Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2026

Unmasking Early Renal Fibrosis in Polycystic Kidney Disease Using Noninvasive Precision Molecular MRI of Collagen

Fibrotic remodeling of extracellular matrix is a central driver of autosomal dominant polycystic kidney disease (ADPKD) progression since early stages of the disease. Unfortunately, it cannot be assessed with currently available methodologies before irreversible structural and functional decline, creating a diagnostic blind spot that hinders accurate early risk stratification and management. Here, we report the development of Gd-hProCA32.Collagen, a collagen -targeted protein MRI contrast agent that enables precision molecular MRI (pMRI) of early fibrosis by directly imaging collagen type I deposition in vivo before conventional laboratory and imaging methods detect changes in kidneys and liver of Pkhd1PCK/PCK (PCK) rats and Pkd2 mutant mice. Gd-hProCA32.Collagen, used at 10-fold lower dose, outperformed the widely clinically used agent gadobutrol (Gadovist), detecting approximately 2.8-fold greater total renal cyst volume ([~]8,500 vs [~]3,000 mm3, p<0.0001) and 1.5-fold higher total cyst count ([~]245 vs [~]160, p<0.0001), with superior T1W and T2W kidney AUC (p<0.01 and p<0.001) and preferential sensitivity to small and medium cysts. Signal enhancement in kidneys and liver correlated strongly with histological collagen burden quantified by Sirius red staining, whereas Gadovist showed no meaningful correlation. Gd-hProCA32.Collagen also enabled in vivo visualization of previously undetectable changes resembling radial striations at sites of microcyst cluster-adjacent microfibrosis and sustained delayed MRI enhancement due to specific collagen binding. These results reveal a previously inaccessible subclinical fibrotic phase of cystic kidney and liver disease and establish collagen-targeted pMRI as a strategy for early noninvasive detection and spatial mapping of multi-organ extracellular matrix remodeling when conventional biomarkers remain non-discriminating. One-sentence summaryWe report a first-in-class collagen-targeted MRI contrast agent with Precision molecular MRI that noninvasively reveals a previously inaccessible subclinical fibrotic phase of polycystic kidney disease across kidney and liver, overcoming limitations of current diagnostic methodology.

molecular biology↗

bioRxiv2026

Prenatal cannabis exposure affects human fetal neurodevelopment: anintegrated multi-omics study

Prenatal cannabis use is on the rise, and observational studies suggest that such use results in neurodevelopmental deficits in the offspring. Because observational studies can be confounded by unaccounted factors, we studied the neurodevelopmental consequences, at the molecular level, of prenatal cannabis use. We applied an integrated multi-omics approach, combining transcriptomics and global proteomics, to first trimester (T1) and second trimester (T2) human fetal brains from pregnancies with and without documented maternal cannabis exposure and no use of drugs of abuse. Prenatal cannabis exposure produced minimal molecular effects in female T1 fetal brains but induced pronounced system-level disruption in male T2 fetal brains. These disrupted pathways have molecular signatures linked to neurodevelopmental and neuropsychiatric disorders, including autism spectrum disorder, schizophrenia-related pathology, and disorders of cortical connectivity, raising significant concerns of prenatal cannabis use.

neuroscience↗

bioRxiv2026

Projectomic Organization of the Serotonin System of the Mouse Brain

The serotonin system innervates nearly the entire brain to support diverse functions, and its dysfunction is implicated in multiple psychiatric disorders. Although recent studies suggested that this anatomically diffuse system supports differentiated rather than uniform modulation, its overall organization is unclear. Here, using systematic whole-brain axon tracing and integrated analyses, we show that the serotonin projectome is organized by functional relatedness rather than physical proximity of its targets. Dorsal and median raphe serotonin neurons partition into five projectomic groups, each preferentially innervating the hippocampus, basal ganglia, cortex, medial interbrain, or brainstem/lateral thalamus, with within-group structure ranging from discrete subgroups to continuous variation. Spatial transcriptomic analyses reveal that each projectomic group corresponds to a distinct combination of transcriptomic clusters, with transcriptome and somatic position jointly predicting projectomic identity. Projection-specific serotonin depletion produces dissociable behavioral phenotypes. Together, projectomic identity emerges as a central axis linking axon collateralization, molecular diversity, and behavioral function.

