Biology subjects

Mattevi, A.

Publications and source records attributed to Mattevi, A..

9 recordsLinked to original sources

bioRxiv2026

L-2-hydroxyglutarate recycling is linked to coenzyme Q biosynthesis

The mitochondrial COQ metabolon catalyzes the late stages of the biosynthesis of coenzyme Q, an essential and ubiquitous cofactor. Here, by integrating coevolution, coexpression, colocalization and domain-fusion analyses, we identify L-2-hydroxyglutarate dehydrogenase (L2HGDH) as an integral component of this assembly. By acting in physical proximity to the COQ metabolon, L2HGDH sustains coenzyme Q production by maintaining the biosynthetic intermediates in their catalytically-active reduced state. Consistently, analysis of fibroblasts and urine samples from patients with primary coenzyme Q deficiency displayed marked accumulation of L-2-hydroxyglutarate. Cryo-electron microscopy reveals that L2HGDH forms a stable complex with COQ3 and COQ6, defining a heterotrimeric assembly that organizes catalytic sites on a shared membrane-facing surface thereby enabling localized quinone reduction. Together, these findings identify L2HGDH as a previously unrecognized component of the COQ metabolon, establish a direct link between central carbon metabolism and coenzyme Q biosynthesis, and expand the functional roles of metabolons in coordinating metabolic flux across distinct pathways.

biochemistry↗

bioRxiv2026

COQ8 chaperones coenzyme Q lipid intermediates through ATP-driven structural gating

Coenzyme Q biosynthesis requires the atypical kinase-like COQ8 proteins, whose ATPase activity streamlines the membrane-associated COQ metabolon, yet its molecular mechanism has remained unclear. Taking advantage of the tetrapod ancestral coenzyme Q biosynthetic machinery and liposomes mimicking the inner mitochondrial membrane, we show that COQ8A and COQ8B act as a streamlining factor for the coenzyme Q metabolon by engaging in loose protein-protein interactions and delivering insoluble biosynthetic intermediates. Structural bioinformatics and pathological-variant-driven mutagenesis reveal that coenzyme Q intermediates are recognized via their head-groups in a pocket whose access is gated by long-range conformational changes controlled by ATP hydrolysis. Finally, it is demonstrated that excess coenzyme Q suppresses binding of early-stage intermediates and thereby abolishes the streamlining effect of COQ8 on the metabolon. Together, these results support a model in which COQ8 functions as a biochemical coenzyme Q sensor that tunes coenzyme Q biosynthesis by coupling ATPase-driven intermediate chaperoning with feedback regulation by the final product. TeaserCOQ8 enhances coenzyme Q metabolic flux via ATP hydrolysis-driven chaperoning of biosynthetic intermediates.

biochemistry↗

bioRxiv2026

The glycine-arginine-rich motif of 53BP1 modulates RNA interactions necessary for its liquid-liquid phase separation during DNA Damage Response

The DNA damage response relies on the rapid assembly of repair factors into foci with properties of liquid-liquid phase separation, driven by de novo transcription of damage-induced RNAs. 53BP1 is a key component of these condensates, yet the molecular determinants driving this process remain unknown. Here, through computational, structural and in vitro approaches, we identify the oligomerization domain of 53BP1 and its glycine-arginine-rich (GAR) motif as crucial for RNA interactions and phase separation. Biophysical characterization reveals that 53BP1-RNA condensates can progressively mature into a more stable state, and that GAR mutants display aberrant material properties. Using a cellular model of telomere fusion events, we demonstrate that the GAR motif is essential for 53BP1-mediated DNA repair, which depends on the combined contributions of RNA binding and appropriate condensate biophysical properties. Therefore, RNA-driven 53BP1 condensation is functionally required to maintain genome integrity.

biophysics↗

bioRxiv2025

Characterization of the Mitomycin C Resistance Protein McrA

McrA from Streptomyces lavendulae is a flavin-dependent enzyme thought to provide self-resistance against the DNA-alkylating antibiotic mitomycin C (MMC). McrA belongs to the berberine bridge enzyme (BBE)-like subfamily of oxidases and catalyzes the oxidation of reduced MMC converting it back into the inactive prodrug form, thereby preventing rearrangement into the reactive quinone methide intermediate. Here we demonstrate the first crystal structure of McrA, allowing us to identify key residues involved in retaining MMC in the active site. Biochemical characterization studies such as pre-steady state kinetics verified McrA oxidase activity, while binding studies demonstrated its ability to recognize oxidized MMC.

