bims-proteo Biomed News
on Proteostasis
Issue of 2022–08–07
25 papers selected by
Eric Chevet, INSERM
  1. Multiple UBX proteins reduce the ubiquitin threshold of the mammalian p97-UFD1-NPL4 unfoldase.
  2. Mechanism of client selection by the protein quality-control factor UBE2O.
  3. TOLLIP-mediated autophagic degradation pathway links the VCP-TMEM63A-DERL1 signaling axis to triple-negative breast cancer progression.
  4. Disease-associated mutations within the yeast DNAJB6 homolog Sis1 slow conformer-specific substrate processing and can be corrected by the modulation of nucleotide exchange factors.
  5. Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation.
  6. Induction of zinc finger protein RNF6 auto-ubiquitination for the treatment of myeloma and chronic myeloid leukemia.
  7. Fic-mediated AMPylation tempers the unfolded protein response during physiological stress.
  8. Ca2+ signalling system initiated by endoplasmic reticulum stress stimulates PERK activation.
  9. SDC1-dependent TGM2 determines radiosensitivity in glioblastoma by coordinating EPG5-mediated fusion of autophagosomes with lysosomes.
  10. KCTD7 mutations impair the trafficking of lysosomal enzymes through CLN5 accumulation to cause neuronal ceroid lipofuscinoses.
  11. trim-21 promotes proteasomal degradation of CED-1 for apoptotic cell clearance in C. elegans.
  12. Selective Secretion of KDEL-Bearing Proteins: Mechanisms and Functions.
  13. PABP/purine-rich motif as an initiation module for cap-independent translation in pattern-triggered immunity.
  14. O-GlcNAcylation stabilizes the autophagy-initiating kinase ULK1 by inhibiting chaperone-mediated autophagy upon HPV infection.
  15. Deficiency of Murine UFM1-Specific E3 Ligase Causes Microcephaly and Inflammation.
  16. Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence.
  17. Role of Long Non-Coding RNA in Regulating ER Stress Response on the Progression of Diabetic Complications.
  18. TGFBR3 supports anoikis through suppressing ATF4 signaling.
  19. Molecular chaperones in DNA repair mechanisms: Role in genomic instability and proteostasis in cancer.
  20. Hypoxia-induced proteasomal degradation of DBC1 by SIAH2 in breast cancer progression.
  21. The E3 ubiquitin ligase HECTD1 contributes to cell proliferation through an effect on mitosis.
  22. Calcium homeostasis and cancer: insights from endoplasmic reticulum-centered organelle communications.
  23. Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state.
  24. Identification of an ERN1 target site within EGFP mRNA.
  25. Deacetylation of ATG4B promotes autophagy initiation under starvation.
  1. Elife. 2022 Aug 03. pii: e76763. [Epub ahead of print]11
    Multiple UBX proteins reduce the ubiquitin threshold of the mammalian p97-UFD1-NPL4 unfoldase.
    Ryo Fujisawa, Cristian Polo Rivera, Karim Labib.
      The p97 / Cdc48 ATPase and its ubiquitin receptors Ufd1-Npl4 are essential to unfold ubiquitylated proteins in many areas of eukaryotic cell biology. In yeast, Cdc48-Ufd1-Npl4 is controlled by a quality control mechanism, whereby substrates must be conjugated to at least five ubiquitins. Here we show that mammalian p97-UFD1-NPL4 is governed by a complex interplay between additional p97 cofactors and the number of conjugated ubiquitins. Using reconstituted assays for the disassembly of ubiquitylated CMG (Cdc45-MCM-GINS) helicase by human p97-UFD1-NPL4, we show that the unfoldase has a high ubiquitin threshold for substrate unfolding, which can be reduced by the UBX proteins UBXN7, FAF1 or FAF2. Our data indicate that the UBX proteins function by binding to p97-UFD1-NPL4 and stabilising productive interactions between UFD1-NPL4 and K48-linked chains of at least five ubiquitins. Stimulation by UBXN7 is dependent upon known ubiquitin binding motifs, whereas FAF1 and FAF2 use a previously uncharacterised coiled-coil domain to reduce the ubiquitin threshold of p97-UFD1-NPL4. We show that deleting the Ubnx7 and Faf1 genes impairs CMG disassembly during S-phase and mitosis and sensitises cells to reduced ubiquitin ligase activity. These findings indicate that multiple UBX proteins are important for the efficient unfolding of ubiquitylated proteins by p97-UFD1-NPL4 in mammalian cells.
    Keywords:  biochemistry; chemical biology; chromosomes; gene expression; human; mouse
    DOI:  https://doi.org/10.7554/eLife.76763
  2. Nat Struct Mol Biol. 2022 Aug 01.
    Mechanism of client selection by the protein quality-control factor UBE2O.
    Matthew C J Yip, Samantha F Sedor, Sichen Shao.
      The E2/E3 enzyme UBE2O ubiquitylates diverse clients to mediate important processes, including targeting unassembled 'orphan' proteins for quality control and clearing ribosomes during erythropoiesis. How quality-control factors, such as UBE2O, select clients on the basis of heterogeneous features is largely unknown. Here, we show that UBE2O client selection is regulated by ubiquitin binding and a cofactor, NAP1L1. Attaching a single ubiquitin onto a client enhances UBE2O binding and multi-mono-ubiquitylation. UBE2O also repurposes the histone chaperone NAP1L1 as an adapter to recruit a subset of clients. Cryo-EM structures of human UBE2O in complex with NAP1L1 reveal a malleable client recruitment interface that is autoinhibited by the intrinsically reactive UBC domain. Adding a ubiquitylated client identifies a distinct ubiquitin-binding SH3-like domain required for client selection. Our findings reveal how multivalency and a feed-forward mechanism drive the selection of protein quality-control clients.
