bims-proteo 2021-03-21 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2021–03–21
38 papers selected by
Eric Chevet, INSERM

J-domain proteins promote client relay from Hsp70 during tail-anchored membrane protein targeting.
Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae.
ATM controls the extent of DNA end resection by eliciting sequential posttranslational modifications of CtIP.
Hsp90-mediated regulation of DYRK3 couples stress granule disassembly and growth via mTORC1 signaling.
Impact of serine protease inhibitor alpha1-antitrypsin on expression of endoplasmic reticulum stress-induced proinflammatory factors in adipocytes.
TEX264 at the intersection of autophagy and DNA repair.
Mutagenesis screen uncovers lifespan extension through integrated stress response inhibition without reduced mRNA translation.
Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor.
p97/VCP is highly expressed in the stem-like cells of breast cancer and controls cancer stemness partly through the unfolded protein response.
Immunoediting role for major vault protein in apoptotic signaling induced by bacterial N-acyl homoserine lactones.
A nuclear-based quality control pathway for non-imported mitochondrial proteins.
Mechanistic basis for ubiquitin modulation of a protein energy landscape.
Ccr4-Not complex subunits Ccr4, Caf1, and Not4 are novel proteolysis factors promoting the degradation of ubiquitin-dependent substrates by the 26S proteasome.
Coordinated Signaling of Activating Transcription Factor 6α and Inositol Requiring Enzyme 1α Regulates Hepatic Stellate Cell-Mediated Fibrogenesis in Mice.
Perspectives on Organelle Interaction, Protein Dysregulation, and Cancer Disease.
Cytosolic protein quality control machinery: Interactions of Hsp70 with a network of co-chaperones and substrates.
Parkin is an E3 ligase for the ubiquitin-like modifier FAT10, which inhibits Parkin activation and mitophagy.
Thapsigargin suppresses alpha 1-acid glycoprotein secretion independently of N-glycosylation and ER stress.
SMURF2-mediated ubiquitin signaling plays an essential role in the regulation of PARP1 PARylating activity, molecular interactions, and functions in mammalian cells.
Activity of the SNARE Protein SNAP29 at the Endoplasmic Reticulum and Golgi Apparatus.
VCP/p97 modulates PtdIns3P production and autophagy initiation.
Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors.
Xbp1s-FoxO1 axis governs lipid accumulation and contractile performance in heart failure with preserved ejection fraction.
Selective autophagy receptor SQSTM1/ p62 inhibits Seneca Valley virus replication by targeting viral VP1 and VP3.
Protein disulphide isomerase inhibition as a potential cancer therapeutic strategy.
A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection.
Sigma receptor knockdown augments dysfunction and apoptosis of beta cells induced by palmitate.
Quantitative Proteomics Reveals that the OGT Interactome is Remodeled in Response to Oxidative Stress.
Protein Trafficking or Cell Signaling: A Dilemma for the Adaptor Protein TOM1.
A Guide To… The Regulation Of Selective Autophagy Receptors.
Deubiquitylation and stabilization of Acf7 by ubiquitin carboxylterminal hydrolase 14 (USP14) is critical for NSCLC migration.
Ubiquitination and the Proteasome as Drug Targets in Trypanosomatid Diseases.
AHR in the intestinal microenvironment: safeguarding barrier function.
Activation of ATF4 triggers trabecular meshwork cell dysfunction and apoptosis in POAG.
Kinetic Characterization of ASXL1/2-Mediated Allosteric Regulation of the BAP1 Deubiquitinase.
Phenotypic screening with target identification and validation in the discovery and development of E3 ligase modulators.
A swine arterivirus deubiquitinase stabilizes two major envelope proteins and promotes production of viral progeny.
O-GlcNAc modification of small heat shock proteins enhances their anti-amyloid chaperone activity.

J Biol Chem. 2021 Mar 16. pii: S0021-9258(21)00324-0. [Epub ahead of print] 100546

J-domain proteins promote client relay from Hsp70 during tail-anchored membrane protein targeting.

Hyunju Cho, Woo Jun Shim, Yumeng Liu, Shu-Ou Shan.

  J-domain proteins (JDPs) play essential roles in assisting Hsp70 function by assisting Hsp70 in client trapping and regulating the Hsp70 ATPase cycle. Here we report that JDPs can further enhance the targeting competence of Hsp70-bound client proteins during tail-anchored protein (TA) biogenesis. In the guided-entry-of-tail-anchored protein (GET) pathway in yeast, nascent TAs are captured by cytosolic Hsp70 and sequentially relayed to downstream chaperones, Sgt2 and Get3, for delivery to the endoplasmic reticulum (ER). We found that two J-domain proteins (JDPs), Ydj1 and Sis1, function in parallel to support TA targeting to the ER in vivo. Biochemical analyses showed that, while Ydj1 and Sis1 differ in their ability to assist Hsp70 in TA trapping, both JDPs enhance the transfer of Hsp70-bound TAs to Sgt2. The ability of the JDPs to regulate the ATPase cycle of Hsp70 is essential for enhancing the transfer competence of Hsp70-bound TAs in vitro and for supporting TA insertion in vivo. These results demonstrate a role of JDPs in regulating the conformation of Hsp70-bound clients during membrane protein biogenesis.

Keywords:  Hsp40; Hsp70; membrane proteins; molecular chaperone; protein targeting; tail-anchored protein

DOI:  https://doi.org/10.1016/j.jbc.2021.100546
Autophagy. 2021 Mar 15. 1-24

Atg9-centered multi-omics integration reveals new autophagy regulators in Saccharomyces cerevisiae.

Di Peng, Chen Ruan, Shanshan Fu, Chengwen He, Jingzhen Song, Hui Li, Yiran Tu, Dachao Tang, Lan Yao, Shaofeng Lin, Ying Shi, Weizhi Zhang, Hao Zhou, Le Zhu, Cong Ma, Cheng Chang, Jie Ma, Zhiping Xie, Chenwei Wang, Yu Xue.

  In Saccharomyces cerevisiae, Atg9 is an important autophagy-related (Atg) protein, and interacts with hundreds of other proteins. How many Atg9-interacting proteins are involved in macroautophagy/autophagy is unclear. Here, we conducted a multi-omic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy, and identified 290 and 256 genes to be markedly regulated by ATG9 in transcriptional and translational levels, respectively. Unexpectedly, we found most of known Atg proteins and autophagy regulators that interact with Atg9 were not significantly changed in the mRNA or protein level during autophagy. Based on a hypothesis that proteins with similar molecular characteristics might have similar functions, we developed a new method named inference of functional interacting partners (iFIP) to integrate the transcriptomic, proteomic and interactomic data, and predicted 42 Atg9-interacting proteins to be potentially involved in autophagy, including 15 known Atg proteins or autophagy regulators. We validated 2 Atg9-interacting partners, Glo3 and Scs7, to be functional in both bulk and selective autophagy. The mRNA and protein expressions but not subcellular localizations of Glo3 and Scs7 were affected with or without ATG9 during autophagy, whereas the colocalizations of the 2 proteins and Atg9 were markedly enhanced at early stages of the autophagic process. Further analyses demonstrated that Glo3 but not Scs7 regulates the retrograde transport of Atg9 during autophagy. A working model was illustrated to highlight the importance of the Atg9 interactome. Taken together, our study not only provided a powerful method for analyzing the multi-omics data, but also revealed 2 new players that regulate autophagy.Abbreviations: ALP: alkaline phosphatase; Arf1: ADP-ribosylation factor 1; Atg: autophagy-related; Co-IP: co-immunoprecipitation; Cvt: cytoplasm-to-vacuole targeting; DEM: differentially expressed mRNA; DEP: differentially expressed protein; DIC: differential interference contrast; E-ratio: enrichment ratio; ER: endoplasmic reticulum; ES: enrichment score; FC: fold change; FPKM: fragments per kilobase of exon per million fragments mapped; GAP: GTPase-activating protein; GFP: green fluorescent protein; GO: gene ontology; GSEA: gene set enrichment analysis; GST: glutathione S-transferase; HA: hemagglutinin; iFIP: inference of functional interacting partners; KO: knockout; LR: logistic regression; OE: over-expression; PAS: phagophore assembly site; PPI: protein-protein interaction; RFP: red fluorescence protein; RNA-seq: RNA sequencing; RT-PCR: real-time polymerase chain reaction; SCC: Spearman's correlation coefficient; SD-N: synthetic minimal medium lacking nitrogen; THANATOS: The Autophagy, Necrosis, ApopTosis OrchestratorS; Vsn: variance stabilization normalization; WT: wild-type.

Keywords:  Atg9; atg9 interactome; autophagy; proteomics; transcriptomics

DOI:  https://doi.org/10.1080/15548627.2021.1898749
Proc Natl Acad Sci U S A. 2021 Mar 23. pii: e2022600118. [Epub ahead of print]118(12):

ATM controls the extent of DNA end resection by eliciting sequential posttranslational modifications of CtIP.

Jinhua Han, Li Wan, Guixing Jiang, Liping Cao, Feiyu Xia, Tian Tian, Xiaomei Zhu, Mingjie Wu, Michael S Y Huen, Yi Wang, Ting Liu, Jun Huang.

