Biology subjects

Dadlez, M.

Publications and source records attributed to Dadlez, M..

13 recordsLinked to original sources

bioRxiv2026

GW182 silencing domain engages the tristetraprolin-binding pocket of CNOT1 to recruit CNOT1 into multiprotein condensates

GW182 recruits the CCR4-NOT deadenylase complex through its CIM1 region, yet the CNOT1 surface mediating this interaction has remained unknown. Using hydrogen- deuterium exchange mass spectrometry, we map CIM1 binding to a hydrophobic groove within CNOT1 residues 800-999. Unexpectedly, this groove coincides with the tristetraprolin (TTP)-binding pocket. CIM1 and the C-terminal TTP peptide engage this surface through a shared RL(P/{zeta})X{Omega} sequence pattern despite lacking overall homology, suggesting a convergently evolved short linear motif (SLiM). We further show that the GW182 silencing domain (GW182 SD) and TTP compete for CNOT1 binding using orthogonal in vitro assays, including a reconstituted liquid-liquid phase separation system in which GW182 SD acts as a scaffold and recruits CNOT1 as a client through specific binding. These findings define a shared CNOT1 recognition site and reveal SLiM-mediated competition as a molecular principle governing CCR4-NOT engagement, with consequences for GW182-driven silencing condensate assembly in vitro. SignificanceGW182 silencing domain binds the tristetraprolin pocket of CNOT1 and recruits it into multiprotein condensates, providing a biophysical framework for coordinated miRNA- and ARE-mediated gene expression regulation.

biophysics↗

bioRxiv2025

A closely related pair of superoxide dismutase isozymes from Staphylococcus aureus show distinct stabilities and proton-exchange dynamics

Changes in biochemical properties, caused by iterative mutations in amino acid sequence, underlie the alterations in protein function over time that underpin the evolutionary process. An example is the switching of an enzymes reliance from one essential metal to an alternative as their catalytic cofactor. We previously described such a neofunctionalisation in Staphylococcus aureus, which altered a superoxide dismutase (SOD) enzyme from being an ancestral manganese-dependent (MnSOD) into an extant isozyme that can equally utilise either manganese or iron, termed cambialism (camSOD). Yet its unclear whether camSOD emergence involved selection solely for cofactor flexibility or whether other biochemical properties also diverged during neofunctionalisation. Here, we have investigated an independent biochemical property of the S. aureus SODs, their structural stability. We demonstrate that the neofunctionalised camSOD exhibits increased stability relative to the ancestral MnSOD. S. aureus camSOD is more resistant to both chemical and thermal unfolding in vitro. Crucially, while both isozymes possess a stable core at the heart of their fold, consisting of regions of the protein localised around the metal cofactor that resist hydrogen-deuterium exchange when exposed to isotopically labelled solvent, this core is larger and more exchange-resistant in camSOD than MnSOD. Thus, during the recent divergence of this SOD pair, two distinct biochemical properties have undergone substantial and rapid evolutionary change. This study paves the way for investigations of the structural and functional relationship between these properties, a SODs metal-preference and stability, and of how these properties were concomitantly selected during neofunctionalisation in the S. aureus lineage.

biochemistry↗

bioRxiv2025

Zika virus capsid protein C (ZIKV-C) interactors network mapped by proteomic analysis of human neural stem cells expressing FLAG-tagged C protein.

Zika virus is a teratogenic pathogen belonging to the Flaviviridae family. It possesses the ability to penetrate the placenta and affect the brain development of a fetus, resulting in microcephaly and functional impairments. Mechanisms of this neurotoxicity are still unclear, but capsid proteins of Zika and related viruses are known to exert apoptotic effect in different types of cells, including neurons. To explore the pathways affected by the presence of ZIKV-C, we have performed MS-based interactomic experiment in human neural stem cells and managed to identify 149 putative interactors. Our results indicate that the nucleus (especially the nucleolus) and the mitochondria are the main sites of interaction of protein C with host proteins. A number of the proteins we identified have significant links to diseases of the nervous system, including neurodevelopmental diseases. Furthermore, for the first time, we have identified MAM-domain containing glycosylphosphatidylinositol anchor protein 1, T-complex protein 1 subunit beta, lysine-tRNA ligase, calumenin as particularly abundant ZIKV protein C interactors. Data are available via ProteomeXchange with identifier PXD064412.