    DOI:  https://doi.org/10.1038/s41594-022-00807-6
  3. Autophagy. 2022 Aug 03. 1-17
    TOLLIP-mediated autophagic degradation pathway links the VCP-TMEM63A-DERL1 signaling axis to triple-negative breast cancer progression.
    Tai-Mei Zhang, Li Liao, Shao-Ying Yang, Min-Ying Huang, Yin-Ling Zhang, Ling Deng, Shu-Yuan Hu, Fan Yang, Fang-Lin Zhang, Zhi-Min Shao, Da-Qiang Li.
      Triple-negative breast cancer (TNBC) is the most challenging breast cancer subtype to treat due to the lack of effective targeted therapies. Transmembrane (TMEM) proteins represent attractive drug targets for cancer therapy, but biological functions of most members of the TMEM family remain unknown. Here, we report for the first time that TMEM63A (transmembrane protein 63A), a poorly characterized TMEM protein with unknown functions in human cancer, functions as a novel oncogene to promote TNBC cell proliferation, migration, and invasion in vitro and xenograft tumor growth and lung metastasis in vivo. Mechanistic investigations revealed that TMEM63A localizes in endoplasmic reticulum (ER) and lysosome membranes, and interacts with VCP (valosin-containing protein) and its cofactor DERL1 (derlin 1). Furthermore, TMEM63A undergoes autophagy receptor TOLLIP-mediated autophagic degradation and is stabilized by VCP through blocking its lysosomal degradation. Strikingly, TMEM63A in turn stabilizes oncoprotein DERL1 through preventing TOLLIP-mediated autophagic degradation. Notably, pharmacological inhibition of VCP by CB-5083 or knockdown of DERL1 partially abolishes the oncogenic effects of TMEM63A on TNBC progression both in vitro and in vivo. Collectively, these findings uncover a previously unknown functional and mechanistic role for TMEM63A in TNBC progression and provide a new clue for targeting TMEM63A-driven TNBC tumors by using a VCP inhibitor.Abbreviations: ATG16L1, autophagy related 16 like 1; ATG5, autophagy related 5; ATP5F1B/ATP5B, ATP synthase F1 subunit beta; Baf-A1, bafilomycin A1; CALCOCO2/NDP52, calcium binding and coiled-coil domain 2; CANX, calnexin; DERL1, derlin 1; EGFR, epidermal growth factor receptor; ER, endoplasmic reticulum; ERAD, endoplasmic reticulum-associated degradation; HSPA8, heat shock protein family A (Hsp70) member 8; IP, immunoprecipitation; LAMP2A, lysosomal associated membrane protein 2; NBR1, NBR1 autophagy cargo receptor; OPTN, optineurin; RT-qPCR, reverse transcription-quantitative PCR; SQSTM1/p62, sequestosome 1; TAX1BP1, Tax1 binding protein 1; TMEM63A, transmembrane protein 63A; TNBC, triple-negative breast cancer; TOLLIP, toll interacting protein; VCP, valosin containing protein.
    Keywords:  Macroautophagic degradation; proteostasis; selective autophagy receptor; transmembrane protein; triple-negative breast cancer
    DOI:  https://doi.org/10.1080/15548627.2022.2103992
  4. Nat Commun. 2022 Aug 05. 13(1): 4570
    Disease-associated mutations within the yeast DNAJB6 homolog Sis1 slow conformer-specific substrate processing and can be corrected by the modulation of nucleotide exchange factors.
    Ankan K Bhadra, Michael J Rau, Jil A Daw, James A J Fitzpatrick, Conrad C Weihl, Heather L True.
      Molecular chaperones, or heat shock proteins (HSPs), protect against the toxic misfolding and aggregation of proteins. As such, mutations or deficiencies within the chaperone network can lead to disease. Dominant mutations within DNAJB6 (Hsp40)-an Hsp70 co-chaperone-lead to a protein aggregation-linked myopathy termed Limb-Girdle Muscular Dystrophy Type D1 (LGMDD1). Here, we used the yeast prion model client in conjunction with in vitro chaperone activity assays to gain mechanistic insights into the molecular basis of LGMDD1. Here, we show how mutations analogous to those found in LGMDD1 affect Sis1 (a functional homolog of human DNAJB6) function by altering the structure of client protein aggregates, interfering with the Hsp70 ATPase cycle, dimerization and substrate processing; poisoning the function of wild-type protein. These results uncover the mechanisms through which LGMDD1-associated mutations alter chaperone activity, and provide insights relevant to potential therapeutic interventions.
    DOI:  https://doi.org/10.1038/s41467-022-32318-9
  5. Cell Rep. 2022 Aug 02. pii: S2211-1247(22)00981-0. [Epub ahead of print]40(5): 111168
    Human UFSP1 is an active protease that regulates UFM1 maturation and UFMylation.
    David Millrine, Thomas Cummings, Stephen P Matthews, Joshua J Peter, Helge M Magnussen, Sven M Lange, Thomas Macartney, Frederic Lamoliatte, Axel Knebel, Yogesh Kulathu.
      An essential first step in the post-translational modification of proteins with UFM1, UFMylation, is the proteolytic cleavage of pro-UFM1 to expose a C-terminal glycine. Of the two UFM1-specific proteases (UFSPs) identified in humans, only UFSP2 is reported to be active, since the annotated sequence of UFSP1 lacks critical catalytic residues. Nonetheless, efficient UFM1 maturation occurs in cells lacking UFSP2, suggesting the presence of another active protease. We herein identify UFSP1 translated from a non-canonical start site to be this protease. Cells lacking both UFSPs show complete loss of UFMylation resulting from an absence of mature UFM1. While UFSP2, but not UFSP1, removes UFM1 from the ribosomal subunit RPL26, UFSP1 acts earlier in the pathway to mature UFM1 and cleave a potential autoinhibitory modification on UFC1, thereby controlling activation of UFMylation. In summary, our studies reveal important distinctions in substrate specificity and localization-dependent functions for the two proteases in regulating UFMylation.
