bims-proteo 2021-01-10 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2021‒01‒10
thirty-nine papers selected by
Eric Chevet
INSERM

The eIF2α kinase HRI triggers the autophagic clearance of cytosolic protein aggregates.
NUPR1 interacts with eIF2a and is required for resolution of the ER-stress response in pancreatic tissue.
Endoplasmic reticulum stress: a key regulator of the follicular microenvironment in the ovary.
Downregulation of miR-17-92 Cluster by PERK Fine-Tunes Unfolded Protein Response Mediated Apoptosis.
Plasma membrane aquaporins interact with the endoplasmic reticulum resident VAP27 proteins at ER-PM contact sites and endocytic structures.
The protein kinase Ire1 impacts pathogenicity of Candida albicans by regulating homeostatic adaptation to endoplasmic reticulum stress.
Molecular basis for ubiquitin ligase CRL2FEM1C-mediated recognition of C-degron.
p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response.
Build-UPS and break-downs: metabolism impacts on proteostasis and aging.
Membrane Protein Quality Control Mechanisms in the Endo-Lysosome System.
MOAP-1-mediated dissociation of p62/SQSTM1 bodies releases Keap1 and suppresses Nrf2 signaling.
FNDC-1-Mediated Mitophagy and ATFS-1 Coordinate to Protect Against Hypoxia-Reoxygenation.
Caspase-8 Inhibition Prevents the Cleavage and Degradation of E3 Ligase Substrate Receptor Cereblon and Potentiates Its Biological Function.
MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor-1.
Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.
TRK-Fused Gene (TFG), a protein involved in protein secretion pathways, is an essential component of the antiviral innate immune response.
HSF-1 displays nuclear stress body formation in multiple tissues in Caenorhabditis elegans upon stress and following the transition to adulthood.
Targeted degradation of the enhancer lysine acetyltransferases CBP and p300.
E3 Ubiquitin Ligases: Key Regulators of TGFβ Signaling in Cancer Progression.
Ubiquitin signalling in neurodegeneration: mechanisms and therapeutic opportunities.
Molecular basis for arginine C-terminal degron recognition by Cul2FEM1 E3 ligase.
Adaptors as the regulators of HECT ubiquitin ligases.
Development of Antibody-Based PROTACs for the Degradation of the Cell-Surface Immune Checkpoint Protein PD-L1.
Nuclear Ubiquitin-Proteasome Pathways in Proteostasis Maintenance.
Homeostatic regulation of STING by retrograde membrane traffic to the ER.
Negative regulation of AMPK signaling by high glucose via E3 ubiquitin ligase MG53.
Mammalian Deubiquitinating Enzyme Inhibitors Display in Vitro and in Vivo Activity against Malaria Parasites and Potentiate Artemisinin Action.
Effects of ER-resident and secreted AGR2 on cell proliferation, migration, invasion, and survival in PANC-1 pancreatic cancer cells.
Selective autophagy of intracellular organelles: recent research advances.
FAT10 protects against ischemia-induced ventricular arrhythmia by decreasing Nedd4-2/Nav1.5 complex formation.
Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity.
Beyond K48 and K63: non-canonical protein ubiquitination.
Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62.
Inhibition of the proteasome and proteaphagy enhances apoptosis in FLT3-ITD-driven acute myeloid leukemia.
Cdc48/Shp1 participates in dissociation of protein complexes to regulate their activity.
Targeting USP47 overcomes tyrosine kinase inhibitor resistance and eradicates leukemia stem/progenitor cells in chronic myelogenous leukemia.
Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes.
Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative.
Studying OTUD6B-OTUB1 Protein-Protein Interaction by Low-Throughput GFP-Trap Assays and High-Throughput AlphaScreen Assays.

J Biol Chem. 2020 Dec 02. pii: S0021-9258(20)00036-8. [Epub ahead of print]296 100050

The eIF2α kinase HRI triggers the autophagic clearance of cytosolic protein aggregates.

Tapas Mukherjee, Valeria Ramaglia, Mena Abdel-Nour, Athanasia A Bianchi, Jessica Tsalikis, Hien N Chau, Suneil K Kalia, Lorraine V Kalia, Jane-Jane Chen, Damien Arnoult, Jennifer L Gommerman, Dana J Philpott, Stephen E Girardin.

  Large cytosolic protein aggregates are removed by two main cellular processes, autophagy and the ubiquitin-proteasome system, and defective clearance of these protein aggregates results in proteotoxicity and cell death. Recently, we found that the eIF2α kinase heme-regulated inhibitory (HRI) induced a cytosolic unfolded protein response to prevent aggregation of innate immune signalosomes, but whether HRI acts as a general sensor of proteotoxicity in the cytosol remains unclear. Here we show that HRI controls autophagy to clear cytosolic protein aggregates when the ubiquitin-proteasome system is inhibited. We further report that silencing the expression of HRI resulted in decreased levels of BAG3 and HSPB8, two proteins involved in chaperone-assisted selective autophagy, suggesting that HRI may control proteostasis in the cytosol at least in part through chaperone-assisted selective autophagy. Moreover, knocking down the expression of HRI resulted in cytotoxic accumulation of overexpressed α-synuclein, a protein known to aggregate in Parkinson's disease, dementia with Lewy bodies, and multiple system atrophy. In agreement with these data, protein aggregate accumulation and microglia activation were observed in the spinal cord white matter of 7-month-old Hri-/- mice as compared with Hri+/+ littermates. Moreover, aged Hri-/- mice showed accumulation of misfolded α-synuclein in the lateral collateral pathway, a region of the sacral spinal cord horn that receives visceral sensory afferents from the bladder and distal colon, a pathological feature common to α-synucleinopathies in humans. Together, these results suggest that HRI contributes to a general cytosolic unfolded protein response that could be leveraged to bolster the clearance of cytotoxic protein aggregates.

Keywords:  BAG3–HSPB8 complex; CASA; HRI; Parkinson’s disease; alpha-synuclein; autophagy; integrated stress response; proteasome; protein aggregation; protein misfolding

DOI:  https://doi.org/10.1074/jbc.RA120.014415
FEBS J. 2021 Jan 06.

NUPR1 interacts with eIF2a and is required for resolution of the ER-stress response in pancreatic tissue.

Maria Teresa Borrello, Patricia Santofimia-Castaño, Marco Bocchio, Angela Listi, Nicolas Fraunhoffer, Philippe Soubeyran, Eric Chevet, Christopher Pin, Juan Iovanna.

  NUPR1 is a stress response protein overexpressed upon cell injury in virtually all organs including the exocrine pancreas. Despite NUPR1's well established role in the response to cell stress, the molecular and structural machineries triggered by NUPR1 activation remain largely debated. In this study, we uncover a new role for NUPR1, participating in the unfolded protein response (UPR) and the integrated stress response (ISR). Biochemical results and ultrastructural morphological observations revealed alterations in the UPR of acinar cells of germline-deleted NUPR1 murine models, consistent with the inability to restore general protein synthesis after stress induction. Bioinformatic analysis of NUPR1-interacting partners showed significant enrichment in translation initiation factors, including eukaryotic initiation factor (eIF) 2α. Co-immunoprecipitation and proximity ligation assays confirmed interaction between NUPR1 and eIF2α and its phosphorylated form (p-eIF2α). Furthermore, our data suggests loss of NUPR1 in cells results in maintained eIF2α phosphorylation and evaluation of nascent proteins by click chemistry revealed that NUPR1-depleted PANC-1 cells displayed a slower post stress protein synthesis recovery when compared to wild-type. Combined, this data proposes a novel role for NUPR1 in the integrated stress response pathway, at least partially through promoting efficient PERK-branch activity and resolution through a unique interaction with eIF2α.

Keywords:  ER-stress; NUPR1; Unfolded Protein Response; eIF2α; protein translation

DOI:  https://doi.org/10.1111/febs.15700
Mol Hum Reprod. 2021 Jan 07. pii: gaaa088. [Epub ahead of print]

Endoplasmic reticulum stress: a key regulator of the follicular microenvironment in the ovary.

Miyuki Harada, Nozomi Takahashi, Jerilee M K Azhary, Chisato Kunitomi, Tomoyuki Fujii, Yutaka Osuga.