molecular biology↗

bioRxiv2025

The molecular properties of the bHLH TCF4 protein as an intrinsically disordered hub transcription factor

1.BackgroundTranscription factor 4 (TCF4) is a member of the basic helix-loop-helix (bHLH) family of transcription factors and guides proper embryogenesis, particularly neurogenesis, myogenesis, heart development and hematopoiesis. bHLH proteins exhibit variations in length, expression patterns and the presence of defined motifs. The interaction of TCF4 with DNA is dependent on the presence of a conserved bHLH domain, particularly the presence of a basic (b) motif. Most mutations in the Tcf4 gene are either associated with the development of serious nervous system disorders, such as Pitt-Hopkins syndrome or schizophrenia, or are lethal. Although TCF4 is essential for the proper development and function of the human body, apart from the isolated bHLH domain, there is a lack of fundamental knowledge about the structure of TCF4. MethodsRecombinant full-length TCF4 was expressed in E. coli cells and purified using chromatographic techniques. To determine the conformation of the polypeptide chain of TCF4, we performed in vitro analysis using hydrogen/deuterium exchange mass spectrometry (HDX-MS). We then determined the dissociation constant (KD) of the TCF4:DNA complex using independent methods, including fluorescence polarization (FP), electrophoretic mobility shift assay (EMSA), and fluorescence correlation spectroscopy (FCS). Finally, we compared the properties of TCF4 in its apo and holo form in relation to the changes of the conformation of the polypeptide chain (HDX-MS), hydrodynamic properties (e.g., sedimentation-velocity analytical ultracentrifugation; SV-AUC), and stability (thermal shift, circular dichroism; CD). ResultsIn this study, we demonstrate the molecular characteristics of full-length TCF4, the dimer of which is one of the largest intrinsically disordered proteins (IDPs) described to date. According to our findings, the structure of TCF4 is extensively disordered. Only the bHLH domain, which comprises 10% of the polypeptide chain, exhibits a stable fold. Strikingly, Ephrussi-box (E-box) binding via the bHLH domain has no significant effect on the disordered nature of TCF4, but it does influence the stability of TCF4. ConclusionsWe suggest that bHLH plays the role of an anchor localizing TCF4 to specific gene sequences. The dual nature of the TCF4 structure, as well as the fact that the intrinsically disordered regions (IDRs) represents most of the protein sequence, suggests that TCF4 may act as a hub transcription factor regulating the expression of specific genes through the interaction of IDRs with gene-specific partners.

molecular biology↗

bioRxiv2024

Integrated proteome and lipidome analyses place OCIAD1 at mitochondria-peroxisome intersection balancing lipid metabolism

OCIAD1 (Ovarian Cancer Immunoreactive Antigen Domain Containing 1) is a membrane protein largely localized to mitochondria, however, its function in health or disease is not well understood. To comprehensively characterize the molecular changes upon lack of OCIAD1, we used mass spectrometry to study the mitochondrial and cellular proteome and lipidome. We find extensive lipidome rearrangement in OCIAD1 KO cells, characterized by two main phenotypes of decreased ether phospholipids and decreased phospholipids with an odd number of carbons. The lipidomic changes suggest alterations in peroxisomal lipid metabolism. At the same time, proteins responsible for mitochondrial fatty acid {beta} oxidation are significantly increased. Together with a global loss in peroxisomal proteins and a meta-analysis of proximity labeling data, this gives a function to the previously observed partial localization of OCIAD1 to peroxisomes. We suggest a role for OCIAD1 in balancing mitochondrial and peroxisomal lipid metabolism, and a direct impact on the key enzymes FAR1 and ACBD3. Summary StatementLipidomics and proteomics of mitochondrial fractions and whole cells lacking the membrane protein OCIAD1 suggest a role as a dually localized protein balancing mitochondrial and peroxisomal lipid metabolism.

cell biology↗

bioRxiv2023

Phosphorylation Promotes Liquid-Liquid Phase Separation of GRP8 and Its Assembly into Stress Granules Upon Salinity Stress in Arabidopsis

