Biology subjects

Gevaert, K.

Publications and source records attributed to Gevaert, K..

At least 19 recordsLinked to original sources

bioRxiv2026

Functional diversification of UBP6 in plant immunity through N-degron pathway regulation

Deubiquitylases are key proteolytic regulators of ubiquitin-dependent cellular processes, catalyzing the removal or remodelling of ubiquitin modifications on substrate proteins, including those targeted for proteasomal degradation. UBIQUITIN PROTEASE (UBP)6 is a deubiquitylase that promotes the abundance of NONEXPRESSOR OF PATHOGENESIS RELATED GENES (NPR)1, a conserved master regulator of plant immunity. Here, we show that the Arabidopsis thaliana protease METACASPASE (MC)9 site-specifically processes UBP6, generating the E157-UBP6 proteoform, whose stability is controlled by the Arginyl-transferase (ATE) N-degron pathway. We observed that pathogen recognition both triggers UBP6 cleavage and leads to conditional stabilisation of E157 UBP6, which is enhanced as the defence response intensifies. Our data suggest that E157 UBP6, which lacks deubiquitylating activity, may induce inhibition of the proteasome, elevating NPR1 levels and enhancing salicylic acid (SA) induced gene activation, all of which collectively contribute to restricting pathogen growth. Thus, UBP6 cleavage and N-degron pathway regulation provide distinct proteoforms of UBP6 with specific effects on the immune processes.

plant biology↗

bioRxiv2026

TRMT10A deficiency and tRNA fragmentation disrupt human pancreatic β-cell identity and insulin maturation

Mutations in the tRNA-modifying enzyme TRMT10A cause a rare monogenic syndrome characterized by early-onset diabetes and neurodevelopmental defects, yet the molecular mechanisms underlying TRMT10A diabetes remain unclear. Using human TRMT10A-deficient (knockout and mutant) induced pluripotent stem cells (iPSCs) differentiated into islet-like aggregates and TRMT10A-silenced EndoC-{beta}H1 human {beta}-cells, we show that TRMT10A deficiency impairs {beta}-cell differentiation, insulin content and glucose-stimulated insulin secretion while inducing widespread transcriptional alterations. These defects are accompanied by oxidative stress, diminished antioxidant capacity, and defective proinsulin processing driven by reduced PCSK1 expression. Mechanistically, the loss of TRMT10A promotes tRNA fragmentation and the generation of fragments derived from the 5 end of tRNAGln-CTG (tDRGln-CTG) that interact with hnRNPM. Our data support the existence of a previously unrecognized hnRNPM-PTBP1 interaction in human {beta}-cells and suggest that this complex may contribute to the regulation of PCSK1 mRNA stability and/or translation. Furthermore, through its interaction with hnRNPM, tDRGln-CTG may alter the function of the complex thereby contributing to reduced PCSK1 expression, defective proinsulin processing, and impaired insulin content. Our findings link tRNA fragmentation, RNA-binding protein networks and insulin maturation, positioning TRMT10A as a critical regulator of {beta}-cell identity and function and uncovering a novel mechanism of {beta}-cell failure in the pathogenesis of diabetes.

molecular biology↗

bioRxiv2026

Experimental mismatch in benchmarking PELSA and LiP-MS

Limited proteolysis coupled to mass spectrometry (LiP-MS) is a peptide-centric conformational proteomics approach during which a brief incubation with a non-specific protease (e.g., proteinase K) under native conditions generates structural fingerprints that report on treatment-induced conformational changes, which is followed by a tryptic digest under denaturing conditions allowing to read out these fingerprints 1. In contrast, the recently introduced peptide-centric local stability assay (PELSA) uses a high trypsin-to-substrate ratio under native conditions to release fully tryptic peptides that reflect structural stability upon ligand binding 2. In their paper, Li et al. compared PELSA and LiP-MS across several benchmarks and reported that PELSA exhibited quantitative sensitivity comparable to or exceeding LiP-MS. Notably, PELSA quantified a 21-fold greater rapamycin-induced change for FKBP1A compared to LiP-MS. Because such claims influence method selection for conformational proteomics, we reanalyzed the publicly deposited datasets underlying these comparisons and assessed the experimental and analytical choices that contributed to the reported effect sizes. Our evaluation indicates that the reported 21-fold difference arises from non-matched experimental conditions and undisclosed data imputation, and that conclusions regarding quantitative superiority or biological interpretability should therefore be treated with caution.

