bims-proteo 2022-01-30 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2022–01–30
forty papers selected by
Eric Chevet, INSERM

Identifying Interaction Partners of Yeast Protein Disulfide Isomerases Using a Small Thiol-Reactive Cross-Linker: Implications for Secretory Pathway Proteostasis.
ER-stress promotes VHL-independent degradation of hypoxia-inducible factors via FBXW1A/βTrCP.
Mixed in chains: NEDD8 polymers in the Protein Quality Control system.
The endoplasmic reticulum chaperone BiP is a closure-accelerating cochaperone of Grp94.
A Retrotranslocation Assay That Predicts Defective VCP/p97-Mediated Trafficking of a Retroviral Signal Peptide.
The transmembrane endoplasmic reticulum-associated E3 ubiquitin ligase TRIM13 restrains the pathogenic-DNA-triggered inflammatory response.
ER stress-induced cell death proceeds independently of the TRAIL-R2 signaling axis in pancreatic β cells.
Disrupting the balance of protein quality control protein UBQLN2 accelerates tau proteinopathy.
Differential roles for DNAJ isoforms in HTT-polyQ and FUS aggregation modulation revealed by chaperone screens.
Molecular Investigation of the Unfolded Protein Response in Select Human Tauopathies.
E3 ubiquitin ligase ASB17 is required for spermiation in mice.
The TGN/EE SNARE protein SYP61 and the ubiquitin ligase ATL31 cooperatively regulate plant responses to carbon/nitrogen conditions in Arabidopsis.
Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis.
Whi3 mnemon association with endoplasmic reticulum membranes confines the memory of deceptive courtship to the yeast mother cell.
The extracellular Ero1α/PDI electron transport system regulates platelet function by increasing glutathione reduction potential.
Molecular regulation of autophagosome formation.
Helicobacter pylori-induced reactive oxygen species direct turnover of CSN-associated STAMBPL1 and augment apoptotic cell death.
A Yeast-Based Functional Assay to Study Plant N-Degron - N-Recognin Interactions.
TRIM34 modulates influenza virus-activated programmed cell death by targeting Z-DNA-binding protein 1 for K63-linked polyubiquitination.
Disruption of actin dynamics induces autophagy of the eukaryotic chaperonin TRiC/CCT.
A novel yeast model detects Nrf2 and Keap1 interactions with Hsp90.
The mammalian trafficking chaperone protein UNC93B1 maintains the ER calcium sensor STIM1 in a dimeric state primed for translocation to the ER cortex.
Fluorescent probes for targeting endoplasmic reticulum: design strategies and their applications.
Cytosolic adaptation to mitochondria-induced proteostatic stress causes progressive muscle wasting.
USP17 is required for peripheral trafficking of lysosomes.
E2-E3 ubiquitin enzyme pairing - partnership in provoking or mitigating cancers.
Deletion of SUMO1 attenuates behavioral and anatomical deficits by regulating autophagic activities in Huntington disease.
COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma.
Endoplasmic reticulum-translocation is essential for APOL1 cellular toxicity.
Ubiquitin ligases: guardians of mammalian development.
Palmitoylation restricts SQSTM1/p62-mediated autophagic degradation of NOD2 to modulate inflammation.
Co-translational membrane targeting and holo-translocon docking of ribosomes translating the SRP receptor.
SUMOylation modulates the function of DDX19 in mRNA export.
Translational control of E2f1 regulates the Drosophila cell cycle.
Small disulfide loops in peptide hormones mediate self-aggregation and secretory granule sorting.
Segregation of the membrane cargoes, BACE1 and amyloid precursor protein (APP) throughout the Golgi apparatus.
AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation.
Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9.
High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.
The deubiquitinating enzyme USP17 regulates c-Myc levels and controls cell proliferation and glycolysis.

Chem Res Toxicol. 2022 Jan 27.

Identifying Interaction Partners of Yeast Protein Disulfide Isomerases Using a Small Thiol-Reactive Cross-Linker: Implications for Secretory Pathway Proteostasis.

Benjamin J Freije, Wilson M Freije, To Uyen Do, Grace E Adkins, Alexander Bruch, Jennifer E Hurtig, Kevin A Morano, Raffael Schaffrath, James D West.

Protein disulfide isomerases (PDIs) function in forming the correct disulfide bonds in client proteins, thereby aiding the folding of proteins that enter the secretory pathway. Recently, several PDIs have been identified as targets of organic electrophiles, yet the client proteins of specific PDIs remain largely undefined. Here, we report that PDIs expressed in Saccharomyces cerevisiae are targets of divinyl sulfone (DVSF) and other thiol-reactive protein cross-linkers. Using DVSF, we identified the interaction partners that were cross-linked to Pdi1 and Eug1, finding that both proteins form cross-linked complexes with other PDIs, as well as vacuolar hydrolases, proteins involved in cell wall biosynthesis and maintenance, and many ER proteostasis factors involved ER stress signaling and ER-associated protein degradation (ERAD). The latter discovery prompted us to examine the effects of DVSF on ER quality control, where we found that DVSF inhibits the degradation of the ERAD substrate CPY*, in addition to covalently modifying Ire1 and blocking the activation of the unfolded protein response. Our results reveal that DVSF targets many proteins within the ER proteostasis network and suggest that these proteins may be suitable targets for covalent therapeutic development in the future.

DOI: https://doi.org/10.1021/acs.chemrestox.1c00376
Redox Biol. 2022 Jan 18. pii: S2213-2317(22)00015-5. [Epub ahead of print]50 102243

ER-stress promotes VHL-independent degradation of hypoxia-inducible factors via FBXW1A/βTrCP.

Daniela Mennerich, Kateryna Kubaichuk, Ghulam S Raza, Dominik C Fuhrmann, Karl-Heinz Herzig, Bernhard Brüne, Thomas Kietzmann.

  Metabolic adaptation and signal integration in response to hypoxic conditions is mainly regulated by hypoxia-inducible factors (HIFs). At the same time, hypoxia induces ROS formation and activates the unfolded protein response (UPR), indicative of endoplasmic reticulum (ER) stress. However, whether ER stress would affect the hypoxia response remains ill-defined. Here we report that feeding mice a high fat diet causes ER stress and attenuates the response to hypoxia. Mechanistically, ER stress promotes HIF-1α and HIF-2α degradation independent of ROS, Ca2+, and the von Hippel-Lindau (VHL) pathway, involving GSK3β and the ubiquitin ligase FBXW1A/βTrCP. Thereby, we reveal a previously unknown function of the GSK3β/HIFα/βTrCP1 axis in ER homeostasis and demonstrate that inhibition of the HIF-1 and HIF-2 response and genetic deficiency of GSK3β affects proliferation, migration, and sensitizes cells for ER stress promoted apoptosis. Vice versa, we show that hypoxia affects the ER stress response mainly through the PERK-arm of the UPR. Overall, we discovered previously unrecognized links between the HIF pathway and the ER stress response and uncovered an essential survival pathway for cells under ER stress.

Keywords:  ER stress; HIF-1α; HIF-2α; Mild hypoxia; UPR

DOI:  https://doi.org/10.1016/j.redox.2022.102243
Semin Cell Dev Biol. 2022 Jan 22. pii: S1084-9521(22)00013-1. [Epub ahead of print]

Mixed in chains: NEDD8 polymers in the Protein Quality Control system.

Igor Meszka, Jolanta Polanowska, Dimitris P Xirodimas.

  Post-translational modification of proteins with the Ubiquitin-like molecule NEDD8 is a critical regulatory mechanism for several biological processes and a potential target for therapeutic intervention. The role of NEDD8 has been mainly characterised through its modification as single moiety on the cullin family of proteins and control of Cullin-Ring-Ligases, but also on non-cullin substrates. In addition to monoNEDDylation, recent studies have now revealed that NEDD8 can also generate diverse polymers. This is either through modification of the 9 available lysines in NEDD8 and the formation of polyNEDD8 chains, or NEDDylation of Ubiquitin and SUMO-2 for the generation of hybrid NEDD8 chains. Here, we review recent findings that characterise the formation of NEDD8 polymers under distinct modes of protein NEDDylation (canonical/atypical) and their potential role as regulatory signals of the proteotoxic stress response and the Protein Quality Control system.

Keywords:  Canonical/atypical NEDDylation; NEDD8 polymers; Protein Quality Control; Proteostasis

DOI:  https://doi.org/10.1016/j.semcdb.2022.01.005
Proc Natl Acad Sci U S A. 2022 Feb 01. pii: e2118793119. [Epub ahead of print]119(5):

The endoplasmic reticulum chaperone BiP is a closure-accelerating cochaperone of Grp94.

Bin Huang, Ming Sun, Reyal Hoxie, Judy L M Kotler, Larry J Friedman, Jeff Gelles, Timothy O Street.

