Biology subjects

Wang, Q.

Publications and source records attributed to Wang, Q..

At least 469 records · Page 26Linked to original sources

bioRxiv2022

Sex and timing of gonadectomy relative to puberty interact to influence weight, body composition, and feeding behaviors in mice

Gonadal sex steroids are important regulators of energy balance in adult rodents, and gonadectomy (GDX) has opposing effects on weight gain in sexually mature males and females. Puberty is associated with the emergence of sex differences in weight, body composition, and feeding behaviors, yet the role of gonadal hormones at puberty remains unclear. To address this, we performed GDX or sham surgery in male and female C57Bl/6 mice at postnatal day (P)25 (prepubertal) or P60 (postpubertal) timepoints and measured weight and body composition for 35 days, after which ad libitum and operant food intake was measured using Feeding Experimentation Device 3 (FED3s) in the home cage. Consistent with previous studies, postpubertal GDX caused weight gain in females and weight loss in males and increased adiposity in both sexes. However, prepubertal GDX decreased weight gain and altered body composition across the adolescent transition (P25 to P60) in males but had no effect in females. Despite the varied effects on weight, GDX decreased food intake and motivation for food as assessed in operant tasks regardless of sex or timing of surgery relative to puberty. Our findings indicate that GDX interacts with both sex and age at surgery to influence weight, body composition, and feeding behavior. HighlightsO_LIGonadectomy had opposing effects on weight in males and females when performed in adulthood. C_LIO_LIGonadectomy performed prior to puberty decreased weight gain in males but did not affect weight gain in females. C_LIO_LIAcross sex and age at surgery, GDX decreased ad libitum food intake and reduced operant responding for food. C_LIO_LIDecreased food intake under effortful conditions was not explained by body weight in GDX mice. C_LI

animal behavior and cognition↗

bioRxiv2022

Mre11 liberates cGAS from nucleosome sequestration during tumorigenesis

Oncogene-induced replication stress generates endogenous DNA damage that activates cGAS/STING-mediated innate immune signaling and tumor suppression1-3. However, the mechanism for cGAS activation by endogenous DNA damage remains enigmatic, particularly given the constitutive inhibition of cGAS by high-affinity histone acidic patch (AP) binding4-10. Here we report an in vivo CRISPR screen that identified the DNA double strand break sensor Mre11 as a suppressor of mammary tumorigenesis induced by Myc overexpression and p53 deficiency. Mre11 antagonizes Myc-induced proliferation through cGAS/STING activation. Direct binding of the Mre11-Rad50-Nbn (MRN) complex to nucleosomes displaces cGAS from AP sequestration, which is required for DNA damage-induced cGAS mobilization and activation by cytosolic DNA. Mre11 is thereby essential for cGAS activation in response to oncogenic stress, cytosolic DNA transfection, and ionizing radiation. Furthermore, we show Mre11-dependent cGAS activation suppresses Myc-induced proliferation through ZBP1/RIPK3/MLKL-mediated necroptosis. In human triple-negative breast cancer, ZBP1 downregulation correlates with increased genome instability, decreased immune infiltration, and poor patient prognosis. These findings establish Mre11 as a critical link between DNA damage and cGAS activation that regulates tumorigenesis through ZBP1-dependent necroptosis. One-sentence summaryMre11 is required for cGAS activation during oncogenic stress and promotes ZBP1-dependent necroptosis.