neuroscience↗

bioRxiv2026

Neryl diphosphate-derived monoterpene biosynthesis via a biosynthetic gene cluster in the liverwort Marchantia polymorpha

Monoterpenes (C10) are a large group of specialized metabolites important for plant interactions with the environment. Their biosynthesis is well understood in seed plants, where geranyl diphosphate serves as the canonical substrate, but knowledge of monoterpene biosynthesis outside seed plants remains very limited. Here, we report neryl diphosphate (NPP)-derived monoterpene biosynthesis via a biosynthetic gene cluster in the liverwort Marchantia polymorpha. MpMTPSL2, a microbial-type terpene synthase, converts NPP into -phellandrene and D-limonene in vitro. CRISPR knockout lines showed reduced production of both monoterpenes, providing direct genetic evidence for its in planta function. MpCPT5, a cis-prenyltransferase (CPT) family member identified through co-expression with MpMTPSL2, was confirmed to encode NPP synthase, as its knockout plants abolished -phellandrene and D-limonene production. Subcellular localization analyses in protoplasts and stable transgenic plants demonstrated that both MpCPT5 and MpMTPSL2 localize to plastids, co-localizing across all cell types with markedly stronger signals in non-green plastids of oil-body cells. Consistent with this, expression of both genes under their respective promoters was nearly abolished in oil-body-deficient mutants and strongly upregulated in a gain-of-function line for oil-body formation. MpMTPSL2 and MpCPT5 are physically linked through a shared bidirectional promoter that drives their coexpression specific to oil body cells, forming a unique biosynthetic gene cluster whose coordinated expression is maintained by PRC2-mediated H3K27me3 repression. Phylogenetic analysis implies that NPP synthases in M. polymorpha and in flowering plants evolved independently from their respective long-chain CPT ancestors. These findings provide new insights into the mechanisms and evolution of monoterpene biosynthesis in non-seed plants. Significance statementMonoterpenes are a diverse group of specialized metabolites produced widely among land plants, yet our understanding of their biosynthesis outside seed plants remains limited. Here we report that in the liverwort Marchantia polymorpha, the non-canonical substrate neryl diphosphate is used for monoterpene biosynthesis. The functions of the monoterpene synthase gene MpMTPSL2 and the neryl diphosphate synthase gene MpCPT5 were demonstrated through CRISPR knockouts. These two genes are physically linked and share a bidirectional promoter. Promoter assays show both genes function in plastids within oil-body cells, revealing cell-type specificity. These findings shew new light on the mechanisms and evolution of monoterpene biosynthesis in non-seed plants.

plant biology↗

bioRxiv2026

Multi-modal MRI characterisation of vascular remodelling, muscle fibre integrity, and inflammatory recovery in a hindlimb ischaemia mouse model

The hindlimb ischaemia (HLI) mouse model is a widely used preclinical model of chronic limb-threatening ischaemia (CLTI). While CLTI involves complex interactions between impaired perfusion, inflammation and muscle wasting, the standard imaging approach, laser Doppler imaging (LDI), only assesses perfusion. MRI is used clinically to assess neural tracts, inflammation, and perfusion in the brain. We therefore evaluated whether a multimodal MRI approach could longitudinally monitor recovery in the HLI mouse model. Mice underwent MRI three days pre-HLI surgery, and on Days +3 and +7 post-surgery, with histology on Day +7. The MRI detected significant increases in muscle volume and inflammation after HLI surgery, with significant decreases in perfusion, vascular length, and muscle fibre integrity. Overall, MRI can monitor inflammation, muscle fibre integrity, and vascular recovery post-HLI and should be applied in future studies to identify mechanisms of therapeutic recovery in a sequential in vivo analysis without requiring animal sacrifice. O_FIG O_LINKSMALLFIG WIDTH=186 HEIGHT=200 SRC="FIGDIR/small/739107v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@100e5d1org.highwire.dtl.DTLVardef@1f0188dorg.highwire.dtl.DTLVardef@1dbdf4forg.highwire.dtl.DTLVardef@21d415_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

biophysics↗

bioRxiv2026

A novel AR molecular glue degrader via bivalent engagement of the N-terminal domain and RNF213-UBE2J2 complex