  Intra-ovarian local factors regulate the follicular microenvironment in coordination with gonadotrophins, thus playing a crucial role in ovarian physiology as well as pathological states such as polycystic ovary syndrome (PCOS). One recently recognized local factor is endoplasmic reticulum (ER) stress, which involves the accumulation of unfolded or misfolded proteins in the ER related to various physiological and pathological conditions that increase the demand for protein folding or attenuate the protein-folding capacity of the organelle. ER stress results in activation of several signal transduction cascades, collectively termed the unfolded protein response (UPR), which affect a wide variety of cellular functions. Recent studies have revealed diverse roles of ER stress in physiological and pathological conditions in the ovary. In this review, we summarize the most current knowledge of the regulatory roles of ER stress in the ovary, in the context of reproduction. The physiological roles of ER stress and the UPR in the ovary remain largely undetermined. On the other hand, activation of ER stress is known to impair follicular and oocyte health in various pathological conditions; moreover, ER stress also contributes to the pathogenesis of several ovarian diseases, including PCOS. Finally, we discuss the potential of ER stress as a novel therapeutic target. Inhibition of ER stress or UPR activation, by treatment with existing chemical chaperones, lifestyle intervention, or the development of small molecules that target the UPR, represents a promising therapeutic strategy.

Keywords:  endometriosis; endoplasmic reticulum stress; follicular microenvironment; granulosa cell; inflammation; oocyte; ovary; oxidative stress; polycystic ovary syndrome; unfolded protein response

DOI:  https://doi.org/10.1093/molehr/gaaa088
Life (Basel). 2021 Jan 06. pii: E30. [Epub ahead of print]11(1):

Downregulation of miR-17-92 Cluster by PERK Fine-Tunes Unfolded Protein Response Mediated Apoptosis.

Danielle E Read, Ananya Gupta, Karen Cawley, Laura Fontana, Patrizia Agostinis, Afshin Samali, Sanjeev Gupta.

  An important event in the unfolded protein response (UPR) is activation of the endoplasmic reticulum (ER) kinase PERK. The PERK signalling branch initially mediates a prosurvival response, which progresses to a proapoptotic response upon prolonged ER stress. However, the molecular mechanisms of PERK-mediated cell death are not well understood. Here we show that expression of the primary miR-17-92 transcript and mature miRNAs belonging to the miR-17-92 cluster are decreased during UPR. We found that miR-17-92 promoter reporter activity was reduced during UPR in a PERK-dependent manner. Furthermore, we show that activity of the miR-17-92 promoter is repressed by ectopic expression of ATF4 and NRF2. Promoter deletion analysis mapped the region responding to UPR-mediated repression to a site in the proximal region of the miR-17-92 promoter. Hypericin-mediated photo-oxidative ER damage reduced the expression of miRNAs belonging to the miR-17-92 cluster in wild-type but not in PERK-deficient cells. Importantly, ER stress-induced apoptosis was inhibited upon miR-17-92 overexpression in SH-SY5Y and H9c2 cells. Our results reveal a novel function for ATF4 and NRF2, where repression of the miR-17-92 cluster plays an important role in ER stress-mediated apoptosis. Mechanistic details are provided for the potentiation of cell death via sustained PERK signalling mediated repression of the miR-17-92 cluster.

Keywords:  ATF4; CHOP; ER stress; NRF2; apoptosis; miR-17-92; microRNAs; unfolded protein response

DOI:  https://doi.org/10.3390/life11010030
New Phytol. 2020 Nov;228(3): 973-988

Plasma membrane aquaporins interact with the endoplasmic reticulum resident VAP27 proteins at ER-PM contact sites and endocytic structures.

Ana Romina Fox, Florencia Scochera, Timothée Laloux, Karolina Filik, Hervé Degand, Pierre Morsomme, Karina Alleva, François Chaumont.

  Plasma membrane (PM) intrinsic proteins (PIPs) are aquaporins facilitating the diffusion of water and small solutes. The functional importance of the PM organisation of PIPs in the interaction with other cellular structures is not completely understood. We performed a pull-down assay using maize (Zea mays) suspension cells expressing YFP-ZmPIP2;5 and validated the protein interactions by yeast split-ubiquitin and bimolecular fluorescence complementation assays. We expressed interacting proteins tagged with fluorescent proteins in Nicotiana benthamiana leaves and performed water transport assays in oocytes. Finally, a phylogenetic analysis was conducted. The PM-located ZmPIP2;5 physically interacts with the endoplasmic reticulum (ER) resident ZmVAP27-1. This interaction requires the ZmVAP27-1 cytoplasmic major sperm domain. ZmPIP2;5 and ZmVAP27-1 localise in close vicinity in ER-PM contact sites (EPCSs) and endocytic structures upon exposure to salt stress conditions. This interaction enhances PM water permeability in oocytes. Similarly, the Arabidopsis ZmVAP27-1 paralogue, AtVAP27-1, interacts with the AtPIP2;7 aquaporin. Together, these data indicate that the PIP2-VAP27 interaction in EPCSs is evolutionarily conserved, and suggest that VAP27 might stabilise the aquaporins and guide their endocytosis in response to salt stress.

Keywords:  aquaporin; endocytosis; endoplasmic reticulum (ER); endoplasmic reticulum–plasma membrane (ER–PM) contact sites (EPCSs); plant vesicle‐associated membrane protein (VAMP)‐associated protein (VAP27); plasma membrane intrinsic protein (PIP)

DOI:  https://doi.org/10.1111/nph.16743
Cell Microbiol. 2021 Jan 05.

The protein kinase Ire1 impacts pathogenicity of Candida albicans by regulating homeostatic adaptation to endoplasmic reticulum stress.

Shabnam Sircaik, Elvira Román, Priyanka Bapat, Keunsook K Lee, David R Andes, Neil A R Gow, Clarissa J Nobile, Jesús Pla, Sneh Lata Panwar.

The unfolded protein response (UPR), crucial for the maintenance of ER homeostasis, is tied to the regulation of multiple cellular processes in pathogenic fungi. Here we show that C. albicans relies on an ER-resident protein, inositol-requiring enzyme 1 (Ire1) for sensing ER stress and activating the UPR. Compromised Ire1 function impacts cellular processes that are dependent on functional secretory homeostasis, as inferred from transcriptional profiling. Concordantly, an Ire1 mutant strain exhibits pleiotropic roles in ER stress response, antifungal tolerance, cell wall regulation and virulence-related traits. Hac1 is the downstream target of C. albicans Ire1 as it initiates the unconventional splicing of the 19 bp intron from HAC1 mRNA during tunicamycin-induced ER stress. Ire1 also activates the UPR in response to perturbations in cell wall integrity and cell membrane homeostasis in a manner that does not necessitate the splicing of HAC1 mRNA. Furthermore, the Ire1 mutant strain was severely defective in hyphal morphogenesis and biofilm formation as well as in establishing a successful infection in vivo. Together, these findings demonstrate that C. albicans Ire1 functions to regulate traits that are essential for virulence and suggests its importance in responding to multiple stresses, thus integrating various stress signals to maintain ER homeostasis. This article is protected by copyright. All rights reserved.

DOI: https://doi.org/10.1111/cmi.13307
Nat Chem Biol. 2021 Jan 04.

Molecular basis for ubiquitin ligase CRL2FEM1C-mediated recognition of C-degron.

Xiaojie Yan, Xiaolu Wang, Yao Li, Mengqi Zhou, Yanjun Li, Lili Song, Wenyi Mi, Jinrong Min, Cheng Dong.

Proteome integrity depends on the ubiquitin-proteasome system to degrade unwanted or abnormal proteins. In addition to the N-degrons, C-terminal residues of proteins can also serve as degradation signals (C-degrons) that are recognized by specific cullin-RING ubiquitin ligases (CRLs) for proteasomal degradation. FEM1C is a CRL2 substrate receptor that targets the C-terminal arginine degron (Arg/C-degron), but the molecular mechanism of substrate recognition remains largely elusive. Here, we present crystal structures of FEM1C in complex with Arg/C-degron and show that FEM1C utilizes a semi-open binding pocket to capture the C-terminal arginine and that the extreme C-terminal arginine is the major structural determinant in recognition by FEM1C. Together with biochemical and mutagenesis studies, we provide a framework for understanding molecular recognition of the Arg/C-degron by the FEM family of proteins.

DOI: https://doi.org/10.1038/s41589-020-00703-4
Nat Commun. 2021 01 04. 12(1): 16

p62/SQSTM1-droplet serves as a platform for autophagosome formation and anti-oxidative stress response.

