Biology subjects

Volkov, A.

Publications and source records attributed to Volkov, A..

8 recordsLinked to original sources

bioRxiv2026

Minimal requirements and evolution of polar membrane targeting in the land plant SOSEKI protein family

Accurate spatial distribution of polar proteins is essential for cell function, but mechanisms underlying polar protein targeting in plants are poorly understood. Here, we dissect the molecular mechanisms underlying the polar targeting of the SOSEKI1 (SOK1) protein in Arabidopsis thaliana. Using extensive mutagenesis and truncation analyses of the polarity domain, we mapped the minimal polarity fragment necessary and sufficient for stable polar targeting to a 25-amino-acid region. This region likely forms an amphipathic helix, and mutations reveal that both its polar and apolar faces are essential for membrane association and polarity. Using phylogenetic analysis, we reconstruct the evolutionary history of the minimal polar targeting region across land plants. Using cross-species expression and protein localization, we infer the ancestral polar SOK localization pattern and show how it remained remarkably conserved, only to diversify upon gene duplication. This work identifies a polar targeting peptide in plants, reveals a mechanism for polar membrane targeting of a plant protein family, and demonstrates both conservation and diversification within this family.

plant biology↗

bioRxiv2026

Multivalent ubiquitin recognition regulates multiple stages of Tau self-assembly

Liquid-liquid phase separation (LLPS) has emerged as an important intermediate in the pathological self-assembly of Tau, yet the molecular mechanisms that regulate this process remain incompletely understood. Although ubiquitin is a prominent component of pathological inclusions in tauopathies and other neurodegenerative diseases, its presence has largely been linked to targeting aberrant proteins for proteasomal or autophagic clearance. Here, we identify Tau as a ubiquitin-binding protein and demonstrate that multivalent, non-covalent ubiquitin recognition regulates multiple stages of Tau self-assembly. Biochemical, biophysical, structural, and computational analyses identified four ubiquitin-binding elements within the Tau microtubule-binding repeat region that engage the canonical hydrophobic patch of ubiquitin, providing a structural basis for multivalent recognition of mono- and poly-ubiquitin species. Functionally, mono- and poly-ubiquitin suppress Tau condensate formation while enhancing the liquid-like properties of condensates that persist. In contrast, mono-ubiquitin selectively enhances aggregation of the disease-linked Tau-P301L variant under conditions without detectable LLPS, demonstrating that ubiquitin exerts distinct effects depending on the molecular context and stage of Tau self-assembly. Together, these findings establish non-covalent ubiquitin recognition as a previously unrecognized mechanism regulating Tau phase behavior and aggregation. More broadly, they expand the role of ubiquitin beyond protein quality control, with ubiquitin architecture providing an additional layer of regulation over Tau condensate formation, dynamics, maturation, and aggregation.

biophysics↗

bioRxiv2026

Systematic proteomics identifies a conserved mechanism for polar targeting of plant cortical proteins

Multicellular development is tightly coupled to the polarization of individual cells, which partitions polar proteins along the cell cortex and can control asymmetric cell division, anisotropic growth, local differentiation or physiology. Mechanisms driving cell polarization have been described in fungi and animals, but these lack counterparts in plants. While several polarized proteins have been identified in plants, the overall mechanisms guiding their polar localization are poorly characterized. Through iterative affinity proteomics on the recently identified SOSEKI polar proteins, we discovered a network of polar proteins that is conserved in the flowering plant Arabidopsis and the liverwort Marchantia. We next used this collection of novel polarized proteins for systematic proximity ligation proteomics in these two species to map their global polar proteome. We identified a subfamily of polarized Protein S-acyl transferase (PAT) enzymes that are required for membrane targeting of Arabidopsis SOSEKI proteins. Using human and fruit fly models, we showed that PAT19 is sufficient for membrane targeting of SOSEKI1, likely through direct palmitoylation. This work demonstrates a conserved mechanism for polar protein targeting in plants and offers a resource for studying polar protein localization.

plant biology↗

bioRxiv2025

Increased clonality, decreased allele diversity and high genetic structure in tetraploid sea anemone Aulactinia stella populations from North Pacific to Atlantic across the Arctic Ocean

Reproductive mode is a key factor shaping genetic diversity, evolutionary potential, and the processes of dispersal and colonization. Clonality is particularly common in harsh environments and at the margins of species ranges, where it supports persistence, enables rapid growth, and promotes the maintenance of locally adapted genotypes. In the rapidly changing Arctic, increasing ecological connectivity is eroding historical barriers for sessile species. Evaluating genetic diversity in this context, before global change further alters Arctic ocean, is essential for understanding evolutionary dynamics during range expansion and for informing conservation strategies. Aulactinia stella is a circumpolar sea anemone with physiological characteristics in laboratory conditions suggesting a potential for clonal reproduction. In this study, we investigated its reproductive modes in natural populations across the Arctic ocean, from the northern Pacific to the Atlantic, and examined how genetic diversity is structured between adults and juveniles at five sampled sites. Across all study sites, we observed only females or individuals lacking gonads, with the exception of Kamchatka, where males were also present. Genetic indices and changes in genotype frequencies between adults and juveniles confirmed that this species reproduces partially by parthenogenesis. Populations on the Atlantic side were highly clonal with clonal rates (c) estimated at 80-99%, whereas populations on the Pacific side reproduced more sexually (c around 50%). Allelic diversity was twice as high in Kamchatka and Kuril populations, suggesting North Pacific coasts being the main last glacial refugia of A. stella. We found a stepping-stone pattern of genetic structure from Kamchatka to Atlantic populations, consistent with contemporary ocean currents and melted summer sea ice. Only a subset of the juvenile genetic diversity, mostly of local origin, was found in the established adults, while juveniles exhibited lower levels of genetic differentiation across the Arctic Ocean. Our findings underscore the need for further ecological and behavioral investigations to elucidate the mechanisms allowing the current possibilities of dispersal of this species across the Arctic Ocean. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=128 SRC="FIGDIR/small/650399v4_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@b395e6org.highwire.dtl.DTLVardef@364804org.highwire.dtl.DTLVardef@1b22eeeorg.highwire.dtl.DTLVardef@1272ae6_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract (photo: Ekaterina Bocharova)

evolutionary biology↗

bioRxiv2022

ChILL & DisCO to discover competitive, connective and allosteric Nanobodies that modulate the SOS1-RAS protein-protein interactions and tune the nucleotide exchange rate

