bims-proteo 2021-09-05 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2021–09–05
38 papers selected by
Eric Chevet, INSERM

iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation.
Influenza A viruses balance ER stress with host protein synthesis shutoff.
Ligandability of E3 Ligases for Targeted Protein Degradation Applications.
Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation.
Neuronal regulated ire-1-dependent mRNA decay controls germline differentiation in Caenorhabditis elegans.
Endoplasmic reticulum tubules limit the size of misfolded protein condensates.
Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway.
Autophagy in major human diseases.
Proteomic analysis demonstrates the role of the quality control protease LONP1 in mitochondrial protein aggregation.
Intramolecular quality control: HIV-1 envelope gp160 signal-peptide cleavage as a functional folding checkpoint.
The role of endoplasmic reticulum stress in astrocytes.
Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation.
The ATP-dependent SWI/SNF and RSC chromatin remodelers cooperatively induce unfolded protein response genes during endoplasmic reticulum stress.
Isolation and analysis of fractions enriched in WrappER-associated mitochondria from mouse liver.
Altered protein abundance and localization inferred from sites of alternative modification by ubiquitin and SUMO.
Insulin/IGF-1 signaling and heat stress differentially regulate HSF1 activities in germline development.
The deubiquitinase USP15 modulates cellular redox and is a therapeutic target in acute myeloid leukemia.
Tril dampens Nodal signaling through Pellino2- and Traf6-mediated activation of Nedd4l.
A (dis)integrated stress response: Genetic diseases of eIF2α regulators.
Ubiquitination of NF-κB p65 by FBXW2 suppresses breast cancer stemness, tumorigenesis, and paclitaxel resistance.
Dissecting multiple roles of SUMOylation in prostate cancer.
A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins.
Introducing Thioredoxin-related Transmembrane Proteins: Emerging Roles of Human TMX and Clinical Implications.
Protein disulphide isomerase (PDI) is protective against amyotrophic lateral sclerosis (ALS)-related mutant Fused in Sarcoma (FUS) in in vitro models.
Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A.
LC3A-mediated autophagy regulates lung cancer cell plasticity.
Rice ubiquitin-conjugating enzyme OsUBC26 is essential for immunity to the blast fungus Magnaporthe oryzae.
Crosstalk between the chloroplast protein import and SUMO systems revealed through genetic and molecular investigation in Arabidopsis.
Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities.
Tools for functional dissection of site-specific O-GlcNAcylation.
Secreted retrovirus-like GAG-domain-containing protein PEG10 is regulated by UBE3A and is involved in Angelman syndrome pathophysiology.
GOLPH3 keeps the Golgi residents at home.
HOIP limits anti-tumor immunity by protecting against combined TNF and IFN-gamma-induced apoptosis.
Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice.
Deubiquitinases in hematological malignancies.
Cancer associated mutations in Sec61γ alter the permeability of the ER translocase.
Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density.
GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles.

Cell Rep. 2021 Aug 31. pii: S2211-1247(21)01085-8. [Epub ahead of print]36(9): 109642

iRQC, a surveillance pathway for 40S ribosomal quality control during mRNA translation initiation.

Danielle M Garshott, Heeseon An, Elayanambi Sundaramoorthy, Marilyn Leonard, Alison Vicary, J Wade Harper, Eric J Bennett.

  Post-translational modification of ribosomal proteins enables rapid and dynamic regulation of protein biogenesis. Site-specific ubiquitylation of 40S ribosomal proteins uS10 and eS10 plays a key role during ribosome-associated quality control (RQC). Distinct, and previously functionally ambiguous, ubiquitylation events on the 40S proteins uS3 and uS5 are induced by diverse proteostasis stressors that impact translation activity. Here, we identify the ubiquitin ligase RNF10 and the deubiquitylating enzyme USP10 as the key enzymes that regulate uS3 and uS5 ubiquitylation. Prolonged uS3 and uS5 ubiquitylation results in 40S, but not 60S, ribosomal protein degradation in a manner independent of canonical autophagy. We show that blocking progression of either scanning or elongating ribosomes past the start codon triggers site-specific ubiquitylation events on ribosomal proteins uS5 and uS3. This study identifies and characterizes a distinct arm in the RQC pathway, initiation RQC (iRQC), that acts on 40S ribosomes during translation initiation to modulate translation activity and capacity.

Keywords:  RNF10; protein homeostasis; ribosome-associated quality control; translation initiation; ubiquitin

DOI:  https://doi.org/10.1016/j.celrep.2021.109642
Proc Natl Acad Sci U S A. 2021 Sep 07. pii: e2024681118. [Epub ahead of print]118(36):

Influenza A viruses balance ER stress with host protein synthesis shutoff.

Beryl Mazel-Sanchez, Justyna Iwaszkiewicz, Joao P P Bonifacio, Filo Silva, Chengyue Niu, Shirin Strohmeier, Davide Eletto, Florian Krammer, Gene Tan, Vincent Zoete, Benjamin G Hale, Mirco Schmolke.

  Excessive production of viral glycoproteins during infections poses a tremendous stress potential on the endoplasmic reticulum (ER) protein folding machinery of the host cell. The host cell balances this by providing more ER resident chaperones and reducing translation. For viruses, this unfolded protein response (UPR) offers the potential to fold more glycoproteins. We postulated that viruses could have developed means to limit the inevitable ER stress to a beneficial level for viral replication. Using a relevant human pathogen, influenza A virus (IAV), we first established the determinant for ER stress and UPR induction during infection. In contrast to a panel of previous reports, we identified neuraminidase to be the determinant for ER stress induction, and not hemagglutinin. IAV relieves ER stress by expression of its nonstructural protein 1 (NS1). NS1 interferes with the host messenger RNA processing factor CPSF30 and suppresses ER stress response factors, such as XBP1. In vivo viral replication is increased when NS1 antagonizes ER stress induction. Our results reveal how IAV optimizes glycoprotein expression by balancing folding capacity.

Keywords:  CPSF30; ER stress; NS1; influenza virus; neuraminidase

DOI:  https://doi.org/10.1073/pnas.2024681118
Biochemistry. 2021 Sep 02.

Ligandability of E3 Ligases for Targeted Protein Degradation Applications.

Bridget P Belcher, Carl C Ward, Daniel K Nomura.

Targeted protein degradation (TPD) using proteolysis targeting chimeras (PROTACs) and molecular glue degraders has arisen as a powerful therapeutic modality for eliminating disease-causing proteins from cells. PROTACs and molecular glue degraders employ heterobifunctional or monovalent small molecules, respectively, to chemically induce the proximity of target proteins with E3 ubiquitin ligases to ubiquitinate and degrade specific proteins via the proteasome. Whereas TPD is an attractive therapeutic strategy for expanding the druggable proteome, only a relatively small number of E3 ligases out of the >600 E3 ligases encoded by the human genome have been exploited by small molecules for TPD applications. Here we review the existing E3 ligases that have thus far been successfully exploited for TPD and discuss chemoproteomics-enabled covalent screening strategies for discovering new E3 ligase recruiters. We also provide a chemoproteomic map of reactive cysteines within hundreds of E3 ligases that may represent potential ligandable sites that can be pharmacologically interrogated to uncover additional E3 ligase recruiters.

DOI: https://doi.org/10.1021/acs.biochem.1c00464
Nat Commun. 2021 Sep 01. 12(1): 5212

Reconstitution defines the roles of p62, NBR1 and TAX1BP1 in ubiquitin condensate formation and autophagy initiation.

Eleonora Turco, Adriana Savova, Flora Gere, Luca Ferrari, Julia Romanov, Martina Schuschnig, Sascha Martens.