Shun Kageyama, Sigurdur Runar Gudmundsson, Yu-Shin Sou, Yoshinobu Ichimura, Naoki Tamura, Saiko Kazuno, Takashi Ueno, Yoshiki Miura, Daisuke Noshiro, Manabu Abe, Tsunehiro Mizushima, Nobuaki Miura, Shujiro Okuda, Hozumi Motohashi, Jin-A Lee, Kenji Sakimura, Tomoyuki Ohe, Nobuo N Noda, Satoshi Waguri, Eeva-Liisa Eskelinen, Masaaki Komatsu.

Autophagy contributes to the selective degradation of liquid droplets, including the P-Granule, Ape1-complex and p62/SQSTM1-body, although the molecular mechanisms and physiological relevance of selective degradation remain unclear. In this report, we describe the properties of endogenous p62-bodies, the effect of autophagosome biogenesis on these bodies, and the in vivo significance of their turnover. p62-bodies are low-liquidity gels containing ubiquitin and core autophagy-related proteins. Multiple autophagosomes form on the p62-gels, and the interaction of autophagosome-localizing Atg8-proteins with p62 directs autophagosome formation toward the p62-gel. Keap1 also reversibly translocates to the p62-gels in a p62-binding dependent fashion to activate the transcription factor Nrf2. Mice deficient for Atg8-interaction-dependent selective autophagy show that impaired turnover of p62-gels leads to Nrf2 hyperactivation in vivo. These results indicate that p62-gels are not simple substrates for autophagy but serve as platforms for both autophagosome formation and anti-oxidative stress.

DOI: https://doi.org/10.1038/s41467-020-20185-1
Cell Death Differ. 2021 Jan 04.

Build-UPS and break-downs: metabolism impacts on proteostasis and aging.

Franziska Ottens, André Franz, Thorsten Hoppe.

Perturbation of metabolism elicits cellular stress which profoundly modulates the cellular proteome and thus protein homeostasis (proteostasis). Consequently, changes in the cellular proteome due to metabolic shift require adaptive mechanisms by molecular protein quality control. The mechanisms vitally controlling proteostasis embrace the entire life cycle of a protein involving translational control at the ribosome, chaperone-assisted native folding, and subcellular sorting as well as proteolysis by the proteasome or autophagy. While metabolic imbalance and proteostasis decline have been recognized as hallmarks of aging and age-associated diseases, both processes are largely considered independently. Here, we delineate how proteome stability is governed by insulin/IGF1 signaling (IIS), mechanistic target of Rapamycin (TOR), 5' adenosine monophosphate-activated protein kinase (AMPK), and NAD-dependent deacetylases (Sir2-like proteins known as sirtuins). This comprehensive overview is emphasizing the regulatory interconnection between central metabolic pathways and proteostasis, indicating the relevance of shared signaling nodes as targets for future therapeutic interventions.

DOI: https://doi.org/10.1038/s41418-020-00682-y
Trends Cell Biol. 2021 Jan 04. pii: S0962-8924(20)30246-4. [Epub ahead of print]

Membrane Protein Quality Control Mechanisms in the Endo-Lysosome System.

Richa Sardana, Scott D Emr.

  Protein quality control (PQC) machineries play a critical role in selective identification and removal of mistargeted, misfolded, and aberrant proteins. This task is extremely complicated due to the enormous diversity of the proteome. It also requires nuanced and careful differentiation between 'normal' and 'folding intermediates' from 'abnormal' and 'misfolded' protein states. Multiple genetic and proteomic approaches have started to delineate the molecular underpinnings of how these machineries recognize their target and how their activity is regulated. In this review, we summarize our understanding of the various E3 ubiquitin ligases and associated machinery that mediate PQC in the endo-lysosome system in yeast and humans, how they are regulated, and mechanisms of target selection, with the intent of guiding future research in this area.

Keywords:  E3 ligase adaptors; E3 ubiquitin ligase; HECT; Nedd4; RING; RING-CH; Rsp5; endo-lysosome system; lysosome; membrane protein quality control

DOI:  https://doi.org/10.1016/j.tcb.2020.11.011
EMBO Rep. 2021 Jan 04. e50854

MOAP-1-mediated dissociation of p62/SQSTM1 bodies releases Keap1 and suppresses Nrf2 signaling.

Chong Teik Tan, Hao-Chun Chang, Qiling Zhou, Chundong Yu, Nai Yang Fu, Kanaga Sabapathy, Victor C Yu.

  Nrf2 signaling is vital for protecting cells against oxidative stress. However, its hyperactivation is frequently found in liver cancer through excessive build-up of p62/SQSTM1 bodies that sequester Keap1, an adaptor of the E3-ubiquitin ligase complex for Nrf2. Here, we report that the Bax-binding protein MOAP-1 regulates p62-Keap1-Nrf2 signaling through disruption of p62 bodies. Upon induction of cellular stresses that stimulate formation of p62 bodies, MOAP-1 is recruited to p62 bodies and reduces their levels independent of the autophagy pathway. MOAP-1 interacts with the PB1-ZZ domains of p62 and interferes with its self-oligomerization and liquid-liquid phase separation, thereby disassembling the p62 bodies. Loss of MOAP-1 can lead to marked upregulation of p62 bodies, enhanced sequestration of Keap1 by p62 and hyperactivation of Nrf2 antioxidant target genes. MOAP-1-deficient mice exhibit an elevated tumor burden with excessive levels of p62 bodies and Nrf2 signaling in a diethylnitrosamine (DEN)-induced hepatocarcinogenesis model. Together, our data define MOAP-1 as a negative regulator of Nrf2 signaling via dissociation of p62 bodies.

Keywords:  MOAP-1; Nrf2; antioxidant signaling; liver cancer; p62/SQSTM1

DOI:  https://doi.org/10.15252/embr.202050854
Autophagy. 2021 Jan 08.

FNDC-1-Mediated Mitophagy and ATFS-1 Coordinate to Protect Against Hypoxia-Reoxygenation.

Yunki Lim, Brandon Berry, Stephanie Viteri, Matthew McCall, Eun Chan Park, Christopher Rongo, Paul S Brookes, Keith Nehrke.

  Mitochondrial quality control (MQC) balances organelle adaptation and elimination, and mechanistic crosstalk between the underlying molecular processes affects subsequent stress outcomes. FUNDC1 (FUN14 domain containing 1) is a mammalian mitophagy receptor that responds to hypoxia-reoxygenation (HR) stress. Here, we provide evidence that FNDC-1 is the C. elegans ortholog of FUNDC1, and that its loss protects against injury in a worm model of HR. This protection depends upon ATFS-1, a transcription factor that is central to the mitochondrial unfolded protein response (UPRmt). Global mRNA and metabolite profiling suggest that atfs-1-dependent stress responses and metabolic remodeling occur in response to the loss of fndc-1. These data support a role for FNDC-1 in non-hypoxic MQC, and further suggest that these changes are prophylactic in relation to subsequent HR. Our results highlight functional coordination between mitochondrial adaptation and elimination that organizes stress responses and metabolic rewiring to protect against HR injury.

Keywords:   C. elegans ; hypoxia-reoxygenation (HR); metabolism; mitochondrial unfolded protein response (UPRmt); mitophagy

DOI:  https://doi.org/10.1080/15548627.2021.1872885
Front Cell Dev Biol. 2020 ;8 605989

Caspase-8 Inhibition Prevents the Cleavage and Degradation of E3 Ligase Substrate Receptor Cereblon and Potentiates Its Biological Function.

Liang Zhou, Wenjun Yu, David S Jayabalan, Ruben Niesvizky, Samie R Jaffrey, Xiangao Huang, Guoqiang Xu.

  Cereblon (CRBN), a substrate receptor of cullin 4-RING E3 ligase (CRL4), mediates the ubiquitination and degradation of constitutive substrates and immunomodulatory drug-induced neo-substrates including MEIS2, c-Jun, CLC1, IKZF1/3, CK1α, and SALL4. It has been reported that CRBN itself could be degraded through the ubiquitin-proteasome system by its associated or other cullin-RING E3 ligases, thus influencing its biological functions. However, it is unknown whether the CRBN stability and its biological function could be modulated by caspases. In this study, using model cell lines, we found that activation of the death receptor using tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) leads to the decreased CRBN protein level. Through pharmacological inhibition and activation of caspase-8 (CASP-8), we disclosed that CASP-8 regulates CRBN cleavage in cell lines. Site mapping experiments revealed that CRBN is cleaved after Asp9 upon CASP-8 activation, resulting in the reduced stability. Using myeloma as a model system, we further revealed that either inhibition or genetic depletion of CASP-8 enhances the anti-myeloma activity of lenalidomide (Len) by impairing CRBN cleavage, leading to the attenuated IKZF1 and IKZF3 protein levels and the reduced viability of myeloma cell lines and primary myeloma cells from patients. The present study discovered that the stability of the substrate receptor of an E3 ligase can be modulated by CASP-8 and suggested that administration of CASP-8 inhibitors enhances the overall effectiveness of Len-based combination therapy in myeloma.