bioinformatics↗

bioRxiv2026

DiaReport: Reproducible Workflow for Differential Expression Analysis and Interactive Reporting in DIA-based Proteomics

SummaryData-independent acquisition (DIA) has become the preferred data acquisition method for mass spectrometry-based proteomics, yet, reproducible workflows for differential expression (DE) analysis and reporting results remain limited. We present DiaReport, an R package that performs precursor- and protein-level DE analysis from DIA-NN output using MSqRob and QFeatures, while generating high-quality, interactive HTML reports through Quarto. DiaReport integrates precursor data, filtering of missing values, normalization, protein summarization and statistical modeling within a single function, supporting both simple pairwise as well as complex experimental designs. The package provides structured outputs and configuration files to ensure computational reproducibility across different studies. To accommodate diverse research needs, DiaReport includes multiple reporting templates tailored to different proteomic applications. Applying DiaReport to an extracellular vesicle (EV) proteomics dataset demonstrates its ability to efficiently analyze DIA data and provide rapid insights into sample quality and protein level differences. Availability and ImplementationDiaReport is an open-source R package available at https://github.com/Gevaert-Lab/diareport. The package is platform-independent and distributed under the MIT license. Reports are generated using Quarto and require only standard R dependencies. Detailed documentation, installation guides and usage vignettes are provided within the repository. The interactive HTML reports discussed in this study, including the UPS2 benchmark and EV case study, are archived on Zenodo (https://doi.org/10.5281/zenodo.18632744 and https://doi.org/10.5281/zenodo.18632731). ContactCorresponding author: Kris Gevaert; kris.gevaert@vib-ugent.be.

bioinformatics↗

bioRxiv2026

Conditional stability of HY5 through the ATE N-degron pathway regulates environmental responses in Arabidopsis thaliana

The N-degron pathways of ubiquitin mediated proteolysis target proteins for degradation dependent on their amino terminal residue, often produced after protease activity. Very few substrates have been identified in plants even though enzymes of these pathways are highly conserved in eukaryotes. Here we identify ELONGATED HYPOCOTYL5 (HY5), an important transcriptional regulator involved in many aspects of plant development, as a target for the endopeptidase METACASPASE (MC)9, producing the carboxy-terminal protein fragment (proteoform) E59-HY5. E59-HY5 is shown to be a substrate of the arginyl transferase (ATE) N-degron pathway, and influences physiological processes known to be controlled by HY5, including photomorphogenesis and the unfolded protein response. Conditional stability of E59-HY5 was shown to result from environmentally controlled ATE function, which may highlight a general mechanism for N-degron pathway regulation of proteoform and proteome function during growth and development.

plant biology↗

bioRxiv2025

Exhaled breath condensate proteomics using amphipols improves protein detection but reveals statistical challenges in respiratory disease biomarker discovery

BackgroundInvasive diagnostic techniques for pleural mesothelioma (PM) delay early detection, underscoring the need for non-invasive biomarkers. Exhaled breath condensate (EBC) is a promising matrix but has extremely low protein concentration. This study applies an amphipol (APol)-based concentration method to enhance detection of potential PM biomarkers in the EBC proteome. MethodsFour replicate EBC samples from a healthy individual were processed using APols or lyophilization. Subsequently, 145 EBC samples from PM patients (n=25), lung cancer patients (n=28), asymptomatic asbestos-exposed individuals (n=60) or healthy controls (n=32) were concentrated with APols and analysed by liquid chromatography coupled with tandem mass spectrometry. Technical variability from batch effects and collection devices was addressed using omicsGMF, for simultaneous imputation and covariates correction. Statistical analysis employed linear models with technical and clinical covariates. ResultsAPols outperformed lyophilization, yielding 1.7-fold higher proteome coverage and improved reproducibility. Although high data missingness was observed, proteome analysis across 145 samples identified 248 unique proteins. OmicsGMF corrected the substantial variability, while maintaining biological signal. Whereas unsupervised clustering did not reveal distinct disease-specific patterns, supervised statistical analysis detected overall subtle differences between clinical groups (PERMANOVA p-value = 0.008), though no individual proteins reached statistical significance after adjustment for technical and clinical covariates and correction for multiple testing. ConclusionAPols outperforms lyophilization for concentrating proteins in low-abundant EBC samples, enabling enhanced proteome coverage for biomarker discovery studies. However, the inherent high variability of EBC proteomes has a strong effect on detecting possible biomarkers across clinical groups. Key messageO_ST_ABSWhat is already known on this topicC_ST_ABSExhaled breath condensate (EBC) is an attractive non-invasive biofluid for respiratory disease biomarker discovery, but no protein biomarkers have reached clinical application despite extensive investigation. What this study addsUsing superior APols-based protein concentration and rigorous analytical and statistical methods in 145 EBC samples, we demonstrate that fundamental limitations - 96% peptide missingness, 80% skin-protein contamination, high variability, low protein identifications and low fold-changes- make EBC unsuitable for reliable protein biomarker discovery, when proper covariate adjustment is applied. How this study might affect research, practice or policyResearchers pursuing EBC proteomics should be cautious, as inadequate handling of missingness and variability, particularly without proper covariate adjustment, may yield findings that do not reflect true biological differences.