  Hsp70 and Hsp90 chaperones provide protein quality control to the cytoplasm, endoplasmic reticulum (ER), and mitochondria. Hsp90 activity is often enhanced by cochaperones that drive conformational changes needed for ATP-dependent closure and capture of client proteins. Hsp90 activity is also enhanced when working with Hsp70, but, in this case, the underlying mechanistic explanation is poorly understood. Here we examine the ER-specific Hsp70/Hsp90 paralogs (BiP/Grp94) and discover that BiP itself acts as a cochaperone that accelerates Grp94 closure. The BiP nucleotide binding domain, which interacts with the Grp94 middle domain, is responsible for Grp94 closure acceleration. A client protein initiates a coordinated progression of steps for the BiP/Grp94 system, in which client binding to BiP causes a conformational change that enables BiP to bind to Grp94 and accelerate its ATP-dependent closure. Single-molecule fluorescence resonance energy transfer measurements show that BiP accelerates Grp94 closure by stabilizing a high-energy conformational intermediate that otherwise acts as an energetic barrier to closure. These findings provide an explanation for enhanced activity of BiP and Grp94 when working as a pair, and demonstrate the importance of a high-energy conformational state in controlling the timing of the Grp94 conformational cycle. Given the high conservation of the Hsp70/Hsp90 system, other Hsp70s may also serve dual roles as both chaperones and closure-accelerating cochaperones to their Hsp90 counterparts.

Keywords:  BiP; Grp94; chaperone; cochaperone

DOI:  https://doi.org/10.1073/pnas.2118793119
mBio. 2022 Jan 04. e0295321

A Retrotranslocation Assay That Predicts Defective VCP/p97-Mediated Trafficking of a Retroviral Signal Peptide.

Poulami Das, Wendy Kaichun Xu, Amit Kumar Singh Gautam, Mary M Lozano, Jaquelin P Dudley.

  Studies of viral replication have provided critical insights into host processes, including protein trafficking and turnover. Mouse mammary tumor virus (MMTV) is a betaretrovirus that encodes a functional 98-amino-acid signal peptide (SP). MMTV SP is generated from both Rem and envelope precursor proteins by signal peptidase cleavage in the endoplasmic reticulum (ER) membrane. We previously showed that SP functions as a human immunodeficiency virus type 1 (HIV-1) Rev-like protein that is dependent on the AAA ATPase valosin-containing protein (VCP)/p97 to subvert ER-associated degradation (ERAD). SP contains a nuclear localization sequence (NLS)/nucleolar localization sequence (NoLS) within the N-terminal 45 amino acids. To directly determine the SP regions needed for membrane extraction and trafficking, we developed a quantitative retrotranslocation assay with biotin acceptor peptide (BAP)-tagged SP proteins. Use of alanine substitution mutants of BAP-tagged MMTV SP in retrotranslocation assays revealed that mutation of amino acids 57 and 58 (M57-58) interfered with ER membrane extraction, whereas adjacent mutations did not. The M57-58 mutant also showed reduced interaction with VCP/p97 in coimmunoprecipitation experiments. Using transfection and reporter assays to measure activity of BAP-tagged proteins, both M57-58 and an adjacent mutant (M59-61) were functionally defective compared to wild-type SP. Confocal microscopy revealed defects in SP nuclear trafficking and abnormal localization of both M57-58 and M59-61. Furthermore, purified glutathione S-transferase (GST)-tagged M57-58 and M59-61 demonstrated reduced ability to oligomerize compared to tagged wild-type SP. These experiments suggest that SP amino acids 57 and 58 are critical for VCP/p97 interaction and retrotranslocation, whereas residues 57 to 61 are critical for oligomerization and nuclear trafficking independent of the NLS/NoLS. Our results emphasize the complex host interactions with long signal peptides. IMPORTANCE Endoplasmic reticulum-associated degradation (ERAD) is a form of cellular protein quality control that is manipulated by viruses, including the betaretrovirus, mouse mammary tumor virus (MMTV). MMTV-encoded signal peptide (SP) has been shown to interact with an essential ERAD factor, VCP/p97 ATPase, to mediate its extraction from the ER membrane, also known as retrotranslocation, for RNA binding and nuclear function. In this paper, we developed a quantitative retrotranslocation assay that identified an SP substitution mutant, which is defective for VCP interaction as well as nuclear trafficking, oligomer formation, and function. An adjacent SP mutant was competent for retrotranslocation and VCP interaction but shared the other defects. Our results revealed the requirement for VCP during SP trafficking and the complex cellular pathways used by long signal peptides.

Keywords:  ERAD; VCP; VCP/p97; betaretrovirus; mouse mammary tumor virus; p97; protein trafficking; retro translocation; signal peptide

DOI:  https://doi.org/10.1128/mBio.02953-21
Sci Adv. 2022 Jan 28. 8(4): eabh0496

The transmembrane endoplasmic reticulum-associated E3 ubiquitin ligase TRIM13 restrains the pathogenic-DNA-triggered inflammatory response.

Xuelian Li, Zhou Yu, Qian Fang, Mingjin Yang, Jiaying Huang, Zheng Li, Jianli Wang, Taoyong Chen.

The endoplasmic reticulum (ER)-localized stimulator of interferon genes (STING) is the core adaptor for the pathogenic-DNA-triggered innate response. Aberrant activation of STING causes autoinflammatory and autoimmune diseases, raising the concern about how STING is finely tuned during innate response to pathogenic DNAs. Here, we report that the transmembrane domain (TM)-containing ER-localized E3 ubiquitin ligase TRIM13 (tripartite motif containing 13) is required for restraining inflammatory response to pathogenic DNAs. TRIM13 deficiency enhances pathogenic-DNA-triggered inflammatory cytokine production, inhibits DNA virus replication, and causes age-related autoinflammation. Mechanistically, TRIM13 interacts with STING via the TM and catalyzes Lys6-linked polyubiquitination of STING, leading to decelerated ER exit and accelerated ER-initiated degradation of STING. STING deficiency reverses the enhanced innate anti-DNA virus response in TRIM13 knockout mice. Our study delineates a potential strategy for controlling the homeostasis of STING by transmembrane ER-associated TRIM13 during the pathogenic-DNA-triggered inflammatory response.

DOI: https://doi.org/10.1126/sciadv.abh0496
Cell Death Discov. 2022 Jan 24. 8(1): 34

ER stress-induced cell death proceeds independently of the TRAIL-R2 signaling axis in pancreatic β cells.

Cathrin Hagenlocher, Robin Siebert, Bruno Taschke, Senait Wieske, Angelika Hausser, Markus Rehm.

Prolonged ER stress and the associated unfolded protein response (UPR) can trigger programmed cell death. Studies in cancer cell lines demonstrated that the intracellular accumulation of TRAIL receptor-2 (TRAIL-R2) and the subsequent activation of caspase-8 contribute significantly to apoptosis induction upon ER stress. While this might motivate therapeutic strategies that promote cancer cell death through ER stress-induced caspase-8 activation, it could also support the unwanted demise of non-cancer cells. Here, we therefore investigated if TRAIL-R2 dependent signaling towards apoptosis can be induced in pancreatic β cells, whose loss by prolonged ER stress is associated with the onset of diabetes. Interestingly, we found that elevated ER stress in these cells does not result in TRAIL-R2 transcriptional induction or elevated protein levels, and that the barely detectable expression of TRAIL-R2 is insufficient to allow TRAIL-induced apoptosis to proceed. Overall, this indicates that apoptotic cell death upon ER stress most likely proceeds independent of TRAIL-R2 in pancreatic β cells. Our findings therefore point to differences in ER stress response and death decision-making between cancer cells and pancreatic β cells and also have implications for future targeted treatment strategies that need to differentiate between ER stress susceptibility of cancer cells and pancreatic β cells.

DOI: https://doi.org/10.1038/s41420-022-00830-y
J Neurosci. 2022 Jan 06. pii: JN-RM-1116-21. [Epub ahead of print]

Disrupting the balance of protein quality control protein UBQLN2 accelerates tau proteinopathy.

Julia E Gerson, Stephanie Sandoval-Pistorius, Jacqueline P Welday, Aleija Rodriguez, Jordan D Gregory, Nyjerus Liggans, Kylie Schache, Xingli Li, Hanna Trzeciakiewicz, Sami Barmada, Lisa M Sharkey, Henry L Paulson.

