bims-proteo 2022-07-17 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2022‒07‒17
29 papers selected by
Eric Chevet
INSERM

Proteasome substrate receptors and their therapeutic potential.
The testis-specific E3 ubiquitin ligase RNF133 is required for fecundity in mice.
Selective autophagy and Golgi quality control in Drosophila.
Exosomes, autophagy and ER stress pathways in human diseases: Cross-regulation and therapeutic approaches.
Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.
A specific EMC subunit supports Dengue virus infection by promoting virus membrane fusion essential for cytosolic genome delivery.
SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells.
A specialized Hsp90 co-chaperone network regulates steroid hormone receptor response to ligand.
Decoding endoplasmic reticulum stress signals in cancer cells and antitumor immunity.
Spatial and Temporal Control of Protein Secretion with Light.
From guide to guard-activation mechanism of the stress-sensing chaperone Get3.
Ubiquitination and deubiquitination of 4E-T regulate neural progenitor cell maintenance and neurogenesis by controlling P-body formation.
Feedforward activation of PRKN/parkin.
Regulation of the COPII secretory machinery via focal adhesions and extracellular matrix signaling.
Trigger factor both holds and folds its client proteins.
USP8 promotes cancer progression and extracellular vesicle-mediated CD8+ T cell exhaustion by deubiquitinating the TGF-β receptor TβRII.
Autophagosomal components recycling on autolysosomes.
Autophagic sequestration of SQSTM1 disrupts the aggresome formation of ubiquitinated proteins during proteasome inhibition.
Human neural progenitors establish a diffusion barrier in the ER membrane during cell division.
The coordination of V-ATPase and ATG16L1 is part of a common mechanism of non-canonical autophagy.
Tex264 Binding to SNX27 Regulates Itgα5 Receptor Membrane Recycling and Affects Cell Migration.
A campaign targeting a conserved Hsp70 binding site uncovers how subcellular localization is linked to distinct biological activities.
Adaptor-Specific Antibody Fragment Inhibitors for the Intracellular Modulation of p97 (VCP) Protein-Protein Interactions.
Autophagy-associated immune dysregulation and hyperplasia in a patient with compound heterozygous mutations in ATG9A.
Identification of ligand linkage vectors for the development of p300/CBP degraders.
Decreasing pdzd8-mediated mito-ER contacts improves organismal fitness and mitigates Aβ42 toxicity.
The clinical relevance of unfolded protein response signaling in breast cancer.
Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES.
PHF20 is crucial for epigenetic control of starvation-induced autophagy through enhancer activation.

Trends Biochem Sci. 2022 Jul 09. pii: S0968-0004(22)00147-5. [Epub ahead of print]

Proteasome substrate receptors and their therapeutic potential.

Vasty Osei-Amponsa, Kylie J Walters.

  The ubiquitin-proteasome system (UPS) is critical for protein quality control and regulating protein lifespans. Following ubiquitination, UPS substrates bind multidomain receptors that, in addition to ubiquitin-binding sites, contain functional domains that bind to deubiquitinating enzymes (DUBs) or the E3 ligase E6AP/UBE3A. We provide an overview of the proteasome, focusing on its receptors and DUBs. We highlight the key role of dynamics and importance of the substrate receptors having domains for both binding and processing ubiquitin chains. The UPS is rich with therapeutic opportunities, with proteasome inhibitors used clinically and ongoing development of small molecule proteolysis targeting chimeras (PROTACs) for the degradation of disease-associated proteins. We discuss the therapeutic potential of proteasome receptors, including hRpn13, for which PROTACs have been developed.

Keywords:  deubiquitinating enzymes; proteasome; substrate receptors; ubiquitin

DOI:  https://doi.org/10.1016/j.tibs.2022.06.006
BMC Biol. 2022 Jul 13. 20(1): 161

The testis-specific E3 ubiquitin ligase RNF133 is required for fecundity in mice.

Kaori Nozawa, Yoshitaka Fujihara, Darius J Devlin, Ricardo E Deras, Katarzyna Kent, Irina V Larina, Kohei Umezu, Zhifeng Yu, Courtney M Sutton, Qiuji Ye, Laura K Dean, Chihiro Emori, Masahito Ikawa, Thomas X Garcia, Martin M Matzuk.

  BACKGROUND: Ubiquitination is a post-translational modification required for a number of physiological functions regulating protein homeostasis, such as protein degradation. The endoplasmic reticulum (ER) quality control system recognizes and degrades proteins no longer needed in the ER through the ubiquitin-proteasome pathway. E2 and E3 enzymes containing a transmembrane domain have been shown to function in ER quality control. The ER transmembrane protein UBE2J1 is a E2 ubiquitin-conjugating enzyme reported to be essential for spermiogenesis at the elongating spermatid stage. Spermatids from Ube2j1 KO male mice are believed to have defects in the dislocation step of ER quality control. However, associated E3 ubiquitin-protein ligases that function during spermatogenesis remain unknown.RESULTS: We identified four evolutionarily conserved testis-specific E3 ubiquitin-protein ligases [RING finger protein 133 (Rnf133); RING finger protein 148 (Rnf148); RING finger protein 151 (Rnf151); and Zinc finger SWIM-type containing 2 (Zswim2)]. Using the CRISPR/Cas9 system, we generated and analyzed the fertility of mutant mice with null alleles for each of these E3-encoding genes, as well as double and triple knockout (KO) mice. Male fertility, male reproductive organ, and sperm-associated parameters were analyzed in detail. Fecundity remained largely unaffected in Rnf148, Rnf151, and Zswim2 KO males; however, Rnf133 KO males displayed severe subfertility. Additionally, Rnf133 KO sperm exhibited abnormal morphology and reduced motility. Ultrastructural analysis demonstrated that cytoplasmic droplets were retained in Rnf133 KO spermatozoa. Although Rnf133 and Rnf148 encode paralogous genes that are chromosomally linked and encode putative ER transmembrane E3 ubiquitin-protein ligases based on their protein structures, there was limited functional redundancy of these proteins. In addition, we identified UBE2J1 as an E2 ubiquitin-conjugating protein that interacts with RNF133.
CONCLUSIONS: Our studies reveal that RNF133 is a testis-expressed E3 ubiquitin-protein ligase that plays a critical role for sperm function during spermiogenesis. Based on the presence of a transmembrane domain in RNF133 and its interaction with the ER containing E2 protein UBE2J1, we hypothesize that these ubiquitin-regulatory proteins function together in ER quality control during spermatogenesis.