Drought and salinity are major environmental stresses affecting plant development and growth. SNF1-related protein kinases type 2 (SnRK2s) are key regulators of the plant responses to water deficit and salt stress. Here, we show that Arabidopsis thaliana Glycine-Rich RNA-Binding Protein 8 (GRP8) is a target of abscisic acid (ABA)-non-activated SnRK2s and negatively regulates root growth and seed germination under salt stress. In response to salinity, GRP8 assembles into stress granules (SGs). We show that in addition to the GRP8 C-terminal glycine-rich intrinsically disordered region (IRD), the N-terminal RNA recognition motif (RRM) plays a key role in this process. Phosphorylation of S27 in the RRM by SnRK2s significantly affects the structural dynamics of GRP8, facilitates its dimerization and subsequent liquid-liquid phase separation. Thus, we show that in addition to the known role of IDRs in recruitment into SGs, the RRM plays a decisive role.

plant biology↗

bioRxiv2023

In vitro methylation of the U7 snRNP subunits Lsm11 and SmE by the PRMT5/MEP50/pICln methylosome

U7 snRNP is a multi-subunit endonuclease required for 3 end processing of metazoan replication-dependent histone pre-mRNAs. In contrast to the spliceosomal snRNPs, U7 snRNP lacks the Sm subunits D1 and D2 and instead contains two related proteins, Lsm10 and Lsm11. The remaining five subunits of the U7 heptameric Sm ring, SmE, F, G, B and D3, are shared with the spliceosomal snRNPs. The pathway that assembles the unique ring of U7 snRNP is unknown. Here, we show that a heterodimer of Lsm10 and Lsm11 tightly interacts with the methylosome, a complex of the arginine methyltransferase PRMT5, MEP50 and pICln known to methylate arginines in the C-terminal regions of the Sm proteins B, D1 and D3 during the spliceosomal Sm ring assembly. Both biochemical and Cryo-EM structural studies demonstrate that the interaction is mediated by PRMT5, which binds and methylates two arginine residues in the N-terminal region of Lsm11. Surprisingly, PRMT5 also methylates an N-terminal arginine in SmE, a subunit that does not undergo this type of modification during the biogenesis of the spliceosomal snRNPs. An intriguing possibility is that the unique methylation pattern of Lsm11 and SmE plays a vital role in the assembly of the U7 snRNP.

biochemistry↗

bioRxiv2022

Keratin 8 is a scaffolding and regulatory protein of ERAD complexes

Early recognition and enhanced degradation of misfolded proteins by the endoplasmic reticulum (ER) quality control and ER-associated degradation (ERAD) cause defective protein secretion and membrane targeting, as exemplified for Z-alpha 1 antitrypsin (Z-A1AT), responsible for alpha-1-antitrypsin deficiency (A1ATD) and F508del-CFTR (cystic fibrosis transmembrane conductance regulator) responsible for cystic fibrosis (CF). Prompted by our previous observation that decreasing Keratin 8 (K8) expression increased trafficking of F508del-CFTR to the plasma membrane, we investigated whether K8 impacts trafficking of soluble misfolded Z-A1AT protein. The subsequent goal of this study was to elucidate the mechanism underlying the K8-dependent regulation of protein trafficking, focusing on the ERAD pathway. The results show that diminishing K8 concentration in HeLa cells enhances secretion of both Z-A1AT and wild type (WT) A1AT with a 13-fold and 4-fold increase, respectively. K8 down-regulation triggers ER failure and cellular apoptosis when ER stress is jointly elicited by conditional expression of the s heavy chains, as previously shown for Hrd1 knock-out. Simultaneous K8 silencing and Hrd1 knock-out did not show any synergistic effect, consistent with K8 acting in the Hrd1-governed ERAD step. Fractionation experiments reveal that K8 is recruited to ERAD complexes containing Derlin2, Sel1 and Hrd1 proteins upon expression of Z/WT-A1AT and F508del-CFTR. Treatment of the cells with c407, a small molecule inhibiting K8 interaction, decreases K8 and Derlin2 recruitment to high-order ERAD complexes. This was associated with increased Z-A1AT secretion in both HeLa and Z-homozygous A1ATD patients respiratory cells. Overall, we provide evidence that K8 acts as an ERAD modulator. It may play a scaffolding protein role for early-stage ERAD complexes, regulating Hrd1-governed retrotranslocation initiation/ubiquitination processes. Targeting K8-containing ERAD complexes is an attractive strategy for the pharmacotherapy of A1ATD.

