Biology subjects

Yue, Y.

Publications and source records attributed to Yue, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Physicochemical compatibility and stability of urapidil-propofol admixtures during simulated Y-site Administration

Background/Objectives: Urapidil with propofol is clinically efficient against elevated blood pressure during sedation. However, their physicochemical compatibility and emulsion stability upon continuous infusion remain unclear. This study aimed to evaluate different mixing ratios and diluents, thereby proving the safety limits for their co-administration. Methods: Urapidil solutions prepared with either sodium chloride (NS) or glucose injection (GS), and emulsified with propofol at different ratios (v/v), were stored for 12 h. Physical compatibility was assessed by visual inspection, pH, osmolality, mean droplet diameter (MDD), polydispersity index (PDI), zeta potential, and percentage of fat globules larger than 5 m (PFAT5). Chemical stability was quantified using high-performance liquid chromatography. Results: pH and osmolality stabilized. Urapidil hydrochloride and propofol contents remained pure at > 95%, MDD was < 500 nm, and PDI was < 0.2. Urapidil proportion in NS was significantly negatively correlated with the zeta potential. PFAT5 was > 0.05% after 2-8 h. In contrast, in GS at a 1:2 ratio, PFAT5 remained < 0.05%, which increased slightly in the 1:1 group at 8 h. PFAT5 stabilized in the high-propofol group (10:1) under all conditions. Conclusions: The chemical compatibility of the admixture was acceptable after 12 h of storage. However, physical compatibility was influenced by the mixing ratio, diluent type, and storage time. For clinical Y-site co-administration, a 10:1 mixing ratio or dilution in 5% GS is recommended. Enhanced proportions must be mixed with NS, while continuous infusion time must be < 2 h to mitigate fat embolism risk.

pharmacology and toxicology↗

bioRxiv2026

Color-dependent foraging in C. elegans integrates chromoprotein photosensitization with bacterial metabolic cues

Animals rely on color to navigate complex environments, yet how eyeless organisms use chromatic information to guide food choice remains poorly understood. Here, we show that Caenorhabditis elegans exhibits robust color dependent foraging driven by microbial chromophores, preferentially consuming red while avoiding blue chromoprotein expressing bacteria across bacterial backgrounds and wild isolates. This discrimination persists in darkness and independently of photoreceptor, revealing a mechanism beyond canonical photoreception. Purified chromoproteins and bacterial metabolite fractions independently reproduce preference, demonstrating complementary chromatic and post ingestive metabolic cues. Mechanistically, blue chromoproteins generate singlet oxygen, producing oxidative stress and remodeling bacterial tryptophan and pterin metabolism, whereas red food promotes serotonin production and feeding-associated neuropeptide signaling. Disrupting serotonin biosynthesis or neuropeptide processing abolishes color preference. Together, our findings reveal a previously unrecognized, novel sensory strategy in which wavelength-selective pigment photochemistry transforms microbial color into metabolic information that is integrated through gut brain neuroendocrine signaling to guide foraging behavior in an eyeless animal.

molecular biology↗

bioRxiv2026

Mosaic foreleg convergence disentangles phylogeny from ecology in Cretaceous amber crickets

Mosaic evolution assembles organisms from ancestral and derived parts, and traits shaped by convergent selection can mislead phylogenetic reconstruction while recording ecology. Disentangling these two signals within the same anatomy is a challenge for placing fossils and reconstructing evolution in deep time. We present a character-partitioning framework that fixes a molecular backbone of living species, projects fossils onto it with partitioned morphological matrices, and quantifies each anatomical module's contribution to phylogenetic placement and ecological prediction. In mid-Cretaceous Myanmar amber crickets, which combine a cricket-like body with mole-cricket-like digging forelegs, the foreleg module drove most phylogenetic distortion and carried most ecological information: removing it restored a convergent living control species to its family and collapsed habitat-prediction accuracy from 77.8% to below the 44.4% baseline. Partitioning convergent modules thus separates phylogenetic signal from ecological information, turning mosaicism from a confound of fossil interpretation into a quantitative record of history and niche.

