bims-proteo 2021-08-22 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2021‒08‒22
forty-three papers selected by
Eric Chevet
INSERM

EVI/WLS function is regulated by ubiquitylation and is linked to ER-associated degradation by ERLIN2.
Identification of Ubiquitin Variants That Inhibit the E2 Ubiquitin Conjugating Enzyme, Ube2k.
Ubiquitin protein helps cells to recover from stress.
Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD.
Fluc-EGFP reporter mice reveal differential alterations of neuronal proteostasis in aging and disease.
Reciprocal antagonistic regulation of E3 ligases controls ACC synthase stability and responses to stress.
Pex30-like proteins function as adaptors at distinct ER membrane contact sites.
Fatty acids impact sarcomere integrity through myristoylation and ER homeostasis.
The Hob proteins are novel and conserved lipid-binding proteins at ER-PM contact sites.
Reconstitution and Structural Analysis of a HECT Ligase-Ubiquitin Complex via an Activity-Based Probe.
IFN-γ-induced ER stress impairs autophagy and triggers apoptosis in lung cancer cells.
Therapeutic targeting of endoplasmic reticulum stress in acute graft-versus-host disease.
Deubiquitinating enzymes (DUBs): regulation, homeostasis, and oxidative stress response.
A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures.
Suppression of Vps13 adaptor protein mutants reveals a central role for PI4P in regulating prospore membrane extension.
The Proteome Folding Problem and Cellular Proteostasis.
The pancreatic β cell response to secretory demands and adaption to stress.
Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase.
An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens.
The unfolded protein response as regulator of cancer stemness and differentiation: mechanisms and implications for cancer therapy.
Titin kinase ubiquitination aligns autophagy receptors with mechanical signals in the sarcomere.
RNF168-mediated localization of BARD1 recruits the BRCA1-PALB2 complex to DNA damage.
UBE2D3 contributes to myocardial ischemia-reperfusion injury by regulating autophagy in dependence of p62/SQSTM1.
eIF4B enhances ATF4 expression and contributes to cellular adaptation to asparagine limitation in BRAF-mutated A375 melanoma.
Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery.
DAXX represents a new type of protein-folding enabler.
Circulating Protein Disulfide Isomerase is associated with increased risk of Thrombosis in JAK2-mutated Myeloproliferative Neoplasms.
ADAR1 limits stress granule formation through both translation-dependent and translation-independent mechanisms.
Cotranslational prolyl hydroxylation is essential for flavivirus biogenesis.
The deubiquitinase USP10 restores PTEN activity and inhibits non-small cell lung cancer cell proliferation.
Interdomain interactions dictate the function of the C. albicans Hsp110 protein Msi3.
The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites.
Sumoylation regulates the assembly and activity of the SMN complex.
UBCH5 family members differentially impact stabilization of mutant p53 via RNF128 Iso1 during Barrett's progression to esophageal adenocarcinoma.
CHIP-dependent regulation of the actin cytoskeleton is linked to neuronal cell membrane integrity.
UBC19 is a new interacting protein of ORANGE for its nuclear localization in Arabidopsis thaliana.
Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis.
Translation initiation factor eIF2Bε promotes Wnt-mediated clonogenicity and global translation in intestinal epithelial cells.
Exploring Ligand-Directed N-Acyl-N-alkylsulfonamide-Based Acylation Chemistry for Potential Targeted Degrader Development.
Bifunctional small molecules that mediate the degradation of extracellular proteins.
Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.
PARylation prevents the proteasomal degradation of topoisomerase I DNA-protein crosslinks and induces their deubiquitylation.
The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation.

J Cell Sci. 2021 Aug 15. pii: jcs257790. [Epub ahead of print]134(16):

EVI/WLS function is regulated by ubiquitylation and is linked to ER-associated degradation by ERLIN2.

Lucie M Wolf, Annika M Lambert, Julie Haenlin, Michael Boutros.

  WNT signalling is important for development in all metazoans and is associated with various human diseases. The ubiquitin-proteasome system (UPS) and regulatory endoplasmic reticulum-associated degradation (ERAD) have been implicated in the production of WNT proteins. Here, we investigated how the WNT secretory factor EVI (also known as WLS) is ubiquitylated, recognised by ERAD components and subsequently removed from the secretory pathway. We performed a focused immunoblot-based RNAi screen for factors that influence EVI/WLS protein stability. We identified the VCP-binding proteins FAF2 and UBXN4 as novel interaction partners of EVI/WLS and showed that ERLIN2 links EVI/WLS to the ubiquitylation machinery. Interestingly, we also found that EVI/WLS is ubiquitylated and degraded in cells irrespective of their level of WNT production. This K11, K48 and K63-linked ubiquitylation is mediated by the E2 ubiquitin-conjugating enzymes UBE2J2, UBE2K and UBE2N, but is independent of the E3 ubiquitin ligases HRD1 (also known as SYVN1) and GP78 (also known as AMFR). Taken together, our study identifies factors that link the UPS to the WNT secretory pathway and provides mechanistic details of the fate of an endogenous substrate of regulatory ERAD in mammalian cells. This article has an associated First Person interview with the first author of the paper.

Keywords:  ERAD; EVI/WLS; Proteolysis; Ubiquitylation; Wnt signalling

DOI:  https://doi.org/10.1242/jcs.257790
ACS Chem Biol. 2021 Aug 16.

Identification of Ubiquitin Variants That Inhibit the E2 Ubiquitin Conjugating Enzyme, Ube2k.

Adam J Middleton, Joan Teyra, Jingyi Zhu, Sachdev S Sidhu, Catherine L Day.

Transfer of ubiquitin to substrate proteins regulates most processes in eukaryotic cells. E2 enzymes are a central component of the ubiquitin machinery, and generally determine the type of ubiquitin signal generated and thus the ultimate fate of substrate proteins. The E2, Ube2k, specifically builds degradative ubiquitin chains on diverse substrates. Here we have identified protein-based reagents, called ubiquitin variants (UbVs), that bind tightly and specifically to Ube2k. Crystal structures reveal that the UbVs bind to the E2 enzyme at a hydrophobic cleft that is distinct from the active site and previously identified ubiquitin binding sites. We demonstrate that the UbVs are potent inhibitors of Ube2k and block both ubiquitin charging of the E2 enzyme and E3-catalyzed ubiquitin transfer. The binding site of the UbVs suggests they directly clash with the ubiquitin activating enzyme, while potentially disrupting interactions with E3 ligases via allosteric effects. Our data reveal the first protein-based inhibitors of Ube2k and unveil a hydrophobic groove that could be an effective target for inhibiting Ube2k and other E2 enzymes.

DOI: https://doi.org/10.1021/acschembio.1c00445
Nature. 2021 Aug 16.

Ubiquitin protein helps cells to recover from stress.

Titus Franzmann, Simon Alberti.



Keywords:  Cell biology; Molecular biology

DOI:  https://doi.org/10.1038/d41586-021-02197-z
Nat Commun. 2021 08 18. 12(1): 5004

Structures of a deAMPylation complex rationalise the switch between antagonistic catalytic activities of FICD.

Luke A Perera, Steffen Preissler, Nathan R Zaccai, Sylvain Prévost, Juliette M Devos, Michael Haertlein, David Ron.

The endoplasmic reticulum (ER) Hsp70 chaperone BiP is regulated by AMPylation, a reversible inactivating post-translational modification. Both BiP AMPylation and deAMPylation are catalysed by a single ER-localised enzyme, FICD. Here we present crystallographic and solution structures of a deAMPylation Michaelis complex formed between mammalian AMPylated BiP and FICD. The latter, via its tetratricopeptide repeat domain, binds a surface that is specific to ATP-state Hsp70 chaperones, explaining the exquisite selectivity of FICD for BiP's ATP-bound conformation both when AMPylating and deAMPylating Thr518. The eukaryotic deAMPylation mechanism thus revealed, rationalises the role of the conserved Fic domain Glu234 as a gatekeeper residue that both inhibits AMPylation and facilitates hydrolytic deAMPylation catalysed by dimeric FICD. These findings point to a monomerisation-induced increase in Glu234 flexibility as the basis of an oligomeric state-dependent switch between FICD's antagonistic activities, despite a similar mode of engagement of its two substrates - unmodified and AMPylated BiP.

DOI: https://doi.org/10.1038/s41467-021-25076-7
EMBO J. 2021 Aug 19. e107260

Fluc-EGFP reporter mice reveal differential alterations of neuronal proteostasis in aging and disease.

Sonja Blumenstock, Elena Katharina Schulz-Trieglaff, Kerstin Voelkl, Anna-Lena Bolender, Paul Lapios, Jana Lindner, Mark S Hipp, F Ulrich Hartl, Rüdiger Klein, Irina Dudanova.

  The cellular protein quality control machinery is important for preventing protein misfolding and aggregation. Declining protein homeostasis (proteostasis) is believed to play a crucial role in age-related neurodegenerative disorders. However, how neuronal proteostasis capacity changes in different diseases is not yet sufficiently understood, and progress in this area has been hampered by the lack of tools to monitor proteostasis in mammalian models. Here, we have developed reporter mice for in vivo analysis of neuronal proteostasis. The mice express EGFP-fused firefly luciferase (Fluc-EGFP), a conformationally unstable protein that requires chaperones for proper folding, and that reacts to proteotoxic stress by formation of intracellular Fluc-EGFP foci and by reduced luciferase activity. Using these mice, we provide evidence for proteostasis decline in the aging brain. Moreover, we find a marked reaction of the Fluc-EGFP sensor in a mouse model of tauopathy, but not in mouse models of Huntington's disease. Mechanistic investigations in primary neuronal cultures demonstrate that different types of protein aggregates have distinct effects on the cellular protein quality control. Thus, Fluc-EGFP reporter mice enable new insights into proteostasis alterations in different diseases.