  DNA end resection is a critical step in the repair of DNA double-strand breaks (DSBs) via homologous recombination (HR). However, the mechanisms governing the extent of resection at DSB sites undergoing homology-directed repair remain unclear. Here, we show that, upon DSB induction, the key resection factor CtIP is modified by the ubiquitin-like protein SUMO at lysine 578 in a PIAS4-dependent manner. CtIP SUMOylation occurs on damaged chromatin and requires prior hyperphosphorylation by the ATM protein kinase. SUMO-modified hyperphosphorylated CtIP is targeted by the SUMO-dependent E3 ubiquitin ligase RNF4 for polyubiquitination and subsequent degradation. Consequently, disruption of CtIP SUMOylation results in aberrant accumulation of CtIP at DSBs, which, in turn, causes uncontrolled excessive resection, defective HR, and increased cellular sensitivity to DSB-inducing agents. These findings reveal a previously unidentified regulatory mechanism that regulates CtIP activity at DSBs and thus the extent of end resection via ATM-dependent sequential posttranslational modification of CtIP.

Keywords:  ATM; CtIP; DNA end resection; homologous recombination; hyperphosphorylation

DOI:  https://doi.org/10.1073/pnas.2022600118
EMBO Rep. 2021 Mar 19. e51740

Hsp90-mediated regulation of DYRK3 couples stress granule disassembly and growth via mTORC1 signaling.

Laura Mediani, Francesco Antoniani, Veronica Galli, Jonathan Vinet, Arianna Dorotea Carrà, Ilaria Bigi, Vadreenath Tripathy, Tatiana Tiago, Marco Cimino, Giuseppina Leo, Triana Amen, Daniel Kaganovich, Cristina Cereda, Orietta Pansarasa, Jessica Mandrioli, Priyanka Tripathi, Dirk Troost, Eleonora Aronica, Johannes Buchner, Anand Goswami, Jared Sterneckert, Simon Alberti, Serena Carra.

  Stress granules (SGs) are dynamic condensates associated with protein misfolding diseases. They sequester stalled mRNAs and signaling factors, such as the mTORC1 subunit raptor, suggesting that SGs coordinate cell growth during and after stress. However, the molecular mechanisms linking SG dynamics and signaling remain undefined. We report that the chaperone Hsp90 is required for SG dissolution. Hsp90 binds and stabilizes the dual-specificity tyrosine-phosphorylation-regulated kinase 3 (DYRK3) in the cytosol. Upon Hsp90 inhibition, DYRK3 dissociates from Hsp90 and becomes inactive. Inactive DYRK3 is subjected to two different fates: it either partitions into SGs, where it is protected from irreversible aggregation, or it is degraded. In the presence of Hsp90, DYRK3 is active and promotes SG disassembly, restoring mTORC1 signaling and translation. Thus, Hsp90 links stress adaptation and cell growth by regulating the activity of a key kinase involved in condensate disassembly and translation restoration.

Keywords:  DYRK3; FUS-ALS; Hsp90; phase separation; stress granules

DOI:  https://doi.org/10.15252/embr.202051740
Biochem Biophys Rep. 2021 Jul;26 100967

Impact of serine protease inhibitor alpha1-antitrypsin on expression of endoplasmic reticulum stress-induced proinflammatory factors in adipocytes.

Yukari Ando, Akito Kuroda, Kazuya Kusama, Takeshi Matsutani, Akihisa Matsuda, Kazuhiro Tamura.

  Obesity-induced endoplasmic reticulum (ER) stress contributes to low-grade chronic inflammation in adipose tissue and may cause metabolic disorders such as diabetes mellitus and dyslipidemia. Identification of high serpina A1 (alpha-1 antitrypsin, A1AT) expression in mouse adipose tissue and adipocytes prompted us to explore the role of A1AT in the inflammatory response of adipocytes under ER stress. We aimed to determine the role of A1AT expression in adipocytes with ER stress during regulation of adipocyte homeostasis and inflammation. To this end, we chemically induced ER stress in A1AT small interfering RNA-transfected differentiating adipocytes using thapsigargin. Induction of CCAAT-enhancer-binding protein homologous protein (CHOP), an ER stress marker, by thapsigargin was lower in A1AT-deficient SW872 adipocytes. Thapsigargin or the proinflammatory cytokine tumor necrosis factor (TNF)α increased basal expression of cytokines such as interleukin (IL)-1β and IL-8 in both SW872 and primary omental adipocytes. This thapsigargin- or TNFα-induced expression of proinflammatory genes was increased by A1AT deficiency. These findings indicate that adipose A1AT may suppress the ER stress response to block excessive expression of proinflammatory factors, which suggests that A1AT protects against adipose tissue dysfunction associated with ER stress activation.

Keywords:  Adipocyte; Alpha-1 antitrypsin; Endoplasmic reticulum stress; Proinflammatory factor

DOI:  https://doi.org/10.1016/j.bbrep.2021.100967
Autophagy. 2021 Mar 17. 1-10

TEX264 at the intersection of autophagy and DNA repair.

John Fielden, Marta Popović, Kristijan Ramadan.

  TEX264 (testes expressed gene 264) is a single-pass transmembrane protein, consisting of an N-terminal hydrophobic region, a gyrase inhibitory (GyrI)-like domain, and a loosely structured C terminus. TEX264 was first identified as an endoplasmic reticulum (ER)-resident Atg8-family-binding protein that mediates the degradation of portions of the ER during starvation (i.e., reticulophagy). More recently, TEX264 was identified as a cofactor of VCP/p97 ATPase that promotes the repair of covalently trapped TOP1 (DNA topoisomerase 1)-DNA crosslinks. This review summarizes the current knowledge of TEX264 as a protein with roles in both autophagy and DNA repair and provides an evolutionary and structural analysis of GyrI proteins. Based on our phylogenetic analysis, we provide evidence that TEX264 is a member of a large superfamily of GyrI-like proteins that evolved in bacteria and are present in metazoans, including invertebrates and chordates.Abbreviations: Atg8: autophagy related 8; Atg39: autophagy related 39; Cdc48: cell division cycle 48; CGAS: cyclic GMP-AMP synthase; DPC: DNA-protein crosslinks; DSB: DNA double-strand break; ER: endoplasmic reticulum; GyrI: gyrase inhibitory domain; LRR: leucine-rich repeat; MAFFT: multiple alignment using fast Fourier transform; MAP1LC3/LC3: microtubule-associated protein 1 light chain 3; MTOR: mechanistic target of rapamycin kinase; STUBL: SUMO targeted ubiquitin ligase; SUMO: small ubiquitin-like modifier; TEX264: testis expressed gene 264; TOP1cc: topoisomerase 1-cleavage complex; UBZ: ubiquitin binding Zn finger domain; VCP: valosin containing protein.

Keywords:  Autophagy; DNA repair; TEX264; gyrase inhibitory-like proteins; nucleophagy; reticulophagy

DOI:  https://doi.org/10.1080/15548627.2021.1894059
Nat Commun. 2021 03 15. 12(1): 1678

Mutagenesis screen uncovers lifespan extension through integrated stress response inhibition without reduced mRNA translation.

Maxime J Derisbourg, Laura E Wester, Ruth Baddi, Martin S Denzel.

Protein homeostasis is modulated by stress response pathways and its deficiency is a hallmark of aging. The integrated stress response (ISR) is a conserved stress-signaling pathway that tunes mRNA translation via phosphorylation of the translation initiation factor eIF2. ISR activation and translation initiation are finely balanced by eIF2 kinases and by the eIF2 guanine nucleotide exchange factor eIF2B. However, the role of the ISR during aging remains poorly understood. Using a genomic mutagenesis screen for longevity in Caenorhabditis elegans, we define a role of eIF2 modulation in aging. By inhibiting the ISR, dominant mutations in eIF2B enhance protein homeostasis and increase lifespan. Consistently, full ISR inhibition using phosphorylation-defective eIF2α or pharmacological ISR inhibition prolong lifespan. Lifespan extension through impeding the ISR occurs without a reduction in overall protein synthesis. Instead, we observe changes in the translational efficiency of a subset of mRNAs, of which the putative kinase kin-35 is required for lifespan extension. Evidently, lifespan is limited by the ISR and its inhibition may provide an intervention in aging.

DOI: https://doi.org/10.1038/s41467-021-21743-x
Cell Mol Biol Lett. 2021 Mar 17. 26(1): 11

Triazoloacridone C-1305 impairs XBP1 splicing by acting as a potential IRE1α endoribonuclease inhibitor.

Sylwia Bartoszewska, Jarosław Króliczewski, David K Crossman, Aneta Pogorzelska, Maciej Bagiński, James F Collawn, Rafal Bartoszewski.

  Inositol requiring enzyme 1 alpha (IRE1α) is one of three signaling sensors in the unfolding protein response (UPR) that alleviates endoplasmic reticulum (ER) stress in cells and functions to promote cell survival. During conditions of irrevocable stress, proapoptotic gene expression is induced to promote cell death. One of the three signaling stressors, IRE1α is an serine/threonine-protein kinase/endoribonuclease (RNase) that promotes nonconventional splicing of XBP1 mRNA that is translated to spliced XBP1 (XBP1s), an active prosurvival transcription factor. Interestingly, elevated IRE1α and XBP1s are both associated with poor cancer survival and drug resistance. In this study, we used next-generation sequencing analyses to demonstrate that triazoloacridone C-1305, a microtubule stabilizing agent that also has topoisomerase II inhibitory activity, dramatically decreases XBP1s mRNA levels and protein production during ER stress conditions, suggesting that C-1305 does this by decreasing IRE1α's endonuclease activity.