cell biology↗

bioRxiv2021

Heterotypic Assembly Mechanism Regulates CHIP E3 Ligase Activity

The E3 ubiquitin ligases CHIP/CHN-1 and UFD-2 team up to accelerate ubiquitin chain formation. However, it remained largely unclear how the high processivity of this E3 set is achieved. Here we studied the molecular mechanism and function of the CHN-1/UFD-2 complex in Caenorhabditis elegans. Our data show that UFD-2 binding promotes the cooperation between CHN-1 and ubiquitin-conjugating E2 enzymes by stabilizing the CHN-1 U-box dimer. The HSP-1 chaperone outcompetes UFD-2 for CHN-1 binding and promotes the auto-inhibited CHN-1 state by acting on the conserved position of the U-box domain. The interaction with UFD-2 enables CHN-1 to efficiently ubiquitinate S-Adenosylhomocysteinase (AHCY-1), an enzyme crucial for lipid metabolism. Our results define the molecular mechanism underlying the synergistic cooperation of CHN-1 and UFD-2 in substrate ubiquitylation. HIGHLIGHTSO_LIE3 ligase UFD-2 stimulates ubiquitylation activity of CHIP/CHN-1 C_LIO_LIUFD-2 binding promotes dimerization of CHIP/CHN-1 U-box domains and utilization of E2 enzymes C_LIO_LIHSP70/HSP-1 by latching the U-box and TPR domains stabilizes the autoinhibitory state of CHIP/CHN-1, limiting interactions with E2s and UFD-2 C_LIO_LIAssembly with UFD-2 enables CHIP/CHN-1 to regulate lipid metabolism by ubiquitylation of S-Adenosylhomocysteinase C_LI

molecular biology↗

bioRxiv2021

ApoE4 disrupts interaction of sortilin with fatty acid-binding protein 7 essential to promote lipid signaling

Sortilin is a receptor for neuronal uptake of apolipoprotein E. Sortilin-dependent uptake of lipidated apoE promotes conversion of polyunsaturated fatty acids (PUFA) into neuromodulators that induce anti-inflammatory gene expression in the brain. This neuroprotective pathway works with apoE3 but is lost with apoE4, the main risk factor for Alzheimers disease (AD). Here, we elucidated steps in cellular handling of lipids through sortilin, and why they are disrupted by apoE4. Combining unbiased proteome screens with analyses in mouse models, we uncover interaction of sortilin with fatty acid-binding protein (FABP) 7, the intracellular carrier for PUFA in the brain. In the presence of apoE3, sortilin promotes functional expression of FABP7 and its ability to elicit lipid-dependent gene transcription. By contrast, apoE4 binding blocks sortilin sorting, causing catabolism of FABP7 and impairing lipid signaling. Reduced FABP7 levels in the brain of AD patients expressing apoE4 substantiate the relevance of these interactions for neuronal lipid homeostasis. Taken together, we document interaction of sortilin with mediators of extracellular and intracellular lipid transport that provides a mechanistic explanation for loss of a neuroprotective lipid metabolism in AD. SUMMARY STATEMENTLipids are central to brain health and defects in brain lipid homeostasis are causal to neurodegenerative processes in Alzheimers disease. Here, we uncovered how the neuronal lipoprotein receptor sortilin interacts with apoE and FABP7, the carriers for extra- and intracellular transport of lipids in the brain, respectively. We show that this interaction enables lipids to control gene transcription via nuclear receptors; and why this presumed neuroprotective lipid action is disturbed in humans who carry the {varepsilon}4 variant of apoE, the most important risk factor for sporadic Alzheimers disease.

cell biology↗

bioRxiv2019

Biochemical, Biophysical, and Functional Analyses of Two Isoforms of the SnRK2 Inhibitor AtSCS