Keywords:  Huntington’s disease; nuclear and cytoplasmic aggregates; protein homeostasis; reporter mouse; tauopathy

DOI:  https://doi.org/10.15252/embj.2020107260
Proc Natl Acad Sci U S A. 2021 Aug 24. pii: e2011900118. [Epub ahead of print]118(34):

Reciprocal antagonistic regulation of E3 ligases controls ACC synthase stability and responses to stress.

Han Yong Lee, Hye Lin Park, Chanung Park, Yi-Chun Chen, Gyeong Mee Yoon.

  Ethylene influences plant growth, development, and stress responses via crosstalk with other phytohormones; however, the underlying molecular mechanisms are still unclear. Here, we describe a mechanistic link between the brassinosteroid (BR) and ethylene biosynthesis, which regulates cellular protein homeostasis and stress responses. We demonstrate that as a scaffold, 1-aminocyclopropane-1-carboxylic acid (ACC) synthases (ACS), a rate-limiting enzyme in ethylene biosynthesis, promote the interaction between Seven-in-Absentia of Arabidopsis (SINAT), a RING-domain containing E3 ligase involved in stress response, and ETHYLENE OVERPRODUCER 1 (ETO1) and ETO1-like (EOL) proteins, the E3 ligase adaptors that target a subset of ACS isoforms. Each E3 ligase promotes the degradation of the other, and this reciprocally antagonistic interaction affects the protein stability of ACS. Furthermore, 14-3-3, a phosphoprotein-binding protein, interacts with SINAT in a BR-dependent manner, thus activating reciprocal degradation. Disrupted reciprocal degradation between the E3 ligases compromises the survival of plants in carbon-deficient conditions. Our study reveals a mechanism by which plants respond to stress by modulating the homeostasis of ACS and its cognate E3 ligases.

Keywords:  ACC synthases; E3 ligases; SINAT; ethylene; reciprocal degradation

DOI:  https://doi.org/10.1073/pnas.2011900118
J Cell Biol. 2021 Oct 04. pii: e202103176. [Epub ahead of print]220(10):

Pex30-like proteins function as adaptors at distinct ER membrane contact sites.

Joana Veríssimo Ferreira, Pedro Carvalho.

Membrane lipids and proteins synthesized in the ER are used for de novo assembly of organelles, such as lipid droplets and peroxisomes. After assembly, the growth of these organelles is supported by ER-derived lipids transferred at membrane contact sites (MCSs). How ER sites for organelle biogenesis and lipid transfer are established and regulated is unclear. Here, we investigate how the ER membrane protein Pex30 and its family members Pex28, Pex29, Pex31, and Pex32 target and function at multiple MCSs. We show that different Pex30 complexes function at distinct ER domains and MCSs. Pex30 targets ER-peroxisome MCSs when bound to Pex28 and Pex32, organizes the nuclear-vacuolar junction when bound to Pex29, and promotes the biogenesis of lipid droplets independently of other family members. Importantly, the reticulon homology domain (RHD) mediates the assembly of the various Pex30 complexes. Given the role of RHD in membrane shaping, our findings offer a mechanistic link between MCS and regulation of membrane curvature.

DOI: https://doi.org/10.1083/jcb.202103176
Cell Rep. 2021 Aug 17. pii: S2211-1247(21)00973-6. [Epub ahead of print]36(7): 109539

Fatty acids impact sarcomere integrity through myristoylation and ER homeostasis.

Hongyun Tang, Mingxue Cui, Min Han.

  Decreased ability to maintain tissue integrity is critically involved in aging and degenerative diseases. Fatty acid (FA) metabolism has a profound impact on animal development and tissue maintenance, but our understanding of the underlying mechanisms is limited. We investigated whether and how FA abundance affects muscle integrity using Caenorhabditis elegans. We show that reducing the overall FA level by blocking FA biosynthesis or inhibiting protein myristoylation leads to disorganization of sarcomere structure and adult-onset paralysis. Further analysis indicates that myristoylation of two ARF guanosine triphosphatases (GTPases) critically mediates the effect of FA deficiency on sarcomere integrity through inducing endoplasmic reticulum (ER) stress and ER unfolded protein response (UPRER), which in turn leads to reduction of the level of sarcomere component PINCH and myosin disorganization. We thus present a mechanism that links FA signal, protein myristoylation, and ER homeostasis with muscle integrity, which provides valuable insights into the regulatory role of nutrients and ER homeostasis in muscle maintenance.

Keywords:  ACS; ER stress; UNC-97/PINCH; acyl-CoA synthetase; arf-1.2; arf-3; eIF-2a; muscle degeneration; myristoylation; xbp-1

DOI:  https://doi.org/10.1016/j.celrep.2021.109539
J Cell Sci. 2022 Mar 01. pii: jcs259086. [Epub ahead of print]135(5):

The Hob proteins are novel and conserved lipid-binding proteins at ER-PM contact sites.

Sarah D Neuman, Jeff R Jorgensen, Amy T Cavanagh, Jeremy T Smyth, Jane E Selegue, Scott D Emr, Arash Bashirullah.

  Membrane contact sites are critical junctures for organelle signaling and communication. Endoplasmic reticulum-plasma membrane (ER-PM) contact sites were the first membrane contact sites to be described; however, the protein composition and molecular function of these sites is still emerging. Here, we leverage yeast and Drosophila model systems to uncover a novel role for the Hobbit (Hob) proteins at ER-PM contact sites. We find that Hobbit localizes to ER-PM contact sites in both yeast cells and the Drosophila larval salivary glands, and this localization is mediated by an N-terminal ER membrane anchor and conserved C-terminal sequences. The C-terminus of Hobbit binds to plasma membrane phosphatidylinositols, and the distribution of these lipids is altered in hobbit mutant cells. Notably, the Hobbit protein is essential for viability in Drosophila, providing one of the first examples of a membrane contact site-localized lipid binding protein that is required for development.

Keywords:   Drosophila ; S. cerevisiae ; ER–PM contact sites; Hobbit; Phosphatidylinositol; Regulated exocytosis; Salivary gland

DOI:  https://doi.org/10.1242/jcs.259086
ACS Chem Biol. 2021 Aug 17.

Reconstitution and Structural Analysis of a HECT Ligase-Ubiquitin Complex via an Activity-Based Probe.

Rahul M Nair, Ayshwarya Seenivasan, Bing Liu, Dan Chen, Edward D Lowe, Sonja Lorenz.

Ubiquitin activity-based probes have proven invaluable in elucidating structural mechanisms in the ubiquitin system by stabilizing transient macromolecular complexes of deubiquitinases, ubiquitin-activating enzymes, and the assemblies of ubiquitin-conjugating enzymes with ubiquitin ligases of the RING-Between-RING and RING-Cysteine-Relay families. Here, we demonstrate that an activity-based probe, ubiquitin-propargylamine, allows for the preparative reconstitution and structural analysis of the interactions between ubiquitin and certain HECT ligases. We present a crystal structure of the ubiquitin-linked HECT domain of HUWE1 that defines a catalytically critical conformation of the C-terminal tail of the ligase for the transfer of ubiquitin to an acceptor protein. Moreover, we observe that ubiquitin-propargylamine displays selectivity among HECT domains, thus corroborating the notion that activity-based probes may provide entry points for the development of specific, active site-directed inhibitors and reporters of HECT ligase activities.

DOI: https://doi.org/10.1021/acschembio.1c00433
Oncoimmunology. 2021 ;10(1): 1962591

IFN-γ-induced ER stress impairs autophagy and triggers apoptosis in lung cancer cells.

Can Fang, Tao Weng, Shaojie Hu, Zhiwei Yuan, Hui Xiong, Bing Huang, Yixin Cai, Lequn Li, Xiangning Fu.

  Interferon-gamma (IFN-γ) is a major effector molecule of immunity and a common feature of tumors responding to immunotherapy. Active IFN-γ signaling can directly trigger apoptosis and cell cycle arrest in human cancer cells. However, the mechanisms underlying these actions remain unclear. Here, we report that IFN-γ rapidly increases protein synthesis and causes the unfolded protein response (UPR), as evidenced by the increased expression of glucose-regulated protein 78, activating transcription factor-4, and c/EBP homologous protein (CHOP) in cells treated with IFN-γ. The JAK1/2-STAT1 and AKT-mTOR signaling pathways are required for IFN-γ-induced UPR. Endoplasmic reticulum (ER) stress promotes autophagy and restores homeostasis. Surprisingly, in IFN-γ-treated cells, autophagy was impaired at the step of autophagosome-lysosomal fusion and caused by a significant decline in the expression of lysosomal membrane protein-1 and -2 (LAMP-1/LAMP-2). The ER stress inhibitor 4-PBA restored LAMP expression in IFN-γ-treated cells. IFN-γ stimulation activated the protein kinase-like ER kinase (PERK)-eukaryotic initiation factor 2a subunit (eIF2α) axis and caused a reduction in global protein synthesis. The PERK inhibitor, GSK2606414, partially restored global protein synthesis and LAMP expression in cells treated with IFN-γ. We further investigated the functional consequences of IFN-γ-induced ER stress. We show that inhibition of ER stress significantly prevents IFN-γ-triggered apoptosis. CHOP knockdown abrogated IFN-γ-mediated apoptosis. Inhibition of ER stress also restored cyclin D1 expression in IFN-γ-treated cells. Thus, ER stress and the UPR caused by IFN-γ represent novel mechanisms underlying IFN-γ-mediated anticancer effects. This study expands our understanding of IFN-γ-mediated signaling and its cellular actions in tumor cells.