The autophagic degradation of misfolded and ubiquitinated proteins is important for cellular homeostasis. In this process, which is governed by cargo receptors, ubiquitinated proteins are condensed into larger structures and subsequently become targets for the autophagy machinery. Here we employ in vitro reconstitution and cell biology to define the roles of the human cargo receptors p62/SQSTM1, NBR1 and TAX1BP1 in the selective autophagy of ubiquitinated substrates. We show that p62 is the major driver of ubiquitin condensate formation. NBR1 promotes condensate formation by equipping the p62-NBR1 heterooligomeric complex with a high-affinity UBA domain. Additionally, NBR1 recruits TAX1BP1 to the ubiquitin condensates formed by p62. While all three receptors interact with FIP200, TAX1BP1 is the main driver of FIP200 recruitment and thus the autophagic degradation of p62-ubiquitin condensates. In summary, our study defines the roles of all three receptors in the selective autophagy of ubiquitin condensates.

DOI: https://doi.org/10.1038/s41467-021-25572-w
Elife. 2021 Sep 03. pii: e65644. [Epub ahead of print]10

Neuronal regulated ire-1-dependent mRNA decay controls germline differentiation in Caenorhabditis elegans.

Mor Levi-Ferber, Rewayd Shalash, Adrien Le-Thomas, Yehuda Salzberg, Maor Shurgi, Jennifer Ic Benichou, Avi Ashkenazi, Sivan Henis-Korenblit.

  Understanding the molecular events that regulate cell pluripotency versus acquisition of differentiated somatic cell fate is fundamentally important. Studies in Caenorhabditis elegans demonstrate that knockout of the germline-specific translation repressor gld-1 causes germ cells within tumorous gonads to form germline-derived teratoma. Previously we demonstrated that endoplasmic reticulum (ER) stress enhances this phenotype to suppress germline tumor progression(Levi-Ferber et al., 2015). Here, we identify a neuronal circuit that non-autonomously suppresses germline differentiation and show that it communicates with the gonad via the neurotransmitter serotonin to limit somatic differentiation of the tumorous germline. ER stress controls this circuit through regulated inositol requiring enzyme-1 (IRE-1)-dependent mRNA decay of transcripts encoding the neuropeptide FLP-6. Depletion of FLP-6 disrupts the circuit's integrity and hence its ability to prevent somatic-fate acquisition by germline tumor cells. Our findings reveal mechanistically how ER stress enhances ectopic germline differentiation and demonstrate that regulated Ire1-dependent decay can affect animal physiology by controlling a specific neuronal circuit.

Keywords:  C. elegans; ER stress; IRE1; RIDD; cell biology; developmental biology; germline; neuronal circuit; pluripotency; teratoma

DOI:  https://doi.org/10.7554/eLife.65644
Elife. 2021 Sep 01. pii: e71642. [Epub ahead of print]10

Endoplasmic reticulum tubules limit the size of misfolded protein condensates.

Smriti Parashar, Ravi Chidambaram, Shuliang Chen, Christina R Liem, Eric Griffis, Gerard G Lambert, Nathan C Shaner, Matthew Wortham, Jesse C Hay, Susan Ferro-Novick.

  The endoplasmic reticulum (ER) is composed of sheets and tubules. Here we report that the COPII coat subunit, SEC24C, works with the long form of the tubular ER-phagy receptor, RTN3, to target dominant-interfering mutant proinsulin Akita puncta to lysosomes. When the delivery of Akita puncta to lysosomes was disrupted, large puncta accumulated in the ER. Unexpectedly, photobleach analysis indicated that Akita puncta behaved as condensates and not aggregates, as previously suggested. Akita puncta enlarged when either RTN3 or SEC24C were depleted, or when ER sheets were proliferated by either knocking out Lunapark or overexpressing CLIMP63. Other ER-phagy substrates that are segregated into tubules behaved like Akita, while a substrate (type I procollagen) that is degraded by the ER-phagy sheets receptor, FAM134B, did not. Conversely, when ER tubules were augmented in Lunapark knock-out cells by overexpressing reticulons, ER-phagy increased and the number of large Akita puncta were reduced. Our findings imply that segregating cargos into tubules has two beneficial roles. First, it localizes mutant misfolded proteins, the receptor and SEC24C to the same ER domain. Second, physically restraining condensates within tubules, before they undergo ER-phagy, prevents them from enlarging and impacting cell health.

Keywords:  cell biology

DOI:  https://doi.org/10.7554/eLife.71642
J Cell Biol. 2021 Nov 01. pii: e202104073. [Epub ahead of print]220(11):

Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway.

James L Shen, Tina M Fortier, Ruoxi Wang, Eric H Baehrecke.

Defects in autophagy cause problems in metabolism, development, and disease. The autophagic clearance of mitochondria, mitophagy, is impaired by the loss of Vps13D. Here, we discover that Vps13D regulates mitophagy in a pathway that depends on the core autophagy machinery by regulating Atg8a and ubiquitin localization. This process is Pink1 dependent, with loss of pink1 having similar autophagy and mitochondrial defects as loss of vps13d. The role of Pink1 has largely been studied in tandem with Park/Parkin, an E3 ubiquitin ligase that is widely considered to be crucial in Pink1-dependent mitophagy. Surprisingly, we find that loss of park does not exhibit the same autophagy and mitochondrial deficiencies as vps13d and pink1 mutant cells and contributes to mitochondrial clearance through a pathway that is parallel to vps13d. These findings provide a Park-independent pathway for Pink1-regulated mitophagy and help to explain how Vps13D regulates autophagy and mitochondrial morphology and contributes to neurodegenerative diseases.

DOI: https://doi.org/10.1083/jcb.202104073
EMBO J. 2021 Aug 30. e108863

Autophagy in major human diseases.

Daniel J Klionsky, Giulia Petroni, Ravi K Amaravadi, Eric H Baehrecke, Andrea Ballabio, Patricia Boya, José Manuel Bravo-San Pedro, Ken Cadwell, Francesco Cecconi, Augustine M K Choi, Mary E Choi, Charleen T Chu, Patrice Codogno, Maria Isabel Colombo, Ana Maria Cuervo, Vojo Deretic, Ivan Dikic, Zvulun Elazar, Eeva-Liisa Eskelinen, Gian Maria Fimia, David A Gewirtz, Douglas R Green, Malene Hansen, Marja Jäättelä, Terje Johansen, Gábor Juhász, Vassiliki Karantza, Claudine Kraft, Guido Kroemer, Nicholas T Ktistakis, Sharad Kumar, Carlos Lopez-Otin, Kay F Macleod, Frank Madeo, Jennifer Martinez, Alicia Meléndez, Noboru Mizushima, Christian Münz, Josef M Penninger, Rushika M Perera, Mauro Piacentini, Fulvio Reggiori, David C Rubinsztein, Kevin M Ryan, Junichi Sadoshima, Laura Santambrogio, Luca Scorrano, Hans-Uwe Simon, Anna Katharina Simon, Anne Simonsen, Alexandra Stolz, Nektarios Tavernarakis, Sharon A Tooze, Tamotsu Yoshimori, Junying Yuan, Zhenyu Yue, Qing Zhong, Lorenzo Galluzzi, Federico Pietrocola.

  Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.

Keywords:  aging; cancer; inflammation; metabolic syndromes; neurodegeneration

DOI:  https://doi.org/10.15252/embj.2021108863
J Biol Chem. 2021 Aug 27. pii: S0021-9258(21)00935-2. [Epub ahead of print] 101134

Proteomic analysis demonstrates the role of the quality control protease LONP1 in mitochondrial protein aggregation.