Tau protein accumulation drives toxicity in several neurodegenerative disorders. To better understand the pathways regulating tau homeostasis in disease, we investigated the role of ubiquilins (UBQLNs)-a class of proteins linked to ubiquitin-mediated protein quality control (PQC) and various neurodegenerative diseases-in regulating tau. Cell-based assays identified UBQLN2 as the primary brain-expressed UBQLN to regulate tau. UBQLN2 efficiently lowered wild-type tau levels irrespective of aggregation, suggesting that UBQLN2 interacts with and regulates tau protein under normal conditions or early in disease. Moreover, UBQLN2 itself proved to be prone to accumulation as insoluble protein in male and female tau transgenic mice and the human tauopathy progressive supranuclear palsy. Genetic manipulation of UBQLN2 in a tauopathy mouse model demonstrated that a physiological UBQLN2 balance is required for tau homeostasis. UBQLN2 overexpression exacerbated phosphorylated tau pathology and toxicity in mice expressing P301S mutant tau, whereas P301S mice lacking UBQLN2 showed significantly reduced phosphorylated tau. Further studies support the view that an imbalance of UBQLN2 perturbs ubiquitin-dependent PQC and autophagy. We conclude that changes in UBQLN2 levels, whether due to pathogenic mutations or secondary to disease states such as tauopathy, contribute to proteostatic imbalances that exacerbate neurodegeneration.SIGNIFICANCE STATEMENT We defined a role for the protein quality control protein, Ubiquilin-2 (UBQLN2), in age-related neurodegenerative tauopathies. This group of disorders is characterized by the accumulation of tau protein aggregates, which differ when UBQLN2 levels are altered. Given the lack of effective disease-modifying therapies for tauopathies and UBQLN2's function in handling various disease-linked proteins, we explored the role of UBQLN2 in regulating tau. We found that UBQLN2 reduced tau levels in cell models but behaved differently in mouse brain, where it accelerated mutant tau pathology and tau-mediated toxicity. A better understanding of the diverse functions of regulatory proteins like UBQLN2 can elucidate some of the causative factors in neurodegenerative disease and outline new routes to therapeutic intervention.

DOI: https://doi.org/10.1523/JNEUROSCI.1116-21.2021
Nat Commun. 2022 Jan 26. 13(1): 516

Differential roles for DNAJ isoforms in HTT-polyQ and FUS aggregation modulation revealed by chaperone screens.

Kinneret Rozales, Amal Younis, Naseeb Saida, Anatoly Meller, Hodaya Goldman, Lior Kellerman, Ronit Heinrich, Shai Berlin, Reut Shalgi.

Protein aggregation is a hallmark of neurodegeneration. Here, we find that Huntington's disease-related HTT-polyQ aggregation induces a cellular proteotoxic stress response, while ALS-related mutant FUS (mutFUS) aggregation leads to deteriorated proteostasis. Further exploring chaperone function as potential modifiers of pathological aggregation in these contexts, we reveal divergent effects of naturally-occurring chaperone isoforms on different aggregate types. We identify a complex of the full-length (FL) DNAJB14 and DNAJB12, that substantially protects from mutFUS aggregation, in an HSP70-dependent manner. Their naturally-occurring short isoforms, however, do not form a complex, and lose their ability to preclude mutFUS aggregation. In contrast, DNAJB12-short alleviates, while DNAJB12-FL aggravates, HTT-polyQ aggregation. DNAJB14-FL expression increases the mobility of mutFUS aggregates, and restores the deteriorated proteostasis in mutFUS aggregate-containing cells and primary neurons. Our results highlight a maladaptive cellular response to pathological aggregation, and reveal a layer of chaperone network complexity conferred by DNAJ isoforms, in regulation of different aggregate types.

DOI: https://doi.org/10.1038/s41467-022-27982-w
J Alzheimers Dis Rep. 2021 ;5(1): 855-869

Molecular Investigation of the Unfolded Protein Response in Select Human Tauopathies.

Aleksandra P Pitera, Iain J Hartnell, Lucy Scullard, Kirsten L Williamson, Delphine Boche, Vincent O'Connor, Katrin Deinhardt.

   Background: Tauopathies are a group of neurodegenerative diseases associated with the accumulation of misfolded tau protein. The mechanisms underpinning tau-dependent proteinopathy remain to be elucidated. A protein quality control pathway within the endoplasmic reticulum, the unfolded protein response (UPR), has been suggested as a possible pathway modulating cellular responses in a range of neurodegenerative diseases, including those associated with misfolded cytosolic tau.
Objective: In this study we investigated three different clinically defined tauopathies to establish whether these diseases are accompanied by the activation of UPR.
Methods: We used PCR and western blotting to probe for the modulation of several reliable UPR markers in mRNA and proteins extracted from three distinct tauopathies: 20 brain samples from Alzheimer's disease patients, 11 from Pick's disease, and 10 from progressive supranuclear palsy. In each disease samples from these patients were compared with equal numbers of age-matched non-demented controls.
Results: Our investigation showed that different markers of UPR are not changed at the late stage of any of the human tauopathies investigated. Interestingly, UPR signatures were often observed in non-demented controls.
Conclusion: These data from late-stage human cortical tissue report an activation of UPR markers within the aged brain across all cohorts investigated and further support the emerging evidence that the accumulation of misfolded cytosolic tau does not drive a disease-associated activation of UPR.

Keywords:  Alzheimer’s disease; BiP; Pick’s disease; XBP-1; endoplasmic reticulum; progressive supranuclear palsy; tau

DOI:  https://doi.org/10.3233/ADR-210050
Transl Androl Urol. 2021 Dec;10(12): 4320-4332

E3 ubiquitin ligase ASB17 is required for spermiation in mice.

Cong Shen, Jinfu Xu, Qiao Zhou, Meng Lin, Jinxing Lv, Xi Zhang, Yangyang Wu, Xia Chen, Jun Yu, Xiaoyan Huang, Bo Zheng.

   Background: A major goal of spermiation is to degrade the apical ectoplasmic specialization (ES) junction between Sertoli cells and elongating spermatids in preparation for the eventual disengagement of spermatids into the lumen. E3 ubiquitin ligases mediate the process of ubiquitination and the subsequent proteasomal degradation, but their specific role during spermiation remains largely unexplored.
Methods: Ankyrin repeat and SOCS box protein 17 (Asb17)-knockout mice were generated via a CRISPR/Cas9 approach. Epididymal sperm parameters were assessed by a computer-assisted sperm analysis (CASA) system, and morphological analysis of testicular tissues were performed based on histological and immunostaining staining, and transmission electron microscopy (TEM). The interactions between ASB17 and Espin (ESPN) were predicted by HawkDock server and validated through protein pull-down and immunoprecipitation assays.
Results: We report that ASB17, an E3 ligase, is required for the completion of spermiation and that mice lacking Asb17 are oligozoospermic owing to spermiation failure. ASB17-deficient mice are fertile; however, spermatids exhibit a disorganized ES junction, resulting in retention within the seminiferous epithelium. Mechanistically, ASB17 deficiency leads to excess accumulation of ESPN, an actin-binding essential structural component of the ES. We determined that ASB17 regulates the removal of the ES through ubiquitin mediated protein degradation of ESPN.
Conclusions: In summary, our study describes a role for ASB17 in the regulation of cell-cell junctions between germ cells and somatic cells in the testis. These findings establish a novel mechanism for the regulatory role of E3 ligases during spermatogenesis.

Keywords:  ASB17; E3 ligase; ESPN; Spermiation; ectoplasmic specialization (ES)

DOI:  https://doi.org/10.21037/tau-21-789
Plant Cell. 2022 Jan 28. pii: koac014. [Epub ahead of print]

The TGN/EE SNARE protein SYP61 and the ubiquitin ligase ATL31 cooperatively regulate plant responses to carbon/nitrogen conditions in Arabidopsis.

Yoko Hasegawa, Thais Huarancca Reyes, Tomohiro Uemura, Anirban Baral, Akari Fujimaki, Yongming Luo, Yoshie Morita, Yasushi Saeki, Shugo Maekawa, Shigetaka Yasuda, Koki Mukuta, Yoichiro Fukao, Keiji Tanaka, Akihiko Nakano, Junpei Takagi, Rishikesh P Bhalerao, Junji Yamaguchi, Takeo Sato.

Ubiquitination is a post-translational modification involving the reversible attachment of the small protein ubiquitin to a target protein. Ubiquitination is involved in numerous cellular processes, including the membrane trafficking of cargo proteins. However, the ubiquitination of the trafficking machinery components and their involvement in environmental responses are not well understood. Here, we report that the Arabidopsis thaliana trans-Golgi network/early endosome (TGN/EE) localized SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein SYP61 interacts with the transmembrane ubiquitin ligase ATL31, a key regulator of resistance to disrupted carbon (C)/nitrogen/(N)-nutrient conditions. SYP61 is a key component of membrane trafficking in Arabidopsis. The subcellular localization of ATL31 was disrupted in knockdown mutants of SYP61, and the insensitivity of ATL31-overexpressing plants to high C/low N-stress was repressed in these mutants, suggesting that SYP61 and ATL31 cooperatively function in plant responses to nutrient stress. SYP61 is ubiquitinated in plants, and its ubiquitination level is upregulated under low C/high N-nutrient conditions. These findings provide important insights into the ubiquitin signaling and membrane trafficking machinery in plants.

DOI: https://doi.org/10.1093/plcell/koac014
Cell Rep. 2022 Jan 25. pii: S2211-1247(21)01801-5. [Epub ahead of print]38(4): 110286

Selective autophagy controls innate immune response through a TAK1/TAB2/SH3PX1 axis.

