bims-proteo Biomed News
on Proteostasis
Issue of 2023–01–01
twenty-one papers selected by
Eric Chevet, INSERM
  1. SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
  2. Cytosolic stress granules relieve the ubiquitin-proteasome system in the nuclear compartment.
  3. A SNX1-SNX2-VAPB partnership regulates endosomal membrane rewiring in response to nutritional stress.
  4. Extracellular Chaperone Networks and the Export of J-Domain Proteins.
  5. Two modes of Cue2-mediated mRNA cleavage with distinct substrate recognition initiate no-go decay.
  6. Phosphorylation of the Hsp90 co-chaperone Hop changes its conformational dynamics and biological function.
  7. Mammalian hybrid prophagophore is a precursor to autophagosomes.
  8. One-Step Sortase-Mediated Chemoenzymatic Semisynthesis of Deubiquitinase-Resistant Ub-Peptide Conjugates.
  9. Endoplasmic reticulum calnexins participate in the primary root growth response to phosphate deficiency.
  10. The UBE2D ubiquitin conjugating enzymes: Potential regulatory hubs in development, disease and evolution.
  11. Regulatory role of endoplasmic reticulum resident chaperone protein ERp29 in anti-murine β-coronavirus host cell response.
  12. SPOP inhibits BRAF-dependent tumorigenesis through promoting non-degradative ubiquitination of BRAF.
  13. A ubiquitination cascade regulating the integrated stress response and survival in carcinomas.
  14. The roles of HSP40/DNAJ protein family in neurodegenerative diseases.
  15. UBE2J1 inhibits colorectal cancer progression by promoting ubiquitination and degradation of RPS3.
  16. Targeted Protein Degradation Induced by HEMTACs Based on HSP90.
  17. TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1.
  18. Targeted degradation via direct 26S proteasome recruitment.
  19. A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
  20. Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.
  21. Small non-coding RNA Interactome Capture reveals pervasive, carbon source-dependent tRNA engagement of yeast glycolytic enzymes.
  1. Proc Natl Acad Sci U S A. 2023 Jan 03. 120(1): e2213703120
    SUMO enhances unfolding of SUMO-polyubiquitin-modified substrates by the Ufd1/Npl4/Cdc48 complex.
    Hyein G Lee, Abigail A Lemmon, Christopher D Lima.
      The Ufd1/Npl4/Cdc48 complex is a universal protein segregase that plays key roles in eukaryotic cellular processes. Its functions orchestrating the clearance or removal of polyubiquitylated targets are established; however, prior studies suggest that the complex also targets substrates modified by the ubiquitin-like protein SUMO. Here, we show that interactions between Ufd1 and SUMO enhance unfolding of substrates modified by SUMO-polyubiquitin hybrid chains by the budding yeast Ufd1/Npl4/Cdc48 complex compared to substrates modified by polyubiquitin chains, a difference that is accentuated when the complex has a choice between these substrates. Incubating Ufd1/Npl4/Cdc48 with a substrate modified by a SUMO-polyubiquitin hybrid chain produced a series of single-particle cryo-EM structures that reveal features of interactions between Ufd1/Npl4/Cdc48 and ubiquitin prior to and during unfolding of ubiquitin. These results are consistent with cellular functions for SUMO and ubiquitin modifications and support a physical model wherein Ufd1/Npl4/Cdc48, SUMO, and ubiquitin conjugation pathways converge to promote clearance of proteins modified with SUMO and polyubiquitin.
    Keywords:  SUMO; quality control; segregase; stress; ubiquitin
    DOI:  https://doi.org/10.1073/pnas.2213703120
  2. EMBO J. 2022 Dec 27. e111802
    Cytosolic stress granules relieve the ubiquitin-proteasome system in the nuclear compartment.
    Shanshan Xu, Maria E Gierisch, Anna Katharina Schellhaus, Ina Poser, Simon Alberti, Florian A Salomons, Nico P Dantuma.
      The role of cytosolic stress granules in the integrated stress response has remained largely enigmatic. Here, we studied the functionality of the ubiquitin-proteasome system (UPS) in cells that were unable to form stress granules. Surprisingly, the inability of cells to form cytosolic stress granules had primarily a negative impact on the functionality of the nuclear UPS. While defective ribosome products (DRiPs) accumulated at stress granules in thermally stressed control cells, they localized to nucleoli in stress granule-deficient cells. The nuclear localization of DRiPs was accompanied by redistribution and enhanced degradation of SUMOylated proteins. Depletion of the SUMO-targeted ubiquitin ligase RNF4, which targets SUMOylated misfolded proteins for proteasomal degradation, largely restored the functionality of the UPS in the nuclear compartment in stress granule-deficient cells. Stress granule-deficient cells showed an increase in the formation of mutant ataxin-1 nuclear inclusions when exposed to thermal stress. Our data reveal that stress granules play an important role in the sequestration of cytosolic misfolded proteins, thereby preventing these proteins from accumulating in the nucleus, where they would otherwise infringe nuclear proteostasis.