Karen Pollecker, Marc Sylvester, Wolfgang Voos.

  The mitochondrial matrix protease LONP1 is an essential part of the organellar protein quality control system. LONP1 has been shown to be involved in respiration control and apoptosis. Furthermore, a reduction in LONP1 level correlates with ageing. Up to now, the effects of a LONP1 defect were mostly studied by utilizing transient, siRNA-mediated knockdown approaches. We generated a new cellular model system for studying the impact of LONP1 on mitochondrial protein homeostasis by a CRISPR/Cas-mediated genetic knockdown (gKD). These cells show a stable reduction of LONP1 along with a mild phenotype characterized by absent morphological differences and only small negative effects on mitochondrial functions under normal culture conditions. To assess the consequences of a permanent LONP1 depletion on the mitochondrial proteome, we analyzed the alterations of protein levels by quantitative mass spectrometry, demonstrating small adaptive changes, in particular with respect to mitochondrial protein biogenesis. In an additional proteomic analysis, we determined the temperature-dependent aggregation behavior of mitochondrial proteins and its dependence on a reduction of LONP1 activity, demonstrating the important role of the protease for mitochondrial protein homeostasis in mammalian cells. We identified a significant number of mitochondrial proteins that are affected by LONP1 activity especially with respect to their stress-induced solubility. Taken together, our results suggest a very good applicability of the LONP1 gKD cell line as a model system for human ageing processes.

Keywords:  Human; LONP1 protease; cell biology; mitochondria; protein aggregation; proteostasis

DOI:  https://doi.org/10.1016/j.jbc.2021.101134
Cell Rep. 2021 Aug 31. pii: S2211-1247(21)01089-5. [Epub ahead of print]36(9): 109646

Intramolecular quality control: HIV-1 envelope gp160 signal-peptide cleavage as a functional folding checkpoint.

Nicholas McCaul, Matthias Quandte, Ilja Bontjer, Guus van Zadelhoff, Aafke Land, Ema T Crooks, James M Binley, Rogier W Sanders, Ineke Braakman.

  Removal of the membrane-tethering signal peptides that target secretory proteins to the endoplasmic reticulum is a prerequisite for proper folding. While generally thought to be removed co-translationally, we report two additional post-targeting functions for the HIV-1 gp120 signal peptide, which remains attached until gp120 folding triggers its removal. First, the signal peptide improves folding fidelity by enhancing conformational plasticity of gp120 by driving disulfide isomerization through a redox-active cysteine. Simultaneously, the signal peptide delays folding by tethering the N terminus to the membrane, until assembly with the C terminus. Second, its carefully timed cleavage represents intramolecular quality control and ensures release of (only) natively folded gp120. Postponed cleavage and the redox-active cysteine are both highly conserved and important for viral fitness. Considering the ∼15% proteins with signal peptides and the frequency of N-to-C contacts in protein structures, these regulatory roles of signal peptides are bound to be more common in secretory-protein biogenesis.

Keywords:  HIV-1; disulfide bond; disulfide isomerization; endoplasmic reticulum; envelope glycoprotein; gp120; membrane tethering; protein folding; redox-active cysteine; signal peptide

DOI:  https://doi.org/10.1016/j.celrep.2021.109646
Glia. 2021 Aug 31.

The role of endoplasmic reticulum stress in astrocytes.

Savannah G Sims, Rylee N Cisney, Marissa M Lipscomb, Gordon P Meares.

  Astrocytes are glial cells that support neurological function in the central nervous system (CNS), in part, by providing structural support for neuronal synapses and blood vessels, participating in electrical and chemical transmission, and providing trophic support via soluble factors. Dysregulation of astrocyte function contributes to neurological decline in CNS diseases. Neurological diseases are highly heterogeneous but share common features of cellular stress including the accumulation of misfolded proteins. Endoplasmic reticulum (ER) stress has been reported in nearly all neurological and neurodegenerative diseases. ER stress occurs when there is an accumulation of misfolded proteins in the ER lumen and the protein folding demand of the ER is overwhelmed. ER stress initiates the unfolded protein response (UPR) to restore homeostasis by abating protein translation and, if the cell is irreparably damaged, initiating apoptosis. Although protein aggregation and misfolding in neurological disease has been well described, cell-specific contributions of ER stress and the UPR in physiological and disease states are poorly understood. Recent work has revealed a role for active UPR signaling that may drive astrocytes toward a maladaptive phenotype in various model systems. In response to ER stress, astrocytes produce inflammatory mediators, have reduced trophic support, and can transmit ER stress to other cells. This review will discuss the current known contributions and consequences of activated UPR signaling in astrocytes.

Keywords:  astrocytes; cell signaling; endoplasmic reticulum; glia; protein folding; translation

DOI:  https://doi.org/10.1002/glia.24082
Protein Sci. 2021 Aug 30.

Quantitative analyses for effects of neddylation on CRL2VHL substrate ubiquitination and degradation.

Kankan Wang, Kurt M Reichermeier, Xing Liu.

  Through catalyzing the ubiquitination of key regulatory proteins, cullin-RING ubiquitin ligases (CRLs) play essential biological roles and their activities are controlled by multiple mechanisms including neddylation, the conjugation of NEDD8 to cullins. Upon neddylation, a CRL, such as the CUL1-based CRL1, undergoes conformational changes that accelerate substrate ubiquitination. Given the structural diversity across subfamilies of CRLs and their substrates, to what extent neddylation modulates the activity of individual CRLs remains to be evaluated. Here, through reconstituting the CRL2 ubiquitination reaction in vitro, we showed that neddylation promotes CRL2VHL -dependent degradation of both full-length HIF1α and the degron peptide of HIF1α, resulting in more than 10-fold increase in the rate of substrate ubiquitination. Consistently, pevonedistat (also known as MLN4924), an inhibitor of neddylation, inhibits the degradation of HIF1α in RCC4 cells stably expressing VHL in cycloheximide chase assays. However, such inhibitory effect of pevonedistat on HIF1α degradation was not observed in HEK293 cells, which was further found to be due to CRL2VHL -independent degradation that was active in HEK293 but not RCC4 cells. After truncating HIF1α to its Carboxy-terminal Oxygen-Dependent Degradation (CODD) domain, we showed that pevonedistat inhibited the degradation of CODD and increased its half-life by six-fold in HEK293 cells. Our results demonstrate that neddylation plays a significant role in activating CRL2, and the cellular activity of CRL2VHL is better reflected by the degradation of CODD than that of HIF1α, especially under conditions where CRL2-independent degradation of HIF1α is active. This article is protected by copyright. All rights reserved.

Keywords:  CODD; CRL2 ubiquitin ligase; neddylation; protein degradation; ubiquitination

DOI:  https://doi.org/10.1002/pro.4176
Biochim Biophys Acta Gene Regul Mech. 2021 Aug 25. pii: S1874-9399(21)00066-3. [Epub ahead of print] 194748

The ATP-dependent SWI/SNF and RSC chromatin remodelers cooperatively induce unfolded protein response genes during endoplasmic reticulum stress.

Rakesh Kumar Sahu, Sakshi Singh, Raghuvir Singh Tomar.