Keywords:  Contraceptive; ERAD; Male infertility; PROTACs; Sperm defects

DOI:  https://doi.org/10.1186/s12915-022-01368-2
Autophagy. 2022 Jul 12. 1-2

Selective autophagy and Golgi quality control in Drosophila.

Raksha Gohel, Ashrafur Rahman, Peter Lőrincz, Anikó Nagy, Gábor Csordás, Yan Zhang, Gábor Juhász, Ioannis P Nezis.

  The LIR motif-docking site (LDS) of Atg8/LC3 proteins is essential for the binding of LC3-interacting region (LIR)-containing proteins and their subsequent degradation by macroautophagy/autophagy. In our recent study, we created a mutated LDS site in Atg8a, the Drosophila homolog of Atg8/LC3 and found that LDS mutants accumulate known autophagy substrates and have reduced lifespan. We also conducted quantitative proteomics analyses and identified several proteins that are enriched in the LDS mutants, including Gmap (Golgi microtubule-associated protein). Gmap contains a LIR motif and accumulates in LDS mutants. We showed that Gmap and Atg8a interact in a LIR-LDS dependent manner and that the Golgi size and morphology are altered in Atg8a-LDS and Gmap-LIR motif mutants. Our findings highlight a role for Gmap in the regulation of Golgiphagy.

Keywords:  Drosophila; Golgi; Golgiphagy; LIR motif; LIR-motif docking site; autophagy

DOI:  https://doi.org/10.1080/15548627.2022.2098765
Biochim Biophys Acta Mol Basis Dis. 2022 Jul 07. pii: S0925-4439(22)00155-7. [Epub ahead of print] 166484

Exosomes, autophagy and ER stress pathways in human diseases: Cross-regulation and therapeutic approaches.

Babak Jahangiri, Ali Kian Saei, Patience O Obi, Narjes Asghari, Shahrokh Lorzadeh, Shirin Hekmatirad, Marveh Rahmati, Fatemeh Velayatipour, Mohammad Hosseni Asghari, Ayesha Saleem, Mohammad Amin Moosavi.

  Exosomal release pathway and autophagy together maintain homeostasis and survival of cells under stressful conditions. Autophagy is a catabolic process through which cell entities, such as malformed biomacromolecules and damaged organelles, are degraded and recycled via the lysosomal-dependent pathway. Exosomes, a sub-type of extracellular vesicles (EVs) formed by the inward budding of multivesicular bodies (MVBs), are mostly involved in mediating communication between cells. The unfolded protein response (UPR) is an adaptive response that is activated to sustain survival in the cells faced with the endoplasmic reticulum (ER) stress through a complex network that involves protein synthesis, exosomes secretion and autophagy. Disruption of the critical crosstalk between EVs, UPR and autophagy may be implicated in various human diseases, including cancers and neurodegenerative diseases, yet the molecular mechanism(s) behind the coordination of these communication pathways remains obscure. Here, we review the available information on the mechanisms that control autophagy, ER stress and EV pathways, with the view that a better understanding of their crosstalk and balance may improve our knowledge on the pathogenesis and treatment of human diseases, where these pathways are dysregulated.

Keywords:  Autophagy; Cancer; Crosstalk; ER stress; Exosomes; Extracellular vesicles; Secretory autophagy; Unfolded protein response

DOI:  https://doi.org/10.1016/j.bbadis.2022.166484
BMC Biol. 2022 Jul 14. 20(1): 162

Systematic prediction of degrons and E3 ubiquitin ligase binding via deep learning.

Chao Hou, Yuxuan Li, Mengyao Wang, Hong Wu, Tingting Li.

  BACKGROUND: Degrons are short linear motifs, bound by E3 ubiquitin ligase to target protein substrates to be degraded by the ubiquitin-proteasome system. Mutations leading to deregulation of degron functionality disrupt control of protein abundance due to mistargeting of proteins destined for degradation and often result in pathologies. Targeting degrons by small molecules also emerges as an exciting drug design strategy to upregulate the expression of specific proteins. Despite their essential function and disease targetability, reliable identification of degrons remains a conundrum. Here, we developed a deep learning-based model named Degpred that predicts general degrons directly from protein sequences.RESULTS: We showed that the BERT-based model performed well in predicting degrons singly from protein sequences. Then, we used the deep learning model Degpred to predict degrons proteome-widely. Degpred successfully captured typical degron-related sequence properties and predicted degrons beyond those from motif-based methods which use a handful of E3 motifs to match possible degrons. Furthermore, we calculated E3 motifs using predicted degrons on the substrates in our collected E3-substrate interaction dataset and constructed a regulatory network of protein degradation by assigning predicted degrons to specific E3s with calculated motifs. Critically, we experimentally verified that a predicted SPOP binding degron on CBX6 prompts CBX6 degradation and mediates the interaction with SPOP. We also showed that the protein degradation regulatory system is important in tumorigenesis by surveying degron-related mutations in TCGA.
CONCLUSIONS: Degpred provides an efficient tool to proteome-wide prediction of degrons and binding E3s singly from protein sequences. Degpred successfully captures typical degron-related sequence properties and predicts degrons beyond those from previously used motif-based methods, thus greatly expanding the degron landscape, which should advance the understanding of protein degradation, and allow exploration of uncharacterized alterations of proteins in diseases. To make it easier for readers to access collected and predicted datasets, we integrated these data into the website http://degron.phasep.pro/ .

Keywords:  Cancer driver mutation; Deep learning; Degron; E3 Ubiquitin ligase; Protein degradation

DOI:  https://doi.org/10.1186/s12915-022-01364-6
PLoS Pathog. 2022 Jul 14. 18(7): e1010717

A specific EMC subunit supports Dengue virus infection by promoting virus membrane fusion essential for cytosolic genome delivery.

Parikshit Bagchi, Kaitlyn Speckhart, Andrew Kennedy, Andrew W Tai, Billy Tsai.

