bims-proteo Biomed News
on Proteostasis
Issue of 2024–02–11
fifty-two papers selected by
Eric Chevet, INSERM
  1. Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.
  2. RACK1 and IRE1 participate in the translational quality control of amyloid precursor protein in Drosophila models of Alzheimer's disease.
  3. Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration.
  4. FicD Sensitizes Cellular Response to Glucose Fluctuations in Mouse Embryonic Fibroblasts.
  5. Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore.
  6. The cyclimids: Degron-inspired cereblon binders for targeted protein degradation.
  7. Highly specific intracellular ubiquitination of a small molecule.
  8. A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting.
  9. RABC1, an Arabidopsis RAB18 regulates binding and subsequent detachment of autophagosomes from the ER in autophagy.
  10. The GATOR2 complex maintains lysosomal-autophagic function by inhibiting the protein degradation of MiT/TFEs.
  11. Role of J-domain proteins in yeast physiology and protein quality control.
  12. Zn2+-dependent functional switching of ERp18, an ER-resident thioredoxin-like protein.
  13. Paraoxonase-like APMAP maintains endoplasmic reticulum-associated lipid and lipoprotein homeostasis.
  14. Rab32 family proteins regulate autophagosomal components recycling.
  15. Translation regulation in response to stress.
  16. Allosteric Hsp70 Modulator YM-1 Induces Degradation of BRD4.
  17. Attenuation of HOIL-1L ligase activity promotes systemic autoimmune disorders by augmenting linear ubiquitin signaling.
  18. Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.
  19. Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases.
  20. Visualizing chaperone-mediated multistep assembly of the human 20S proteasome.
  21. J-domain proteins: From molecular mechanisms to diseases.
  22. Multiple genes core to ERAD, macro-autophagy and lysosomal degradation pathways participate in the proteostasis response in α1-antitrypsin deficiency.
  23. A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy.
  24. ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons.
  25. Direct binding to sterols accelerates endoplasmic reticulum-associated degradation of HMG CoA reductase.
  26. Translation selectively destroys non-functional transcription complexes.
  27. Stress Biology: Complexity and Multifariousness in Health and Disease.
  28. A compact regulatory RNA element in mouse Hsp70 mRNA.
  29. RNF220-mediated K63-linked polyubiquitination stabilizes Olig proteins during oligodendroglial development and myelination.
  30. Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes.
  31. PPTC7 limits mitophagy through proximal and dynamic interactions with BNIP3 and NIX.
  32. Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors.
  33. Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3KBTBD2.
  34. Patient derived model of UBA5- associated encephalopathy identifies defects in neurodevelopment and highlights potential therapies.
  35. APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size.
  36. NEDD4L intramolecular Interactions regulate its auto- and substrate NaV1.5 ubiquitination.
  37. Knockout of PA200 improves proteasomal degradation and myelination in a proteotoxic neuropathy.
  38. WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration.
  39. Characterization of ATG8-family protein phosphorylation by Phos-tag gel for autophagy study.
  40. Ataxin-2 sequesters Raptor into aggregates and impairs cellular mTORC1 signaling.
  41. Regulation of proteostasis and innate immunity via mitochondria-nuclear communication.
  42. Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal.
  43. Characterizing ATP processing by the AAA+ protein p97 at the atomic level.
  44. Discovery of Novel PROTAC Degraders of p300/CBP as Potential Therapeutics for Hepatocellular Carcinoma.
  45. Contact-FP: A Dimerization-Dependent Fluorescent Protein Toolkit for Visualizing Membrane Contact Site Dynamics.
  46. Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer.
  47. Mitochondrial outer membrane integrity regulates a ubiquitin-dependent and NF-κB-mediated inflammatory response.
  48. Deficient tRNA posttranscription modification dysregulated the mitochondrial quality controls and apoptosis.
  49. Integrated Stress Response Potentiates Ponatinib-Induced Cardiotoxicity.
  50. ISR inhibition reverses pancreatic β-cell failure in Wolfram syndrome models.
  51. Tracing back primed resistance in cancer via sister cells.
  52. Senescent cells and macrophages cooperate through a multi-kinase signaling network to promote intestinal transformation in Drosophila.
  1. Nat Struct Mol Biol. 2024 Feb 07.
    Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases.
    Joanna Liwocha, Jerry Li, Nicholas Purser, Chutima Rattanasopa, Samuel Maiwald, David T Krist, Daniel C Scott, Barbara Steigenberger, J Rajan Prabu, Brenda A Schulman, Gary Kleiger.
      E3 ubiquitin ligases, in collaboration with E2 ubiquitin-conjugating enzymes, modify proteins with poly-ubiquitin chains. Cullin-RING ligase (CRL) E3s use Cdc34/UBE2R-family E2s to build Lys48-linked poly-ubiquitin chains to control an enormous swath of eukaryotic biology. Yet the molecular mechanisms underlying this exceptional linkage specificity and millisecond kinetics of poly-ubiquitylation remain unclear. Here we obtain cryogenic-electron microscopy (cryo-EM) structures that provide pertinent insight into how such poly-ubiquitin chains are forged. The CRL RING domain not only activates the E2-bound ubiquitin but also shapes the conformation of a distinctive UBE2R2 loop, positioning both the ubiquitin to be transferred and the substrate-linked acceptor ubiquitin within the active site. The structures also reveal how the ubiquitin-like protein NEDD8 uniquely activates CRLs during chain formation. NEDD8 releases the RING domain from the CRL, but unlike previous CRL-E2 structures, does not contact UBE2R2. These findings suggest how poly-ubiquitylation may be accomplished by many E2s and E3s.
    DOI:  https://doi.org/10.1038/s41594-023-01206-1
  2. J Biol Chem. 2024 Feb 02. pii: S0021-9258(24)00095-4. [Epub ahead of print] 105719
    RACK1 and IRE1 participate in the translational quality control of amyloid precursor protein in Drosophila models of Alzheimer's disease.
    Yu Li, Dongyue Liu, Xuejing Zhang, Suman Rimal, Bingwei Lu, Shuangxi Li.
      Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by dysregulation of the expression and processing of the amyloid precursor protein (APP). Protein quality control systems are dedicated to remove faulty and deleterious proteins to maintain cellular protein homeostasis (proteostasis). Identidying mechanisms underlying APP protein regulation is crucial for understanding AD pathogenesis. However, the factors and associated molecular mechanisms regulating APP protein quality control remain poorly defined. In this study, we show that mutant APP with its mitochondrial-targeting sequence ablated exhibited predominant endoplasmic reticulum (ER) distribution and led to aberrant ER morphology, deficits in locomotor activity, and shortened lifespan. We searched for regulators that could counteract the toxicity caused by the ectopic expression of this mutant APP. Genetic removal of the ribosome-associated quality control (RQC) factor RACK1 resulted in reduced levels of ectopically expressed mutant APP. By contrast, gain of RACK1 function increased mutant APP level. Additionally, overexpression of the ER stress regulator (IRE1) resulted in reduced levels of ectopically expressed mutant APP. Mechanistically, the RQC related ATPase VCP/p97 and the E3 ubiquitin ligase Hrd1 were required for the reduction of mutant APP level by IRE1. These factors also regulated the expression and toxicity of ectopically expressed wild type APP, supporting their relevance to APP biology. Our results reveal functions of RACK1 and IRE1 in regulating the quality control of APP homeostasis and mitigating its pathogenic effects, with implications for the understanding and treatment of AD.
    Keywords:  Drosophila; ER; IRE1; Proteostasis; RACK1; amyloid precursor protein (APP); ribosome-associated quality control (RQC)
    DOI:  https://doi.org/10.1016/j.jbc.2024.105719
  3. bioRxiv. 2024 Jan 25. pii: 2024.01.24.577043. [Epub ahead of print]
    Spatial proteomics of ER tubules reveals CLMN, an ER-actin tether at focal adhesions that promotes cell migration.
    Holly Merta, Tadamoto Isogai, Blessy Paul, Gaudenz Danuser, W Mike Henne.
      The endoplasmic reticulum (ER) is structurally and functionally diverse, yet how its functions are organized within morphological subdomains is incompletely understood. Utilizing TurboID-based proximity labeling and CRISPR knock-in technologies, here we map the proteomic landscape of the human ER and nuclear envelope. Spatial proteomics reveals enrichments of proteins into ER tubules, sheets, and nuclear envelope. We uncover an ER-enriched actin-binding protein, Calmin (CLMN), and define it as an ER-actin tether that localizes to focal adhesions adjacent to ER tubules. CLMN depletion perturbs focal adhesion disassembly, actin dynamics, and cell movement. Mechanistically, CLMN-depleted cells also exhibit defects in calcium signaling near ER-actin interfaces, suggesting CLMN promotes calcium signaling near adhesions to facilitate their disassembly. Collectively, we map the sub-organelle proteome landscape of the ER, identify CLMN as an ER-actin tether, and describe a non-canonical mechanism by which ER tubules engage actin to regulate cell migration.
    DOI:  https://doi.org/10.1101/2024.01.24.577043
  4. bioRxiv. 2024 Jan 23. pii: 2024.01.22.576705. [Epub ahead of print]
    FicD Sensitizes Cellular Response to Glucose Fluctuations in Mouse Embryonic Fibroblasts.
    Burak Gulen, Lisa N Kinch, Kelly A Servage, Aubrie Blevins, Nathan M Stewart, Hillery F Gray, Amanda K Casey, Kim Orth.
      During homeostasis, the endoplasmic reticulum (ER) maintains productive transmembrane and secretory protein folding that is vital for proper cellular function. The ER-resident HSP70 chaperone, BiP, plays a pivotal role in sensing ER stress to activate the unfolded protein response (UPR). BiP function is regulated by the bifunctional enzyme FicD that mediates AMPylation and deAMPylation of BiP in response to changes in ER stress. AMPylated BiP acts as a molecular rheostat to regulate UPR signaling, yet little is known about the molecular consequences of FicD loss. In this study, we investigate the role of FicD in mouse embryonic fibroblast (MEF) response to pharmacologically and metabolically induced ER stress. We find differential BiP AMPylation signatures when comparing robust chemical ER stress inducers to physiological glucose starvation stress and recovery. Wildtype MEFs respond to pharmacological ER stress by downregulating BiP AMPylation. Conversely, BiP AMPylation in wildtype MEFs increases upon metabolic stress induced by glucose starvation. Deletion of FicD results in widespread gene expression changes under baseline growth conditions. In addition, FicD null MEFs exhibit dampened UPR signaling, altered cell stress recovery response, and unconstrained protein secretion. Taken together, our findings indicate that FicD is important for tampering UPR signaling, stress recovery, and the maintenance of secretory protein homeostasis.
    Significance Statement: The chaperone BiP plays a key quality control role in the endoplasmic reticulum, the cellular location for the production, folding, and transport of secreted proteins. The enzyme FicD regulates BiP's activity through AMPylation and deAMPylation. Our study unveils the importance of FicD in regulating BiP and the unfolded protein response (UPR) during stress. We identify distinct BiP AMPylation signatures for different stressors, highlighting FicD's nuanced control. Deletion of FicD causes widespread gene expression changes, disrupts UPR signaling, alters stress recovery, and perturbs protein secretion in cells. These observations underscore the pivotal contribution of FicD for preserving secretory protein homeostasis. Our findings deepen the understanding of FicD's role in maintaining cellular resilience and open avenues for therapeutic strategies targeting UPR-associated diseases.