    Keywords:  SUMO; protein quality control; proteostasis; stress granules; ubiquitin-proteasome system
    DOI:  https://doi.org/10.15252/embj.2022111802
  3. Life Sci Alliance. 2023 Mar;pii: e202201652. [Epub ahead of print]6(3):
    A SNX1-SNX2-VAPB partnership regulates endosomal membrane rewiring in response to nutritional stress.
    Juliane Da Graça, Juliette Charles, Morgane Djebar, Karla Alvarez-Valadez, Joëlle Botti, Etienne Morel.
      Nutrient deprivation ("starvation") is a major catabolic stress faced by mammalian cells in both pathological and physiological situations. Starvation induces autophagosome biogenesis in the immediate vicinity of ER and leads to lysosome spatial repositioning, but little is known about the consequences of nutritional stress on endosomes. Here, we report that starvation induces tethering of endosomal tubules to ER subregions, fostering autophagosome assembly. We show that this endosomal membrane generation is regulated by sorting nexin 1 (SNX1) protein and is important for the autophagic response. These newly formed SNX1 endosomal tubules establish connections with ER subdomains engaged in early autophagic machinery mobilization. Such endosome-ER transient tethers are regulated by a local dialog between SNX2, an endosomal partner of SNX1, and VAPB, an ER protein associated with autophagy initiation stage regulation. We propose that in a very early response to starvation, SNX1 and SNX2 cooperation induces and regulates endosomal membrane tubulation towards VAPB-positive ER subdomains involved in autophagosome biogenesis, highlighting the contribution of early endosomes in the cellular response to nutritional stress.
    DOI:  https://doi.org/10.26508/lsa.202201652
  4. J Biol Chem. 2022 Dec 26. pii: S0021-9258(22)01283-2. [Epub ahead of print] 102840
    Extracellular Chaperone Networks and the Export of J-Domain Proteins.
    Janice E A Braun.
      An extracellular network of molecular chaperones protects a diverse array of proteins that reside in or pass-through extracellular spaces. Proteins in the extracellular milieu face numerous challenges that can lead to protein misfolding and aggregation. As a checkpoint for proteins that move between cells, extracellular chaperone networks are of growing clinical relevance. J-domain proteins (JDPs) are ubiquitous molecular chaperones that are known for their essential roles in a wide array of fundamental cellular processes through their regulation of Hsp70s. As the largest molecular chaperone family, JDPs have long been recognized for their diverse functions within cells. Some JDPs are elegantly selective for their 'client proteins', some do not discriminate among substrates and others act co-operatively on the same target. The realization that JDPs are exported through both classical and unconventional secretory pathways has fueled investigation into the roles that JDPs play in protein quality control and intercellular communication. The proposed functions of exported JDPs are diverse. Studies suggest that export of DnaJB11 enhances extracellular proteostasis, that intercellular movement of DnaJB1 or DnaJB6 enhances the proteostasis capacity in recipient cells, while the import of DnaJB8 increases resistance to chemotherapy in recipient cancer cells. In addition, the export of DnaJC5 and concurrent DnaJC5-dependent ejection of dysfunctional and aggregation-prone proteins are implicated in the prevention of neurodegeneration. This review provides a brief overview of the current understanding of the extracellular chaperone networks and outlines the first wave of studies describing the cellular export of JDPs.
    Keywords:  DnaJ; EVs; J Domain Proteins; JDP; exosomes; extracellular chaperones; extracellular vesicles; misfolded proteins; molecular chaperones
    DOI:  https://doi.org/10.1016/j.jbc.2022.102840
  5. Nucleic Acids Res. 2022 Dec 30. pii: gkac1172. [Epub ahead of print]
    Two modes of Cue2-mediated mRNA cleavage with distinct substrate recognition initiate no-go decay.
    Shota Tomomatsu, Atsuya Watanabe, Petr Tesina, Satoshi Hashimoto, Ken Ikeuchi, Sihan Li, Yoshitaka Matsuo, Roland Beckmann, Toshifumi Inada.