evolutionary biology↗

bioRxiv2026

Proteoform Barcode: An Intuitive Visualization Framework for Top-Down Proteomics

Top-down proteomics (TDP) advances biomedical research by providing a birds-eye view of proteoforms in cells, tissues, and biofluids. Thousands of proteoforms can be characterized using well-established TDP technologies, and potential proteoform biomarkers of diseases have been discovered. However, there is a lack of an easy and biologically informative approach to present the quantitative global TDP data. Here, we present proteoform barcode as a straightforward visualization approach that simultaneously displays proteoform abundance and their associated Gene Ontology (GO) biological processes, converting a list of proteoforms to a biologically informative image. The proteoform barcode allows 1) a global view of proteoforms (i.e., relative abundance and functional information) in complex biological systems (i.e., bacteria, yeast, human cells, and human plasma) and 2) the accurate distinction of samples in diverse biological conditions (i.e., control and disease) assisted by machine learning approaches. The proteoform barcode, assisted by the random forest model, accurately separated the human plasma samples of healthy controls and early-stage breast cancer. The data demonstrates the high potential of the proteoform barcode-based approach for early diagnosis of diseases in an easy and biologically informative manner.

systems biology↗

bioRxiv2026

CLASP2 promotes repair of kinesin-1 damage to the microtubule lattice

Microtubules are cytoskeletal polymers that play essential roles in eukaryotic cells, including structural support, cell division, and intracellular transport. During intracellular transport, kinesin motor proteins move cargo along microtubule tracks via their processive stepping. Recent studies have shown that the kinesin-1 KIF5C can damage the microtubule lattice while stepping. Microtubule damage can be repaired through incorporation of new tubulin subunits, however, excessive lattice damage results in microtubule breakage and disassembly. To identify cellular factors involved in microtubule repair, we performed an siRNA screen targeting microtubule-associated proteins (MAPs) known to regulate microtubule dynamics and stability. Based on the results, we investigated whether the end binding protein EB1 and cytoplasmic linker-associated protein 2 (CLASP2) contribute to repair of microtubule damage. To test this, we used a microtubule destruction assay in which damage was induced in microtubules gliding over surfaces coated with wild-type or mutant KIF5C proteins. Our findings suggest that CLASP2 directly facilitates microtubule repair, whereas EB1 does not. We further examined CLASP function using a microtubule repair assay and found that CLASP2 promotes repair by enhancing tubulin incorporation and reducing microtubule breakage. Together, these findings demonstrate that CLASP proteins play an important role in repairing and protecting against lattice damage caused by kinesin-1 motor activity. Our results further suggest that MAPs can directly regulate microtubule lattice integrity under mechanical stress generated by motor protein-driven intracellular transport.

Cell Biology↗

bioRxiv2026

Balancing of immune activation and suppression during phage infection

Signaling-based anti-bacteriophage systems such as CBASS and Thoeris synthesize infection-triggered nucleotide signals that activate anti-phage effectors1,2. However, the phage features sensed by these systems and the mechanisms phages use to evade signaling immunity remain poorly understood. Here, studying clinically relevant Pseudomonas aeruginosa phages from the Migulavirinae family3, we show that closely related phages encode subtle allelic variation in side tail fiber proteins that determine sensitivity to type II Thoeris. In parallel, these same phages encode an "anti-defense hotspot" that contains three adjacent genes that are each sufficient to facilitate phage evasion of both CBASS and Thoeris defenses, counter-balancing the activating proteins. Comparative analysis of this anti-signaling hotspot across the broader family of related N4-like phages uncovered a new Thoeris anti-defense (Tad) protein that sponges NAD-derived molecules (e.g. gcADPR) and exhibits sequence and structural similarity to a poorly characterized nucleotide-binding region of the human ryanodine receptor. Together, these findings reveal how the balance between immune activation and antagonism shifts phage outcomes and reveals a surprising similarity between a phage molecular sponge and an important human protein.