  The SWI/SNF subfamily remodelers (SWI/SNF and RSC) generally promote gene expression by displacing or evicting nucleosomes at the promoter regions. Their action creates a nucleosome-depleted region where transcription machinery accesses the DNA. Their involvement has been shown critical for inducing stress-responsive transcription programs. Although the role of SWI/SNF and RSC complexes in transcription regulation of heat shock responsive genes is well studied, their involvement at other pathways such as unfolded protein response (UPR) and protein quality control (PQC) is less known. This study shows that SWI/SNF occupies promoters of UPR, HSP and PQC genes in response to unfolded protein stress, and its recruitment at UPR promoters depends on Hac1 transcription factor and other epigenetic factors like Ada2 and Ume6. Disruption of SWI/SNF's activity does not affect the remodeling of these promoters or gene expression. However, inactivation of RSC and SWI/SNF together diminishes expression of most of the UPR, HSP and PQC genes tested. Furthermore, RSC and SWI/SNF colocalize at these promoters, suggesting that these two remodelers functionally cooperate to induce stress-responsive genes under proteotoxic conditions.

Keywords:  Chromatin remodeling complexes; ER stress; RSC; SWI/SNF; Transcription regulation; UPR

DOI:  https://doi.org/10.1016/j.bbagrm.2021.194748
STAR Protoc. 2021 Sep 17. 2(3): 100752

Isolation and analysis of fractions enriched in WrappER-associated mitochondria from mouse liver.

Nicolò Ilacqua, Irene Anastasia, Luca Pellegrini.

  The endoplasmic reticulum (ER) plays a central role in lipid homeostasis, but the role of individual ER subdomains in lipid biology has not been elucidated. WrappER is a curved wrapping type of rough-ER that establishes extensive contacts with almost every mitochondria of the hepatocyte in the mouse liver. Here, we describe a protocol for isolation of fractions enriched in wrappER-associated mitochondria from the mouse liver. We also provide techniques for assessing its quality by electron microscopy and biochemical/proteomic analysis. For complete information on the use and execution of this protocol, please refer to Anastasia et al. (2021).

Keywords:  Cell Biology; Cell separation/fractionation; Metabolism; Protein Biochemistry

DOI:  https://doi.org/10.1016/j.xpro.2021.100752
J Mol Biol. 2021 Aug 28. pii: S0022-2836(21)00452-6. [Epub ahead of print] 167219

Altered protein abundance and localization inferred from sites of alternative modification by ubiquitin and SUMO.

Adi Ulman, Tal Levin, Bareket Dassa, Aaron Javitt, Assaf Kacen, Merav D Shmueli, Avital Eisenberg-Lerner, Daoud Sheban, Simon Fishllevich, Emmanuel D Levy, Yifat Merbl.

  Protein modification by ubiquitin or SUMO can alter the function, stability or activity of target proteins. Previous studies have identified thousands of substrates that were modified by ubiquitin or SUMO on the same lysine residue. However, it remains unclear whether such overlap could result from a mere higher solvent accessibility, whether proteins containing those sites are associated with specific functional traits, and whether selectively perturbing their modification by ubiquitin or SUMO could result in different phenotypic outcomes. Here, we mapped reported lysine modification sites across the human proteome and found an enrichment of sites reported to be modified by both ubiquitin and SUMO. Our analysis uncovered thousands of proteins containing such sites, which we term Sites of Alternative Modification (SAMs). Among more than 36,000 sites reported to be modified by SUMO, 51.8% have also been reported to be modified by ubiquitin. SAM-containing proteins are associated with diverse biological functions including cell cycle, DNA damage, and transcriptional regulation. As such, our analysis highlights numerous proteins and pathways as putative targets for further elucidating the crosstalk between ubiquitin and SUMO. Comparing the biological and biochemical properties of SAMs versus other non-overlapping modification sites revealed that these sites were associated with altered cellular localization or abundance of their host proteins. Lastly, using S. cerevisiae as model, we show that mutating the SAM motif in a protein can influence its ubiquitination as well as its localization and abundance.

Keywords:  PTM Profiling; PTM: post-translational modification; SAM; SUMO; Ubl: Ubiquitin-like; lysine; proteostasis; site of alternative modification; systems biology; ubiquitin

DOI:  https://doi.org/10.1016/j.jmb.2021.167219
Cell Rep. 2021 Aug 31. pii: S2211-1247(21)01061-5. [Epub ahead of print]36(9): 109623

Insulin/IGF-1 signaling and heat stress differentially regulate HSF1 activities in germline development.

Stacey L Edwards, Purevsuren Erdenebat, Allison C Morphis, Lalit Kumar, Lai Wang, Tomasz Chamera, Constantin Georgescu, Jonathan D Wren, Jian Li.

  Germline development is sensitive to nutrient availability and environmental perturbation. Heat shock transcription factor 1 (HSF1), a key transcription factor driving the cellular heat shock response (HSR), is also involved in gametogenesis. The precise function of HSF1 (HSF-1 in C. elegans) and its regulation in germline development are poorly understood. Using the auxin-inducible degron system in C. elegans, we uncovered a role of HSF-1 in progenitor cell proliferation and early meiosis and identified a compact but important transcriptional program of HSF-1 in germline development. Interestingly, heat stress only induces the canonical HSR in a subset of germ cells but impairs HSF-1 binding at its developmental targets. Conversely, insulin/insulin growth factor 1 (IGF-1) signaling dictates the requirement for HSF-1 in germline development and functions through repressing FOXO/DAF-16 in the soma to activate HSF-1 in germ cells. We propose that this non-cell-autonomous mechanism couples nutrient-sensing insulin/IGF-1 signaling to HSF-1 activation to support homeostasis in rapid germline growth.

Keywords:  HSF1; germline development; heat shock response; insulin/IGF-1 signaling; proteostasis

DOI:  https://doi.org/10.1016/j.celrep.2021.109623
Leukemia. 2021 Aug 31.

The deubiquitinase USP15 modulates cellular redox and is a therapeutic target in acute myeloid leukemia.

Madeline Niederkorn, Chiharu Ishikawa, Kathleen M Hueneman, James Bartram, Emily Stepanchick, Joshua R Bennett, Ashley E Culver-Cochran, Lyndsey C Bolanos, Emma Uible, Kwangmin Choi, Mark Wunderlich, John P Perentesis, Timothy M Chlon, Marie-Dominique Filippi, Daniel T Starczynowski.

Ubiquitin-specific peptidase 15 (USP15) is a deubiquitinating enzyme implicated in critical cellular and oncogenic processes. We report that USP15 mRNA and protein are overexpressed in human acute myeloid leukemia (AML) as compared to normal hematopoietic progenitor cells. This high expression of USP15 in AML correlates with KEAP1 protein and suppression of NRF2. Knockdown or deletion of USP15 in human and mouse AML models significantly impairs leukemic progenitor function and viability and de-represses an antioxidant response through the KEAP1-NRF2 axis. Inhibition of USP15 and subsequent activation of NRF2 leads to redox perturbations in AML cells, coincident with impaired leukemic cell function. In contrast, USP15 is dispensable for human and mouse normal hematopoietic cells in vitro and in vivo. A preclinical small-molecule inhibitor of USP15 induced the KEAP1-NRF2 axis and impaired AML cell function, suggesting that targeting USP15 catalytic function can suppress AML. Based on these findings, we report that USP15 drives AML cell function, in part, by suppressing a critical oxidative stress sensor mechanism and permitting an aberrant redox state. Furthermore, we postulate that inhibition of USP15 activity with small molecule inhibitors will selectively impair leukemic progenitor cells by re-engaging homeostatic redox responses while sparing normal hematopoiesis.

DOI: https://doi.org/10.1038/s41375-021-01394-z
Proc Natl Acad Sci U S A. 2021 Sep 07. pii: e2104661118. [Epub ahead of print]118(36):

Tril dampens Nodal signaling through Pellino2- and Traf6-mediated activation of Nedd4l.