      Ribosome collisions are recognized by E3 ubiquitin ligase Hel2/ZNF598, leading to RQC (ribosome-associated quality control) and to endonucleolytic cleavage and degradation of the mRNA termed NGD (no-go decay). NGD in yeast requires the Cue2 endonuclease and occurs in two modes, either coupled to RQC (NGDRQC+) or RQC uncoupled (NGDRQC-). This is mediated by an unknown mechanism of substrate recognition by Cue2. Here, we show that the ubiquitin binding activity of Cue2 is required for NGDRQC- but not for NGDRQC+, and that it involves the first two N-terminal Cue domains. In contrast, Trp122 of Cue2 is crucial for NGDRQC+. Moreover, Mbf1 is required for quality controls by preventing +1 ribosome frameshifting induced by a rare codon staller. We propose that in Cue2-dependent cleavage upstream of the collided ribosomes (NGDRQC-), polyubiquitination of eS7 is recognized by two N-terminal Cue domains of Cue2. In contrast, for the cleavage within collided ribosomes (NGDRQC+), the UBA domain, Trp122 and the interaction between Mbf1 and uS3 are critical.
    DOI:  https://doi.org/10.1093/nar/gkac1172
  6. J Mol Biol. 2022 Dec 23. pii: S0022-2836(22)00558-7. [Epub ahead of print] 167931
    Phosphorylation of the Hsp90 co-chaperone Hop changes its conformational dynamics and biological function.
    Matteo Castelli, Kaushik Bhattacharya, Ernest Abboud, Stefano A Serapian, Didier Picard, Giorgio Colombo.
      The molecular chaperones Hsp90 and Hsp70 and their regulatory co-chaperone Hop play a key role at the crossroads of the folding pathways of numerous client proteins by forming fine-tuned multiprotein complexes. Alterations of the biomolecules involved may functionally impact the chaperone machinery: here, we integrate simulations and experiments to unveil how Hop conformational fitness and interactions can be controlled by the perturbation of just one residue. Specifically, we unveil how mechanisms mediated by Hop residue Y354 control Hop open and closed states, which affect binding of Hsp70/Hsp90. Phosphorylation or mutation of Hop-Y354 are shown to favor structural ensembles that are indeed not optimal for stable interactions with Hsp90 and Hsp70. This disfavors cellular accumulation of the stringent Hsp90 clients glucocorticoid receptor and the viral tyrosine kinase v-Src, with detrimental effects on v-Src activity. Our results show how the post-translational modification of a specific residue in Hop provides a regulation mechanism for the larger chaperone complex of which it is part. In this framework, the effects of one single alteration are amplified at the cellular level through the perturbation of protein-interaction networks.
    Keywords:  Conformational Selection; Hsp90, Hsp70; Molecular Chaperones; Molecular Dynamics; Post-Translational Modification
    DOI:  https://doi.org/10.1016/j.jmb.2022.167931
  7. Autophagy. 2022 Dec 26.
    Mammalian hybrid prophagophore is a precursor to autophagosomes.
    Suresh Kumar, Ruheena Javed, Masroor A Paddar, Eeva-Liisa Eskelinen, Graham S Timmins, Vojo Deretic.
      SUMMARYThe precursors to mammalian autophagosomes originate from pre-existing membranes contributed by a number of sources, and subsequently enlarge through intermembrane lipid transfer, then close to sequester the cargo, and merge with lysosomes to degrade the cargo. Using cellular and in vitro membrane fusion analyses coupled with proteomic and biochemical studies we show that autophagosomes are formed from a hybrid membrane compartment referred to as a prophagophore or HyPAS (hybrid preautophagosomal structure). HyPAS is initially LC3-negative and subsequently becomes an LC3-positive phagophore. The prophagophore emerges through fusion of RB1CC1/FIP200-containing vesicles, derived from the cis-Golgi, with endosomally derived ATG16L1 membranes. A specialized Ca2+-responsive apparatus controls prophagophore biogenesis and can be modulated by pharmacological agents such as SIGMAR1 agonists and antagonists including chloroquine. Autophagic prophagophore formation is inhibited during SARS-CoV-2 infection and is recapitulated by expression of SARS-CoV-2 nsp6. These findings show that mammalian autophagosomal prophagophores emerge via the convergence of secretory and endosomal pathways in a process that is targeted by microbial factors including coronaviral membrane proteins.
    Keywords:  Autophagy; COVID19; Golgi; HyPAS prophagophore; LC3; calcium; endoplasmic reticulum; endosome; syntaxin
    DOI:  https://doi.org/10.1080/15548627.2022.2161728
  8. ACS Omega. 2022 Dec 20. 7(50): 46693-46701
    One-Step Sortase-Mediated Chemoenzymatic Semisynthesis of Deubiquitinase-Resistant Ub-Peptide Conjugates.
    Avinash K Singh, Sumit Murmu, Artur Krężel.