microbiology↗

bioRxiv2026

Aberrant cortical subcortical somatosensory network organization is associated with impaired tactile-motion perception in akinetic-rigid Parkinson's disease

BackgroundParkinsons disease (PD) is associated with somatosensory dysfunction, yet higher-order tactile-motion processing and its neural basis remain poorly understood. Here, we combined psychophysical assessment of tactile-motion perception with resting-state functional MRI (rs-fMRI) to investigate how altered sensorimotor network organization relates to tactile perceptual deficits in akinetic-rigid dominant PD (PDAR). MethodsForty-six participants (25 PDAR and 21 healthy controls, HCs) underwent clinical evaluation and resting-state functional MRI scanning. A subset of participants (15 PDAR and 15 HCs) additionally completed a tactile-motion perception task assessing directional bias and speed sensitivity. ROI-to-ROI functional connectivity analyses were performed within a customized 26-node sensorimotor and cortico-basal ganglia-thalamo-cortical (CBGTC) network. ResultsCompared with HCs, PDAR patients exhibited significantly altered tactile-motion perception, including greater directional bias (p = 0.047) and reduced sensitivity to dynamic tactile speed (p < 0.001), reflecting diminished sensitivity to mid-to-high speeds. Resting-state functional connectivity analyses revealed widespread reductions in connectivity within cortical somatosensory regions (Areas 1, 2, 3a, 3b, 5), particularly between primary somatosensory and motor cortices. In contrast, increased connectivity was observed between basal ganglia-thalamic structures and cortical sensorimotor regions, including thalamus-M1 and GPi-sensorimotor connections (all p-FDR < 0.05). ConclusionsThese findings demonstrate a dual pattern of sensorimotor network reorganization in PDAR, characterized by disrupted cortical somatosensory integration alongside enhanced subcortical-cortical coupling. The present study provides evidence that higher-order tactile-motion dysfunction in PD is associated with large-scale abnormalities in distributed sensorimotor networks and highlights the somatosensory system as a potential target for future therapeutic intervention.

neuroscience↗

bioRxiv2026

Retinoic acid resolves the conflict between X-chromosome inactivation and pluripotency program in female cleavage-stage embryos

The tight coupling of X-chromosome inactivation (XCI) and pluripotency is a paradigm of holistic developmental regulation, and their inverse correlation enables XCI establishment during implantation. In contrast, the co-establishment of imprinted XCI (iXCI) and pluripotency program in female preimplantation embryos challenges the holistic pattern, but how embryos coordinate the two remains unknown. Here, we find that Nanog during the cleavage stage strongly represses the co-upregulated Rnf12-Xist axis, the triggering signaling of iXCI, creating a conflict that threatens iXCI. We identify retinoic acid (RA) as the coordinator that resolves the conflict and safeguards iXCI. RA activates its receptor RARG to evict NANOG from Rnf12 5region, avoiding NANOGs threat. In vivo, either maternal vitamin A deficiency or embryonic RA synthesis defects results in impaired iXCI and female-biased embryonic lethality. Thus, we highlight RA as a master regulator to holistically balance iXCI and pluripotency during cleavage stages, thereby ensuring proper female embryogenesis.

developmental biology↗

bioRxiv2026

Visual experience drives functional reorganization of cortical GABAergic circuits

Sensory experience shapes the development and function of neocortical circuits. Although repeated exposure to sensory stimuli can alter cortical responses, the precise relationship between sensory experience and circuit interactions remains unclear. Here, we examine how cortical circuits are shaped by repeated exposure to varied visual stimuli. We find that visually evoked beta activity, a prominent pattern of visually evoked activity that relies on somatostatin-expressing (SST) GABAergic interneurons, is robustly potentiated by visual experience. Enhanced visual experience leads to increased responses in SST interneurons and suppressed responses in vasoactive intestinal peptide-expressing (VIP) interneurons. In association with this rebalancing of cortical inhibitory activity, experience increases the recruitment and visual selectivity of excitatory neurons. This enhancement is associated with increased SST-IN influence on nearby pyramidal neurons and requires SST-IN activity during visual experience. Visual experience thus selectively reorganizes adult dendrite-targeting inhibitory circuits, promoting network synchrony and enhancing sensory encoding by excitatory neurons.

