bims-proteo 2022-01-02 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2022–01–02
eightteen papers selected by
Eric Chevet, INSERM

MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51.
Analysis of Pancreatic Acinar Protein Solubility in Autophagy-Deficient Mice.
PUB22 and PUB23 U-box E3 ubiquitin ligases negatively regulate 26S proteasome activity under proteotoxic stress conditions.
Kinetic control of nascent protein biogenesis by peptide deformylase.
The ER stress sensor inositol-requiring enzyme 1α in Kupffer cells promotes hepatic ischemia-reperfusion injury.
State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools.
The ASCC2 CUE domain in the ALKBH3-ASCC DNA repair complex recognizes adjacent ubiquitins in K63-linked polyubiquitin.
The chemical biology of ubiquitin.
Autophagy mediates ER stress and inflammation in Helicobacter pylori-related gastric cancer.
Immune regulator LGP2 targets Ubc13/UBE2N to mediate widespread interference with K63 polyubiquitination and NF-κB activation.
AP2M1 mediates autophagy-induced CLDN2 (claudin 2) degradation through endocytosis and interaction with LC3 and reduces intestinal epithelial tight junction permeability.
Kaposi's sarcoma herpesvirus activates the hypoxia response to usurp HIF2α-dependent translation initiation for replication and oncogenesis.
Biogenesis of secretory immunoglobulin M requires intermediate non-native disulfide bonds and engagement of the protein disulfide isomerase ERp44.
p53 regulates skeletal muscle mitophagy and mitochondrial quality control following denervation-induced muscle disuse.
p16 Represses DNA Damage Repair via a Novel Ubiquitin-Dependent Signaling Cascade.
Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis.
Ever-Expanding NGLY1 biology.
Converging roles of PSENEN/PEN2 and CLN3 in the autophagy-lysosome system.

J Biochem. 2021 Dec 29. pii: mvab153. [Epub ahead of print]

MITOL regulates phosphatidic acid-binding activity of RMDN3/PTPIP51.

Naoki Ito, Takara Takahashi, Isshin Shiiba, Shun Nagashima, Ryoko Inatome, Shigeru Yanagi.

  The transfer of phospholipids from the endoplasmic reticulum to mitochondria via the mitochondria-endoplasmic reticulum (ER) contact site (MERCS) is essential for maintaining mitochondrial function and integrity. Here, we identified RMDN3/PTPIP51, possessing phosphatidic acid (PA)-transfer activity, as a neighboring protein of the mitochondrial E3 ubiquitin ligase MITOL/MARCH5 by proximity-dependent biotin labeling using APEX2. We found that MITOL interacts with and ubiquitinates RMDN3. Mutational analysis identified lysine residue 89 in RMDN3 as a site of ubiquitination by MITOL. Loss of MITOL or the substitution of lysine 89 to arginine in RMDN3 significantly reduced the PA-binding activity of RMDN3, suggesting that MITOL regulates the transport of PA to mitochondria by activating RMDN3. Our findings imply that ubiquitin signaling regulates phospholipid transport at the MERCS.

Keywords:  E3 ubiquitin ligase; MITOL; RMDN3; mitochondria-ER contact site; phospholipid

DOI:  https://doi.org/10.1093/jb/mvab153
Methods Mol Biol. 2022 ;2445 243-253

Analysis of Pancreatic Acinar Protein Solubility in Autophagy-Deficient Mice.

Matthew Smith, Carla Salomo-Coll, Morwenna Muir, Simon Wilkinson.

  Autophagy of the endoplasmic reticulum, or ER-phagy, maintains the homeostasis of the secretory pathway. This is particularly prominent in specialized secretory cells such as the acinar cells of the exocrine pancreas. The role for such a homeostatic pathway during ageing of mammals is modelled best by in vivo genetic or pharmacologic intervention in mice. This is due to the paucity of cellular models that can maintain acinar identity outside of an animal. Here we present methods for isolation of soluble and insoluble protein fractions of ER luminal proteins from the pancreas, alongside RNA. Analysis of these macromolecules allows inference of changes in ER luminal proteostasis upon autophagy-targeted interventions. These methods will likely be more widely applicable, beyond autophagy research.

Keywords:  Autophagy; ER stress; ER-phagy; Endoplasmic reticulum; Pancreas; UPR

DOI:  https://doi.org/10.1007/978-1-0716-2071-7_15
J Integr Plant Biol. 2021 Dec 28.