    DOI:  https://doi.org/10.1101/2024.01.22.576705
  5. Sci Adv. 2024 Feb 09. 10(6): eadj8027
    Three-step docking by WIPI2, ATG16L1, and ATG3 delivers LC3 to the phagophore.
    Shanlin Rao, Marvin Skulsuppaisarn, Lisa M Strong, Xuefeng Ren, Michael Lazarou, James H Hurley, Gerhard Hummer.
      The covalent attachment of ubiquitin-like LC3 proteins (microtubule-associated proteins 1A/1B light chain 3) prepares the autophagic membrane for cargo recruitment. We resolve key steps in LC3 lipidation by combining molecular dynamics simulations and experiments in vitro and in cellulo. We show how the E3-like ligaseautophagy-related 12 (ATG12)-ATG5-ATG16L1 in complex with the E2-like conjugase ATG3 docks LC3 onto the membrane in three steps by (i) the phosphatidylinositol 3-phosphate effector protein WD repeat domain phosphoinositide-interacting protein 2 (WIPI2), (ii) helix α2 of ATG16L1, and (iii) a membrane-interacting surface of ATG3. Phosphatidylethanolamine (PE) lipids concentrate in a region around the thioester bond between ATG3 and LC3, highlighting residues with a possible role in the catalytic transfer of LC3 to PE, including two conserved histidines. In a near-complete pathway from the initial membrane recruitment to the LC3 lipidation reaction, the three-step targeting of the ATG12-ATG5-ATG16L1 machinery establishes a high level of regulatory control.
    DOI:  https://doi.org/10.1126/sciadv.adj8027
  6. Cell Chem Biol. 2024 Jan 31. pii: S2451-9456(24)00039-4. [Epub ahead of print]
    The cyclimids: Degron-inspired cereblon binders for targeted protein degradation.
    Saki Ichikawa, N Connor Payne, Wenqing Xu, Chia-Fu Chang, Nandini Vallavoju, Spencer Frome, Hope A Flaxman, Ralph Mazitschek, Christina M Woo.
      Cereblon (CRBN) is an E3 ligase substrate adapter widely exploited for targeted protein degradation (TPD) strategies. However, achieving efficient and selective target degradation is a preeminent challenge with ligands that engage CRBN. Here, we report that the cyclimids, ligands derived from the C-terminal cyclic imide degrons of CRBN, exhibit distinct modes of interaction with CRBN and offer a facile approach for developing potent and selective bifunctional degraders. Quantitative TR-FRET-based characterization of 60 cyclimid degraders in binary and ternary complexes across different substrates revealed that ternary complex binding affinities correlated strongly with cellular degradation efficiency. Our studies establish the unique properties of the cyclimids as versatile warheads in TPD and a systematic biochemical approach for quantifying ternary complex formation to predict their cellular degradation activity, which together will accelerate the development of ligands that engage CRBN.
    Keywords:  CoraFluor; E3 ligase; PROTAC; TR-FRET; cereblon; cyclimids; degrader; targeted protein degradation assay; ternary complex
    DOI:  https://doi.org/10.1016/j.chembiol.2024.01.003
  7. bioRxiv. 2024 Jan 28. pii: 2024.01.26.577493. [Epub ahead of print]
    Highly specific intracellular ubiquitination of a small molecule.
    Weicheng Li, Enrique M Garcia-Rivera, Dylan C Mitchell, Joel M Chick, Micah Maetani, John M Knapp, Geoffrey M Matthews, Ryosuke Shirasaki, Ricardo de Matos Simoes, Vasanthi Viswanathan, John L Pulice, Matthew G Rees, Jennifer A Roth, Steven P Gygi, Constantine S Mitsiades, Cigall Kadoch, Stuart L Schreiber, Jonathan M L Ostrem.
      Ubiquitin is a small, highly conserved protein that acts as a posttranslational modification in eukaryotes. Ubiquitination of proteins frequently serves as a degradation signal, marking them for disposal by the proteasome. Here, we report a novel small molecule from a diversity-oriented synthesis library, BRD1732, that is directly ubiquitinated in cells, resulting in dramatic accumulation of inactive ubiquitin monomers and polyubiquitin chains causing broad inhibition of the ubiquitin-proteasome system. Ubiquitination of BRD1732 and its associated cytotoxicity are stereospecific and dependent upon two homologous E3 ubiquitin ligases, RNF19A and RNF19B. Our finding opens the possibility for indirect ubiquitination of a target through a ubiquitinated bifunctional small molecule, and more broadly raises the potential for posttranslational modification in trans .
    DOI:  https://doi.org/10.1101/2024.01.26.577493
  8. J Cell Biol. 2024 Apr 01. pii: e202307094. [Epub ahead of print]223(4):
    A role for Vps13-mediated lipid transfer at the ER-endosome contact site in ESCRT-mediated sorting.
    Sho W Suzuki, Matthew West, Yichen Zhang, Jenny S Fan, Rachel T Roberts, Greg Odorizzi, Scott D Emr.
      Endosomes are specialized organelles that function in the secretory and endocytic protein sorting pathways. Endocytosed cell surface receptors and transporters destined for lysosomal degradation are sorted into intraluminal vesicles (ILVs) at endosomes by endosomal sorting complexes required for transport (ESCRT) proteins. The endosomes (multivesicular bodies, MVBs) then fuse with the lysosome. During endosomal maturation, the number of ILVs increases, but the size of endosomes does not decrease despite the consumption of the limiting membrane during ILV formation. Vesicle-mediated trafficking is thought to provide lipids to support MVB biogenesis. However, we have uncovered an unexpected contribution of a large bridge-like lipid transfer protein, Vps13, in this process. Here, we reveal that Vps13-mediated lipid transfer at ER-endosome contact sites is required for the ESCRT pathway. We propose that Vps13 may play a critical role in supplying lipids to the endosome, ensuring continuous ESCRT-mediated sorting during MVB biogenesis.
    DOI:  https://doi.org/10.1083/jcb.202307094
  9. Autophagy. 2024 Feb 07.
    RABC1, an Arabidopsis RAB18 regulates binding and subsequent detachment of autophagosomes from the ER in autophagy.
    Yang Shao, Jiaqi Sun, Hugo Zheng.
      Macroautophagy/autophagy is a strategy cells use to cope with detrimental conditions, e.g. nutrient deficiency. Phagophores, the precursors to autophagosomes, are initiated and expanded on the endoplasmic reticulum (ER). However, how phagophores and completed autophagosomes are linked to the ER remains incompletely understood. We recently unveiled a RAB GTPase-based linkage between the two structures. RABC1 is a plant member of RABC/RAB18 GTPases. Our biochemical and microscopy data indicated that RABC1 promotes autophagy in response to nutrient starvation, but not under ER stress. Under nutrient-starvation conditions, active RABC1 interacts with ATG18a on the ER, controlling the association of ATG18a to the ER. Subsequently, active RABC1 is turned off allowing expanded phagophores or autophagosomes to detach from the ER. Our work identifies a RAB GTPase-mediated autophagy process in plant cells, opening a door for improving crop productivity in the changing environment.
    Keywords:  ATG18; RABC1; TOR; autophagosomes; endoplasmic reticulum; nutrient starvation
    DOI:  https://doi.org/10.1080/15548627.2024.2314415
  10. Mol Cell. 2024 Jan 31. pii: S1097-2765(24)00048-0. [Epub ahead of print]
    The GATOR2 complex maintains lysosomal-autophagic function by inhibiting the protein degradation of MiT/TFEs.
    Shu Yang, Chun-Yuan Ting, Mary A Lilly.
      Lysosomes are central to metabolic homeostasis. The microphthalmia bHLH-LZ transcription factors (MiT/TFEs) family members MITF, TFEB, and TFE3 promote the transcription of lysosomal and autophagic genes and are often deregulated in cancer. Here, we show that the GATOR2 complex, an activator of the metabolic regulator TORC1, maintains lysosomal function by protecting MiT/TFEs from proteasomal degradation independent of TORC1, GATOR1, and the RAG GTPase. We determine that in GATOR2 knockout HeLa cells, members of the MiT/TFEs family are ubiquitylated by a trio of E3 ligases and are degraded, resulting in lysosome dysfunction. Additionally, we demonstrate that GATOR2 protects MiT/TFE proteins in pancreatic ductal adenocarcinoma and Xp11 translocation renal cell carcinoma, two cancers that are driven by MiT/TFE hyperactivation. In summary, we find that the GATOR2 complex has independent roles in TORC1 regulation and MiT/TFE protein protection and thus is central to coordinating cellular metabolism with control of the lysosomal-autophagic system.
    Keywords:  E3 ligases; GATOR2; MiT/TFEs; TORC1; autophagy; lysosome; pancreatic ductal adenocarcinoma; renal cell carcinoma; ubiquitination
    DOI:  https://doi.org/10.1016/j.molcel.2024.01.012
  11. J Mol Biol. 2024 Feb 06. pii: S0022-2836(24)00056-1. [Epub ahead of print] 168484
    Role of J-domain proteins in yeast physiology and protein quality control.
    Carmen Ruger-Herreros, Lucia Svoboda, Axel Mogk, Bernd Bukau.
      The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The numbers of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
    DOI:  https://doi.org/10.1016/j.jmb.2024.168484
  12. Cell Rep. 2024 Jan 30. pii: S2211-1247(24)00010-X. [Epub ahead of print] 113682
    Zn2+-dependent functional switching of ERp18, an ER-resident thioredoxin-like protein.
    Chika Tsutsumi, Kaiku Uegaki, Riyuji Yamashita, Ryo Ushioda, Kazuhiro Nagata.
      ERp18 is an endoplasmic reticulum (ER)-resident thioredoxin (Trx) family protein, similar to cytosolic Trx1. The Trx-like domain occupies a major portion of the whole ERp18 structure, which is postulated to be an ER paralog of cytosolic Trx1. Here, we elucidate that zinc ion (Zn2+) binds ERp18 through its catalytic motif, triggering oligomerization of ERp18 from a monomer to a trimer. While the monomeric ERp18 has disulfide oxidoreductase activity, the trimeric ERp18 acquires scavenger activity for hydrogen peroxide (H2O2) in the ER. Depletion of ERp18 thus causes the accumulation of H2O2, which is produced during the oxidative folding of nascent polypeptides in the ER. ERp18 knockdown in C. elegans without Prx4 and GPx7/8, both of which are also known to have H2O2 scavenging activity in the ER, shortened the lifespan, suggesting that ERp18 may form a primitive and essential H2O2 scavenging system for the maintenance of redox homeostasis in the ER.
    Keywords:  CP: Cell biology; ERp18; Zn(2+); aging; endoplasmic reticulum; hydrogen peroxide
    DOI:  https://doi.org/10.1016/j.celrep.2024.113682
  13. bioRxiv. 2024 Jan 27. pii: 2024.01.26.577049. [Epub ahead of print]
    Paraoxonase-like APMAP maintains endoplasmic reticulum-associated lipid and lipoprotein homeostasis.
    Blessy Paul, Holly Merta, Rupali Ugrankar-Banerjee, Monica Hensley, Son Tran, Goncalo Dias do Vale, Jeffrey G McDonald, Steven A Farber, W Mike Henne.