Hyung-Seok Kim, Yangsook Song Green, Yuanyuan Xie, Jan L Christian.

  Toll-like receptor 4 (Tlr) interactor with leucine-rich repeats (Tril) functions as a Tlr coreceptor to mediate innate immunity in adults. In Xenopus embryos, Tril triggers degradation of the transforming growth factor β (Tgf-ß) family inhibitor, Smad7. This enhances bone morphogenetic protein (Bmp) signaling to enable ventral mesoderm to commit to a blood fate. Here, we show that Tril simultaneously dampens Nodal signaling by catalytically activating the ubiquitin ligase NEDD4 Like (Nedd4l). Nedd4l then targets Nodal receptors for degradation. How Tril signals are transduced in a nonimmune context is unknown. We identify the ubiquitin ligase Pellino2 as a protein that binds to the cytoplasmic tail of Tril and subsequently forms a complex with Nedd4l and another E3 ligase, TNF-receptor associated factor 6 (Traf6). Pellino2 and Traf6 are essential for catalytic activation of Nedd4l, both in Xenopus and in mammalian cells. Traf6 ubiquitinates Nedd4l, which is then recruited to membrane compartments where activation occurs. Collectively, our findings reveal that Tril initiates a noncanonical Tlr-like signaling cascade to activate Nedd4l, thereby coordinately regulating the Bmp and Nodal arms of the Tgf-ß superfamily during vertebrate development.

Keywords:  Nedd4l; Nodal; Pellino; Tril; Xenopus

DOI:  https://doi.org/10.1073/pnas.2104661118
Wiley Interdiscip Rev RNA. 2021 Aug 31. e1689

A (dis)integrated stress response: Genetic diseases of eIF2α regulators.

Alyssa M English, Katelyn M Green, Stephanie L Moon.

  The integrated stress response (ISR) is a conserved mechanism by which eukaryotic cells remodel gene expression to adapt to intrinsic and extrinsic stressors rapidly and reversibly. The ISR is initiated when stress-activated protein kinases phosphorylate the major translation initiation factor eukaryotic translation initiation factor 2ɑ (eIF2ɑ), which globally suppresses translation initiation activity and permits the selective translation of stress-induced genes including important transcription factors such as activating transcription factor 4 (ATF4). Translationally repressed messenger RNAs (mRNAs) and noncoding RNAs assemble into cytoplasmic RNA-protein granules and polyadenylated RNAs are concomitantly stabilized. Thus, regulated changes in mRNA translation, stability, and localization to RNA-protein granules contribute to the reprogramming of gene expression that defines the ISR. We discuss fundamental mechanisms of RNA regulation during the ISR and provide an overview of a growing class of genetic disorders associated with mutant alleles of key translation factors in the ISR pathway. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications RNA in Disease and Development > RNA in Disease Translation > Translation Regulation RNA in Disease and Development > RNA in Development.

Keywords:  RNA-protein granules; eIF2α; genetic diseases; integrated stress response; translation

DOI:  https://doi.org/10.1002/wrna.1689
Cell Death Differ. 2021 Aug 31.

Ubiquitination of NF-κB p65 by FBXW2 suppresses breast cancer stemness, tumorigenesis, and paclitaxel resistance.

Chune Ren, Xue Han, Chao Lu, Tingting Yang, Pengyun Qiao, Yonghong Sun, Zhenhai Yu.

The F-box and WD-repeat-containing protein 2 (FBXW2) plays a crucial role as an E3 ligase in regulating tumorigenesis. However, the functions of FBXW2 in breast cancer are still unknown. Here, we find that nuclear factor-kB (NF-κB) p65 is a new substrate of FBXW2. FBXW2 directly binds to p65, leading to its ubiquitination and degradation. Interestingly, p300 acetylation of p65 blocks FBXW2 induced p65 ubiquitination. FBXW2-p65 axis is a crucial regulator of SOX2-induced stemness in breast cancer. Moreover, FBXW2 inhibits breast tumor growth by regulating p65 degradation in vitro and in vivo. FBXW2 overexpression abrogates the effects of p65 on paclitaxel resistance in vitro and in vivo. Furthermore, FBXW2 induced p65 degradation is also confirmed in FBXW2-knockout mice. Our results identify FBXW2 as an important E3 ligase for p65 degradation, which provide insights into the tumor suppressor functions of FBXW2 in breast cancer.

DOI: https://doi.org/10.1038/s41418-021-00862-4
Cancer Lett. 2021 Aug 28. pii: S0304-3835(21)00431-6. [Epub ahead of print]521 88-97

Dissecting multiple roles of SUMOylation in prostate cancer.

Yishu Wang, Jianxiu Yu.

  Protein modification with small ubiquitin-like modifiers (SUMOs) plays dual roles in prostate cancer (PCa) tumorigenesis and development. Any intermediary of the SUMO conjugation cycle going awry may forfeit the balance between tumorigenic potential and anticancer effects. Deregulated SUMOylation on the androgen receptor and oncoproteins also takes part in this pathological process, as exemplified by STAT3/NF-κB and tumor suppressors such as PTEN and p53. Here, we outline recent developments and discoveries of SUMOylation in PCa and present an overview of its multiple roles in PCa tumorigenesis/promotion and suppression, while elucidating its potential as a therapeutic target for PCa.

Keywords:  Prostate cancer (PCa); SUMOs; SUMOylation; Therapeutic intervention

DOI:  https://doi.org/10.1016/j.canlet.2021.08.034
JACS Au. 2021 Jun 28. 1(6): 777-785

A Chemical Toolbox for Labeling and Degrading Engineered Cas Proteins.

Rodrigo A Gama-Brambila, Jie Chen, Yasamin Dabiri, Georg Tascher, Václav Němec, Christian Münch, Guangqi Song, Stefan Knapp, Xinlai Cheng.

The discovery of clustered regularly interspaced short palindromic repeats and their associated proteins (Cas) has revolutionized the field of genome and epigenome editing. A number of new methods have been developed to precisely control the function and activity of Cas proteins, including fusion proteins and small-molecule modulators. Proteolysis-targeting chimeras (PROTACs) represent a new concept using the ubiquitin-proteasome system to degrade a protein of interest, highlighting the significance of chemically induced protein-E3 ligase interaction in drug discovery. Here, we engineered Cas proteins (Cas9, dCas9, Cas12, and Cas13) by inserting a Phe-Cys-Pro-Phe (FCPF) amino acid sequence (known as the π-clamp system) and demonstrate that the modified CasFCPF proteins can be (1) labeled in live cells by perfluoroaromatics carrying the fluorescein or (2) degraded by a perfluoroaromatics-functionalized PROTAC (PROTAC-FCPF). A proteome-wide analysis of PROTAC-FCPF-mediated Cas9FCPF protein degradation revealed a high target specificity, suggesting a wide range of applications of perfluoroaromatics-induced proximity in the regulation of stability, activity, and functionality of any FCPF-tagging protein.

DOI: https://doi.org/10.1021/jacsau.1c00007
Antioxid Redox Signal. 2021 Sep 01.

Introducing Thioredoxin-related Transmembrane Proteins: Emerging Roles of Human TMX and Clinical Implications.

Yoshiyuki Matsuo.