Keywords:  ER stress; IFN-γ; LAMP; apoptosis; autophagy; lung adenocarcinoma

DOI:  https://doi.org/10.1080/2162402X.2021.1962591
Haematologica. 2021 Aug 19.

Therapeutic targeting of endoplasmic reticulum stress in acute graft-versus-host disease.

Eileen Haring, Geoffroy Andrieux, Franziska M Uhl, Máté Krausz, Michele Proietti, Barbara Sauer, Philipp R Esser, Stefan F Martin, Dietmar Pfeifer, Annette Schmitt-Graeff, Justus Duyster, Natalie Köhler, Bodo Grimbacher, Melanie Boerries, Konrad Aumann, Robert Zeiser, Petya Apostolova.

Acute graft-versus-host disease (GVHD) is a life-threatening complication of allogeneic hematopoietic cell transplantation (allo-HCT), a potentially curative treatment for leukemia. Endoplasmic reticulum (ER) stress occurs when the protein folding capacity of the ER is oversaturated. How ER stress modulates tissue homeostasis in the context of alloimmunity is not well understood. We show that ER stress contributes to intestinal tissue injury during GVHD and can be targeted pharmacologically. We observed high levels of ER stress upon GVHD onset in a murine allo-HCT model and in human biopsies. These levels correlated with GVHD severity, underscoring a novel therapeutic potential. Elevated ER stress resulted in increased cell death of intestinal organoids. In a conditional knockout model, deletion of the ER stress regulator transcription factor Xbp1 in intestinal epithelial cells induced a general ER stress signaling disruption and aggravated GVHD lethality. This phenotype was mediated by changes in the production of anti-microbial peptides and the microbiome composition as well as activation of pro-apoptotic signaling. Inhibition of inositol-requiring enzyme 1 alpha (IRE1α), the most conserved signaling branch in ER stress, reduced GVHD development in mice. IRE1α blockade by the small molecule inhibitor 4µ8c improved intestinal cell viability, without impairing hematopoietic regeneration and T cell activity against tumor cells. Our findings in patient samples and mice indicate that excessive ER stress propagates tissue injury during GVHD. Reducing ER stress could improve the outcome of patients suffering from GVHD.

DOI: https://doi.org/10.3324/haematol.2021.278387
J Biol Chem. 2021 Aug 12. pii: S0021-9258(21)00880-2. [Epub ahead of print] 101077

Deubiquitinating enzymes (DUBs): regulation, homeostasis, and oxidative stress response.

Nathan A Snyder, Gustavo M Silva.

  Ubiquitin signaling is a conserved, widespread, and dynamic system in which protein substrates are rapidly modified by ubiquitin to impact protein activity, localization or stability. To regulate this system, deubiquitinating enzymes (DUBs) counter the signal induced by ubiquitin conjugases and ligases by removing ubiquitin from these substrates. Many DUBs selectively regulate physiological pathways employing conserved mechanisms of ubiquitin bond cleavage. DUB activity is highly regulated in dynamic environments through protein-protein interaction, post-translational modification, and relocalization. The largest family of DUBs, cysteine proteases, are also sensitive to regulation by oxidative stress, as reactive oxygen species (ROS) directly modify the catalytic cysteine required for their enzymatic activity. Current research has implicated DUB activity in human diseases, including various cancers and neurodegenerative disorders. Due to their selectivity and functional roles, DUBs have become important targets for therapeutic development to treat these conditions. This review will discuss the main classes of DUBs and their regulatory mechanisms with a particular focus on DUB redox regulation and its physiological impact during oxidative stress.

Keywords:  DUB; deubiquitination; enzymatic regulation; oxidative stress; redox signaling; translation; ubiquitin

DOI:  https://doi.org/10.1016/j.jbc.2021.101077
Nat Microbiol. 2021 Aug 16.

A heat-shock response regulated by the PfAP2-HS transcription factor protects human malaria parasites from febrile temperatures.

Elisabet Tintó-Font, Lucas Michel-Todó, Timothy J Russell, Núria Casas-Vila, David J Conway, Zbynek Bozdech, Manuel Llinás, Alfred Cortés.

Periodic fever is a characteristic clinical feature of human malaria, but how parasites survive febrile episodes is not known. Although the genomes of Plasmodium species encode a full set of chaperones, they lack the conserved eukaryotic transcription factor HSF1, which activates the expression of chaperones following heat shock. Here, we show that PfAP2-HS, a transcription factor in the ApiAP2 family, regulates the protective heat-shock response in Plasmodium falciparum. PfAP2-HS activates the transcription of hsp70-1 and hsp90 at elevated temperatures. The main binding site of PfAP2-HS in the entire genome coincides with a tandem G-box DNA motif in the hsp70-1 promoter. Engineered parasites lacking PfAP2-HS have reduced heat-shock survival and severe growth defects at 37 °C but not at 35 °C. Parasites lacking PfAP2-HS also have increased sensitivity to imbalances in protein homeostasis (proteostasis) produced by artemisinin, the frontline antimalarial drug, or the proteasome inhibitor epoxomicin. We propose that PfAP2-HS contributes to the maintenance of proteostasis under basal conditions and upregulates specific chaperone-encoding genes at febrile temperatures to protect the parasite against protein damage.

DOI: https://doi.org/10.1038/s41564-021-00940-w
PLoS Genet. 2021 Aug;17(8): e1009727

Suppression of Vps13 adaptor protein mutants reveals a central role for PI4P in regulating prospore membrane extension.

Tsuyoshi S Nakamura, Yasuyuki Suda, Kenji Muneshige, Yuji Fujieda, Yuuya Okumura, Ichiro Inoue, Takayuki Tanaka, Tetsuo Takahashi, Hideki Nakanishi, Xiao-Dong Gao, Yasushi Okada, Aaron M Neiman, Hiroyuki Tachikawa.

Vps13 family proteins are proposed to function in bulk lipid transfer between membranes, but little is known about their regulation. During sporulation of Saccharomyces cerevisiae, Vps13 localizes to the prospore membrane (PSM) via the Spo71-Spo73 adaptor complex. We previously reported that loss of any of these proteins causes PSM extension and subsequent sporulation defects, yet their precise function remains unclear. Here, we performed a genetic screen and identified genes coding for a fragment of phosphatidylinositol (PI) 4-kinase catalytic subunit and PI 4-kinase noncatalytic subunit as multicopy suppressors of spo73Δ. Further genetic and cytological analyses revealed that lowering PI4P levels in the PSM rescues the spo73Δ defects. Furthermore, overexpression of VPS13 and lowering PI4P levels synergistically rescued the defect of a spo71Δ spo73Δ double mutant, suggesting that PI4P might regulate Vps13 function. In addition, we show that an N-terminal fragment of Vps13 has affinity for the endoplasmic reticulum (ER), and ER-plasma membrane (PM) tethers localize along the PSM in a manner dependent on Vps13 and the adaptor complex. These observations suggest that Vps13 and the adaptor complex recruit ER-PM tethers to ER-PSM contact sites. Our analysis revealed that involvement of a phosphoinositide, PI4P, in regulation of Vps13, and also suggest that distinct contact site proteins function cooperatively to promote de novo membrane formation.

DOI: https://doi.org/10.1371/journal.pgen.1009727
J Mol Biol. 2021 Aug 12. pii: S0022-2836(21)00430-7. [Epub ahead of print] 167197

The Proteome Folding Problem and Cellular Proteostasis.

Evan T Powers, Lila M Gierasch.

  Stunning advances have been achieved in addressing the protein folding problem, providing deeper understanding of the mechanisms by which proteins navigate energy landscapes to reach their native states and enabling powerful algorithms to connect sequence to structure. However, the realities of the in vivo protein folding problem remain a challenge to reckon with. Here, we discuss the concept of the "proteome folding problem"-the problem of how organisms build and maintain a functional proteome-by admitting that folding energy landscapes are characterized by many misfolded states and that cells must deploy a network of chaperones and degradation enzymes to minimize deleterious impacts of these off-pathway species. The resulting proteostasis network is an inextricable part of in vivo protein folding and must be understood in detail if we are to solve the proteome folding problem. We discuss how the development of computational models for the proteostasis network's actions and the relationship to the biophysical properties of the proteome has begun to offer new insights and capabilities.

Keywords:  Protein folding; chaperone; computational modeling; energy landscape; proteome folding; proteostasis

DOI:  https://doi.org/10.1016/j.jmb.2021.167197
Endocrinology. 2021 Aug 18. pii: bqab173. [Epub ahead of print]

The pancreatic β cell response to secretory demands and adaption to stress.