Keywords:  ER stress; IRE1α; UPR; XBP1s

DOI:  https://doi.org/10.1186/s11658-021-00255-y
Cell Death Dis. 2021 Mar 17. 12(4): 286

p97/VCP is highly expressed in the stem-like cells of breast cancer and controls cancer stemness partly through the unfolded protein response.

Chuang Li, Yongsheng Huang, Qianqian Fan, Hongyang Quan, Yeqing Dong, Meng Nie, Jiaqi Wang, Fucun Xie, Jiang Ji, Lan Zhou, Zhi Zheng, Lin Wang.

p97/VCP, an evolutionarily concerned ATPase, partakes in multiple cellular proteostatic processes, including the endoplasmic reticulum (ER)-associated protein degradation (ERAD). Elevated expression of p97 is common in many cancers and is often associated with poor survival. Here we report that the levels of p97 positively correlated with the histological grade, tumor size, and lymph node metastasis in breast cancers. We further examined p97 expression in the stem-like cancer cells or cancer stem cells (CSCs), a cell population that purportedly underscores cancer initiation, therapeutic resistance, and recurrence. We found that p97 was consistently at a higher level in the CD44+/CD24-, ALDH+, or PKH26+ CSC populations than the respective non-CSC populations in human breast cancer tissues and cancer cell lines and p97 expression also positively correlated with that of SOX2, another CSC marker. To assess the role of p97 in breast cancers, cancer proliferation, mammosphere, and orthotopic growth were analyzed. Similarly as p97 depletion, two pharmacological inhibitors, which targets the ER-associated p97 or globally inhibits p97's ATPase activity, markedly reduced cancer growth and the CSC population. Importantly, depletion or inhibition of p97 greatly suppressed the proliferation of the ALDH+ CSCs and the CSC-enriched mammospheres, while exhibiting much less or insignificant inhibitory effects on the non-CSC cancer cells. Comparable phenotypes produced by blocking ERAD suggest that ER proteostasis is essential for the CSC integrity. Loss of p97 gravely activated the unfolded protein response (UPR) and modulated the expression of multiple stemness and pluripotency regulators, including C/EBPδ, c-MYC, SOX2, and SKP2, which collectively contributed to the demise of CSCs. In summary, p97 controls the breast CSC integrity through multiple targets, many of which directly affect cancer stemness and are induced by UPR activation. Our findings highlight the importance of p97 and ER proteostasis in CSC biology and anticancer therapy.

DOI: https://doi.org/10.1038/s41419-021-03555-5
Proc Natl Acad Sci U S A. 2021 Mar 23. pii: e2012529118. [Epub ahead of print]118(12):

Immunoediting role for major vault protein in apoptotic signaling induced by bacterial N-acyl homoserine lactones.

Josep Rayo, Rachel Gregor, Nicholas T Jacob, Rambabu Dandela, Luba Dubinsky, Alex Yashkin, Alexander Aranovich, Manikandan Thangaraj, Orna Ernst, Eran Barash, Sergey Malitsky, Bogdan I Florea, Bastiaan P Krom, Erik A C Wiemer, Valerie A Kickhoefer, Leonard H Rome, John C Mathison, Gunnar F Kaufmann, Herman S Overkleeft, Benjamin F Cravatt, Tsaffrir Zor, Kim D Janda, Richard J Ulevitch, Vladimir V Kravchenko, Michael M Meijler.

  The major vault protein (MVP) mediates diverse cellular responses, including cancer cell resistance to chemotherapy and protection against inflammatory responses to Pseudomonas aeruginosa Here, we report the use of photoactive probes to identify MVP as a target of the N-(3-oxo-dodecanoyl) homoserine lactone (C12), a quorum sensing signal of certain proteobacteria including P. aeruginosa. A treatment of normal and cancer cells with C12 or other N-acyl homoserine lactones (AHLs) results in rapid translocation of MVP into lipid raft (LR) membrane fractions. Like AHLs, inflammatory stimuli also induce LR-localization of MVP, but the C12 stimulation reprograms (functionalizes) bioactivity of the plasma membrane by recruiting death receptors, their apoptotic adaptors, and caspase-8 into LR. These functionalized membranes control AHL-induced signaling processes, in that MVP adjusts the protein kinase p38 pathway to attenuate programmed cell death. Since MVP is the structural core of large particles termed vaults, our findings suggest a mechanism in which MVP vaults act as sentinels that fine-tune inflammation-activated processes such as apoptotic signaling mediated by immunosurveillance cytokines including tumor necrosis factor-related apoptosis inducing ligand (TRAIL).

Keywords:  bacterial signaling; cross-kingdom communication; immunoediting; immunosurveillance

DOI:  https://doi.org/10.1073/pnas.2012529118
Elife. 2021 Mar 18. pii: e61230. [Epub ahead of print]10

A nuclear-based quality control pathway for non-imported mitochondrial proteins.

Viplendra Ps Shakya, William A Barbeau, Tianyao Xiao, Christina S Knutson, Max H Schuler, Adam L Hughes.

  Mitochondrial import deficiency causes cellular toxicity due to the accumulation of non-imported mitochondrial precursor proteins, termed mitoprotein-induced stress. Despite the burden mis-localized mitochondrial precursors place on cells, our understanding of the systems that dispose of these proteins is incomplete. Here, we cataloged the location and steady-state abundance of mitochondrial precursor proteins during mitochondrial impairment in S. cerevisiae. We found that a number of non-imported mitochondrial proteins localize to the nucleus, where they are subjected to proteasome-dependent degradation through a process we term nuclear-associated mitoprotein degradation (mitoNUC). Recognition and destruction of mitochondrial precursors by the mitoNUC pathway requires the presence of an N-terminal mitochondrial targeting sequence (MTS) and is mediated by combined action of the E3 ubiquitin ligases San1, Ubr1, and Doa10. Impaired breakdown of precursors leads to alternative sequestration in nuclear-associated foci. These results identify the nucleus as an important destination for the disposal of non-imported mitochondrial precursors.

Keywords:  S. cerevisiae; cell biology

DOI:  https://doi.org/10.7554/eLife.61230
Proc Natl Acad Sci U S A. 2021 Mar 23. pii: e2025126118. [Epub ahead of print]118(12):

Mechanistic basis for ubiquitin modulation of a protein energy landscape.

Emma C Carroll, Naomi R Latorraca, Johanna M Lindner, Brendan C Maguire, Jeffrey G Pelton, Susan Marqusee.

  Ubiquitin is a common posttranslational modification canonically associated with targeting proteins to the 26S proteasome for degradation and also plays a role in numerous other nondegradative cellular processes. Ubiquitination at certain sites destabilizes the substrate protein, with consequences for proteasomal processing, while ubiquitination at other sites has little energetic effect. How this site specificity-and, by extension, the myriad effects of ubiquitination on substrate proteins-arises remains unknown. Here, we systematically characterize the atomic-level effects of ubiquitination at various sites on a model protein, barstar, using a combination of NMR, hydrogen-deuterium exchange mass spectrometry, and molecular dynamics simulation. We find that, regardless of the site of modification, ubiquitination does not induce large structural rearrangements in the substrate. Destabilizing modifications, however, increase fluctuations from the native state resulting in exposure of the substrate's C terminus. Both of the sites occur in regions of barstar with relatively high conformational flexibility. Nevertheless, destabilization appears to occur through different thermodynamic mechanisms, involving a reduction in entropy in one case and a loss in enthalpy in another. By contrast, ubiquitination at a nondestabilizing site protects the substrate C terminus through intermittent formation of a structural motif with the last three residues of ubiquitin. Thus, the biophysical effects of ubiquitination at a given site depend greatly on local context. Taken together, our results reveal how a single posttranslational modification can generate a broad array of distinct effects, providing a framework to guide the design of proteins and therapeutics with desired degradation and quality control properties.

Keywords:  energy landscape; hydrogen exchange; molecular dynamics; ubiquitin

DOI:  https://doi.org/10.1073/pnas.2025126118
Biochim Biophys Acta Mol Cell Res. 2021 Mar 13. pii: S0167-4889(21)00064-1. [Epub ahead of print] 119010

Ccr4-Not complex subunits Ccr4, Caf1, and Not4 are novel proteolysis factors promoting the degradation of ubiquitin-dependent substrates by the 26S proteasome.

Ganapathi Kandasamy, Ashis Kumar Pradhan, R Palanimurugan.