SNF1-related protein kinases 2 (SnRK2s) are key signaling elements that regulate abscisic acid (ABA)-dependent plant development and responses to environmental stresses. Our previous data showed that the SnRK2-interacting Calcium Sensor (SCS) is an inhibitor of SnRK2 activity. In Arabidopsis thaliana, the use of alternative transcription start sites located within AtSCS gene results in two in-frame transcripts and subsequently two proteins, which differ only by the sequence position of the N-terminus. We described the longer AtSCS-A earlier, and now we describe the shorter AtSCS-B and compare both isoforms. The two forms differ significantly in their expression profiles in plant organs and in response to environmental stresses, in calcium binding properties, and conformational dynamics in the presence and absence of Ca2+. The results show that only AtSCS-A has the features of a calcium sensor. Both forms inhibit SnRK2 activity, but differ with respect to calcium dependence, as AtSCS-A requires calcium for inhibition, while AtSCS-B does not. Analysis of Arabidopsis plants stably expressing 35S::AtSCS-A-c-myc or 35S::AtSCS-B-c-myc in the scs-1 knockout mutant revealed that in planta both forms are negative regulators of the SnRK2 activity induced in response to ABA and regulate plant defense against water deficit. Moreover, the data present biochemical, biophysical, and functional properties of EF-hand-like motifs in plant proteins.\n\nOne sentence SummaryTwo isoforms of SnRK2-interacting calcium sensor are expressed in Arabidopsis; they differ in calcium binding properties, but both of them inhibit SnRK2s and subsequently fine tune ABA signaling.

plant biology↗

bioRxiv2019

Mitochondria biogenesis in the synapse is supported by local translation

Synapses are the regions of the neuron that enable the transmission and propagation of action potentials on the cost of high energy consumption and elevated demand for mitochondrial ATP production. The rapid changes in local energetic requirements at dendritic spines imply the role of mitochondria in the maintenance of their homeostasis. Using global proteomic analysis supported with complementary experimental approaches, we show that an important pool of mitochondrial proteins is locally produced at the synapse indicating that mitochondrial biogenesis takes place locally to maintain the pool of functional mitochondria in axons and dendrites. Furthermore, we show that stimulation of synaptoneurosomes induces the local synthesis of mitochondrial proteins that are transported to the mitochondria and incorporated into the protein supercomplexes of the respiratory chain.\n\nSynopsis\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=187 SRC=\"FIGDIR/small/789164v1_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (47K):\norg.highwire.dtl.DTLVardef@1813d6forg.highwire.dtl.DTLVardef@1e85cd3org.highwire.dtl.DTLVardef@2656f7org.highwire.dtl.DTLVardef@1177d7d_HPS_FORMAT_FIGEXP M_FIG Mitochondria biogenesis in the synapse is supported by local translation\n\nC_FIG O_LIMitochondrial proteins represent a large pool of proteins synthesized locally at the synapse\nC_LIO_LINewly synthesized mitochondrial proteins are imported into the mitochondria and incorporated into the respiratory chain complexes\nC_LIO_LIUncoupling of mitochondria and blocking mitochondrial import inhibits incorporation of de novo synthesized proteins into the mitochondrial protein complexes\nC_LI

neuroscience↗

bioRxiv2018

Inhibition of proteasomal degradation rescues a pathogenic variant of mitochondrial Respiratory chain assembly 1 factor

Nuclear and mitochondrial genome mutations lead to various mitochondrial diseases, many of which affect the mitochondrial respiratory chain. The proteome of the intermembrane space (IMS) of mitochondria consists of several important assembly factors that participate in the biogenesis of mitochondrial respiratory chain complexes. The present study comprehensively analyzed a recently identified IMS protein, RESpiratory chain Assembly 1 (RESA1) factor, or cytochrome c oxidase assembly factor 7 (COA7) that is associated with a rare form of mitochondrial leukoencephalopathy and complex IV deficiency. We found that RESA1 requires the mitochondrial IMS import and assembly (MIA) pathway for efficient accumulation in the IMS. We also found that pathogenic mutant versions of RESA1 are imported slower than the wild type protein, and mislocalized mutant proteins are degraded in the cytosol by proteasome machinery. Interestingly, proteasome inhibition rescued both the mitochondrial localization of mutant RESA1 and complex IV activity in patient-derived fibroblasts. We propose that proteasome inhibition is a novel therapeutic approach for a broad range of mitochondrial pathologies that are associated with the excessive degradation of mitochondrial proteins that is caused by genetic mutations or biogenesis defects.

biochemistry↗