SIGNIFICANCE: The presence of a large number of thioredoxin superfamily members suggests a complex mechanism of redox-based regulation in mammalian cells. However, whether these members are functionally redundant or play separate and distinct roles in each cellular compartment remains to be elucidated. Recent advances: In the mammalian endoplasmic reticulum (ER), approximately 20 thioredoxin-like proteins have been identified. Most ER oxidoreductases are soluble proteins located in the luminal compartment, while a small family of five thioredoxin-related transmembrane proteins (TMX) also reside in the ER membrane and play crucial roles with specialized functions.
CRITICAL ISSUES: In addition to the predicted function of ER protein quality control, several independent studies have suggested the diverse roles of TMX family proteins in the regulation of cellular processes, including calcium homeostasis, bioenergetics, and thiol-disulfide exchange in the extracellular space. Moreover, recent studies have provided evidence of their involvement in the pathogenesis of various diseases.
FUTURE DIRECTIONS: Extensive research is required to unravel the physiological roles of TMX family proteins. Given that membrane-associated proteins are prime targets for drug discovery in a variety of human diseases, expanding our knowledge on the mechanistic details of TMX action on the cell membrane will provide molecular basis for developing novel diagnostic and therapeutic approaches as a potent molecular target in a clinical setting.

DOI: https://doi.org/10.1089/ars.2021.0187
Sci Rep. 2021 Sep 02. 11(1): 17557

Protein disulphide isomerase (PDI) is protective against amyotrophic lateral sclerosis (ALS)-related mutant Fused in Sarcoma (FUS) in in vitro models.

S Parakh, E R Perri, M Vidal, J Sultana, S Shadfar, P Mehta, A Konopka, C J Thomas, D M Spencer, J D Atkin.

Mutations in Fused in Sarcoma (FUS) are present in familial and sporadic cases of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). FUS is localised in the nucleus where it has important functions in DNA repair. However, in ALS/FTD, mutant FUS mislocalises from the nucleus to the cytoplasm where it forms inclusions, a key pathological hallmark of neurodegeneration. Mutant FUS also inhibits protein import into the nucleus, resulting in defects in nucleocytoplasmic transport. Fragmentation of the neuronal Golgi apparatus, induction of endoplasmic reticulum (ER) stress, and inhibition of ER-Golgi trafficking are also associated with mutant FUS misfolding in ALS. Protein disulphide isomerase (PDI) is an ER chaperone previously shown to be protective against misfolding associated with mutant superoxide dismutase 1 (SOD1) and TAR DNA-binding protein-43 (TDP-43) in cellular and zebrafish models. However, a protective role against mutant FUS in ALS has not been previously described. In this study, we demonstrate that PDI is protective against mutant FUS. In neuronal cell line and primary cultures, PDI restores defects in nuclear import, prevents the formation of mutant FUS inclusions, inhibits Golgi fragmentation, ER stress, ER-Golgi transport defects, and apoptosis. These findings imply that PDI is a new therapeutic target in FUS-associated ALS.

DOI: https://doi.org/10.1038/s41598-021-96181-2
Cell Rep. 2021 Aug 31. pii: S2211-1247(21)01076-7. [Epub ahead of print]36(9): 109633

Not4 and Not5 modulate translation elongation by Rps7A ubiquitination, Rli1 moonlighting, and condensates that exclude eIF5A.

George E Allen, Olesya O Panasenko, Zoltan Villanyi, Marina Zagatti, Benjamin Weiss, Lucile Pagliazzo, Susanne Huch, Christine Polte, Szabolcs Zahoran, Christopher S Hughes, Vicent Pelechano, Zoya Ignatova, Martine A Collart.

  In this work, we show that Not4 and Not5 from the Ccr4-Not complex modulate translation elongation dynamics and change ribosome A-site dwelling occupancy in a codon-dependent fashion. These codon-specific changes in not5Δ cells are very robust and independent of codon position within the mRNA, the overall mRNA codon composition, or changes of mRNA expression levels. They inversely correlate with codon-specific changes in cells depleted for eIF5A and positively correlate with those in cells depleted for ribosome-recycling factor Rli1. Not5 resides in punctate loci, co-purifies with ribosomes and Rli1, but not with eIF5A, and limits mRNA solubility. Overexpression of wild-type or non-complementing Rli1 and loss of Rps7A ubiquitination enable Not4 E3 ligase-dependent translation of polyarginine stretches. We propose that Not4 and Not5 modulate translation elongation dynamics to produce a soluble proteome by Rps7A ubiquitination, dynamic condensates that limit mRNA solubility and exclude eIF5A, and a moonlighting function of Rli1.

Keywords:  Condensates; Not1; Not4; Not5; Rli1; codon optimality; eIF5A; translation elongation

DOI:  https://doi.org/10.1016/j.celrep.2021.109633
Autophagy. 2021 Sep 01. 1-14

LC3A-mediated autophagy regulates lung cancer cell plasticity.

Chia-Cheng Miao, Wen Hwang, Ling-Yi Chu, Li-Hao Yang, Cam-Thu Ha, Pei-Yu Chen, Ming-Han Kuo, Sheng-Chieh Lin, Ya-Yu Yang, Shuang-En Chuang, Chia-Cherng Yu, Shien-Tung Pan, Mou-Chieh Kao, Chuang-Rung Chang, Yu-Ting Chou.

   ABBREVIATIONS: ATG14: autophagy related 14; CDH2: cadherin 2; ChIP-qPCR: chromatin immunoprecipitation quantitative polymerase chain reaction; CQ: chloroquine; ECAR: extracellular acidification rate; EMT: epithelial-mesenchymal transition; EPCAM: epithelial cell adhesion molecule; MAP1LC3A/LC3A: microtubule associated protein 1 light chain 3 alpha; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MAP1LC3C/LC3C: microtubule associated protein 1 light chain 3 gamma; NDUFV2: NADH:ubiquinone oxidoreductase core subunit V2; OCR: oxygen consumption rate; ROS: reactive oxygen species; RT-qPCR: reverse-transcriptase quantitative polymerase chain reaction; SC: scrambled control; shRNA: short hairpin RNA; SNAI2: snail family transcriptional repressor 2; SOX2: SRY-box transcription factor 2; SQSTM1/p62: sequestosome 1; TGFB/TGF-β: transforming growth factor beta; TOMM20: translocase of outer mitochondrial membrane 20; ZEB1: zinc finger E-box binding homeobox 1.

Keywords:  Autophagy; LC3A; SOX2; cancer cell plasticity; lung cancer; mitochondria dynamics

DOI:  https://doi.org/10.1080/15548627.2021.1964224
Mol Plant Pathol. 2021 Aug 30.

Rice ubiquitin-conjugating enzyme OsUBC26 is essential for immunity to the blast fungus Magnaporthe oryzae.

Xin Liu, Linlin Song, Heng Zhang, Yijuan Lin, Xiaolei Shen, Jiayuan Guo, Meiling Su, Gaosheng Shi, Zonghua Wang, Guo-Dong Lu.

  The functions of ubiquitin-conjugating enzymes (E2) in plant immunity are not well understood. In this study, OsUBC26, a rice ubiquitin-conjugating enzyme, was characterized in the defence against Magnaporthe oryzae. The expression of OsUBC26 was induced by M. oryzae inoculation and methyl jasmonate treatment. Both RNA interference lines and CRISPR/Cas9 null mutants of OsUBC26 reduced rice resistance to M. oryzae. WRKY45 was down-regulated in OsUBC26 null mutants. In vitro E2 activity assay indicated that OsUBC26 is an active ubiquitin-conjugating enzyme. Yeast two-hybrid assays using OsUBC26 as bait identified the RING-type E3 ligase UCIP2 as an interacting protein. Coimmunoprecipitation assays confirmed the interaction between OsUBC26 and UCIP2. The CRISPR/Cas9 mutants of UCIP2 also showed compromised resistance to M. oryzae. Yeast two-hybrid screening using UCIP2 as bait revealed that APIP6 is a binding partner of UCIP2. Moreover, OsUBC26 working with APIP6 ubiquitinateds AvrPiz-t, an avirulence effector of M. oryzae, and OsUBC26 null mutation impaired the proteasome degradation of AvrPiz-t in rice cells. In summary, OsUBC26 plays important roles in rice disease resistance by regulating WRKY45 expression and working with E3 ligases such as APIP6 to counteract the effector protein AvrPiz-t from M. oryzae.