  Degradation of short-lived and abnormal proteins is essential for normal cellular homeostasis. In eukaryotes, such unstable cellular proteins are selectively degraded by the ubiquitin proteasome system (UPS). Abnormalities in protein degradation by the UPS have been linked to several human diseases. Ccr4, Caf1, and Not4 proteins are known components of the Ccr4-Not multimeric complex. Ccr4 and Caf1 have established roles in transcription, mRNA de-adenylation and RNA degradation etc., while Not4 was shown to have important roles in regulating translation and protein quality control pathways. Here we show that Ccr4, Caf1, and Not4 have a novel function at a post-ubiquitylation step in the UPS pathway by promoting ubiquitin-dependent degradation of short-lived proteins by the 26S proteasome. Using a substrate of the well-studied ubiquitin fusion degradation (UFD) pathway, we found that its UPS-mediated degradation was severely impaired upon deletion of CCR4, CAF1, or NOT4 genes in Saccharomyces cerevisiae. Additionally, we show that Ccr4, Caf1, and Not4 bind to cellular ubiquitin conjugates, and that Ccr4 and Caf1 proteins interact with the proteasome. In contrast to Ccr4, Caf1, and Not4, other subunits of the Ccr4-Not complex are dispensable for UFD substrate degradation. From our findings we conclude that the Ccr4-Not complex subunits Ccr4, Caf1, and Not4 have a novel function outside of the canonical Ccr4-Not complex as a factor targeting ubiquitylated substrates for proteasomal degradation.

Keywords:  Caf1,; Ccr4-Not complex,; N-end rule pathway,; Not4; Ubiquitin fusion degradation (UFD),

DOI:  https://doi.org/10.1016/j.bbamcr.2021.119010
Am J Physiol Gastrointest Liver Physiol. 2021 Mar 17.

Coordinated Signaling of Activating Transcription Factor 6α and Inositol Requiring Enzyme 1α Regulates Hepatic Stellate Cell-Mediated Fibrogenesis in Mice.

Fei Xue, Jianwen Lu, Samuel C Buchl, Liankang Sun, Vijay H Shah, Harmeet Malhi, Jessica L Maiers.

   BACKGROUND/AIMS: Liver injury and the Unfolded Protein Response (UPR) are tightly linked, but their relationship differs with cell-type and injurious stimuli. UPR initiation promotes hepatic stellate cell (HSC) activation and fibrogenesis, but the underlying mechanisms are unclear. Despite the complexity and overlap downstream of UPR transducers IRE1α, ATF6α, and PERK, previous research in HSCs primarily focused on IRE1α. Here, we interrogated the fibrogenic role of ATF6α or PERK in vitro and HSC-specific UPR signaling in vivo.
METHODS/RESULTS: Overexpression of ATF6α, but not the PERK effector ATF4, promoted HSC activation and fibrogenic gene transcription in immortalized HSCs. Furthermore, ATF6α inhibition through Ceapin-A7, or Atf6a deletion, disrupted TGFβ-mediated activation of primary hHSCs or mHSCs respectively. We interrogated the fibrogenic role of ATF6α in vivo through conditional HSC-specific Atf6a deletion. Atf6aHSCΔ/Δ mice displayed reduced fibrosis and HSC activation following bile-duct ligation (BDL) or CCl4-induced injury. The Atf6aHSCΔ/Δ phenotype differed from HSC-specific Ire1a deletion, as Ire1aHSCΔ/Δ mice showed reduced fibrogenic gene transcription no changes in fibrosis compared to Ire1afl/fl mice following BDL. Interestingly, ATF6α signaling increased in Ire1aΔ/Δ HSCs, while IRE1α signaling was upregulated in Atf6aΔ/Δ HSCs. Finally, we asked whether co-deletion of Arf6a and Ire1a additively limits fibrosis. Unexpectedly, fibrosis worsened in Atf6aHSCΔ/ΔIre1aHSCΔ/Δ mice following BDL, and Atf6aΔ/ΔIre1aΔ/Δ mHSCs showed increased fibrogenic gene transcription.
CONCLUSIONS: ATF6α and IRE1α individually promote fibrogenic transcription in HSCs and ATF6α drives fibrogenesis in vivo. Unexpectedly, disruption of both pathways sensitizes the liver to fibrogenesis, suggesting that fine-tuned UPR signaling is critical for regulating HSC activation and fibrogenesis.

Keywords:  ER Stress; Endoplasmic Reticulum; Hepatic Fibrosis; Unfolded Protein Response

DOI:  https://doi.org/10.1152/ajpgi.00453.2020
Front Cell Dev Biol. 2021 ;9 613336

Perspectives on Organelle Interaction, Protein Dysregulation, and Cancer Disease.

Paula Díaz, Alejandra Sandoval-Bórquez, Roberto Bravo-Sagua, Andrew F G Quest, Sergio Lavandero.

  In recent decades, compelling evidence has emerged showing that organelles are not static structures but rather form a highly dynamic cellular network and exchange information through membrane contact sites. Although high-throughput techniques facilitate identification of novel contact sites (e.g., organelle-organelle and organelle-vesicle interactions), little is known about their impact on cellular physiology. Moreover, even less is known about how the dysregulation of these structures impacts on cellular function and therefore, disease. Particularly, cancer cells display altered signaling pathways involving several cell organelles; however, the relevance of interorganelle communication in oncogenesis and/or cancer progression remains largely unknown. This review will focus on organelle contacts relevant to cancer pathogenesis. We will highlight specific proteins and protein families residing in these organelle-interfaces that are known to be involved in cancer-related processes. First, we will review the relevance of endoplasmic reticulum (ER)-mitochondria interactions. This section will focus on mitochondria-associated membranes (MAMs) and particularly the tethering proteins at the ER-mitochondria interphase, as well as their role in cancer disease progression. Subsequently, the role of Ca2+ at the ER-mitochondria interphase in cancer disease progression will be discussed. Members of the Bcl-2 protein family, key regulators of cell death, also modulate Ca2+ transport pathways at the ER-mitochondria interphase. Furthermore, we will review the role of ER-mitochondria communication in the regulation of proteostasis, focusing on the ER stress sensor PERK (PRKR-like ER kinase), which exerts dual roles in cancer. Second, we will review the relevance of ER and mitochondria interactions with other organelles. This section will focus on peroxisome and lysosome organelle interactions and their impact on cancer disease progression. In this context, the peroxisome biogenesis factor (PEX) gene family has been linked to cancer. Moreover, the autophagy-lysosome system is emerging as a driving force in the progression of numerous human cancers. Thus, we will summarize our current understanding of the role of each of these organelles and their communication, highlighting how alterations in organelle interfaces participate in cancer development and progression. A better understanding of specific organelle communication sites and their relevant proteins may help to identify potential pharmacological targets for novel therapies in cancer control.

Keywords:  cancer; endoplasmic reticulum; interorganelle communication; lysosome; mitochondria; peroxisome

DOI:  https://doi.org/10.3389/fcell.2021.613336
Exp Biol Med (Maywood). 2021 Mar 17. 1535370221999812

Cytosolic protein quality control machinery: Interactions of Hsp70 with a network of co-chaperones and substrates.

Chamithi Karunanayake, Richard C Page.

  The chaperone heat shock protein 70 (Hsp70) and its network of co-chaperones serve as a central hub of cellular protein quality control mechanisms. Domain organization in Hsp70 dictates ATPase activity, ATP dependent allosteric regulation, client/substrate binding and release, and interactions with co-chaperones. The protein quality control activities of Hsp70 are classified as foldase, holdase, and disaggregase activities. Co-chaperones directly assisting protein refolding included J domain proteins and nucleotide exchange factors. However, co-chaperones can also be grouped and explored based on which domain of Hsp70 they interact. Here we discuss how the network of cytosolic co-chaperones for Hsp70 contributes to the functions of Hsp70 while closely looking at their structural features. Comparison of domain organization and the structures of co-chaperones enables greater understanding of the interactions, mechanisms of action, and roles played in protein quality control.

Keywords:  BAG; CHIP; GrpE; Hip; Hop; Hsp110; Hsp40; Hsp70; Hsp90; J domain protein; SMADs; co-chaperones; molecular chaperones; nucleotide exchange factor; protein quality control

DOI:  https://doi.org/10.1177/1535370221999812
Cell Rep. 2021 Mar 16. pii: S2211-1247(21)00171-6. [Epub ahead of print]34(11): 108857

Parkin is an E3 ligase for the ubiquitin-like modifier FAT10, which inhibits Parkin activation and mitophagy.

Nicola D Roverato, Carolin Sailer, Nicola Catone, Annette Aichem, Florian Stengel, Marcus Groettrup.

  Parkin is an E3 ubiquitin ligase belonging to the RING-between-RING family. Mutations in the Parkin-encoding gene PARK2 are associated with familial Parkinson's disease. Here, we investigate the interplay between Parkin and the inflammatory cytokine-induced ubiquitin-like modifier FAT10. FAT10 targets hundreds of proteins for degradation by the 26S proteasome. We show that FAT10 gets conjugated to Parkin and mediates its degradation in a proteasome-dependent manner. Parkin binds to the E2 enzyme of FAT10 (USE1), auto-FAT10ylates itself, and facilitates FAT10ylation of the Parkin substrate Mitofusin2 in vitro and in cells, thus identifying Parkin as a FAT10 E3 ligase. On mitochondrial depolarization, FAT10ylation of Parkin inhibits its activation and ubiquitin-ligase activity causing impairment of mitophagy progression and aggravation of rotenone-mediated death of dopaminergic neuronal cells. In conclusion, FAT10ylation inhibits Parkin and mitophagy rendering FAT10 a likely inflammation-induced exacerbating factor and potential drug target for Parkinson's disease.