    Keywords:  CP: Cell biology; CP: Molecular biology; ER; UBA5; UFC1; UFM1; cysteine protease; endoplasmic reticulum; membrane protein; ribosome; ubiquitin; ubiquitin-like modifier
    DOI:  https://doi.org/10.1016/j.celrep.2022.111168
  6. J Biol Chem. 2022 Aug 01. pii: S0021-9258(22)00756-6. [Epub ahead of print] 102314
    Induction of zinc finger protein RNF6 auto-ubiquitination for the treatment of myeloma and chronic myeloid leukemia.
    Haixia Zhuang, Ying Ren, Chenyu Mao, Yueya Zhong, Zubin Zhang, Biyin Cao, Yuming Zhang, Jinqi Huang, Guoqiang Xu, Zhenqian Huang, Yujia Xu, Xinliang Mao.
      The zinc finger ubiquitin ligase RNF6 has been proposed as a potential therapeutic target in several cancers, but understanding its molecular mechanism of degradation has been elusive. In the present study, we find that RNF6 is degraded via auto-ubiquitination in a manner dependent on its Really Interesting New Gene (RING) domain. We determine that when the RING domain is deleted (ΔRING) or the core cysteine residues in the zinc finger are mutated (C632S/C635S), the wild-type protein, but not the ΔRING or mutant RNF6 protein, undergoes polyubiquitination. We also identify USP7 as a deubiquitinase of RNF6 by tandem mass spectrometry. We show that USP7 interacts with RNF6 and abolishes its K48-linked polyubiquitination, thereby preventing its degradation. In contrast, we found a USP7-specific inhibitor promotes RNF6 polyubiquitination, degradation, and cell death. Furthermore, we demonstrate anti-leukemic drug Nilotinib and anti-myeloma drug Panobinostat (LBH589) induce RNF6 K48-linked polyubiquitination and degradation in both multiple myeloma (MM) and leukemia cells. In agreement with our hypothesis on the mode of RNF6 degradation, we show these drugs promote RNF6 auto-ubiquitination in an in vitro ubiquitination system without other E3 ligases. Consistently, re-expression of RNF6 ablates drug-induced MM and leukemia cell apoptosis. Therefore, our results reveal that RNF6 is a RING E3 ligase that undergoes auto-ubiquitination, which could be abolished by USP7 and induced by anti-cancer drugs. We propose chemical induction of RNF6 auto-ubiquitination and degradation could be a novel strategy for the treatment of hematological malignancies including MM and leukemia.
    Keywords:  RNF6; USP7; auto-ubiquitination; leukemia; myeloma
    DOI:  https://doi.org/10.1016/j.jbc.2022.102314
  7. Proc Natl Acad Sci U S A. 2022 Aug 09. 119(32): e2208317119
    Fic-mediated AMPylation tempers the unfolded protein response during physiological stress.
    Amanda K Casey, Hillery F Gray, Suneeta Chimalapati, Genaro Hernandez, Andrew T Moehlman, Nathan Stewart, Hazel A Fields, Burak Gulen, Kelly A Servage, Karoliina Stefanius, Aubrie Blevins, Bret M Evers, Helmut Krämer, Kim Orth.
      The proper balance of synthesis, folding, modification, and degradation of proteins, also known as protein homeostasis, is vital to cellular health and function. The unfolded protein response (UPR) is activated when the mechanisms maintaining protein homeostasis in the endoplasmic reticulum become overwhelmed. However, prolonged or strong UPR responses can result in elevated inflammation and cellular damage. Previously, we discovered that the enzyme filamentation induced by cyclic-AMP (Fic) can modulate the UPR response via posttranslational modification of binding immunoglobulin protein (BiP) by AMPylation during homeostasis and deAMPylation during stress. Loss of fic in Drosophila leads to vision defects and altered UPR activation in the fly eye. To investigate the importance of Fic-mediated AMPylation in a mammalian system, we generated a conditional null allele of Fic in mice and characterized the effect of Fic loss on the exocrine pancreas. Compared to controls, Fic-/- mice exhibit elevated serum markers for pancreatic dysfunction and display enhanced UPR signaling in the exocrine pancreas in response to physiological and pharmacological stress. In addition, both fic-/- flies and Fic-/- mice show reduced capacity to recover from damage by stress that triggers the UPR. These findings show that Fic-mediated AMPylation acts as a molecular rheostat that is required to temper the UPR response in the mammalian pancreas during physiological stress. Based on these findings, we propose that repeated physiological stress in differentiated tissues requires this rheostat for tissue resilience and continued function over the lifetime of an animal.
    Keywords:  AMPylation; ER stress; Fic; pancreas; unfolded protein response
    DOI:  https://doi.org/10.1073/pnas.2208317119
  8. Cell Calcium. 2022 Jul 20. pii: S0143-4160(22)00095-1. [Epub ahead of print]106 102622
    Ca2+ signalling system initiated by endoplasmic reticulum stress stimulates PERK activation.
    Constanza Feliziani, Macarena Fernandez, Gonzalo Quassollo, Deborah Holstein, Sebastián M Bairo, James C Paton, Adrienne W Paton, Juan de Batista, James D Lechleiter, Mariana Bollo.
      The accumulation of unfolded proteins within the Endoplasmic Reticulum (ER) activates a signal transduction pathway termed the unfolded protein response (UPR), which attempts to restore ER homoeostasis. If this cannot be done, UPR signalling ultimately induces apoptosis. Ca2+ depletion in the ER is a potent inducer of ER stress. Despite the ubiquity of Ca2+ as an intracellular messenger, the precise mechanism(s) by which Ca2+ release affects the UPR remains unknown. Tethering a genetically encoded Ca2+ indicator (GCamP6) to the ER membrane revealed novel Ca2+ signalling events initiated by Ca2+ microdomains in human astrocytes under ER stress, induced by tunicamycin (Tm), an N-glycosylation inhibitor, as well as in a cell model deficient in all three inositol triphosphate receptor isoforms. Pharmacological and molecular studies indicate that these local events are mediated by translocons and that the Ca2+ microdomains impact (PKR)-like-ER kinase (PERK), an UPR sensor, activation. These findings reveal the existence of a Ca2+ signal mechanism by which stressor-mediated Ca2+ release regulates ER stress.