PUB22 and PUB23 U-box E3 ubiquitin ligases negatively regulate 26S proteasome activity under proteotoxic stress conditions.

Min Yong Ahn, Dong Hye Seo, Woo Taek Kim.

  The mechanism regulating proteasomal activity under proteotoxic stress conditions remains unclear. Here, we showed that arsenite-induced proteotoxic stress resulted in upregulation of Arabidopsis homologous PUB22 and PUB23 U-box E3 ubiquitin ligases and that pub22pub23 double mutants displayed arsenite-insensitive seed germination and root growth phenotypes. PUB22/PUB23 downregulated 26S proteasome activity by promoting the dissociation of the 19S regulatory particle from the holo-proteasome complex, resulting in intracellular accumulation of UbG76V -GFP, an artificial substrate of the proteasome complex, and insoluble poly-ubiquitinated proteins. These results suggest that PUB22/PUB23 play a critical role in arsenite-induced proteotoxic stress response via negative regulation of 26S proteasome integrity. This article is protected by copyright. All rights reserved.

Keywords:  26S proteasome complex; Arabidopsis thaliana; U-box E3 ligases PUB22/23; proteotoxic stress; sodium arsenite

DOI:  https://doi.org/10.1111/jipb.13209
Sci Rep. 2021 Dec 27. 11(1): 24457

Kinetic control of nascent protein biogenesis by peptide deformylase.

Lena A K Bögeholz, Evan Mercier, Wolfgang Wintermeyer, Marina V Rodnina.

Synthesis of bacterial proteins on the ribosome starts with a formylated methionine. Removal of the N-terminal formyl group is essential and is carried out by peptide deformylase (PDF). Deformylation occurs co-translationally, shortly after the nascent-chain emerges from the ribosomal exit tunnel, and is necessary to allow for further N-terminal processing. Here we describe the kinetic mechanism of deformylation by PDF of ribosome-bound nascent-chains and show that PDF binding to and dissociation from ribosomes is rapid, allowing for efficient scanning of formylated substrates in the cell. The rate-limiting step in the PDF mechanism is a conformational rearrangement of the nascent-chain that takes place after cleavage of the formyl group. Under conditions of ongoing translation, the nascent-chain is deformylated rapidly as soon as it becomes accessible to PDF. Following deformylation, the enzyme is slow in releasing the deformylated nascent-chain, thereby delaying further processing and potentially acting as an early chaperone that protects short nascent chains before they reach a length sufficient to recruit other protein biogenesis factors.

DOI: https://doi.org/10.1038/s41598-021-03969-3
J Biol Chem. 2021 Dec 22. pii: S0021-9258(21)01342-9. [Epub ahead of print] 101532

The ER stress sensor inositol-requiring enzyme 1α in Kupffer cells promotes hepatic ischemia-reperfusion injury.

Jie Cai, Xiaoge Zhang, Peng Chen, Yang Li, Songzi Liu, Qian Liu, Hanyong Zhang, Zhuyin Wu, Ke Song, Jianmiao Liu, Bo Shan, Yong Liu.

  Hepatic ischemia/reperfusion (I/R) injury is an inflammation-mediated process arising from ischemia/reperfusion-elicited stress in multiple cell types, causing liver damage during surgical procedures and often resulting in liver failure. Endoplasmic reticulum (ER) stress triggers the activation of the unfolded protein response (UPR) and is implicated in tissue injuries, including hepatic I/R injury. However, the cellular mechanism that links the UPR signaling to local inflammatory responses during hepatic I/R injury remains largely obscure. Here, we report that IRE1α, a critical ER-resident transmembrane signal transducer of the UPR, plays an important role in promoting Kupffer cell-mediated liver inflammation and hepatic I/R injury. Utilizing a mouse model in which IRE1α is specifically ablated in myeloid cells, we found that abrogation of IRE1α markedly attenuated necrosis and cell death in the liver, accompanied by reduced neutrophil infiltration and liver inflammation following hepatic I/R injury. Mechanistic investigations in mice as well as in primary Kupffer cells revealed that loss of IRE1α in Kupffer cells not only blunted the activation of the NLRP3 inflammasome and IL-1β production, but also suppressed the expression of the inducible nitric oxide synthase (iNos) and pro-inflammatory cytokines. Moreover, pharmacological inhibition of IRE1α's RNase activity was able to attenuate inflammasome activation and iNos expression in Kupffer cells, leading to alleviation of hepatic I/R injury in mice. Collectively, these results demonstrate that Kupffer cell IRE1α mediates local inflammatory damage during hepatic I/R injury. Our findings suggest that IRE1α RNase activity may serve as a promising target for therapeutic treatment of ischemia/reperfusion-associated liver inflammation and dysfunction.