pathology↗

bioRxiv2025

Advancing DIA-based Limited Proteolysis Workflows: introducing DIA-LiPA

Limited proteolysis coupled to mass spectrometry (LiP-MS) probes protein conformational dynamics, but interpretation of LiP-MS data is complicated by heterogenous proteolytic cleavage patterns and missing data. Recent advances in data-independent acquisition (DIA) and machine learning-based search engines promise improved sensitivity and reproducibility, yet their performance in LiP-MS workflows remains underexplored. We systematically evaluated selected library-free DIA workflows using a rapamycin-treated human cell lysate and a yeast heat shock dataset, benchmarking DIA-NN and Spectronaut for identification depth, reproducibility and false discovery rate control. Our results show that library-free approaches achieve high sensitivity, eliminating the experimental overhead and sample requirements associated with empirical libraries. Building on these advances, we introduce a DIA-based Limited Proteolysis data Analysis pipeline (DIA-LiPA), a data analysis workflow tailored for LiP-MS data that integrates semi-tryptic- and tryptic-level precursor data and accounts for missingness to enable structural interpretation. Validation across multiple datasets confirmed that DIA-LiPA reproduces known structural signatures and uncovers additional regulatory patterns, providing a robust framework for mechanistic insights into protein dynamics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/687786v2_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@19fc486org.highwire.dtl.DTLVardef@1f74b7org.highwire.dtl.DTLVardef@127db11org.highwire.dtl.DTLVardef@19f5b88_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

MLMarker: A machine learning framework for tissue inference and biomarker discovery

MLMarker is a machine learning tool that computes continuous tissue similarity scores for proteomics data, addressing the challenge of interpreting complex or sparse datasets. Trained on 34 healthy tissues, its Random Forest model generates probabilistic predictions with SHAP-based protein-level explanations. A penalty factor corrects for missing proteins, improving robustness for low-coverage samples. Across three public datasets, MLMarker revealed brain-like signatures in cerebral melanoma metastases, achieved high accuracy in a pan-cancer cohort, and identified brain and pituitary origins in biofluids. MLMarker provides an interpretable framework for tissue inference and hypothesis generation, available as a Python package and Streamlit app.

bioinformatics↗

bioRxiv2025

Collisional cross-section prediction for multiconformational peptide ions with IM2Deep

Peptide collisional cross-section (CCS) prediction is complicated by the tendency of peptide ions to exhibit multiple conformations in the gas phase. This adds further complexity to downstream analysis of proteomics data, for example for identification or quantification through feature finding. Here, we present an improved version of IM2Deep that is trained on a carefully curated dataset to predict CCS values of multiconformational peptides. The training data is derived from a large and comprehensive set of publicly available datasets. This comprehensive training dataset together with a tailored architecture allows for the accurate CCS prediction of multiple peptide conformational states. Furthermore, the enhanced IM2Deep model also retains high precision for peptides with a single observed conformation. IM2Deep is publicly available under a permissive open source license at https://github.com/compomics/IM2Deep.

bioinformatics↗

bioRxiv2025

Detection of human unannotated microproteins by mass spectrometry-based proteomics: a community assessment