Michael A Kalwat, Donalyn Scheuner, Karina Rodrigues Dos Santos, Decio L Eizirik, Melanie H Cobb.

  Pancreatic β cells dedicate much of their protein translation capacity to produce insulin to maintain glucose homeostasis. In response to increased secretory demand, β cells can compensate by increasing insulin production capability even in the face of protracted peripheral insulin resistance. The ability to amplify insulin secretion in response to hyperglycemia is a critical facet of β cell function, and the exact mechanisms by which this occurs have been studied for decades. To adapt to the constant and fast changing demands for insulin production, β cells utilize the unfolded protein response of the endoplasmic reticulum. Failure of these compensatory mechanisms contributes to both type 1 and 2 diabetes. Additionally, studies in which β cells are 'rested' by reducing endogenous insulin demand have shown promise as a therapeutic strategy that could be applied more broadly. Here we review recent findings in β cells pertaining to the metabolic amplifying pathway, the unfolded protein response, and potential advances in therapeutics based on β cell rest.

Keywords:  beta cell rest; endoplasmic reticulum stress; insulin secretion; pancreatic islet beta cell; unfolded protein response

DOI:  https://doi.org/10.1210/endocr/bqab173
ACS Synth Biol. 2021 Aug 16.

Engineering Single Pan-Specific Ubiquibodies for Targeted Degradation of All Forms of Endogenous ERK Protein Kinase.

Erin A Stephens, Morgan B Ludwicki, Bunyarit Meksiriporn, Mingji Li, Tianzheng Ye, Connor Monticello, Katherine J Forsythe, Lutz Kummer, Pengbo Zhou, Andreas Plückthun, Matthew P DeLisa.

  Ubiquibodies (uAbs) are a customizable proteome editing technology that utilizes E3 ubiquitin ligases genetically fused to synthetic binding proteins to steer otherwise stable proteins of interest (POIs) to the 26S proteasome for degradation. The ability of engineered uAbs to accelerate the turnover of exogenous or endogenous POIs in a post-translational manner offers a simple yet robust tool for dissecting diverse functional properties of cellular proteins as well as for expanding the druggable proteome to include tumorigenic protein families that have yet-to-be successfully drugged by conventional inhibitors. Here, we describe the engineering of uAbs composed of human carboxyl-terminus of Hsc70-interacting protein (CHIP), a highly modular human E3 ubiquitin ligase, tethered to differently designed ankyrin repeat proteins (DARPins) that bind to nonphosphorylated (inactive) and/or doubly phosphorylated (active) forms of extracellular signal-regulated kinase 1 and 2 (ERK1/2). Two of the resulting uAbs were found to be global ERK degraders, pan-specifically capturing all endogenous ERK1/2 protein forms and redirecting them to the proteasome for degradation in different cell lines, including MCF7 breast cancer cells. Taken together, these results demonstrate how the substrate specificity of an E3 ubiquitin ligase can be reprogrammed to generate designer uAbs against difficult-to-drug targets, enabling a modular platform for remodeling the mammalian proteome.

Keywords:  DARPins; E3 ubiquitin ligase; nonantibody scaffolds; protein degrader; targeted protein degradation; ubiquibodies

DOI:  https://doi.org/10.1021/acssynbio.1c00357
Elife. 2021 Aug 20. pii: e69142. [Epub ahead of print]10

An engineered transcriptional reporter of protein localization identifies regulators of mitochondrial and ER membrane protein trafficking in high-throughput CRISPRi screens.

Robert W Coukos, David Yao, Mateo Lopez Sanchez, Eric T Strand, Meagan E Olive, Namrata D Udeshi, Jonathan S Weissman, Steven A Carr, Michael C Bassik, Alice Y Ting.

  The trafficking of specific protein cohorts to correct subcellular locations at correct times is essential for every signaling and regulatory process in biology. Gene perturbation screens could provide a powerful approach to probe the molecular mechanisms of protein trafficking, but only if protein localization or mislocalization can be tied to a simple and robust phenotype for cell selection, such as cell proliferation or fluorescence-activated cell sorting (FACS). To empower the study of protein trafficking processes with gene perturbation, we developed a genetically-encoded molecular tool named HiLITR. HiLITR converts protein colocalization into proteolytic release of a membrane-anchored transcription factor, which drives the expression of a chosen reporter gene. Using HiLITR in combination with FACS-based CRISPRi screening in human cell lines, we identified genes that influence the trafficking of mitochondrial and ER tail-anchored proteins. We show that loss of the SUMO E1 component SAE1 results in mislocalization and destabilization of many mitochondrial tail-anchored proteins. We also demonstrate a distinct regulatory role for EMC10 in the ER membrane complex, opposing the transmembrane-domain insertion activity of the complex. Through transcriptional integration of complex cellular functions, HiLITR expands the scope of biological processes that can be studied by genetic perturbation screening technologies.

Keywords:  biochemistry; cell biology; chemical biology; human

DOI:  https://doi.org/10.7554/eLife.69142
Biochem Pharmacol. 2021 Aug 16. pii: S0006-2952(21)00353-1. [Epub ahead of print] 114737

The unfolded protein response as regulator of cancer stemness and differentiation: mechanisms and implications for cancer therapy.

Dong Liang, Mohammad Khoonkari, Tony Avril, Eric Chevet, Frank A E Kruyt.

  The unfolded protein response (UPR) is an adaptive mechanism that regulates protein and cellular homeostasis. Three endoplasmic reticulum (ER) membrane localized stress sensors, IRE1, PERK and ATF6, coordinate the UPR in order to maintain ER proteostasis and cell survival, or induce cell death when homeostasis cannot be restored. However, recent studies have identified alternative functions for the UPR in developmental biology processes and cell fate decisions under both normal and cancerous conditions. In cancer, increasing evidence points towards the involvement of the three UPR sensors in oncogenic reprogramming and the regulation of tumor cells endowed with stem cell properties, named cancer stem cells (CSCs), that are considered to be the most malignant cells in tumors. Here we review the reported roles and underlying molecular mechanisms of the three UPR sensors in regulating stemness and differentiation, particularly in solid tumor cells, processes that have a major impact on tumor aggressiveness. Mainly PERK and IRE1 branches of the UPR were found to regulate CSCs and tumor development and examples are provided for breast cancer, colon cancer and aggressive brain tumors, glioblastoma. Although the underlying mechanisms and interactions between the different UPR branches in regulating stemness in cancer need to be further elucidated, we propose that PERK and IRE1 targeted therapy could inhibit self-renewal of CSCs or induce differentiation that is predicted to have therapeutic benefit. For this, more specific UPR modulators need to be developed with favorable pharmacological properties that together with patient stratification will allow optimal evaluation in clinical studies.

Keywords:  IRE1; PERK; cancer stem cells; therapy; tumor formation; unfolded protein response

DOI:  https://doi.org/10.1016/j.bcp.2021.114737
EMBO Rep. 2021 Aug 17. e48018

Titin kinase ubiquitination aligns autophagy receptors with mechanical signals in the sarcomere.

Julius Bogomolovas, Jennifer R Fleming, Barbara Franke, Bruno Manso, Bernd Simon, Alexander Gasch, Marija Markovic, Thomas Brunner, Ralph Knöll, Ju Chen, Siegfried Labeit, Martin Scheffner, Christine Peter, Olga Mayans.

  Striated muscle undergoes remodelling in response to mechanical and physiological stress, but little is known about the integration of such varied signals in the myofibril. The interaction of the elastic kinase region from sarcomeric titin (A168-M1) with the autophagy receptors Nbr1/p62 and MuRF E3 ubiquitin ligases is well suited to link mechanosensing with the trophic response of the myofibril. To investigate the mechanisms of signal cross-talk at this titin node, we elucidated its 3D structure, analysed its response to stretch using steered molecular dynamics simulations and explored its functional relation to MuRF1 and Nbr1/p62 using cellular assays. We found that MuRF1-mediated ubiquitination of titin kinase promotes its scaffolding of Nbr1/p62 and that the process can be dynamically down-regulated by the mechanical unfolding of a linker sequence joining titin kinase with the MuRF1 receptor site in titin. We propose that titin ubiquitination is sensitive to the mechanical state of the sarcomere, the regulation of sarcomere targeting by Nbr1/p62 being a functional outcome. We conclude that MuRF1/Titin Kinase/Nbr1/p62 constitutes a distinct assembly that predictably promotes sarcomere breakdown in inactive muscle.

Keywords:  X-ray crystallography; cellular signalling; mechanotransduction; steered molecular dynamics simulations; ubiquitination

DOI:  https://doi.org/10.15252/embr.201948018
Nat Commun. 2021 08 18. 12(1): 5016

RNF168-mediated localization of BARD1 recruits the BRCA1-PALB2 complex to DNA damage.

John J Krais, Yifan Wang, Pooja Patel, Jayati Basu, Andrea J Bernhardy, Neil Johnson.