Targeted protein degradation enables the elimination of disease-relevant proteins through induced proximity between E3 ligases and substrates. Current androgen receptor (AR) therapies act via the ligand-binding domain (LBD) but fail against constitutively active LBD mutants or splice variants such as AR-V7. Here, we identify GZL626, a small-molecule degrader that induces proteasome-dependent degradation of both full-length AR and AR-V7. GZL626 suppresses AR transcriptional activity, inhibits proliferation of AR-positive prostate cancer cells, and blocks SARS-CoV-2 infection. Mechanistically, GZL626 binds the intrinsically disordered AR N-terminal domain (NTD) and promotes formation of a noncanonical RNF213-UBE2J2-AR ternary complex that drives AR ubiquitination and degradation. The AR DNA-binding domain (DBD) acts as a structural hub within this assembly. Distinct from PROTACs or classical molecular glues, GZL626 engages both AR and RNF213 bivalently, remodeling protein interactions to stabilize a functional E3-E2-substrate complex. These findings establish GZL626 as a first-in-class NTD degrader with potential to overcome resistance in advanced prostate cancer.

biophysics↗

bioRxiv2026

A superfolding sfPepper enables superresolution and single-molecule RNA imaging in live cells

Fluorescent RNAs (FRs) have emerged as powerful tools for the visualization of RNA in live cells. However, the poor folding of FRs is a major limiting factor in many advanced RNA imaging applications. Here, we describe a novel strategy to significantly increase the folding efficiency of FRs. By introducing a stabilizing stem and performing targeted mutagenesis at key junction regions, we develop a superfolder variant of the Pepper aptamer, termed sfPepper, that exhibits a striking twofold increase in folding efficiency compared with Pepper under physiological conditions. sfPepper exhibits much improved thermostability and reduced ion dependence and, most importantly, is substantially brighter than Pepper in live cells. sfPepper enables robust imaging of diverse noncoding RNAs and messenger RNAs with increased signal-to-background ratios and stimulated emission depletion (STED) superresolution imaging of CUG trinucleotide repeat-containing toxic RNAs. Remarkably, only four sfPepper repeats facilitate sensitive single-molecule mRNA tracking, revealing dynamic heterogeneity among ER-associated mRNA molecules. Together, this study establishes an efficient strategy for improving FR folding and offers a powerful tool for fluorescently labelling RNAs in live cells.

molecular biology↗

bioRxiv2026

Systematic identification of cell division proteins in haloarchaea and the discovery of a membrane anchor for the Z ring

Most archaea rely on the tubulin-like protein FtsZ for division. In the last decade, several novel cell division proteins have been discovered in the model haloarchaeon Haloferax volcanii which contains two FtsZ proteins, FtsZ1 and FtsZ2. However, the composition of this FtsZ-based archaeal divisome is largely uncharacterized. Here, using in vivo crosslinking coupled with immunoprecipitation and mass spectrometry (CLIP-MS), we identified ten proteins that localize to the division site, including wide-spread proteins predicted to be involved in DNA binding and energy metabolism. Deletion analysis indicate that most of these proteins have a modest or minor impact on cell division, but HVO_0399, renamed as Cell Division Protein C (CdpC), is important for cell division and functions as a membrane anchor for FtsZ1. CdpC consists of three domains, an N-terminal domain (NTD) containing an amphipathic helix critical for membrane binding, a long intrinsically disordered linker, and a C-terminal domain (CTD) that binds FtsZ1 with high affinity and likely promotes its polymerization. Notably, both the NTD and CTD of CdpC harbor a zinc finger that is indispensable for its function. Phylogenetic analysis indicates that CdpC sequences evolved fast across haloarchaea, but exhibited high conservation in domain structure and critical residues found in this study. Overall, our study expands the repertoire of candidate division proteins and establishes CdpC as a membrane anchor for FtsZ1 in haloarchaea. These findings pave the way for in-depth studies of arcaheal cell division and broaden the function of zinc finger proteins in archaea.