cell biology↗

bioRxiv2022

Heterotrophic bacteria drive sulfide oxidation in coastal sediments

Sulfate reduction and sulfur oxidation are very active in coastal sediments. They shape the biogeochemistry and microbial ecology at hot places of organic matter metabolism. Different from the well-studied sulfate reduction, sulfur oxidation in coastal sediments is still full of questions. Herein, we investigated the distribution of reduced sulfur compounds in differently layers of coastal sediments at the Yellow sea and found that sulfide (H2S), sulfane sulfur (S0), and thiosulfate mainly accumulated in anaerobic sediments and were mostly oxidized in anoxic and oxic interface in the sediments and the sea water. Bacterial community analysis indicated that heterotrophic bacteria are dominating species in surface sediments and sea water. Metagenome analysis showed that two sulfur-oxidizing genes encoding sulfide:quinone oxidoreductases (SQR) and persufide dioxygenases (PDO), were sharply more abundant than other sulfur-oxidizing genes in the coastal sediments. Since members of the marine Roseobacter clade were dominant in coastal waters and sediments, we studied the sulfur oxidation pathway in the Roseobacter Ruegeria pomeroyi DSS-3 and found that sulfide:quinone oxidoreductase, persulfide dioxygenase, and sulfite-oxidizing enzyme were the main enzymes for the oxidation of H2S, zerovalent sulfur, and sulfite/thiosulfate. This study, for the first time, clarified the dominating function of heterotrophic bacteria in sulfur oxidation in the coastal sediments and sea water. IMPORTANCECoastal sediments are the most productive ecosystems. We performed the microbial community diversity and metagenomic analysis of seawater and coastal sediments of the Yellow Sea and explored the sulfur oxidation process in them. We found that heterotrophic bacteria are dominating species in surface sediments and sea water, sulfide and sulfane sulfur were mostly oxidized in surface sediments, and the genes encoding SQR, PDO, and SOE are abundant. Using Ruegeria pomeroyi DSS-3 as the model strain, we studied how these enzymes cooperate to oxidize H2S to sulfate. Thus, this research revealed the critical role of heterotrophic bacteria in sulfur oxidation in coastal sediments and sea water.

microbiology↗

bioRxiv2022

Integrated proteomics reveals the landscape of autophagy degradation in human neurons and autophagy receptors regulating neuronal activity

Autophagy is a catabolic and self-degradative process crucial for maintaining cellular homeostasis. Malfunctional autophagy is implicated in neurodevelopmental and neurodegenerative diseases. However, the exact role and targets of autophagy in human neurons remain elusive. Here we reported a systematic investigation of neuronal autophagy targets through integrated proteomics. Deep proteomic profiling of multiple autophagy-deficient lines of human induced neurons, mouse brains, and LC3-interactome uncovers a role of neuronal autophagy in targeting primarily endoplasmic reticulum (ER), mitochondria, endosome, Golgi apparatus, synaptic vesicle (SV) proteins, and cAMP-PKA pathway, for degradation. Tubular ER and specific SV proteins are significant autophagy cargos in the axons. Functional validation identified calumenin as an ER resident autophagy receptor and illuminated a role of autophagy in regulating PKA and neuronal activity through AKAP11-mediated degradation. Our study thus reveals the landscape of autophagy degradation in human neurons and offers molecular insight into mechanisms of neurological disorders linked to autophagy deficiency. HighlightO_LIIntegrated proteomics reveals the landscape of autophagy degradation in human neurons C_LIO_LIAutophagy clears tubular ER and selective ER and synaptic vesicle proteins in neurons C_LIO_LICalumenin is an ER resident autophagy receptor C_LIO_LIAutophagy controls PKA pathway and neuronal activity through autophagy receptor AKAP11 C_LI

neuroscience↗

bioRxiv2022

Characterization of the Human Immunodeficiency Virus (HIV-1) Envelope Glycoprotein Conformational States on Infectious Virus Particles

