for effective repair.

cell biology↗

bioRxiv2025

Conformational Dynamics and Membrane Insertion Mechanism of B4GALNT1 in Ganglioside Synthesis

Glycosphingolipids (GSLs) are crucial membrane components involved in essential cellular pathways. Complex GSLs, known as gangliosides, are synthesised in the ER/Golgi by a series of glycosyltransferase enzymes. Imbalances in GSL metabolism can lead to severe diseases, often affecting the nervous system. B4GALNT1 is a key enzyme in the ganglioside synthetic pathway, synthesising complex gangliosides including GM2 and GD2 from GM3 and GD3. These products are precursors to the major brain gangliosides. Loss of B4GALNT1 function causes hereditary spastic paraplegia 26 (HSP26), while its overexpression is linked to cancers including childhood neuroblastoma. Here, we present crystal structures of the homodimeric B4GALNT1 enzyme demonstrating conformational changes upon binding of donor substrate ligands and product. These structures support a catalytic mechanism that involves dynamic remodelling of the substrate binding site during catalysis. We also demonstrate that processing of lipid substrates by B4GALNT1 is severely compromised when surface loops flanking the active site are mutated from hydrophobic residues to polar. Molecular dynamics simulations support that these loops can insert into the lipid bilayer explaining how B4GALNT1 accesses and processes lipid substrates. By combining structure prediction and molecular simulations we propose that this mechanism of dynamic membrane insertion is exploited by other, structurally distinct GSL synthesising enzymes.

biochemistry↗

bioRxiv2024

Molecular Insights into Neuronal Dysfunction in GM2 Gangliosidoses

Glycosphingolipids (GSL) are important bioactive components of cellular membranes. Complex GSLs, containing sialic acid residues are known as gangliosides and are highly abundant in the brain. Diseases of ganglioside metabolism often result in severe, early-onset neurodegeneration. The ganglioside GM2 is the substrate of the hydrolytic lysosomal {beta}- hexosaminidase A (HexA) enzyme and when subunits of this enzyme are non-functional, GM2 lipid accumulates in cells leading to the GM2 gangliosidoses, Tay-Sachs and Sandhoff diseases. We have developed high-quality i3Neuron-based models of Tay-Sachs and Sandhoff diseases, that demonstrate storage of GM2, formation of membrane whorls and accumulation of endolysosomal proteins consistent with disease phenotypes. Importantly, in addition to lysosomal dysfunction, the composition of the plasma membrane (PM) is significantly impacted in these diseases with changes in the abundance of both lipids and proteins. The changes to the PM proteome are driven in part by exocytosis of lysosomal material resulting in the aberrant accumulation of lysosomal proteins and lipids on the cell surface. The altered abundance of GM2 at the PM was striking, bringing the abundance of this precursor lipid up to that of the common neuronal gangliosides. Furthermore, the PM profiling identifies significant changes in synaptic protein abundances with direct functional impact on neuronal activity including rapid electrical firing consistent with neuronal hyperactivity. This work provides mechanistic insights into neuronal dysfunction in the GM2 gangliosidoses and highlights that these are also severe PM disorders. This work has broad implications for other lysosomal storage disorders and late-onset neurodegenerative diseases involving sphingolipid dysregulation.

neuroscience↗

bioRxiv2022

The structure of a Plasmodium vivax Tryptophan Rich Antigen suggests a lipid binding function for a pan-Plasmodium multi-gene family

Tryptophan Rich Antigens (TRAgs) are encoded by a multi-gene family in all Plasmodium species, significantly expanded in P. vivax, but their function is not currently known. We show that multiple P. vivax TRAgs are expressed on the merozoite surface and that one, PVP01_0000100 binds red blood cells with a strong preference for reticulocytes. Solving the structure of the C-terminal tryptophan rich domain that defines the TRAg family revealed a three-helical bundle that is conserved across Plasmodium and has homology with lipid-binding BAR domains involved in membrane remodelling. Biochemical assays confirmed that this domain has lipid binding activity with preference for sulfatide, a glycosphingolipid present in the outer leaflet of plasma membranes. Deletion of the putative orthologue in P. knowlesi, PKNH_1300500, impacts invasion in reticulocytes, suggesting a role for membrane remodelling during this essential process. Together, this work suggests a molecular function for the TRAg family for the first time.