Keywords:  ER stress; Hepatic ischemia/reperfusion injury; IRE1α; Inflammation; Kupffer cells

DOI:  https://doi.org/10.1016/j.jbc.2021.101532
Semin Cell Dev Biol. 2021 Dec 24. pii: S1084-9521(21)00307-4. [Epub ahead of print]

State of the art in (semi-)synthesis of Ubiquitin- and Ubiquitin-like tools.

Yara Huppelschoten, Gerbrand J van der Heden van Noort.

  Protein ubiquitination is a key post-translational modification in regulating many fundamental cellular processes and dysregulation of these processes can give rise to a vast array of diseases. Unravelling the molecular mechanisms of ubiquitination hence is an important area in current ubiquitin research with as aim to understand this enigmatic process. The complexity of ubiquitin (Ub) signaling arises from the large variety of Ub conjugates, where Ub is attached to other Ub proteins, Ub-like proteins, and protein substrates. The chemical preparation of such Ub conjugates in high homogeneity and in adequate amounts contributes greatly to the deciphering of Ub signaling. The strength of these chemically synthesized conjugates lies in the chemo-selectivity in which they can be created that are sometimes difficult to obtain using biochemical methodology. In this review, we will discuss the progress in the chemical protein synthesis of state-of-the-art Ub and Ub-like chemical probes, their unique concepts and related discoveries in the ubiquitin field.

Keywords:  Activity-based probes; Chemical protein synthesis; Ubiquitin(l)

DOI:  https://doi.org/10.1016/j.semcdb.2021.11.025
J Biol Chem. 2021 Dec 28. pii: S0021-9258(21)01355-7. [Epub ahead of print] 101545

The ASCC2 CUE domain in the ALKBH3-ASCC DNA repair complex recognizes adjacent ubiquitins in K63-linked polyubiquitin.

Patrick M Lombardi, Sara Haile, Timur Rusanov, Rebecca Rodell, Rita Anoh, Julia G Baer, Kate A Burke, Lauren N Gray, Abigail R Hacker, Kayla R Kebreau, Christine K Ngandu, Hannah A Orland, Emmanuella Osei-Asante, Dhane P Schmelyun, Devin E Shorb, Shaheer H Syed, Julianna M Veilleux, Ananya Majumdar, Nima Mosammaparast, Cynthia Wolberger.

  Alkylation of DNA and RNA is a potentially toxic lesion that can result in mutations and even cell death. In response to alkylation damage, K63-linked polyubiquitin chains are assembled that localize the ALKBH3-ASCC repair complex to damage sites in the nucleus. The protein ASCC2, a subunit of the ASCC complex, selectively binds K63-linked polyubiquitin chains via its CUE domain. The basis for polyubiquitin binding specificity was unclear, since CUE domains in other proteins typically bind a single ubiquitin and do not discriminate among different polyubiquitin linkage types. We report here that the ASCC2 CUE domain selectively binds K63-linked diubiquitin by contacting both the distal and proximal ubiquitin. Whereas the ASCC2 CUE domain binds the distal ubiquitin in a manner similar to that reported for other CUE domains bound to a single ubiquitin, the contacts with the proximal ubiquitin are unique to ASCC2. Residues in the N-terminal portion of the ASCC2 α1 helix contribute to the binding interaction with the proximal ubiquitin of K63-linked diubiquitin. Mutation of residues within the N-terminal portion of the ASCC2 α1 helix decreases ASCC2 recruitment in response to DNA alkylation, supporting the functional significance of these interactions during the alkylation damage response. Our study reveals the versatility of CUE domains in ubiquitin recognition.