Keywords:  TRAIL; anti-myeloma activity; caspase-8; cell viability; cereblon; cleavage; lenalidomide; multiple myeloma

DOI:  https://doi.org/10.3389/fcell.2020.605989
Elife. 2021 Jan 08. pii: e60191. [Epub ahead of print]10

MYC regulates ribosome biogenesis and mitochondrial gene expression programs through its interaction with host cell factor-1.

Tessa M Popay, Jing Wang, Clare M Adams, Gregory Caleb Howard, Simona G Codreanu, Stacy D Sherrod, John A McLean, Lance R Thomas, Shelly L Lorey, Yuichi J Machida, April M Weissmiller, Christine M Eischen, Qi Liu, William P Tansey.

  The oncoprotein transcription factor MYC is a major driver of malignancy and a highly validated but challenging target for the development of anticancer therapies. Novel strategies to inhibit MYC may come from understanding the co-factors it uses to drive pro-tumorigenic gene expression programs, providing their role in MYC activity is understood. Here we interrogate how one MYC co-factor, host cell factor (HCF)-1, contributes to MYC activity in a human Burkitt lymphoma setting. We identify genes connected to mitochondrial function and ribosome biogenesis as direct MYC/HCF-1 targets and demonstrate how modulation of the MYC-HCF-1 interaction influences cell growth, metabolite profiles, global gene expression patterns, and tumor growth in vivo. This work defines HCF-1 as a critical MYC co-factor, places the MYC-HCF-1 interaction in biological context, and highlights HCF-1 as a focal point for development of novel anti-MYC therapies.

Keywords:  MYC; cancer; cancer biology; human; mouse; ribosome biogenesis

DOI:  https://doi.org/10.7554/eLife.60191
Genome Biol. 2021 Jan 05. 22(1): 16

Disome-seq reveals widespread ribosome collisions that promote cotranslational protein folding.

Taolan Zhao, Yan-Ming Chen, Yu Li, Jia Wang, Siyu Chen, Ning Gao, Wenfeng Qian.

  BACKGROUND: The folding of proteins is challenging in the highly crowded and sticky environment of a cell. Regulation of translation elongation may play a crucial role in ensuring the correct folding of proteins. Much of our knowledge regarding translation elongation comes from the sequencing of mRNA fragments protected by single ribosomes by ribo-seq. However, larger protected mRNA fragments have been observed, suggesting the existence of an alternative and previously hidden layer of regulation.RESULTS: In this study, we performed disome-seq to sequence mRNA fragments protected by two stacked ribosomes, a product of translational pauses during which the 5'-elongating ribosome collides with the 3'-paused one. We detected widespread ribosome collisions that are related to slow ribosome release when stop codons are at the A-site, slow peptide bond formation from proline, glycine, asparagine, and cysteine when they are at the P-site, and slow leaving of polylysine from the exit tunnel of ribosomes. The structure of disomes obtained by cryo-electron microscopy suggests a different conformation from the substrate of the ribosome-associated protein quality control pathway. Collisions occurred more frequently in the gap regions between α-helices, where a translational pause can prevent the folding interference from the downstream peptides. Paused or collided ribosomes are associated with specific chaperones, which can aid in the cotranslational folding of the nascent peptides.
CONCLUSIONS: Therefore, cells use regulated ribosome collisions to ensure protein homeostasis.

Keywords:  Cotranslational protein folding; Disome structure; Disome-seq; Protein homeostasis; Ribosome collision; Ribosome release; Ribosome-associated chaperones; Translation elongation; Translational pause

DOI:  https://doi.org/10.1186/s13059-020-02256-0
PLoS Pathog. 2021 Jan;17(1): e1009111

TRK-Fused Gene (TFG), a protein involved in protein secretion pathways, is an essential component of the antiviral innate immune response.

Kashif Aziz Khan, Alexandre Marineau, Priscilla Doyon, Mariana Acevedo, Étienne Durette, Anne-Claude Gingras, Marc J Servant.

Antiviral innate immune response to RNA virus infection is supported by Pattern-Recognition Receptors (PRR) including RIG-I-Like Receptors (RLR), which lead to type I interferons (IFNs) and IFN-stimulated genes (ISG) production. Upon sensing of viral RNA, the E3 ubiquitin ligase TNF Receptor-Associated Factor-3 (TRAF3) is recruited along with its substrate TANK-Binding Kinase (TBK1), to MAVS-containing subcellular compartments, including mitochondria, peroxisomes, and the mitochondria-associated endoplasmic reticulum membrane (MAM). However, the regulation of such events remains largely unresolved. Here, we identify TRK-Fused Gene (TFG), a protein involved in the transport of newly synthesized proteins to the endomembrane system via the Coat Protein complex II (COPII) transport vesicles, as a new TRAF3-interacting protein allowing the efficient recruitment of TRAF3 to MAVS and TBK1 following Sendai virus (SeV) infection. Using siRNA and shRNA approaches, we show that TFG is required for virus-induced TBK1 activation resulting in C-terminal IRF3 phosphorylation and dimerization. We further show that the ability of the TRAF3-TFG complex to engage mTOR following SeV infection allows TBK1 to phosphorylate mTOR on serine 2159, a post-translational modification shown to promote mTORC1 signaling. We demonstrate that the activation of mTORC1 signaling during SeV infection plays a positive role in the expression of Viperin, IRF7 and IFN-induced proteins with tetratricopeptide repeats (IFITs) proteins, and that depleting TFG resulted in a compromised antiviral state. Our study, therefore, identifies TFG as an essential component of the RLR-dependent type I IFN antiviral response.

DOI: https://doi.org/10.1371/journal.ppat.1009111
Cell Stress Chaperones. 2021 Jan 04.

HSF-1 displays nuclear stress body formation in multiple tissues in Caenorhabditis elegans upon stress and following the transition to adulthood.

Andrew Deonarine, Matt W G Walker, Sandy D Westerheide.

  The transcription factor heat shock factor-1 (HSF-1) regulates the heat shock response (HSR), a cytoprotective response induced by proteotoxic stresses. Data from model organisms has shown that HSF-1 also has non-stress biological roles, including roles in the regulation of development and longevity. To better study HSF-1 function, we created a C. elegans strain containing HSF-1 tagged with GFP at its endogenous locus utilizing CRISPR/Cas9-guided transgenesis. We show that the HSF-1::GFP CRISPR worm strain behaves similarly to wildtype worms in response to heat and other stresses, and in other physiological processes. HSF-1 was expressed in all tissues assayed. Immediately following the initiation of reproduction, HSF-1 formed nuclear stress bodies, a hallmark of activation, throughout the germline. Upon the transition to adulthood, of HSF-1 nuclear stress bodies appeared in most somatic cells. Genetic loss of the germline suppressed nuclear stress body formation with age, suggesting that the germline influences HSF-1 activity. Interestingly, we found that various neurons did not form nuclear stress bodies after transitioning to adulthood. Therefore, the formation of HSF-1 nuclear stress bodies upon the transition to adulthood does not occur in a synchronous manner in all cell types. In sum, these studies enhance our knowledge of the expression and activity of the aging and proteostasis factor HSF-1 in a tissue-specific manner with age.

Keywords:  Aging; C. elegans; Cell stress; HSF-1; Heat shock response; Nuclear stress bodies

DOI:  https://doi.org/10.1007/s12192-020-01188-9
Cell Chem Biol. 2020 Dec 31. pii: S2451-9456(20)30513-4. [Epub ahead of print]

Targeted degradation of the enhancer lysine acetyltransferases CBP and p300.

Raghu Vannam, Jan Sayilgan, Samuel Ojeda, Barbara Karakyriakou, Eileen Hu, Johannes Kreuzer, Robert Morris, Xcanda Ixchel Herrera Lopez, Sumit Rai, Wilhelm Haas, Michael Lawrence, Christopher J Ott.