microbiology↗

bioRxiv2026

LARP4 is a B cell-specific metabolic checkpoint for plasma cell differentiation and a therapeutic target in systemic lupus erythematosus

RNA-binding protein LARP4 plays an important role in T cell activation and differentiation, but its role in B cell biology and the pathogenesis of systemic lupus erythematosus (SLE) remains unclear. This study found that LARP4 was specifically highly expressed in B cells of SLE patients and was positively correlated with disease activity. By constructing T cell-specific and B cell-specific conditional knockout mice, we found that deletion of LARP4 in B cells, but not in T cells, significantly alleviated pristane-induced and Bm12-induced lupus nephritis. Further analysis showed that LARP4 deletion selectively inhibited B cell differentiation into plasma cells, but did not affect germinal center B cell formation. Integrated transcriptomic and metabolomics analyses revealed that this effect is due to reduced phosphatidic acid synthesis and decreased mTORC1 activity caused by mitochondrial oxidative phosphorylation dysfunction. Furthermore, we used LIPEP, a LARP4 inhibitory peptide that effectively mimicked the therapeutic effects of LARP4 gene knockout in the MRL/lpr spontaneous lupus model and outperformed cyclophosphamide in reducing glomerular immune complex deposition and improving extrarenal dermatitis. These results indicates that LARP4 is a key metabolic checkpoint regulating B cell differentiation into Plasma cells and suggest that it may be a potential therapeutic target for SLE.

immunology↗

bioRxiv2026

Teneurins Are SPARCL1 Receptors

Extensive experiments document that SPARCL1, a secreted protein that is produced primarily by astrocytes in brain and endothelia throughout the body and that is also known as Hevin, enhances synapse formation. However, the mode of action of SPARCL1 at synapses remains unclear owing to divergent results in the literature. Here, we use cultured neurons from newborn male and female mouse embryos to show that the C-terminal follistatin-like and Ca2+-binding domains of SPARCL1, which account for only 35% of the total SPARCL1 sequence, are sufficient to potently enhance synapse numbers. SPARCL1 acts at nanomolar concentrations at which SPARCL1 does not robustly bind to neurexins, neuroligins or neurexin/neuroligin complexes but avidly interacts with all teneurins. Strikingly, the follistatin-like domain of SPARCL1 on its own strongly binds to teneurins but is unable to stimulate synapse formation. Only when combined with the SPARCL1 Ca2+- binding domain does the follistatin-like domain induce synapses, suggesting that SPARCL1 enhances synapse numbers by binding to teneurins via its C-terminal follistatin-like domain and by activating synapse formation via its Ca2+-binding domain. SIGNIFICANCE STATEMENTSPARCL1 (also known as Hevin) is a synaptogenic factor that is produced primarily by astrocytes in brain, and that enhances synapse formation. How SPARCL1 acts at synapses, however, remains unclear because divergent results describe its binding partners at synapses and the sequences involved in its synaptogenic activity remain unclear. In the present study, we show that SPARCL1 avidly binds to the presynaptic teneurins adhesion molecules, that this binding is mediated by its small follistatin-like domain, and that its synaptogenic activity requires both its follistatin-like and its Ca2+-binding EC domains. Thus, our results suggest that SPARCL1 is recruited to developing synapses by binding of its follistatin-like domain to teneurins and then induces synapse assembly via its Ca2+-binding domain.

neuroscience↗

bioRxiv2026

Charge Imbalance Drives Salt-Optimized Nucleosome Phase Separation under Physiological Conditions