    Keywords:  (PKR)-like-ER kinase (PERK); Calcium signalling; Inositol triphosphate receptor; Translocon; Unfolded protein response
    DOI:  https://doi.org/10.1016/j.ceca.2022.102622
  9. Autophagy. 2022 Aug 01. 1-19
    SDC1-dependent TGM2 determines radiosensitivity in glioblastoma by coordinating EPG5-mediated fusion of autophagosomes with lysosomes.
    Wang Zheng, Qianping Chen, Hongxia Liu, Liang Zeng, Yuchuan Zhou, Xinglong Liu, Yang Bai, Jianghong Zhang, Yan Pan, Chunlin Shao.
      Glioblastoma multiforme (GBM) is the most common brain malignancy insensitive to radiotherapy (RT). Although macroautophagy/autophagy was reported to be a fundamental factor prolonging the survival of tumors under radiotherapeutic stress, the autophagic biomarkers coordinated to radioresistance of GBM are still lacking in clinical practice. Here we established radioresistant GBM cells and identified their protein profiles using tandem mass tag (TMT) quantitative proteomic analysis. It was found that SDC1 and TGM2 proteins were overexpressed in radioresistant GBM cells and tissues and they contributed to the poor prognosis of RT. Knocking down SDC1 and TGM2 inhibited the fusion of autophagosomes with lysosomes and thus enhanced the radiosensitivity of GBM cells. After irradiation, TGM2 bound with SDC1 and transported it from the cell membrane to lysosomes, and then bound to LC3 through its two LC3-interacting regions (LIRs), coordinating the encounter between autophagosomes and lysosomes, which should be a prerequisite for lysosomal EPG5 to recognize LC3 and subsequently stabilize the STX17-SNAP29-VAMP8 QabcR SNARE complex assembly. Moreover, when combined with RT, cystamine dihydrochloride (a TGM2 inhibitor) extended the lifespan of GBM-bearing mice. Overall, our findings demonstrated the EPG5 tethering mode with SDC1 and TGM2 during the fusion of autophagosomes with lysosomes, providing new insights into the molecular mechanism and therapeutic target underlying radioresistant GBM.Abbreviations: BafA1: bafilomycin A1; CQ: chloroquine; Cys-D: cystamine dihydrochloride; EPG5: ectopic P-granules 5 autophagy tethering factor; GBM: glioblastoma multiforme; GFP: green fluorescent protein; LAMP2: lysosomal associated membrane protein 2; LIRs: LC3-interacting regions; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; NC: negative control; RFP: red fluorescent protein; RT: radiotherapy; SDC1: syndecan 1; SNAP29: synaptosome associated protein 29; SQSTM1/p62: sequestosome 1; STX17: syntaxin 17; TGM2: transglutaminase 2; TMT: tandem mass tag; VAMP8: vesicle associated membrane protein 8; WT: wild type.
    Keywords:  Autophagosome maturation; EPG5; SDC1; TGM2; glioblastoma; radioresistance biomarkers
    DOI:  https://doi.org/10.1080/15548627.2022.2105562
  10. Sci Adv. 2022 Aug 05. 8(31): eabm5578
    KCTD7 mutations impair the trafficking of lysosomal enzymes through CLN5 accumulation to cause neuronal ceroid lipofuscinoses.
    Yalan Wang, Xiaotong Cao, Pei Liu, Weijia Zeng, Rui Peng, Qing Shi, Kai Feng, Pingzhao Zhang, Huiru Sun, Chenji Wang, Hongyan Wang.
      Lysosomes are central organelles for cellular degradation and energy metabolism. Neuronal ceroid lipofuscinoses (NCLs) are a group of the most common neurodegenerative lysosomal storage disorders characterized by intracellular accumulation of ceroid in neurons. Mutations in KCTD7, a gene encoding an adaptor of the CUL3-RING E3 ubiquitin ligase (CRL3) complex, are categorized as a unique NCL subtype. However, the underlying mechanisms remain elusive. Here, we report various lysosomal and autophagic defects in KCTD7-deficient cells. Mechanistically, the CRL3-KCTD7 complex degrades CLN5, whereas patient-derived KCTD7 mutations disrupt the interaction between KCTD7-CUL3 or KCTD7-CLN5 and ultimately lead to excessive accumulation of CLN5. The accumulated CLN5 disrupts the interaction between CLN6/8 and lysosomal enzymes at the endoplasmic reticulum (ER), subsequently impairing ER-to-Golgi trafficking of lysosomal enzymes. Our findings reveal previously unrecognized roles of KCTD7-mediated CLN5 proteolysis in lysosomal homeostasis and demonstrate that KCTD7 and CLN5 are biochemically linked and function in a common neurodegenerative pathway.
    DOI:  https://doi.org/10.1126/sciadv.abm5578
  11. Elife. 2022 Aug 05. pii: e76436. [Epub ahead of print]11
    trim-21 promotes proteasomal degradation of CED-1 for apoptotic cell clearance in C. elegans.
    Lei Yuan, Peiyao Li, Huiru Jing, Qian Zheng, Hui Xiao.