Human immunodeficiency virus (HIV-1) entry into cells involves triggering of the viral envelope glycoprotein (Env) trimer ((gp120/gp41)3) by the primary receptor, CD4, and coreceptors, CCR5 or CXCR4. The pretriggered (State-1) conformation of the mature (cleaved) Env is targeted by broadly neutralizing antibodies (bNAbs), which are inefficiently elicited compared with poorly neutralizing antibodies (pNAbs). Here we characterize variants of the moderately triggerable HIV-1AD8 Env on virions produced by an infectious molecular proviral clone; such virions contain more cleaved Env than pseudotyped viruses. We identified three types of cleaved wild-type AD8 Env trimers on virions: 1) State-1-like trimers preferentially recognized by bNAbs and exhibiting strong subunit association; 2) trimers recognized by pNAbs directed against the gp120 coreceptor-binding region and exhibiting weak, detergent-sensitive subunit association; and 3) a minor gp41-only population. The first Env population was enriched and the other Env populations reduced by introducing State-1-stabilizing changes in the AD8 Env or by treatment of the virions with crosslinker or the State-1-preferring entry inhibitor, BMS-806. These stabilized AD8 Envs were also more resistant to gp120 shedding induced by a CD4-mimetic compound or by incubation on ice. Conversely, a State-1-destabilized, CD4-independent AD8 Env variant exhibited weaker bNAb recognition and stronger pNAb recognition. Similar relationships between Env triggerability and antigenicity/shedding propensity on virions were observed for other HIV-1 strains. Our results show that State-1 Envs on virions can be significantly enriched by optimizing Env cleavage; stabilizing the pretriggered conformation by Env modification, crosslinking or BMS-806 treatment; strengthening Env subunit interactions; and using CD4-negative producer cells. IMPORTANCEEfforts to develop an effective HIV-1 vaccine have been frustrated by the inability to elicit broad neutralizing antibodies that recognize multiple virus strains. Such antibodies are able to bind a particular shape of the HIV-1 envelope glycoprotein trimer, as it exists on a viral membrane but before engaging receptors on the host cell. Here, we establish simple yet powerful assays to characterize the envelope glycoproteins in a natural context on virus particles. We find that, depending on the HIV-1 strain, some envelope glycoproteins change shape and fall apart, creating decoys that can potentially divert the host immune response. We identify requirements to keep the relevant envelope glycoprotein target for broad neutralizing antibodies intact on virus-like particles. These studies suggest strategies that should facilitate efforts to produce and use virus-like particles as vaccine immunogens.

microbiology↗

bioRxiv2022

Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants

The SARS-CoV-2 Omicron variant continues to evolve, with new BQ and XBB subvariants now rapidly expanding in Europe/US and Asia, respectively. As these new subvariants have additional spike mutations, they may possess altered antibody evasion properties. Here, we report that neutralization of BQ.1, BQ.1.1, XBB, and XBB.1 by sera from vaccinees and infected persons was markedly impaired, including sera from individuals who were boosted with a WA1/BA.5 bivalent mRNA vaccine. Compared to the ancestral strain D614G, serum neutralizing titers against BQ and XBB subvariants were lower by 13-81-fold and 66-155-fold, respectively, far beyond what had been observed to date. A panel of monoclonal antibodies capable of neutralizing the original Omicron variant, including those with Emergency Use Authorization, were largely inactive against these new subvariants. The spike mutations that conferred antibody resistance were individually studied and structurally explained. Finally, the ACE2-binding affinities of the spike proteins of these novel subvariants were found to be similar to those of their predecessors. Taken together, our findings indicate that BQ and XBB subvariants present serious threats to the efficacy of current COVID-19 vaccines, render inactive all authorized monoclonal antibodies, and may have gained dominance in the population because of their advantage in evading antibodies.

microbiology↗

bioRxiv2022

OPUS-DSD: Deep Structural Disentanglement for cryo-EM Single Particle Analysis

Many Cryo-EM datasets contain structural heterogeneity due to functional or nonfunctional dynamics that conventional reconstruction methods may fail to resolve. Here we propose a new method, OPUS-DSD (Deep Structural Disentanglement), which can reliably reconstruct the structural landscape of cryo-EM data by directly translating the 2D cryo-EM images into 3D structures. The method adopts a convolutional neural network and is regularized by a latent space prior that encourages the encoding of structural information. The performance of OPUS-DSD was systematically compared to a previously reported method, cryoDRGN, on synthetic and real cryo-EM data. It consistently outperformed existing methods, resolved large or small structural heterogeneity, and improved the final reconstructions of tested systems even on highly noisy cryo-EM data. The results have shown that OPUS-DSD should be particularly suitable for cases in which the high structural flexibilities cannot easily be represented by rigid-body movements. Therefore, OPUS-DSD represents a valuable tool that can not only recover functionally-important structural dynamics missed in a traditional cryo-EM refinement, but also improve the final reconstruction by increasing homogeneity in a dataset. OPUS-DSD is available at https://github.com/alncat/opusDSD.