      Oxidative stress perturbs lipid homeostasis and contributes to metabolic diseases. Though ignored compared to mitochondrial oxidation, the endoplasmic reticulum (ER) generates reactive oxygen species requiring antioxidant quality control. Using multi-organismal profiling featuring Drosophila , zebrafish, and mammalian cells, here we characterize the paraoxonase-like APMAP as an ER-localized protein that promotes redox and lipid homeostasis and lipoprotein maturation. APMAP-depleted mammalian cells exhibit defective ER morphology, elevated ER and oxidative stress, lipid droplet accumulation, and perturbed ApoB-lipoprotein homeostasis. Critically, APMAP loss is rescued with chemical antioxidant NAC. Organismal APMAP depletion in Drosophila perturbs fat and lipoprotein homeostasis, and zebrafish display increased vascular ApoB-containing lipoproteins, particles that are atherogenic in mammals. Lipidomics reveals altered polyunsaturated phospholipids and increased ceramides upon APMAP loss, which perturbs ApoB-lipoprotein maturation. These ApoB-associated defects are rescued by inhibiting ceramide synthesis. Collectively, we propose APMAP is an ER-localized antioxidant that promotes lipid and lipoprotein homeostasis.
    Key findings summary: APMAP localizes primarily to the ER network in human cells and Drosophila fat body tissue, and is a type II integral membrane protein Loss of APMAP or Drosophila APMAP (dAPMAP) causes ER membrane expansion, elevates CHOP-associated ER stress, promotes LD accumulation, and alters ApoB-lipoprotein secretion APMAP-depleted cells and dAPMAP-depleted Drosophila fat tissue exhibit defective redox homeostasis; phenotypes associated with APMAP loss are rescued by antioxidant NAC Zebrafish-based LipoGlo reporter reveals that loss of apmap in zebrafish causes increased vascular ApoB-containing lipoproteins Lipidomic profiling indicates that APMAP loss reduces PUFA-phospholipids and elevates intracellular ceramides, which perturbs ApoB maturation.
    DOI:  https://doi.org/10.1101/2024.01.26.577049
  14. J Cell Biol. 2024 Mar 04. pii: e202306040. [Epub ahead of print]223(3):
    Rab32 family proteins regulate autophagosomal components recycling.
    Zhe Wu, Huilin Que, Chuangpeng Li, Li Yan, Shixuan Wang, Yueguang Rong.
      In autophagy, autophagosomes deliver the lumenal contents to lysosomes for degradation via autophagosome-lysosome fusion. In contrast, autophagosome outer membrane components were recycled via autophagosomal components recycling (ACR), which is mediated by the recycler complex. The recycler complex, composed of SNX4, SNX5, and SNX17, cooperate with the dynein-dynactin complex to mediate ACR. However, how ACR is regulated remains unknown. Here, we found that Rab32 family proteins localize to autolysosomes and are required for ACR, rather than other autophagosomal or lysosomal Rab proteins. The GTPase activity of Rab32 family proteins, governed by their guanine nucleotide exchange factor and GTPase-activating protein, plays a key role in regulating ACR. This regulation occurs through the control of recycler complex formation, as well as the connection between the recycler-cargo and dynactin complex. Together, our study reveals an unidentified Rab32 family-dependent regulatory mechanism for ACR.
    DOI:  https://doi.org/10.1083/jcb.202306040
  15. FEBS J. 2024 Feb 03.
    Translation regulation in response to stress.
    Thomas D Williams, Adrien Rousseau.
      Cell stresses occur in a wide variety of settings: in disease, during industrial processes, and as part of normal day-to-day rhythms. Adaptation to these stresses requires cells to alter their proteome. Cells modify the proteins they synthesize to aid proteome adaptation. Changes in both mRNA transcription and translation contribute to altered protein synthesis. Here, we discuss the changes in translational mechanisms that occur following the onset of stress, and the impact these have on stress adaptation.
    Keywords:  mRNA; proteostasis; signalling; stress; translation
    DOI:  https://doi.org/10.1111/febs.17076
  16. Chem Pharm Bull (Tokyo). 2024 ;72(2): 161-165
    Allosteric Hsp70 Modulator YM-1 Induces Degradation of BRD4.
    Yugo Mishima, Shusuke Tomoshige, Shinichi Sato, Minoru Ishikawa.
      YM-1, an allosteric modulator of heat-shock 70 kDa protein (Hsp70), inhibits cancer cell growth, but the mechanism is not yet fully understood. Here, we show that YM-1 induces the degradation of bromodomain containing 4 (BRD4), which mediates oncogene expression. Overall, our results indicate that YM-1 promotes the binding of HSP70 to BRD4, and this in turn promotes the ubiquitination of BRD4 by C-terminus of Hsc70-interacting protein (CHIP), an E3 ubiquitin ligase working in concert with Hsp70, leading to proteasomal degradation of BRD4. This YM-1-induced decrease of BRD4 would contribute at least in part to the inhibition of cancer cell growth.
    Keywords:  YM-1; bromodomain containing 4 (BRD4); cancer treatment; heat-shock 70 kDa protein (Hsp70); protein degradation
    DOI:  https://doi.org/10.1248/cpb.c23-00543
  17. JCI Insight. 2024 Feb 08. pii: e171108. [Epub ahead of print]9(3):
    Attenuation of HOIL-1L ligase activity promotes systemic autoimmune disorders by augmenting linear ubiquitin signaling.
    Yasuhiro Fuseya, Keiichiro Kadoba, Xiaoxi Liu, Hiroyuki Suetsugu, Takeshi Iwasaki, Koichiro Ohmura, Takayuki Sumida, Yuta Kochi, Akio Morinobu, Chikashi Terao, Kazuhiro Iwai.
      Linear ubiquitin chains, which are generated specifically by the linear ubiquitin assembly complex (LUBAC) ubiquitin ligase, play crucial roles in immune signaling, including NF-κB activation. LUBAC comprises catalytic large isoform of heme-oxidized iron regulatory protein 2 ubiquitin ligase 1 (HOIL-1L) interacting protein (HOIP), accessory HOIL-1L, and SHANK-associated RH domain-interacting protein (SHARPIN). Deletion of the ubiquitin ligase activity of HOIL-1L, an accessory ligase of LUBAC, augments LUBAC functions by enhancing LUBAC-mediated linear ubiquitination, which is catalyzed by HOIP. Here, we show that HOIL-1L ΔRING1 mice, which exhibit augmented LUBAC functions upon loss of the HOIL-1L ligase, developed systemic lupus erythematosus (SLE) and Sjögren's syndrome in a female-dominant fashion. Augmented LUBAC activity led to hyperactivation of both lymphoid and myeloid cells. In line with the findings in mice, we sought to identify missense single nucleotide polymorphisms/variations of the RBCK1/HOIL-1L gene in humans that attenuate HOIL-1L ligase activity. We found that the R464H variant, which is encoded by rs774507518 within the RBCK1/HOIL-1L gene, attenuated HOIL-1L ligase activity and augmented LUBAC-mediated immune signaling, including that mediated by Toll-like receptors. We also found that rs774507518 was enriched significantly in patients with SLE, strongly suggesting that RBCK1/HOIL-1L is an SLE susceptibility gene and that augmented linear ubiquitin signaling generated specifically by LUBAC underlies the pathogenesis of this prototype systemic autoimmune disease.
    Keywords:  Autoimmune diseases; Autoimmunity; Cell Biology; Lupus
    DOI:  https://doi.org/10.1172/jci.insight.171108
  18. Nat Struct Mol Biol. 2024 Feb 08.
    Structural mechanisms of autoinhibition and substrate recognition by the ubiquitin ligase HACE1.
    Jonas Düring, Madita Wolter, Julia J Toplak, Camilo Torres, Olexandr Dybkov, Thornton J Fokkens, Katherine E Bohnsack, Henning Urlaub, Wieland Steinchen, Christian Dienemann, Sonja Lorenz.
      Ubiquitin ligases (E3s) are pivotal specificity determinants in the ubiquitin system by selecting substrates and decorating them with distinct ubiquitin signals. However, structure determination of the underlying, specific E3-substrate complexes has proven challenging owing to their transient nature. In particular, it is incompletely understood how members of the catalytic cysteine-driven class of HECT-type ligases (HECTs) position substrate proteins for modification. Here, we report a cryogenic electron microscopy (cryo-EM) structure of the full-length human HECT HACE1, along with solution-based conformational analyses by small-angle X-ray scattering and hydrogen-deuterium exchange mass spectrometry. Structure-based functional analyses in vitro and in cells reveal that the activity of HACE1 is stringently regulated by dimerization-induced autoinhibition. The inhibition occurs at the first step of the catalytic cycle and is thus substrate-independent. We use mechanism-based chemical crosslinking to reconstitute a complex of activated, monomeric HACE1 with its major substrate, RAC1, determine its structure by cryo-EM and validate the binding mode by solution-based analyses. Our findings explain how HACE1 achieves selectivity in ubiquitinating the active, GTP-loaded state of RAC1 and establish a framework for interpreting mutational alterations of the HACE1-RAC1 interplay in disease. More broadly, this work illuminates central unexplored aspects in the architecture, conformational dynamics, regulation and specificity of full-length HECTs.
    DOI:  https://doi.org/10.1038/s41594-023-01203-4
  19. Proteins. 2024 Feb 09.
    Application of AlphaFold models in evaluating ligandable cysteines across E3 ligases.
    Patrick Koldenhof, Martijn P Bemelmans, Brahma Ghosh, Kelly L Damm-Ganamet, Herman W T van Vlijmen, Vineet Pande.
      Proteolysis Targeting Chimeras (PROTACs) are an emerging therapeutic modality and chemical biology tools for Targeted Protein Degradation (TPD). PROTACs contain a ligand targeting the protein of interest, a ligand recruiting an E3 ligase and a linker connecting these two ligands. There are over 600 E3 ligases known so far, but only a handful have been exploited for TPD applications. A key reason for this is the scarcity of ligands binding various E3 ligases and the paucity of structural data available, which complicates ligand design across the family. In this study, we aim to progress PROTAC discovery by proposing a shortlist of E3 ligases that can be prioritized for covalent targeting by performing systematic structural ligandability analysis on a chemoproteomic dataset of potentially reactive cysteines across hundreds of E3 ligases. One of the goals of this study is to apply AlphaFold (AF) models for ligandability evaluations, as for a vast majority of these ligases an experimental structure is not available in the protein data bank (PDB). Using a combination of pocket features, AF model quality and additional aspects, we propose a shortlist of E3 ligases and corresponding cysteines that can be prioritized to potentially discover covalent ligands and expand the PROTAC toolbox.
    Keywords:  AlphaFold; E3 ligases; PROTAC; SiteMap; chemoproteomic data; cysteines; ligandability
    DOI:  https://doi.org/10.1002/prot.26675
  20. bioRxiv. 2024 Jan 28. pii: 2024.01.27.577538. [Epub ahead of print]
    Visualizing chaperone-mediated multistep assembly of the human 20S proteasome.
    Frank Adolf, Jiale Du, Ellen A Goodall, Richard M Walsh, Shaun Rawson, Susanne von Gronau, J Wade Harper, John Hanna, Brenda A Schulman.