Keywords:  DNA damage response; alkylation damage; immunofluorescence microscopy; isothermal titration calorimetry (ITC); nuclear magnetic resonance (NMR); polyubiquitin; signaling; site-directed mutagenesis; ubiquitin; ubiquitin-binding domain

DOI:  https://doi.org/10.1016/j.jbc.2021.101545
Biochim Biophys Acta Gen Subj. 2021 Dec 28. pii: S0304-4165(21)00238-5. [Epub ahead of print] 130079

The chemical biology of ubiquitin.

George M Burslem.

  This mini-review will cover the various chemical biology approaches employed to prepare and modulate ubiquitin chains and the ubiquitin-proteasome system. Emphasis will be given to the biochemistry and chemical biology of poly-ubiquitin chain preparation as a tool to elucidate its roles in biological systems as well as the hijacking of the ubiquitin proteasome system using heterobifunctional compounds to induce intracellular ubiquitination.

Keywords:  Chemical biology; Protein synthesis; Ubiquitin

DOI:  https://doi.org/10.1016/j.bbagen.2021.130079
Gut Microbes. 2022 Jan-Dec;14(1):14(1): 2015238

Autophagy mediates ER stress and inflammation in Helicobacter pylori-related gastric cancer.

M C Mommersteeg, I Simovic, B Yu, S A V van Nieuwenburg, I M J Bruno, M Doukas, E J Kuipers, M C W Spaander, M P Peppelenbosch, N Castaño-Rodríguez, G M Fuhler.

  Autophagy is a cellular degradation mechanism, which is triggered by the bacterium Helicobacter pylori. A single nucleotide polymorphism (SNP) in the autophagy gene ATG16L1 (rs2241880, G-allele) has been shown to dysregulate autophagy and increase intestinal endoplasmic reticulum (ER) stress. Here, we investigate the role of this SNP in H. pylori-mediated gastric carcinogenesis and its molecular pathways. ATG16L1 rs2241880 was genotyped in subjects from different ethnic cohorts (Dutch and Australian) presenting with gastric (pre)malignant lesions of various severity. Expression of GRP78 (a marker for ER stress) was assessed in gastric tissues. The effect of ATG16L1 rs2241880 on H. pylori-mediated ER stress and pro-inflammatory cytokine induction was investigated in organoids and CRISPR/Cas9 modified cell lines. Development of gastric cancer was associated with the ATG16L1 rs2241880 G-allele. Intestinal metaplastic cells in gastric tissue of patients showed increased levels of ER-stress. In vitro models showed that H. pylori increases autophagy while reducing ER stress, which appeared partly mediated by the ATG16L1 rs2241880 genotype. H. pylori-induced IL-8 production was increased while TNF-α production was decreased, in cells homozygous for the G-allele. The ATG16L1 rs2241880 G-allele is associated with progression of gastric premalignant lesions and cancer. Modulation of H. pylori-induced ER stress pathways and pro-inflammatory mediators by ATG16L1 rs2441880 may underlie this increased risk.

Keywords:  ATG16L1; ER stress; Helicobacter pylori; Intestinal metaplasia; atrophic gastritis; autophagy; gastric cancer; inflammation

DOI:  https://doi.org/10.1080/19490976.2021.2015238
Cell Rep. 2021 Dec 28. pii: S2211-1247(21)01675-2. [Epub ahead of print]37(13): 110175

Immune regulator LGP2 targets Ubc13/UBE2N to mediate widespread interference with K63 polyubiquitination and NF-κB activation.

Jessica J Lenoir, Jean-Patrick Parisien, Curt M Horvath.

  Lysine 63-linked polyubiquitin (K63-Ub) chains activate a range of cellular immune and inflammatory signaling pathways, including the mammalian antiviral response. Interferon and antiviral genes are triggered by TRAF family ubiquitin ligases that form K63-Ub chains. LGP2 is a feedback inhibitor of TRAF-mediated K63-Ub that can interfere with diverse immune signaling pathways. Our results demonstrate that LGP2 inhibits K63-Ub by association with and sequestration of the K63-Ub-conjugating enzyme, Ubc13/UBE2N. The LGP2 helicase subdomain, Hel2i, mediates protein interaction that engages and inhibits Ubc13/UBE2N, affecting control over a range of K63-Ub ligase proteins, including TRAF6, TRIM25, and RNF125, all of which are inactivated by LGP2. These findings establish a unifying mechanism for LGP2-mediated negative regulation that can modulate a variety of K63-Ub signaling pathways.