biophysics↗

bioRxiv2022

A novel crosstalk between Nrf2 and Smad2/3 bridged by two nuanced Keap1 isoforms

The Keap1-Nrf2 signalling to transcriptionally regulate antioxidant response element (ARE)-driven target genes has been accepted as key redox-sensitive pathway governing a vast variety of cellular stresses during healthy survival and disease development. Herein, we identified two nuanced isoforms and {beta} of Keap1, arising from its first and another in-frame translation starting codons, respectively. In identifying those differential expression genes monitored by Keap1 and/or Keap1{beta}, an unusual interaction of Keap1 with Smad2/3 was discovered by parsing transcriptome sequencing, Keap1-interacting protein profiling and relevant immunoprecipitation data. Further examination validated that Smad2/3 enable physical interaction with Keap1, as well as its isoforms and {beta}, by both EDGETSD and DLG motifs in the linker regions between their MH1 and MH2 domains, such that the stability of Smad2/3 and its transcriptional activity are enhanced with the prolonged half-lives and signalling responses from the cytoplasmic to nuclear compartments. The activation of Smad2/3 by Keap1, Keap1 or Keap1{beta} was likely contributable to a coordinative or another competitive effect of Nrf2, particularly in distinct Keap1-based cellular responses to its cognate growth factor or redox stress. Overall, this discovery presents a novel functional bridge crossing both the Keap1-Nrf2 redox signalling and the TGF-{beta}1-Smad2/3 pathways in healthy growth and development.

cell biology↗

bioRxiv2022

Running ahead of evolution - AI based simulation for predicting future high-risk SARS-CoV-2 variants

The never-ending emergence of SARS-CoV-2 variations of concern (VOCs) has challenged the whole world for pandemic control. In order to develop effective drugs and vaccines, one needs to efficiently simulate SARS-CoV-2 spike receptor binding domain (RBD) mutations and identify high-risk variants. We pretrain a large protein language model with approximately 408 million protein sequences and construct a high-throughput screening for the prediction of binding affinity and antibody escape. As the first work on SARS-CoV-2 RBD mutation simulation, we successfully identify mutations in the RBD regions of 5 VOCs and can screen millions of potential variants in seconds. Our workflow scales to 4096 NPUs with 96.5% scalability and 493.9x speedup in mixed precision computing, while achieving a peak performance of 366.8 PFLOPS (reaching 34.9% theoretical peak) on Pengcheng Cloudbrain-II. Our method paves the way for simulating coronavirus evolution in order to prepare for a future pandemic that will inevitably take place. Our models are released at https://github.com/ZhiweiNiepku/SARS-CoV-2_mutation_simulation to facilitate future related work. JustificationWe develop a novel multi-constraint variation prediction framework to simulate SARS-CoV-2 RBD mutations, reaching a peak performance of 366.8 PFLOPS with 96.5% scalability and achieving 493.9x speedup. Our method facilitates the prediction and prioritization of future high-risk variants for the early deployment of drugs and vaccines. Performance attributes O_TBL View this table: org.highwire.dtl.DTLVardef@1b1873aorg.highwire.dtl.DTLVardef@25314eorg.highwire.dtl.DTLVardef@1c80130org.highwire.dtl.DTLVardef@1c61b21org.highwire.dtl.DTLVardef@11f21c5_HPS_FORMAT_FIGEXP M_TBL C_TBL Overview of the problemCoronavirus Disease 2019 (COVID-19) has spread rapidly to more than 200 countries or regions since December 2019. Due to its high infectivity, there have been over 645 million confirmed cases, including approximately 6.6 million deaths, reported by the World Health Organization (WHO) as of December 20221. In addition to being a serious threat to human health, COVID-19 has had a catastrophic impact on the global economy.

bioinformatics↗

bioRxiv2022

Lysosomes mediate the mitochondrial UPR via mTORC1-dependent ATF4 phosphorylation