Dengue virus (DENV) represents the most common human arboviral infection, yet its cellular entry mechanism remains unclear. The multi-subunit endoplasmic reticulum membrane complex (EMC) supports DENV infection, in part, by assisting the biosynthesis of viral proteins critical for downstream replication steps. Intriguingly, the EMC has also been shown to act at an earlier step prior to viral protein biogenesis, although this event is not well-defined. Here we demonstrate that the EMC subunit EMC4 promotes fusion of the DENV and endosomal membranes during entry, enabling delivery of the viral genome into the cytosol which is then targeted to the ER for viral protein biosynthesis. We also found that EMC4 mediates ER-to-endosome transfer of phosphatidylserine, a phospholipid whose presence in the endosome facilitates DENV-endosomal membrane fusion. These findings clarify the EMC-dependent DENV early entry step, suggesting a mechanism by which an ER-localized host factor can regulate viral fusion at the endosome.

DOI: https://doi.org/10.1371/journal.ppat.1010717
bioRxiv. 2022 Jun 13. pii: 2021.12.30.474519. [Epub ahead of print]

SARS-CoV-2 diverges from other betacoronaviruses in only partially activating the IRE1α/XBP1 ER stress pathway in human lung-derived cells.

Long C Nguyen, David M Renner, Diane Silva, Dongbo Yang, Nicholas Parenti, Kaeri M Medina, Vlad Nicolaescu, Haley Gula, Nir Drayman, Andrea Valdespino, Adil Mohamed, Christopher Dann, Kristin Wannemo, Lydia Robinson-Mailman, Alan Gonzalez, Letícia Stock, Mengrui Cao, Zeyu Qiao, Raymond E Moellering, Savas Tay, Glenn Randall, Michael F Beers, Marsha Rich Rosner, Scott A Oakes, Susan R Weiss.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has killed over 6 million individuals worldwide and continues to spread in countries where vaccines are not yet widely available, or its citizens are hesitant to become vaccinated. Therefore, it is critical to unravel the molecular mechanisms that allow SARS-CoV-2 and other coronaviruses to infect and overtake the host machinery of human cells. Coronavirus replication triggers endoplasmic reticulum (ER) stress and activation of the unfolded protein response (UPR), a key host cell pathway widely believed essential for viral replication. We examined the master UPR sensor IRE1α kinase/RNase and its downstream transcription factor effector XBP1s, which is processed through an IRE1α-mediated mRNA splicing event, in human lung-derived cells infected with betacoronaviruses. We found human respiratory coronavirus OC43 (HCoV-OC43), Middle East respiratory syndrome coronavirus (MERS-CoV), and murine coronavirus (MHV) all induce ER stress and strongly trigger the kinase and RNase activities of IRE1α as well as XBP1 splicing. In contrast, SARS-CoV-2 only partially activates IRE1α through autophosphorylation, but its RNase activity fails to splice XBP1. Moreover, while IRE1α was dispensable for replication in human cells for all coronaviruses tested, it was required for maximal expression of genes associated with several key cellular functions, including the interferon signaling pathway, during SARS-CoV-2 infection. Our data suggest that SARS-CoV-2 actively inhibits the RNase of autophosphorylated IRE1α, perhaps as a strategy to eliminate detection by the host immune system.IMPORTANCE: SARS-CoV-2 is the third lethal respiratory coronavirus after MERS-CoV and SARS-CoV to emerge this century, causing millions of deaths world-wide. Other common coronaviruses such as HCoV-OC43 cause less severe respiratory disease. Thus, it is imperative to understand the similarities and differences among these viruses in how each interacts with host cells. We focused here on the inositol-requiring enzyme 1α (IRE1α) pathway, part of the host unfolded protein response to virus-induced stress. We found that while MERS-CoV and HCoV-OC43 fully activate the IRE1α kinase and RNase activities, SARS-CoV-2 only partially activates IRE1α, promoting its kinase activity but not RNase activity. Based on IRE1α-dependent gene expression changes during infection, we propose that SARS-CoV-2 prevents IRE1α RNase activation as a strategy to limit detection by the host immune system.

DOI: https://doi.org/10.1101/2021.12.30.474519
Cell Rep. 2022 Jul 12. pii: S2211-1247(22)00833-6. [Epub ahead of print]40(2): 111039

A specialized Hsp90 co-chaperone network regulates steroid hormone receptor response to ligand.

Sarah J Backe, Rebecca A Sager, Bethany R Regan, Julian Sit, Lauren A Major, Gennady Bratslavsky, Mark R Woodford, Dimitra Bourboulia, Mehdi Mollapour.

  Heat shock protein-90 (Hsp90) chaperone machinery is involved in the stability and activity of its client proteins. The chaperone function of Hsp90 is regulated by co-chaperones and post-translational modifications. Although structural evidence exists for Hsp90 interaction with clients, our understanding of the impact of Hsp90 chaperone function toward client activity in cells remains elusive. Here, we dissect the impact of recently identified higher eukaryotic co-chaperones, FNIP1/2 (FNIPs) and Tsc1, toward Hsp90 client activity. Our data show that Tsc1 and FNIP2 form mutually exclusive complexes with FNIP1, and that unlike Tsc1, FNIP1/2 interact with the catalytic residue of Hsp90. Functionally, these co-chaperone complexes increase the affinity of the steroid hormone receptors glucocorticoid receptor and estrogen receptor to their ligands in vivo. We provide a model for the responsiveness of the steroid hormone receptor activation upon ligand binding as a consequence of their association with specific Hsp90:co-chaperone subpopulations.

Keywords:  CP: Molecular biology; FNIP1; FNIP2; Hsp90; Tsc1; androgen receptor; chaperone; chaperone code; co-chaperone; glucocorticoid receptor; steroid hormone receptors

DOI:  https://doi.org/10.1016/j.celrep.2022.111039
Trends Cancer. 2022 Jul 08. pii: S2405-8033(22)00134-0. [Epub ahead of print]

Decoding endoplasmic reticulum stress signals in cancer cells and antitumor immunity.

Camilla Salvagno, Jessica K Mandula, Paulo C Rodriguez, Juan R Cubillos-Ruiz.