microbiology↗

bioRxiv2022

Altered plasma membrane abundance of the sulfatide-binding protein NF155 links glycosphingolipid imbalances to demyelination

Myelin is a multi-layered membrane that tightly wraps neuronal axons enabling efficient, high-speed signal propagation. The axon and myelin sheath form tight contacts, mediated by specific plasma membrane proteins and lipids, and disruption of these contacts causes devastating demyelinating diseases. Using two cell-based models of demyelinating sphingolipidoses, we demonstrate that altered lipid metabolism changes the abundance of specific plasma membrane proteins. These altered membrane proteins have known roles in cell adhesion and signalling, with several implicated in neurological diseases. The cell surface abundance of the adhesion molecule Neurofascin, a protein critical for the maintenance of myelin-axon contacts, changes following disruption to sphingolipid metabolism. This provides a direct molecular link between altered lipid abundance and myelin stability. We show that the Neurofascin isoform NF155, but not NF186, interacts directly and specifically with the sphingolipid sulfatide via multiple binding sites and that this interaction requires the full-length extracellular domain of NF155. We demonstrate that NF155 adopts an S-shaped conformation and preferrentially binds sulfatide-containing membranes in cis, with important implications for protein arrangement in the tight axon-myelin space. Our work links glycosphingolipid imbalances to disturbance of membrane protein abundance and demonstrates how this may be driven by direct protein-lipid interactions, providing a mechanistic framework to understand the pathogenesis of galactosphingolipidoses.

neuroscience↗

bioRxiv2022

Attenuation hotspots in neurotropic human astroviruses

During the last decade, the detection of neurotropic astroviruses has increased dramatically. The MLB genogroup of astroviruses represents a genetically distinct group of zoonotic astroviruses associated with gastroenteritis and severe neurological complications in young children, the immunocompromised and the elderly. Using different virus evolution approaches, we identified dispensable regions in the 3' end of the capsid-coding region responsible for attenuation of MLB astroviruses in susceptible cell lines. To create recombinant viruses with identified deletions, MLB reverse genetics and replicon systems were developed. Recombinant truncated MLB viruses had wild type-like or enhanced growth and replication properties in permissive cells but were strongly attenuated in iPSC-derived neuronal cultures confirming the location of neurotropism determinants. This approach can be used for the development of vaccine candidates using attenuated astroviruses that infect humans, livestock animals and poultry.

microbiology↗

bioRxiv2022

Structural determinants of homophilic adhesion by receptor tyrosine phosphatases

The type IIB receptor protein tyrosine phosphatases (R2B RPTPs) are cell surface transmembrane proteins that engage in cell adhesion via their extracellular domains (ECDs) and cell signaling via their cytoplasmic phosphatase domains. The ECDs of R2B RPTPs form stable, homophilic, trans interactions between adjacent cell membranes. Previous work has demonstrated how one family member, PTPRM, forms homodimers; however, the determinants of homophilic specificity remain unknown. We have solved the X-ray crystal structure of the membrane-distal, N-terminal domains of PTPRK that form a head-to-tail dimer consistent with intermembrane adhesion. Comparison with the PTPRM structure demonstrates inter-domain conformational differences that may define homophilic specificity. Using small-angle X-ray scattering we determined the solution structures of the full-length ECDs of PTPRM and PTPRK, identifying that both are rigid, extended molecules that differ in their overall long-range conformation. Furthermore, we identify one residue, W351, within the interaction interface that differs between PTPRM and PTPRK and show that mutation to glycine, the equivalent residue in PTPRM, abolishes PTPRK dimer formation in vitro. This comparison of two members of the receptor tyrosine phosphatase family suggest that homophilic specificity is driven by a combination of shape complementarity and specific but limited sequence differences. SIGNIFICANCE STATEMENTCell-cell contacts are dynamically regulated, in part, by the actions of tyrosine kinases and phosphatases. The R2B family of receptor tyrosine phosphatases combine an adhesive extracellular domain with intracellular catalytic domains that bind and dephosphorylate key cell adhesion and polarity proteins. Previous work demonstrated that the extracellular domains form head-to-tail homodimers but, as the interface was composed of residues conserved across the family, homophilic specificity determinants remained unclear. We have used a range of structural techniques including X-ray crystallography, small angle X-ray scattering and AlphaFold modelling to demonstrate that, despite their similarity, two members of the R2B family possess significant differences in their overall shape. Our results support that a combination of subtle shape and sequence variations may determine homophilic binding.