DNA damage prompts a diverse range of alterations to the chromatin landscape. The RNF168 E3 ubiquitin ligase catalyzes the mono-ubiquitination of histone H2A at lysine (K)13/15 (mUb-H2A), forming a binding module for DNA repair proteins. BRCA1 promotes homologous recombination (HR), in part, through its interaction with PALB2, and the formation of a larger BRCA1-PALB2-BRCA2-RAD51 (BRCA1-P) complex. The mechanism by which BRCA1-P is recruited to chromatin surrounding DNA breaks is unclear. In this study, we reveal that an RNF168-governed signaling pathway is responsible for localizing the BRCA1-P complex to DNA damage. Using mice harboring a Brca1CC (coiled coil) mutation that blocks the Brca1-Palb2 interaction, we uncovered an epistatic relationship between Rnf168- and Brca1CC alleles, which disrupted development, and reduced the efficiency of Palb2-Rad51 localization. Mechanistically, we show that RNF168-generated mUb-H2A recruits BARD1 through a BRCT domain ubiquitin-dependent recruitment motif (BUDR). Subsequently, BARD1-BRCA1 accumulate PALB2-RAD51 at DNA breaks via the CC domain-mediated BRCA1-PALB2 interaction. Together, these findings establish a series of molecular interactions that connect the DNA damage signaling and HR repair machinery.

DOI: https://doi.org/10.1038/s41467-021-25346-4
Cell Signal. 2021 Aug 12. pii: S0898-6568(21)00207-2. [Epub ahead of print] 110118

UBE2D3 contributes to myocardial ischemia-reperfusion injury by regulating autophagy in dependence of p62/SQSTM1.

Xun Wang, Ping Yang, Yongliang Jiang, Yazhou Xu, Nan Wang, Peng Rao, Lin Yang, Lin Sun, Di Lu.

  The impairment of autophagic flux has been widely recognized in myocardial ischemia-reperfusion (I/R) injury, but its underlying mechanism contributing to impaired autophagic flux is poorly understood. As celluar major degradation systems, autophagy and ubiquitin proteasome(UPS) participate in the multitudinous progression of disease by interactive relationship. Especially UBE2D3, the ubiquitin-binding enzyme E2 family, is closely related to the regulation impairment of autophagic flux under I/R in our study. Therefore, this study aims to further explore the regulatory mechanism of UBE2D3 in I/R induced autophagy. We determined interference with UBE2D3 alleviated injury of myocardial cells both in vivo and in vitro. Conversely, when inhibiting proteasome function by injecting MG-132, myocardial infarct size of rats became increasingly enhanced, along with the high expression levels of LDH and CK-MB in serum, compared with myocardial I/R injury without treatment of MG-132. This had been caused by UBE2D3 promoting p62/SQSTM1(p62) ubiquitination(Ub), which lead to worsen the impairment of autophagic flux induced by myocardial I/R injury. In addition, UBE2D3 could also participate in the regulation of autophagy by negatively regulating mTOR. But more surprisingly, this mechanism was independent of the known mTOR-beclin1 pathway. These results suggested that in myocardial I/R injury, UBE2D3 promoted p62 ubiquitination to aggravate the impairment of autophagic flux. Moreover, mTOR was also involved in its regulation of autophagic flux in a way escaped from beclin1.

Keywords:  Autophagy; Myocardial ischemia-reperfusion injury; UBE2D3; Ubiquitylation; p62/SQSTM1

DOI:  https://doi.org/10.1016/j.cellsig.2021.110118
Biochem Biophys Res Commun. 2021 Aug 10. pii: S0006-291X(21)01176-1. [Epub ahead of print]573 93-99

eIF4B enhances ATF4 expression and contributes to cellular adaptation to asparagine limitation in BRAF-mutated A375 melanoma.

Yukie Iwao, Yuka Okamoto, Hitomi Shirahama, Satomi Tsukahara, Akihiro Tomida.

  ATF4 is a crucial transcription factor in the integrated stress response, a major adaptive signaling pathway activated by tumor microenvironment and therapeutic stresses. BRAF inhibitors, such as vemurafenib, induce ATF4 in BRAF-mutated melanoma cells, but the mechanisms of ATF4 induction are not fully elucidated. Here, we show that ATF4 expression can be upregulated by eukaryotic initiation factor 4B (eIF4B) in BRAF-mutated A375 cells. Indeed, eIF4B knockout (KO) prevented ATF4 induction and activation of the uORF-mediated ATF4 translation mechanism during vemurafenib treatment, which were effectively recovered by the rescue of eIF4B. Transcriptome analysis revealed that eIF4B KO selectively influenced ATF4-target gene expression among the overall gene expression changed by vemurafenib. Interestingly, eIF4B supported cellular proliferation under asparagine-limited conditions, possibly through the eIF4B-ATF4 pathway. Our findings indicate that eIF4B can regulate ATF4 expression, thereby contributing to cellular stress adaptation, which could be targeted as a therapeutic approach against malignancies, including melanoma.

Keywords:  ATF4; Asparagine limitation; BRAF mutation; Melanoma; eIF4B; vemurafenib

DOI:  https://doi.org/10.1016/j.bbrc.2021.08.022
Nat Commun. 2021 08 17. 12(1): 4980

Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery.

Wei Qin, Samuel A Myers, Dominique K Carey, Steven A Carr, Alice Y Ting.

Proximity labeling (PL) with genetically-targeted promiscuous enzymes has emerged as a powerful tool for unbiased proteome discovery. By combining the spatiotemporal specificity of PL with methods for functional protein enrichment, we show that it is possible to map specific protein subclasses within distinct compartments of living cells. In particular, we develop a method to enrich subcompartment-specific RNA binding proteins (RBPs) by combining peroxidase-catalyzed PL with organic-aqueous phase separation of crosslinked protein-RNA complexes ("APEX-PS"). We use APEX-PS to generate datasets of nuclear, nucleolar, and outer mitochondrial membrane (OMM) RBPs, which can be mined for novel functions. For example, we find that the OMM RBP SYNJ2BP retains specific nuclear-encoded mitochondrial mRNAs at the OMM during translation stress, facilitating their local translation and import of protein products into the mitochondrion during stress recovery. Functional PL in general, and APEX-PS in particular, represent versatile approaches for the discovery of proteins with novel function in specific subcellular compartments.

DOI: https://doi.org/10.1038/s41467-021-25259-2
Nature. 2021 Aug 18.

DAXX represents a new type of protein-folding enabler.

Liangqian Huang, Trisha Agrawal, Guixin Zhu, Sixiang Yu, Liming Tao, JiaBei Lin, Ronen Marmorstein, James Shorter, Xiaolu Yang.

Protein quality control systems are crucial for cellular function and organismal health. At present, most known protein quality control systems are multicomponent machineries that operate via ATP-regulated interactions with non-native proteins to prevent aggregation and promote folding1, and few systems that can broadly enable protein folding by a different mechanism have been identified. Moreover, proteins that contain the extensively charged poly-Asp/Glu (polyD/E) region are common in eukaryotic proteomes2, but their biochemical activities remain undefined. Here we show that DAXX, a polyD/E protein that has been implicated in diverse cellular processes3-10, possesses several protein-folding activities. DAXX prevents aggregation, solubilizes pre-existing aggregates and unfolds misfolded species of model substrates and neurodegeneration-associated proteins. Notably, DAXX effectively prevents and reverses aggregation of its in vivo-validated client proteins, the tumour suppressor p53 and its principal antagonist MDM2. DAXX can also restore native conformation and function to tumour-associated, aggregation-prone p53 mutants, reducing their oncogenic properties. These DAXX activities are ATP-independent and instead rely on the polyD/E region. Other polyD/E proteins, including ANP32A and SET, can also function as stand-alone, ATP-independent molecular chaperones, disaggregases and unfoldases. Thus, polyD/E proteins probably constitute a multifunctional protein quality control system that operates via a distinctive mechanism.

DOI: https://doi.org/10.1038/s41586-021-03824-5
Clin Cancer Res. 2021 Aug 16. pii: clincanres.1140.2021. [Epub ahead of print]

Circulating Protein Disulfide Isomerase is associated with increased risk of Thrombosis in JAK2-mutated Myeloproliferative Neoplasms.

Anish V Sharda, Thomas Bogue, Alexandra Barr, Lourdes Mendez, Robert Flaumenhaft, Jeffrey I Zwicker.

PURPOSE: Thromboembolic events (TE) are the most common complications of myeloproliferative neoplasms (MPN). Clinical parameters including patient age and mutation-status are used to risk-stratify patients with MPN, but a true biomarker of TE risk is lacking. Protein disulfide isomerase (PDI), an endoplasmic reticulum protein vital for protein folding, also possesses essential extracellular functions, including regulation of thrombus formation. Pharmacologic PDI inhibition prevents thrombus formation, but whether pathologic increases in PDI increase TE risk remains unknown.EXPERIMENTAL DESIGN: We evaluated the association of plasma PDI levels and risk of TE in a cohort of patients with MPN with established diagnosis of polycythemia vera (PV) or essential thrombocythemia (ET), compared to healthy controls. Plasma PDI was measured at enrollment and subjects followed prospectively for development of TE.
RESULTS: A subset of patients, primarily JAK2-mutated MPN, had significantly elevated plasma PDI levels as compared to controls. Plasma PDI was functionally active. There was no association between PDI levels and clinical parameters typically used to risk-stratify patients with MPN. The risk of TE was 8-fold greater in those with PDI levels above 2.5 ng/ml. Circulating endothelial cells from JAK2-mutated MPN patients, but not platelets, demonstrated augmented PDI release, suggesting endothelial activation as a source of increased plasma PDI in MPN.
CONCLUSIONS: The observed association between plasma PDI levels and increased risk of TE in patients with JAK2-mutated MPN has both prognostic and therapeutic implications.