      Dedicated assembly factors orchestrate stepwise production of many molecular machines, including the 28-subunit proteasome core particle (CP) that mediates protein degradation. Here, we report cryo-EM reconstructions of seven recombinant human subcomplexes that visualize all five chaperones and the three active site propeptides across a wide swath of the assembly pathway. Comparison of these chaperone-bound intermediates and a matching mature CP reveals molecular mechanisms determining the order of successive subunit additions, and how proteasome subcomplexes and assembly factors structurally adapt upon progressive subunit incorporation to stabilize intermediates, facilitate the formation of subsequent intermediates, and ultimately rearrange to coordinate proteolytic activation with gated access to active sites. The structural findings reported here explain many previous biochemical and genetic observations. This work establishes a methodologic approach for structural analysis of multiprotein complex assembly intermediates, illuminates specific functions of assembly factors, and reveals conceptual principles underlying human proteasome biogenesis.
    DOI:  https://doi.org/10.1101/2024.01.27.577538
  21. Cell Stress Chaperones. 2023 Dec 23. pii: S1355-8145(23)02244-7. [Epub ahead of print]29(1): 21-33
    J-domain proteins: From molecular mechanisms to diseases.
    Jaroslaw Marszalek, Paolo De Los Rios, Douglas Cyr, Matthias P Mayer, Vasista Adupa, Claes Andréasson, Gregory L Blatch, Janice E A Braun, Jeffrey L Brodsky, Bernd Bukau, J Paul Chapple, Charlotte Conz, Sébastien Dementin, Pierre Genevaux, Olivier Genest, Pierre Goloubinoff, Jason Gestwicki, Colin M Hammond, Justin K Hines, Koji Ishikawa, Lukasz A Joachimiak, Janine Kirstein, Krzysztof Liberek, Dejana Mokranjac, Nadinath Nillegoda, Carlos H I Ramos, Mathieu Rebeaud, David Ron, Sabine Rospert, Chandan Sahi, Reut Shalgi, Bartlomiej Tomiczek, Ryo Ushioda, Elizaveta Ustyantseva, Yihong Ye, Maciej Zylicz, Harm H Kampinga.
      J-domain proteins (JDPs) are the largest family of chaperones in most organisms, but much of how they function within the network of other chaperones and protein quality control machineries is still an enigma. Here, we report on the latest findings related to JDP functions presented at a dedicated JDP workshop in Gdansk, Poland. The report does not include all (details) of what was shared and discussed at the meeting, because some of these original data have not yet been accepted for publication elsewhere or represented still preliminary observations at the time.
    Keywords:  Evolution; Hsp70 cycle; JDP
    DOI:  https://doi.org/10.1016/j.cstres.2023.12.002
  22. Cell Mol Gastroenterol Hepatol. 2024 Feb 07. pii: S2352-345X(24)00034-1. [Epub ahead of print]
    Multiple genes core to ERAD, macro-autophagy and lysosomal degradation pathways participate in the proteostasis response in α1-antitrypsin deficiency.
    Jie Li, Francesca Moretti, Tunda Hidvegi, Sanja Sviben, James Aj Fitzpatrick, Hemalatha Sundaramoorthi, Stephen C Pak, Gary A Silverman, Britta Knapp, Ireos Filipuzzi, John Alford, John Reece-Hoyes, Florian Nigsch, Leon O Murphy, Beat Nyfeler, David H Perlmutter.
       BACKGROUND: In the classical form of α1-antitrypsin deficiency (ATD), the misfolded α1-antitrypsin Z (ATZ) variant accumulates in the endoplasmic reticulum (ER) of liver cells. A gain-of-function proteotoxic mechanism is responsible for chronic liver disease in a sub-group of homozygotes. Proteostatic response pathways, including conventional ERAD and autophagy, have been proposed as the mechanisms that allow cellular adaptation and presumably protection from the liver disease phenotype. Recent studies have concluded that a distinct lysosomal pathway called ERLAD completely supplants the role of the conventional macro-autophagy pathway in degradation of ATZ. Here we used several state-of-the-art approaches to more fully characterize the proteostatic responses in cellular systems that model ATD.
    METHODS: We used CRISPR-mediated genome editing coupled to a cell selection step by FACS to carry out screening for proteostasis genes that regulate ATZ accumulation and combined that with selective genome editing in two other model systems.
    RESULTS: ERAD genes are key early regulators and multiple autophagy genes, from classical as well as from ERLAD and other newly described ER-phagy pathways, participate in degradation of ATZ in a manner that is temporally regulated and evolves as ATZ accumulation persists. Time-dependent changes in gene expression are accompanied by specific ultrastructural changes including dilation of the ER, formation of globular inclusions, budding of autophagic vesicles and alterations in the overall shape and component parts of mitochondria.
    CONCLUSIONS: Macro-autophagy is a critical component of the proteostasis response to cellular ATZ accumulation and it becomes more important over time as ATZ synthesis continues unabated. Multiple sub-types of macro-autophagy and non-autophagic lysosomal degradative pathways are needed to respond to the high concentrations of misfolded protein that characterizes ATD and these pathways are attractive candidates for genetic variants that predispose to the hepatic phenotype.
    Keywords:  Autophagy; aggregation-prone proteins; liver disease; proteasome; α1-antitrypsin deficiency
    DOI:  https://doi.org/10.1016/j.jcmgh.2024.02.006
  23. Nat Cell Biol. 2024 Feb 05.
    A metabolite sensor subunit of the Atg1/ULK complex regulates selective autophagy.
    A S Gross, R Ghillebert, M Schuetter, E Reinartz, A Rowland, B C Bishop, M Stumpe, J Dengjel, M Graef.
      Cells convert complex metabolic information into stress-adapted autophagy responses. Canonically, multilayered protein kinase networks converge on the conserved Atg1/ULK kinase complex (AKC) to induce non-selective and selective forms of autophagy in response to metabolic changes. Here we show that, upon phosphate starvation, the metabolite sensor Pho81 interacts with the adaptor subunit Atg11 at the AKC via an Atg11/FIP200 interaction motif to modulate pexophagy by virtue of its conserved phospho-metabolite sensing SPX domain. Notably, core AKC components Atg13 and Atg17 are dispensable for phosphate starvation-induced autophagy revealing significant compositional and functional plasticity of the AKC. Our data indicate that, instead of functioning as a selective autophagy receptor, Pho81 compensates for partially inactive Atg13 by promoting Atg11 phosphorylation by Atg1 critical for pexophagy during phosphate starvation. Our work shows Atg11/FIP200 adaptor subunits bind not only selective autophagy receptors but also modulator subunits that convey metabolic information directly to the AKC for autophagy regulation.
    DOI:  https://doi.org/10.1038/s41556-024-01348-4
  24. Stem Cell Reports. 2024 Jan 20. pii: S2213-6711(24)00005-5. [Epub ahead of print]
    ALS-related p97 R155H mutation disrupts lysophagy in iPSC-derived motor neurons.
    Jacob A Klickstein, Michelle A Johnson, Pantelis Antonoudiou, Jamie Maguire, Joao A Paulo, Steve P Gygi, Chris Weihl, Malavika Raman.
      Mutations in the AAA+ ATPase p97 cause multisystem proteinopathy 1, which includes amyotrophic lateral sclerosis; however, the pathogenic mechanisms that contribute to motor neuron loss remain obscure. Here, we use two induced pluripotent stem cell models differentiated into spinal motor neurons to investigate how p97 mutations perturb the motor neuron proteome. Using quantitative proteomics, we find that motor neurons harboring the p97 R155H mutation have deficits in the selective autophagy of lysosomes (lysophagy). p97 R155H motor neurons are unable to clear damaged lysosomes and have reduced viability. Lysosomes in mutant motor neurons have increased pH compared with wild-type cells. The clearance of damaged lysosomes involves UBXD1-p97 interaction, which is disrupted in mutant motor neurons. Finally, inhibition of the ATPase activity of p97 using the inhibitor CB-5083 rescues lysophagy defects in mutant motor neurons. These results add to the evidence that endo-lysosomal dysfunction is a key aspect of disease pathogenesis in p97-related disorders.
    Keywords:  ALS; autophagy; galectin; lysophagy; lysosome; mitochondria; p97; proteomics
    DOI:  https://doi.org/10.1016/j.stemcr.2024.01.002
  25. Proc Natl Acad Sci U S A. 2024 Feb 13. 121(7): e2318822121
    Direct binding to sterols accelerates endoplasmic reticulum-associated degradation of HMG CoA reductase.
    Rebecca A Faulkner, Yangyan Yang, Jet Tsien, Tian Qin, Russell A DeBose-Boyd.
      The maintenance of cholesterol homeostasis is crucial for normal function at both the cellular and organismal levels. Two integral membrane proteins, 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR) and Scap, are key targets of a complex feedback regulatory system that operates to ensure cholesterol homeostasis. HMGCR catalyzes the rate-limiting step in the transformation of the 2-carbon precursor acetate to 27-carbon cholesterol. Scap mediates proteolytic activation of sterol regulatory element-binding protein-2 (SREBP-2), a membrane-bound transcription factor that controls expression of genes involved in the synthesis and uptake of cholesterol. Sterol accumulation triggers binding of HMGCR to endoplasmic reticulum (ER)-localized Insig proteins, leading to the enzyme's ubiquitination and proteasome-mediated ER-associated degradation (ERAD). Sterols also induce binding of Insigs to Scap, which leads to sequestration of Scap and its bound SREBP-2 in the ER, thereby preventing proteolytic activation of SREBP-2 in the Golgi. The oxygenated cholesterol derivative 25-hydroxycholesterol (25HC) and the methylated cholesterol synthesis intermediate 24,25-dihydrolanosterol (DHL) differentially modulate HMGCR and Scap. While both sterols promote binding of HMGCR to Insigs for ubiquitination and subsequent ERAD, only 25HC inhibits the Scap-mediated proteolytic activation of SREBP-2. We showed previously that 1,1-bisphosphonate esters mimic DHL, accelerating ERAD of HMGCR while sparing SREBP-2 activation. Building on these results, our current studies reveal specific, Insig-independent photoaffinity labeling of HMGCR by photoactivatable derivatives of the 1,1-bisphosphonate ester SRP-3042 and 25HC. These findings disclose a direct sterol binding mechanism as the trigger that initiates the HMGCR ERAD pathway, providing valuable insights into the intricate mechanisms that govern cholesterol homeostasis.
    Keywords:  ER-associated degradation; cholesterol; isoprenoids; sterols; ubiquitination
    DOI:  https://doi.org/10.1073/pnas.2318822121
  26. Nature. 2024 Feb 07.
    Translation selectively destroys non-functional transcription complexes.
    Jason Woodgate, Hamed Mosaei, Pavel Brazda, Flint Stevenson-Jones, Nikolay Zenkin.
      Transcription elongation stalls at lesions in the DNA template1. For the DNA lesion to be repaired, the stalled transcription elongation complex (EC) has to be removed from the damaged site2. Here we show that translation, which is coupled to transcription in bacteria, actively dislodges stalled ECs from the damaged DNA template. By contrast, paused, but otherwise elongation-competent, ECs are not dislodged by the ribosome. Instead, they are helped back into processive elongation. We also show that the ribosome slows down when approaching paused, but not stalled, ECs. Our results indicate that coupled ribosomes functionally and kinetically discriminate between paused ECs and stalled ECs, ensuring the selective destruction of only the latter. This functional discrimination is controlled by the RNA polymerase's catalytic domain, the Trigger Loop. We show that the transcription-coupled DNA repair helicase UvrD, proposed to cause backtracking of stalled ECs3, does not interfere with ribosome-mediated dislodging. By contrast, the transcription-coupled DNA repair translocase Mfd4 acts synergistically with translation, and dislodges stalled ECs that were not destroyed by the ribosome. We also show that a coupled ribosome efficiently destroys misincorporated ECs that can cause conflicts with replication5. We propose that coupling to translation is an ancient and one of the main mechanisms of clearing non-functional ECs from the genome.