      Post-translational modifications (PTMs) of proteins increase the functional diversity of the proteome and play crucial regulatory roles in cellular processes. Ubiquitination is a highly regulated and reversible PTM accomplished by a complex multistep process with the sequential action of several specific ubiquitinating (E1-E3) and deubiquitinating enzymes. The different types of ubiquitination (mono-, poly-mono-, and poly-) and the presence of several target sites in a single substrate add to its complexity, which makes the in vitro reconstitution of this ubiquitin (Ub) machinery a quite cumbersome process. Defects in components of the ubiquitination process also contribute to disease pathogenesis, especially cancer and neurodegeneration. This makes them of interest as potential therapeutic targets. Therefore, the development of efficient and reliable methods that will generate a highly homogeneous ubiquitinated peptide and protein conjugate is a topical subject area of research. In this report, we describe the development of a simple and efficient in vitro sortase-mediated chemoenzymatic strategy for semisynthesis of defined and homogeneous ubiquitin conjugates with more than 90% yield. This was achieved by engineering a sortase recognition motif in the dynamic C-terminus of ubiquitin and its conjugation to an isopeptide-linked di-Gly appended peptide LMFK(ε-GG)TEG corresponding to the ubiquitination site residues 383LMFKTEG389 of p53. The defined and homogeneous ubiquitin conjugates were also weighed for their recognition propensity by deubiquitinating enzymes. This facile semisynthesis of ubiquitin conjugates establishes a simple one-step sortase-mediated chemoenzymatic route for the synthesis of homogeneous and defined isopeptide-linked polypeptides and will help in understanding the complexity of the ubiquitination machinery as well as designing isopeptide drugs and therapeutics.
    DOI:  https://doi.org/10.1021/acsomega.2c05652
  9. Plant Physiol. 2022 Dec 26. pii: kiac595. [Epub ahead of print]
    Endoplasmic reticulum calnexins participate in the primary root growth response to phosphate deficiency.
    Jonatan Montpetit, Joaquín Clúa, Yi-Fang Hsieh, Evangelia Vogiatzaki, Jens Müller, Steffen Abel, Richard Strasser, Yves Poirier.
      Accumulation of incompletely folded proteins in the endoplasmic reticulum (ER) leads to ER stress, activates ER protein degradation pathways, and upregulates genes involved in protein folding. This process is known as the unfolded protein response (UPR). The role of ER protein folding in plant responses to nutrient deficiencies is unclear. We analyzed Arabidopsis (Arabidopsis thaliana) mutants affected in ER protein quality control and established that both CALNEXIN (CNX) genes function in the primary root's response to phosphate (Pi) deficiency. CNX1 and CNX2 are homologous ER lectins promoting protein folding of N-glycosylated proteins via the recognition of the GlcMan9GlcNAc2 glycan. Growth of cnx1-1 and cnx2-2 single mutants was similar to that of the wild type under high and low Pi conditions, but the cnx1-1 cnx2-2 double mutant showed decreased primary root growth under low Pi conditions due to reduced meristematic cell division. This phenotype was specific to Pi deficiency; the double mutant responded normally to osmotic and salt stress. Expression of CNX2 mutated in amino acids involved in binding the GlcMan9GlcNAc2 glycan failed to complement the cnx1-1 cnx2-2 mutant. The root growth phenotype was Fe dependent and was associated with root apoplastic Fe accumulation. Two genes involved in Fe-dependent inhibition of primary root growth under Pi deficiency, the ferroxidase LOW PHOSPHATE 1 (LPR1) and P5-type ATPase PLEIOTROPIC DRUG RESISTANCE 2 (PDR2) were epistatic to CNX1/CNX2. Overexpressing PDR2 failed to complement the cnx1-1 cnx2-2 root phenotype. The cnx1-1 cnx2-2 mutant showed no evidence of UPR activation, indicating a limited effect on ER protein folding. CNX might process a set of N-glycosylated proteins specifically involved in the response to Pi deficiency.
    DOI:  https://doi.org/10.1093/plphys/kiac595
  10. Front Cell Dev Biol. 2022 ;10 1058751
    The UBE2D ubiquitin conjugating enzymes: Potential regulatory hubs in development, disease and evolution.
    Monica Roman-Trufero, Niall Dillon.
      Ubiquitination of cellular proteins plays critical roles in key signalling pathways and in the regulation of protein turnover in eukaryotic cells. E2 ubiquitin conjugating enzymes function as essential intermediates in ubiquitination reactions by acting as ubiquitin donors for the E3 ubiquitin ligase enzymes that confer substrate specificity. The members of the UBE2D family of E2 enzymes are involved in regulating signalling cascades through ubiquitination of target proteins that include receptor tyrosine kinases (RTKs) and components of the Hedgehog, TGFβ and NFκB pathways. UBE2D enzymes also function in transcriptional control by acting as donors for ubiquitination of histone tails by the Polycomb protein Ring1B and the DNA methylation regulator UHRF1 as well as having roles in DNA repair and regulation of the level of the tumour suppressor p53. Here we review the functional roles and mechanisms of regulation of the UBE2D proteins including recent evidence that regulation of the level of UBE2D3 is critical for controlling ubiquitination of specific targets during development. Cellular levels of UBE2D3 have been shown to be regulated by phosphorylation, which affects folding of the protein, reducing its stability. Specific variations in the otherwise highly conserved UBE2D3 protein sequence in amniotes and in a subgroup of teleost fishes, the Acanthomorpha, suggest that the enzyme has had important roles during vertebrate evolution.