Keywords:  DHX58; IFN; K63-Ub; LGP2; RNF125; TRAF6; TRIM25; UBE2N; Ubc13

DOI:  https://doi.org/10.1016/j.celrep.2021.110175
Autophagy. 2021 Dec 29. 1-18

AP2M1 mediates autophagy-induced CLDN2 (claudin 2) degradation through endocytosis and interaction with LC3 and reduces intestinal epithelial tight junction permeability.

Ashwinkumar Subramenium Ganapathy, Kushal Saha, Eric Suchanec, Vikash Singh, Aayush Verma, Gregory Yochum, Walter Koltun, Meghali Nighot, Thomas Ma, Prashant Nighot.

  The intestinal epithelial tight junctions (TJs) provide barrier against paracellular permeation of lumenal antigens. Defects in TJ barrier such as increased levels of pore-forming TJ protein CLDN2 (claudin-2) is associated with inflammatory bowel disease. We have previously reported that starvation-induced macroautophagy/autophagy enhances the TJ barrier by degrading pore-forming CLDN2. In this study, we examined the molecular mechanism underlying autophagy-induced CLDN2 degradation. CLDN2 degradation was persistent in multiple modes of autophagy induction. Immunolocalization, membrane fractionation, and pharmacological inhibition studies showed increased clathrin-mediated CLDN2 endocytosis upon starvation. Inhibition of clathrin-mediated endocytosis negated autophagy-induced CLDN2 degradation and enhancement of the TJ barrier. The co-immunoprecipitation studies showed increased association of CLDN2 with clathrin and adaptor protein AP2 (AP2A1 and AP2M1 subunits) as well as LC3 and lysosomes upon starvation, signifying the role of clathrin-mediated endocytosis in autophagy-induced CLDN2 degradation. The expression and phosphorylation of AP2M1 was increased upon starvation. In-vitro, in-vivo (mouse colon), and ex-vivo (human colon) inhibition of AP2M1 activation prevented CLDN2 degradation. AP2M1 knockout prevented autophagy-induced CLDN2 degradation via reduced CLDN2-LC3 interaction. Site-directed mutagenesis revealed that AP2M1 binds to CLDN2 tyrosine motifs (YXXФ) (67-70 and 148-151). Increased baseline expression of CLDN2 and TJ permeability along with reduced CLDN2-AP2M1-LC3 interactions in ATG7 knockout cells validated the role of autophagy in modulation of CLDN2 levels. Acute deletion of Atg7 in mice increased CLDN2 levels and the susceptibility to experimental colitis. The autophagy-regulated molecular mechanisms linking CLDN2, AP2M1, and LC3 may provide therapeutic tools against intestinal inflammation.Abbreviations: Amil: amiloride; AP2: adaptor protein complex 2; AP2A1: adaptor related protein complex 2 subunit alpha 1; AP2M1: adaptor related protein complex 2 subunit mu 1; ATG7: autophagy related 7; CAL: calcitriol; Cas9: CRISPR-associated protein 9; Con: control; CPZ: chlorpromazine; DSS: dextran sodium sulfate; EBSS: Earle's balanced salt solution; IBD: inflammatory bowel disease; TER: trans-epithelial resistance; KD: knockdown; KO: knockout; MAP1LC3/LC3: microtubule associated protein 1 light chain 3; MβCD: Methyl-β-cyclodextrin; MET: metformin; MG132: carbobenzoxy-Leu-Leu-leucinal; MTOR: mechanistic target of rapamycin kinase; NT: non target; RAPA: rapamycin; RES: resveratrol; SMER: small-molecule enhancer 28; SQSTM1: sequestosome 1; ST: starvation; ULK1: unc-51 like autophagy activating kinase 1; WT: wild type.

Keywords:  Autophagy; CLDN2; inflammatory bowel disease; intestinal permeability; tight junction

DOI:  https://doi.org/10.1080/15548627.2021.2016233
Cell Rep. 2021 Dec 28. pii: S2211-1247(21)01640-5. [Epub ahead of print]37(13): 110144

Kaposi's sarcoma herpesvirus activates the hypoxia response to usurp HIF2α-dependent translation initiation for replication and oncogenesis.