  The tumor microenvironment (TME) provokes endoplasmic reticulum (ER) stress in malignant cells and infiltrating immune populations. Sensing and responding to ER stress is coordinated by the unfolded protein response (UPR), an integrated signaling pathway governed by three ER stress sensors: activating transcription factor (ATF6), inositol-requiring enzyme 1α (IRE1α), and protein kinase R (PKR)-like ER kinase (PERK). Persistent UPR activation modulates malignant progression, tumor growth, metastasis, and protective antitumor immunity. Hence, therapies targeting ER stress signaling can be harnessed to elicit direct tumor killing and concomitant anticancer immunity. We highlight recent findings on the role of the ER stress responses in onco-immunology, with an emphasis on genetic vulnerabilities that render tumors highly sensitive to therapeutic UPR modulation.

Keywords:  ER stress; cancer therapy; immune cells; tumor microenvironment; unfolded protein response

DOI:  https://doi.org/10.1016/j.trecan.2022.06.006
Methods Mol Biol. 2022 ;2473 29-45

Spatial and Temporal Control of Protein Secretion with Light.

Ashley M Bourke, Matthew J Kennedy.

  How newly synthesized integral membrane proteins and secreted factors are sorted and trafficked to the appropriate location in different cell types remains an important problem in cell biology. One powerful approach for elucidating the trafficking route of a specific protein is to sequester it following synthesis in the endoplasmic reticulum and trigger its release with an externally applied cue. Combined with fluorescent probes, this approach can be used to directly visualize each trafficking step as cargo molecules progress through the different organelles of the secretory network. Here, we discuss design strategies and practical implementation of an inducible protein secretion system we recently developed (zapalog mediated ER trap: zapERtrap) that allows one to use light to initiate secretory trafficking from targeted cells or subcellular domains. We provide detailed protocols for experiments using this approach to visualize protein trafficking from the endoplasmic reticulum to the plasma membrane in fibroblast cell lines and primary cultured neurons.

Keywords:  Chemo-optogenetic system; Inducible ER release; Protein secretion; Secretory trafficking

DOI:  https://doi.org/10.1007/978-1-0716-2209-4_4
Mol Cell. 2022 Jul 09. pii: S1097-2765(22)00598-6. [Epub ahead of print]

From guide to guard-activation mechanism of the stress-sensing chaperone Get3.

Kathrin Ulrich, Ákos Farkas, Olivia Chan, Olivia Katamanin, Blanche Schwappach, Ursula Jakob.

  Oxidative stress conditions can cause ATP depletion, oxidative protein unfolding, and potentially toxic protein aggregation. To alleviate this proteotoxic stress, the highly conserved yeast protein, Get3, switches from its guiding function as an ATP-dependent targeting factor for tail-anchored proteins to its guarding function as an ATP-independent molecular chaperone that prevents irreversible protein aggregation. Here, we demonstrate that activation of Get3's chaperone function follows a tightly orchestrated multi-step process, centered around the redox status of two conserved cysteines, whose reactivity is directly controlled by Get3's nucleotide-binding state. Thiol oxidation causes local unfolding and the transition into chaperone-active oligomers. Vice versa, inactivation requires the reduction of Get3's cysteines followed by ATP-binding, which allows the transfer of bound client proteins to ATP-dependent chaperone systems for their effective refolding. Manipulating this fine-tuned cycle of activation and inactivation in yeast impairs oxidative stress resistance and growth, illustrating the necessity to tightly control Get3's intrinsic chaperone function.

Keywords:  chaperone; oxidative stress; protein folding; proteostasis; redox

DOI:  https://doi.org/10.1016/j.molcel.2022.06.015
Cell Rep. 2022 Jul 12. pii: S2211-1247(22)00868-3. [Epub ahead of print]40(2): 111070

Ubiquitination and deubiquitination of 4E-T regulate neural progenitor cell maintenance and neurogenesis by controlling P-body formation.

Shreeya Kedia, Mohamad-Reza Aghanoori, Kaylan M L Burns, Maneesha Subha, Laura Williams, Pengqiang Wen, Drayden Kopp, Sarah L Erickson, Emily M Harvey, Xin Chen, Michelle Hua, Jose Uriel Perez, Fatin Ishraque, Guang Yang.

  During embryogenesis, neural stem/progenitor cells (NPCs) proliferate and differentiate to form brain tissues. Here, we show that in the developing murine cerebral cortex, the balance between the NPC maintenance and differentiation is coordinated by ubiquitin signals that control the formation of processing bodies (P-bodies), cytoplasmic membraneless organelles critical for cell state regulation. We find that the deubiquitinase Otud4 and the E3 ligase Trim56 counter-regulate the ubiquitination status of a core P-body protein 4E-T to orchestrate the assembly of P-bodies in NPCs. Aberrant induction of 4E-T ubiquitination promotes P-body assembly in NPCs and causes a delay in their cell cycle progression and differentiation. In contrast, loss of 4E-T ubiquitination abrogates P-bodies and results in premature neurogenesis. Thus, our results reveal a critical role of ubiquitin-dependent regulation of P-body formation in NPC maintenance and neurogenesis during brain development.

Keywords:  4E-T; CP; Molecular biology; Otud4; Trim56; brain development; cerebral cortex; deubiquitination; neural stem cells; neurogenesis; processing bodies; ubiquitination

DOI:  https://doi.org/10.1016/j.celrep.2022.111070
Autophagy. 2022 Jul 15. 1-2

Feedforward activation of PRKN/parkin.

Rayan Fakih, Véronique Sauvé, Kalle Gehring.

  Parkinson disease is a neurodegenerative disorder characterized by the progressive loss of dopaminergic neurons in the midbrain. The majority of early onset forms of Parkinson disease are a result of autosomal mutations in PRKN (parkin RBR E3 ubiquitin protein ligase) and PINK1 (PTEN induced kinase 1), which together regulate the clearance of damaged mitochondria from cells through selective autophagy of mitochondria (mitophagy). In a pair of recent papers, we characterized a secondary mechanism of activation of PRKN by PINK1 that is responsible for approximately a quarter of mitophagy in a cellular model. Our deepening understanding of PRKN-PINK1 signaling affords hope for the development of small molecule therapeutics for the treatment of Parkinson disease.