    Keywords:  UBE2D3; development; evolution; phosphorylation; ubiquitination
    DOI:  https://doi.org/10.3389/fcell.2022.1058751
  11. J Biol Chem. 2022 Dec 23. pii: S0021-9258(22)01279-0. [Epub ahead of print] 102836
    Regulatory role of endoplasmic reticulum resident chaperone protein ERp29 in anti-murine β-coronavirus host cell response.
    Abhishek Bose, Grishma Kasle, Rishika Jana, Mahua Maulik, Deepthi Thomas, Vaishali Mulchandani, Priyanka Mukherjee, Michael Koval, Jayasri Das Sarma.
      Gap junctional intercellular communication (GJIC) involving astrocytes is important for proper CNS homeostasis. As determined in our previous studies, trafficking of the predominant astrocyte GJ protein, Connexin43 (Cx43), is disrupted in response to infection with a neurotropic murine β-coronavirus (MHV-A59). However, how host factors are involved in Cx43 trafficking and the infection response is not clear. Here, we show that Cx43 retention due to MHV-A59 infection was associated with increased ER stress and reduced expression of chaperone protein ERp29. Treatment of MHV-A59-infected astrocytes with the chemical chaperone 4-sodium phenylbutyrate (4-PBA) increased ERp29 expression, rescued Cx43 transport to the cell surface, increased GJIC, and reduced ER stress. We obtained similar results using an astrocytoma cell line (DBT) upon MHV-A59 infection. Critically, DBT cells transfected to express exogenous ERp29 were resistant to MHV-A59 infection and showed increased Cx43-mediated GJIC. Treatment with Cx43 mimetic peptides inhibited GJIC and increased viral susceptibility, demonstrating a role for intercellular communication in reducing MHV-A59 infectivity. Taken together, these results support a therapeutically targetable ERp29-dependent mechanism where β-coronavirus infectivity is modulated by reducing ER stress and rescuing Cx43 trafficking and function.
    Keywords:  Connexin43; ER stress; ERp29; MHV-A59; astrocytes; gap junctional intercellular communication (GJIC); murine coronavirus (mCoV); β-coronavirus infection
    DOI:  https://doi.org/10.1016/j.jbc.2022.102836
  12. Cell Biosci. 2022 Dec 30. 12(1): 211
    SPOP inhibits BRAF-dependent tumorigenesis through promoting non-degradative ubiquitination of BRAF.
    Kai Feng, Qing Shi, Dongyue Jiao, Yingji Chen, Wanqi Yang, Ke Su, Yalan Wang, Yan Huang, Pingzhao Zhang, Yao Li, Chenji Wang.
       BACKGROUND: The gene encoding the E3 ubiquitin ligase substrate-binding adapter Speckle-type BTB/POZ protein (SPOP) is frequently mutated in prostate cancer (PCa) and endometrial cancer (EC); however, the molecular mechanisms underlying the contribution of SPOP mutations to tumorigenesis remain poorly understood.
    METHODS: BRAF harbors a potential SPOP-binding consensus motif (SBC) motif. Co-immunoprecipitation assays demonstrated that BRAF interacts with SPOP. A series of functional analyses in cell lines were performed to investigate the biological significance of MAPK/ERK activation caused by SPOP mutations.
    RESULTS: Cytoplasmic SPOP binds to and induces non-degradative ubiquitination of BRAF, thereby reducing the interaction between BRAF and other core components of the MAPK/ERK pathway. SPOP ablation increased MAPK/ERK activation. EC- or PCa-associated SPOP mutants showed a reduced capacity to bind and ubiquitinate BRAF. Moreover, cancer-associated BRAF mutations disrupted the BRAF-SPOP interaction and allowed BRAF to evade SPOP-mediated ubiquitination, thereby upregulating MAPK/ERK signaling and enhancing the neoplastic phenotypes of cancer cells.
    CONCLUSIONS: Our findings provide new insights into the molecular link between SPOP mutation-driven tumorigenesis and aberrant BRAF-dependent activation of the MAPK/ERK pathway.
    Keywords:  BRAF; MAPK/ERK; Mutation; SPOP; Ubiquitination
    DOI:  https://doi.org/10.1186/s13578-022-00950-z
  13. Cancer Discov. 2022 Dec 28. pii: CD-22-1230. [Epub ahead of print]
    A ubiquitination cascade regulating the integrated stress response and survival in carcinomas.