Omayra Méndez-Solís, Mourad Bendjennat, Julian Naipauer, Phaedra R Theodoridis, J J David Ho, Ramiro E Verdun, Joshua M Hare, Ethel Cesarman, Stephen Lee, Enrique A Mesri.

  Kaposi's sarcoma herpesvirus (KSHV) is an angiogenesis-inducing oncovirus whose ability to usurp the oxygen-sensing machinery is central to its oncogenicity. By upregulating the hypoxia-inducible factors (HIFs), KSHV reprograms infected cells to a hypoxia-like state, triggering angiogenesis. Here we identify a link between KSHV replicative biology and oncogenicity by showing that KSHV's ability to regulate HIF2α levels and localization to the endoplasmic reticulum (ER) in normoxia enables translation of viral lytic mRNAs through the HIF2α-regulated eIF4E2 translation-initiation complex. This mechanism of translation in infected cells is critical for lytic protein synthesis and contributes to KSHV-induced PDGFRA activation and VEGF secretion. Thus, KSHV regulation of the oxygen-sensing machinery allows virally infected cells to initiate translation via the mTOR-dependent eIF4E1 or the HIF2α-dependent, mTOR-independent, eIF4E2. This "translation initiation plasticity" (TRIP) is an oncoviral strategy used to optimize viral protein expression that links molecular strategies of viral replication to angiogenicity and oncogenesis.

Keywords:  EPAS1; HHV-8; KSHV; Kaposi’s sarcoma herpesvirus; PDGFRA; eIF4E2 cap binding; hypoxia-inducible factors; oxygen-regulated translation initiation; viral oncogenesis; viral replication

DOI:  https://doi.org/10.1016/j.celrep.2021.110144
EMBO J. 2021 Dec 27. e108518

Biogenesis of secretory immunoglobulin M requires intermediate non-native disulfide bonds and engagement of the protein disulfide isomerase ERp44.

Chiara Giannone, Maria Rita Chelazzi, Andrea Orsi, Tiziana Anelli, Tuan Nguyen, Johannes Buchner, Roberto Sitia.

  Antibodies of the immunoglobulin M (IgM) class represent the frontline of humoral immune responses. They are secreted as planar polymers in which flanking µ2 L2 "monomeric" subunits are linked by two disulfide bonds, one formed by the penultimate cysteine (C575) in the tailpiece of secretory µ chains (µs tp) and the second by C414 in the Cµ3. The latter bond is not present in membrane IgM. Here, we show that C575 forms a non-native, intra-subunit disulfide bond as a key step in the biogenesis of secretory IgM. The abundance of this unexpected intermediate correlates with the onset and extent of polymerization. The rearrangement of the C-terminal tails into a native quaternary structure is guaranteed by the engagement of protein disulfide isomerase ERp44, which attacks the non-native C575 bonds. The resulting conformational changes promote polymerization and formation of C414 disulfide linkages. This unusual assembly pathway allows secretory polymers to form without the risk of disturbing the role of membrane IgM as part of the B cell antigen receptor.

Keywords:  ERp44; disulfide bonds; polymeric immunoglobulins; protein quality control; secretion

DOI:  https://doi.org/10.15252/embj.2021108518
J Biol Chem. 2021 Dec 24. pii: S0021-9258(21)01350-8. [Epub ahead of print] 101540

p53 regulates skeletal muscle mitophagy and mitochondrial quality control following denervation-induced muscle disuse.

Jonathan M Memme, Ashley N Oliveira, David A Hood.

  Persistent inactivity promotes skeletal muscle atrophy, marked by mitochondrial aberrations that affect strength, mobility, and metabolic health leading to the advancement of disease. Mitochondrial quality control (MQC) pathways include biogenesis (synthesis), mitophagy/lysosomal turnover, and the mitochondrial unfolded protein response (UPRmt) which serve to maintain an optimal organelle network. Tumor suppressor p53 has been implicated in regulating muscle mitochondria in response to cellular stress; however, its role in the context of muscle disuse has yet to be explored, and whether p53 is necessary for MQC remains unclear. To address this, we subjected p53 muscle-specific knockout (mKO) and wild-type (WT) mice to unilateral denervation. Transcriptomic and pathway analyses revealed dysregulation of pathways pertaining to mitochondrial function, and especially turnover, in mKO muscle following denervation. Protein and mRNA data of the MQC pathways indicated activation of the UPRmt and mitophagy-lysosome systems along with reductions in mitochondrial biogenesis and content in WT and mKO tissue following chronic denervation. However, p53 ablation also attenuated the expression of autophagy/mitophagy machinery, reduced autophagic flux, and enhanced lysosomal dysfunction. While similar reductions in mitochondrial biogenesis and content were observed between genotypes, MQC dysregulation exacerbated mitochondrial dysfunction in mKO fibers, evidenced by elevated reactive oxygen species (ROS). Moreover, acute experiments indicate that p53 mediates the expression of transcriptional regulators of MQC pathways as early as 1 day following denervation. Together, our data illustrate exacerbated mitochondrial dysregulation with denervation stress in p53 mKO tissue, thus indicating that p53 contributes to organellar maintenance via regulation of MQC pathways during muscle atrophy.