Lysosomes are central platforms for not only the degradation of macromolecules but also the integration of multiple signaling pathways. However, whether and how lysosomes mediate the mitochondrial stress response (MSR) remain largely unknown. Here, we demonstrate that lysosomal acidification via the vacuolar H+-ATPase (v-ATPase) is essential for the transcriptional activation of the mitochondrial unfolded protein response (UPRmt). Mitochondrial stress stimulates v-ATPase-mediated lysosomal activation of the mechanistic target of rapamycin complex 1 (mTORC1), which then directly phosphorylates the MSR transcription factor, activating transcription factor 4 (ATF4). Disruption of mTORC1-dependent ATF4 phosphorylation blocks the UPRmt, but not other similar stress responses, such as the UPRER. Finally, ATF4 phosphorylation downstream of the v-ATPase/mTORC1 signaling is indispensable for sustaining mitochondrial redox homeostasis and protecting cells from reactive oxygen species (ROS)-associated cell death upon mitochondrial stress. Thus, v-ATPase/mTORC1-mediated ATF4 phosphorylation via lysosomes links mitochondrial stress to UPRmt activation and mitochondrial function resilience.

cell biology↗

bioRxiv2022

Distinct structure and gating mechanism in diverse NMDA receptors with GluN2C and GluN2D subunits

N-Methyl-D-Aspartate (NMDA) receptors are essential for many brain functions. These receptors are heterotetramers typically comprising two GluN1 subunits and two GluN2 subunits. The latter could alternate among four subtypes (N2A-N2D) and determine the functional diversity of NMDA receptors1, 2. For example, receptors containing N2C or N2D exhibit 50-fold lower channel open probability (Po) than those containing N2A (ref.3-5). Structures of N2A- and N2B-containing receptors have been extensively characterized, providing molecular basis for understanding NMDA receptor function6-14. Here we report the cryo-EM structures of N1-N2D and N1-N2C di-heterotetramers (di-receptors), and N1-N2A-N2C tri-heterotetramer (tri-receptor) at a resolution up to 3.0 [A]. Structural analysis showed that the bilobate N-terminal domain (NTD) in N2D adopted an intrinsic closed conformation, leading to a compact NTD tetramer in N1-N2D receptor. Functional studies further demonstrated that, in di-receptors containing N2D but not N2A or N2B, crosslinking NTD at the tetrameric interface had no effect on channel activity, while crosslinking ligand-binding domain (LBD) of two N1 protomers significantly elevated Po. Surprisingly, we found that the N1-N2C di-receptors spontaneously oscillated between symmetric and asymmetric conformation. The later one occupied a predominant population, whereby two N2C protomers exhibited distinct conformation. This asymmetry, which was also found to a lesser extent in N1-N2A di-receptor10, was further locked by the binding of an N2C-specific allosteric potentiator PYD-106 to a unique binding pocket between NTD and LBD in only one N2C protomer. Finally, N2A and N2C in the N1-N2A-N2C tri-receptor displayed the conformation close to that found in one protomer of N1-N2A and N1-N2C di-receptors, respectively. These findings provide a comprehensive structural understanding of diverse functional properties of major NMDA receptor subtypes.

neuroscience↗

bioRxiv2022

Phase-separating pyrenoid proteins form complexes in the dilute phase

While most studies of biomolecular phase separation have focused on the condensed phase, relatively little is known about the dilute phase. Theory suggests that stable complexes form in the dilute phase of two-component phase-separating systems, impacting phase separation; however, these complexes have not been interrogated experimentally. We show that such complexes indeed exist, using an in vitro reconstitution system of a phase-separated organelle, the algal pyrenoid, consisting of purified proteins Rubisco and EPYC1. Applying fluorescence correlation spectroscopy (FCS) to measure diffusion coefficients, we found that complexes form in the dilute phase with or without condensates present. The majority of these complexes contain exactly one Rubisco molecule. Additionally, we developed a simple analytical model which recapitulates experimental findings and provides molecular insights into the dilute phase organization. Thus, our results demonstrate the existence of protein complexes in the dilute phase, which could play a significant role in the stability, dynamics, and regulation of condensates.

biophysics↗

bioRxiv2022

Mechanism of repression of the glycerol utilization operon in Borrelia burgdorferi