neuroscience↗

bioRxiv2026

Salmonella exploits metal-responsive UMPylation to enable intracellular biphasic growth and antibiotic tolerance

Salmonella develops profound antibiotic tolerance during in vivo infection, directly contributing to antimicrobial treatment failure. Although phenotypic heterogeneity in bacterial growth rates underlies this tolerance, the exact mechanisms remain elusive. Here, we reveal that Salmonella exhibits a biphasic growth pattern within macrophages, with initial antibiotic levels modulating lag phase duration. Crucially, this growth plasticity is orchestrated by metal ion homeostasis and a reversible PTM-mediated protein phase transitions. Mechanistically, under stress conditions, enhanced Mn2+ uptake activates the UMPylator YdiU, which modifies critical translational machinery components such as elongation factor TufA. These modifications induce protein aggregation, leading to translational arrest and growth stasis. Conversely, upon stress alleviation, Salmonella accumulates Mg2+ and effluxes Mn2+, then the de-UMPylase YdiV is activated, which resolves protein aggregates to enable rapid bacterial resuscitation and proliferation. This metal-responsive proteostatic switch represents an evolutionarily conserved strategy for bacterial stress adaptation, with broad implications for combating antimicrobial tolerance. SIGNIFICANCE STATEMENTAntibiotic tolerance, a key cause of treatment failure in chronic infections, is often linked to bacterial phenotypic heterogeneity, yet the underlying regulatory mechanisms remain largely understood. This study uncovers a fundamental survival strategy employed by intracellular pathogen Salmonella, where host-derived manganese acts as a critical signal to induce a reversible, dormant state. We demonstrate that stress-induced Mn2+ influx activates widespread protein UMPylation, which functions as a molecular glue to drive the aggregation of essential proteins, thereby halting bacterial growth and conferring antibiotic tolerance. Crucially, this state is reversible upon stress relief through Mn2+ efflux and subsequent de-UMPylation, enabling rapid bacterial resuscitation. As an evolutionarily conserved mechanism of adaptive tolerance, this metal-ion-responsive switch, mediated by reversible protein UMPylation, identifies a key target for developing therapeutics against persistent bacterial infections.

microbiology↗

bioRxiv2026

Decades of dreams coming true: capillary zone electrophoresis-mass spectrometry for reproducible multi-level proteomics

Capillary zone electrophoresis (CZE)-mass spectrometry (MS) has been proposed as a powerful analytical tool for bottom-up, top-down, and native proteomics (multi-level proteomics) decades ago to analyze complex biological samples at the levels of peptides (bottom-up), proteoforms (top-down), and complexoforms (native). However, its broad adoption has been impeded by the limited robustness and reproducibility. Here, we present multi-level proteomics data from nearly 170 CZE-MS runs ([~]170 hours of instrument time), demonstrating qualitatively (i.e., the number of identified peptides and proteoforms, the number of detected complexoforms, and their migration time) and quantitatively (i.e., peptide, proteoform, and complexoform intensity) reproducible measurement of complex samples with varying levels of complexity, i.e., Escherichia coli cells, HeLa cells, and human plasma. CZE-MS-based native proteomics enabled the detection of hundreds of complexoforms up to 800 kDa from the complex systems via consuming only nanograms of protein material. The results indicate that CZE-MS is sensitive and reproducible enough for broad adoption for multi-level proteomics-based biomedical research.

systems biology↗

bioRxiv2025

Organization of mouse prefrontal cortex subnetwork revealed by spatial single-cell multi-omic analysis of SPIDER-Seq