biochemistry↗

bioRxiv2025

Complete Enzyme Clustering Enhances Coenzyme Q Biosynthesisvia Substrate Channeling

Metabolons - transient assemblies of sequential metabolic enzymes - facilitate the reactions of multi-step metabolic pathways, yet, how they mechanistically bolster metabolic flux remains unknown. Here, we investigate the molecular determinants of metabolon formation in coenzyme Q (CoQ) biosynthesis using coarse-grained molecular dynamics simulations and biochemical experiments. We show that the COQ metabolon forms at the critical region of a phase transition, where both metabolon clustering and metabolic flux exhibit coordinated sigmoidal responses to changes in protein-protein interaction strength. These complete metabolons enable substrate channeling between sequential enzymes, leading to a crucial enhancement of CoQ production efficiency. Selectively disrupting protein-protein interactions and randomly shuffling the interaction network demonstrate that protein-proximity rather than fine structure of the metabolon clusters is imperative for substrate channeling. Grounded in both experiment and simulation, these findings provide a framework for understanding the organization and function of metabolons across diverse metabolic pathways.

biophysics↗

bioRxiv2025

LSD1 serine 166 is a phosphorylation switch for chromatinlandscaping, gene activation, and tissue remodeling

LSD1 is a histone 3 (H3) demethylase that can either repress or activate gene expression. We discover here that the so far enigmatic balance between these two activities in non-hormonal cancer cells is regulated by phosphorylation of serine 166 (S166) on LSD1. SET-mediated Protein Phosphatase 2A (PP2A) inhibition in KRAS mutant cells promotes S166 phosphorylation. Endogenous LSD1 S166 alanine mutant (S166A) cells display H3 lysine 9 demethylation and acetylation, euchromatin, and gene activation. Mechanistically this is explained by the impaired interaction of S166A mutant LSD1 with repressor proteins SNAI2 and MYBP1. Functionally LSD1 S166A mutant cells display augmented beta1 integrin activity and stress fiber formation, and the mutant xenograft tumors have altered tumor microenvironment associated with increased macrophage recruitment. Collectively, PP2A-regulated S166 of LSD1 is a phosphorylation switch for epigenetic gene activation in non-hormonal cancer cells. Conceptually we demonstrate how dephosphorylation of one amino acid on a non-histone protein shapes chromatin landscape in cancer cells, and modify tumor stroma, and immune cell content. Highlights* Mechanism for gene activation by LSD1 in non-hormonal cancers * Single phosphorylation switch in a non-histone protein controls epigenetic landscape * Epigenetic protein phosphorylation in cancer cells shapes tumour immune microenvironment * Novel function for Protein Phosphatase 2A (PP2A) in epigenome regulation via LSD1 Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=185 SRC="FIGDIR/small/653937v1_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@19548b3org.highwire.dtl.DTLVardef@1d7fd4dorg.highwire.dtl.DTLVardef@13707b3org.highwire.dtl.DTLVardef@1da7b71_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Asymmetric Engagement of Dimeric CRL3KBTBD4 by the Molecular Glue UM171 Licenses Degradation of HDAC1/2 Complexes

UM171 is a potent small molecule agonist of ex vivo human hematopoietic stem cell (HSC) self-renewal1, a process that is tightly controlled by epigenetic regulation. By co-opting KBTBD4, a substrate receptor of the CULLIN3-RING E3 ubiquitin ligase complex, UM171 promotes the degradation of members of the CoREST transcriptional corepressor complex, thereby limiting HSC attrition2,3. However, the direct target and mechanism of action of UM171 remain unclear. Here, we reveal that UM171 acts as a molecular glue to induce high-affinity interactions between KBTBD4 and HDAC1 to promote the degradation of select HDAC1/2 corepressor complexes. Through proteomics and chemical inhibitor studies, we discover that the principal target of UM171 is HDAC1/2. Cryo-electron microscopy (cryo-EM) analysis of dimeric KBTBD4 bound to UM171 and the LSD1-HDAC1-CoREST complex unveils an unexpected asymmetric assembly, in which a single UM171 molecule enables a pair of KBTBD4 KELCH-repeat propeller domains to recruit HDAC1 by clamping on its catalytic domain. One of the KBTBD4 propellers partially masks the rim of the HDAC1 active site pocket, which is exploited by UM171 to extend the E3-neo-substrate interface. The other propeller cooperatively strengthens HDAC1 binding via a separate and distinct interface. The overall neomorphic interaction is further buttressed by an endogenous cofactor of HDAC1-CoREST, inositol hexakisphosphate, which makes direct contacts with KBTBD4 and acts as a second molecular glue. The functional relevance of the quaternary complex interaction surfaces defined by cryo-EM is demonstrated by in situ base editor scanning of KBTBD4 and HDAC1. By delineating the direct target of UM171 and its mechanism of action, our results reveal how the cooperativity offered by a large dimeric CRL E3 family can be leveraged by a small molecule degrader and establish for the first time a dual molecular glue paradigm.