    DOI:  https://doi.org/10.1038/s41586-023-07014-3
  27. Cell Stress Chaperones. 2024 Feb 02. pii: S1355-8145(24)00046-4. [Epub ahead of print]
    Stress Biology: Complexity and Multifariousness in Health and Disease.
    Matthias P Mayer, Laura Blair, Gregory L Blatch, Thiago J Borges, Ahmed Chadli, Gabriela Chiosis, Aurélie de Thonel, Albena Dinkova-Kostova, Heath Ecroyd, Adrienne L Edkins, Takanori Eguchi, Monika Fleshner, Kevin P Foley, Sotirios Fragkostefanakis, Jason Gestwicki, Pierre Goloubinoff, Jennifer A Heritz, Christine M Heske, Jonathan D Hibshman, Jenny Joutsen, Wei Li, Michael Lynes, Marc L Mendillo, Nahid Mivechi, Fortunate Mokoena, Yuka Okusha, Veena Prahlad, Elizabeth Repasky, Sara Sannino, Federica Scalia, Reut Shalgi, Lea Sistonen, Emily Sontag, Patricija van Oosten-Hawle, Anniina Vihervaara, Anushka Wickramaratne, Shawn Xiang Yang Wang, Tawanda Zininga.
      Preserving and regulating cellular homeostasis in the light of changing environmental conditions or developmental processes is of pivotal importance for single cellular and multicellular organisms alike. To counteract an imbalance in cellular homeostasis transcriptional programs evolved, called the heat shock response (HSR), unfolded protein response (UPR) and integrated stress response (ISR), that act cell-autonomously in most cells but in multicellular organisms are subjected to cell-nonautonomous regulation. These transcriptional programs downregulate expression of most genes but increase expression of heat shock genes, including genes encoding molecular chaperones and proteases, proteins involved in repair of stress-induced damage to macromolecules and cellular structures. 61 years after the discovery of the heat shock response by Ferruccio Ritossa many aspects of stress biology are still enigmatic. Recent progress in the understanding of stress responses and molecular chaperones was reported at the 12th International Symposium on Heat Shock Proteins in Biology, Medicine and the Environment in the Old Town Alexandria, VA, USA from 28th to 31st of October 2023.
    DOI:  https://doi.org/10.1016/j.cstres.2024.01.006
  28. NAR Mol Med. 2024 Jan;1(1): ugae002
    A compact regulatory RNA element in mouse Hsp70 mRNA.
    Wenshuai Wang, Fei Liu, Maria Vera Ugalde, Anna Marie Pyle.
      Hsp70 (70 kDa heat shock protein) performs molecular chaperone functions by assisting the folding of newly synthesized and misfolded proteins, thereby counteracting various cell stresses and preventing multiple diseases, including neurodegenerative disorders and cancers. It is well established that, immediately after heat shock, Hsp70 gene expression is mediated by a canonical mechanism of cap-dependent translation. However, the molecular mechanism of Hsp70 expression during heat shock remains elusive. Intriguingly, the 5' end of Hsp70 messenger RNA (mRNA) appears to form a compact structure with the potential to regulate protein expression in a cap-independent manner. Here, we determined the minimal length of the mHsp70 5'-terminal mRNA sequence that is required for RNA folding into a highly compact structure. This span of this RNA element was mapped and the secondary structure characterized by chemical probing, resulting in a secondary structural model that includes multiple stable stems, including one containing the canonical start codon. All of these components, including a short stretch of the 5' open reading frame (ORF), were shown to be vital for RNA folding. This work provides a structural basis for future investigations on the role of translational regulatory structures in the 5' untranslated region and ORF sequences of Hsp70 during heat shock.
    DOI:  https://doi.org/10.1093/narmme/ugae002
  29. Sci Adv. 2024 Feb 09. 10(6): eadk3931
    RNF220-mediated K63-linked polyubiquitination stabilizes Olig proteins during oligodendroglial development and myelination.
    Yuwei Li, Li Pear Wan, Ning-Ning Song, Yu-Qiang Ding, Shuhua Zhao, Jianqin Niu, Bingyu Mao, Nengyin Sheng, Pengcheng Ma.
      Maldevelopment of oligodendroglia underlies neural developmental disorders such as leukodystrophy. Precise regulation of the activity of specific transcription factors (TFs) by various posttranslational modifications (PTMs) is required to ensure proper oligodendroglial development and myelination. However, the role of ubiquitination of these TFs during oligodendroglial development is yet unexplored. Here, we find that RNF220, a known leukodystrophy-related E3 ubiquitin ligase, is required for oligodendroglial development. RNF220 depletion in oligodendrocyte lineage cells impedes oligodendrocyte progenitor cell proliferation, differentiation, and (re)myelination, which consequently leads to learning and memory defects. Mechanistically, RNF220 targets Olig1/2 for K63-linked polyubiquitination and stabilization during oligodendroglial development. Furthermore, in a knock-in mouse model of leukodystrophy-related RNF220R365Q mutation, the ubiquitination and stabilization of Olig proteins are deregulated in oligodendroglial cells. This results in pathomimetic oligodendroglial developmental defects, impaired myelination, and abnormal behaviors. Together, our evidence provides an alternative insight into PTMs of oligodendroglial TFs and how this essential process may be implicated in the etiology of leukodystrophy.
    DOI:  https://doi.org/10.1126/sciadv.adk3931
  30. Nucleic Acids Res. 2024 Feb 07. pii: gkae067. [Epub ahead of print]
    Evolving precision: rRNA expansion segment 7S modulates translation velocity and accuracy in eukaryal ribosomes.
    Robert Rauscher, Cristian Eggers, Lyudmila Dimitrova-Paternoga, Vaishnavi Shankar, Alessia Rosina, Marina Cristodero, Helge Paternoga, Daniel N Wilson, Sebastian A Leidel, Norbert Polacek.
      Ribosome-enhanced translational miscoding of the genetic code causes protein dysfunction and loss of cellular fitness. During evolution, open reading frame length increased, necessitating mechanisms for enhanced translation fidelity. Indeed, eukaryal ribosomes are more accurate than bacterial counterparts, despite their virtually identical, conserved active centers. During the evolution of eukaryotic organisms ribosome expansions at the rRNA and protein level occurred, which potentially increases the options for translation regulation and cotranslational events. Here we tested the hypothesis that ribosomal RNA expansions can modulate the core function of the ribosome, faithful protein synthesis. We demonstrate that a short expansion segment present in all eukaryotes' small subunit, ES7S, is crucial for accurate protein synthesis as its presence adjusts codon-specific velocities and guarantees high levels of cognate tRNA selection. Deletion of ES7S in yeast enhances mistranslation and causes protein destabilization and aggregation, dramatically reducing cellular fitness. Removal of ES7S did not alter ribosome architecture but altered the structural dynamics of inter-subunit bridges thus affecting A-tRNA selection. Exchanging the yeast ES7S sequence with the human ES7S increases accuracy whereas shortening causes the opposite effect. Our study demonstrates that ES7S provided eukaryal ribosomes with higher accuracy without perturbing the structurally conserved decoding center.
    DOI:  https://doi.org/10.1093/nar/gkae067
  31. bioRxiv. 2024 Jan 25. pii: 2024.01.24.576953. [Epub ahead of print]
    PPTC7 limits mitophagy through proximal and dynamic interactions with BNIP3 and NIX.
    Lianjie Wei, Mehmet Oguz Gok, Jordyn D Svoboda, Merima Forny, Jonathan R Friedman, Natalie M Niemi.
      PPTC7 is a mitochondrial-localized PP2C phosphatase that maintains mitochondrial protein content and metabolic homeostasis. We previously demonstrated that knockout of Pptc7 elevates mitophagy in a BNIP3- and NIX-dependent manner, but the mechanisms by which PPTC7 influences receptor-mediated mitophagy remain ill-defined. Here, we demonstrate that loss of PPTC7 upregulates BNIP3 and NIX post-transcriptionally and independent of HIF-1α stabilization. On a molecular level, loss of PPTC7 prolongs the half-life of BNIP3 and NIX while blunting their accumulation in response to proteasomal inhibition, suggesting that PPTC7 promotes the ubiquitin-mediated turnover of BNIP3 and NIX. Consistently, overexpression of PPTC7 limits the accumulation of BNIP3 and NIX protein levels in response to pseudohypoxia, a well-known inducer of mitophagy. This PPTC7-mediated suppression of BNIP3 and NIX protein expression requires an intact PP2C catalytic motif but is surprisingly independent of its mitochondrial targeting, indicating that PPTC7 influences mitophagy outside of the mitochondrial matrix. We find that PPTC7 exists in at least two distinct states in cells: a longer isoform, which likely represents full length protein, and a shorter isoform, which likely represents an imported, matrix-localized phosphatase pool. Importantly, anchoring PPTC7 to the outer mitochondrial membrane is sufficient to blunt BNIP3 and NIX accumulation, and proximity labeling and fluorescence co-localization experiments suggest that PPTC7 associates with BNIP3 and NIX within the native cellular environment. Importantly, these associations are enhanced in cellular conditions that promote BNIP3 and NIX turnover, demonstrating that PPTC7 is dynamically recruited to BNIP3 and NIX to facilitate their degradation. Collectively, these data reveal that a fraction of PPTC7 dynamically localizes to the outer mitochondrial membrane to promote the proteasomal turnover of BNIP3 and NIX.
    DOI:  https://doi.org/10.1101/2024.01.24.576953
  32. Nat Commun. 2024 Feb 08. 15(1): 1170
    Molecular basis of SAP05-mediated ubiquitin-independent proteasomal degradation of transcription factors.
    Xiaojie Yan, Xinxin Yuan, Jianke Lv, Bing Zhang, Yongle Huang, Qianqian Li, Jinfeng Ma, Yanran Li, Xiaolu Wang, Yao Li, Ying Yu, Quanyan Liu, Tong Liu, Wenyi Mi, Cheng Dong.
      SAP05, a secreted effector by the obligate parasitic bacteria phytoplasma, bridges host SPL and GATA transcription factors (TFs) to the 26 S proteasome subunit RPN10 for ubiquitination-independent degradation. Here, we report the crystal structures of SAP05 in complex with SPL5, GATA18 and RPN10, which provide detailed insights into the protein-protein interactions involving SAP05. SAP05 employs two opposing lobes with an acidic path and a hydrophobic path to contact TFs and RPN10, respectively. Our crystal structures, in conjunction with mutagenesis and degradation assays, reveal that SAP05 targets plant GATAs but not animal GATAs dependent on their direct salt-bridged electrostatic interactions. Additionally, SAP05 hijacks plant RPN10 but not animal RPN10 due to structural steric hindrance and the key hydrophobic interactions. This study provides valuable molecular-level information into the modulation of host proteins to prevent insect-borne diseases.