      The phagocytic receptor CED-1 mediates apoptotic cell recognition by phagocytic cells, enabling cell corpse clearance in Caenorhabditis elegans. Whether appropriate levels of CED-1 are maintained for executing the engulfment function remains unknown. Here, we identified the C. elegans E3 ubiquitin ligase tripartite motif containing-21 (TRIM-21) as a component of the CED-1 pathway for apoptotic cell clearance. When the NPXY motif of CED-1 was bound to the adaptor protein CED-6 or the YXXL motif of CED-1 was phosphorylated by tyrosine kinase SRC-1 and subsequently bound to the adaptor protein NCK-1 containing the SH2 domain, TRIM-21 functioned in conjunction with UBC-21 to catalyze K48-linked poly-ubiquitination on CED-1, targeting it for proteasomal degradation. In the absence of TRIM-21, CED-1 accumulated post-translationally and drove cell corpse degradation defects, as evidenced by direct binding to VHA-10. These findings reveal a unique mechanism for the maintenance of appropriate levels of CED-1 to regulate apoptotic cell clearance.
    Keywords:  C. elegans; cell biology
    DOI:  https://doi.org/10.7554/eLife.76436
  12. Front Cell Dev Biol. 2022 ;10 967875
    Selective Secretion of KDEL-Bearing Proteins: Mechanisms and Functions.
    F C Palazzo, R Sitia, T Tempio.
      In multicellular organisms, cells must continuously exchange messages with the right meaning, intensity, and duration. Most of these messages are delivered through cognate interactions between membrane and secretory proteins. Their conformational maturation is assisted by a vast array of chaperones and enzymes, ensuring the fidelity of intercellular communication. These folding assistants reside in the early secretory compartment (ESC), a functional unit that encompasses endoplasmic reticulum (ER), intermediate compartment and cis-Golgi. Most soluble ESC residents have C-terminal KDEL-like motifs that prevent their transport beyond the Golgi. However, some accumulate in the ER, while others in downstream stations, implying different recycling rates. Moreover, it is now clear that cells can actively secrete certain ESC residents but not others. This essay discusses the physiology of their differential intracellular distribution, and the mechanisms that may ensure selectivity of release.
    Keywords:  ERp44; Golgi; KDEL receptors; PDI; endoplasmic recticulum; protein folding; protein quality control; protein secretion
    DOI:  https://doi.org/10.3389/fcell.2022.967875
  13. Cell. 2022 Jul 29. pii: S0092-8674(22)00789-9. [Epub ahead of print]
    PABP/purine-rich motif as an initiation module for cap-independent translation in pattern-triggered immunity.
    Jinlong Wang, Xing Zhang, George H Greene, Guoyong Xu, Xinnian Dong.
      Upon stress, eukaryotes typically reprogram their translatome through GCN2-mediated phosphorylation of the eukaryotic translation initiation factor, eIF2α, to inhibit general translation initiation while selectively translating essential stress regulators. Unexpectedly, in plants, pattern-triggered immunity (PTI) and response to other environmental stresses occur independently of the GCN2/eIF2α pathway. Here, we show that while PTI induces mRNA decapping to inhibit general translation, defense mRNAs with a purine-rich element ("R-motif") are selectively translated using R-motif as an internal ribosome entry site (IRES). R-motif-dependent translation is executed by poly(A)-binding proteins (PABPs) through preferential association with the PTI-activating eIFiso4G over the repressive eIF4G. Phosphorylation by PTI regulators mitogen-activated protein kinase 3 and 6 (MPK3/6) inhibits eIF4G's activity while enhancing PABP binding to the R-motif and promoting eIFiso4G-mediated defense mRNA translation, establishing a link between PTI signaling and protein synthesis. Given its prevalence in both plants and animals, the PABP/R-motif translation initiation module may have a broader role in reprogramming the stress translatome.
    Keywords:  IRES; MPK3/MPK6; PABP; R-motif; RACK1; cap-independent translation; eIF4G; eIFiso4G; pattern-triggered immunity; translational reprogramming
    DOI:  https://doi.org/10.1016/j.cell.2022.06.037
  14. J Biol Chem. 2022 Aug 02. pii: S0021-9258(22)00783-9. [Epub ahead of print] 102341
    O-GlcNAcylation stabilizes the autophagy-initiating kinase ULK1 by inhibiting chaperone-mediated autophagy upon HPV infection.
    Yingxin Shi, Sheng Yan, Guang-Can Shao, Jinglong Wang, Yong-Ping Jian, Bo Liu, Yanqiu Yuan, Ke Qin, Shanshan Nai, Xiahe Huang, Yingchun Wang, Zhenghui Chen, Xing Chen, Meng-Qiu Dong, Yiqun Geng, Zhi-Xiang Xu, Jing Li.
      Human papillomaviruses (HPVs) cause a subset of cases of head and neck squamous cell carcinomas (HNSCCs). Previously, we demonstrated that HPV16 oncogene E6 or E6/E7 transduction increases the abundance of O-linked GlcNAcylation (O-GlcNAc) transferase (OGT), but the OGT substrates and cellular pathways affected by this increase are unclear. Here, we focus on the effects of O-GlcNAcylation on HPV-positive HNSCCs. We found that upon HPV infection, ULK1, an autophagy-initiating kinase, is hyper-O-GlcNAcylated, stabilized, and linked with autophagy elevation. Through mass spectrometry, we identified that ULK1 is O-GlcNAcylated at Ser409, which is distinct from the previously reported Thr635/Thr754 sites. It has been demonstrated that PKCαmediates phosphorylation of ULK1 at Ser423, which attenuates its stability by shunting ULK1 to the chaperone-mediated autophagy (CMA) pathway. Using biochemical assays, we demonstrate that ULK1 Ser409Ser410 O-GlcNAcylation antagonizes its phosphorylation at Ser423. Moreover, we found that mutations of Ser409A and its neighboring site Ser410A (2A) render ULK1 less stable by promoting interaction with the CMA chaperone Hsc70. Further, we determined that ULK1-2A mutants attenuate the association of ULK1 with STX17, which is vital for the fusion between autophagosomes and lysosomes. Analysis of The Cancer Genome Atlas (TCGA) database reveals that ULK1 is upregulated in HPV-positive HNSCCs and its level positively correlates with HNSCC patient survival. Overall, our work demonstrates that O-GlcNAcylation of ULK1 is altered in response to environmental changes. O-GlcNAcylation of ULK1 at Ser409 and perhaps at its neighboring Ser410 stabilizes ULK1, and this might underlie the molecular mechanism of HPV-positive HNSCC patient survival.