Lyme disease pathogen Borrelia burgdorferi, switches carbohydrate utilization while transmitting between two disparate hosts, an Ixodes tick vector and a mammalian host. The ability to use glycerol is important for B. burgdorferi to colonize and persist in the tick vector, and expression of the glpFKD (glp) operon for glycerol uptake/utilization is tightly regulated during the enzootic cycle of B. burgdorferi between ticks and mammals. In present study, we identified a cis element within the 5 untranslated region of glp that negatively regulates the glp expression. This repression of glp is independent of RpoS. We further show that BadR directly binds to this cis element and represses glp. The efficiency of BadR binding in the presence of c-di-GMP and various carbohydrates were also assessed. This finding, along with previous findings of positive regulation of glp expression by the c-di-GMP signaling pathway and negative regulation by the alternative sigma factor RpoS, demonstrates that B. burgdorferi employs multi-layer regulatory mechanisms to coordinate glp expression during its enzootic cycle.

microbiology↗

bioRxiv2022

USP10 strikes down Wnt/β-catenin signaling by dual-wielding deubiquitinase activity and phase transition potential

Wnt/{beta}-catenin signaling is a conserved pathway crucially governing development, homeostasis and oncogenesis. Discovery of novel regulators holds great values in both basic and translational research. Through screening, we identified a deubiquitinase (DUB) USP10 as a novel and critical modulator of {beta}-catenin. Mechanistically, USP10 binds to key scaffold Axin1 via conserved motifs and stabilizes Axin1 through K48-linked deubiquitination, and surprisingly, tethers Axin1 and {beta}-catenin physically while promoting phase separation for {beta}-catenin suppression regardless of its enzymatic activity. Functionally, USP10 prominently regulates embryonic development and intestinal homeostasis by antagonizing {beta}-catenin via DUB activity. In colorectal cancer, USP10 substantially represses cancer growth mainly through physical binding compensation and phase separation promotion and correlates with Wnt/{beta}-catenin magnitude clinically. Collectively, we discovered USP10 functioning in multiple biological processes against {beta}-catenin and unearthed a novel enzyme-dependent and -independent "dual-regulating" mechanism by which USP10 utilizes parallelly and context-dependently. USP10 inhibitor was suggested in treating certain Wnt-related diseases.

cell biology↗

bioRxiv2022

Hormone-induced enhancer assembly requires an optimal level of hormone receptor multivalent interactions

Transcription factors (TFs) activate enhancers to drive cell-specific gene programs in response to signals, but our understanding of enhancer assembly during signaling events is incomplete. Here, we show that Androgen Receptor (AR), a steroid hormone-regulated transcription factor, forms condensates through multivalent interactions in response to androgen signaling to orchestrate enhancer assembly. We demonstrate that the intrinsically disordered N-terminal domain (NTD) of AR drives 1,6-Hexanediol-sensitive condensate formation and that NTD deletion or aromatic residue mutation reduces AR self-association and abolishes AR transcriptional activity. AR NTD can be substituted by intrinsically disordered regions (IDRs) from selective proteins for AR condensation capacity and transactivation function. Surprisingly, strengthened AR condensation capacity caused by extending the polyQ tract within AR NTD also leads to impaired transcriptional activity without affecting AR binding on enhancers. Furthermore, either NTD deletion or polyQ extension reduces heterotypic multivalent interactions between AR and other enhancer components. These results suggest the importance of an optimal level of AR condensation in mediating AR-AR homotypic and AR-cofactor heterotypic interactions to regulate enhancer assembly in response to signals. Our study supports the notion that alteration of the fine-tuned multivalent IDR-IDR interactions might underlie AR-related human pathologies, thereby providing novel molecular insights for potential therapeutic strategies to treat prostate cancer and other AR-involved diseases by targeting AR multivalent interactions.

molecular biology↗

bioRxiv2022

Integrated PET and confocal imaging informs a functional timeline for the dynamic process of vascular reconnection during grafting.