Keywords:  Autophagy; Parkinson disease; kinase; mitochondria; neurodegenerative disease; protein phosphorylation; ubiquitin

DOI:  https://doi.org/10.1080/15548627.2022.2100615
J Cell Biol. 2022 Aug 01. pii: e202110081. [Epub ahead of print]221(8):

Regulation of the COPII secretory machinery via focal adhesions and extracellular matrix signaling.

Juan Jung, Muzamil Majid Khan, Jonathan Landry, Aliaksandr Halavatyi, Pedro Machado, Miriam Reiss, Rainer Pepperkok.

Proteins that enter the secretory pathway are transported from their place of synthesis in the endoplasmic reticulum to the Golgi complex by COPII-coated carriers. The networks of proteins that regulate these components in response to extracellular cues have remained largely elusive. Using high-throughput microscopy, we comprehensively screened 378 cytoskeleton-associated and related proteins for their functional interaction with the coat protein complex II (COPII) components SEC23A and SEC23B. Among these, we identified a group of proteins associated with focal adhesions (FERMT2, MACF1, MAPK8IP2, NGEF, PIK3CA, and ROCK1) that led to the downregulation of SEC23A when depleted by siRNA. Changes in focal adhesions induced by plating cells on ECM also led to the downregulation of SEC23A and decreases in VSVG transport from ER to Golgi. Both the expression of SEC23A and the transport defect could be rescued by treatment with a focal adhesion kinase inhibitor. Altogether, our results identify a network of cytoskeleton-associated proteins connecting focal adhesions and ECM-related signaling with the gene expression of the COPII secretory machinery and trafficking.

DOI: https://doi.org/10.1083/jcb.202110081
Nat Commun. 2022 Jul 15. 13(1): 4126

Trigger factor both holds and folds its client proteins.

Kevin Wu, Thomas C Minshull, Sheena E Radford, Antonio N Calabrese, James C A Bardwell.

ATP-independent chaperones like trigger factor are generally assumed to play passive roles in protein folding by acting as holding chaperones. Here we show that trigger factor plays a more active role. Consistent with a role as an aggregation inhibiting chaperone, we find that trigger factor rapidly binds to partially folded glyceraldehyde 3-phosphate dehydrogenase (GAPDH) and prevents it from non-productive self-association by shielding oligomeric interfaces. In the traditional view of holding chaperone action, trigger factor would then be expected to transfer its client to a chaperone foldase system for complete folding. Unexpectedly, we noticed that GAPDH folds into a monomeric but otherwise rather native-like intermediate state while trigger factor-bound. Upon release from trigger factor, the mostly folded monomeric GAPDH rapidly self-associates into its native tetramer and acquires enzymatic activity without needing additional folding factors. The mechanism we propose here for trigger factor bridges the holding and folding activities of chaperone function.

DOI: https://doi.org/10.1038/s41467-022-31767-6
EMBO J. 2022 Jul 11. e108791

USP8 promotes cancer progression and extracellular vesicle-mediated CD8+ T cell exhaustion by deubiquitinating the TGF-β receptor TβRII.

Feng Xie, Xiaoxue Zhou, Heyu Li, Peng Su, Sijia Liu, Ran Li, Jing Zou, Xiang Wei, Chen Pan, Zhengkui Zhang, Min Zheng, Zhuang Liu, Xuli Meng, Huib Ovaa, Peter Ten Dijke, Fangfang Zhou, Long Zhang.

  TGF-β signaling is a key player in tumor progression and immune evasion, and is associated with poor response to cancer immunotherapies. Here, we identified ubiquitin-specific peptidase 8 (USP8) as a metastasis enhancer and a highly active deubiquitinase in aggressive breast tumors. USP8 acts both as a cancer stemness-promoting factor and an activator of the TGF-β/SMAD signaling pathway. USP8 directly deubiquitinates and stabilizes the type II TGF-β receptor TβRII, leading to its increased expression in the plasma membrane and in tumor-derived extracellular vesicles (TEVs). Increased USP8 activity was observed in patients resistant to neoadjuvant chemotherapies. USP8 promotes TGF-β/SMAD-induced epithelial-mesenchymal transition (EMT), invasion, and metastasis in tumor cells. USP8 expression also enables TβRII+ circulating extracellular vesicles (crEVs) to induce T cell exhaustion and chemoimmunotherapy resistance. Pharmacological inhibition of USP8 antagonizes TGF-β/SMAD signaling, and reduces TβRII stability and the number of TβRII+ crEVs to prevent CD8+ T cell exhaustion and to reactivate anti-tumor immunity. Our findings not only reveal a novel mechanism whereby USP8 regulates the cancer microenvironment but also demonstrate the therapeutic advantages of engineering USP8 inhibitors to simultaneously suppress metastasis and improve the efficacy of cancer immunotherapy.

Keywords:  TβRII; USP8; cancer immunotherapy; deubiquitinase; metastasis

DOI:  https://doi.org/10.15252/embj.2021108791
Trends Cell Biol. 2022 Jul 12. pii: S0962-8924(22)00151-9. [Epub ahead of print]

Autophagosomal components recycling on autolysosomes.

Yufen Wang, Huilin Que, Yueguang Rong.

  Autophagy is a multistage, intracellular process. Here, we highlight a recently identified autophagosomal components recycling (ACR) stage and the recycler complex (SNX4-SNX5-SNX17), which mediates recycling of autophagosomal outer membrane proteins on the autolysosome surface immediately following autophagosome-lysosome fusion. This discovery opens numerous research directions into the postfusion fate of autophagosomes.

Keywords:  ATG9A; STX17; autophagosomal components recycling; autophagy; lysosome

DOI:  https://doi.org/10.1016/j.tcb.2022.06.012
Cell Death Dis. 2022 Jul 15. 13(7): 615

Autophagic sequestration of SQSTM1 disrupts the aggresome formation of ubiquitinated proteins during proteasome inhibition.

Chenliang Zhang, Chen Huang, Hongwei Xia, Huanji Xu, Qiulin Tang, Feng Bi.