Deciphering the connectome, anatomy, transcriptome and spatial-omics integrated multi-modal brain atlas and the underlying organization principles remains a great challenge. We developed a Single-cell Projectome-transcriptome In situ Deciphering Sequencing (SPIDER-Seq) technique by combining viral barcoding tracing with single-cell sequencing and spatial-omics. This empowers us to delineate a integrated single-cell spatial molecular, cellular, anatomic and projectomic atlas of mouse prefrontal cortex (PFC). The projectomic and transcriptomic cell clusters display distinct modular organization principles, but are coordinately configured in the PFC. The projection neurons gradiently occupied different territories in the PFC aligning with their wiring patterns. Importantly, they show higher co-projection probability to the downstream nuclei with reciprocal circuit connections. Moreover, we integrated projectomic atlas with their distinct spectrum of neurotransmitter/neuropeptide and the receptors-related gene profiles and depicted PFC neural signal transmission network. By which, we uncovered potential mechanisms underlying the complexity and specificity of neural transmission. Finally, leveraging machine learning, we predicted neuron projections with high accuracy by combining gene profiles and spatial information. As a proof of concept, we used this model to predict projections of fear recall engram neurons. This study facilitates our understanding of brain multi-modal network and neural computation.

neuroscience↗

bioRxiv2025

Noninvasive enrichment of circulating tumor biomarkers in a mouse model of diffuse midline glioma using focused ultrasound

BackgroundDiagnosing diffuse midline glioma (DMG) through invasive tissue biopsies is challenging due to the tumors eloquent location at the pons. Liquid biopsies offer a promising noninvasive alternative; however, their limited detection sensitivity and lack of information on the source of biomarkers pose great challenges. This study aimed to evaluate the feasibility and safety of using focused ultrasound (FUS) with microbubbles to enrich circulating DMG tumor biomarkers in blood and cerebrospinal fluid (CSF) using a mouse model. MethodsMurine DMG cells, transfected with enhanced green fluorescent protein (EGFP) and firefly luciferase (Fluc) genes, were orthotopically injected into the mouse brain. Magnetic resonance imaging was used to guide FUS targeting of the DMG tumor. Droplet digital PCR assays were developed to detect circulating tumor DNA (ctDNA) and RNA (ctRNA) of EGFP and Fluc in blood and CSF samples collected after FUS. ResultsFUS enhanced the plasma levels of EGFP ctRNA by 5.4-fold (p=0.0112), compared with liquid biopsy without FUS. CSF EGFP ctDNA was increased by 2.5-fold (p=0.0253), and Fluc ctDNA was increased by 2.6-fold (p=0.0253) with FUS. No brain tissue damage was associated with FUS sonication. ConclusionsThis study demonstrated the feasibility and safety of FUS in enriching tumor biomarkers in blood and CSF in a mouse model of DMG. The enrichment ratio for circulating biomarkers depends on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc). These findings support the potential future application of FUS to advance the diagnosis of DMG through liquid biopsy. Key pointsO_LIddPCR assays were developed to detect plasma and CSF ctDNA and ctRNA in a mouse model of DMG C_LIO_LIFUS with microbubbles enriched ctDNA and ctRNA in the blood and CSF of a mouse model of DMG C_LIO_LIThe enrichment ratio on circulating biomarkers is dependent on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc) C_LI Importance of the studyLiquid biopsy via detecting circulating tumor biomarkers holds enormous clinical value in the diagnosis of diffuse midline glioma (DMG), where the eloquent location of the tumor poses significant risks to invasive surgical tissue biopsies. However, the effectiveness of liquid biopsy is hindered by its low sensitivity and the lack of information about the source of biomarkers. This study demonstrated that noninvasive and spatially targeted FUS treatment can release tumor-derived DNA and RNA into the blood and CSF in a mouse model of DMG. This study also found that the enrichment effect of FUS on circulating biomarkers depends on the source (plasma vs. CSF), analyte type (ctDNA vs. ctRNA), and individual marker (EGFP vs. Fluc). This study opens new avenues for advancing noninvasive DMG diagnosis through FUS-enhanced liquid biopsy (sonobiopsy).