    DOI:  https://doi.org/10.1038/s41467-024-45521-7
  33. Nat Struct Mol Biol. 2024 Feb 08.
    Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3KBTBD2.
    Yuxia Hu, Zhao Zhang, Qiyu Mao, Xiang Zhang, Aihua Hao, Yu Xun, Yeda Wang, Lin Han, Wuqiang Zhan, Qianying Liu, Yue Yin, Chao Peng, Eva Marie Y Moresco, Zhenguo Chen, Bruce Beutler, Lei Sun.
      Phosphatidylinositol 3-kinase α, a heterodimer of catalytic p110α and one of five regulatory subunits, mediates insulin- and insulin like growth factor-signaling and, frequently, oncogenesis. Cellular levels of the regulatory p85α subunit are tightly controlled by regulated proteasomal degradation. In adipose tissue and growth plates, failure of K48-linked p85α ubiquitination causes diabetes, lipodystrophy and dwarfism in mice, as in humans with SHORT syndrome. Here we elucidated the structures of the key ubiquitin ligase complexes regulating p85α availability. Specificity is provided by the substrate receptor KBTBD2, which recruits p85α to the cullin3-RING E3 ubiquitin ligase (CRL3). CRL3KBTBD2 forms multimers, which disassemble into dimers upon substrate binding (CRL3KBTBD2-p85α) and/or neddylation by the activator NEDD8 (CRL3KBTBD2~N8), leading to p85α ubiquitination and degradation. Deactivation involves dissociation of NEDD8 mediated by the COP9 signalosome and displacement of KBTBD2 by the inhibitor CAND1. The hereby identified structural basis of p85α regulation opens the way to better understanding disturbances of glucose regulation, growth and cancer.
    DOI:  https://doi.org/10.1038/s41594-023-01182-6
  34. bioRxiv. 2024 Jan 27. pii: 2024.01.25.577254. [Epub ahead of print]
    Patient derived model of UBA5- associated encephalopathy identifies defects in neurodevelopment and highlights potential therapies.
    Helen Chen, Yong-Dong Wang, Aidan W Blan, Edith P Almanza-Fuerte, Emily S Bonkowski, Richa Bajpai, Shondra M Pruett-Miller, Heather C Mefford.
      UBA5 encodes for the E1 enzyme of the UFMylation cascade, which plays an essential role in ER homeostasis. The clinical phenotypes of UBA5-associated encephalopathy include developmental delays, epilepsy and intellectual disability. To date, there is no humanized neuronal model to study the cellular and molecular consequences of UBA5 pathogenic variants. We developed and characterized patient-derived cortical organoid cultures and identified defects in GABAergic interneuron development. We demonstrated aberrant neuronal firing and microcephaly phenotypes in patient-derived organoids. Mechanistically, we show that ER homeostasis is perturbed along with exacerbated unfolded protein response pathway in cells and organoids expressing UBA5 pathogenic variants. We also assessed two gene expression modalities that augmented UBA5 expression to rescue aberrant molecular and cellular phenotypes. Our study provides a novel humanized model that allows further investigations of UBA5 variants in the brain and highlights novel systemic approaches to alleviate cellular aberrations for this rare, developmental disorder.
    One-sentence summary: Patient derived model of UBA5-assoicated DEE recapitulated disease phenotype, revealed defects in neurodevelopment, and highlighted potential therapies.
    DOI:  https://doi.org/10.1101/2024.01.25.577254
  35. J Cell Biol. 2024 Apr 01. pii: e202305003. [Epub ahead of print]223(4):
    APOE traffics to astrocyte lipid droplets and modulates triglyceride saturation and droplet size.
    Ian A Windham, Alex E Powers, Joey V Ragusa, E Diane Wallace, Maria Clara Zanellati, Victoria H Williams, Colby H Wagner, Kristen K White, Sarah Cohen.
      The E4 variant of APOE strongly predisposes individuals to late-onset Alzheimer's disease. We demonstrate that in response to lipogenesis, apolipoprotein E (APOE) in astrocytes can avoid translocation into the endoplasmic reticulum (ER) lumen and traffic to lipid droplets (LDs) via membrane bridges at ER-LD contacts. APOE knockdown promotes fewer, larger LDs after a fatty acid pulse, which contain more unsaturated triglyceride after fatty acid pulse-chase. This LD size phenotype was rescued by chimeric APOE that targets only LDs. Like APOE depletion, APOE4-expressing astrocytes form a small number of large LDs enriched in unsaturated triglyceride. Additionally, the LDs in APOE4 cells exhibit impaired turnover and increased sensitivity to lipid peroxidation. Our data indicate that APOE plays a previously unrecognized role as an LD surface protein that regulates LD size and composition. APOE4 causes aberrant LD composition and morphology. Our study contributes to accumulating evidence that APOE4 astrocytes with large, unsaturated LDs are sensitized to lipid peroxidation, which could contribute to Alzheimer's disease risk.
    DOI:  https://doi.org/10.1083/jcb.202305003
  36. J Biol Chem. 2024 Feb 01. pii: S0021-9258(24)00091-7. [Epub ahead of print] 105715
    NEDD4L intramolecular Interactions regulate its auto- and substrate NaV1.5 ubiquitination.
    Katharine M Wright, Sara Nathan, Hanjie Jiang, Wendy Xia, HyoJeon Kim, Nourdine Chakouri, Justin N Nwafor, Lucile Fossier, Lakshmi Srinivasan, Zan Chen, Tatiana Boronina, Jeremy Post, Suman Paul, Robert N Cole, Manu Ben-Johny, Philip A Cole, Sandra B Gabelli.
      NEDD4L is a HECT-type E3 ligase that catalyzes the addition of ubiquitin to intracellular substrates such as the cardiac voltage-gated sodium channel, NaV1.5. The intramolecular interactions of NEDD4L regulate its enzymatic activity which is essential for proteostasis. For NaV1.5, this process is critical as alterations in Na+ current is involved in cardiac diseases including arrhythmias and heart failure. In this study, we perform extensive biochemical and functional analyses that implicate the C2 domain and the first WW-linker (1,2-linker) in the auto-regulatory mechanism of NEDD4L. Through in vitro and electrophysiological experiments, the NEDD4L 1,2-linker was determined to be important in substrate ubiquitination of NaV1.5. We establish the preferred sites of ubiquitination of NEDD4L to be in the second WW-linker (2,3-linker). Interestingly, NEDD4L ubiquitinates the cytoplasmic linker between the first and second transmembrane domains of the channel (DI-DII) of NaV1.5. Moreover, we design a genetically encoded modulator of Nav1.5 that achieves Na+ current reduction using the NEDD4L HECT domain as cargo of a NaV1.5-binding nanobody. These investigations elucidate the mechanisms regulating the NEDD4 family and furnish a new molecular framework for understanding NaV1.5 ubiquitination.
    Keywords:  E3 Ligases; HECT; NEDD4-2; NEDD4L; NanoMaN; Nav1.5; PTM; SCN5A; Ubiquitin; Voltage-Gated Sodium Channel; electrophysiology; mass spectrometry; nanobody; post translational modification; proteostasis; transthioesterification
    DOI:  https://doi.org/10.1016/j.jbc.2024.105715
  37. Life Sci Alliance. 2024 Apr;pii: e202302349. [Epub ahead of print]7(4):
    Knockout of PA200 improves proteasomal degradation and myelination in a proteotoxic neuropathy.
    Jordan Js VerPlank, Joseph M Gawron, Nicholas J Silvestri, Lawrence Wrabetz, Maria Laura Feltri.
      The cellular response to a decrease in protein degradation by 26S proteasomes in chronic diseases is poorly understood. Pharmacological inhibition of proteasomes increases the expression of proteasome subunits and Proteasome Activator 200 (PA200), an alternative proteasome activator. In the S63del mouse model of the peripheral neuropathy Charcot Marie Tooth 1B (CMT1B), proteasomal protein degradation is decreased and proteasome gene expression is increased. Here, we show an increase in PA200 and PA200-bound proteasomes in the peripheral nerves of S63del mice. To test genetically whether the upregulation of PA200 was compensatory, we generated S63del//PA200-/- mice. Unexpectedly, in the sciatic nerves of these mice, there was greater proteasomal protein degradation than in S63del, less polyubiquitinated proteins and markers of the unfolded protein response, and a greater amount of assembled, active 26S proteasomes. These changes were not seen in PA200-/- controls and were therefore specific to the neuropathy. Furthermore, in S63del//PA200-/- mice, myelin thickness and nerve conduction were restored to WT levels. Thus, the upregulation of PA200 is maladaptive in S63del mice and its genetic ablation prevented neuropathy.
    DOI:  https://doi.org/10.26508/lsa.202302349
  38. bioRxiv. 2024 Jan 23. pii: 2024.01.22.576497. [Epub ahead of print]
    WHAMM functions in kidney reabsorption and polymerizes actin to promote autophagosomal membrane closure and cargo sequestration.
    Alyssa M Coulter, Valerie Cortés, Corey J Theodore, Rachel E Cianciolo, Ron Korstanje, Kenneth G Campellone.
      The actin cytoskeleton is essential for many functions of eukaryotic cells, but the factors that nucleate actin assembly are not well understood at the organismal level or in the context of disease. To explore the function of the actin nucleation factor WHAMM in mice, we examined how Whamm inactivation impacts kidney physiology and cellular proteostasis. We show that male WHAMM knockout mice excrete elevated levels of albumin, glucose, phosphate, and amino acids, and display abnormalities of the kidney proximal tubule, suggesting that WHAMM activity is important for nutrient reabsorption. In kidney tissue, the loss of WHAMM results in the accumulation of the lipidated autophagosomal membrane protein LC3, indicating an alteration in autophagy. In mouse fibroblasts and human proximal tubule cells, WHAMM and its binding partner the Arp2/3 complex control autophagic membrane closure and cargo receptor recruitment. These results reveal a role for WHAMM-mediated actin assembly in maintaining kidney function and promoting proper autophagosome membrane remodeling.
    DOI:  https://doi.org/10.1101/2024.01.22.576497
  39. STAR Protoc. 2024 Feb 05. pii: S2666-1667(24)00037-6. [Epub ahead of print]5(1): 102872
    Characterization of ATG8-family protein phosphorylation by Phos-tag gel for autophagy study.
    Gayoung Seo, Wenqi Wang.
      Autophagy supports cell survival under different stress conditions, where ATG8-family proteins are required for autophagosome biogenesis/maturation and selective autophagy. Here, we present a protocol for studying ATG8-family protein phosphorylation using Phos-tag gel, a modified SDS-PAGE system, when the related phosphorylation site information and/or specific phospho-antibody are unavailable. We describe steps for generating GST-ATG8 proteins in bacteria, purifying S protein-Flag-SBP protein (SFB)-tagged kinasefrom cells, preparing gel, and an in vitro kinase assay. We then detail procedures for western blotting and image processing. For complete details on the use and execution of this protocol, please refer to Seo et al.1.
    Keywords:  Protein Biochemistry; Protein expression and purification; Signal Transduction
    DOI:  https://doi.org/10.1016/j.xpro.2024.102872
  40. FEBS J. 2024 Feb 03.
    Ataxin-2 sequesters Raptor into aggregates and impairs cellular mTORC1 signaling.