Thousands of short open reading frames (sORFs) are translated outside of annotated coding sequences. Recent studies have pioneered searching for sORF-encoded microproteins in mass spectrometry (MS)- based proteomics and peptidomics datasets. Here, we assessed literature-reported MS-based identifications of unannotated human proteins. We find that studies vary by three orders of magnitude in the number of unannotated proteins they report. Of nearly 10,000 reported sORF-encoded peptides, 96% were unique to a single study, and 12% mapped to annotated proteins or proteoforms. Manual curation of a benchmark dataset of 406 manually evaluated spectra from 204 sORF-encoded proteins revealed large variation in peptide-spectrum match (PSM) quality between studies, with immunopeptidomics studies generally reporting higher quality PSMs than conventional enzymatic digests of whole cell lysates. We estimate that 65% of predicted sORF-encoded protein detections in immunopeptidomics studies were supported by high-quality PSMs versus 7.8% in non-immunopeptidomics datasets. Our work stresses the need for standardized protocols and analysis workflows to guide future advancements in microprotein detection by MS towards uncovering how many human microproteins exist.

genomics↗

bioRxiv2025

Lack of AtMC1 catalytic activity triggers autoimmunity dependent on NLR stability

Plants utilize cell surface-localized pattern recognition receptors (PRRs) and intracellular nucleotide-binding leucine-rich repeat (NLR) receptors to detect non-self and elicit robust immune responses. Fine-tuning the homeostasis of these receptors is critical to prevent their hyperactivation. Here, we show that Arabidopsis plants lacking metacaspase 1 (AtMC1) display autoimmunity dependent on immune signalling components downstream of NLR and PRR activation. Overexpression of a catalytically inactive AtMC1 in an atmc1 background triggers severe autoimmunity partially dependent on the same immune signalling components. Overexpression of the E3 ligase SNIPER1, a master regulator of NLR homeostasis, fully reverts the AtMC1-dependent autoimmunity phenotype, inferring that a broad defect in NLR turnover may underlie the severe phenotype observed. Catalytically inactive AtMC1 localizes to punctate structures that are degraded through autophagy. Altogether and considering previous evidence on the proteostatic functions of AtMC1, we speculate that Wt AtMC1 may either directly or indirectly control NLR protein levels, thereby preventing autoimmunity.

plant biology↗

bioRxiv2025

A 96well ultrafiltration approach for the high-throughput proteome analysis of extracellular vesicles isolated from conditioned medium

1.Extracellular vesicles (EVs), nanoscale vesicles that are secreted by cells, are critical mediators of intercellular communication and play a crucial role in diverse pathologies such as cancer development. Therefore, EVs are regarded as having high potential in the clinic, both for diagnostic and therapeutic applications. Unfortunately, EVs reside in complex biofluids and their consistent isolation at sufficient purity for mass spectrometry-based proteomics has proven to be challenging, especially when increased high-throughput is required. Here, we describe the incorporation of our previously reported filter-aided EV enrichment (FAEVEr) strategy for the isolation of EVs from conditioned medium, from harvest to proteomic analysis completely to a streamlined 96well format. We compared our approach with ultracentrifugation, the most widely used method for EV enrichment, in terms of protein identifications, consistency, reproducibility and overall performance, including the invested time, resources and required expertise. In addition, our results show that including relative high percentages of TWEEN-20, a mild detergent, markedly improves the final purity of the EV proteome by removing the bulk of non-EV proteins (e.g. serum proteins) and significantly increases the number of identified transmembrane proteins. Moreover, our FAEVEr 96well strategy improves the overall reproducibility with a consistent number of protein identifications and decreased number of missing values across replicates. This promotes the validity and comparability between results, which is essential in both a clinical and research setting, where consistency is paramount. 3. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/634668v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@b45d01org.highwire.dtl.DTLVardef@1460cd0org.highwire.dtl.DTLVardef@1f345fcorg.highwire.dtl.DTLVardef@77c223_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2024