Keywords:   Magnaporthe oryzae ; AvrPiz-t; OsUBC26; WRKY45; plant immunity; rice; ubiquitin-conjugating enzyme

DOI:  https://doi.org/10.1111/mpp.13132
Elife. 2021 Sep 02. pii: e60960. [Epub ahead of print]10

Crosstalk between the chloroplast protein import and SUMO systems revealed through genetic and molecular investigation in Arabidopsis.

Samuel Watson, Na Li, Yiting Ye, Feijie Wu, Qihua Ling, R Paul Jarvis.

  The chloroplast proteome contains thousands of different proteins that are encoded by the nuclear genome. These proteins are imported into the chloroplast via the action of the TOC translocase and associated downstream systems. Our recent work has revealed that the stability of the TOC complex is dynamically regulated by the ubiquitin-dependent chloroplast-associated protein degradation (CHLORAD) pathway. Here, we demonstrate that the TOC complex is also regulated by the SUMO system. Arabidopsis mutants representing almost the entire SUMO conjugation pathway can partially suppress the phenotype of ppi1, a pale-yellow mutant lacking the Toc33 protein. This suppression is linked to increased abundance of TOC proteins and improvements in chloroplast development. Moreover, data from molecular and biochemical experiments support a model in which the SUMO system directly regulates TOC protein stability. Thus, we have identified a regulatory link between the SUMO system and the chloroplast protein import machinery.

Keywords:  A. thaliana; cell biology; plant biology

DOI:  https://doi.org/10.7554/eLife.60960
RSC Chem Biol. 2020 Jun 01. 1(2): 42-55

Neighborhood watch: tools for defining locale-dependent subproteomes and their contextual signaling activities.

Marcus J C Long, Yi Zhao, Yimon Aye.

Transient associations between numerous organelles-e.g., the endoplasmic reticulum and the mitochondria-forge highly-coordinated, particular environments essential for cross-compartment information flow. Our perspective summarizes chemical-biology tools that have enabled identifying proteins present within these itinerant communities against the bulk proteome, even when a particular protein's presence is fleeting/substoichiometric. However, proteins resident at these ephemeral junctions also experience transitory changes to their interactomes, small-molecule signalomes, and, importantly, functions. Thus, a thorough census of sub-organellar communities necessitates functionally probing context-dependent signaling properties of individual protein-players. Our perspective accordingly further discusses how repurposing of existing tools could allow us to glean a functional understanding of protein-specific signaling activities altered as a result of organelles pulling together. Collectively, our perspective strives to usher new chemical-biology techniques that could, in turn, open doors to modulate functions of specific subproteomes/organellar junctions underlying the nuanced regulatory subsystem broadly termed as contactology.

DOI: https://doi.org/10.1039/d0cb00041h
RSC Chem Biol. 2020 Aug 01. 1(3): 98-109

Tools for functional dissection of site-specific O-GlcNAcylation.

Andrii Gorelik, Daan M F van Aalten.

Protein O-GlcNAcylation is an abundant post-translational modification of intracellular proteins with the monosaccharide N-acetylglucosamine covalently tethered to serines and threonines. Modification of proteins with O-GlcNAc is required for metazoan embryo development and maintains cellular homeostasis through effects on transcription, signalling and stress response. While disruption of O-GlcNAc homeostasis can have detrimental impact on cell physiology and cause various diseases, little is known about the functions of individual O-GlcNAc sites. Most of the sites are modified sub-stoichiometrically which is a major challenge to the dissection of O-GlcNAc function. Here, we discuss the application, advantages and limitations of the currently available tools and technologies utilised to dissect the function of O-GlcNAc on individual proteins and sites in vitro and in vivo. Additionally, we provide a perspective on future developments required to decipher the protein- and site-specific roles of this essential sugar modification.

DOI: https://doi.org/10.1039/d0cb00052c
Cell Rep Med. 2021 Aug 17. 2(8): 100360

Secreted retrovirus-like GAG-domain-containing protein PEG10 is regulated by UBE3A and is involved in Angelman syndrome pathophysiology.

Nikhil J Pandya, Congwei Wang, Veronica Costa, Paul Lopatta, Sonja Meier, F Isabella Zampeta, A Mattijs Punt, Edwin Mientjes, Philip Grossen, Tania Distler, Manuel Tzouros, Yasmina Martí, Balazs Banfai, Christoph Patsch, Soren Rasmussen, Marius Hoener, Marco Berrera, Thomas Kremer, Tom Dunkley, Martin Ebeling, Ben Distel, Ype Elgersma, Ravi Jagasia.

  Angelman syndrome (AS) is a neurodevelopmental disorder caused by the loss of maternal UBE3A, a ubiquitin protein ligase E3A. Here, we study neurons derived from patients with AS and neurotypical individuals, and reciprocally modulate UBE3A using antisense oligonucleotides. Unbiased proteomics reveal proteins that are regulated by UBE3A in a disease-specific manner, including PEG10, a retrotransposon-derived GAG protein. PEG10 protein increase, but not RNA, is dependent on UBE3A and proteasome function. PEG10 binds to both RNA and ataxia-associated proteins (ATXN2 and ATXN10), localizes to stress granules, and is secreted in extracellular vesicles, modulating vesicle content. Rescue of AS patient-derived neurons by UBE3A reinstatement or PEG10 reduction reveals similarity in transcriptome changes. Overexpression of PEG10 during mouse brain development alters neuronal migration, suggesting that it can affect brain development. These findings imply that PEG10 is a secreted human UBE3A target involved in AS pathophysiology.

Keywords:  Angelman syndrome; PEG10; RNA-binding protein; UBE3A; extracellular vesicles; hiPSC neurons; retroviral GAG; stress granules

DOI:  https://doi.org/10.1016/j.xcrm.2021.100360
J Cell Biol. 2021 Oct 04. pii: e202108147. [Epub ahead of print]220(10):

GOLPH3 keeps the Golgi residents at home.

Martin Lowe.

In this issue of JCB, Welch et al. (2021. J. Cell Biol.https://doi.org/10.1083/jcb.202106115) show that GOLPH3 mediates the sorting of numerous Golgi proteins into recycling COPI transport vesicles. This explains how many resident proteins are retained at the Golgi and reveals a key role for GOLPH3 in maintaining Golgi homeostasis.

DOI: https://doi.org/10.1083/jcb.202108147
EMBO Rep. 2021 Sep 01. e53391

HOIP limits anti-tumor immunity by protecting against combined TNF and IFN-gamma-induced apoptosis.

Andrew J Freeman, Stephin J Vervoort, Jessica Michie, Kelly M Ramsbottom, John Silke, Conor J Kearney, Jane Oliaro.