    Ya-Jun Liu, Jian-Yang Wang, Xiang-Le Zhang, Lei-Lei Jiang, Hong-Yu Hu.
      Ataxin-2 (Atx2) is a polyglutamine (polyQ) protein, in which abnormal expansion of the polyQ tract can trigger protein aggregation and consequently cause spinocerebellar ataxia type 2 (SCA2), but the mechanism underlying how Atx2 aggregation leads to proteinopathy remains elusive. Here, we investigate the molecular mechanism and cellular consequences of Atx2 aggregation by molecular cell biology approaches. We have revealed that either normal or polyQ-expanded Atx2 can sequester Raptor, a component of mammalian target of rapamycin complex 1 (mTORC1), into aggregates based on their specific interaction. Further research indicates that the polyQ tract and the N-terminal region (residues 1-784) of Atx2 are responsible for the specific sequestration. Moreover, this sequestration leads to suppression of the mTORC1 activity as represented by down-regulation of phosphorylated P70S6K, which can be reversed by overexpression of Raptor. As mTORC1 is a key regulator of autophagy, Atx2 aggregation and sequestration also induces autophagy by upregulating LC3-II and reducing phosphorylated ULK1 levels. This study proposes that Atx2 sequesters Raptor into aggregates, thereby impairing cellular mTORC1 signaling and inducing autophagy, and will be beneficial for a better understanding of the pathogenesis of SCA2 and other polyQ diseases.
    Keywords:  Raptor; aggregation; ataxin-2; mTORC1 signaling; sequestration
    DOI:  https://doi.org/10.1111/febs.17081
  41. J Cell Biol. 2024 Mar 04. pii: e202310005. [Epub ahead of print]223(3):
    Regulation of proteostasis and innate immunity via mitochondria-nuclear communication.
    Sookyung Kim, Theresa R Ramalho, Cole M Haynes.
      Mitochondria are perhaps best known as the "powerhouse of the cell" for their role in ATP production required for numerous cellular activities. Mitochondria have emerged as an important signaling organelle. Here, we first focus on signaling pathways mediated by mitochondria-nuclear communication that promote protein homeostasis (proteostasis). We examine the mitochondrial unfolded protein response (UPRmt) in C. elegans, which is regulated by a transcription factor harboring both a mitochondrial- and nuclear-targeting sequence, the integrated stress response in mammals, as well as the regulation of chromatin by mitochondrial metabolites. In the second section, we explore the role of mitochondria-to-nuclear communication in the regulation of innate immunity and inflammation. Perhaps related to their prokaryotic origin, mitochondria harbor molecules also found in viruses and bacteria. If these molecules accumulate in the cytosol, they elicit the same innate immune responses as viral or bacterial infection.
    DOI:  https://doi.org/10.1083/jcb.202310005
  42. Nat Cell Biol. 2024 Feb 08.
    Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal.
    Laura E Newman, Sammy Weiser Novak, Gladys R Rojas, Nimesha Tadepalle, Cara R Schiavon, Danielle A Grotjahn, Christina G Towers, Marie-Ève Tremblay, Matthew P Donnelly, Sagnika Ghosh, Michaela Medina, Sienna Rocha, Ricardo Rodriguez-Enriquez, Joshua A Chevez, Ian Lemersal, Uri Manor, Gerald S Shadel.
      Mitochondrial DNA (mtDNA) encodes essential subunits of the oxidative phosphorylation system, but is also a major damage-associated molecular pattern (DAMP) that engages innate immune sensors when released into the cytoplasm, outside of cells or into circulation. As a DAMP, mtDNA not only contributes to anti-viral resistance, but also causes pathogenic inflammation in many disease contexts. Cells experiencing mtDNA stress caused by depletion of the mtDNA-packaging protein, transcription factor A, mitochondrial (TFAM) or during herpes simplex virus-1 infection exhibit elongated mitochondria, enlargement of nucleoids (mtDNA-protein complexes) and activation of cGAS-STING innate immune signalling via mtDNA released into the cytoplasm. However, the relationship among aberrant mitochondria and nucleoid dynamics, mtDNA release and cGAS-STING activation remains unclear. Here we show that, under a variety of mtDNA replication stress conditions and during herpes simplex virus-1 infection, enlarged nucleoids that remain bound to TFAM exit mitochondria. Enlarged nucleoids arise from mtDNA experiencing replication stress, which causes nucleoid clustering via a block in mitochondrial fission at a stage when endoplasmic reticulum actin polymerization would normally commence, defining a fission checkpoint that ensures mtDNA has completed replication and is competent for segregation into daughter mitochondria. Chronic engagement of this checkpoint results in enlarged nucleoids trafficking into early and then late endosomes for disposal. Endosomal rupture during transit through this endosomal pathway ultimately causes mtDNA-mediated cGAS-STING activation. Thus, we propose that replication-incompetent nucleoids are selectively eliminated by an adaptive mitochondria-endosomal quality control pathway that is prone to innate immune system activation, which might represent a therapeutic target to prevent mtDNA-mediated inflammation during viral infection and other pathogenic states.
    DOI:  https://doi.org/10.1038/s41556-023-01343-1
  43. Nat Chem. 2024 Feb 07.
    Characterizing ATP processing by the AAA+ protein p97 at the atomic level.
    Mikhail Shein, Manuel Hitzenberger, Tat Cheung Cheng, Smruti R Rout, Kira D Leitl, Yusuke Sato, Martin Zacharias, Eri Sakata, Anne K Schütz.
      The human enzyme p97 regulates various cellular pathways by unfolding hundreds of protein substrates in an ATP-dependent manner, making it an essential component of protein homeostasis and an impactful pharmacological target. The hexameric complex undergoes substantial conformational changes throughout its catalytic cycle. Here we elucidate the molecular motions that occur at the active site in the temporal window immediately before and after ATP hydrolysis by merging cryo-EM, NMR spectroscopy and molecular dynamics simulations. p97 populates a metastable reaction intermediate, the ADP·Pi state, which is poised between hydrolysis and product release. Detailed snapshots reveal that the active site is finely tuned to trap and eventually discharge the cleaved phosphate. Signalling pathways originating at the active site coordinate the action of the hexamer subunits and couple hydrolysis with allosteric conformational changes. Our multidisciplinary approach enables a glimpse into the sophisticated spatial and temporal orchestration of ATP handling by a prototype AAA+ protein.
    DOI:  https://doi.org/10.1038/s41557-024-01440-0
  44. J Med Chem. 2024 Feb 05.
    Discovery of Novel PROTAC Degraders of p300/CBP as Potential Therapeutics for Hepatocellular Carcinoma.
    Qi Chang, Jiayi Li, Yue Deng, Ruilin Zhou, Bingwei Wang, Yujie Wang, Mingming Zhang, Xun Huang, Yingxia Li.
      Adenoviral E1A binding protein 300 kDa (p300) and its closely related paralog CREB binding protein (CBP) are promising therapeutic targets for human cancer. Here, we report the first discovery of novel potent small-molecule PROTAC degraders of p300/CBP against hepatocellular carcinoma (HCC), one of the most common solid tumors. Based upon the clinical p300/CBP bromodomain inhibitor CCS1477, a conformational restriction strategy was used to optimize the linker to generate a series of PROTACs, culminating in the identification of QC-182. This compound effectively induces p300/CBP degradation in the SK-HEP-1 HCC cells in a dose-, time-, and ubiquitin-proteasome system-dependent manner. QC-182 significantly downregulates p300/CBP-associated transcriptome in HCC cells, leading to more potent cell growth inhibition compared to the parental inhibitors and the reported degrader dCBP-1. Notably, QC-182 potently depletes p300/CBP proteins in mouse SK-HEP-1 xenograft tumor tissue. QC-182 is a promising lead compound toward the development of p300/CBP-targeted HCC therapy.
    DOI:  https://doi.org/10.1021/acs.jmedchem.3c01468
  45. Contact (Thousand Oaks). 2024 Jan-Dec;7:7 25152564241228911
    Contact-FP: A Dimerization-Dependent Fluorescent Protein Toolkit for Visualizing Membrane Contact Site Dynamics.
    Gregory E Miner, Sidney Y Smith, Wendy K Showalter, Christina M So, Joey V Ragusa, Alex E Powers, Maria Clara Zanellati, Chih-Hsuan Hsu, Michelle F Marchan, Sarah Cohen.
      Membrane contact sites (MCSs) are sites of close apposition between two organelles used to exchange ions, lipids, and information. Cells respond to changing environmental or developmental conditions by modulating the number, extent, or duration of MCSs. Because of their small size and dynamic nature, tools to study the dynamics of MCSs in live cells have been limited. Dimerization-dependent fluorescent proteins (ddFPs) targeted to organelle membranes are an ideal tool for studying MCS dynamics because they reversibly interact to fluoresce specifically at the interface between two organelles. Here, we build on previous work using ddFPs as sensors to visualize the morphology and dynamics of MCSs. We engineered a suite of ddFPs called Contact-FP that targets ddFP monomers to lipid droplets (LDs), the endoplasmic reticulum (ER), mitochondria, peroxisomes, lysosomes, plasma membrane, caveolae, and the cytoplasm. We show that these probes correctly localize to their target organelles. Using LDs as a test case, we demonstrate that Contact-FP pairs specifically localize to the interface between two target organelles. Titration of LD-mitochondria ddFPs revealed that these sensors can be used at high concentrations to drive MCSs or can be titrated down to minimally perturb and visualize endogenous MCSs. We show that Contact-FP probes can be used to: (1) visualize LD-mitochondria MCS dynamics, (2) observe changes in LD-mitochondria MCS dynamics upon overexpression of PLIN5, a known LD-mitochondrial tether, and (3) visualize two MCSs that share one organelle simultaneously (e.g., LD-mitochondria and LD-ER MCSs). Contact-FP probes can be optimized to visualize MCSs between any pair of organelles represented in the toolkit.
    Keywords:  biosensors; caveolae; endoplasmic reticulum; fluorescent proteins; lipid droplets; lysosomes; membrane contact sites; mitochondria; organelles; peroxisomes; plasma membrane
    DOI:  https://doi.org/10.1177/25152564241228911
  46. Proteins. 2024 Feb 05.
    Computational evidences of a misfolding event in an aggregation-prone light chain preceding the formation of the non-native pathogenic dimer.
    Fausta Desantis, Mattia Miotto, Edoardo Milanetti, Giancarlo Ruocco, Lorenzo Di Rienzo.
      Antibody light chain amyloidosis is a disorder in which protein aggregates, mainly composed of immunoglobulin light chains, deposit in diverse tissues impairing the correct functioning of organs. Interestingly, due to the high susceptibility of antibodies to mutations, AL amyloidosis appears to be strongly patient-specific. Indeed, every patient will display their own mutations that will make the proteins involved prone to aggregation thus hindering the study of this disease on a wide scale. In this framework, determining the molecular mechanisms that drive the aggregation could pave the way to the development of patient-specific therapeutics. Here, we focus on a particular patient-derived light chain, which has been experimentally characterized. We investigated the early phases of the aggregation pathway through extensive full-atom molecular dynamics simulations, highlighting a structural rearrangement and the exposure of two hydrophobic regions in the aggregation-prone species. Next, we moved to consider the pathological dimerization process through docking and molecular dynamics simulations, proposing a dimeric structure as a candidate pathological first assembly. Overall, our results shed light on the first phases of the aggregation pathway for a light chain at an atomic level detail, offering new structural insights into the corresponding aggregation process.