Biases in the Parsortix system observed with pancreatic cancer cell lines

Pancreatic cancer has a 5-year survival rate of merely 12%. The high rate of late-stage diagnoses underscores the need for reliable biomarkers for early detection and disease monitoring. Circulating tumor cells (CTCs) have emerged as a promising biomarker, yet their detection remains challenging due to their rarity and phenotypic diversity. This study evaluates the Parsortix(R) system, a microfluidic device designed to enrich CTCs based on size and deformability, using pancreatic cancer cell lines. As increasing evidence indicates that during epithelial to mesenchymal transition (EMT) a cells deformability increases, we evaluated to what extent the Parsortix(R) system was biased towards epithelial cancer cells. First, the EMT stage of three pancreatic cancer cell lines, CAPAN-1, PANC-1 and MIA PaCa-2, was assessed using immunocytochemistry, flow cytometry and proteomics. CAPAN-1 cells were classified as epithelial, MIA PaCa-2 cells exhibited a mesenchymal-like phenotype, and PANC-1 cells demonstrated a hybrid phenotype. Then, by spiking these cells into blood samples, we determined the Parsortix(R) systems ability to recover the cancer cells. Our results indicated that epithelial and hybrid phenotypes are more efficiently captured (62.6 {+/-} 18.5% and 65.4 {+/-} 11.1%) than mesenchymal cancer cells (32.8 {+/-} 10.2%). To confirm these findings, spike-in experiments were repeated using an EMT inducible cell line. Again, significantly lower recovery rates were found for the cells in a mesenchymal-like state (31.5 {+/-} 6.4%) compared to those in an epithelial state (47.56 {+/-} 7.2%). In conclusion, the Parsortix(R) system may underestimate the presence of mesenchymal CTCs.

cancer biology↗

bioRxiv2024

Olduvai domain expression downregulates mitochondrial pathways: implications for human brain evolution and neoteny

Olduvai (formerly DUF1220) protein domains, encoded by the NBPF gene family, have undergone the greatest human lineage-specific copy-number expansion of any coding sequence in the genome and strongly correlate with brain size and neuron number across primates. Here we show that Olduvai domains act in a dosage-dependent manner to suppress mitochondrial metabolism. Transcriptomic, proteomic, and live-cell imaging analyses of cells overexpressing NBPF1 (which encodes seven Olduvai domains) reveal pronounced downregulation of mitochondrial pathways, including electron transport chain components and NADH dehydrogenase activity, as well as reduced mitochondrial abundance. By limiting energy availability, this suppression delays cellular maturation and developmental timing. We propose that the resulting prolongation of neurogenesis increases neuron production, providing a mechanistic link between Olduvai copy number expansion and the evolutionary enlargement of the human brain. This dosage-sensitive mitochondrial regulation may also contribute to broader neotenic features of human development, offering a unifying molecular mechanism for brain expansion and the neotenic traits that distinguish humans from other primates.

genomics↗

bioRxiv2023

CysQuant: simultaneous quantification of cysteine oxidation and protein abundance using data dependent or independent acquisition mass spectrometry

Protein cysteinyl thiols are susceptible to reduction-oxidation reactions that can influence protein function. Accurate quantification of cysteine oxidation is therefore crucial for decoding protein redox regulation. Here, we present CysQuant, a novel approach for simultaneous quantification of cysteine oxidation degrees and protein abundancies. CysQuant involves light/heavy iodoacetamide isotopologues for differential labeling of reduced and reversibly oxidized cysteines analyzed by data-dependent acquisition (DDA) or data-independent acquisition mass spectrometry (DIA-MS). Using plexDIA with in silico predicted spectral libraries, we quantified an average of 18% cysteine oxidation in Arabidopsis thaliana by DIA-MS, including a subset of highly oxidized cysteines forming disulfide bridges in AlphaFold2 predicted structures. Applying CysQuant to Arabidopsis seedlings exposed to excessive light, we successfully quantified the well-established increased reduction of Calvin-Benson cycle enzymes and discovered yet uncharacterized redox-sensitive disulfides in chloroplastic enzymes. Overall, CysQuant is a highly versatile tool for assessing the cysteine modification status that can be widely applied across various mass spectrometry platforms and organisms.

molecular biology↗

bioRxiv2023

Filter-aided extracellular vesicle enrichment (FAEVEr)