Grafting is a widely used agricultural technique that involves the physical joining of separate plant parts so they form a unified vascular system, enabling beneficial traits from independent genotypes to be captured in a single plant. This simple, yet powerful tool has been used for thousands of years to improve abiotic and biotic stress tolerance, enhance yield, and alter plant architecture in diverse crop systems. Despite the global importance and ancient history of grafting, our understanding of the fundamental biological processes that make this technique successful remains limited, making it difficult to efficiently expand on new genotypic graft combinations. One of the key determinants of successful grafting is the formation of the graft junction, an anatomically unique region where xylem and phloem strands connect between newly joined plant parts to form a unified vascular system. Here, we use an integrated imaging approach to establish a spatiotemporal framework for graft junction formation in the model crop Solanum lycopersicum (tomato), a plant that is commonly grafted worldwide to boost yield and improve abiotic and biotic stress resistance. By combining Positron Emission Tomography (PET), a technique that enables the spatio-temporal tracking of radiolabeled molecules, with high-resolution laser scanning confocal microscopy (LSCM), we are able to merge detailed, anatomical differentiation of the graft junction with a quantitative timeline for when xylem and phloem connections are functionally re-established. In this timeline, we identify a 72-hour window when anatomically connected xylem and phloem strands regain functional capacity, with phloem restoration typically preceding xylem restoration by about 24-hours. Furthermore, we identify heterogeneity in this developmental and physiological timeline that corresponds with microvariability in the physical contact between newly joined rootstock-scion tissues. Our integration of PET and confocal imaging technologies provides a spatio-temporal timeline that will enable future investigations into cellular and tissue patterning events that underlie successful versus failed vascular restoration across the graft junction.

plant biology↗

bioRxiv2022

Palmitoylation regulates neuropilin-2 localization and function in cortical neurons and conveys specificity to semaphorin signaling via palmitoyl acyltransferases

Secreted semaphorin 3F (Sema3F) and semaphorin 3A (Sema3A) exhibit remarkably distinct effects on deep layer excitatory cortical pyramidal neurons; Sema3F mediates dendritic spine pruning, whereas Sema3A promotes the elaboration of basal dendrites. Sema3F and Sema3A signal through distinct holoreceptors that include neuropilin-2 (Nrp-2)/plexinA3 (PlexA3) and neuropilin-1 (Nrp-1)/PlexA4, respectively. We find that Nrp-2 and Nrp-1 are S-palmitoylated in cortical neurons and that palmitoylation of select Nrp-2 cysteines is required for its proper subcellular localization and also for Sema3F/Nrp-2-dependent dendritic spine pruning in cortical neurons, both in vitro and in vivo. Moreover, we show that the palmitoyl acyltransferase DHHC15 is required for Nrp-2 palmitoylation and Sema3F/Nrp-2-dependent dendritic spine pruning, but it is dispensable for Nrp-1 palmitoylation and Sema3A/Nrp-1-dependent basal dendritic elaboration. Therefore, palmitoyl acyltransferase-substrate specificity is essential for establishing compartmentalized neuronal structure and functional responses to extrinsic guidance cues. HIGHLIGHTSO_LINeuropilins (Nrps) are S-palmitoylated in vitro and in vivo in the central nervous system C_LIO_LIS-palmitoylation of select Nrp-2 cysteines confers subcellular localization specificity and is required for semaphorin 3F-dependent dendritic spine pruning in cortical neurons C_LIO_LIDistinct palmitoyl acyltransferases mediate Nrp-2 and Nrp-1 palmitoylation and function, imparting specificity to semaphorin signaling C_LI

neuroscience↗

bioRxiv2022

The protist ubiquitin ligase effector PbE3-2 targets RD21A to impede plant immunity

Clubroot caused by the soil-borne protist pathogen Plasmodiophora brassicae is one of the most devastating diseases of Brassica oil and vegetable crops worldwide. Understanding the pathogen infection strategy is crucial for the development of disease control. However, the molecular mechanism by which this pathogen promotes infection remains largely unknown. Here, we identified a P. brassicae-secreted effector PbE3-2 that impedes plant immunity by ubiquitinating the immune regulator RD21A for degradation. Overexpression of PbE3-2 in Arabidopsis thaliana resulted in higher susceptibility to P. brassicae and decreases in chitin-triggered reactive oxygen species burst and expression of marker genes in salicylic acid signaling. PbE3-2 interacted with and ubiquitinated RD21A in vitro and in vivo. Mutant plants deficient in RD21A exhibited similar susceptibility and compromsied immune responses as in PbE3-2 overexpression plants. These results suggest that P. brassicae promotes clubroot disease through RD21A degradation mediated by the effector PbE3-2. As PbE3-2 is widely conserved across different P. brassicae pathotypes, the degradation of RD21A by PbE3-2 might be a prevalent infection strategy in this pathogen.

microbiology↗