Aggresome formation is a protective cellular response to counteract proteasome dysfunction by sequestering misfolded proteins and reducing proteotoxic stress. Autophagic degradation of the protein aggregates is considered to be a key compensating mechanism for balancing proteostasis. However, the precise role of autophagy in proteasome inhibition-induced aggresome biogenesis remains unclear. Herein, we demonstrate that in the early stage of proteasome inhibition, the maturation of the autophagosome is suppressed, which facilitates aggresome formation of misfolded proteins. Proteasome inhibition-induced phosphorylation of SQSTM1 T269/S272 inhibits its autophagic receptor activity and promotes aggresome formation of misfolded proteins. Inhibiting SQSTM1 T269/S272 phosphorylation using Doramapimod aggravates proteasome inhibitor-mediated cell damage and tumor suppression. Taken together, our data reveal a negative effect of autophagy on aggresome biogenesis and cell damage upon proteasome inhibition. Our study suggests a novel therapeutic intervention for proteasome inhibitor-mediated tumor treatment.

DOI: https://doi.org/10.1038/s41419-022-05061-8
Development. 2022 Jul 11. pii: dev.200613. [Epub ahead of print]

Human neural progenitors establish a diffusion barrier in the ER membrane during cell division.

Muhammad Khadeesh Bin Imtiaz, Lars N Royall, Daniel Gonzalez-Bohorquez, Sebastian Jessberger.

  Asymmetric segregation of cellular components regulates the fate and behavior of somatic stem cells. Similar to dividing budding yeast and precursor cells in C. elegans, it has been shown that mouse neural progenitors establish a diffusion barrier in the membrane of the endoplasmic reticulum (ER), which has been associated with asymmetric partitioning of damaged proteins and cellular age. However, the existence of an ER-diffusion barrier in human cells remains unknown. Here we used fluorescence loss in photobleaching (FLIP) imaging to show that human embryonic stem cell (hESC)- and induced pluripotent stem cell (iPSC)-derived neural progenitor cells establish an ER-diffusion barrier during cell division. The human ER-diffusion barrier is regulated via Lamin-dependent mechanisms and is associated with asymmetric segregation of mono- and polyubiquitinated, damaged proteins. Further, forebrain regionalized organoids derived from hESCs were used to show the establishment of an ER-membrane diffusion barrier in more naturalistic tissues mimicking early steps of human brain development. Thus, the data provided here show that human neural progenitors establish a diffusion barrier during cell division in the membrane of the ER, which may allow for asymmetric segregation of cellular components, contributing to the fate and behavior of human neural progenitor cells.

Keywords:  Cell division; Diffusion barrier; ER membrane; Human neural progenitor; Neurogenesis

DOI:  https://doi.org/10.1242/dev.200613
Autophagy. 2022 Jul 09.

The coordination of V-ATPase and ATG16L1 is part of a common mechanism of non-canonical autophagy.

Yuchen Lei, Daniel J Klionsky.

  The conjugation of Atg8-family proteins with phospholipids on the double-membrane phagophore is one of the hallmarks of macroautopahgy/autophagy. However, in the past decades, Atg8-family proteins are also found on single-membrane structures, including the phagosome, endosome and lysosome. While the physiological importance of the non-canonical Atg8-family protein conjugation has been demonstrated, the mechanism of this process and the underlying regulation are still not very clear. In a recent paper, Hooper et al. found that during LC3-associated phagocytosis, reactive oxygen species are required for V-ATPase assembly, which is essential for the subsequent LC3 conjugation to the phagosome. Enhanced V-ATPase assembly and the direct engagement of ATG16L1 are also observed in a wide range of non-canonical Atg8-family protein conjugation processes, defining the V-ATPase and ATG16L1 as taking part in a common mechanism.

Keywords:  ATG16L1; Atg8 conjugation; LAP; ROS; V-ATPase; non-canonical autophagy

DOI:  https://doi.org/10.1080/15548627.2022.2100678
Biomed Res Int. 2022 ;2022 4304419

Tex264 Binding to SNX27 Regulates Itgα5 Receptor Membrane Recycling and Affects Cell Migration.

Xiao-Hui Xu, Qian-Wen Yang, Chang-Ling Yue, Yun-Yi Zhu, Zhao-Huan Zhang.

Tex264 is an endoplasmic reticulum (ER) membrane protein that was recently demonstrated to act as an ER-phagy receptor under starvation conditions to mediate endoplasmic reticulum autophagy. However, how Tex264 functions in the central nervous system (CNS) and tumors is unclear. Here, we identified 89 proteins from the rat brain that may specifically interact with Tex264 and confirmed the interaction between sorting nexin 27 (SNX27) and Tex264 by coimmunoprecipitation and immunofluorescence. Our results indicated that Tex264 may promote recycling of membrane proteins from endosomes to the cell plasma membrane by recruiting SNX27 retromer vesicles. siRNA-mediated knockdown of TEX264 in HeLa cells did not affect cell proliferation but did significantly inhibit cell migration through a mechanism that may involve a reduction in SNX27-mediated Itgα5 receptor membrane recycling. Results of this study helped identify potential binding Tex264 partners and provide insights into Tex264 functions in the CNS and in tumors.

DOI: https://doi.org/10.1155/2022/4304419
Cell Chem Biol. 2022 Jul 05. pii: S2451-9456(22)00238-0. [Epub ahead of print]

A campaign targeting a conserved Hsp70 binding site uncovers how subcellular localization is linked to distinct biological activities.

Hao Shao, Shuhei Taguwa, Luke Gilbert, Arielle Shkedi, Sara Sannino, Christopher J Guerriero, Zachary J Gale-Day, Zapporah T Young, Jeffrey L Brodsky, Jonathan Weissman, Jason E Gestwicki, Judith Frydman.

  The potential of small molecules to localize within subcellular compartments is rarely explored. To probe this question, we measured the localization of Hsp70 inhibitors using fluorescence microscopy. We found that even closely related analogs had dramatically different distributions, with some residing predominantly in the mitochondria and others in the ER. CRISPRi screens supported this idea, showing that different compounds had distinct chemogenetic interactions with Hsp70s of the ER (HSPA5/BiP) and mitochondria (HSPA9/mortalin) and their co-chaperones. Moreover, localization seemed to determine function, even for molecules with conserved binding sites. Compounds with distinct partitioning have distinct anti-proliferative activity in breast cancer cells compared with anti-viral activity in cellular models of Dengue virus replication, likely because different sets of Hsp70s are required in these processes. These findings highlight the contributions of subcellular partitioning and chemogenetic interactions to small molecule activity, features that are rarely explored during medicinal chemistry campaigns.