    Keywords:  Light Chain Amyloidosis; Molecular dynamics simulation; Pathogenic Dimerization; Protein Aggregation; Protein misfolding
    DOI:  https://doi.org/10.1002/prot.26672
  47. EMBO J. 2024 Feb 09.
    Mitochondrial outer membrane integrity regulates a ubiquitin-dependent and NF-κB-mediated inflammatory response.
    Esmee Vringer, Rosalie Heilig, Joel S Riley, Annabel Black, Catherine Cloix, George Skalka, Alfredo E Montes-Gómez, Aurore Aguado, Sergio Lilla, Henning Walczak, Mads Gyrd-Hansen, Daniel J Murphy, Danny T Huang, Sara Zanivan, Stephen Wg Tait.
      Mitochondrial outer membrane permeabilisation (MOMP) is often essential for apoptosis, by enabling cytochrome c release that leads to caspase activation and rapid cell death. Recently, MOMP has been shown to be inherently pro-inflammatory with emerging cellular roles, including its ability to elicit anti-tumour immunity. Nonetheless, how MOMP triggers inflammation and how the cell regulates this remains poorly defined. We find that upon MOMP, many proteins localised either to inner or outer mitochondrial membranes are ubiquitylated in a promiscuous manner. This extensive ubiquitylation serves to recruit the essential adaptor molecule NEMO, leading to the activation of pro-inflammatory NF-κB signalling. We show that disruption of mitochondrial outer membrane integrity through different means leads to the engagement of a similar pro-inflammatory signalling platform. Therefore, mitochondrial integrity directly controls inflammation, such that permeabilised mitochondria initiate NF-κB signalling.
    Keywords:  Cell Death; Inflammation; Mitochondria; NF-κB; Ubiquitin
    DOI:  https://doi.org/10.1038/s44318-024-00044-1
  48. iScience. 2024 Feb 16. 27(2): 108883
    Deficient tRNA posttranscription modification dysregulated the mitochondrial quality controls and apoptosis.
    Yunfan He, Gao Zhu, Xincheng Li, Mi Zhou, Min-Xin Guan.
      Mitochondria are dynamic organelles in cellular metabolism and physiology. Mitochondrial DNA (mtDNA) mutations are associated with a broad spectrum of clinical abnormalities. However, mechanisms underlying mtDNA mutations regulate intracellular signaling related to the mitochondrial and cellular integrity are less explored. Here, we demonstrated that mt-tRNAMet 4435A>G mutation-induced nucleotide modification deficiency dysregulated the expression of nuclear genes involved in cytosolic proteins involved in oxidative phosphorylation system (OXPHOS) and impaired the assemble and integrity of OXPHOS complexes. These dysfunctions caused mitochondrial dynamic imbalance, thereby increasing fission and decreasing fusion. Excessive fission impaired the process of autophagy including initiation phase, formation, and maturation of autophagosome. Strikingly, the m.4435A>G mutation upregulated the PARKIN dependent mitophagy pathways but downregulated the ubiquitination-independent mitophagy. These alterations promoted intrinsic apoptotic process for the removal of damaged cells. Our findings provide new insights into mechanism underlying deficient tRNA posttranscription modification regulated intracellular signaling related to the mitochondrial and cellular integrity.
    Keywords:  Cell biology; Molecular physiology; Properties of biomolecules
    DOI:  https://doi.org/10.1016/j.isci.2024.108883
  49. Circ Res. 2024 Feb 07.
    Integrated Stress Response Potentiates Ponatinib-Induced Cardiotoxicity.
    Gege Yan, Zhenbo Han, Youjeong Kwon, Jordan Jousma, Sarath Babu Nukala, Benjamin L Prosser, Xiaoping Du, Sandra Pinho, Sang-Bing Ong, Won Hee Lee, Sang-Ging Ong.
       BACKGROUND: Mitochondrial dysfunction is a primary driver of cardiac contractile failure; yet, the cross talk between mitochondrial energetics and signaling regulation remains obscure. Ponatinib, a tyrosine kinase inhibitor used to treat chronic myeloid leukemia, is among the most cardiotoxic tyrosine kinase inhibitors and causes mitochondrial dysfunction. Whether ponatinib-induced mitochondrial dysfunction triggers the integrated stress response (ISR) to induce ponatinib-induced cardiotoxicity remains to be determined.
    METHODS: Using human-induced pluripotent stem cells-derived cardiomyocytes (hiPSC-CMs) and a recently developed mouse model of ponatinib-induced cardiotoxicity, we performed proteomic analysis, molecular and biochemical assays to investigate the relationship between ponatinib-induced mitochondrial stress and ISR and their role in promoting ponatinib-induced cardiotoxicity.
    RESULTS: Proteomic analysis revealed that ponatinib activated the ISR in cardiac cells. We identified GCN2 (general control nonderepressible 2) as the eIF2α (eukaryotic translation initiation factor) kinase responsible for relaying mitochondrial stress signals to trigger the primary ISR effector-ATF4 (activating transcription factor 4), upon ponatinib exposure. Mechanistically, ponatinib treatment exerted inhibitory effects on ATP synthase activity and reduced its expression levels resulting in ATP deficits. Perturbed mitochondrial function resulting in ATP deficits then acts as a trigger of GCN2-mediated ISR activation, effects that were negated by nicotinamide mononucleotide, an NAD+ precursor, supplementation. Genetic inhibition of ATP synthase also activated GCN2. Interestingly, we showed that the decreased abundance of ATP also facilitated direct binding of ponatinib to GCN2, unexpectedly causing its activation most likely because of a conformational change in its structure. Importantly, administering an ISR inhibition, ISRIB, protected human-induced pluripotent stem cell-derived cardiomyocytes against ponatinib. Ponatinib-treated mice also exhibited reduced cardiac function, effects that were attenuated upon systemic ISRIB administration. Importantly, ISRIB does not affect the antitumor effects of ponatinib in vitro.
    CONCLUSIONS: Neutralizing ISR hyperactivation could prevent or reverse ponatinib-induced cardiotoxicity. The findings that compromised ATP production potentiates GCN2-mediated ISR activation have broad implications across various cardiac diseases. Our results also highlight an unanticipated role of ponatinib in causing direct activation of a kinase target despite its role as an ATP-competitive kinase inhibitor.
    Keywords:  cardiotoxicity; mice; mitochondria; ponatinib; proteomics
    DOI:  https://doi.org/10.1161/CIRCRESAHA.123.323683
  50. Cell Death Differ. 2024 Feb 06.
    ISR inhibition reverses pancreatic β-cell failure in Wolfram syndrome models.
    Rui Hu, Xiangyi Chen, Qiang Su, Zhaoyue Wang, Xushu Wang, Mengting Gong, Minglu Xu, Rongrong Le, Yawei Gao, Peng Dai, Zhen-Ning Zhang, Li Shao, Weida Li.
      Pancreatic β-cell failure by WFS1 deficiency is manifested in individuals with wolfram syndrome (WS). The lack of a suitable human model in WS has impeded progress in the development of new treatments. Here, human pluripotent stem cell derived pancreatic islets (SC-islets) harboring WFS1 deficiency and mouse model of β cell specific Wfs1 knockout were applied to model β-cell failure in WS. We charted a high-resolution roadmap with single-cell RNA-seq (scRNA-seq) to investigate pathogenesis for WS β-cell failure, revealing two distinct cellular fates along pseudotime trajectory: maturation and stress branches. WFS1 deficiency disrupted β-cell fate trajectory toward maturation and directed it towards stress trajectory, ultimately leading to β-cell failure. Notably, further investigation of the stress trajectory identified activated integrated stress response (ISR) as a crucial mechanism underlying WS β-cell failure, characterized by aberrant eIF2 signaling in WFS1-deficient SC-islets, along with elevated expression of genes in regulating stress granule formation. Significantly, we demonstrated that ISRIB, an ISR inhibitor, efficiently reversed β-cell failure in WFS1-deficient SC-islets. We further validated therapeutic efficacy in vivo with β-cell specific Wfs1 knockout mice. Altogether, our study provides novel insights into WS pathogenesis and offers a strategy targeting ISR to treat WS diabetes.
    DOI:  https://doi.org/10.1038/s41418-024-01258-w
  51. Nat Commun. 2024 Feb 07. 15(1): 1158
    Tracing back primed resistance in cancer via sister cells.
    Jun Dai, Shuyu Zheng, Matías M Falco, Jie Bao, Johanna Eriksson, Sanna Pikkusaari, Sofia Forstén, Jing Jiang, Wenyu Wang, Luping Gao, Fernando Perez-Villatoro, Olli Dufva, Khalid Saeed, Yinyin Wang, Ali Amiryousefi, Anniina Färkkilä, Satu Mustjoki, Liisa Kauppi, Jing Tang, Anna Vähärautio.
      Exploring non-genetic evolution of cell states during cancer treatments has become attainable by recent advances in lineage-tracing methods. However, transcriptional changes that drive cells into resistant fates may be subtle, necessitating high resolution analysis. Here, we present ReSisTrace that uses shared transcriptomic features of sister cells to predict the states priming treatment resistance. Applying ReSisTrace in ovarian cancer cells perturbed with olaparib, carboplatin or natural killer (NK) cells reveals pre-resistant phenotypes defined by proteostatic and mRNA surveillance features, reflecting traits enriched in the upcoming subclonal selection. Furthermore, we show that DNA repair deficiency renders cells susceptible to both DNA damaging agents and NK killing in a context-dependent manner. Finally, we leverage the obtained pre-resistance profiles to predict and validate small molecules driving cells to sensitive states prior to treatment. In summary, ReSisTrace resolves pre-existing transcriptional features of treatment vulnerability, facilitating both molecular patient stratification and discovery of synergistic pre-sensitizing therapies.
    DOI:  https://doi.org/10.1038/s41467-024-45478-7
  52. Dev Cell. 2024 Jan 31. pii: S1534-5807(24)00029-7. [Epub ahead of print]
    Senescent cells and macrophages cooperate through a multi-kinase signaling network to promote intestinal transformation in Drosophila.
    Ishwaree Datta, Erdem Bangi.
      Cellular senescence is a conserved biological process that plays a crucial and context-dependent role in cancer. The highly heterogeneous and dynamic nature of senescent cells and their small numbers in tissues make in vivo mechanistic studies of senescence challenging. As a result, how multiple senescence-inducing signals are integrated in vivo to drive senescence in only a small number of cells is unclear. Here, we identify cells that exhibit multiple features of senescence in a Drosophila model of intestinal transformation, which emerge in response to concurrent activation of AKT, JNK, and DNA damage signaling within transformed tissue. Eliminating senescent cells, genetically or by treatment with senolytic compounds, reduces overgrowth and improves survival. We find that senescent cells promote tumorigenesis by recruiting Drosophila macrophages to the transformed tissue, which results in non-autonomous activation of JNK signaling. These findings identify senescent cell-macrophage interactions as an important driver of epithelial transformation.
    Keywords:  Drosophila; cell signaling; colon cancer; hemocyte; macrophage; senescence
    DOI:  https://doi.org/10.1016/j.devcel.2024.01.009
This page is being maintained by Thomas Krichel. It was last updated on 2024‒11‒22 at 4:27.