Keywords:  FAT10; Parkin; Parkinson’s disease; mitophagy; ubiquitin-like modifier

DOI:  https://doi.org/10.1016/j.celrep.2021.108857
Biochem Biophys Res Commun. 2021 Mar 16. pii: S0006-291X(21)00399-5. [Epub ahead of print]552 30-36

Thapsigargin suppresses alpha 1-acid glycoprotein secretion independently of N-glycosylation and ER stress.

Nanami Goto, Shusaku Shibutani, Noboru Miura, Rie Watanabe, Hiroyuki Iwata.

  Alpha-1 acid glycoprotein (AGP) is a major acute-phase protein that is involved in drug/ligand binding and regulation of immune response. In response to inflammation, AGP secretion from the liver increases, resulting in elevated concentration of plasma AGP. AGP exhibits multiple N-glycosylation sites, and thus, is highly glycosylated. Although AGP glycosylation is considered to affect its functions, the significance of AGP glycosylation for its secretion is unclear. In this study, we investigated the effects of AGP glycosylation using glycosylation-deficient mouse AGP mutants lacking one, four, or all five N-glycosylation sites. Furthermore, we examined the effects of endoplasmic reticulum (ER) stress-inducing reagents, including tunicamycin and thapsigargin, which induce ER stress in an N-glycosylation-dependent and -independent manner, respectively. Here, we found that glycosylation deficiency and ER stress induce a little or no effect on AGP secretion. Conversely, thapsigargin significantly suppressed AGP secretion in glycosylation-independent manner. These findings indicate that AGP secretion is regulated via thapsigargin-sensitive pathway that might be further controlled by the intracellular calcium concentrations.

Keywords:  Alpha 1-acid glycoprotein; Endoplasmic reticulum stress; N-Glycosylation; Thapsigargin; Tunicamycin

DOI:  https://doi.org/10.1016/j.bbrc.2021.03.017
FASEB J. 2021 Apr;35(4): e21436

SMURF2-mediated ubiquitin signaling plays an essential role in the regulation of PARP1 PARylating activity, molecular interactions, and functions in mammalian cells.

Nataša Ilić, Yulei Tao, Sandy Boutros-Suleiman, Venkata Narasimha Kadali, Andrea Emanuelli, Gal Levy-Cohen, Michael Blank.

  Poly(ADP-ribose) polymerase 1 (PARP1) is a key molecular stress sensor and response mediator implicated in multiple cellular functions in health and diseases. Despite its importance and intrinsic involvement in pivotal molecular and cellular processes, including DNA repair, transcription regulation, chromatin organization, and cell death, the regulatory mechanisms of PARP1 are poorly understood. In this study, we show that SMURF2, a HECT-type E3 ubiquitin ligase and suggested tumor suppressor, physically interacts with PARP1 in different cellular settings, directly ubiquitinates it in vitro and stimulates its PARylation activity in cells, the phenomenon that required SMURF2 E3 ubiquitin ligase function. Intriguingly, in the cellular environment SMURF2 was found to regulate the dynamic exchange of ubiquitin moieties on PARP1, mostly decreasing its monoubiquitination. Through the set of systematic mass spectrometry analyses conducted on SMURF2-modified cells, we identified on PARP1 18 lysine residues (out of 126 present in PARP1) as sites which ubiquitination was considerably affected by SMURF2. Subsequent site-directed mutagenesis coupled with in cellula ubiquitination and PARylation assays unveiled K222 as a critical site enabling a cross talk between SMURF2-modulated monoubiquitination of PARP1 and its activity, and pointed to K498, S507, and a KTR triad (K498/K521/K524) as the main auto-PARylation sites affected by SMURF2. The results also uncovered that SMURF2 controls PARP1 interactome, influencing its functions and expression in a context-dependent manner. Taken together, these findings suggest that SMURF2-mediated ubiquitin signaling plays an essential role in PARP1 regulation, beyond the regulation of its protein expression.

Keywords:  PARP1; PARylation; SMURF2; interactome; ubiquitinome

DOI:  https://doi.org/10.1096/fj.202001759R
Front Cell Dev Biol. 2021 ;9 637565

Activity of the SNARE Protein SNAP29 at the Endoplasmic Reticulum and Golgi Apparatus.

Elena Morelli, Elisa A Speranza, Enrica Pellegrino, Galina V Beznoussenko, Francesca Carminati, Massimiliano Garré, Alexander A Mironov, Marco Onorati, Thomas Vaccari.

  Snap29 is a conserved regulator of membrane fusion essential to complete autophagy and to support other cellular processes, including cell division. In humans, inactivating SNAP29 mutations causes CEDNIK syndrome, a rare multi-systemic disorder characterized by congenital neuro-cutaneous alterations. The fibroblasts of CEDNIK patients show alterations of the Golgi apparatus (GA). However, whether and how Snap29 acts at the GA is unclear. Here we investigate SNAP29 function at the GA and endoplasmic reticulum (ER). As part of the elongated structures in proximity to these membrane compartments, a pool of SNAP29 forms a complex with Syntaxin18, or with Syntaxin5, which we find is required to engage SEC22B-loaded vesicles. Consistent with this, in HeLa cells, in neuroepithelial stem cells, and in vivo, decreased SNAP29 activity alters GA architecture and reduces ER to GA trafficking. Our data reveal a new regulatory function of Snap29 in promoting secretory trafficking.

Keywords:  Golgi apparatus; SEC22B; SNAP29 gene; SNARE protein; Syntaxin 5; endoplasmic reticulum; vesicle fusion

DOI:  https://doi.org/10.3389/fcell.2021.637565
Autophagy. 2021 Mar 09. 1-2

VCP/p97 modulates PtdIns3P production and autophagy initiation.

Lidia Wrobel, Sandra M Hill, Avraham Ashkenazi, David C Rubinsztein.

  VCP/p97 is an essential multifunctional protein implicated in a plethora of intracellular quality control systems, and abnormal function of VCP is the underlying cause of several neurodegenerative disorders. We reported that VCP regulates the levels of the macroautophagy/autophagy-inducing lipid phosphatidylinositol-3-phosphate (PtdIns3P) by modulating the activity of the BECN1 (beclin 1)-containing phosphatidylinositol 3-kinase (PtdIns3K) complex. VCP stimulates the deubiquitinase activity of ATXN3 (ataxin 3) to stabilize BECN1 protein levels and also interacts with and promotes the assembly and kinase activity of the PtdIns3K complex. Acute inhibition of VCP activity impairs autophagy induction, demonstrated by a diminished PtdIns3P production and decreased recruitment of early autophagy markers WIPI2 and ATG16L1. Thus, VCP promotes autophagosome biogenesis, in addition to its previously described role in autophagosome maturation.

Keywords:  ATXN3; PI(3)P; PI3K; VCP/p97; autophagy initiation; beclin 1

DOI:  https://doi.org/10.1080/15548627.2021.1898742
iScience. 2021 Mar 19. 24(3): 102196

Impaired phosphatidylethanolamine metabolism activates a reversible stress response that detects and resolves mutant mitochondrial precursors.

Pingdewinde N Sam, Elizabeth Calzada, Michelle Grace Acoba, Tian Zhao, Yasunori Watanabe, Anahita Nejatfard, Jonathan C Trinidad, Timothy E Shutt, Sonya E Neal, Steven M Claypool.

  Phosphatidylethanolamine (PE) made in mitochondria has long been recognized as an important precursor for phosphatidylcholine production that occurs in the endoplasmic reticulum (ER). Recently, the strict mitochondrial localization of the enzyme that makes PE in the mitochondrion, phosphatidylserine decarboxylase 1 (Psd1), was questioned. Since a dual localization of Psd1 to the ER would have far-reaching implications, we initiated our study to independently re-assess the subcellular distribution of Psd1. Our results support the unavoidable conclusion that the vast majority, if not all, of functional Psd1 resides in the mitochondrion. Through our efforts, we discovered that mutant forms of Psd1 that impair a self-processing step needed for it to become functional are dually localized to the ER when expressed in a PE-limiting environment. We conclude that severely impaired cellular PE metabolism provokes an ER-assisted adaptive response that is capable of identifying and resolving nonfunctional mitochondrial precursors.

Keywords:  Cell Biology; Molecular Physiology; Proteomics

DOI:  https://doi.org/10.1016/j.isci.2021.102196
Nat Commun. 2021 03 16. 12(1): 1684

Xbp1s-FoxO1 axis governs lipid accumulation and contractile performance in heart failure with preserved ejection fraction.

Gabriele G Schiattarella, Francisco Altamirano, Soo Young Kim, Dan Tong, Anwarul Ferdous, Hande Piristine, Subhajit Dasgupta, Xuliang Wang, Kristin M French, Elisa Villalobos, Stephen B Spurgin, Maayan Waldman, Nan Jiang, Herman I May, Theodore M Hill, Yuxuan Luo, Heesoo Yoo, Vlad G Zaha, Sergio Lavandero, Thomas G Gillette, Joseph A Hill.