  The enhancer factors CREB-binding protein (CBP) and p300 (also known as KAT3A and KAT3B) maintain gene expression programs through lysine acetylation of chromatin and transcriptional regulators and by scaffolding functions mediated by several protein-protein interaction domains. Small molecule inhibitors that target some of these domains have been developed; however, they cannot completely ablate p300/CBP function in cells. Here we describe a chemical degrader of p300/CBP, dCBP-1. Leveraging structures of ligand-bound p300/CBP domains, we use in silico modeling of ternary complex formation with the E3 ubiquitin ligase cereblon to enable degrader design. dCBP-1 is exceptionally potent at killing multiple myeloma cells and can abolish the enhancer that drives MYC oncogene expression. As an efficient degrader of this unique class of acetyltransferases, dCBP-1 is a useful tool alongside domain inhibitors for dissecting the mechanism by which these factors coordinate enhancer activity in normal and diseased cells.

Keywords:  CBP; HAT; KAT; PROTAC; enhancer; histone acetyltransferase; lysine acetyltransferase; multiple myeloma; p300

DOI:  https://doi.org/10.1016/j.chembiol.2020.12.004
Int J Mol Sci. 2021 Jan 06. pii: E476. [Epub ahead of print]22(2):

E3 Ubiquitin Ligases: Key Regulators of TGFβ Signaling in Cancer Progression.

Abhishek Sinha, Prasanna Vasudevan Iyengar, Peter Ten Dijke.

  Transforming growth factor β (TGFβ) is a secreted growth and differentiation factor that influences vital cellular processes like proliferation, adhesion, motility, and apoptosis. Regulation of the TGFβ signaling pathway is of key importance to maintain tissue homeostasis. Perturbation of this signaling pathway has been implicated in a plethora of diseases, including cancer. The effect of TGFβ is dependent on cellular context, and TGFβ can perform both anti- and pro-oncogenic roles. TGFβ acts by binding to specific cell surface TGFβ type I and type II transmembrane receptors that are endowed with serine/threonine kinase activity. Upon ligand-induced receptor phosphorylation, SMAD proteins and other intracellular effectors become activated and mediate biological responses. The levels, localization, and function of TGFβ signaling mediators, regulators, and effectors are highly dynamic and regulated by a myriad of post-translational modifications. One such crucial modification is ubiquitination. The ubiquitin modification is also a mechanism by which crosstalk with other signaling pathways is achieved. Crucial effector components of the ubiquitination cascade include the very diverse family of E3 ubiquitin ligases. This review summarizes the diverse roles of E3 ligases that act on TGFβ receptor and intracellular signaling components. E3 ligases regulate TGFβ signaling both positively and negatively by regulating degradation of receptors and various signaling intermediates. We also highlight the function of E3 ligases in connection with TGFβ's dual role during tumorigenesis. We conclude with a perspective on the emerging possibility of defining E3 ligases as drug targets and how they may be used to selectively target TGFβ-induced pro-oncogenic responses.

Keywords:  E3 Ligase; PROTAC; SMAD; SMURF; TGFβ; cancer; signaling; tumor; ubiquitin

DOI:  https://doi.org/10.3390/ijms22020476
Cell Death Differ. 2021 Jan 07.

Ubiquitin signalling in neurodegeneration: mechanisms and therapeutic opportunities.

Marlene F Schmidt, Zhong Yan Gan, David Komander, Grant Dewson.

Neurodegenerative diseases are characterised by progressive damage to the nervous system including the selective loss of vulnerable populations of neurons leading to motor symptoms and cognitive decline. Despite millions of people being affected worldwide, there are still no drugs that block the neurodegenerative process to stop or slow disease progression. Neuronal death in these diseases is often linked to the misfolded proteins that aggregate within the brain (proteinopathies) as a result of disease-related gene mutations or abnormal protein homoeostasis. There are two major degradation pathways to rid a cell of unwanted or misfolded proteins to prevent their accumulation and to maintain the health of a cell: the ubiquitin-proteasome system and the autophagy-lysosomal pathway. Both of these degradative pathways depend on the modification of targets with ubiquitin. Aging is the primary risk factor of most neurodegenerative diseases including Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis. With aging there is a general reduction in proteasomal degradation and autophagy, and a consequent increase of potentially neurotoxic protein aggregates of β-amyloid, tau, α-synuclein, SOD1 and TDP-43. An often over-looked yet major component of these aggregates is ubiquitin, implicating these protein aggregates as either an adaptive response to toxic misfolded proteins or as evidence of dysregulated ubiquitin-mediated degradation driving toxic aggregation. In addition, non-degradative ubiquitin signalling is critical for homoeostatic mechanisms fundamental for neuronal function and survival, including mitochondrial homoeostasis, receptor trafficking and DNA damage responses, whilst also playing a role in inflammatory processes. This review will discuss the current understanding of the role of ubiquitin-dependent processes in the progressive loss of neurons and the emergence of ubiquitin signalling as a target for the development of much needed new drugs to treat neurodegenerative disease.

DOI: https://doi.org/10.1038/s41418-020-00706-7
Nat Chem Biol. 2021 Jan 04.

Molecular basis for arginine C-terminal degron recognition by Cul2FEM1 E3 ligase.

Xinyan Chen, Shanhui Liao, Yaara Makaros, Qiong Guo, Zhongliang Zhu, Rina Krizelman, Karin Dahan, Xiaoming Tu, Xuebiao Yao, Itay Koren, Chao Xu.

Degrons are elements within protein substrates that mediate the interaction with specific degradation machineries to control proteolysis. Recently, a few classes of C-terminal degrons (C-degrons) that are recognized by dedicated cullin-RING ligases (CRLs) have been identified. Specifically, CRL2 using the related substrate adapters FEM1A/B/C was found to recognize C degrons ending with arginine (Arg/C-degron). Here, we uncover the molecular mechanism of Arg/C-degron recognition by solving a subset of structures of FEM1 proteins in complex with Arg/C-degron-bearing substrates. Our structural research, complemented by binding assays and global protein stability (GPS) analyses, demonstrates that FEM1A/C and FEM1B selectively target distinct classes of Arg/C-degrons. Overall, our study not only sheds light on the molecular mechanism underlying Arg/C-degron recognition for precise control of substrate turnover, but also provides valuable information for development of chemical probes for selectively regulating proteostasis.

DOI: https://doi.org/10.1038/s41589-020-00704-3
Cell Death Differ. 2021 Jan 05.

Adaptors as the regulators of HECT ubiquitin ligases.

Sonia Shalini Shah, Sharad Kumar.

The HECT (homologous to E6AP C-terminus) ubiquitin ligases (E3s) are a small family of highly conserved enzymes involved in diverse cellular functions and pathological conditions. Characterised by a C-terminal HECT domain that accepts ubiquitin from E2 ubiquitin conjugating enzymes, these E3s regulate key signalling pathways. The activity and functional regulation of HECT E3s are controlled by several factors including post-translational modifications, inter- and intramolecular interactions and binding of co-activators and adaptor proteins. In this review, we focus on the regulation of HECT E3s by accessory proteins or adaptors and discuss various ways by which adaptors mediate their regulatory roles to affect physiological outcomes. We discuss common features that are conserved from yeast to mammals, regardless of the type of E3s as well as shed light on recent discoveries explaining some existing enigmas in the field.

DOI: https://doi.org/10.1038/s41418-020-00707-6
J Am Chem Soc. 2021 Jan 04.

Development of Antibody-Based PROTACs for the Degradation of the Cell-Surface Immune Checkpoint Protein PD-L1.

Adam D Cotton, Duy P Nguyen, Josef A Gramespacher, Ian B Seiple, James A Wells.

Targeted protein degradation has emerged as a new paradigm to manipulate cellular proteostasis. Proteolysis-targeting chimeras (PROTACs) are bifunctional small molecules that recruit an E3 ligase to a target protein of interest, promoting its ubiquitination and subsequent degradation. Here, we report the development of antibody-based PROTACs (AbTACs), fully recombinant bispecific antibodies that recruit membrane-bound E3 ligases for the degradation of cell-surface proteins. We show that an AbTAC can induce the lysosomal degradation of programmed death-ligand 1 by recruitment of the membrane-bound E3 ligase RNF43. AbTACs represent a new archetype within the PROTAC field to target cell-surface proteins with fully recombinant biological molecules.

DOI: https://doi.org/10.1021/jacs.0c10008
Biomolecules. 2021 Jan 04. pii: E54. [Epub ahead of print]11(1):

Nuclear Ubiquitin-Proteasome Pathways in Proteostasis Maintenance.

Dina Franić, Klara Zubčić, Mirta Boban.