    Keywords:  Chaperone-mediated autophagy; HNSCC; HPV; Macroautophagy; O-GlcNAc; ULK1
    DOI:  https://doi.org/10.1016/j.jbc.2022.102341
  15. Mol Neurobiol. 2022 Aug 06.
    Deficiency of Murine UFM1-Specific E3 Ligase Causes Microcephaly and Inflammation.
    Jie Zhang, Huabin Zhu, Siyang Liu, Michaela Quintero, Tianyi Zhu, Renshi Xu, Yafei Cai, Ye Han, Honglin Li.
      The UFM1 conjugation system is a Ubiquitin (Ub)-like modification system that is essential for animal development and normal physiology of multiple tissues and organs. It consists of UFM1, a Ub-like modifier, and the UFM1-specific enzymes (namely E1 enzyme UBA5, E2 enzyme UFC1 E2, and E3 ligases) that catalyze conjugation of UFM1 to its specific protein targets. Clinical studies have identified rare genetic variants in human UFM1, UBA5 and UFC1 genes that were linked to early-onset encephalopathy and defective brain development, strongly suggesting the critical role of the UFM1 system in the nervous system. Yet, the physiological function of this system in adult brain remains not defined. In this study, we investigated the role of UFM1 E3 ligase in adult mouse and found that both UFL1 and UFBP1 proteins, two components of UFM1 E3 ligase, are essential for survival of mature neurons in adult mouse. Neuron-specific deletion of either UFL1 or UFBP1 led to significant neuronal loss and elevation of inflammatory response. Interestingly, loss of one allele of UFBP1 genes caused the occurrence of seizure-like events. Our study has provided genetic evidence for the indispensable role of UFM1 E3 ligase in mature neurons and further demonstrated the importance of the UFM1 system in the nervous system.
    Keywords:  Microcephaly; Neuronal death; Seizure; UFBP1; UFL1; UFM1; UFMylation
    DOI:  https://doi.org/10.1007/s12035-022-02979-0
  16. Life Sci Alliance. 2022 Dec;pii: e202201492. [Epub ahead of print]5(12):
    Ubiquitome profiling reveals a regulatory pattern of UPL3 with UBP12 on metabolic-leaf senescence.
    Wei Lan, Weibo Ma, Shuai Zheng, Yuhao Qiu, Han Zhang, Haisen Lu, Yu Zhang, Ying Miao.
      The HECT-type UPL3 ligase plays critical roles in plant development and stress protection, but understanding of its regulation remains limited. Here, the multi-omics analyses of ubiquitinated proteins in upl3 mutants were performed. A landscape of UPL3-dependent ubiquitinated proteins is constructed: Preferential ubiquitination of proteins related to carbon fixation represented the largest set of proteins with increased ubiquitination in the upl3 plant, including most of carbohydrate metabolic enzymes, BRM, and variant histone, whereas a small set of proteins with reduced ubiquitination caused by the upl3 mutation were linked to cysteine/methionine synthesis, as well as hexokinase 1 (HXK1) and phosphoenolpyruvate carboxylase 2 (PPC2). Notably, ubiquitin hydrolase 12 (UBP12), BRM, HXK1, and PPC2 were identified as the UPL3-interacting partners in vivo and in vitro. Characterization of brm, upl3, ppc2, gin2, and ubp12 mutant plants and proteomic and transcriptomic analysis suggested that UPL3 fine-tunes carbohydrate metabolism, mediating cellular senescence by interacting with UBP12, BRM, HXK1, and PPC2. Our results highlight a regulatory pattern of UPL3 with UBP12 as a hub of regulator on proteolysis-independent regulation and proteolysis-dependent degradation.
    DOI:  https://doi.org/10.26508/lsa.202201492
  17. Curr Gene Ther. 2022 Aug 01.
    Role of Long Non-Coding RNA in Regulating ER Stress Response on the Progression of Diabetic Complications.
    Ramanarayanan Vijayalalitha, Architha Tca, George Raj Juanitaa, Ravichandran Jayasuriya, Karan Naresh Amin, Kunka Mohanram Ramkumar.
      Chronic hyperglycemia damages the nerves, blood vessels, culminating in other vascular complications. Such complications enhance cytokine, oxidative and endoplasmic reticulum (ER) stress. ER is the primary organelle where proteins are synthesised and attains confirmatory changes before its site of destination. Perturbation of ER homeostasis activates signaling sensors within its lumen, the unfolded protein response (UPR) that orchestrates ER stress and is extensively studied. Increased ER stress markers are reported in diabetic complications in addition to lncRNA that acts as an upstream marker inducing ER stress response. This review focuses on the mechanisms of lncRNA that regulate ER stress markers, especially during the progression of diabetic complications. Through this systemic review, we showcase the dysfunctional lncRNAs that acts as a leading cause of ER stress response on the progression of diabetic complications.
    Keywords:  ER stress; diabetic complications; lncRNA
    DOI:  https://doi.org/10.2174/1566523222666220801141450
  18. J Cell Sci. 2022 Aug 01. pii: jcs.258396. [Epub ahead of print]
    TGFBR3 supports anoikis through suppressing ATF4 signaling.
    Yu-Jhen Hsu, Yih-Jia Yin, Kai-Feng Tsai, Cian-Chun Jian, Zi-Wen Liang, Chien-Yu Hsu, Chun-Chao Wang.