Heart failure with preserved ejection fraction (HFpEF) is now the dominant form of heart failure and one for which no efficacious therapies exist. Obesity and lipid mishandling greatly contribute to HFpEF. However, molecular mechanism(s) governing metabolic alterations and perturbations in lipid homeostasis in HFpEF are largely unknown. Here, we report that cardiomyocyte steatosis in HFpEF is coupled with increases in the activity of the transcription factor FoxO1 (Forkhead box protein O1). FoxO1 depletion, as well as over-expression of the Xbp1s (spliced form of the X-box-binding protein 1) arm of the UPR (unfolded protein response) in cardiomyocytes each ameliorates the HFpEF phenotype in mice and reduces myocardial lipid accumulation. Mechanistically, forced expression of Xbp1s in cardiomyocytes triggers ubiquitination and proteasomal degradation of FoxO1 which occurs, in large part, through activation of the E3 ubiquitin ligase STUB1 (STIP1 homology and U-box-containing protein 1) a novel and direct transcriptional target of Xbp1s. Our findings uncover the Xbp1s-FoxO1 axis as a pivotal mechanism in the pathogenesis of cardiometabolic HFpEF and unveil previously unrecognized mechanisms whereby the UPR governs metabolic alterations in cardiomyocytes.

DOI: https://doi.org/10.1038/s41467-021-21931-9
Autophagy. 2021 Mar 14. 1-13

Selective autophagy receptor SQSTM1/ p62 inhibits Seneca Valley virus replication by targeting viral VP1 and VP3.

Wei Wen, Xiangmin Li, Mengge Yin, Haoyuan Wang, Liuxin Qin, Hui Li, Wenqiang Liu, Zekai Zhao, Qiongqiong Zhao, Huanchun Chen, Junjie Hu, Ping Qian.

  Macroautophagy/autophagy plays a critical role in antiviral immunity through targeting viruses and initiating host immune responses. The receptor protein, SQSTM1/p62 (sequestosome 1), plays a vital role in selective autophagy. It serves as a receptor targeting ubiquitinated proteins or pathogens to phagophores for degradation. In this study, we explored the reciprocal regulation between selective autophagy receptor SQSTM1 and Seneca Valley virus (SVV). SVV infection induced autophagy. Autophagy promoted SVV infection in pig cells but played opposite functions in human cells. Overexpression of SQSTM1 decreased viral protein production and reduced viral titers. Further study showed that SQSTM1 interacted with SVV VP1 and VP3 independent of its UBA domain. SQSTM1 targeted SVV VP1 and VP3 to phagophores for degradation to inhibit viral replication. To counteract this, SVV evolved strategies to circumvent the host autophagic machinery to promote viral replication. SVV 3Cpro targeted the receptor SQSTM1 for cleavage at glutamic acid 355, glutamine 392, and glutamine 395 and abolished its capacity to mediate selective autophagy. At the same time, the 3Cpro-mediated SQSTM1 cleavage products lost the ability to inhibit viral propagation. Collectively, our results provide evidence for selective autophagy in host against viruses and reveal potential viral strategies to evade autophagic machinery for successful pathogenesis. Abbreviations: Baf.A1: bafilomycin A1; Co-IP: co-immunoprecipitation; hpi: h post-infection; LIR: LC3-interacting region; MAP1LC3B/LC3B: microtubule-associated protein 1 light chain 3 beta; MOI: multiplicity of infection; PB1: N-terminal Phox/Bem1p; Rap.: rapamycin; Seneca Valley virus: SVV; SQSTM1/p62: sequestosome 1; SQSTM1-N355: residues 1 to 355 of SQSTM1; SQSTM1-C355: residues 355 to 478 of SQSTM1; SQSTM1-N392: residues 1 to 392 of SQSTM1; SQSTM1-C392: residues 392 to 478 of SQSTM1; SQSTM1-N388: residues 1 to 388 of SQSTM1; SQSTM1-N397: residues 1 to 397 of SQSTM1; UBA: ubiquitin association; Ubi: ubiquitin.

Keywords:  3C protease; SQSTM1; VP1; VP3; cleavage; selective autophagy

DOI:  https://doi.org/10.1080/15548627.2021.1897223
Cancer Med. 2021 Mar 20.

Protein disulphide isomerase inhibition as a potential cancer therapeutic strategy.

Lauren E Powell, Paul A Foster.

  The protein disulphide isomerase (PDI) gene family is a large, diverse group of enzymes recognised for their roles in disulphide bond formation within the endoplasmic reticulum (ER). PDI therefore plays an important role in ER proteostasis, however, it also shows involvement in ER stress, a characteristic recognised in multiple disease states, including cancer. While the exact mechanisms by which PDI contributes to tumorigenesis are still not fully understood, PDI exhibits clear involvement in the unfolded protein response (UPR) pathway. The UPR acts to alleviate ER stress through the activation of ER chaperones, such as PDI, which act to refold misfolded proteins, promoting cell survival. PDI also acts as an upstream regulator of the UPR pathway, through redox regulation of UPR stress receptors. This demonstrates the pro-protective roles of PDI and highlights PDI as a potential therapeutic target for cancer treatment. Recent research has explored the use of PDI inhibitors with PACMA 31 in particular, demonstrating promising anti-cancer effects in ovarian cancer. This review discusses the properties and functions of PDI family members and focuses on their potential as a therapeutic target for cancer treatment.

Keywords:  cancer; protein disulphide isomerase; protein disulphide isomerase inhibitors

DOI:  https://doi.org/10.1002/cam4.3836
Cell Rep. 2021 Mar 16. pii: S2211-1247(21)00173-X. [Epub ahead of print]34(11): 108859

A genome-wide CRISPR screen identifies UFMylation and TRAMP-like complexes as host factors required for hepatitis A virus infection.

Jessie Kulsuptrakul, Ruofan Wang, Nathan L Meyers, Melanie Ott, Andreas S Puschnik.

  Hepatitis A virus (HAV) is a positive-sense RNA virus causing acute inflammation of the liver. Here, using a genome-scale CRISPR screen, we provide a comprehensive picture of the cellular factors that are exploited by HAV. We identify genes involved in sialic acid/ganglioside biosynthesis and members of the eukaryotic translation initiation factor complex, corroborating their putative roles for HAV. Additionally, we uncover all components of the cellular machinery for UFMylation, a ubiquitin-like protein modification. We show that HAV translation specifically depends on UFM1 conjugation of the ribosomal protein RPL26. Furthermore, we find that components related to the yeast Trf4/5-Air1/2-Mtr4 polyadenylation (TRAMP) complex are required for viral translation independent of controlling viral poly(A) tails or RNA stability. Finally, we demonstrate that pharmacological inhibition of the TRAMP-like complex decreases HAV replication in hepatocyte cells and human liver organoids, thus providing a strategy for host-directed therapy of HAV infection.

Keywords:  CRISPR screen; PAPD5; PAPD7; RPL26; TENT4; UFM1; UFMylation; ZCCHC14; hepatitis A virus; host factor

DOI:  https://doi.org/10.1016/j.celrep.2021.108859
Exp Biol Med (Maywood). 2021 Mar 09. 1535370221997780

Sigma receptor knockdown augments dysfunction and apoptosis of beta cells induced by palmitate.

Mengting Ke, Guangzhen He, Huawei Wang, Siyuan Cheng, Yancheng Xu.

  Sigma-1 receptor (Sig-1R) is located in the endoplasmic reticulum (ER) and clustered on the mitochondria related endoplasmic membranes, which are involved in the regulation of nervous system disease. Here, we designed Sig-1R silence MIN6 cells and studied the influence of Sig-1R silence on beta cells. We showed Sig-1R inactivation in MIN6 cells could not only decrease cell proliferation but also inhibit cell cycle, and this inhibitory effect on cell cycle might be achieved by regulating the FoxM1/Plk1/Cenpa pathway. Moreover, Sig-1R deficiency increased MIN6 cells sensitivity to lipotoxicity, exaggerated palmitate (PA)-induced apoptosis, and impaired insulin secretion. On the other hand, ER chaperone GRP78 and ER proapoptotic molecules CHOP increased in Sig-1R knockdown MIN6 cells. The ATP level decreased and reactive oxygen species (ROS) increased in this kind of cells. Furthermore not only GRP78 and CHOP levels, but also ATP and ROS levels changed more in Sig-1R silence cells after cultured with PA. Therefore, Sig-1R deficiency exaggerated PA induced beta cells apoptosis by aggravating ER stress and mitochondrial dysfunction. Together, our study showed that Sig-1R might influence the proliferation, apoptosis, and function of beta cells.

Keywords:  ER stress; Sig-1R; apoptosis; beta cells; lipotoxicity; mitochondrial dysfunction

DOI:  https://doi.org/10.1177/1535370221997780
Mol Cell Proteomics. 2021 Mar 11. pii: S1535-9476(21)00042-6. [Epub ahead of print] 100069

Quantitative Proteomics Reveals that the OGT Interactome is Remodeled in Response to Oxidative Stress.

Marissa Martinez, Santosh Renuse, Simion Kreimer, Robert O'Meally, Peter Natov, Anil K Madugundu, Raja Sekhar Nirujogi, Raiha Tahir, Robert Cole, Akhilesh Pandey, Natasha E Zachara.