Liquid-liquid phase separation (LLPS) of chromatin contributes to genome organization and regulates genome accessibility to control gene expression. Despite advances in identifying the environmental conditions that promote chromatin condensation, the specific molecular interactions that initiate condensate formation, as well as the physical mechanisms by which DNA mechanics and epigenetic modifications modulate the resulting interaction network, remain unclear. Here, we utilize a residue-resolution, coarse-grained protein-DNA model to simulate nucleosome interactions across diverse ionic and structural conditions. Our simulations reveal non-monotonic salt-dependent phase-separation behavior, with optimal nucleosome condensation occurring under physiological salt conditions. Such a behavior was caused by the charge-imbalanced polyampholytic nature of nucleosomes, which drives competition between local protein-DNA attractions and global DNA-DNA repulsion. We further demonstrate that the conformational flexibility of nucleosomal DNA promotes unwrapping of DNA from the histone core, thereby strengthening histone-DNA interactions and enhancing condensate formation. Finally, we show that acetylation of histone H3 and H4 tails significantly reduces inter-nucleosomal interactions and increases nucleosome dynamics within condensates. Together, our study establishes a quantitative link between microscopic molecular interactions and macroscopic material properties, providing new insights into how mechanical constraints and epigenetic modifications could cooperatively tune genome architecture.

biophysics↗

bioRxiv2026

Conserved and specialized features of thalamocortical wiring revealed by single-cell projection mapping in mouse and marmoset

Across mammals, brain regions can duplicate, expand, and diversify, requiring long-range connectivity to accommodate species-specific specializations while preserving globally ordered wiring. This challenge is especially pronounced in primate thalamocortical circuits, where select cortical fields and their thalamic partners have expanded disproportionately. Although gene expression in the thalamus follows broad and conserved gradients, how thalamocortical projections are organized at single-neuron resolution, and how this organization is reshaped by expansion, remain unknown. Here, we investigate thalamocortical projection organization by in situ sequencing and BARseq projection mapping in marmosets and mice. We profiled the gene expression of 1.5 million marmoset neurons and jointly measured gene expression and cortical projections in 708 marmoset and 1,518 mouse neurons that spanned multiple thalamic nuclei. In both species, projections of individual neurons targeted diverse areas that together spanned a large fraction of the cortex. Comparing projections at the single-neuron level and local neighborhood level revealed that marmoset thalamocortical projections were more spatially segregated, producing a point-to-point architecture. Strikingly, this local specialization coexisted with a conserved gradient that predominated over discrete anatomical borders: In the higher-order sensory thalamus of both species, gene expression and projections varied continuously across nucleus borders, and borders had only a small effect on projections. Furthermore, in both marmoset and mouse, gene expression gradients were associated with the anteroposterior locations of cortical targets. These results reconcile discrete nucleus and gradient-based models of thalamic organization and suggest that primate circuit specialization is superimposed on a conserved molecular-projection gradient.

neuroscience↗

bioRxiv2026

PTPRJ Drives Clonal Selection in CEBPA mutated AML

Transcription factor CEBPA is mutated in 10-15% of acute myeloid leukaemia (AML), a haematopoietic malignancy with high mortality. CEBPA mutations show a distinct pattern, and most patients are biallelic, carrying both an in-frame C-terminal mutation and a frameshift N-terminal mutation on opposing alleles. Rare N-terminal germline cases have 100% penetrance to AML, all with an acquired a C-terminal mutation. This suggests a selective pressure from one CEBPA mutation to develop another. Our zebrafish models faithfully recapitulate the human disease. All biallelic mutant combinations die by 4-6 weeks of age, with pre-leukaemic haematopoietic stem cell (HSC) expansion. C-terminal and N-terminal mutants show phenotypic differences in myeloid-primed HSC and differences in the myeloid differentiation block. RNA-Seq identified differentially expressed genes in opposing vectors. We identified phosphatase receptor PTPRJ as a candidate driver of clonal selection, with knock-out of ptprja in our fish accelerating pre-leukaemic expansion of HSC in C-terminal mutants, decelerating it in N-terminal mutants. Cebpa-mutant murine cells exhibit changes in differentiation and a clonal advantage with loss of Ptprj, which perturbs key signalling pathways. Our data suggest that PTPRJ contributes to the mechanism of leukaemogenesis in CEBPA mutant AML by driving the selective pressure from each mutation to develop the other.