molecular biology↗

bioRxiv2024

LSD1 inhibition suppresses ASCL1 and de-represses YAP1 to drive potent activity against neuroendocrine prostate cancer

Progression to lethal metastatic castration-resistant prostate cancer (mCRPC) is driven in part by epigenetic modulators such as LSD1 (KDM1A), a lysine-specific demethylase. Yet, mCRPC is increasingly recognized as a highly heterogeneous disease whose classification into subtypes is defined by the extent of androgen receptor (AR) and/or neuroendocrine (NE) characteristics. Meanwhile, the role of LSD1 in driving the different subtypes of mCRPC has remained unclear. Here, we assess the necessity of LSD1 in driving progression of mCRPC subtypes including AR+/NE- (ARPC), AR-/NE+ (NEPC), AR+/NE+ (amphicrine; AMPC), and AR-/NE- (double-negative; DNPC) through the use of LSD1 inhibitors in clinical development. LSD1 inhibition (LSD1i) was observed to be highly effective in restricting growth of NEPC, and efficacy was associated with TP53 loss-of-function. Mice bearing NEPC patient-derived xenografts treated with the LSD1 inhibitors, bomedemstat (MK-3543) or iadademstat (ORY-1001), exhibited suppression of the NE transcriptional profile, including ASCL1. LSD1i also induced expression and activity of YAP1, a non-NE transcription factor canonically silenced in NEPC (YAPOFF cancer), thereby switching NEPC from a YAPOFF to a YAPON cancer class. Therapeutically-induced YAPON NEPC tumors exhibited cell cycle arrest and repression of proliferative transcriptional programs. Importantly, the LSD1i-mediated YAPON state induced sensitivity to an inhibitor of YAP/TEAD function, IAG933, which extended antitumor efficacy against NEPC. Altogether, these findings indicate that patients diagnosed with NEPC may obtain greater relative benefit from LSD1-targeted therapies compared to those with other mCRPC subtypes and that dual inhibition of LSD1 and YAP/TEAD function demonstrates a promising treatment strategy potentially extending to other YAPOFF cancers. SignificanceAcross prostate cancer subtypes, NEPC is exceptionally responsive to LSD1 inhibition and this response is enhanced in combination with a YAP/TEAD disruptor which may improve patient selection and outcomes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=171 HEIGHT=200 SRC="FIGDIR/small/576106v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@77332eorg.highwire.dtl.DTLVardef@1c127d0org.highwire.dtl.DTLVardef@1cec77org.highwire.dtl.DTLVardef@e87ed7_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2023

The catalytic-independent function of LSD1 modulates the epigenetic landscape of mouse embryonic stem cells

Lysine-specific histone demethylase 1 (LSD1), which demethylates mono- or di-methylated histone H3 on lysine 4 (H3K4me1/2), is essential for early embryogenesis and development. Here we show that LSD1 is dispensable for embryonic stem cell (ESC) self-renewal but is required for ESC growth and differentiation. Reexpression of a catalytically-dead LSD1 (LSD1MUT) recovers the proliferation capability of ESCs, yet the enzymatic activity of LSD1 is essential to ensure proper differentiation. Indeed, a gain of H3K4me1 in Lsd1 knockout (KO) ESCs does not lead to major changes in global gene expression programs related to stemness. However, ablation of LSD1 but not LSD1MUT results in decreased DNMT1 and UHRF1 proteins coupled to global hypomethylation. We show that both LSD1 and LSD1MUT control protein stability of UHRF1 and DNMT1 through interaction with the ubiquitin-specific peptidase 7 (USP7) and, consequently, inhibiting DNMT1 and UHRF1 ubiquitylation. Our studies elucidate for the first time a novel mechanism by which the scaffolding function of LSD1 controls DNA methylation in ESCs.

molecular biology↗