bioengineering↗

bioRxiv2025

Genetic and Functional Characterization of AMH Signaling in Zebrafish - Evidence for Roles of Amh-Bmpr2a-Bmpr1bb Pathway in Controlling Gonadal Homeostasis

Anti-Mullerian hormone (AMH), a member of the TGF-{beta} superfamily, plays a crucial role in Mullerian duct regression in mammals. AMH signals through a specific type II receptor (AMHRII) and a type I receptor to activate the downstream Smad1/5/9 signaling pathway. Interestingly, non-mammalian vertebrates, including teleosts, also express AMH despite lacking Mullerian ducts. Accumulating evidence indicates that AMH influences gonadal development and function across vertebrates. Intriguingly, zebrafish, a popular model organism, possesses AMH (Amh/amh) but lacks specific type II receptor (Amhr2). Based on our previous studies and data from others, we propose that Amh may signal through a novel pathway in zebrafish involving the BMP type II receptor Bmpr2a and type I receptor Bmpr1bb. In this study, we provide genetic and functional evidence for the existence of the Amh-Bmpr2a-Bmpr1bb signaling pathway in zebrafish and its role in controlling gonadal homeostasis. Our experimental data excluded the participation of Bmpr2b and Bmpr1ba, paralogues of Bmpr2a and Bmpr1bb respectively, in Amh signaling. Additionally, we also provide genetic evidence that the phenotypes exhibited by amh, bmpr2a, and bmpr1bb mutants, i.e., gonadal hypertrophy, were all dependent on gonadotropin signaling, and that the two gonadotropins (FSH and LH) showed similar potency in driving the development of hypertrophic gonadal growth resulting from dysfunction in the Amh-Bmpr2a-Bmpr1bb signaling pathway. In summary, the present study provides comprehensive evidence for Amh signaling through Bmpr2a-Bmpr1bb pathway and its interplay with gonadotropins in controlling germ cell proliferation and differentiation.

genetics↗

bioRxiv2025

Circulating Lipids are Associated with PTSD Severity and Predict Symptomatic PTSD in a Cohort of Veterans and Service Members

Post-traumatic stress disorder (PTSD) is characterized by chronic stress, alterations in mood, and avoidance after a traumatic event has occurred. While recovery can occur, many PTSD patients suffer life-long impairments. In combat veterans, high rates of PTSD contribute to increased rates of depression and anxiety and a higher likelihood of suicidal ideation. The lack of biological markers for psychiatric conditions such as PTSD highlights the need for omics-based approaches to diagnosis. Discovery of novel blood-based biomarkers could aid in the development of treatments or therapies, quantify groups for those at the highest risk of adverse events, and provide insight into the molecular underpinnings of PTSD. This study used untargeted lipidomics to analyze 602 circulating lipid species in blood from a cohort of 133 veterans and combat members with varying severities of PTSD. We discovered five circulating lipids, including serum total cholesterol, cholesterol ether (ChE(18:2)), and lipids associated with metabolic dysfunction (cardiolipin : CL(87:7), monolysocardiolipin : MLCL(50:4), and phosphatidylethanolamine plasmalogen/ether lipid : PE(18:1e_20:3)) that correlated significantly with increasing PTSD severity after adjustment for multiple comparisons. Additionally, we showed that symptomatic PTSD patients could be separated from asymptomatic controls using these lipid species. This study contributes to the limited research surrounding the role of circulating lipids in PTSD.

neuroscience↗

bioRxiv2025

Accessibility of the unstructured α-tubulin C-terminal tail is controlled by microtubule lattice conformation