  Protein homeostasis, or proteostasis, is crucial for the functioning of a cell, as proteins that are mislocalized, present in excessive amounts, or aberrant due to misfolding or other type of damage can be harmful. Proteostasis includes attaining the correct protein structure, localization, and the formation of higher order complexes, and well as the appropriate protein concentrations. Consequences of proteostasis imbalance are evident in a range of neurodegenerative diseases characterized by protein misfolding and aggregation, such as Alzheimer's, Parkinson's, and amyotrophic lateral sclerosis. To protect the cell from the accumulation of aberrant proteins, a network of protein quality control (PQC) pathways identifies the substrates and direct them towards refolding or elimination via regulated protein degradation. The main pathway for degradation of misfolded proteins is the ubiquitin-proteasome system. PQC pathways have been first described in the cytoplasm and the endoplasmic reticulum, however, accumulating evidence indicates that the nucleus is an important PQC compartment for ubiquitination and proteasomal degradation of not only nuclear, but also cytoplasmic proteins. In this review, we summarize the nuclear ubiquitin-proteasome pathways involved in proteostasis maintenance in yeast, focusing on inner nuclear membrane-associated degradation (INMAD) and San1-mediated protein quality control.

Keywords:  inner nuclear membrane; nucleus; proteasome; protein misfolding; protein quality control; proteostasis; ubiquitin; yeast

DOI:  https://doi.org/10.3390/biom11010054
Nat Commun. 2021 01 04. 12(1): 61

Homeostatic regulation of STING by retrograde membrane traffic to the ER.

Kojiro Mukai, Emari Ogawa, Rei Uematsu, Yoshihiko Kuchitsu, Fumika Kiku, Takefumi Uemura, Satoshi Waguri, Takehiro Suzuki, Naoshi Dohmae, Hiroyuki Arai, Anthony K Shum, Tomohiko Taguchi.

Coat protein complex I (COP-I) mediates the retrograde transport from the Golgi apparatus to the endoplasmic reticulum (ER). Mutation of the COPA gene, encoding one of the COP-I subunits (α-COP), causes an immune dysregulatory disease known as COPA syndrome. The molecular mechanism by which the impaired retrograde transport results in autoinflammation remains poorly understood. Here we report that STING, an innate immunity protein, is a cargo of the retrograde membrane transport. In the presence of the disease-causative α-COP variants, STING cannot be retrieved back to the ER from the Golgi. The forced Golgi residency of STING results in the cGAS-independent and palmitoylation-dependent activation of the STING downstream signaling pathway. Surf4, a protein that circulates between the ER/ ER-Golgi intermediate compartment/ Golgi, binds STING and α-COP, and mediates the retrograde transport of STING to the ER. The STING/Surf4/α-COP complex is disrupted in the presence of the disease-causative α-COP variant. We also find that the STING ligand cGAMP impairs the formation of the STING/Surf4/α-COP complex. Our results suggest a homeostatic regulation of STING at the resting state by retrograde membrane traffic and provide insights into the pathogenesis of COPA syndrome.

DOI: https://doi.org/10.1038/s41467-020-20234-9
Mol Cell. 2020 Dec 24. pii: S1097-2765(20)30900-X. [Epub ahead of print]

Negative regulation of AMPK signaling by high glucose via E3 ubiquitin ligase MG53.

Peng Jiang, Lejiao Ren, Li Zhi, Zhong Yu, Fengxiang Lv, Fengli Xu, Wei Peng, Xiaoyu Bai, Kunlun Cheng, Li Quan, Xiuqin Zhang, Xianhua Wang, Yan Zhang, Dan Yang, Xinli Hu, Rui-Ping Xiao.

As a master regulator of metabolism, AMP-activated protein kinase (AMPK) is activated upon energy and glucose shortage but suppressed upon overnutrition. Exaggerated negative regulation of AMPK signaling by nutrient overload plays a crucial role in metabolic diseases. However, the mechanism underlying the negative regulation is poorly understood. Here, we demonstrate that high glucose represses AMPK signaling via MG53 (also called TRIM72) E3-ubiquitin-ligase-mediated AMPKα degradation and deactivation. Specifically, high-glucose-stimulated reactive oxygen species (ROS) signals AKT to phosphorylate AMPKα at S485/491, which facilitates the recruitment of MG53 and the subsequent ubiquitination and degradation of AMPKα. In addition, high glucose deactivates AMPK by ROS-dependent suppression of phosphorylation of AMPKα at T172. These findings not only delineate the mechanism underlying the impairment of AMPK signaling in overnutrition-related diseases but also highlight the significance of keeping the yin-yang balance of AMPK signaling in the maintenance of metabolic homeostasis.

DOI: https://doi.org/10.1016/j.molcel.2020.12.008
ACS Infect Dis. 2021 Jan 05.

Mammalian Deubiquitinating Enzyme Inhibitors Display in Vitro and in Vivo Activity against Malaria Parasites and Potentiate Artemisinin Action.

Nelson V Simwela, Katie R Hughes, Michael T Rennie, Michael P Barrett, Andrew P Waters.

  The ubiquitin proteasome system (UPS) is an emerging drug target in malaria due to its essential role in the parasite's life cycle stages as well its contribution to resistance to artemisinins. Polymorphisms in the Kelch13 gene of Plasmodium falciparum are primary markers of artemisinin resistance and among other things are phenotypically characterized by an overactive UPS. Inhibitors targeting the proteasome, critical components of the UPS, display activity in malaria parasites and synergize artemisinin action. Here we report the activity of small molecule inhibitors targeting mammalian deubiquitinating enzymes, DUBs (upstream UPS components), in malaria parasites. We show that generic DUB inhibitors can block intraerythrocytic development of malaria parasites in vitro and possess antiparasitic activity in vivo and can be used in combination with additive to synergistic effect. We also show that inhibition of these upstream components of the UPS can potentiate the activity of artemisinin in vitro as well as in vivo to the extent that artemisinin resistance can be overcome. Combinations of DUB inhibitors anticipated to target different DUB activities and downstream proteasome inhibitors are even more effective at improving the potency of artemisinins than either inhibitors alone, providing proof that targeting multiple UPS activities simultaneously could be an attractive approach to overcoming artemisinin resistance. These data further validate the parasite UPS as a target to both enhance artemisinin action and potentially overcome resistance. Lastly, we confirm that DUB inhibitors can be developed into in vivo antimalarial drugs with promise for activity against all of human malaria and could thus further exploit their current pursuit as anticancer agents in rapid drug repurposing programs.

Keywords:  artemisinin; malaria; potentiation; resistance; synergy; ubiquitin proteasome system

DOI:  https://doi.org/10.1021/acsinfecdis.0c00580
BMC Cancer. 2021 Jan 07. 21(1): 33

Effects of ER-resident and secreted AGR2 on cell proliferation, migration, invasion, and survival in PANC-1 pancreatic cancer cells.

Xian Hong, Zhi-Xuan Li, Jie Hou, Hui-Yu Zhang, Chun-Yan Zhang, Jian Zhang, He Sun, Li-Hong Pang, Tao Wang, Zhi-Hui Deng.

  BACKGROUND: Anterior gradient-2 (AGR2) is a proto-oncogene involved in tumorigenesis and cancer progression. AGR2, predominantly localized in the endoplasmic reticulum (ER), is also a secreted protein detected in the extracellular compartment in multiple cancers. However, the biological functions of intracellular and extracellular AGR2 remain to be elucidated.METHODS: Based on the biochemical structure of AGR2 protein, PANC-1 pancreatic cancer cells stably expressing ER-resident or secreted AGR2 were generated by a lentivirus-mediated stable overexpression system. The capacities of cell proliferation, migration, invasion and survival were assessed in PANC-1 stable cells. Moreover, EGFR expression and activation were determined to explore the possible mechanism of AGR2 roles in pancreatic cancer tumorigenesis.
RESULTS: It was discovered that secreted AGR2, but not ER-resident AGR2, promotes cell proliferation, migration and invasion of PANC-1 cells. Moreover, the data indicated that both the ER-resident and the secreted AGR2 enhance the survival capacity of PANC-1 cells after tunicamycin-induced ER stress and gemcitabine treatment. However, EGFR expression and activation were not found to be involved in AGR2-dependent oncogenic phenotypes in PANC-1 cells.
CONCLUSIONS: Secreted AGR2 is predominantly involved in cell proliferation, migration and invasion in PANC-1 pancreatic cancer cells. Both secreted and ER-resident AGR2 contribute to the survival of PANC-1 cells under the challenging conditions. These findings provide insight into how different localizations of AGR2 have contributed to pancreatic cancer growth, metastasis, and drug sensitivity.