cancer biology↗

bioRxiv2026

Cell-type-specific coupling of single-unit spikes and cortical ripples in macaque and human V1

Cortical ripples are brief high-frequency (80-150 Hz) oscillatory bursts in the extracellular potential, associated with memory and attention. So far, it is unclear whether they are brain-state specific and which neuron types participate in their generation. We report cortical ripples in macaque V1 at rest, present with both eyes open and closed. Using massively parallel Utah array recordings, we identify six single-unit classes and describe their relation to ripple-band oscillations. The classes differ in firing-rate modulation, phase-locking strength, and preferred ripple-band phase. One class of putative deep-layer neurons exhibits non-sinusoidal phase locking, explained by a simple thresholding mechanism in a computational model. During ripples, most units fire irregularly with transient regular bursts. The ripple-associated spiking organisation is largely preserved during natural-image viewing and confirmed in V1 of a blind human. Together, these findings suggest cortical ripples arise from a shared circuit conserved across species and conditions.

neuroscience↗

bioRxiv2026

Nuclear Cx43 restrains microglial neurotoxicity during brain development

Microglia are essential for sculpting the developing brain, yet the molecular mechanisms that select beneficial overreactive phagocytosis remain incompletely understood. Connexin 43 (Cx43, encoded by GJA1 in humans) is best known as a gap junction and hemichannel protein, although its non-canonical, channel-independent functions are increasingly recognized. We found that Cx43 is highly expressed in microglia during the perinatal period in human and mouse, whereas proportion of full-length multimeric Cx43 unexpectedly localizes to the nucleoplasm. Deletion of microglial Cx43 in mice during development instigates a transient neurotoxic state with microgliosis, upregulated phagocytic and complement pathways, excessive neuronal apoptosis, translating into depressive-like and cognitive deficits in the adulthood. Notably, neither microglia-specific deletion of Cx43 in adulthood nor hemichannel blockade recapitulate these changes, indicating a channel-independent, developmental stage-specific neuroprotective mechanism. Nucleus-targeted Cx43 overexpression suppresses neurotoxic markers and neural apoptosis. Nuclear Cx43 interacts with transcriptional regulators to restrain proinflammatory gene programs, nuclear import of Cx43 is driven by neurogenic niche-derived bFGF, which triggers AKT-mediated phosphorylation of a C-terminal nucleus localization signal (NLS), 14-3-3 binding, and importin-dependent nucleus translocation. These findings reveal a developmentally restricted nuclear Cx43 function that restrains microglial neurotoxicity while promoting microglial physiological functions thus expanding connexin biology to transcriptional co-regulation and pointing to a potential avenue for therapeutic intervention.

neuroscience↗

bioRxiv2026

HiFi-ST: High-Fidelity Reconstruction of Continuous Spatial Transcriptomic Expression Fields via Conditional Neural Fields

Spatial transcriptomics characterizes tissue-scale gene expression patterns, yet its observations are sparse discrete samples of an underlying continuous molecular field, leading to spatial aliasing and sub-resolution information loss. Existing methods usually formulate this task as spot-level point regression, making it difficult to capture both expression continuity and the regional nature of observation. Here, we propose HiFi-ST, a conditional neural field framework for continuous spatial transcriptomics modeling. HiFi-ST formulates spatial gene expression prediction as continuous expression field learning, models each spot as a regional observation over a finite support domain, approximates local integration through Monte Carlo sampling, and integrates multiscale tissue feature extraction with FiLM-based conditional modulation to improve modeling of complex spatial heterogeneity and consistency with the underlying measurement process. Systematic evaluation on three independent datasets (HER2+, cSCC, and Alex_NatGen) showed that HiFi-ST outperformed mclSTExp, BLEEP, THItoGene, His2ST, and HisToGene on key metrics. On HER2+, HiFi-ST achieved an average PCC improvement of 65.1% and an average MSE reduction of 40.9%; on cSCC, PCC improved by 10.2% and MSE decreased by 51.2%; on Alex_NatGen, PCC improved by 80.0% and MSE decreased by 16.3%. In addition, the learned multiscale tissue representations supported downstream spatial immunoanalysis, including assisted identification of candidate TLS regions. Overall, HiFi-ST provides a unified framework bridging discrete measurements and continuous expression field reconstruction for tumor microenvironment analysis and spatial immune structure characterization.