biochemistry↗

bioRxiv2022

Herpes simplex virus 1 protein pUL21 stimulates cellular ceramide transport by activating CERT

Herpes simplex virus (HSV)-1 dramatically alters the architecture and protein composition of cellular membranes during infection, but its effects upon membrane lipid composition remain unclear. HSV-1 pUL21 is a virus-encoded protein phosphatase adaptor that promotes dephosphorylation of multiple cellular and virus proteins, including the cellular ceramide transport protein CERT. CERT mediates non- vesicular transport of ceramide from the ER to the trans-Golgi network, whereupon ceramide is converted to sphingomyelin and other sphingolipids that play important roles in cell proliferation, cell signalling and membrane trafficking. Using click chemistry to profile the kinetics of sphingolipid metabolism in cultured cells, we show that pUL21-mediated dephosphorylation activates CERT and increases the rate of ceramide to sphingomyelin conversion. Purified pUL21 and full-length CERT interact with sub-micromolar affinity and we map the domains responsible for the interaction. Solving the solution structure of the pUL21 C-terminal domain in complex with the CERT PH and START domains using small-angle X-ray scattering allows us to identify a single amino acid mutation on the surface of pUL21 that disrupts CERT binding in vitro and in cultured cells. Sphingolipid profiling demonstrates that ceramide to sphingomyelin conversion is severely diminished in the context of HSV- 1 infection, a defect that is compounded when infecting with a virus encoding the mutated form of pUL21 that lacks the ability to activate CERT. However, virus replication and spread are not significantly altered when pUL21-mediated CERT dephosphorylation is abolished, highlighting that dephosphorylation of other cellular and/or viral targets underpins the important role of pUL21 in HSV-1 biology. SignificanceHerpes simplex virus (HSV)-1 causes a life-long dormant infection of neurons, sporadically reactivating to manifest as cold-sores or genital herpes. While the impact of HSV-1 upon the protein content of infected cells has been well studied, we know relatively little about its impact upon cellular lipids. Using bioorthogonal labelling in cultured cells we show that HSV-1 protein pUL21 activates the key cellular lipid transport protein CERT to accelerate the conversion of ceramide to sphingomyelin. HSV-1 infection dramatically alters the kinetics of ceramide metabolism, leading to ceramide accumulation. Mutation of HSV-1 pUL21 to prevent CERT activation further enhances ceramide accumulation but this does not alter the replication or spread of HSV-1, highlighting that other cellular and/or viral proteins represent the critical targets of pUL21-mediated dephosphorylation in cultured cells.

microbiology↗

bioRxiv2022

Molecular mechanism of Afadin substrate recruitment to the receptor phosphatase PTPRK via its pseudophosphatase domain

Protein tyrosine phosphatase receptor-type kappa (PTPRK) is a transmembrane receptor that links extracellular homophilic interactions to intracellular catalytic activity. Previously we showed that PTPRK promotes cell-cell adhesion by selectively dephosphorylating several cell junction regulators including the protein Afadin (Fearnley et al., 2019). Here we demonstrate that Afadin is recruited for dephosphorylation by directly binding to the PTPRK D2 pseudophosphatase domain. We mapped this interaction to a putative coiled coil (CC) domain in Afadin that is separated by more than 100 amino acids from the substrate pTyr residue. We identify the residues that define PTP specificity, explaining how Afadin is selectively dephosphorylated by PTPRK yet not by the closely-related receptor tyrosine phosphatase PTPRM. Our work demonstrates that PTP substrate specificity can be determined by protein-protein interactions distal to the active site. This explains how PTPRK and other PTPs achieve substrate specificity despite a lack of specific sequence context at the substrate pTyr. Furthermore, by demonstrating that these interactions are phosphorylation-independent and mediated via binding to a non-catalytic domain, we highlight how receptor PTPs could function as intracellular scaffolds in addition to catalyzing protein dephosphorylation.

molecular biology↗