    Lisa D Cervia, Tsukasa Shibue, Ashir A Borah, Benjamin Gaeta, Linh He, Lisa Leung, Naomi Li, Sydney M Moyer, Brian H Shim, Nancy Dumont, Alfredo Gonzalez, Nolan R Bick, Mariya Kazachkova, Joshua M Dempster, John Michael Krill-Burger, Federica Piccioni, Namrata D Udeshi, Meagan E Olive, Steven A Carr, David E Root, James M McFarland, Francisca Vazquez, William C Hahn.
      Systematic identification of signaling pathways required for the fitness of cancer cells will facilitate the development of new cancer therapies. We used gene essentiality measurements in 1,086 cancer cell lines to identify selective co-essentiality modules and found that a ubiquitin ligase complex composed of UBA6, BIRC6, KCMF1 and UBR4, which is required for the survival of a subset of epithelial tumors that exhibit a high degree of aneuploidy. Suppressing BIRC6 in cell lines that are dependent on this complex led to a substantial reduction in cell fitness in vitro and potent tumor regression in vivo. Mechanistically, BIRC6 suppression resulted in selective activation of the integrated stress response (ISR) by stabilization of the heme-regulated inhibitor (HRI), a direct ubiquitination target of the UBA6/BIRC6/KCMF1/UBR4 complex. These observations uncover a novel ubiquitination cascade that regulates ISR and highlight the potential of ISR activation as a new therapeutic strategy.
    DOI:  https://doi.org/10.1158/2159-8290.CD-22-1230
  14. Zhejiang Da Xue Xue Bao Yi Xue Ban. 2022 Nov 25. 51(5): 640-646
    The roles of HSP40/DNAJ protein family in neurodegenerative diseases.
    Yinghui He, Zhiping Wang.
      Molecular chaperones and co-chaperones facilitate the assembly of newly synthesized polypeptides and refolding of unfolded or misfolded proteins, thereby maintaining protein homeostasis in cells. As co-chaperones of the master chaperone heat shock protein (HSP) 70, the HSP40 (DNAJ) proteins are largest chaperone family in eukaryotic cells. They contain a characteristic J-domain which mediates interaction with HSP70, thereby helping protein folding. It is well perceived that protein homeostasis is vital for neuronal health. DNAJ family proteins have been linked to the occurrence and progression of neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, Huntington's disease, spinocerebellar ataxia, Charcot-Marie-Tooth disease, spinal muscular atrophy, distal hereditary motor neuropathy, limb-girdle type muscular dystrophy, neuronal ceroid lipofuscinosis and essential tremor in recent studies. DNAJA1 effectively degrades huntington aggregates; DNAJB1 can degrade protein aggregates ataxin-3; DNAJB2 can inhibit the formation of huntington aggregates; DNAJB6 can inhibit the aggregation of Aβ 42 and α-synuclein; DNAJC5 can promote the release of TDP-43, τ protein, and α-synuclein into the extracellular space. Mutations in the essential tremor-associated DNAJC13 gene can prevent endosome protein trafficking. This article reviews the mechanism of DNAJ protein family in neurodegenerative diseases.
    Keywords:  DNAJ; HSP40; Molecular chaperones; Neurodegenerative diseases; Protein homeostasis; Review
    DOI:  https://doi.org/10.3724/zdxbyxb-2021-0406
  15. Oncogene. 2022 Dec 26.
    UBE2J1 inhibits colorectal cancer progression by promoting ubiquitination and degradation of RPS3.
    Tuo Wang, Chi Jin, Peng Yang, Zhihao Chen, Jiangzhou Ji, Qingyang Sun, Sheng Yang, Yifei Feng, Junwei Tang, Yueming Sun.
      Ubiquitin-conjugating enzyme E2 J1 (UBE2J1) has been proven to participate in the ubiquitination of multiple substrate proteins. However, the underlying mechanisms of UBE2J1 as a ubiquitin-conjugating enzyme participating in cancer development and progression remain largely unknown. Here, we identified that UBE2J1 is downregulated in colorectal cancer (CRC) tissues and cell lines which are mediated by DNA hypermethylation of its promoter, and decreased UBE2J1 is associated with poor prognosis. Functionally, UBE2J1 serving as a suppressor gene inhibits the proliferation and metastasis of CRC cells. Mechanistically, UBE2J1-TRIM25, forming an E2-E3 complex, physically interacts with and targets RPS3 for ubiquitination and degradation at the K214 residue. The downregulated RPS3 caused by UBE2J1 overexpression restrains NF-κB translocation into the nucleus and therefore inactivates the NF-κB signaling pathway. Our study revealed a novel role of UBE2J1-mediated RPS3 poly-ubiquitination and degradation in disrupting the NF-κB signaling pathway, which may serve as a novel and promising biomarker and therapeutic target for CRC.