Panagiotis Tsapras, Stavroula Petridi, Selina Chan, Marta Geborys, Anne-Claire Jacomin, Antonia P Sagona, Pascal Meier, Ioannis P Nezis.

  Selective autophagy is a catabolic route that turns over specific cellular material for degradation by lysosomes, and whose role in the regulation of innate immunity is largely unexplored. Here, we show that the apical kinase of the Drosophila immune deficiency (IMD) pathway Tak1, as well as its co-activator Tab2, are both selective autophagy substrates that interact with the autophagy protein Atg8a. We also present a role for the Atg8a-interacting protein Sh3px1 in the downregulation of the IMD pathway, by facilitating targeting of the Tak1/Tab2 complex to the autophagy platform through its interaction with Tab2. Our findings show the Tak1/Tab2/Sh3px1 interactions with Atg8a mediate the removal of the Tak1/Tab2 signaling complex by selective autophagy. This in turn prevents constitutive activation of the IMD pathway in Drosophila. This study provides mechanistic insight on the regulation of innate immune responses by selective autophagy.

Keywords:  Drosophila; IMD; Sh3px1; Tab2; Tak1; autophagy; chronic inflammation; innate immunity

DOI:  https://doi.org/10.1016/j.celrep.2021.110286
Curr Biol. 2022 Jan 24. pii: S0960-9822(22)00013-6. [Epub ahead of print]

Whi3 mnemon association with endoplasmic reticulum membranes confines the memory of deceptive courtship to the yeast mother cell.

Yasmin Lau, Henry Patrick Oamen, Marcel Grogg, Iuliia Parfenova, Juha Saarikangas, Robin Hannay, Richard Alan Nichols, Donald Hilvert, Yves Barral, Fabrice Caudron.

Prion-like proteins are involved in many aspects of cellular physiology, including cellular memory. In response to deceptive courtship, budding yeast escapes pheromone-induced cell-cycle arrest through the coalescence of the G1/S inhibitor Whi3 into a dominant, inactive super-assembly. Whi3 is a mnemon (Whi3mnem), a protein that conformational change maintains as a trait in the mother cell but is not inherited by the daughter cells. How the maintenance and asymmetric inheritance of Whi3mnem are achieved is unknown. Here, we report that Whi3mnem is closely associated with endoplasmic reticulum (ER) membranes and is retained in the mother cell by the lateral diffusion barriers present at the bud neck. Strikingly, barrier defects made Whi3mnem propagate in a mitotically stable, prion-like manner. The amyloid-forming glutamine-rich domain of Whi3 was required for both mnemon and prion-like behaviors. Thus, we propose that Whi3mnem is in a self-templating state, lending temporal maintenance of memory, whereas its association with the compartmentalized membranes of the ER prevents infectious propagation to the daughter cells. These results suggest that confined self-templating super-assembly is a powerful mechanism for the long-term encoding of information in a spatially defined manner. Yeast courtship may provide insights on how individual synapses become potentiated in neuronal memory.

DOI: https://doi.org/10.1016/j.cub.2022.01.002
Redox Biol. 2022 Jan 20. pii: S2213-2317(22)00016-7. [Epub ahead of print]50 102244

The extracellular Ero1α/PDI electron transport system regulates platelet function by increasing glutathione reduction potential.

Lu Wang, Xi Wang, Xiying Lv, Qiushuo Jin, Hongcai Shang, Chih-Chen Wang, Lei Wang.

  Protein disulfide isomerase (PDI), an oxidoreductase, possesses two vicinal cysteines in the -Cys-Gly-His-Cys-motif that either form a disulfide bridge (S-S) or exist in a sulfhydryl form (-SH), forming oxidized or reduced PDI, respectively. PDI has been proven to be critical for platelet aggregation, thrombosis, and hemostasis, and PDI inhibition is being evaluated as a novel antithrombotic strategy. The redox states of functional PDI during the regulation of platelet aggregation, however, remain to be elucidated. Endoplasmic reticulum (ER) oxidoreductin-1α (Ero1α) and PDI constitute the pivotal oxidative folding pathway in the ER and play an important role in ER redox homeostasis. Whether Ero1α and PDI constitute an extracellular electron transport pathway to mediate platelet aggregation is an open question. Here, we found that oxidized but not reduced PDI promotes platelet aggregation. On the platelet surface, Ero1α constitutively oxidizes PDI and further regulates platelet aggregation in a glutathione-dependent manner. The Ero1α/PDI system oxidizes reduced glutathione (GSH) and establishes a reduction potential optimal for platelet aggregation. Therefore, platelet aggregation is mediated by the Ero1α-PDI-GSH electron transport system on the platelet surface. We further showed that targeting the functional interplay between PDI and Ero1α by small molecule inhibitors may be a novel strategy for antithrombotic therapy.

Keywords:  Ero1α; Glutathione; PDI; Platelet; Redox

DOI:  https://doi.org/10.1016/j.redox.2022.102244
Biochem Soc Trans. 2022 Jan 25. pii: BST20210819. [Epub ahead of print]

Molecular regulation of autophagosome formation.

Yan Hu, Fulvio Reggiori.

  Macroautophagy, hereafter autophagy, is a degradative process conserved among eukaryotes, which is essential to maintain cellular homeostasis. Defects in autophagy lead to numerous human diseases, including various types of cancer and neurodegenerative disorders. The hallmark of autophagy is the de novo formation of autophagosomes, which are double-membrane vesicles that sequester and deliver cytoplasmic materials to lysosomes/vacuoles for degradation. The mechanism of autophagosome biogenesis entered a molecular era with the identification of autophagy-related (ATG) proteins. Although there are many unanswered questions and aspects that have raised some controversies, enormous advances have been done in our understanding of the process of autophagy in recent years. In this review, we describe the current knowledge about the molecular regulation of autophagosome formation, with a particular focus on budding yeast and mammalian cells.

Keywords:  ATG proteins; autophagy; degradation; lysosomes; phagophore; sequestration

DOI:  https://doi.org/10.1042/BST20210819
Cell Mol Life Sci. 2022 Jan 23. 79(2): 86

Helicobacter pylori-induced reactive oxygen species direct turnover of CSN-associated STAMBPL1 and augment apoptotic cell death.

Supattra Chaithongyot, Michael Naumann.

  Deubiquitinylases (DUBs) are central regulators of the ubiquitin system involved in protein regulation and cell signalling and are important for a variety of physiological processes. Most DUBs are cysteine proteases, and few other proteases are metalloproteases of the JAB1/MPN +/MOV34 protease family (JAMM). STAM-binding protein like 1 (STAMBPL1), a member of the JAMM family, cleaves ubiquitin bonds and has a function in regulating cell survival, Tax-mediated nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) activation and epithelial-mesenchymal transition. However, the molecular mechanism by which STAMBPL1 influences cell survival is not well defined, especially with regard to its deubiquitinylation function. Here, we show that reactive oxygen species (ROS) induced by chemotherapeutic agents or the human microbial pathogen Helicobacter pylori can induce cullin 1-RING ubiquitin ligase (CRL1) and 26S proteasome-dependent degradation STAMBPL1. Interestingly, STAMBPL1 has a direct interaction with the constitutive photomorphogenic 9 (COP9 or CSN) signalosome subunits CSN5 and CSN6. The interaction with the CSN is required for the stabilisation and function of the STAMBPL1 protein. In addition, STAMBPL1 deubiquitinylates the anti-apoptotic protein Survivin and thus ameliorates cell survival. In summary, our data reveal a previously unknown mechanism by which the deubiquitinylase STAMBPL1 and the E3 ligase CRL1 balance the level of Survivin degradation and thereby determine apoptotic cell death. In response to genotoxic stress, the degradation of STAMBPL1 augments apoptotic cell death. This new mechanism may be useful to develop therapeutic strategies targeting STAMBPL1 in tumours that have high STAMBPL1 and Survivin protein levels.

Keywords:  Cullin-RING-ubiquitin ligase; Genotoxic stress; Ubiquitinylation

DOI:  https://doi.org/10.1007/s00018-022-04135-2
Front Plant Sci. 2021 ;12 806129

A Yeast-Based Functional Assay to Study Plant N-Degron - N-Recognin Interactions.

Aida Kozlic, Nikola Winter, Theresia Telser, Jakob Reimann, Katrin Rose, Lilian Nehlin, Sophie Berckhan, Gunjan Sharma, Charlene Dambire, Tinne Boeckx, Michael J Holdsworth, Andreas Bachmair.

  The N-degron pathway is a branch of the ubiquitin-proteasome system where amino-terminal residues serve as degradation signals. In a synthetic biology approach, we expressed ubiquitin ligase PRT6 and ubiquitin conjugating enzyme 2 (AtUBC2) from Arabidopsis thaliana in a Saccharomyces cerevisiae strain with mutation in its endogenous N-degron pathway. The two enzymes re-constitute part of the plant N-degron pathway and were probed by monitoring the stability of co-expressed GFP-linked plant proteins starting with Arginine N-degrons. The novel assay allows for straightforward analysis, whereas in vitro interaction assays often do not allow detection of the weak binding of N-degron recognizing ubiquitin ligases to their substrates, and in planta testing is usually complex and time-consuming.