The dynamic modification of specific serine and threonine residues of intracellular proteins by O-linked N-acetyl-β-D-glucosamine (O-GlcNAc) mitigates injury and promotes cytoprotection in a variety of stress models. The O-GlcNAc transferase (OGT) and the O-GlcNAcase (OGA) are the sole enzymes that add and remove O-GlcNAc, respectively, from thousands of substrates. It remains unclear how just two enzymes can be specifically controlled to affect glycosylation of target proteins and signaling pathways both basally and in response to stress. Several lines of evidence suggest that protein interactors regulate these responses by affecting OGT and OGA activity, localization and substrate specificity. To provide insight into the mechanisms by which OGT function is controlled, we have utilized quantitative proteomics to define OGT's basal and stress-induced interactomes. OGT and its interaction partners were immunoprecipitated from OGT wild-type, null and hydrogen peroxide treated cell lysates that had been isotopically labeled with light, medium and heavy lysine and arginine (stable isotopic labeling of amino acids in cell culture [SILAC]). In total, more than 130 proteins were found to interact with OGT, many of which change their association upon hydrogen peroxide stress. These proteins include the major OGT cleavage and glycosylation substrate, host cell factor 1, which demonstrated a time-dependent dissociation following stress. To validate less-well characterized interactors, such as glyceraldehyde 3-phosphate dehydrogenase and histone deacetylase 1, we turned to parallel reaction monitoring, which recapitulated our discovery-based SILAC approach. Although the majority of proteins identified are novel OGT interactors, 64% of them are previously characterized glycosylation targets that contain varied domain architecture and function. Together these data demonstrate that OGT interacts with unique and specific interactors in a stress-responsive manner.

DOI: https://doi.org/10.1016/j.mcpro.2021.100069
Front Cell Dev Biol. 2021 ;9 643769

Protein Trafficking or Cell Signaling: A Dilemma for the Adaptor Protein TOM1.

Tiffany G Roach, Heljä K M Lång, Wen Xiong, Samppa J Ryhänen, Daniel G S Capelluto.

  Lysosomal degradation of ubiquitinated transmembrane protein receptors (cargo) relies on the function of Endosomal Sorting Complex Required for Transport (ESCRT) protein complexes. The ESCRT machinery is comprised of five unique oligomeric complexes with distinct functions. Target of Myb1 (TOM1) is an ESCRT protein involved in the initial steps of endosomal cargo sorting. To exert its function, TOM1 associates with ubiquitin moieties on the cargo via its VHS and GAT domains. Several ESCRT proteins, including TOLLIP, Endofin, and Hrs, have been reported to form a complex with TOM1 at early endosomal membrane surfaces, which may potentiate the role of TOM1 in cargo sorting. More recently, it was found that TOM1 is involved in other physiological processes, including autophagy, immune responses, and neuroinflammation, which crosstalk with its endosomal cargo sorting function. Alteration of TOM1 function has emerged as a phosphoinositide-dependent survival mechanism for bacterial infections and cancer progression. Based on current knowledge of TOM1-dependent cellular processes, this review illustrates how TOM1 functions in coordination with an array of protein partners under physiological and pathological scenarios.

Keywords:  ESCRT; Endofin; TOL; TOLLIP; TOM1; endosome; phosphoinositides

DOI:  https://doi.org/10.3389/fcell.2021.643769
FEBS J. 2021 Mar 17.

A Guide To… The Regulation Of Selective Autophagy Receptors.

A Gubas, I Dikic.

  Autophagy is a highly conserved catabolic process cells use to maintain their homeostasis by degrading misfolded, damaged, and excessive proteins, non-functional organelles, foreign pathogens, and other cellular components. Hence, autophagy can be non-selective, where bulky portions of the cytoplasm are degraded upon stress, or a highly selective process, where pre-selected cellular components are degraded. To distinguish between different cellular components, autophagy employs selective autophagy receptors, which will link the cargo to the autophagy machinery, thereby sequestering it in the autophagosome for its subsequent degradation in the lysosome. Autophagy receptors undergo post-translational and structural modifications to fulfil their role in autophagy, or upon executing their role, for their own degradation. We highlight the four most prominent protein modifications - phosphorylation, ubiquitination, acetylation, and oligomerisation - that are essential for autophagy receptor recruitment, function, and turnover. Understanding the regulation of selective autophagy receptors will provide deeper insights into the pathway and open up potential therapeutic avenues.

Keywords:  Autophagy; oligomerisation; phosphorylation; receptor; ubiquitination

DOI:  https://doi.org/10.1111/febs.15824
J Biosci. 2021 ;pii: 19. [Epub ahead of print]46

Deubiquitylation and stabilization of Acf7 by ubiquitin carboxylterminal hydrolase 14 (USP14) is critical for NSCLC migration.

Guobei Yan, N A Liu, Junhua Wang, Jun Tian, Hongbin Liu, Suping Li, Wenchao Liu, Xiaoliang Li, Kai Li, Hong Wang.

The ubiquitin-proteasome system is an essential regulator of Acf7, which serves as a key effector for the maintenance of the EMT program and migration. However, the precise mechanism for the deubiquitination of Acf7 is still not fully understood. Using a proteomic approach, we identified ubiquitin-specific peptidase 14 (USP14) as an Acf7-associated deubiquitinase. Our findings show that there was an interaction between USP14 and Acf7. The expression of USP14 and Acf7 were elevated in lung cancer tissues compared to adjacent normal cells. Employing the overexpression of USP14 and the USP14 knockdown assay indicated that USP14 can greatly increase the steady-state levels of Acf7 by inhibiting the degradation of Acf7 through the ubiquitin- proteasome pathway. Here we identified USP14 as a deubiquitinating enzyme that regulated Acf7 ubiquitination and protein levels. Moreover, knockdown of USP14 inhibited cell migration, however, overexpression of wild-type USP14 but not USP14 mutants promoted cell migration. Together, these results suggest that USP14 plays an important role in the NSCLC migration through modulating Acf7 stability.
Front Chem. 2020 ;8 630888

Ubiquitination and the Proteasome as Drug Targets in Trypanosomatid Diseases.

Marie-José Bijlmakers.

  The eukaryotic pathogens Trypanosoma brucei, Trypanosoma cruzi and Leishmania are responsible for debilitating diseases that affect millions of people worldwide. The numbers of drugs available to treat these diseases, Human African Trypanosomiasis, Chagas' disease and Leishmaniasis are very limited and existing treatments have substantial shortcomings in delivery method, efficacy and safety. The identification and validation of novel drug targets opens up new opportunities for the discovery of therapeutic drugs with better efficacy and safety profiles. Here, the potential of targeting the ubiquitin-proteasome system in these parasites is reviewed. Ubiquitination is the posttranslational attachment of one or more ubiquitin proteins to substrates, an essential eukaryotic mechanism that regulates a wide variety of cellular processes in many different ways. The best studied of these is the delivery of ubiquitinated substrates for degradation to the proteasome, the major cellular protease. However, ubiquitination can also regulate substrates in proteasome-independent ways, and proteasomes can degrade proteins to some extent in ubiquitin-independent ways. Because of these widespread roles, both ubiquitination and proteasomal degradation are essential for the viability of eukaryotes and the proteins that mediate these processes are therefore attractive drug targets in trypanosomatids. Here, the current understanding of these processes in trypanosomatids is reviewed. Furthermore, significant recent progress in the development of trypanosomatid-selective proteasome inhibitors that cure mouse models of trypanosomatid infections is presented. In addition, the targeting of the key enzyme in ubiquitination, the ubiquitin E1 UBA1, is discussed as an alternative strategy. Important differences between human and trypanosomatid UBA1s in susceptibility to inhibitors predicts that the selective targeting of these enzymes in trypanosomatids may also be feasible. Finally, it is proposed that activating enzymes of the ubiquitin-like proteins SUMO and NEDD8 may represent drug targets in these trypanosomatids as well.

Keywords:  drug target; leishmania; proteasome; trypanosoma; ubiqutination

DOI:  https://doi.org/10.3389/fchem.2020.630888
Nat Rev Gastroenterol Hepatol. 2021 Mar 19.

AHR in the intestinal microenvironment: safeguarding barrier function.

Brigitta Stockinger, Kathleen Shah, Emma Wincent.

Mammalian aryl hydrocarbon receptor (AHR) is a ligand-dependent transcription factor that belongs to the basic helix-loop-helix (bHLH)-PAS family of transcription factors, which are evolutionarily conserved environmental sensors. In the absence of ligands, AHR resides in the cytoplasm in a complex with molecular chaperones such as HSP90, XAP2 and p23. Upon ligand binding, AHR translocates into the nuclear compartment, where it dimerizes with its partner protein, AHR nuclear translocator (ARNT), an obligatory partner for the DNA-binding and functional activity. Historically, AHR had mostly been considered as a key intermediary for the detrimental effects of environmental pollutants on the body. However, following the discovery of AHR-mediated functions in various immune cells, as well as the emergence of non-toxic 'natural' AHR ligands, this view slowly began to change, and the study of AHR-deficient mice revealed a plethora of important beneficial functions linked to AHR activation. This Review focuses on regulation of the AHR pathway and the barrier-protective roles AHR has in haematopoietic, as well as non-haematopoietic, cells within the intestinal microenvironment. It covers the nature of AHR ligands and feedback regulation of the AHR pathway, outlining the currently known physiological functions in immune, epithelial, endothelial and neuronal cells of the intestine.