    DOI:  https://doi.org/10.1038/s41388-022-02581-7
  16. J Med Chem. 2022 Dec 27.
    Targeted Protein Degradation Induced by HEMTACs Based on HSP90.
    Zhenzhen Li, Siyue Ma, Ling Zhang, Shuxin Zhang, Zhao Ma, Lupei Du, Minyong Li.
      Targeted protein degradation (TPD) strategies open up new avenues for therapeutics and provide powerful tools for biological inquiry. Herein, we present a brand-new approach, termed heat shock protein 90 (HSP90)-mediated targeting chimeras (HEMTACs), to induce intracellular protein degradation by bridging a target protein to HSP90 to drive the downregulation of proteins. We successfully showcase HEMTACs for cyclin-dependent kinase 4 and 6 (CDK4/6) by using a flexible linker to connect the targeting warhead of CDK4/6 with the HSP90 ligand. Overall, our study delivers a series of evidence that HEMTACs can serve as a valuable addition to TPD strategies, most prominently proteolysis-targeting chimera technology.
    DOI:  https://doi.org/10.1021/acs.jmedchem.2c01648
  17. J Cell Biol. 2023 Feb 06. pii: e202108144. [Epub ahead of print]222(2):
    TBK1 phosphorylation activates LIR-dependent degradation of the inflammation repressor TNIP1.
    Jianwen Zhou, Nikoline Lander Rasmussen, Hallvard Lauritz Olsvik, Vyacheslav Akimov, Zehan Hu, Gry Evjen, Stéphanie Kaeser-Pebernard, Devanarayanan Siva Sankar, Carole Roubaty, Pauline Verlhac, Nicole van de Beck, Fulvio Reggiori, Yakubu Princely Abudu, Blagoy Blagoev, Trond Lamark, Terje Johansen, Jörn Dengjel.
      Limitation of excessive inflammation due to selective degradation of pro-inflammatory proteins is one of the cytoprotective functions attributed to autophagy. In the current study, we highlight that selective autophagy also plays a vital role in promoting the establishment of a robust inflammatory response. Under inflammatory conditions, here TLR3-activation by poly(I:C) treatment, the inflammation repressor TNIP1 (TNFAIP3 interacting protein 1) is phosphorylated by Tank-binding kinase 1 (TBK1) activating an LIR motif that leads to the selective autophagy-dependent degradation of TNIP1, supporting the expression of pro-inflammatory genes and proteins. This selective autophagy efficiently reduces TNIP1 protein levels early (0-4 h) upon poly(I:C) treatment to allow efficient initiation of the inflammatory response. At 6 h, TNIP1 levels are restored due to increased transcription avoiding sustained inflammation. Thus, similarly as in cancer, autophagy may play a dual role in controlling inflammation depending on the exact state and timing of the inflammatory response.
    DOI:  https://doi.org/10.1083/jcb.202108144
  18. Nat Chem Biol. 2023 Jan;19(1): 55-63
    Targeted degradation via direct 26S proteasome recruitment.
    Charlene Bashore, Sumit Prakash, Matthew C Johnson, Ryan J Conrad, Ivy A Kekessie, Suzie J Scales, Noriko Ishisoko, Tracy Kleinheinz, Peter S Liu, Nataliya Popovych, Aaron T Wecksler, Lijuan Zhou, Christine Tam, Inna Zilberleyb, Rajini Srinivasan, Robert A Blake, Aimin Song, Steven T Staben, Yingnan Zhang, David Arnott, Wayne J Fairbrother, Scott A Foster, Ingrid E Wertz, Claudio Ciferri, Erin C Dueber.
      Engineered destruction of target proteins by recruitment to the cell's degradation machinery has emerged as a promising strategy in drug discovery. The majority of molecules that facilitate targeted degradation do so via a select number of ubiquitin ligases, restricting this therapeutic approach to tissue types that express the requisite ligase. Here, we describe a new strategy of targeted protein degradation through direct substrate recruitment to the 26S proteasome. The proteolytic complex is essential and abundantly expressed in all cells; however, proteasomal ligands remain scarce. We identify potent peptidic macrocycles that bind directly to the 26S proteasome subunit PSMD2, with a 2.5-Å-resolution cryo-electron microscopy complex structure revealing a binding site near the 26S pore. Conjugation of this macrocycle to a potent BRD4 ligand enabled generation of chimeric molecules that effectively degrade BRD4 in cells, thus demonstrating that degradation via direct proteasomal recruitment is a viable strategy for targeted protein degradation.