Keywords:  Arabidopsis thaliana; N-degron pathway; N-recognin; PRT6; synthetic biology; ubiquitin-dependent proteolysis; yeast-based assay

DOI:  https://doi.org/10.3389/fpls.2021.806129
J Biol Chem. 2022 Jan 20. pii: S0021-9258(22)00051-5. [Epub ahead of print] 101611

TRIM34 modulates influenza virus-activated programmed cell death by targeting Z-DNA-binding protein 1 for K63-linked polyubiquitination.

Xiaoyan Wang, Jing Xiong, Diwei Zhou, Shanfeng Zhang, Li Wang, Qingqing Tian, Changming Li, Jie Liu, Yaping Wu, Junying Li, Jun Wang.

  Z-DNA-binding protein 1 (ZBP1) is an innate sensor of influenza A virus (IAV) that participates in IAV-induced programmed cell death. Nevertheless, little is known about the upstream signaling pathways regulating ZBP1. We found that a member of the tripartite motif (TRIM) family, TRIM34, interacted with ZBP1 to promote its K63-linked polyubiquitination. Using a series of genetic approaches, we provide in vitro and in vivo evidence indicating that IAV triggered cell death and inflammatory responses via dependent on TRIM34/ZBP1 interaction. TRIM34 and ZBP1 expression and interaction protected mice from death during IAV infection owing to reduced inflammatory responses and epithelial damage. Additionally, analysis of clinical samples revealed that TRIM34 associates with ZBP1 and mediates ZBP1 polyubiquitination in vivo. Higher levels of proinflammatory cytokines correlated with higher levels of ZBP1 in IAV-infected patients. Taken together, we conclude that TRIM34 serves as a critical regulator of IAV-induced programmed cell death by mediating the K63-linked polyubiquitination of ZBP1.

Keywords:  Influenza A virus; Programmed cell death; TRIM34; ZBP1; polyubiquitination

DOI:  https://doi.org/10.1016/j.jbc.2022.101611
Cell Death Discov. 2022 Jan 25. 8(1): 37

Disruption of actin dynamics induces autophagy of the eukaryotic chaperonin TRiC/CCT.

Yuki Date, Akira Matsuura, Eisuke Itakura.

Autophagy plays important role in the intracellular protein quality control system by degrading abnormal organelles and proteins, including large protein complexes such as ribosomes. The eukaryotic chaperonin tailless complex polypeptide 1 (TCP1) ring complex (TRiC), also called chaperonin-containing TCP1 (CCT), is a 1-MDa hetero-oligomer complex comprising 16 subunits that facilitates the folding of ~10% of the cellular proteome that contains actin. However, the quality control mechanism of TRiC remains unclear. To monitor the autophagic degradation of TRiC, we generated TCP1α-RFP-GFP knock-in HeLa cells using a CRISPR/Cas9-knock-in system with an RFP-GFP donor vector. We analyzed the autophagic degradation of TRiC under several stress conditions and found that treatment with actin (de)polymerization inhibitors increased the lysosomal degradation of TRiC, which was localized in lysosomes and suppressed by deficiency of autophagy-related genes. Furthermore, we found that treatment with actin (de)polymerization inhibitors increased the association between TRiC and unfolded actin, suggesting that TRiC was inactivated. Moreover, unfolded actin mutants were degraded by autophagy. Taken together, our results indicate that autophagy eliminates inactivated TRiC, serving as a quality control system.

DOI: https://doi.org/10.1038/s41420-022-00828-6
Dis Model Mech. 2022 Jan 28. pii: dmm.049258. [Epub ahead of print]

A novel yeast model detects Nrf2 and Keap1 interactions with Hsp90.

Vy Ngo, Anne Brickenden, Hansen Liu, Cynthia Yeung, Wing-Yiu Choy, Martin L Duennwald.

  Nrf2 is the master transcriptional regulator of cellular responses against oxidative stress. It is chiefly regulated by Keap1, a substrate adaptor protein that mediates Nrf2 degradation. Nrf2 activity is also influenced by many other protein interactions that provide Keap1-independent regulation. To study Nrf2 regulation, we establish and characterize yeast models expressing human Nrf2, Keap1, and other proteins that interact with and regulate Nrf2. Yeast models have been well-established as powerful tools to study protein function and genetic and physical protein-protein interactions. In this work, we recapitulate previously described Nrf2 interactions in yeast and discover that Nrf2 interacts with the molecular chaperone Hsp90. Our work establishes yeast as a useful tool to study Nrf2 interactions and provides novel insight into the crosstalk between the antioxidant response and the heat shock response.

Keywords:  Hsp90; Keap1; Molecular chaperones; Nrf2; Protein interactions; Yeast model

DOI:  https://doi.org/10.1242/dmm.049258
J Biol Chem. 2022 Jan 20. pii: S0021-9258(22)00047-3. [Epub ahead of print] 101607

The mammalian trafficking chaperone protein UNC93B1 maintains the ER calcium sensor STIM1 in a dimeric state primed for translocation to the ER cortex.

Wen-An Wang, Nicolas Demaurex.

  The stromal interaction molecule 1 (STIM1) is an endoplasmic reticulum (ER) Ca2+ sensor that regulates the activity of Orai plasma membrane Ca2+ channels to mediate the store-operated Ca2+ entry (SOCE) pathway essential for immunity. Unc-93 homologue B1 (UNC93B1) is a multiple membrane-spanning ER protein that acts as a trafficking chaperone by guiding nucleic-acid sensing toll-like receptors (TLRs) to their respective endosomal signaling compartments. We previously showed that UNC93B1 interacts with STIM1 to promote antigen cross-presentation in dendritic cells, but the STIM1 binding site(s) and activation step(s) impacted by this interaction remained unknown. In this study, we show that UNC93B1 interacts with STIM1 in the ER lumen by binding to residues in close proximity to the transmembrane domain. Cysteine cross-linking in-vivo showed that UNC93B1 binding promotes the zipping of transmembrane and proximal cytosolic helices within resting STIM1 dimers, priming STIM1 for translocation. In addition, we show that UNC93B1 deficiency reduces SOCE and STIM1/Orai1 interactions and targets STIM1 to lighter ER domains, while UNC93B1 expression accelerates the recruitment of STIM1 to cortical ER domains. We conclude that UNC93B1 therefore acts as a trafficking chaperone by maintaining the pool of resting STIM1 proteins in a state primed for activation, enabling their rapid translocation in an extended conformation to cortical ER signaling compartments.

Keywords:  calcium signaling; innate immunity; ion channels; membrane contact sites; protein trafficking

DOI:  https://doi.org/10.1016/j.jbc.2022.101607
Chem Commun (Camb). 2022 Jan 28.

Fluorescent probes for targeting endoplasmic reticulum: design strategies and their applications.

Deepmala Singh, Deeksha Rajput, Sriram Kanvah.

Advances in developing organic fluorescent probes and fluorescence imaging techniques have enhanced our understanding of cell biology. The endoplasmic reticulum (ER) is a dynamic structure that plays a crucial role in protein synthesis, post-translational modifications, and lipid metabolism. The malfunction of ER contributes to several physiological and pathological conditions. Therefore, the investigations on the imaging and role of ER have attracted a lot of attention. Due to their simplicity, synthetic tunability, photostability, high quantum yields, easier cellular uptake, and lower cytotoxicity, organic fluorophores offer invaluable tools for the precision targeting of various cellular organelles and probe ER dynamics. The precision staining is made possible by incorporating specific functional groups having preferential and local organelle biomolecular interactions. For instance, functional moieties such as methyl sulfonamide, sulfonylurea, and pentafluorophenyl assist in ER targeting and thus have become essential tools to probe a deeper understanding of their dynamics. Furthermore, dual-function fluorescent probes that simultaneously image ER and detect specific physiological parameters or biological analytes were achieved by introducing special recognition or chemically reactive sites. This article attempts to comprehensively capture various design strategies currently employed by researchers utilizing small organic molecules to target the ER and detect specific analytes.

DOI: https://doi.org/10.1039/d1cc06944f
iScience. 2022 Jan 21. 25(1): 103715

Cytosolic adaptation to mitochondria-induced proteostatic stress causes progressive muscle wasting.

Xiaowen Wang, Frank A Middleton, Rabi Tawil, Xin Jie Chen.