      Epithelial morphogenesis and oncogenic transformation can cause loss of cell adhesion, and detached cells are eliminated by anoikis. Here, we reveal that transforming growth factor beta receptor 3 (TGFBR3) acts as an anoikis mediator through the coordination of activating transcription factor 4 (ATF4). In breast cancer, TGFBR3 is progressively lost, but elevated TGFBR3 is associated with a histologic subtype characterized by cellular adhesion defects. Dissecting the impact of extracellular matrix (ECM) deprivation, we demonstrate that ECM loss promotes TGFBR3 expression, which in turn differentiates cell aggregates to a prosurvival phenotype and drives the intrinsic apoptotic pathway. We demonstrate that inhibition of TGFBR3 impairs epithelial anoikis by activating ATF4 signaling. These preclinical findings provide a rationale for therapeutic inhibition of ATF4 in the subgroup of breast cancer patients with low TGFBR3 expression.
    Keywords:  Activating transcription factor 4; Anoikis; Breast cancer; Integrated stress response; Transforming growth factor beta
    DOI:  https://doi.org/10.1242/jcs.258396
  19. Life Sci. 2022 Jul 30. pii: S0024-3205(22)00552-5. [Epub ahead of print] 120852
    Molecular chaperones in DNA repair mechanisms: Role in genomic instability and proteostasis in cancer.
    Adria Hasan, Suroor Fatima Rizvi, Sana Parveen, Snober S Mir.
      Cells are exposed to several environmental or chemical stressors that may cause DNA damage. DNA damage alters the normal functioning of the cell and contributes to several diseases, including cancer. Cells either induce DNA damage repair pathways or programmed cell death pathways to prevent disease formation depending on the severity of the stress and the damage caused. The DNA repair mechanisms are crucial to maintaining genome stability. During this adaptive response, the heat shock proteins (HSPs) are the key players. HSPs are overexpressed during genotoxic stress, but the role of different molecular players in the interaction between HSPs and DNA repair proteins is still poorly understood. As DNA damage promotes genomic instability and proteotoxic stress, modulating the protein quality control systems like the HSPs network could be a promising strategy for targeting disease pathologies associated with genomic instability, such as cancer. Hence, this review highlights the role of HSPs in DNA repair pathways. Further, the review also provides an outlook on the role of genomic instability and protein homeostasis in cancer, which is crucial to understanding the mechanisms behind its survival and developing novel targeted therapies.
    Keywords:  DNA damage response; DNA repair; Genomic instability; Molecular chaperones; Proteostasis
    DOI:  https://doi.org/10.1016/j.lfs.2022.120852
  20. Elife. 2022 Aug 01. pii: e81247. [Epub ahead of print]11
    Hypoxia-induced proteasomal degradation of DBC1 by SIAH2 in breast cancer progression.
    Qiangqiang Liu, Qian Luo, Jianyu Feng, Yanping Zhao, Biao Ma, Hongcheng Cheng, Tian Zhao, Hong Lei, Chenglong Mu, Linbo Chen, Yuanyuan Meng, Jiaojiao Zhang, Yijia Long, Jingyi Su, Guo Chen, Yanjun Li, Gang Hu, Xudong Liao, Quan Chen, Yushan Zhu.
      DBC1 has been characterized as a key regulator of physiological and pathophysiological activities, such as DNA damage, senescence and tumorigenesis. However, the mechanism by which the functional stability of DBC1 is regulated has yet to be elucidated. Here, we report that the ubiquitination-mediated degradation of DBC1 is regulated by the E3 ubiquitin ligase SIAH2 and deubiquitinase OTUD5 under hypoxic stress. Mechanistically, hypoxia promoted DBC1 to interact with SIAH2 but not OTUD5, resulting in the ubiquitination and subsequent degradation of DBC1 through the ubiquitin-proteasome pathway. SIAH2 knockout inhibited tumor cell proliferation and migration, which could be rescued by double knockout of SIAH2/CCAR2. Human tissue microarray analysis further revealed that the SIAH2/DBC1 axis was responsible for tumor progression under hypoxic stress. These findings define a key role of the hypoxia-mediated SIAH2-DBC1 pathway in the progression of human breast cancer and provide novel insights into the metastatic mechanism of breast cancer.
    Keywords:  cancer biology; cell biology; mouse
    DOI:  https://doi.org/10.7554/eLife.81247
  21. Sci Rep. 2022 Aug 01. 12(1): 13160
    The E3 ubiquitin ligase HECTD1 contributes to cell proliferation through an effect on mitosis.
    Natalie Vaughan, Nico Scholz, Catherine Lindon, Julien D F Licchesi.
      The cell cycle is tightly regulated by protein phosphorylation and ubiquitylation events. During mitosis, the multi-subunit cullin-RING E3 ubiquitin ligase APC/c functions as a molecular switch which signals for one cell to divide into two daughter cells, through the ubiquitylation and proteasomal degradation of mitotic cyclins. The contributions of other E3 ligase families during cell cycle progression remain less well understood. Similarly, the roles of ubiquitin chain types beyond homotypic K48 chains in S-phase or branched K11/K48 chains during mitosis, also remain to be fully determined. Our recent findings that HECTD1 ubiquitin ligase activity assembles branched K29/K48 ubiquitin linkages prompted us to evaluate HECTD1 function during the cell cycle. We used transient knockdown and genetic knockout to show that HECTD1 depletion in HEK293T and HeLa cells decreases cell number and we established that this is mediated through loss of ubiquitin ligase activity. Interestingly, we found that HECTD1 depletion increases the proportion of cells with aligned chromosomes (Prometa/Metaphase) and we confirmed this molecularly using phospho-Histone H3 (Ser28) as a marker of mitosis. Time-lapse microscopy of NEBD to anaphase onset established that HECTD1-depleted cells take on average longer to go through mitosis. In line with this data, HECTD1 depletion reduced the activity of the Spindle Assembly Checkpoint, and BUB3, a component of the Mitosis Checkpoint Complex, was identified as novel HECTD1 interactor. BUB3, BUBR1 or MAD2 protein levels remained unchanged in HECTD1-depleted cells. Overall, this study reveals a novel putative role for HECTD1 during mitosis and warrants further work to elucidate the mechanisms involved.