genomics↗

bioRxiv2026

NLR from soybean Rsv1 locus confers broad-spectrum resistance to soybean mosaic virus G1-G7 strains by recognizing viral P3 protein

Nucleotide-binding leucine-rich repeat (NLR) immune receptor genes are of significant value in disease resistance breeding and the control of viral diseases. Soybean mosaic virus (SMV) poses a serious threat to soybean production and the Rsv1 locus in soybean cultivar Suweon 97 confers broad-spectrum resistance against SMV strains G1 to G7; however, this locus harbors no fewer than 18 NLR genes, and thus the broad-spectrum antiviral mechanisms underlying the Rsv1 locus remain poorly understood to date. Here, we established a rapid and highly efficient screening system for cloning NLR genes from soybean Rsv1 locus and identified a broad-spectrum antiviral NLR gene 13g184900 from this highly complicated locus. The NLR encoded by 13g184900 can recognize viral P3 protein from all SMV strains (G1-G7) and another potyvirus Bean common mosaic virus (BCMV). The coiled-coil (CC) domain of this NLR directly interacts with viral P3 protein. Additionally, we showed that this NLR originated from wild soybean accession in East China and has been introduced into several soybean cultivars during domestication. Collectively, we developed a high-throughput screening system for identifying NLR genes in soybean and our study provides new mechanistic perspective on how the Rsv1 locus mediates the broad-spectrum resistance to all SMV G1-G7 strains.

plant biology↗

bioRxiv2026

Selective knockout of PKA regulatory subunits reveal opposite catalytic and metabolic consequences with implications for Alzheimer's disease

cAMP-dependent Protein Kinase A (PKA) is a master regulator of cell signaling involved in energy metabolism, synaptic plasticity, and stress response. Dysregulated PKA signaling is implicated in diseases including neurodegeneration and cancer. PKA catalytic activity is regulated by two nonredundant regulatory subunits, Type I (RI/RI{beta}) and Type II (RII/RII{beta}), whose divergent functions are not fully understood. We generated double-knockout (KO) cell lines of RI/RI{beta} and RII/RII{beta} subunits and performed multiplexed MS-based proteomic and phosphoproteomic profiling under basal and glucose-perturbed conditions. We found that RI and RII loss drives distinct, and often opposite, remodeling of the cellular proteome and phosphoproteome. While both mutants blunted metabolic flexibility to glycolytic stressors and stimuli, RI and RII KO cells exhibited elevated and depressed glycolytic signaling, respectively. Interestingly, RI KO increased the abundance and kinase activity of the PKA catalytic subunit C isoform, leading to an increase in PKA substrate phosphorylation, whereas RII KO decreased the abundance, kinase activity, and substrate phosphorylation by the catalytic subunit C{beta} isoform. Notably, one of the most differentially affected PKA sites between RI and RII KOs maps to Tau, whose hyperphosphorylation is a hallmark of Alzheimers disease. Loss of RI increased Tau phosphorylation, which was not only caused by increased PKA catalytic activity, but also a higher binding affinity of Tau to RII subunits on the negatively-charged flexible linker region. Overall, the present study demonstrates that PKA RI and RII subunits play nonredundant roles in modulating PKA activity, metabolic flexibility, and phospho-regulation of key disease-associated substrates such as Tau.

biochemistry↗