DOI: https://doi.org/10.1038/s41575-021-00430-8
Aging (Albany NY). 2021 Mar 10. 13

Activation of ATF4 triggers trabecular meshwork cell dysfunction and apoptosis in POAG.

Ying Ying, Ran Xue, Yangfan Yang, Sarah X Zhang, Hui Xiao, Huazhang Zhu, Jingming Li, Guo Chen, Yiming Ye, Minbin Yu, Xing Liu, Yimin Zhong.

  Primary open angle glaucoma (POAG) is the leading cause of irreversible blindness. Dysfunction of the trabecular meshwork (TM), resulting in decreased outflow of aqueous humor and increased intraocular pressure (IOP), plays an important role in the pathogenesis of POAG. However, the underlying mechanisms still remain unclear. In this study, we demonstrated that the eIF2-α/ATF4/CHOP branch of unfolded protein response (UPR) was activated in human trabecular meshwork cells (HTMCs) upon tert-butyl hydroperoxide (TBHP) exposure. Inhibition of ATF4 ameliorated TBHP-induced apoptosis and inflammatory cytokine production, while ectopic expression of ATF4 increased the expression of endothelial leukocyte adhesion molecule (ELAM)-1 and IL-8 in HTMCs. Furthermore, we found that ATF4 inhibition reduced tunicamycin-induced caspase-3 activation, ROS production, ELAM-1 expression, and HTMCs phagocytosis impairment. By an in vivo study in mice, we showed that overexpression of ATF4 in the TM induced C/EBP homologous protein (CHOP) expression and TM cells apoptosis, contributing to inflammatory cytokine production, and probably IOP elevation. More importantly, upregulation of ATF4 and CHOP, and colocalization of ATF4 with ELAM-1 were found in the TM of POAG patients. These results suggest that ATF4 is a critical mediator of oxidative stress and ER stress-induced TM cell dysfunction and apoptosis in POAG.

Keywords:  activating transcription factor 4; endoplasmic reticulum stress; oxidative stress; primary open angle glaucoma; trabecular meshwork

DOI:  https://doi.org/10.18632/aging.202677
Mol Cancer Res. 2021 Mar 17. pii: molcanres.0080.2020. [Epub ahead of print]

Kinetic Characterization of ASXL1/2-Mediated Allosteric Regulation of the BAP1 Deubiquitinase.

Hongzhuang Peng, Joel Cassel, Daniel S McCracken, Jeremy W Prokop, Eleonora Sementino, Mitchell Cheung, Paul R Collop, Alexander Polo, Surbhi Joshi, Jacob P Mandell, Kasirajan Ayyanathan, David Hinds, S Bruce Malkowicz, J William Harbour, Anne M Bowcock, Joseph Salvino, Eileen J Kennedy, Joseph R Testa, Frank J Rauscher.

BAP1 is an ubiquitin hydrolase whose deubiquitinase activity is mediated by polycomb group-like protein ASXL2. Cancer-related BAP1 mutations/deletions lead to loss-of-function by targeting the catalytic (UCH) or ULD domains of BAP1, and the latter disrupts binding to ASXL2, an obligate partner for BAP1 enzymatic activity. However, the biochemical and biophysical properties of domains involved in forming the enzymatically active complex are unknown. Here, we report the molecular dynamics, kinetics and stoichiometry of these interactions. We demonstrate that interactions between BAP1 and ASXL2 are direct, specific, and stable to biochemical and biophysical manipulations as detected by isothermal titration calorimetry, GST association, and optical biosensor assays. Association of the ASXL2-AB box greatly stimulates BAP1 activity. A stable ternary complex is formed, comprised of the BAP1-UCH, BAP1-ULD, and ASXL2-AB domains. Stoichiometric analysis revealed that one molecule of the ULD domain directly interacts with one molecule of the AB box. Real-time kinetics analysis of the ULD/AB protein complex to the BAP1 UCH domain, based on SPR, indicated that formation of the ULD/AB complex with the UCH domain is a single-step event with fast association and slow dissociation rates. In vitro experiments validated in cells that ASXL-AB box directly regulates BAP1 activity. Implications: Collectively, these data elucidate molecular interactions between specific protein domains regulating BAP1 deubiquitinase activity, thus establishing a foundation for small-molecule approaches to reactivate latent wild-type BAP1 catalytic activity in BAP1-mutant cancers.

DOI: https://doi.org/10.1158/1541-7786.MCR-20-0080
Cell Chem Biol. 2021 Mar 18. pii: S2451-9456(21)00096-9. [Epub ahead of print]28(3): 283-299

Phenotypic screening with target identification and validation in the discovery and development of E3 ligase modulators.

Nil Ege, Habib Bouguenina, Marianthi Tatari, Rajesh Chopra.

  The use of phenotypic screening was central to the discovery and development of novel thalidomide analogs, the IMiDs (immunomodulatory drugs) agents. With the discovery that these agents bind the E3 ligase, CRL4CRBN, and alter its substrate specificity, there has been a great deal of endeavor to discover other small molecules that can modulate alternative E3 ligases. Furthermore, the chemical properties necessary for drug discovery and the rules by which neo-substrates are selected for degradation are being defined in the context of phenotypic alterations in specific cellular systems. This review gives a detailed summary of these recent advances and the methodologies being exploited to understand the mechanism of action of emerging protein degradation therapies.

Keywords:  E3 ligase modulators; drug discovery; phenotypic screening; targeted protein degradation

DOI:  https://doi.org/10.1016/j.chembiol.2021.02.011
PLoS Pathog. 2021 Mar;17(3): e1009403

A swine arterivirus deubiquitinase stabilizes two major envelope proteins and promotes production of viral progeny.

Rui Guo, Xingyu Yan, Yanhua Li, Jin Cui, Saurav Misra, Andrew E Firth, Eric J Snijder, Ying Fang.

Arteriviruses are enveloped positive-strand RNA viruses that assemble and egress using the host cell's exocytic pathway. In previous studies, we demonstrated that most arteriviruses use a unique -2 ribosomal frameshifting mechanism to produce a C-terminally modified variant of their nonstructural protein 2 (nsp2). Like full-length nsp2, the N-terminal domain of this frameshift product, nsp2TF, contains a papain-like protease (PLP2) that has deubiquitinating (DUB) activity, in addition to its role in proteolytic processing of replicase polyproteins. In cells infected with porcine reproductive and respiratory syndrome virus (PRRSV), nsp2TF localizes to compartments of the exocytic pathway, specifically endoplasmic reticulum-Golgi intermediate compartment (ERGIC) and Golgi complex. Here, we show that nsp2TF interacts with the two major viral envelope proteins, the GP5 glycoprotein and membrane (M) protein, which drive the key process of arterivirus assembly and budding. The PRRSV GP5 and M proteins were found to be poly-ubiquitinated, both in an expression system and in cells infected with an nsp2TF-deficient mutant virus. In contrast, ubiquitinated GP5 and M proteins did not accumulate in cells infected with the wild-type, nsp2TF-expressing virus. Further analysis implicated the DUB activity of the nsp2TF PLP2 domain in deconjugation of ubiquitin from GP5/M proteins, thus antagonizing proteasomal degradation of these key viral structural proteins. Our findings suggest that nsp2TF is targeted to the exocytic pathway to reduce proteasome-driven turnover of GP5/M proteins, thus promoting the formation of GP5-M dimers that are critical for arterivirus assembly.

DOI: https://doi.org/10.1371/journal.ppat.1009403
Nat Chem. 2021 Mar 15.

O-GlcNAc modification of small heat shock proteins enhances their anti-amyloid chaperone activity.

Aaron T Balana, Paul M Levine, Timothy W Craven, Somnath Mukherjee, Nichole J Pedowitz, Stuart P Moon, Terry T Takahashi, Christian F W Becker, David Baker, Matthew R Pratt.

A major role for the intracellular post-translational modification O-GlcNAc appears to be the inhibition of protein aggregation. Most of the previous studies in this area focused on O-GlcNAc modification of the amyloid-forming proteins themselves. Here we used synthetic protein chemistry to discover that O-GlcNAc also activates the anti-amyloid activity of certain small heat shock proteins (sHSPs), a potentially more important modification event that can act broadly and substoichiometrically. More specifically, we found that O-GlcNAc increases the ability of sHSPs to block the amyloid formation of both α-synuclein and Aβ(1-42). Mechanistically, we show that O-GlcNAc near the sHSP IXI-domain prevents its ability to intramolecularly compete with substrate binding. Finally, we found that, although O-GlcNAc levels are globally reduced in Alzheimer's disease brains, the modification of relevant sHSPs is either maintained or increased, which suggests a mechanism to maintain these potentially protective O-GlcNAc modifications. Our results have important implications for neurodegenerative diseases associated with amyloid formation and potentially other areas of sHSP biology.

DOI: https://doi.org/10.1038/s41557-021-00648-8