Protein-protein interactions (PPIs) are central in cell metabolism but research tools for the structural and functional characterization of these PPIs are often missing. Here we introduce novel and broadly applicable immunization (Cross-link PPIs and immunize llamas, ChILL) and selection strategies (Display and co-selection, DisCO) for the discovery of diverse Nanobodies that either stabilize or disrupt PPIs in a single experiment. We applied ChILL and DisCO to identify competitive, connective or fully allosteric Nanobodies that inhibit or facilitate the formation of the SOS1*RAS complex and modulate the nucleotide exchange rate on this pivotal GTPase in vitro and RAS signalling in cellulo. One of these connective Nanobodies fills a cavity that was previously identified as the binding pocket for a series of therapeutic lead compounds. The long complementarity-determining region (CDR3) that penetrates this binding pocket serves as an innovative pharmacophore for extending the repertoire of potential leads.

bioengineering↗

bioRxiv2022

The Proxitome of Arabidopsis Processing Bodies Reveals a Condensate-Membrane Interface Instructing Actin-Driven Directional Growth

Cellular condensates can comprise membrane-less ribonucleoprotein assemblies with liquid-like properties. These cellular condensates influence various biological outcomes, but their liquidity hampers their isolation and characterization. Here, we investigated the composition of the condensates known as processing bodies (PBs) in the model plant Arabidopsis through a proximity-biotinylation pipeline. Using in situ protein-protein interaction approaches, genetics and high-resolution imaging, we show that PBs comprise networks that interface with membranes. Surprisingly, the conserved component of PBs, DECAPPING PROTEIN 1 (DCP1), can interface with unique plasma membrane subdomains that include cell edges and vertices. We characterized these plasma membrane interfaces and discovered a developmental module that can control cell shape. This module is modulated by the liquid-like properties of DCP1 and the actin-nucleating SCAR-WAVE complex, whereby the DCP1-SCAR-WAVE interaction confines actin nucleation. This study reveals an unexpected repertoire for a conserved condensate at unique membrane-condensate interfaces.

cell biology↗

bioRxiv2021

Interactome and structural basis for targeting the human T-cell leukemia virus Tax oncoprotein

Human T-cell leukemia virus type-1 (HTLV-1) is the causative agent of adult T-cell leukemia (ATL). Although ATL is a well-characterized T-cell neoplasm, linked to intermittent expression of the viral Tax-1 protein, there is currently no strategy to target Tax-1 functions using small molecules. Here, we report a comprehensive interaction map between Tax-1 and human PDZ domain-containing proteins (hPDZome). We show that Tax-1 interacts with more than one-third of hPDZome components, including proteins involved in cell cycle, cell-cell junctions, cytoskeleton organization, and membrane complex assembly. Using nuclear magnetic resonance (NMR) spectroscopy, we have determined the structural basis of the interaction between the C-terminal PDZ binding motif (PBM) of Tax-1, and the PDZ domains of syntenin-1, an evolutionary conserved hub that controls exosome trafficking. Finally, we have used confocal imaging, molecular modelling, NMR and mammalian cell-based assays to demonstrate that the Tax-1/syntenin-1 interaction is amenable to small-molecule inhibition. Altogether, our study highlights the biological significance of Tax-PDZ interactome and its interplay with exosome formation. It shows a direct link between extracellular vesicles and HTLV-1 transmission, providing a novel framework for the design of targeted therapies for HTLV-1-induced diseases.

biochemistry↗

bioRxiv2018

Radiotherapy and cisplatin increase immunotherapy efficacy by enabling local and systemic intratumoral T-cell activity

To increase cancer immunotherapy success, PD-1 blockade must be combined with rationally selected treatments. Here, we examined in a poorly immunogenic mouse breast cancer model the potential of antibody-based immunomodulation and conventional anti-cancer treatments to collaborate with anti-PD-1 treatment. One important requirement to improve anti-PD-1-mediated tumor control was to promote tumor-specific cytotoxic T cell (CTL) priming, which was achieved by stimulating the CD137 costimulatory receptor. A second requirement was to overrule PD-1-unrelated mechanisms of CTL suppression in the tumor micro-environment (TME). This was achieved by radiotherapy and cisplatin treatment. In the context of CD137/PD-1-targeting immunotherapy, radiotherapy allowed for tumor elimination by altering the TME, rather than intrinsic CTL functionality. Combining this radioimmunotherapy regimen with low-dose cisplatin improved CTL-dependent regression of a contralateral tumor outside the radiation field. Thus, systemic tumor control may be achieved by combining immunotherapy protocols that promote T cell priming with (chemo)radiation protocols that permit CTL activity in both the irradiated tumor and (occult) metastases.\n\nSummary statementThis study reveals that radiotherapy and cisplatin can be re-purposed to improve antibody-based immunotherapy success in poorly immunogenic breast cancer by overruling PD-1 unrelated mechanisms of T cell suppression in the tumor micro-environment.

cancer biology↗