Keywords:  Hsp70; allosteric inhibitors; anti-cancer; antivirals; chaperones; chemical biology; subcellular localization

DOI:  https://doi.org/10.1016/j.chembiol.2022.06.006
J Am Chem Soc. 2022 Jul 12.

Adaptor-Specific Antibody Fragment Inhibitors for the Intracellular Modulation of p97 (VCP) Protein-Protein Interactions.

Ziwen Jiang, Yu-Hsuan Kuo, Mengqi Zhong, Jianchao Zhang, Xin X Zhou, Lijuan Xing, James A Wells, Yanzhuang Wang, Michelle R Arkin.

Protein-protein interactions (PPIs) form complex networks to drive cellular signaling and cellular functions. Precise modulation of a target PPI helps explain the role of the PPI in cellular events and possesses therapeutic potential. For example, valosin-containing protein (VCP/p97) is a hub protein that interacts with more than 30 adaptor proteins involved in various cellular functions. However, the role of each p97 PPI during the relevant cellular event is underexplored. The development of small-molecule PPI modulators remains challenging due to a lack of grooves and pockets in the relatively large PPI interface and the fact that a common binding groove in p97 binds to multiple adaptors. Here, we report an antibody fragment-based modulator for the PPI between p97 and its adaptor protein NSFL1C (p47). We engineered these antibody modulators by phage display against the p97-interacting domain of p47 and minimizing binding to other p97 adaptors. The selected antibody fragment modulators specifically disrupt the intracellular p97/p47 interaction. The potential of this antibody platform to develop PPI inhibitors in therapeutic applications was demonstrated through the inhibition of Golgi reassembly, which requires the p97/p47 interaction. This study presents a unique approach to modulate specific intracellular PPIs using engineered antibody fragments, demonstrating a method to dissect the function of a PPI within a convoluted PPI network.

DOI: https://doi.org/10.1021/jacs.2c03665
Autophagy. 2022 Jul 15. 1-14

Autophagy-associated immune dysregulation and hyperplasia in a patient with compound heterozygous mutations in ATG9A.

Guowu Hu, Pia J Hauk, Nannan Zhang, Waleed Elsegeiny, Carlos M Guardia, Amy Kullas, Kevin Crosby, Robin R Deterding, Michaela Schedel, Paul Reynolds, Jordan K Abbott, Vijaya Knight, Stefania Pittaluga, Mark Raffeld, Sergio D Rosenzweig, Juan S Bonifacino, Gulbu Uzel, Peter R Williamson, Erwin W Gelfand.

  ABBREVIATIONS: BCL2: BCL2 apoptosis regulator; BCL10: BCL10 immune signaling adaptor; CARD11: caspase recruitment domain family member 11; CBM: CARD11-BCL10-MALT1; CR2: complement C3d receptor 2; EBNA: Epstein Barr nuclear antigen; EBV: Epstein-Barr virus; FCGR3A; Fc gamma receptor IIIa; GLILD: granulomatous-lymphocytic interstitial lung disease; HV: healthy volunteer; IKBKB/IKB kinase: inhibitor of nuclear factor kappa B kinase subunit beta; IL2RA: interleukin 2 receptor subunit alpha; MALT1: MALT1 paracaspase; MS4A1: membrane spanning 4-domain A1; MTOR: mechanistic target of rapamycin kinase; MYC: MYC proto-oncogene, bHLH: transcription factor; NCAM1: neural cell adhesion molecule 1; NFKB: nuclear factor kappa B; NIAID: National Institute of Allergy and Infectious Diseases; NK: natural killer; PTPRC: protein tyrosine phosphatase receptor type C; SELL: selectin L; PBMCs: peripheral blood mononuclear cells; TR: T cell receptor; Tregs: regulatory T cells; WT: wild-type.

Keywords:  ATG9A; MTOR; NFKB; T-cell signaling; cellular proliferation; rapamycin

DOI:  https://doi.org/10.1080/15548627.2022.2093028
RSC Med Chem. 2022 Jun 22. 13(6): 726-730

Identification of ligand linkage vectors for the development of p300/CBP degraders.

Duncan K Brownsey, Ben C Rowley, Evgueni Gorobets, Koichiro Mihara, Ranjan Maity, James W Papatzimas, Benjamin S Gelfand, Morley D Hollenberg, Nizar J Bahlis, Darren J Derksen.

To develop new degrader molecules from an existing protein ligand a linkage vector must be identified and then joined with a suitable E3 ligase without disrupting binding to the respective targets. This is typically achieved through empirically evaluating the degradation efficacy of a series of synthetic degraders. Our strategy for determining optimal linkage sites utilises biotinylated protein ligands, linked via potential conjugation sites of an inhibitor to confirm whether target protein is maintained after forming a conjugate. This method provides low-cost, qualitative evidence that the addition of a linker moiety at a specific position can be tolerated, guiding further optimisation. We demonstrate the application of this method through the exploration of linkage vectors on A-485, a known ligand of p300/CBP, and found a conjugation site through a urea moiety. Pomalidomide was then conjugated through this site with several different linkers and cell viability and degradation were assessed for this library using a myeloma cell line, MM1.S. Compound 18i, with a PEG4 linker, was found to be the most effective p300 degrader and linker length greater than 10 atoms afforded enhanced degradation.

DOI: https://doi.org/10.1039/d1md00070e
Life Sci Alliance. 2022 Nov;pii: e202201531. [Epub ahead of print]5(11):

Decreasing pdzd8-mediated mito-ER contacts improves organismal fitness and mitigates Aβ42 toxicity.

Victoria L Hewitt, Leonor Miller-Fleming, Madeleine J Twyning, Simonetta Andreazza, Francesca Mattedi, Julien Prudent, Franck Polleux, Alessio Vagnoni, Alexander J Whitworth.