  The success of cancer immunotherapy is limited to a subset of patients, highlighting the need to identify the processes by which tumors evade immunity. Using CRISPR/Cas9 screening, we reveal that melanoma cells lacking HOIP, the catalytic subunit of LUBAC, are highly susceptible to both NK and CD8+ T-cell-mediated killing. We demonstrate that HOIP-deficient tumor cells exhibit increased sensitivity to the combined effect of the inflammatory cytokines, TNF and IFN-γ, released by NK and CD8+ T cells upon target recognition. Both genetic deletion and pharmacological inhibition of HOIP augment tumor cell sensitivity to combined TNF and IFN-γ. Together, we unveil a protective regulatory axis, involving HOIP, which limits a transcription-dependent form of cell death that engages both intrinsic and extrinsic apoptotic machinery upon exposure to TNF and IFN-γ. Our findings highlight HOIP inhibition as a potential strategy to harness and enhance the killing capacity of TNF and IFN-γ during immunotherapy.

Keywords:  CRISPR screen; HOIP; IFN-gamma; TNF; immunotherapy

DOI:  https://doi.org/10.15252/embr.202153391
Nat Commun. 2021 Sep 01. 12(1): 5204

Dynamic tracking and identification of tissue-specific secretory proteins in the circulation of live mice.

Kwang-Eun Kim, Isaac Park, Jeesoo Kim, Myeong-Gyun Kang, Won Gun Choi, Hyemi Shin, Jong-Seo Kim, Hyun-Woo Rhee, Jae Myoung Suh.

Secretory proteins are an essential component of interorgan communication networks that regulate animal physiology. Current approaches for identifying secretory proteins from specific cell and tissue types are largely limited to in vitro or ex vivo models which often fail to recapitulate in vivo biology. As such, there is mounting interest in developing in vivo analytical tools that can provide accurate information on the origin, identity, and spatiotemporal dynamics of secretory proteins. Here, we describe iSLET (in situ Secretory protein Labeling via ER-anchored TurboID) which selectively labels proteins that transit through the classical secretory pathway via catalytic actions of Sec61b-TurboID, a proximity labeling enzyme anchored in the ER lumen. To validate iSLET in a whole-body system, we express iSLET in the mouse liver and demonstrate efficient labeling of liver secretory proteins which could be tracked and identified within circulating blood plasma. Furthermore, proteomic analysis of the labeled liver secretome enriched from liver iSLET mouse plasma is highly consistent with previous reports of liver secretory protein profiles. Taken together, iSLET is a versatile and powerful tool for studying spatiotemporal dynamics of secretory proteins, a valuable class of biomarkers and therapeutic targets.

DOI: https://doi.org/10.1038/s41467-021-25546-y
Biomark Res. 2021 Aug 28. 9(1): 66

Deubiquitinases in hematological malignancies.

Hu Lei, Jiaqi Wang, Jiacheng Hu, Qian Zhu, Yingli Wu.

  Deubiquitinases (DUBs) are enzymes that control the stability, interactions or localization of most cellular proteins by removing their ubiquitin modification. In recent years, some DUBs, such as USP7, USP9X and USP10, have been identified as promising therapeutic targets in hematological malignancies. Importantly, some potent inhibitors targeting the oncogenic DUBs have been developed, showing promising inhibitory efficacy in preclinical models, and some have even undergone clinical trials. Different DUBs perform distinct function in diverse hematological malignancies, such as oncogenic, tumor suppressor or context-dependent effects. Therefore, exploring the biological roles of DUBs and their downstream effectors will provide new insights and therapeutic targets for the occurrence and development of hematological malignancies. We summarize the DUBs involved in different categories of hematological malignancies including leukemia, multiple myeloma and lymphoma. We also present the recent development of DUB inhibitors and their applications in hematological malignancies. Together, we demonstrate DUBs as potential therapeutic drug targets in hematological malignancies.

Keywords:  Deubiquitinases; Hematological malignancies; Leukemia; Lymphoma; Multiple myeloma

DOI:  https://doi.org/10.1186/s40364-021-00320-w
PLoS Genet. 2021 Aug 30. 17(8): e1009780

Cancer associated mutations in Sec61γ alter the permeability of the ER translocase.

Christopher M Witham, Aleshanee L Paxman, Lamprini Baklous, Robert F L Steuart, Benjamin L Schulz, Carl J Mousley.

Translocation of secretory and integral membrane proteins across or into the ER membrane occurs via the Sec61 complex, a heterotrimeric protein complex possessing two essential sub-units, Sec61p/Sec61α and Sss1p/Sec61γ and the non-essential Sbh1p/Sec61β subunit. In addition to forming a protein conducting channel, the Sec61 complex maintains the ER permeability barrier, preventing flow of molecules and ions. Loss of Sec61 integrity is detrimental and implicated in the progression of disease. The Sss1p/Sec61γ C-terminus is juxtaposed to the key gating module of Sec61p/Sec61α and is important for gating the translocon. Inspection of the cancer genome database identifies six mutations in highly conserved amino acids of Sec61γ/Sss1p. We identify that five out of the six mutations identified affect gating of the ER translocon, albeit with varying strength. Together, we find that mutations in Sec61γ that arise in malignant cells result in altered translocon gating dynamics, this offers the potential for the translocon to represent a target in co-therapy for cancer treatment.

DOI: https://doi.org/10.1371/journal.pgen.1009780
Nat Methods. 2021 Sep 03.

Nascent Ribo-Seq measures ribosomal loading time and reveals kinetic impact on ribosome density.

Johanna Schott, Sonja Reitter, Doris Lindner, Jan Grosser, Marius Bruer, Anjana Shenoy, Tamar Geiger, Arthur Mathes, Gergana Dobreva, Georg Stoecklin.

In general, mRNAs are assumed to be loaded with ribosomes instantly upon entry into the cytoplasm. To measure ribosome density (RD) on nascent mRNA, we developed nascent Ribo-Seq by combining Ribo-Seq with progressive 4-thiouridine labeling. In mouse macrophages, we determined experimentally the lag between the appearance of nascent mRNA and its association with ribosomes, which was calculated to be 20-22 min for bulk mRNA. In mouse embryonic stem cells, nRibo-Seq revealed an even stronger lag of 35-38 min in ribosome loading. After stimulation of macrophages with lipopolysaccharide, the lag between cytoplasmic and translated mRNA leads to uncoupling between input and ribosome-protected fragments, which gives rise to distorted RD measurements under conditions where mRNA amounts are far from steady-state expression. As a result, we demonstrate that transcriptional changes affect RD in a passive way.

DOI: https://doi.org/10.1038/s41592-021-01250-z
J Cell Biol. 2021 Oct 04. pii: e202106115. [Epub ahead of print]220(10):

GOLPH3 and GOLPH3L are broad-spectrum COPI adaptors for sorting into intra-Golgi transport vesicles.

Lawrence G Welch, Sew-Yeu Peak-Chew, Farida Begum, Tim J Stevens, Sean Munro.

The fidelity of Golgi glycosylation is, in part, ensured by compartmentalization of enzymes within the stack. The COPI adaptor GOLPH3 has been shown to interact with the cytoplasmic tails of a subset of Golgi enzymes and direct their retention. However, other mechanisms of retention, and other roles for GOLPH3, have been proposed, and a comprehensive characterization of the clientele of GOLPH3 and its paralogue GOLPH3L is lacking. GOLPH3's role is of particular interest as it is frequently amplified in several solid tumor types. Here, we apply two orthogonal proteomic methods to identify GOLPH3+3L clients and find that they act in diverse glycosylation pathways or have other roles in the Golgi. Binding studies, bioinformatics, and a Golgi retention assay show that GOLPH3+3L bind the cytoplasmic tails of their clients through membrane-proximal positively charged residues. Furthermore, deletion of GOLPH3+3L causes multiple defects in glycosylation. Thus, GOLPH3+3L are major COPI adaptors that impinge on most, if not all, of the glycosylation pathways of the Golgi.

DOI: https://doi.org/10.1083/jcb.202106115