    DOI:  https://doi.org/10.1038/s41589-022-01218-w
  19. Mol Syst Biol. 2022 Dec 27. e11147
    A single-cell RNA labeling strategy for measuring stress response upon tissue dissociation.
    Anika Neuschulz, Olga Bakina, Victor Badillo-Lisakowski, Pedro Olivares-Chauvet, Thomas Conrad, Michael Gotthardt, Helmut Kettenmann, Jan Philipp Junker.
      Tissue dissociation, a crucial step in single-cell sample preparation, can alter the transcriptional state of a sample through the intrinsic cellular stress response. Here we demonstrate a general approach for measuring transcriptional response during sample preparation. In our method, transcripts made during dissociation are labeled for later identification upon sequencing. We found general as well as cell-type-specific dissociation response programs in zebrafish larvae, and we observed sample-to-sample variation in the dissociation response of mouse cardiomyocytes despite well-controlled experimental conditions. Finally, we showed that dissociation of the mouse hippocampus can lead to the artificial activation of microglia. In summary, our approach facilitates experimental optimization of dissociation procedures as well as computational removal of transcriptional perturbation response.
    Keywords:  RNA labeling; SLAM-seq; cellular stress response; single-cell transcriptomics; tissue dissociation
    DOI:  https://doi.org/10.15252/msb.202211147
  20. Cell Rep Med. 2022 Dec 23. pii: S2666-3791(22)00441-4. [Epub ahead of print] 100877
    Proteomics separates adult-type diffuse high-grade gliomas in metabolic subgroups independent of 1p/19q codeletion and across IDH mutational status.
    Jakob Maximilian Bader, Nikolaus Deigendesch, Martin Misch, Matthias Mann, Arend Koch, Felix Meissner.
      High-grade adult-type diffuse gliomas are malignant neuroepithelial tumors with poor survival rates in combined chemoradiotherapy. The current WHO classification is based on IDH1/2 mutational and 1p/19q codeletion status. Glioma proteome alterations remain undercharacterized despite their promise for a better molecular patient stratification and therapeutic target identification. Here, we use mass spectrometry to characterize 42 formalin-fixed, paraffin-embedded (FFPE) samples from IDH-wild-type (IDHwt) gliomas, IDH-mutant (IDHmut) gliomas with and without 1p/19q codeletion, and non-neoplastic controls. Based on more than 5,500 quantified proteins and 5,000 phosphosites, gliomas separate by IDH1/2 mutational status but not by 1p/19q status. Instead, IDHmut gliomas split into two proteomic subtypes with widespread perturbations, including aerobic/anaerobic energy metabolism. Validations with three independent glioma proteome datasets confirm these subgroups and link the IDHmut subtypes to the established proneural and classic/mesenchymal subtypes in IDHwt glioma. This demonstrates common phenotypic subtypes across the IDH status with potential therapeutic implications for patients with IDHmut gliomas.
    Keywords:  1p/19q codeletion; IDH; glioblastoma; glioma; isocitrate dehydrogenase; proteomics
    DOI:  https://doi.org/10.1016/j.xcrm.2022.100877
  21. RNA. 2022 Dec 27. pii: rna.079408.122. [Epub ahead of print]
    Small non-coding RNA Interactome Capture reveals pervasive, carbon source-dependent tRNA engagement of yeast glycolytic enzymes.
    Claudio Asencio, Thomas Schwarzl, Sudeep Sahadevan, Matthias W Hentze.
      Small non-coding RNAs fulfill key functions in cellular and organismal biology, typically working in concert with RNA-binding proteins (RBPs). While proteome-wide methodologies have enormously expanded the repertoire of known RBPs, these methods do not distinguish RBPs binding to small non-coding RNAs from the rest. To specifically identify this relevant subclass of RBPs, we developed small non-coding RNA interactome capture (snRIC2C) based on the differential RNA-binding capacity of silica matrices (2C). We define the S. cerevisiae proteome of nearly 300 proteins that specifically binds to RNAs smaller than 200 nucleotides in length (snRBPs), identifying informative distinctions from the total RNA-binding proteome determined in parallel. Strikingly, the snRBPs include most glycolytic enzymes from yeast. With further methodological developments using silica matrices, 12 tRNAs were identified as specific binders of the glycolytic enzyme GAPDH. We show that tRNA engagement of GAPDH is carbon source-dependent and regulated by the RNA polymerase III repressor Maf1, suggesting a regulatory interaction between glycolysis and RNA polymerase III activity. We conclude that snRIC2C and other 2C-derived methods greatly facilitate the study of RBPs, revealing previously unrecognised interactions.
    Keywords:  GPADH; Glycolytic enzymes; small non-coding RNA binding proteome; snRIC2C; tRNA
    DOI:  https://doi.org/10.1261/rna.079408.122
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