Mitochondria-ER contact sites (MERCs) orchestrate many important cellular functions including regulating mitochondrial quality control through mitophagy and mediating mitochondrial calcium uptake. Here, we identify and functionally characterize the Drosophila ortholog of the recently identified mammalian MERC protein, Pdzd8. We find that reducing pdzd8-mediated MERCs in neurons slows age-associated decline in locomotor activity and increases lifespan in Drosophila. The protective effects of pdzd8 knockdown in neurons correlate with an increase in mitophagy, suggesting that increased mitochondrial turnover may support healthy aging of neurons. In contrast, increasing MERCs by expressing a constitutive, synthetic ER-mitochondria tether disrupts mitochondrial transport and synapse formation, accelerates age-related decline in locomotion, and reduces lifespan. Although depletion of pdzd8 prolongs the survival of flies fed with mitochondrial toxins, it is also sufficient to rescue locomotor defects of a fly model of Alzheimer's disease expressing Amyloid β42 (Aβ42). Together, our results provide the first in vivo evidence that MERCs mediated by the tethering protein pdzd8 play a critical role in the regulation of mitochondrial quality control and neuronal homeostasis.

DOI: https://doi.org/10.26508/lsa.202201531
Am J Cancer Res. 2022 ;12(6): 2627-2640

The clinical relevance of unfolded protein response signaling in breast cancer.

Masanori Oshi, Arya Mariam Roy, Shipra Gandhi, Yoshihisa Tokumaru, Li Yan, Akimitsu Yamada, Itaru Endo, Kazuaki Takabe.

Protein homeostasis regulated by the Endoplasmic Reticulum (ER) is a recognized process involved in cancer progression. ER stress activates the Unfolded Protein Response (UPR) and has been implicated in a variety of cancers. Given the role of the UPR activation in carcinogenesis, we hypothesized that UPR activation could be associated with pathological progression, higher clinical stage, and worse survival in breast cancer. A total of 4,416 breast cancer patients from multiple independent cohorts were analyzed. We defined the UPR pathway score by the degree of enrichment by Gene Set Variant Analysis and median was used to divide high vs. low score groups in each cohort. High UPR breast cancer significantly enriched not only cell proliferation-related but also other pro-cancerous gene sets consistently in both METABIC and GSE96058 cohort. Majority of UPR pathway score high cells in the bulk tumor were tumor cells compared to other cells, including stromal, T-, B-, and myeloid-cells (P<0.001). UPR score was significantly associated with advanced stage, high grade, and triple negative breast cancer (TNBC) (all P<0.001). High UPR breast cancer was associated with worse patient survival in both cohorts (all P<0.001). Among breast cancer subtype, ER-positive/HER2-negative breast cancer with high UPR was significantly associated with worse survival, but neither HER-positive nor TNBC. High UPR ER-positive/HER2-negative breast cancer was infiltrated with high level of Th1 and Th2 cells, M1 macrophage, and plasma cells. On the other hand, they were significantly infiltrated with high level of several types of stromal cells in tumor microenvironment (all P<0.001). Finally, high UPR metastatic breast cancer was also associated with worse patient survival (P=0.041). UPR signaling is associated with cancer aggressiveness, and worse survival, especially ER-positive/HER2-negative breast cancer subtype.

Keywords: Biomarker; breast cancer; gene expression; hormonal; unfolded protein response
EMBO J. 2022 Jul 13. e110581

Molecular architecture of 40S translation initiation complexes on the hepatitis C virus IRES.

Zuben P Brown, Irina S Abaeva, Swastik De, Christopher U T Hellen, Tatyana V Pestova, Joachim Frank.

  Hepatitis C virus mRNA contains an internal ribosome entry site (IRES) that mediates end-independent translation initiation, requiring a subset of eukaryotic initiation factors (eIFs). Biochemical studies revealed that direct binding of the IRES to the 40S ribosomal subunit places the initiation codon into the P site, where it base pairs with eIF2-bound Met-tRNAiMet forming a 48S initiation complex. Subsequently, eIF5 and eIF5B mediate subunit joining, yielding an elongation-competent 80S ribosome. Initiation can also proceed without eIF2, in which case Met-tRNAiMet is recruited directly by eIF5B. However, the structures of initiation complexes assembled on the HCV IRES, the transitions between different states, and the accompanying conformational changes have remained unknown. To fill these gaps, we now obtained cryo-EM structures of IRES initiation complexes, at resolutions up to 3.5 Å, that cover all major stages from the initial ribosomal association, through eIF2-containing 48S initiation complexes, to eIF5B-containing complexes immediately prior to subunit joining. These structures provide insights into the dynamic network of 40S/IRES contacts, highlight the role of IRES domain II, and reveal conformational changes that occur during the transition from eIF2- to eIF5B-containing 48S complexes and prepare them for subunit joining.

Keywords:  eIF2; eIF5B; hepatitis C virus IRES; ribosome; translation initiation

DOI:  https://doi.org/10.15252/embj.2022110581
Nucleic Acids Res. 2022 Jul 13. pii: gkac584. [Epub ahead of print]

PHF20 is crucial for epigenetic control of starvation-induced autophagy through enhancer activation.

Se Won Park, Jaehoon Kim, Sungryong Oh, Jeongyoon Lee, Joowon Cha, Hyun Sik Lee, Keun Il Kim, Daechan Park, Sung Hee Baek.

Autophagy is a catabolic pathway that maintains cellular homeostasis under various stress conditions, including conditions of nutrient deprivation. To elevate autophagic flux to a sufficient level under stress conditions, transcriptional activation of autophagy genes occurs to replenish autophagy components. Thus, the transcriptional and epigenetic control of the genes regulating autophagy is essential for cellular homeostasis. Here, we applied integrated transcriptomic and epigenomic profiling to reveal the roles of plant homeodomain finger protein 20 (PHF20), which is an epigenetic reader possessing methyl binding activity, in controlling the expression of autophagy genes. Phf20 deficiency led to impaired autophagic flux and autophagy gene expression under glucose starvation. Interestingly, the genome-wide characterization of chromatin states by Assay for Transposase-Accessible Chromatin (ATAC)-sequencing revealed that the PHF20-dependent chromatin remodelling occurs in enhancers that are co-occupied by dimethylated lysine 36 on histone H3 (H3K36me2). Importantly, the recognition of H3K36me2 by PHF20 was found to be highly correlated with increased levels of H3K4me1/2 at the enhancer regions. Collectively, these results indicate that PHF20 regulates autophagy genes through enhancer activation via H3K36me2 recognition as an epigenetic reader. Our findings emphasize the importance of nuclear events in the regulation of autophagy.

DOI: https://doi.org/10.1093/nar/gkac584