DOI: https://doi.org/10.1158/1078-0432.CCR-21-1140
J Cell Sci. 2021 Aug 16. pii: jcs.258783. [Epub ahead of print]

ADAR1 limits stress granule formation through both translation-dependent and translation-independent mechanisms.

Giulia A Corbet, James M Burke, Roy Parker.

  Stress granules (SGs) are cytoplasmic assemblies of RNA and protein that form when translation is repressed during the integrated stress response (ISR). SGs assemble from the combination of RNA-RNA, RNA-protein, and protein-protein interactions between mRNPs. The protein Adenosine deaminase acting on RNA 1 (ADAR1) recognizes and modifies dsRNAs within cells to prevent an aberrant innate immune response. ADAR1 localizes to SGs, and since RNA-RNA interactions contribute to SG assembly and dsRNA induces SGs, we examined how ADAR1 affects SG formation. First, we demonstrate that ADAR1 depletion triggers SGs by allowing endogenous dsRNA to activate the ISR through PKR activation and translation repression. However, we also show that ADAR1 limits SG formation independently of translation inhibition. ADAR1 repression of SGs is independent of deaminase activity, but dependent on dsRNA-binding activity, suggesting a model where ADAR1 binding limits RNA-RNA and/or RNA-protein interactions necessary for recruitment to SGs. Given that ADAR1 expression is induced during viral infection, these findings have implications for ADAR1's role in the antiviral response.

Keywords:  ADAR1; Stress granules

DOI:  https://doi.org/10.1242/jcs.258783
Nature. 2021 Aug 18.

Cotranslational prolyl hydroxylation is essential for flavivirus biogenesis.

Ranen Aviner, Kathy H Li, Judith Frydman, Raul Andino.

Viral pathogens are an ongoing threat to public health worldwide. Analysing their dependence on host biosynthetic pathways could lead to effective antiviral therapies1. Here we integrate proteomic analyses of polysomes with functional genomics and pharmacological interventions to define how enteroviruses and flaviviruses remodel host polysomes to synthesize viral proteins and disable host protein production. We find that infection with polio, dengue or Zika virus markedly modifies polysome composition, without major changes to core ribosome stoichiometry. These viruses use different strategies to evict a common set of translation initiation and RNA surveillance factors from polysomes while recruiting host machineries that are specifically required for viral biogenesis. Targeting these specialized viral polysomes could provide a new approach for antiviral interventions. For example, we find that both Zika and dengue use the collagen proline hydroxylation machinery to mediate cotranslational modification of conserved proline residues in the viral polyprotein. Genetic or pharmacological inhibition of proline hydroxylation impairs nascent viral polyprotein folding and induces its aggregation and degradation. Notably, such interventions prevent viral polysome remodelling and lower virus production. Our findings delineate the modular nature of polysome specialization at the virus-host interface and establish a powerful strategy to identify targets for selective antiviral interventions.

DOI: https://doi.org/10.1038/s41586-021-03851-2
J Biol Chem. 2021 Aug 17. pii: S0021-9258(21)00891-7. [Epub ahead of print] 101088

The deubiquitinase USP10 restores PTEN activity and inhibits non-small cell lung cancer cell proliferation.

Yuanming He, Shuoyi Jiang, Chenyu Mao, Hui Zheng, Biyin Cao, Zubin Zhang, Jun Zhao, Yuanying Zeng, Xinliang Mao.

  The phosphatase and tensin homolog deleted on chromosome ten (PTEN) protein is a key player in tumorigenesis of non-small cell lung cancer, and was recently found to be inactivated by TRIM25-mediated K63-linked polyubiquitination. However, the deubiquitinase coordinates TRIM25 in PTEN ubiquitination is still elusive. In the present study, we found that this K63-linked polyubiquitination could be ablated by the ubiquitin-specific protease 10 (USP10) in a screen against a panel of deubiquitinases. We found using co-immununoprecipitation/immunoblotting that USP10 interacted with PTEN and reduced the K63-linked polyubiquitination of PTEN mediated by TRIM25 in non-small cell lung cancer (NSCLC) cells. Moreover, USP10, but not its inactive C424A deubiquitinating mutant or other deubiquitinases, abolished PTEN from K63-linked polyubiquitination mediated by TRIM25. In contrast to TRIM25, USP10 restored PTEN phosphatase activity and reduced the production of the secondary messenger PI(3,4,5)P3, thereby inhibiting AKT/mTOR pro-growth signaling transduction in NSCLC cells. Moreover, USP10 was downregulated in NSCLC cell lines and primary tissues, whereas TRIM25 was upregulated. Consistent with its molecular activity, re-expression of USP10 suppressed NSCLC cell proliferation and migration while knockout of USP10 promoted NSCLC cell proliferation and migration. In conclusion, the present study demonstrates that USP10 coordinates TRIM25 to modulate PTEN activity. Specifically, USP10 activates PTEN by preventing its K63-linked polyubiquitination mediated by TRIM25 and suppresses the AKT/mTOR signaling pathway thereby inhibiting NSCLC proliferation, indicating that it may be a potential drug target for cancer treatment.

Keywords:  K63-linked polyubiquitination; NSCLC; PTEN; USP10; deubiquitinase

DOI:  https://doi.org/10.1016/j.jbc.2021.101088
J Biol Chem. 2021 Aug 14. pii: S0021-9258(21)00885-1. [Epub ahead of print] 101082

Interdomain interactions dictate the function of the C. albicans Hsp110 protein Msi3.

Hongtao Li, Liqing Hu, Crist Cuffee, Mahetab Mohamed, Qianbin Li, Qingdai Liu, Lei Zhou, Qinglian Liu.

  Heat Shock Proteins of 110 kDa (Hsp110s), a unique class of molecular chaperones, are essential for maintaining protein homeostasis. Hsp110s exhibit a strong chaperone activity preventing protein aggregation (the "holdase" activity) and also function as the major nucleotide-exchange factor (NEF) for Hsp70 chaperones. Hsp110s contain two functional domains: a nucleotide-binding domain (NBD) and substrate-binding domain (SBD). ATP binding is essential for Hsp110 function and results in close contacts between the NBD and SBD. However, the molecular mechanism of this ATP-induced allosteric coupling remains poorly defined. In this study, we carried out biochemical analysis on Msi3, the sole Hsp110 in Candida albicans, to dissect the unique allosteric coupling of Hsp110s using three mutations affecting the domain-domain interface. All the mutations abolished both the in vivo and in vitro functions of Msi3. While the ATP-bound state was disrupted in all mutants, only mutation of the NBD-SBDβ interfaces showed significant ATPase activity, suggesting that the full-length Hsp110s have an ATPase that is mainly suppressed by NBD-SBDβ contacts. Moreover, the high-affinity ATP binding unexpectedly appears to require these NBD-SBD contacts. Remarkably, the "holdase" activity was largely intact for all mutants tested while NEF activity was mostly compromised, although both activities strictly depended on the ATP-bound state, indicating different requirements for these two activities. Stable peptide substrate binding to Msi3 led to dissociation of the NBD-SBD contacts and compromised interactions with Hsp70. Taken together, our data demonstrate that the exceptionally strong NBD-SBD contacts in Hsp110s dictate the unique allosteric coupling and biochemical activities.

Keywords:  ATPase; Hsp110; Hsp70; allosteric regulation; heat shock protein (HSP); molecular chaperone; peptides; protein folding; proteostasis

DOI:  https://doi.org/10.1016/j.jbc.2021.101082
Life Sci Alliance. 2021 Oct;pii: e202101152. [Epub ahead of print]4(10):

The structure and flexibility analysis of the Arabidopsis synaptotagmin 1 reveal the basis of its regulation at membrane contact sites.

Juan L Benavente, Dritan Siliqi, Lourdes Infantes, Laura Lagartera, Alberto Mills, Federico Gago, Noemí Ruiz-López, Miguel A Botella, María J Sánchez-Barrena, Armando Albert.

Non-vesicular lipid transfer at ER and plasma membrane (PM) contact sites (CS) is crucial for the maintenance of membrane lipid homeostasis. Extended synaptotagmins (E-Syts) play a central role in this process as they act as molecular tethers of ER and PM and as lipid transfer proteins between these organelles. E-Syts are proteins constitutively anchored to the ER through an N-terminal hydrophobic segment and bind the PM via a variable number of C-terminal C2 domains. Synaptotagmins (SYTs) are the plant orthologous of E-Syts and regulate the ER-PM communication in response to abiotic stress. Combining different structural and biochemical techniques, we demonstrate that the binding of SYT1 to lipids occurs through a Ca2+-dependent lipid-binding site and by a site for phosphorylated forms of phosphatidylinositol, thus integrating two different molecular signals in response to stress. In addition, we show that SYT1 displays three highly flexible hinge points that provide conformational freedom to facilitate lipid extraction, protein loading, and subsequent transfer between PM and ER.

DOI: https://doi.org/10.26508/lsa.202101152
Nat Commun. 2021 08 19. 12(1): 5040

Sumoylation regulates the assembly and activity of the SMN complex.

Giulietta M Riboldi, Irene Faravelli, Takaaki Kuwajima, Nicolas Delestrée, Georgia Dermentzaki, Mariangels De Planell-Saguer, Paola Rinchetti, Le Thi Hao, Christine C Beattie, Stefania Corti, Serge Przedborski, George Z Mentis, Francesco Lotti.