AbstractExtracellular vesicles (EVs), membrane-delimited nanovesicles that are secreted by cells into the extracellular environment, are gaining substantial interest due to their involvement in cellular homeostasis and their contribution to disease pathology. The latter in particular has led to an exponential increase in interest in EVs as they are considered to be circulating packages containing potential biomarkers and are also a possible biological means to deliver drugs in a cell-specific manner. However, several challenges hamper straightforward proteome analysis of EVs as they are generally low abundant and reside in complex biological matrices. These matrices typically contain abundant protein concentrations that vastly exceed those of the EV proteome. Therefore, extensive EV isolation and purification protocols are imperative and many have been developed, including (density) ultracentrifugation, size-exclusion and precipitation methods. Here, we describe filter-aided extracellular vesicle enrichment (FAEVEr) as an approach based on 300 kDa MWCO filtration that allows the processing of multiple samples in parallel within a reasonable timeframe and at moderate cost. We demonstrate that FAEVEr is capable of quantitatively retaining EV particles on filters, whilst allowing extensive washing with the mild detergent TWEEN-20 to remove interfering non-EV proteins. The retained particles are directly lysed on the filter for a complete recovery of the EV protein cargo towards proteome analysis. Here, we validate and optimize FAEVEr on recombinant EV material and apply it on conditioned medium as well as on complex serum. Our results indicate that EVs isolated from MCF7 cells cultured with or without serum have a drastic different proteome because of nutrient deprivation.

cell biology↗

bioRxiv2023

Antagonism and selective modulation of the human glucocorticoid receptor both reduce recruitment of p300/CBP and the Mediator complex

Exogenous glucocorticoids are frequently used to treat inflammatory disorders and as adjuncts for treatment of solid cancers. However, their use is associated with severe side effects and therapy resistance. Novel glucocorticoid receptor (GR) ligands with a patient-validated reduced side effect profile have not yet reached the clinic. GR is a member of the nuclear receptor family of transcription factors and heavily relies on interactions with coregulator proteins for its transcriptional activity. To elucidate the role of the GR interactome in the differential transcriptional activity of GR following treatment with agonists, antagonists, or lead selective GR agonists and modulators (SEGRAMs), we generated comprehensive interactome maps by high-confidence proximity proteomics in lung epithelial carcinoma cells. We found that the GR antagonist RU486 and the SEGRAM Dagrocorat both reduced GR interaction with CREB-binding protein (CBP)/p300 and the Mediator complex when compared to the full GR agonist Dexamethasone. Our data offer new insights into the role of differential coregulator recruitment in shaping ligand-specific GR-mediated transcriptional responses. In BriefGlucocorticoids are commonly prescribed for the treatment of inflammatory disorders but are associated with severe side effects. Novel glucocorticoid receptor (GR) ligands with strong anti-inflammatory effects but reduced side effects are still sought after. Despite decades-long GR research, there is still an incomplete understanding of the molecular mechanisms driving context-specific GR activity. Using proximity labeling proteomics, we identified CREB-binding protein (CBP), p300 and the Mediator complex as potential crucial GR coregulators driving ligand-induced changes in GRs transcriptional activity. HighlightsO_LIGlucocorticoids (GCs), potent anti-inflammatory agents, can elicit side effects C_LIO_LIMore selective GCs, causing less side effects, are currently still unavailable C_LIO_LILack of fundamental insights on context-specific actions of the GC receptor (GR) C_LIO_LIWe mapped ligand-specific GR interactomes using proximity labeling proteomics C_LIO_LIp300/CBP and Mediator undergo ligand-dependent changes in interaction with GR C_LI

molecular biology↗

bioRxiv2023

Seed Longevity is Controlled by Metacaspases

To survive extreme desiccation, seeds enter dormancy that can last millennia. This dormancy involves the accumulation of protective but structurally disordered storage proteins through unknown adjustments of proteolytic surveillance mechanisms. Mutation of all six types II metacaspases (MCAs)-II in the model plant Arabidopsis revealed their essential role in modulating these proteolytic mechanisms. MCA-II mutant seeds fail to properly target at the endoplasmic reticulum (ER) the AAA ATPase Cell Division Cycle 48 (CDC48) to dispose of misfolded proteins. MCA-IIs cleave a CDC48 adaptor, the ubiquitination regulatory X domain-containing (PUX) responsible for localizing CDC48 to the lipid droplets. When cleaved, CDC48-PUX is inactivated and allows a lipid droplet-to-ER shuttling of CDC48, an important step in the regulation of seeds lifespan. In sum, we uncover antagonism between proteolytic pathways bestowing longevity. One-Sentence SummaryMetacaspase proteases confer seed longevity by antagonizing CDC48 activity.

plant biology↗