Keywords:  lysosome; mitochondria; mitochondrial biogenesis; mitochondrial quality control; mitophagy; muscle atrophy; p53; skeletal muscle; transcriptomics; unfolded protein response (UPR)

DOI:  https://doi.org/10.1016/j.jbc.2021.101540
Cancer Res. 2021 Dec 29. pii: canres.2101.2021. [Epub ahead of print]

p16 Represses DNA Damage Repair via a Novel Ubiquitin-Dependent Signaling Cascade.

David P Molkentine, Jessica M Molkentine, Kathleen A Bridges, David R Valdecanas, Annika Dhawan, Reshub Bahri, Andrew J Hefner, Manish Kumar, Liangpeng Yang, Mohamed Abdelhakiem, Phillip M Pifer, Vlad Sandulache, Aakash Sheth, Beth M Beadle, Howard D Thames, Kathryn A Mason, Curtis R Pickering, Raymond E Meyn, Heath D Skinner.

Squamous cell carcinoma driven by human papillomavirus (HPV) is more sensitive to DNA-damaging therapies than its HPV-negative counterpart. Here we show that p16, the clinically utilized surrogate for HPV positivity, renders cells more sensitive to radiation via a ubiquitin-dependent signaling pathway, linking high levels of this protein to increased activity of the transcription factor SP1, increased HUWE1 transcription, and degradation of ubiquitin-specific protease 7 (USP7) and TRIP12. Activation of this pathway in HPV-positive disease led to decreased homologous recombination (HR) and improved response to radiation, a phenomenon that can be recapitulated in HPV-negative disease using USP7 inhibitors in clinical development. This p16-driven axis induced sensitivity to PARP inhibition and potentially leads to "BRCAness" in head and neck squamous cell carcinoma (HNSCC) cells. Thus, these findings support a functional role for p16 in HPV-positive tumors in driving response to DNA damage, which can be exploited to improve outcomes in both HPV-positive and HPV-negative HNSCC patients.

DOI: https://doi.org/10.1158/0008-5472.CAN-21-2101
Semin Cancer Biol. 2021 Dec 22. pii: S1044-579X(21)00300-X. [Epub ahead of print]

Characterizing and exploiting the many roles of aberrant H2B monoubiquitination in cancer pathogenesis.

Lucile M Jeusset, Kirk J McManus.

  Monoubiquitination of histone H2B on lysine 120 (H2Bub1) is implicated in the control of multiple essential processes, including transcription, DNA damage repair and mitotic chromosome segregation. Accordingly, aberrant regulation of H2Bub1 can induce transcriptional reprogramming and genome instability that may promote oncogenesis. Remarkably, alterations of the ubiquitin ligases and deubiquitinating enzymes regulating H2Bub1 are emerging as ubiquitous features in cancer, further supporting the possibility that the misregulation of H2Bub1 is an underlying mechanism contributing to cancer pathogenesis. To date, aberrant H2Bub1 dynamics have been reported in multiple cancer types and are associated with transcriptional changes that promote oncogenesis in a cancer type-specific manner. Owing to the multi-functional nature of H2Bub1, misregulation of its writers and erasers may drive disease initiation and progression through additional synergistic processes. Accordingly, understanding the molecular determinants and pathogenic impacts associated with aberrant H2Bub1 regulation may reveal novel drug targets and therapeutic vulnerabilities that can be exploited to develop innovative precision medicine strategies that better combat cancer. In this review, we present the normal functions of H2Bub1 in the control of DNA-associated processes and describe the pathogenic implications associated with its misregulation in cancer. We further discuss the challenges coupled with the development of therapeutic strategies targeting H2Bub1 misregulation and expose the potential benefits of designing treatments that synergistically exploit the multiple functionalities of H2Bub1 to improve treatment selectivity and efficacy.