  Mitochondrial dysfunction causes muscle wasting in many diseases and probably also during aging. The underlying mechanism is poorly understood. We generated transgenic mice with unbalanced mitochondrial protein loading and import, by moderately overexpressing the nuclear-encoded adenine nucleotide translocase, Ant1. We found that these mice progressively lose skeletal muscle. Ant1-overloading reduces mitochondrial respiration. Interestingly, it also induces small heat shock proteins and aggresome-like structures in the cytosol, suggesting increased proteostatic burden due to accumulation of unimported mitochondrial preproteins. The transcriptome of Ant1-transgenic muscles is drastically remodeled to counteract proteostatic stress, by repressing protein synthesis and promoting proteasomal function, autophagy, and lysosomal amplification. These proteostatic adaptations collectively reduce protein content thereby reducing myofiber size and muscle mass. Thus, muscle wasting can occur as a trade-off of adaptation to mitochondria-induced proteostatic stress. This finding could have implications for understanding the mechanism of muscle wasting, especially in diseases associated with Ant1 overexpression, including facioscapulohumeral dystrophy.

Keywords:  Biological sciences; Cell biology; Cellular physiology; Functional aspects of cell biology

DOI:  https://doi.org/10.1016/j.isci.2021.103715
EMBO Rep. 2022 Jan 26. e51932

USP17 is required for peripheral trafficking of lysosomes.

Jia Lin, Aidan P McCann, Naphannop Sereesongsaeng, Jonathan M Burden, Alhareth A Alsa'd, Roberta E Burden, Ileana Micu, Richard Williams, Sandra Van Schaeybroeck, Emma Evergren, Paul Mullan, Jeremy C Simpson, Christopher J Scott, James F Burrows.

  Expression of the deubiquitinase USP17 is induced by multiple stimuli, including cytokines (IL-4/6), chemokines (IL-8, SDF1), and growth factors (EGF), and several studies indicate it is required for cell proliferation and migration. However, the mechanisms via which USP17 impacts upon these cellular functions are unclear. Here, we demonstrate that USP17 depletion prevents peripheral lysosome positioning, as well as trafficking of lysosomes to the cell periphery in response to EGF stimulation. Overexpression of USP17 also increases secretion of the lysosomal protease cathepsin D. In addition, USP17 depletion impairs plasma membrane repair in cells treated with the pore-forming toxin streptolysin O, further indicating that USP17 is required for lysosome trafficking to the plasma membrane. Finally, we demonstrate that USP17 can deubiquitinate p62, and we propose that USP17 can facilitate peripheral lysosome trafficking by opposing the E3 ligase RNF26 to untether lysosomes from the ER and facilitate lysosome peripheral trafficking, lysosome protease secretion, and plasma membrane repair.

Keywords:  EGF; USP17; exocytosis; lysosome

DOI:  https://doi.org/10.15252/embr.202051932
Biochim Biophys Acta Rev Cancer. 2022 Jan 21. pii: S0304-419X(22)00004-X. [Epub ahead of print] 188679

E2-E3 ubiquitin enzyme pairing - partnership in provoking or mitigating cancers.

Shu-Chun Chang, Bo-Xiang Zhang, Jeak Ling Ding.

  The ubiquitin-proteasome system (UPS) modulates carcinogenesis through ubiquitination of cancer-related target proteins, leading to their degradation in the proteasome. This may deactivate tumor suppressors or activate tumor promoters- either way causing homeostatic imbalance. As major components of the UPS, the E2 and E3 enzymes are recognized as pivotal determinants of substrate recognition and ubiquitination. Identification of E2-E3 pairing selectivity is particularly pertinent to early diagnosis and potential development of targeted cancer therapeutics. This review is motivated by recent findings and new insights into the molecular dynamics of ubiquitination triggered by specific E2-E3 pairing, leading to cancer initiation and progression if cancer suppressors are degraded or cancer suppression (if cancer promoters are degraded), respectively. We provide an overview of strategies employed in screening for E2-E3 interactions based on up-to-date studies focusing on the E2-E3 interface motifs. Of considerable recent interest is how E2 and E3 might switch their functional partnerships via UBE2O, which suggests an emerging significance on how UBE2O might influence E2-E3 pairing. Thus, a reflection on the role of UBE2O is included. Finally, we deliberate on the rational and cautious development of anti-cancer cocktail drugs which specifically target E2-E3 interacting residues for precision in cancer-killing with minimal side-effects. To this end, a list of potential future research is proposed.

Keywords:  Carcinogenesis; E2-E3 enzyme pairing; Tumor microenvironment (TME); UBE2O; UPS screening approaches; Ubiquitin-proteasome system (UPS)

DOI:  https://doi.org/10.1016/j.bbcan.2022.188679
Proc Natl Acad Sci U S A. 2022 Feb 01. pii: e2107187119. [Epub ahead of print]119(5):

Deletion of SUMO1 attenuates behavioral and anatomical deficits by regulating autophagic activities in Huntington disease.

Uri Nimrod Ramírez-Jarquín, Manish Sharma, Wuyue Zhou, Neelam Shahani, Srinivasa Subramaniam.

  The CAG expansion of huntingtin (mHTT) associated with Huntington disease (HD) is a ubiquitously expressed gene, yet it prominently damages the striatum and cortex, followed by widespread peripheral defects as the disease progresses. However, the underlying mechanisms of neuronal vulnerability are unclear. Previous studies have shown that SUMO1 (small ubiquitin-like modifier-1) modification of mHtt promotes cellular toxicity, but the in vivo role and functions of SUMO1 in HD pathogenesis are unclear. Here, we report that SUMO1 deletion in Q175DN HD-het knockin mice (HD mice) prevented age-dependent HD-like motor and neurological impairments and suppressed the striatal atrophy and inflammatory response. SUMO1 deletion caused a drastic reduction in soluble mHtt levels and nuclear and extracellular mHtt inclusions while increasing cytoplasmic mHtt inclusions in the striatum of HD mice. SUMO1 deletion promoted autophagic activity, characterized by augmented interactions between mHtt inclusions and a lysosomal marker (LAMP1), increased LC3B- and LAMP1 interaction, and decreased interaction of sequestosome-1 (p62) and LAMP1 in DARPP-32-positive medium spiny neurons in HD mice. Depletion of SUMO1 in an HD cell model also diminished the mHtt levels and enhanced autophagy flux. In addition, the SUMOylation inhibitor ginkgolic acid strongly enhanced autophagy and diminished mHTT levels in human HD fibroblasts. These results indicate that SUMO is a critical therapeutic target in HD and that blocking SUMO may ameliorate HD pathogenesis by regulating autophagy activities.

Keywords:  gene expression; motor abnormality; neurodegeneration; posttranslational modification; striatal vulnerability

DOI:  https://doi.org/10.1073/pnas.2107187119
Mol Neurobiol. 2022 Jan 27.

COP1 Acts as a Ubiquitin Ligase for PCDH9 Ubiquitination and Degradation in Human Glioma.

Kunlin Zhou, Lei Wang, Yuelin Liu, Zhiyi Liu, Bin Zhang, Hengliang Shi.

  Constitutive photomorphogenic 1 (COP1, also known as RFWD2), a ring-finger-type E3 ubiquitin ligase, has been reported to play a pivotal role in the regulation of cell growth, apoptosis, and DNA repair. Accumulating evidence has suggested that COP1 plays a role in tumorigenesis by triggering the ubiquitination and degradation of its substrates, but the potential mechanism remains unclear. In this study, COP1 was used as a bait in a yeast two-hybrid experiment to screen COP1-interacting proteins in a human brain cDNA library, and the results indicated that protocadherin 9 (PCDH9) was a potential binding protein of COP1. The interaction between and colocalization of COP1 and PCDH9 was further confirmed by coimmunoprecipitation (co-IP) assay and immunofluorescent staining. Subsequently, we demonstrated that COP1 acted as an E3 ligase to promote the ubiquitination and degradation of PCDH9 through the proteasome pathway in glioma cells. Furthermore, we identified that the type of COP1 mediated PCDH9 ubiquitination was Lys48-linked polyubiquitination. Finally, we found that the COP1 protein level was inversely correlated with the PCDH9 protein level in human glioma tissues. Taken together, our results suggest that COP1 is an E3 ubiquitin ligase for PCDH9 and reveal an important mechanism for PCDH9 regulation in human glioma.

Keywords:  COP1; Glioma; PCDH9; Ubiquitination

DOI:  https://doi.org/10.1007/s12035-021-02634-0
iScience. 2022 Jan 21. 25(1): 103717

Endoplasmic reticulum-translocation is essential for APOL1 cellular toxicity.

Etty Kruzel-Davila, Ira Bavli-Kertselli, Ayala Ofir, Amber M Cheatham, Revital Shemer, Eid Zaknoun, Sergiy Chornyy, Orly Tabachnikov, Shamara E Davis, Atanu K Khatua, Karl Skorecki, Waldemar Popik.