Keywords:  AGR2; Drug sensitivity; ER stress; Pancreatic cancer

DOI:  https://doi.org/10.1186/s12885-020-07743-y
Theranostics. 2021 ;11(1): 222-256

Selective autophagy of intracellular organelles: recent research advances.

Wen Li, Pengcheng He, Yuge Huang, Yi-Fang Li, Jiahong Lu, Min Li, Hiroshi Kurihara, Zhuo Luo, Tian Meng, Mashun Onishi, Changle Ma, Lei Jiang, Yongquan Hu, Qing Gong, Dongxing Zhu, Yiming Xu, Rong Liu, Lei Liu, Cong Yi, Yushan Zhu, Ningfang Ma, Koji Okamoto, Zhiping Xie, Jinbao Liu, Rong-Rong He, Du Feng.

  Macroautophagy (hereafter called autophagy) is a highly conserved physiological process that degrades over-abundant or damaged organelles, large protein aggregates and invading pathogens via the lysosomal system (the vacuole in plants and yeast). Autophagy is generally induced by stress, such as oxygen-, energy- or amino acid-deprivation, irradiation, drugs, etc. In addition to non-selective bulk degradation, autophagy also occurs in a selective manner, recycling specific organelles, such as mitochondria, peroxisomes, ribosomes, endoplasmic reticulum (ER), lysosomes, nuclei, proteasomes and lipid droplets (LDs). This capability makes selective autophagy a major process in maintaining cellular homeostasis. The dysfunction of selective autophagy is implicated in neurodegenerative diseases (NDDs), tumorigenesis, metabolic disorders, heart failure, etc. Considering the importance of selective autophagy in cell biology, we systemically review the recent advances in our understanding of this process and its regulatory mechanisms. We emphasize the 'cargo-ligand-receptor' model in selective autophagy for specific organelles or cellular components in yeast and mammals, with a focus on mitophagy and ER-phagy, which are finely described as types of selective autophagy. Additionally, we highlight unanswered questions in the field, helping readers focus on the research blind spots that need to be broken.

Keywords:  ER-phagy; autophagy receptor; lipophagy; lysophagy; mitophagy; nucleophagy; pexophagy; proteaphagy; ribophagy; selective autophagy

DOI:  https://doi.org/10.7150/thno.49860
Cell Death Dis. 2021 Jan 05. 12(1): 25

FAT10 protects against ischemia-induced ventricular arrhythmia by decreasing Nedd4-2/Nav1.5 complex formation.

Xiao Liu, Jin Ge, Chen Chen, Yang Shen, Jinyan Xie, Xin Zhu, Menglu Liu, Jinzhu Hu, Leifeng Chen, Linjuan Guo, Qiongqiong Zhou, Xia Yan, Yuming Qiu, Rong Wan, Ali J Marian, Kui Hong.

The human leukocyte antigen F-associated transcript 10 (FAT10) is a member of the small ubiquitin-like protein family that binds to its target proteins and subjects them to degradation by the ubiquitin-proteasome system (UPS). In the heart, FAT10 plays a cardioprotective role and affects predisposition to cardiac arrhythmias after myocardial ischemia (MI). However, whether and how FAT10 influences cardiac arrhythmias is unknown. We investigated the role of FAT10 in regulating the sodium channel Nav1.5, a major regulator of cardiac arrhythmias. Fat10 was conditionally deleted in cardiac myocytes using Myh6-Cre and Fat10F/F mice (cFat10-/-). Compared with their wild-type littermates, cFat10-/- mice showed prolonged RR, PR, and corrected QT (QTc) intervals, were more likely to develop ventricular arrhythmia, and had increased mortality after MI. Patch-clamp studies showed that the peak Na+ current was reduced, and the late Na+ current was significantly augmented, resulting in a decreased action potential amplitude and delayed depolarization. Immunoblot and immunofluorescence analyses showed that the expression of the membrane protein Nav1.5 was decreased. Coimmunoprecipitation experiments demonstrated that FAT10 stabilized Nav1.5 expression by antagonizing Nav1.5 ubiquitination and degradation. Specifically, FAT10 bound to the lysine residues in the C-terminal fragments of Nav1.5 and decreased the binding of Nav1.5 to the Nedd4-2 protein, a ubiquitin E3 ligase, preventing degradation of the Nav1.5 protein. Collectively, our findings showed that deletion of the Fat10 in cardiac myocytes led to increased cardiac arrhythmias and increased mortality after MI. Thus, FAT10 protects against ischemia-induced ventricular arrhythmia by binding to Nav1.5 and preventing its Neddylation and degradation by the UPS after MI.

DOI: https://doi.org/10.1038/s41419-020-03290-3
Cell Chem Biol. 2021 Jan 04. pii: S2451-9456(20)30516-X. [Epub ahead of print]

Proteomics of broad deubiquitylase inhibition unmasks redundant enzyme function to reveal substrates and assess enzyme specificity.

Valentina Rossio, Joao A Paulo, Joel Chick, Bradley Brasher, Steven P Gygi, Randall W King.

  Deubiquitylating enzymes (DUBs) counteract ubiquitylation to control stability or activity of substrates. Identification of DUB substrates is challenging because multiple DUBs can act on the same substrate, thwarting genetic approaches. Here, we circumvent redundancy by chemically inhibiting multiple DUBs simultaneously in Xenopus egg extract. We used quantitative mass spectrometry to identify proteins whose ubiquitylation or stability is altered by broad DUB inhibition, and confirmed their DUB-dependent regulation with human orthologs, demonstrating evolutionary conservation. We next extended this method to profile DUB specificity. By adding recombinant DUBs to extract where DUB activity was broadly inhibited, but ubiquitylation and degradation were active at physiological rates, we profiled the ability of DUBs to rescue degradation of these substrates. We found that USP7 has a unique ability to broadly antagonize degradation. Together, we present an approach to identify DUB substrates and characterize DUB specificity that overcomes challenges posed by DUB redundancy.

Keywords:  TMT-proteomics; UPS substrates; USP7; Xenopus; deubiquitylating enzymes; proteasomal degradation; ubiquitin

DOI:  https://doi.org/10.1016/j.chembiol.2020.12.007
Cell Mol Biol Lett. 2021 Jan 05. 26(1): 1

Beyond K48 and K63: non-canonical protein ubiquitination.

Michal Tracz, Wojciech Bialek.

  Protein ubiquitination has become one of the most extensively studied post-translational modifications. Originally discovered as a critical element in highly regulated proteolysis, ubiquitination is now regarded as essential for many other cellular processes. This results from the unique features of ubiquitin (Ub) and its ability to form various homo- and heterotypic linkage types involving one of the seven different lysine residues or the free amino group located at its N-terminus. While K48- and K63-linked chains are broadly covered in the literature, the other types of chains assembled through K6, K11, K27, K29, and K33 residues deserve equal attention in the light of the latest discoveries. Here, we provide a concise summary of recent advances in the field of these poorly understood Ub linkages and their possible roles in vivo.

Keywords:  Atypical ubiquitination; Non-canonical; Ubiquitin; Ubiquitin chains

DOI:  https://doi.org/10.1186/s11658-020-00245-6
Nat Struct Mol Biol. 2021 Jan 04.

Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62.

Samuel Itskanov, Katie M Kuo, James C Gumbart, Eunyong Park.

Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. In the present study, we determined cryo-electron microscopy (cryo-EM) structures of several variants of Sec61-Sec62-Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and luminal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation.

DOI: https://doi.org/10.1038/s41594-020-00541-x
FEBS Open Bio. 2021 Jan;11(1): 48-60

Inhibition of the proteasome and proteaphagy enhances apoptosis in FLT3-ITD-driven acute myeloid leukemia.

Rosa G Lopez-Reyes, Grégoire Quinet, Maria Gonzalez-Santamarta, Clément Larrue, Jean-Emmanuel Sarry, Manuel S Rodriguez.