Microtubules are cytoskeletal filaments that self-assemble from the protein tubulin, a heterodimer of -tubulin and {beta}-tubulin, and are important for cell mechanics, migration, and division. Much work has focused on how the nucleotide state of {beta}-tubulin regulates the structure and dynamics of microtubules. In contrast, less is known about the structure and function of the C-terminal tails (CTTs) of - and {beta}-tubulin which are thought to freely protrude from the surface of the microtubule. To study the CTT of -tubulin, we developed three different biosensors that bind the tyrosinated -tubulin CTT (Y-CTT). Surprisingly, live imaging of the probes indicates that the Y-CTT is minimally accessible along the microtubule lattice under normal cellular conditions. Lattice binding of the Y-CTT probes can be increased by three different ways of changing the tubulin conformational state: the drug Taxol, expression of microtubule-associated proteins (MAPs) that recognize or promote an expanded tubulin conformation, or expression of tubulin that cannot hydrolyze GTP. Molecular dynamics simulations indicate that the Y-CTT undergoes numerous transient interactions with the bodies of -tubulin and {beta}-tubulin in the lattice, and that the frequency of these interactions is regulated by the tubulin nucleotide state. These findings suggest that accessibility of the Y-CTT is locally governed by nucleotide- and MAP-dependent conformational changes to tubulin subunits within the microtubule lattice.

cell biology↗

bioRxiv2025

MATCAP1 preferentially binds an expanded tubulin conformation to generate detyrosinated and ?C2 a-tubulin

Microtubules are cytoskeletal filaments with critical roles in cell division, cell motility, intracellular trafficking, and cilium function. In cells, subsets of microtubules are selectively marked by posttranslational modifications (PTMs), which control the ability of microtubule-associated proteins (MAPs) and molecular motors to engage microtubules. Detyrosination ({Delta}Y) and {Delta}C2 are PTMs of -tubulin, wherein one or two residues, respectively, are enzymatically removed from the C-terminus of the protein. How specific patterns of PTMs are generated in cells is not understood. Here, we use in vitro reconstitution assays to investigate the microtubule binding behavior of metallopeptidase MATCAP1 and the mechanism by which it generates {Delta}Y and {Delta}C2 modifications of -tubulin. We demonstrate that MATCAP1 preferentially binds to microtubules composed of tubulin subunits in an expanded conformation, which can be induced by preventing {beta}-tubulin GTP hydrolysis, Taxol treatment, or kinesin-1 stepping. MATCAP1 binds to expanded microtubule lattices with long dwell time and sequentially removes the terminal tyrosine residue to generate {Delta}Y-microtubules and the penultimate glutamate residue to generate {Delta}C2-microtubules. Thus, the lattice conformation of microtubules is a key factor that gates the binding and activity of MATCAP1.

cell biology↗

bioRxiv2025

Micron-scale protein transport along microtubules by kinesin-driven shepherding

How microscopic interactions give rise to cellular-scale order in the crowded environment of cells remains an open problem. Far-from-equilibrium mixtures of active and passive molecules self-organize, but the principles remain unclear. Microtubules are cytoskeletal polymers composed of 13 protofilaments bound by mixtures of actively moving motors and passively diffusing microtubule-associated proteins (MAPs), serving as a model system for self-organization on a multi-lane lattice. Here, we combine computational modeling, analytic theory, and in vitro reconstitution to demonstrate that motors can "shepherd" diffusive MAPs by rectifying Brownian motion into net directional drift without motor-MAP binding. Our model reveals that biased movement increases when fewer protofilaments are accessible or when lateral diffusion between protofilaments is limited, identifying local dimensionality and diffusion as key parameters governing spatial patterning. Notably, shepherding depends not on individual motor processivity but on the total number of motors bound to microtubules. We experimentally recapitulate micron-scale shepherding with a kinesin-1 motor (K401) and a diffusive MAP (PRC1), which show no detectable binding. These findings reveal shepherding as an emergent mechanism by which ensembles of motors generate micron-scale spatial patterning and transport of MAPs without direct binding interactions.

biophysics↗