  Two variants at the APOL1 gene, encoding apolipoprotein L1, account for more than 70% of the increased risk for chronic kidney disease in individuals of African ancestry. While the initiating event for APOL1 risk variant cell injury remains to be clarified, we explored the possibility of blocking APOL1 toxicity at a more upstream level. We demonstrate that deletion of the first six amino acids of exon 4 abrogates APOL1 cytotoxicity by impairing APOL1 translocation to the lumen of ER and splicing of the signal peptide. Likewise, in orthologous systems, APOL1 lethality was partially abrogated in yeast strains and flies with reduced dosage of genes encoding ER translocon proteins. An inhibitor of ER to Golgi trafficking reduced lethality as well. We suggest that targeting the MSALFL sequence or exon 4 skipping may serve as potential therapeutic approaches to mitigate the risk of CKD caused by APOL1 renal risk variants.

Keywords:  Cell biology; Cellular physiology; Functional aspects of cell biology

DOI:  https://doi.org/10.1016/j.isci.2021.103717
Nat Rev Mol Cell Biol. 2022 Jan 25.

Ubiquitin ligases: guardians of mammalian development.

David A Cruz Walma, Zhuoyao Chen, Alex N Bullock, Kenneth M Yamada.

Mammalian development demands precision. Millions of molecules must be properly located in temporal order, and their function regulated, to orchestrate important steps in cell cycle progression, apoptosis, migration and differentiation, to shape developing embryos. Ubiquitin and its associated enzymes act as cellular guardians to ensure precise spatio-temporal control of key molecules during each of these important cellular processes. Loss of precision results in numerous examples of embryological disorders or even cancer. This Review discusses the crucial roles of E3 ubiquitin ligases during key steps of early mammalian development and their roles in human disease, and considers how new methods to manipulate and exploit the ubiquitin regulatory machinery - for example, the development of molecular glues and PROTACs - might facilitate clinical therapy.

DOI: https://doi.org/10.1038/s41580-021-00448-5
Cell Death Differ. 2022 Jan 22.

Palmitoylation restricts SQSTM1/p62-mediated autophagic degradation of NOD2 to modulate inflammation.

Lingli Zhou, Xing He, Liqiu Wang, Ping Wei, Zhe Cai, Song Zhang, Shouheng Jin, Huasong Zeng, Jun Cui.

The nucleotide-binding oligomerization domain protein 2 (NOD2) senses bacterial peptidoglycan to induce proinflammatory and antimicrobial responses. Dysregulation of NOD2 signaling is involved in multiple inflammatory disorders. Recently, S-palmitoylation, a novel type of post-translational modification, is reported to play a crucial role in membrane association and ligand-induced signaling of NOD2, yet its influence on the stability of NOD2 is unclear. Here we show that inhibition of S-palmitoylation facilitates the SQSTM1/p62-mediated autophagic degradation of NOD2, while S-palmitoylation of NOD2 by ZDHHC5 promotes the stability of NOD2. Furthermore, we identify a gain-of-function R444C variant of NOD2 short isoform (NOD2s-R444C) in autoinflammatory disease, which induces excessive inflammation through its high S-palmitoylation level. Mechanistically, the NOD2s-R444C variant possesses a stronger binding ability to ZDHHC5, which promotes its S-palmitoylation, and restricts its autophagic degradation by reducing its interaction with SQSTM1/p62. Taken together, our study reveals the regulatory role of S-palmitoylation in controlling NOD2 stability through the crosstalk with autophagy, and provides insights into the association between dysfunctional S-palmitoylation and the occurrence of inflammatory diseases.

DOI: https://doi.org/10.1038/s41418-022-00942-z
J Mol Biol. 2022 Jan 20. pii: S0022-2836(22)00023-7. [Epub ahead of print] 167459

Co-translational membrane targeting and holo-translocon docking of ribosomes translating the SRP receptor.

Michal Mayer, Lulu Winer, Amihai Karniel, Elhanan Pinner, Eliane H Yardeni, David Morgenstern, Eitan Bibi.

  Many integral membrane proteins are produced by translocon-associated ribosomes. The assembly of ribosomes translating membrane proteins on the translocons is mediated by a conserved system, composed of the signal recognition particle and its receptor (FtsY in Escherichia coli). FtsY is a peripheral membrane protein, and its role late during membrane protein targeting involves interactions with the translocon. However, earlier stages in the pathway have remained obscure, namely, how FtsY targets the membrane in vivo and where it initially docks. Our previous studies have demonstrated co-translational membrane-targeting of FtsY translation intermediates and identified a nascent FtsY targeting-peptide. Here, in a set of in vivo experiments, we utilized tightly stalled FtsY translation intermediates, pull-down assays and site-directed cross-linking, which revealed FtsY-nascent chain-associated proteins in the cytosol and on the membrane. Our results demonstrate interactions between the FtsY-translating ribosomes and cytosolic chaperones, which are followed by directly docking on the translocon. In support of this conclusion, we show that translocon over-expression increases dramatically the amount of membrane associated FtsY-translating ribosomes. The co-translational contacts of the FtsY nascent chains with the translocon differ from its post-translational contacts, suggesting a major structural maturation process. The identified interactions led us to propose a model for how FtsY may target the membrane co-translationally. On top of our past observations, the current results may add another tier to the hypothesis that FtsY act stoichiometrically in targeting ribosomes to the membrane in a constitutive manner.

Keywords:  FtsY; Holo-translocon; Membrane protein biogenesis; Membrane ribosomes; SRP-receptor; SecA; SecDFYajC; SecYEG; Trigger factor (TF); YfgM, Co-translational targeting; YidC

DOI:  https://doi.org/10.1016/j.jmb.2022.167459
J Cell Sci. 2022 Jan 26. pii: jcs.259449. [Epub ahead of print]

SUMOylation modulates the function of DDX19 in mRNA export.

Poulomi Banerjee, Shubha Markande, Misha Kalarikkal, Jomon Joseph.

  Nuclear export of mRNAs is a critical regulatory step in eukaryotic gene expression. The mRNA transcript undergoes extensive processing, and is loaded with a set of RNA-binding proteins (RBPs) to form export-competent messenger ribonucleoprotein particles (mRNPs) in the nucleus. During the transit of mRNPs through the nuclear pore complex (NPC), the DEAD-box ATPase - DDX19 - remodels mRNPs at the cytoplasmic side of the NPC, by removing a subset of RNA-binding proteins to terminate mRNP export. This requires the RNA-dependent ATPase activity of DDX19 and its dynamic interactions with Gle1 and Nup214. However, the regulatory mechanisms underlying these interactions are unclear. We find that DDX19 gets covalently attached with a small ubiquitin-like modifier (SUMO) at lysine 26, which enhances its interaction with Gle1. Furthermore, a SUMOylation-defective mutant of human DDX19B, K26R, failed to provide a complete rescue of the mRNA export defect caused by DDX19 depletion. Collectively, our results suggest that SUMOylation fine-tunes the function of DDX19 in mRNA export by regulating its interaction with Gle1. This study identifies SUMOylation of DDX19 as a modulatory mechanism during the mRNA export process.

Keywords:  DDX19; Gle1; MRNA export; Nup358; SUMO

DOI:  https://doi.org/10.1242/jcs.259449
Proc Natl Acad Sci U S A. 2022 Jan 25. pii: e2113704119. [Epub ahead of print]119(4):

Translational control of E2f1 regulates the Drosophila cell cycle.

Jan Inge Øvrebø, Mary-Rose Bradley-Gill, Norman Zielke, Minhee Kim, Marco Marchetti, Jonathan Bohlen, Megan Lewis, Monique van Straaten, Nam-Sung Moon, Bruce A Edgar.

  E2F transcription factors are master regulators of the eukaryotic cell cycle. In Drosophila, the sole activating E2F, E2F1, is both required for and sufficient to promote G1→S progression. E2F1 activity is regulated both by binding to RB Family repressors and by posttranscriptional control of E2F1 protein levels by the EGFR and TOR signaling pathways. Here, we investigate cis-regulatory elements in the E2f1 messenger RNA (mRNA) that enable E2f1 translation to respond to these signals and promote mitotic proliferation of wing imaginal disc and intestinal stem cells. We show that small upstream open reading frames (uORFs) in the 5' untranslated region (UTR) of the E2f1 mRNA limit its translation, impacting rates of cell proliferation. E2f1 transgenes lacking these 5'UTR uORFs caused TOR-independent expression and excess cell proliferation, suggesting that TOR activity can bypass uORF-mediated translational repression. EGFR signaling also enhanced translation but through a mechanism less dependent on 5'UTR uORFs. Further, we mapped a region in the E2f1 mRNA that contains a translational enhancer, which may also be targeted by TOR signaling. This study reveals translational control mechanisms through which growth signaling regulates cell cycle progression.

Keywords:  E2F1; TOR; cell cycle; translational control; uORF

DOI:  https://doi.org/10.1073/pnas.2113704119
Life Sci Alliance. 2022 May;pii: e202101279. [Epub ahead of print]5(5):

Small disulfide loops in peptide hormones mediate self-aggregation and secretory granule sorting.

Jennifer Reck, Nicole Beuret, Erhan Demirci, Cristina Prescianotto-Baschong, Martin Spiess.