SMN is a ubiquitously expressed protein and is essential for life. SMN deficiency causes the neurodegenerative disease spinal muscular atrophy (SMA), the leading genetic cause of infant mortality. SMN interacts with itself and other proteins to form a complex that functions in the assembly of ribonucleoproteins. SMN is modified by SUMO (Small Ubiquitin-like Modifier), but whether sumoylation is required for the functions of SMN that are relevant to SMA pathogenesis is not known. Here, we show that inactivation of a SUMO-interacting motif (SIM) alters SMN sub-cellular distribution, the integrity of its complex, and its function in small nuclear ribonucleoproteins biogenesis. Expression of a SIM-inactivated mutant of SMN in a mouse model of SMA slightly extends survival rate with limited and transient correction of motor deficits. Remarkably, although SIM-inactivated SMN attenuates motor neuron loss and improves neuromuscular junction synapses, it fails to prevent the loss of sensory-motor synapses. These findings suggest that sumoylation is important for proper assembly and function of the SMN complex and that loss of this post-translational modification impairs the ability of SMN to correct selective deficits in the sensory-motor circuit of SMA mice.

DOI: https://doi.org/10.1038/s41467-021-25272-5
Cell Mol Gastroenterol Hepatol. 2021 Aug 17. pii: S2352-345X(21)00170-3. [Epub ahead of print]

UBCH5 family members differentially impact stabilization of mutant p53 via RNF128 Iso1 during Barrett's progression to esophageal adenocarcinoma.

Paramita Ray, Derek J Nancarrow, Daysha Ferrer-Torres, Zhuwen Wang, May San Martinho, Tonaye Hinton, Joshua H Wu, Angeline Wu, Danielle Kim Turgeon, Max A Hammer, Michael K Dame, Theodore S Lawrence, Patrick J O'Brien, Jason R Spence, David G Beer, Dipankar Ray.

  BACKGROUND & AIMS: TP53 mutations underlie Barrett's (BE) progression to dysplasia and cancer. During BE progression, the ubiquitin ligase (E3) RNF128/GRAIL switches expression from isoform 2 (Iso2) to Iso1 stabilizing mutant p53. However, the ubiquitin conjugating enzyme (E2) that partners with Iso1 to stabilize mutant p53 is unknown.METHODS: Single-cell RNA sequencing of paired normal esophagus and BE tissues identified candidate E2s, further investigated in expression data from BE to esophageal adenocarcinoma (EAC) progression samples. Biochemical and cellular studies helped clarify RNF128-E2 role on mutant p53 stability.
RESULTS: The UBE2D family member 2D3 (UBCH5C) is the most abundant E2 in normal esophagus. However, during BE to EAC progression, loss of UBE2D3 copy number and reduced expression of RNF128 Iso2 were noted, two known p53 degraders. In contrast, expression of UBE2D1 (UBCH5A) and RNF128 Iso1 in dysplastic BE and EAC forms an inactive E2-E3 complex, stabilizing mutant p53. To destabilize mutant p53, we targeted RNF128 Iso1 either by mutating asparagine (N48, 59 and 101) residues to block glycosylation to facilitate β-TrCP1-mediated degradation or by mutating proline (P54 and 105) residues to restore p53 polyubiquitinating ability. Additionally, either loss of UBCH5A catalytic activity, or disruption of the Iso1-UBCH5A interaction promoted Iso1 loss. Consequently, overexpression of either catalytically-dead, or Iso1-binding deficient UBCH5A mutants destabilized Iso1 to degrade mutant p53, thus compromising the clonogenic survival of mutant p53-dependent BE cells.
CONCLUSION: Loss of RNF128 Iso2-UBCH5C and persistence of the Iso1-UBCH5A complex favors mutant p53 stability to promote BE cells survival. Therefore, targeting of Iso1-UBCH5A may provide a novel therapeutic strategy to prevent BE progression.

Keywords:  Barrett’s esophagus; RNF128-UBCH5 complex; esophageal adenocarcinoma; p53 protein stability

DOI:  https://doi.org/10.1016/j.jcmgh.2021.08.003
iScience. 2021 Aug 20. 24(8): 102878

CHIP-dependent regulation of the actin cytoskeleton is linked to neuronal cell membrane integrity.

Catarina Dias, Erisa Nita, Jakub Faktor, Ailish C Tynan, Lenka Hernychova, Borivoj Vojtesek, Jesper Nylandsted, Ted R Hupp, Tilo Kunath, Kathryn L Ball.

  CHIP is an E3-ubiquitin ligase that contributes to healthy aging and has been characterized as neuroprotective. To elucidate dominant CHIP-dependent changes in protein steady-state levels in a patient-derived human neuronal model, CHIP function was ablated using gene-editing and an unbiased proteomic analysis conducted to compare knock-out and wild-type isogenic induced pluripotent stem cell (iPSC)-derived cortical neurons. Rather than a broad effect on protein homeostasis, loss of CHIP function impacted on a focused cohort of proteins from actin cytoskeleton signaling and membrane integrity networks. In support of the proteomics, CHIP knockout cells had enhanced sensitivity to induced membrane damage. We conclude that the major readout of CHIP function in cortical neurons derived from iPSC of a patient with elevate α-synuclein, Parkinson's disease and dementia, is the modulation of substrates involved in maintaining cellular "health". Thus, regulation of the actin cytoskeletal and membrane integrity likely contributes to the neuroprotective function(s) of CHIP.

Keywords:  bioinformatics; cell biology; omics; organizational aspects of cell biology; proteomics

DOI:  https://doi.org/10.1016/j.isci.2021.102878
Plant Signal Behav. 2021 Aug 18. 1964847

UBC19 is a new interacting protein of ORANGE for its nuclear localization in Arabidopsis thaliana.

Wei-Cai Chen, Qi Wang, Tian-Jun Cao, Shan Lu.

  ORANGE (OR) is a member of the DnaJ-like zinc finger domain-containing protein family, of which all orthologs share a highly conserved quadruple repeat of the CxxCxxxG signatures at their C-termini. Dual subcellular localization and different interacting partner proteins have been reported for OR. In plastids, OR interacts with phytoene synthase, the entry enzyme for carotenoid biosynthesis, to promote chromoplast biogenesis and carotenoid accumulation in non-pigmented tissues. In the nucleus, OR interacts with the eukaryotic release factor eRF1-2 to regulate cell elongation in the petiole, and with the transcription factor TCP14 to repress the expression of Early Light-Induced Proteins (ELIPs) and chloroplast biogenesis in de-etiolating cotyledons. In this study, we demonstrated the E2 ubiquitin-conjugating enzyme UBC19 as a new interacting partner of OR. The lysine58 of OR was found to be ubiquitinated, and OR lost its nuclear localization and the capability in repressing ELIPs when lysine58 was substituted by alanine. Our findings raised the possibility that the ubiquitination by UBC19 is essential for the nuclear localization of OR.

Keywords:  De-etiolation; ORANGE; UBC19; nucleus; protein-protein interaction

DOI:  https://doi.org/10.1080/15592324.2021.1964847
Thorax. 2021 Aug 16. pii: thoraxjnl-2021-216882. [Epub ahead of print]

Inhibition of PDIA3 in club cells attenuates osteopontin production and lung fibrosis.

Amit Kumar, Evan Elko, Sierra R Bruno, Zoe F Mark, Nicolas Chamberlain, Bethany Korwin Mihavics, Ravishankar Chandrasekaran, Joseph Walzer, Mona Ruban, Clarissa Gold, Ying Wai Lam, Sudhir Ghandikota, Anil G Jegga, Jose L Gomez, Yvonne Mw Janssen-Heininger, Vikas Anathy.

  BACKGROUND: The role of club cells in the pathology of idiopathic pulmonary fibrosis (IPF) is not well understood. Protein disulfide isomerase A3 (PDIA3), an endoplasmic reticulum-based redox chaperone required for the functions of various fibrosis-related proteins; however, the mechanisms of action of PDIA3 in pulmonary fibrosis are not fully elucidated.OBJECTIVES: To examine the role of club cells and PDIA3 in the pathology of pulmonary fibrosis and the therapeutic potential of inhibition of PDIA3 in lung fibrosis.
METHODS: Role of PDIA3 and aberrant club cells in lung fibrosis was studied by analyses of human transcriptome dataset from Lung Genomics Research Consortium, other public resources, the specific deletion or inhibition of PDIA3 in club cells and blocking SPP1 downstream of PDIA3 in mice.
RESULTS: PDIA3 and club cell secretory protein (SCGB1A1) signatures are upregulated in IPF compared with control patients. PDIA3 or SCGB1A1 increases also correlate with a decrease in lung function in patients with IPF. The bleomycin (BLM) model of lung fibrosis showed increases in PDIA3 in SCGB1A1 cells in the lung parenchyma. Ablation of Pdia3, specifically in SCGB1A1 cells, decreases parenchymal SCGB1A1 cells along with fibrosis in mice. The administration of a PDI inhibitor LOC14 reversed the BLM-induced parenchymal SCGB1A1 cells and fibrosis in mice. Evaluation of PDIA3 partners revealed that SPP1 is a major interactor in fibrosis. Blocking SPP1 attenuated the development of lung fibrosis in mice.
CONCLUSIONS: Our study reveals a new relationship with distally localised club cells, PDIA3 and SPP1 in lung fibrosis and inhibition of PDIA3 or SPP1 attenuates lung fibrosis.