    DOI:  https://doi.org/10.1038/s41598-022-16965-y
  22. Trends Cell Biol. 2022 Jul 29. pii: S0962-8924(22)00174-X. [Epub ahead of print]
    Calcium homeostasis and cancer: insights from endoplasmic reticulum-centered organelle communications.
    Shanliang Zheng, Xingwen Wang, Dong Zhao, Hao Liu, Ying Hu.
      Calcium ion (Ca2+) is a ubiquitous and versatile signaling molecule controlling a wide variety of cellular processes, such as proliferation, cell death, migration, and immune response, all fundamental processes essential for the establishment of cancer. In recent decades, the loss of Ca2+ homeostasis has been considered an important driving force in the initiation and progression of malignant diseases. The primary intracellular Ca2+ store, the endoplasmic reticulum (ER), plays an essential role in maintaining Ca2+ homeostasis by coordinating with other organelles and the plasma membrane. Here, we discuss the dysregulation of ER-centered Ca2+ homeostasis in cancer, summarize Ca2+-based anticancer therapeutics, and highlight the significance of furthering our understanding of Ca2+ homeostasis regulation in cancer.
    Keywords:  calcium homeostasis; endoplasmic reticulum; intra-organelle communication; mitochondria; oncogene; tumor suppressor
    DOI:  https://doi.org/10.1016/j.tcb.2022.07.004
  23. J Biol Chem. 2022 Jul 31. pii: S0021-9258(22)00763-3. [Epub ahead of print] 102321
    Cleavage of mitochondrial homeostasis regulator PGAM5 by the intramembrane protease PARL is governed by transmembrane helix dynamics and oligomeric state.
    Verena Siebert, Mara Silber, Elena Heuten, Claudia Muhle-Goll, Marius K Lemberg.
      The intramembrane protease PARL acts as a crucial mitochondrial safeguard by cleaving the mitophagy regulators PINK1 and PGAM5. Depending on the stress level, PGAM5 can either stimulate cell survival or cell death. In contrast to PINK1, which is constantly cleaved in healthy mitochondria and only active when the inner mitochondrial membrane is depolarized, PGAM5 processing is inversely regulated. However, determinants of PGAM5 that indicate it as a conditional substrate for PARL have not been rigorously investigated, and it is unclear how uncoupling the mitochondrial membrane potential affects its processing compared to that of PINK1. Here, we show that several polar transmembrane residues in PGAM5 distant from the cleavage site serve as key determinants for its PARL-catalyzed cleavage. Our NMR analysis indicates that a short N-terminal amphipathic helix, followed by a kink and a C-terminal transmembrane helix harboring the scissile peptide bond, are key for a productive interaction with PARL. Furthermore, we also show that PGAM5 is stably inserted into the inner mitochondrial membrane until uncoupling the membrane potential triggers its disassembly into monomers, which are then cleaved by PARL. In conclusion, we propose a model in which PGAM5 is slowly processed by PARL-catalyzed cleavage that is influenced by multiple hierarchical substrate features, including a membrane potential-dependent oligomeric switch.
    Keywords:  PGAM5; helix dynamics; intramembrane proteolysis; oligomeric state; rhomboid serine protease
    DOI:  https://doi.org/10.1016/j.jbc.2022.102321
  24. J Cell Biochem. 2022 Jul 31.
    Identification of an ERN1 target site within EGFP mRNA.
    Marius W Baeken, Yohei Yokobayashi.
      EGFP (enhanced green fluorescent protein) is one of the most common tools used in life sciences, including research focusing on proteostasis. Here we report that ERN1 (endoplasmic reticulum to nucleus signaling 1), which is upregulated by UPR (unfolded protein response), targets an RNA hairpin loop motif in EGFP mRNA. A silent mutation introduced into EGFP mRNA abolished the ERN1-dependent mRNA decay. Therefore, experiments that employ EGFP as a reporter gene in studies that involve upregulation of the UPR pathway should be interpreted carefully, and a mutant devoid of the ERN1 target motif may be more suitable for such studies.
    Keywords:  EGFP; ERN1; IRE1; proteostasis; unfolded protein response
    DOI:  https://doi.org/10.1002/jcb.30314
  25. Sci Adv. 2022 Aug 05. 8(31): eabo0412
    Deacetylation of ATG4B promotes autophagy initiation under starvation.
    Liangbo Sun, Haojun Xiong, Lingxi Chen, Xufang Dai, Xiaojing Yan, Yaran Wu, Mingzhen Yang, Meihua Shan, Tao Li, Jie Yao, Wenbin Jiang, Haiyan He, Fengtian He, Jiqin Lian.
      Eukaryotes initiate autophagy when facing environmental changes such as a lack of external nutrients. However, the mechanisms of autophagy initiation are still not fully elucidated. Here, we showed that deacetylation of ATG4B plays a key role in starvation-induced autophagy initiation. Specifically, we demonstrated that ATG4B is activated during starvation through deacetylation at K39 by the deacetylase SIRT2. Moreover, starvation triggers SIRT2 dephosphorylation and activation in a cyclin E/CDK2 suppression-dependent manner. Meanwhile, starvation down-regulates p300, leading to a decrease in ATG4B acetylation at K39. K39 deacetylation also enhances the interaction of ATG4B with pro-LC3, which promotes LC3-II formation. Furthermore, an in vivo experiment using Sirt2 knockout mice also confirmed that SIRT2-mediated ATG4B deacetylation at K39 promotes starvation-induced autophagy initiation. In summary, this study reveals an acetylation-dependent regulatory mechanism that controls the role of ATG4B in autophagy initiation in response to nutritional deficiency.
    DOI:  https://doi.org/10.1126/sciadv.abo0412
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