Unlike constitutively secreted proteins, peptide hormones are stored in densely packed secretory granules, before regulated release upon stimulation. Secretory granules are formed at the TGN by self-aggregation of prohormones as functional amyloids. The nonapeptide hormone vasopressin, which forms a small disulfide loop, was shown to be responsible for granule formation of its precursor in the TGN as well as for toxic fibrillar aggregation of unfolded mutants in the ER. Several other hormone precursors also contain similar small disulfide loops suggesting their function as a general device to mediate aggregation for granule sorting. To test this hypothesis, we studied the capacity of small disulfide loops of different hormone precursors to mediate aggregation in the ER and the TGN. They indeed induced ER aggregation in Neuro-2a and COS-1 cells. Fused to a constitutively secreted reporter protein, they also promoted sorting into secretory granules, enhanced stimulated secretion, and increased Lubrol insolubility in AtT20 cells. These results support the hypothesis that small disulfide loops act as novel signals for sorting into secretory granules by self-aggregation.

DOI: https://doi.org/10.26508/lsa.202101279
Traffic. 2022 Jan 25.

Segregation of the membrane cargoes, BACE1 and amyloid precursor protein (APP) throughout the Golgi apparatus.

Lou Fourriere, Ellie Hyun-Jung Cho, Paul A Gleeson.

  The intracellular trafficking of BACE1 and APP regulates amyloid-β production. Our previous work demonstrated that newly synthesised BACE1 and APP are segregated into distinct trafficking pathways from the trans-Golgi network (TGN), and that alterations in their trafficking leads to an increase in Aβ production in non-neuronal and neuronal cells. However, it is not known whether BACE1 and APP are transported through the Golgi stacks together and sorted at the TGN or segregated prior to arrival at the TGN. To address this question, we have used high-resolution Airyscan technology followed by Huygens deconvolution to quantify the overlap of BACE1 and APP in Golgi subcompartments in HeLa cells and primary neurons. Here we show that APP and BACE1 are segregated, on exit from the endoplasmic reticulum and in the cis-Golgi and throughout the Golgi stack. In contrast, the transferrin receptor, which exits the TGN in AP-1 mediated transport carriers as for BACE1, colocalizes with BACE1, but not APP, throughout the Golgi stack. The segregation of APP and BACE1 is independent of the Golgi ribbon structure and the cytoplasmic domain of the cargo. Overall, our findings reveal the segregation of different membrane cargoes early in the secretory pathway, a finding relevant to the regulation of APP processing events. This article is protected by copyright. All rights reserved.

Keywords:  Airyscan microscopy; amyloid precursor protein (APP); beta-secretase 1 (BACE1); colocalization; segregation; trans-Golgi network (TGN)

DOI:  https://doi.org/10.1111/tra.12831
FEBS J. 2022 Jan 26.

AKT1 mediates multiple phosphorylation events that functionally promote HSF1 activation.

Wen-Cheng Lu, Ramsey Omari, Haimanti Ray, John Wang, Imade Williams, Curteisha Jacobs, Natasha Hockaden, Matthew L Bochman, Richard L Carpenter.

  The heat stress response activates the transcription factor heat shock factor 1 (HSF1), which subsequently upregulates heat shock proteins to maintain the integrity of the proteome. HSF1 activation requires nuclear localization, trimerization, DNA binding, phosphorylation, and gene transactivation. Phosphorylation at S326 is an important regulator of HSF1 transcriptional activity. Phosphorylation at S326 is mediated by AKT1, mTOR, p38, MEK1, and DYRK2. Here, we observed activation of HSF1 by AKT1 independently of mTOR. AKT2 also phosphorylated S326 of HSF1 but showed weak ability to activate HSF1. Similarly, mTOR, p38, MEK1, and DYRK2 all phosphorylated S326 but AKT1 was the most potent activator. Mass spectrometry showed that AKT1 also phosphorylated HSF1 at T142, S230, and T527 in addition to S326 whereas the other kinases did not. Subsequent investigation revealed that phosphorylation at T142 is necessary for HSF1 trimerization and that S230, S326, and T527 are required for HSF1 gene transactivation and recruitment of TFIIB and CDK9. Interestingly, T527 as a phosphorylated residue has not been previously shown and sits in the transactivation domain, further implying a role for this site in HSF1 gene transactivation. This study suggests that HSF1 hyperphosphorylation is targeted and these specific residues have direct function in regulating HSF1 transcriptional activity.

Keywords:  AKT1; HSF1; heat shock; phosphorylation

DOI:  https://doi.org/10.1111/febs.16375
Neuron. 2022 Jan 20. pii: S0896-6273(21)01076-X. [Epub ahead of print]

Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9.

Sisi Yang, Daehun Park, Laura Manning, Sarah E Hill, Mian Cao, Zhao Xuan, Ian Gonzalez, Yongming Dong, Benjamin Clark, Lin Shao, Ifechukwu Okeke, Agustin Almoril-Porras, Jihong Bai, Pietro De Camilli, Daniel A Colón-Ramos.

  Autophagy is a cellular degradation pathway essential for neuronal health and function. Autophagosome biogenesis occurs at synapses, is locally regulated, and increases in response to neuronal activity. The mechanisms that couple autophagosome biogenesis to synaptic activity remain unknown. In this study, we determine that trafficking of ATG-9, the only transmembrane protein in the core autophagy pathway, links the synaptic vesicle cycle with autophagy. ATG-9-positive vesicles in C. elegans are generated from the trans-Golgi network via AP-3-dependent budding and delivered to presynaptic sites. At presynaptic sites, ATG-9 undergoes exo-endocytosis in an activity-dependent manner. Mutations that disrupt endocytosis, including a lesion in synaptojanin 1 associated with Parkinson's disease, result in abnormal ATG-9 accumulation at clathrin-rich synaptic foci and defects in activity-induced presynaptic autophagy. Our findings uncover regulated key steps of ATG-9 trafficking at presynaptic sites and provide evidence that ATG-9 exo-endocytosis couples autophagosome biogenesis at presynaptic sites with the activity-dependent synaptic vesicle cycle.

Keywords:  AP-3; ATG-9; Golgi apparatus; Parkinson’s disease; autophagy; clathrin; endocytosis; neuronal activity; synaptic vesicle cycle; synaptojanin 1/unc-26

DOI:  https://doi.org/10.1016/j.neuron.2021.12.031
Nat Commun. 2022 Jan 25. 13(1): 476

High-resolution structures of a thermophilic eukaryotic 80S ribosome reveal atomistic details of translocation.

Miglė Kišonaitė, Klemens Wild, Karine Lapouge, Thomas Ruppert, Irmgard Sinning.

Ribosomes are complex and highly conserved ribonucleoprotein assemblies catalyzing protein biosynthesis in every organism. Here we present high-resolution cryo-EM structures of the 80S ribosome from a thermophilic fungus in two rotational states, which due to increased 80S stability provide a number of mechanistic details of eukaryotic translation. We identify a universally conserved 'nested base-triple knot' in the 26S rRNA at the polypeptide tunnel exit with a bulged-out nucleotide that likely serves as an adaptable element for nascent chain containment and handover. We visualize the structure and dynamics of the ribosome protective factor Stm1 upon ribosomal 40S head swiveling. We describe the structural impact of a unique and essential m1acp3 Ψ 18S rRNA hyper-modification embracing the anticodon wobble-position for eukaryotic tRNA and mRNA translocation. We complete the eEF2-GTPase switch cycle describing the GDP-bound post-hydrolysis state. Taken together, our data and their integration into the structural landscape of 80S ribosomes furthers our understanding of protein biogenesis.

DOI: https://doi.org/10.1038/s41467-022-27967-9
FEBS Lett. 2022 Jan 25.

The deubiquitinating enzyme USP17 regulates c-Myc levels and controls cell proliferation and glycolysis.

Mai Nagasaka, Yasumichi Inoue, Manaka Yoshida, Chiharu Miyajima, Daisuke Morishita, Muneshige Tokugawa, Haruna Nakamoto, Mayumi Sugano, Nobumichi Ohoka, Hidetoshi Hayashi.

  The c-Myc oncoprotein is frequently overexpressed in human cancers and is essential for cancer cell proliferation. The dysregulation of ubiquitin-proteasome-mediated degradation is one of the contributing factors to the up-regulated expression of c-Myc in human cancers. We herein identified USP17 as a novel deubiquitinating enzyme that regulates c-Myc levels and controls cell proliferation and glycolysis. The overexpression of USP17 stabilized the c-Myc protein by promoting its deubiquitination. In contrast, the knockdown of USP17 promoted c-Myc degradation and reduced c-Myc levels. The knockdown of USP17 also suppressed cell proliferation and glycolysis. Collectively, the present results reveal a novel role for USP17 in the regulation of c-Myc stability, and suggest its potential as a therapeutic target for cancer treatment.

Keywords:  USP17; c-Myc; deubiquitination; glycolysis; proliferation

DOI:  https://doi.org/10.1002/1873-3468.14296