Keywords:  Cancer; Genome instability; H2B; Transcription; Ubiquitination

DOI:  https://doi.org/10.1016/j.semcancer.2021.12.007
J Biochem. 2021 Dec 31. pii: mvab134. [Epub ahead of print]

Ever-Expanding NGLY1 biology.

Tadashi Suzuki, Yukiko Yoshida.

The cytosolic peptide:N-glycanase (PNGase; NGLY1 in humans) is a deglycosylating enzyme that is widely conserved in eukaryotes. This enzyme is involved in the degradation of misfolded N-glycoproteins that are destined for proteasomal degradation in the cytosol, a process that is called endoplasmic reticulum (ER)-associated degradation (ERAD). Although the physiological significance of NGLY1 remained unknown until recently, the discovery of NGLY1 deficiency, a human genetic disorder bearing mutations in the NGLY1 gene, has led to explosive research progress regarding the functional characterization of this enzyme. For example, it is now known that NGLY1 can also act as an "editing enzyme" to convert N-glycosylated asparagine residues to aspartate residues, thus introducing negative charges into a core peptide and modulating the function of the target molecule. Diverse biological processes have also been found to be affected by compromised NGLY1 activity. In this special issue, recent research progress on the functional characterization of NGLY1 and its orthologues in worm/fly/rodents, assay methods/biomarkers useful for the development of therapeutics, and the comprehensive transcriptome/proteome of NGLY1-KO cells as well as patient-derived cells are discussed.

DOI: https://doi.org/10.1093/jb/mvab134
Autophagy. 2021 Dec 29. 1-18

Converging roles of PSENEN/PEN2 and CLN3 in the autophagy-lysosome system.

Marcel Klein, Abuzar Kaleem, Sandra Oetjen, Daniela Wünkhaus, Lars Binkle, Sandra Schilling, Milena Gjorgjieva, Ralf Scholz, Doris Gruber-Schoffnegger, Stephan Storch, Stefan Kins, Gerard Drewes, Sabine Hoffmeister-Ullerich, Dietmar Kuhl, Guido Hermey.

  PSENEN/PEN2 is the smallest subunit of the γ-secretase complex, an intramembrane protease that cleaves proteins within their transmembrane domains. Mutations in components of the γ-secretase underlie familial Alzheimer disease. In addition to its proteolytic activity, supplementary, γ-secretase independent, functions in the macroautophagy/autophagy-lysosome system have been proposed. Here, we screened for PSENEN-interacting proteins and identified CLN3. Mutations in CLN3 are causative for juvenile neuronal ceroid lipofuscinosis, a rare lysosomal storage disorder considered the most common neurodegenerative disease in children. As mutations in the PSENEN and CLN3 genes cause different neurodegenerative diseases, understanding shared cellular functions of both proteins might be pertinent for understanding general cellular mechanisms underlying neurodegeneration. We hypothesized that CLN3 modulates γ-secretase activity and that PSENEN and CLN3 play associated roles in the autophagy-lysosome system. We applied CRISPR gene-editing and obtained independent isogenic HeLa knockout cell lines for PSENEN and CLN3. Following previous studies, we demonstrate that PSENEN is essential for forming a functional γ-secretase complex and is indispensable for γ-secretase activity. In contrast, CLN3 does not modulate γ-secretase activity to a significant degree. We observed in PSENEN- and CLN3-knockout cells corresponding alterations in the autophagy-lysosome system. These include reduced activity of lysosomal enzymes and lysosome number, an increased number of autophagosomes, increased lysosome-autophagosome fusion, and elevated levels of TFEB (transcription factor EB). Our study strongly suggests converging roles of PSENEN and CLN3 in the autophagy-lysosome system in a γ-secretase activity-independent manner, supporting the idea of common cytopathological processes underlying different neurodegenerative diseases.

Keywords:  Alzheimer disease; cln3 disease; knockout cells; neuronal ceroid lipofuscinosis; transcription factor eb; γ-secretase

DOI:  https://doi.org/10.1080/15548627.2021.2016232