Keywords:  idiopathic pulmonary fibrosis; interstitial fibrosis

DOI:  https://doi.org/10.1136/thoraxjnl-2021-216882
Stem Cell Res. 2021 Aug 11. pii: S1873-5061(21)00346-9. [Epub ahead of print]55 102499

Translation initiation factor eIF2Bε promotes Wnt-mediated clonogenicity and global translation in intestinal epithelial cells.

W L Smit, R J de Boer, B J Meijer, C N Spaan, M van Roest, P J Koelink, J Koster, E Dekker, T E M Abbink, M S van der Knaap, G R van den Brink, V Muncan, J Heijmans.

  Modulation of global mRNA translation, which is essential for intestinal stem cell function, is controlled by Wnt signaling. Loss of tumor supressor APC in stem cells drives adenoma formation through hyperactivion of Wnt signaling and dysregulated translational control. It is unclear whether factors that coordinate global translation in the intestinal epithelium are needed for APC-driven malignant transformation. Here we identified nucleotide exchange factor eIF2Bε as a translation initiation factor involved in Wnt-mediated intestinal epithelial stemness. Using eIF2BεArg191His mice with a homozygous point mutation that leads to dysfunction in the enzymatic activity, we demonstrate that eIF2Bε is involved in small intestinal crypt formation, stemness marker expression, and secreted Paneth cell-derived granule formation. Wnt hyperactivation in ex vivo eIF2BεArg191His organoids, using a GSK3β inhibitor to mimic Apc driven transformation, shows that eIF2Bε is essential for Wnt-mediated clonogenicity and associated increase of the global translational capacity. Finally, we observe high eIF2Bε expression in human colonic adenoma tissues, exposing eIF2Bε as a potential target of CRC stem cells with aberrant Wnt signaling.

Keywords:  APC; Global mRNA translation; Intestinal stemness; Wnt signaling; eIF2B epsilon

DOI:  https://doi.org/10.1016/j.scr.2021.102499
ACS Med Chem Lett. 2021 Aug 12. 12(8): 1302-1307

Exploring Ligand-Directed N-Acyl-N-alkylsulfonamide-Based Acylation Chemistry for Potential Targeted Degrader Development.

Mingxing Teng, Jie Jiang, Scott B Ficarro, Hyuk-Soo Seo, Jae Hyun Bae, Katherine A Donovan, Eric S Fischer, Tinghu Zhang, Sirano Dhe-Paganon, Jarrod A Marto, Nathanael S Gray.

Ligand-directed bioconjugation strategies have been used for selective protein labeling in live cells or tissue samples in applications such as live-cell imaging. Here we hypothesized that a similar strategy could be used for targeted protein degradation. To test this possibility, we developed a series of CDK2-targeting N-acyl-N-alkylsulfonamide (NASA)-containing acylation probes. The probes featured three components: a CDK2 homing ligand, a CRL4CRBN E3 ligase recruiting ligand, and a NASA functionality. We determined that upon target binding, NASA-mediated reaction resulted in selective functionalization of Lys89 on purified or native CDK2. However, we were unable to observe CDK2 degradation, which is in contrast to the efficient degradation achieved by the use of a structurally similar reversible bivalent degrader. Our analysis suggests that the lack of degradation is due to the failure to form a productive CDK2:CRBN complex. Therefore, although this work demonstrates that NASA chemistry can be used for protein labeling, whether this strategy could enable efficient protein degradation remains an open question.

DOI: https://doi.org/10.1021/acsmedchemlett.1c00285
Nat Chem Biol. 2021 Aug 19.

Bifunctional small molecules that mediate the degradation of extracellular proteins.

David F Caianiello, Mengwen Zhang, Jason D Ray, Rebecca A Howell, Jake C Swartzel, Emily M J Branham, Egor Chirkin, Venkata R Sabbasani, Angela Z Gong, David M McDonald, Viswanathan Muthusamy, David A Spiegel.

Targeted protein degradation (TPD) has emerged as a promising therapeutic strategy. Most TPD technologies use the ubiquitin-proteasome system, and are therefore limited to targeting intracellular proteins. To address this limitation, we developed a class of modular, bifunctional synthetic molecules called MoDE-As (molecular degraders of extracellular proteins through the asialoglycoprotein receptor (ASGPR)), which mediate the degradation of extracellular proteins. MoDE-A molecules mediate the formation of a ternary complex between a target protein and ASGPR on hepatocytes. The target protein is then endocytosed and degraded by lysosomal proteases. We demonstrated the modularity of the MoDE-A technology by synthesizing molecules that induce depletion of both antibody and proinflammatory cytokine proteins. These data show experimental evidence that nonproteinogenic, synthetic molecules can enable TPD of extracellular proteins in vitro and in vivo. We believe that TPD mediated by the MoDE-A technology will have widespread applications for disease treatment.

DOI: https://doi.org/10.1038/s41589-021-00851-1
Nucleic Acids Res. 2021 Aug 17. pii: gkab730. [Epub ahead of print]

Charcot-Marie-Tooth mutation in glycyl-tRNA synthetase stalls ribosomes in a pre-accommodation state and activates integrated stress response.

Samantha Mendonsa, Nicolai von Kuegelgen, Lucija Bujanic, Marina Chekulaeva.

Toxic gain-of-function mutations in aminoacyl-tRNA synthetases cause a degeneration of peripheral motor and sensory axons, known as Charcot-Marie-Tooth (CMT) disease. While these mutations do not disrupt overall aminoacylation activity, they interfere with translation via an unknown mechanism. Here, we dissect the mechanism of function of CMT mutant glycyl-tRNA synthetase (CMT-GARS), using high-resolution ribosome profiling and reporter assays. We find that CMT-GARS mutants deplete the pool of glycyl-tRNAGly available for translation and inhibit the first stage of elongation, the accommodation of glycyl-tRNA into the ribosomal A-site, which causes ribosomes to pause at glycine codons. Moreover, ribosome pausing activates a secondary repression mechanism at the level of translation initiation, by inducing the phosphorylation of the alpha subunit of eIF2 and the integrated stress response. Thus, CMT-GARS mutant triggers translational repression via two interconnected mechanisms, affecting both elongation and initiation of translation.

DOI: https://doi.org/10.1093/nar/gkab730
Nat Commun. 2021 08 18. 12(1): 5010

PARylation prevents the proteasomal degradation of topoisomerase I DNA-protein crosslinks and induces their deubiquitylation.

Yilun Sun, Jiji Chen, Shar-Yin N Huang, Yijun P Su, Wenjie Wang, Keli Agama, Sourav Saha, Lisa M Jenkins, John M Pascal, Yves Pommier.

Poly(ADP)-ribosylation (PARylation) regulates chromatin structure and recruits DNA repair proteins. Using single-molecule fluorescence microscopy to track topoisomerase I (TOP1) in live cells, we found that sustained PARylation blocked the repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) in a similar fashion as inhibition of the ubiquitin-proteasome system (UPS). PARylation of TOP1-DPC was readily revealed by inhibiting poly(ADP-ribose) glycohydrolase (PARG), indicating the otherwise transient and reversible PARylation of the DPCs. As the UPS is a key repair mechanism for TOP1-DPCs, we investigated the impact of TOP1-DPC PARylation on the proteasome and found that the proteasome is unable to associate with and digest PARylated TOP1-DPCs. In addition, PARylation recruits the deubiquitylating enzyme USP7 to reverse the ubiquitylation of PARylated TOP1-DPCs. Our work identifies PARG as repair factor for TOP1-DPCs by enabling the proteasomal digestion of TOP1-DPCs. It also suggests the potential regulatory role of PARylation for the repair of a broad range of DPCs.

DOI: https://doi.org/10.1038/s41467-021-25252-9
J Biol Chem. 2021 Aug 12. pii: S0021-9258(21)00878-4. [Epub ahead of print] 101075

The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation.

Saikat Bhattacharya, Jeffrey J Lange, Michaella Levy, Laurence Florens, Michael P Washburn, Jerry L Workman.

  SETD2 is an important methyltransferase that methylates substrates crucial substrates such as histone H3, tubulin, and STAT1, and also physically interacts with transcription and splicing regulators such as Pol II and various hnRNPs. Notably, SETD2 has a functionally uncharacterized extended N-terminal region, the removal of which leads to its stabilization. How this region regulates SETD2 half-life is unclear. Here we show that SETD2 consists of multiple long disordered regions across its length which cumulatively destabilize the protein by facilitating its proteasomal degradation. SETD2 disordered regions can reduce the half-life of the yeast homolog Set2 in mammalian cells as well as in yeast, demonstrating the importance of intrinsic structural features in regulating protein half-life. In addition to the shortened half-life, by performing fluorescence recovery after photobleaching (FRAP) assay we found that SETD2 forms liquid droplets in vivo, another property associated with proteins that contain disordered regions. The phase-separation behavior of SETD2 is exacerbated upon the removal of its N-terminal segment and results in activator-independent histone H3K36 methylation. Our findings reveal that disordered region-facilitated proteolysis is an important mechanism governing SETD2 function.

Keywords:  chromatin; histone; intrinsically disordered protein; proteasome; protein degradation

DOI:  https://doi.org/10.1016/j.jbc.2021.101075