  Acute myeloid leukaemia (AML) is a clonal disorder that affects hematopoietic stem cells or myeloid progenitors. One of the most common mutations that results in AML occurs in the gene encoding fms-like tyrosine kinase 3 (FLT3). Previous studies have demonstrated that AML cells expressing FLT3-internal tandem duplication (ITD) are more sensitive to the proteasome inhibitor bortezomib (Bz) than FLT3 wild-type cells, with this cytotoxicity being mediated by autophagy (Atg). Here, we show that proteasome inhibition with Bz results in modest but consistent proteaphagy in MOLM-14 leukemic cells expressing the FLT3-ITD mutation, but not in OCI-AML3 leukemic cells with wild-type FLT3. Chemical inhibition of Atg with bafilomycin A simultaneously blocked proteaphagy and resulted in the accumulation of the p62 Atg receptor in Bz-treated MOLM-14 cells. The use of ubiquitin traps revealed that ubiquitin plays an important role in proteasome-Atg cross-talk. The p62 inhibitor verteporfin blocked proteaphagy and, importantly, resulted in accumulation of high molecular weight forms of p62 and FLT3-ITD in Bz-treated MOLM-14 cells. Both Atg inhibitors enhanced Bz-induced apoptosis in FLT3-ITD-driven leukemic cells, highlighting the therapeutic potential of these treatments.

Keywords:  AML; FLT3‐ITD; bortezomib; leukaemia; proteaphagy; ubiquitin

DOI:  https://doi.org/10.1002/2211-5463.12950
Curr Genet. 2021 Jan 03.

Cdc48/Shp1 participates in dissociation of protein complexes to regulate their activity.

Linda Lauinger, Karin Flick, Peter Kaiser.

  The AAA-ATPase p97/Cdc48 is one of the most abundant proteins in eukaryotes, and owing to its multiple functions, is considered the swiss army knife of cells. Recent findings demonstrate that p97/Cdc48 and its cofactor p47/Shp1 control the heavy metal stress response by active, signal-triggered disassembly of a multisubunit ubiquitin ligase. Here we review this pathway and describe recently achieved mechanistic insight into the role of p47/Shp1 in this process.

Keywords:  Cadmium response; Cdc48/p97; SCF ubiquitin ligase; Shp1/p47

DOI:  https://doi.org/10.1007/s00294-020-01136-1
Nat Commun. 2021 01 04. 12(1): 51

Targeting USP47 overcomes tyrosine kinase inhibitor resistance and eradicates leukemia stem/progenitor cells in chronic myelogenous leukemia.

Hu Lei, Han-Zhang Xu, Hui-Zhuang Shan, Meng Liu, Ying Lu, Zhi-Xiao Fang, Jin Jin, Bo Jing, Xin-Hua Xiao, Shen-Meng Gao, Feng-Hou Gao, Li Xia, Li Yang, Li-Gen Liu, Wei-Wei Wang, Chuan-Xu Liu, Yin Tong, Yun-Zhao Wu, Jun-Ke Zheng, Guo-Qiang Chen, Li Zhou, Ying-Li Wu.

Identifying novel drug targets to overcome resistance to tyrosine kinase inhibitors (TKIs) and eradicating leukemia stem/progenitor cells are required for the treatment of chronic myelogenous leukemia (CML). Here, we show that ubiquitin-specific peptidase 47 (USP47) is a potential target to overcome TKI resistance. Functional analysis shows that USP47 knockdown represses proliferation of CML cells sensitive or resistant to imatinib in vitro and in vivo. The knockout of Usp47 significantly inhibits BCR-ABL and BCR-ABLT315I-induced CML in mice with the reduction of Lin-Sca1+c-Kit+ CML stem/progenitor cells. Mechanistic studies show that stabilizing Y-box binding protein 1 contributes to USP47-mediated DNA damage repair in CML cells. Inhibiting USP47 by P22077 exerts cytotoxicity to CML cells with or without TKI resistance in vitro and in vivo. Moreover, P22077 eliminates leukemia stem/progenitor cells in CML mice. Together, targeting USP47 is a promising strategy to overcome TKI resistance and eradicate leukemia stem/progenitor cells in CML.

DOI: https://doi.org/10.1038/s41467-020-20259-0
Elife. 2021 Jan 06. pii: e61539. [Epub ahead of print]10

Ral GTPases promote breast cancer metastasis by controlling biogenesis and organ targeting of exosomes.

Shima Ghoroghi, Benjamin Mary, Annabel Larnicol, Nandini Asokan, Annick Klein, Naël Osmani, Ignacio Busnelli, François Delalande, Nicodème Paul, Sébastien Halary, Frédéric Gros, Laetitia Fouillen, Anne-Marie Haeberle, Cathy Royer, Coralie Spiegelhalter, Gwennan André-Grégoire, Vincent Mittelheisser, Alexandre Detappe, Kendelle Murphy, Paul Timpson, Raphaël Carapito, Marcel Blot-Chabaud, Julie Gavard, Christine Carapito, Nicolas Vitale, Olivier Lefebvre, Jacky G Goetz, Vincent Hyenne.

  Cancer extracellular vesicles (EVs) shuttle at distance and fertilize pre-metastatic niches facilitating subsequent seeding by tumor cells. However, the link between EV secretion mechanisms and their capacity to form pre-metastatic niches remains obscure. Using mouse models, we show that GTPases of the Ral family control, through the phospholipase D1, multi-vesicular bodies homeostasis and tune the biogenesis and secretion of pro-metastatic EVs. Importantly, EVs from RalA or RalB depleted cells have limited organotropic capacities in vivo and are less efficient in promoting metastasis. RalA and RalB reduce the EV levels of the adhesion molecule MCAM/CD146, which favors EV-mediated metastasis by allowing EVs targeting to the lungs. Finally, RalA, RalB and MCAM/CD146, are factors of poor prognosis in breast cancer patients. Altogether, our study identifies RalGTPases as central molecules linking the mechanisms of EVs secretion and cargo loading to their capacity to disseminate and induce pre-metastatic niches in a CD146 dependent manner.

Keywords:  cancer biology; cell biology; human; mouse; zebrafish

DOI:  https://doi.org/10.7554/eLife.61539
Nat Commun. 2021 01 05. 12(1): 121

Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative.

Man Pan, Qingyun Zheng, Yuanyuan Yu, Huasong Ai, Yuan Xie, Xin Zeng, Chu Wang, Lei Liu, Minglei Zhao.

p97, also known as valosin-containing protein (VCP) or Cdc48, plays a central role in cellular protein homeostasis. Human p97 mutations are associated with several neurodegenerative diseases. Targeting p97 and its cofactors is a strategy for cancer drug development. Despite significant structural insights into the fungal homolog Cdc48, little is known about how human p97 interacts with its cofactors. Recently, the anti-alcohol abuse drug disulfiram was found to target cancer through Npl4, a cofactor of p97, but the molecular mechanism remains elusive. Here, using single-particle cryo-electron microscopy (cryo-EM), we uncovered three Npl4 conformational states in complex with human p97 before ATP hydrolysis. The motion of Npl4 results from its zinc finger motifs interacting with the N domain of p97, which is essential for the unfolding activity of p97. In vitro and cell-based assays showed that the disulfiram derivative bis-(diethyldithiocarbamate)-copper (CuET) can bypass the copper transporter system and inhibit the function of p97 in the cytoplasm by releasing cupric ions under oxidative conditions, which disrupt the zinc finger motifs of Npl4, locking the essential conformational switch of the complex.

DOI: https://doi.org/10.1038/s41467-020-20359-x
Methods Mol Biol. 2021 ;2261 381-394

Studying OTUD6B-OTUB1 Protein-Protein Interaction by Low-Throughput GFP-Trap Assays and High-Throughput AlphaScreen Assays.

Elisabeth Weber, Kenji Schorpp, Kamyar Hadian.

  Protein-protein interactions (PPI) are involved in a myriad of cellular processes, and their deregulation can lead to many diseases. One such process is protein ubiquitination that requires an orchestrated action of three key enzymes to add ubiquitin moieties to substrate proteins. Importantly, this process is reversible through deubiquitinating enzymes. Both ubiquitination and deubiquitination require many PPIs that once classified can be utilized to identify small molecule inhibitors counteracting these reactions. Here, we study the protein-protein interaction between the two deubiquitinating enzymes OTUB1 and OTUD6B and report for the first time that both proteins directly interact with each other. We describe the GFP-Trap immunoprecipitation as a cell-based method to analyze the OTUD6B-OTUB1 interaction in the cellular context and the AlphaScreen (amplified luminescent proximity homogeneous assay) assay as a tool to detect direct interactions and to search for PPI inhibitors.

Keywords:  AlphaScreen; DUB; Deubiquitinase; GFP-trap; Homogeneous proximity assay; Immunoprecipitation; OTUB1; OTUD6B; Protein–protein interactions; Ubiquitin

DOI:  https://doi.org/10.1007/978-1-0716-1186-9_23