bims-proteo 2023-09-24 papers

bims-proteo

Biomed News

on Proteostasis

Issue of 2023–09–24
23 papers selected by
Eric Chevet, INSERM

ER-trafficking triggers NRF1 ubiquitination to promote its proteolytic activation.
Proteotoxic stress and the ubiquitin proteasome system.
Mechanistic characterization of disulfide bond reduction of an ERAD substrate mediated by cooperation between ERdj5 and BiP.
Temporal landscape of mitochondrial proteostasis governed by the UPRmt.
Defining E3 ligase-substrate relationships through multiplex CRISPR screening.
Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping.
Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C).
ER stress elicits non-canonical CASP8 (caspase 8) activation on autophagosomal membranes to induce apoptosis.
Unlocking DCAFs To Catalyze Degrader Development: An Arena for Innovative Approaches.
Changing the guard - nuclear pore complex quality control.
Regulation of nucleo-cytosolic 26S proteasome translocation by aromatic amino acids via mTOR is essential for cell survival under stress.
Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress.
Exploring The "Misfolding Problem" by Systematic Discovery and Analysis of Functional-But-Degraded Proteins.
Ksp1 is an autophagic receptor protein for the Snx4-assisted autophagy of Ssn2/Med13.
A mechanism that ensures non-selective cytoplasm degradation by autophagy.
PerTurboID, A targeted in situ method reveals the impact of kinase deletion on its local protein environment in the cytoadhesion complex of malaria causing parasites.
Dynamic association of the intramembrane proteases SPPL2a/b and their substrates with tetraspanin-enriched microdomains.
Protocol for quantifying the in vivo rate of protein degradation in mice using a pulse-chase technique.
PKR-mediated stress response enhances dengue and Zika virus replication.
Regulation of cellular cholesterol distribution via non-vesicular lipid transport at ER-Golgi contact sites.
Endoplasmic Reticulum Stress in Pancreatic β-Cells Induces Incretin Desensitization and β-Cell Dysfunction via ATF4-Mediated PDE4D Expression.
UBC13-mediated template switching promotes replication stress resistance in FBH1-deficient cells.
E3 ubiquitin ligase RNF187 promotes growth of spermatogonia via lysine 48-linked polyubiquitination-mediated degradation of KRT36/KRT84.

iScience. 2023 Oct 20. 26(10): 107777

ER-trafficking triggers NRF1 ubiquitination to promote its proteolytic activation.

Claire Chavarria, Léa Zaffalon, Sérgio T Ribeiro, Mélanie Op, Manfredo Quadroni, Maria Sofia Iatrou, Chloé Chapuis, Fabio Martinon.

  The transcription factor NRF1 resides in the endoplasmic reticulum (ER) and is constantly transported to the cytosol for proteasomal degradation. However, when the proteasome is defective, NRF1 escapes degradation and undergoes proteolytic cleavage by the protease DDI2, generating a transcriptionally active form that restores proteostasis, including proteasome function. The mechanisms that regulate NRF1 proteolytic activation and transcriptional potential remain poorly understood. This study demonstrates that the ER is a crucial regulator of NRF1 function by orchestrating its ubiquitination through the E3 ubiquitin ligase HRD1. We show that HRD1-mediated NRF1 ubiquitination is necessary for DDI2-mediated processing in cells. Furthermore, we found that deficiency in both RAD23A and RAD23B impaired DDI2-mediated NRF1 processing, indicating that these genes are essential components of the DDI2 proteolytic machinery. Our findings highlight the intricate mechanism by which the ER activates NRF1 to coordinate the transcriptional activity of an adaptation response in cells.

Keywords:  Biochemistry; Biological sciences; Cell biology; Natural sciences

DOI:  https://doi.org/10.1016/j.isci.2023.107777
Semin Cell Dev Biol. 2023 Sep 19. pii: S1084-9521(23)00161-1. [Epub ahead of print]

Proteotoxic stress and the ubiquitin proteasome system.

Rachel Kandel, Jasmine Jung, Sonya Neal.

  The ubiquitin proteasome system maintains protein homeostasis by regulating the breakdown of misfolded proteins, thereby preventing misfolded protein aggregates. The efficient elimination is vital for preventing damage to the cell by misfolded proteins, known as proteotoxic stress. Proteotoxic stress can lead to the collapse of protein homeostasis and can alter the function of the ubiquitin proteasome system. Conversely, impairment of the ubiquitin proteasome system can also cause proteotoxic stress and disrupt protein homeostasis. This review examines two impacts of proteotoxic stress, 1) disruptions to ubiquitin homeostasis (ubiquitin stress) and 2) disruptions to proteasome homeostasis (proteasome stress). Here, we provide a mechanistic description of the relationship between proteotoxic stress and the ubiquitin proteasome system. This relationship is illustrated by findings from several protein misfolding diseases, mainly neurodegenerative diseases, as well as from basic biology discoveries from yeast to mammals. In addition, we explore the importance of the ubiquitin proteasome system in endoplasmic reticulum quality control, and how proteotoxic stress at this organelle is alleviated. Finally, we highlight how cells utilize the ubiquitin proteasome system to adapt to proteotoxic stress and how the ubiquitin proteasome system can be genetically and pharmacologically manipulated to maintain protein homeostasis.

Keywords:  Aggregates; Deubiquitinase; Neurodegeneration; Nrf1; Proteasome; Proteasome stress; Protein misfolding; Proteotoxic stress; Ubiquitin; Ubiquitin proteasome system; Ubiquitin stress; Unfolded protein response; Usp14

DOI:  https://doi.org/10.1016/j.semcdb.2023.08.002
J Biol Chem. 2023 Sep 20. pii: S0021-9258(23)02302-5. [Epub ahead of print] 105274

Mechanistic characterization of disulfide bond reduction of an ERAD substrate mediated by cooperation between ERdj5 and BiP.

Xiaohan Cai, Shogo Ito, Kentaro Noi, Michio Inoue, Ryo Ushioda, Yukinari Kato, Kazuhiro Nagata, Kenji Inaba.

  Endoplasmic reticulum (ER)-associated degradation (ERAD) is a protein quality control process that eliminates misfolded proteins from the ER. DnaJ homolog subfamily C member 10 (ERdj5) is a protein disulfide isomerase (PDI) family member that accelerates ER-associated degradation (ERAD) by reducing disulfide bonds of aberrant proteins with the help of an ER-resident chaperone BiP. However, the detailed mechanisms by which ERdj5 acts in concert with BiP are poorly understood. In this study, we reconstituted an in vitro system that monitors ERdj5-mediated reduction of disulfide-linked J-chain oligomers, known to be physiological ERAD substrates. Biochemical analyses using purified proteins revealed that J-chain oligomers were reduced to monomers by ERdj5 in a stepwise manner via trimeric and dimeric intermediates, and BiP synergistically enhanced this action in an ATP-dependent manner. Single-molecule observations of ERdj5-catalyzed J-chain disaggregation using high-speed atomic force microscopy (HS-AFM) demonstrated the stochastic release of small J-chain oligomers through repeated actions of ERdj5 on peripheral and flexible regions of large J-chain aggregates. Using systematic mutational analyses, ERAD substrate disaggregation mediated by ERdj5 and BiP was dissected at the molecular level.

Keywords:  BiP; ER proteostasis; ER-associated degradation; ERdj5; J-chain; high-speed AFM

DOI:  https://doi.org/10.1016/j.jbc.2023.105274
Sci Adv. 2023 Sep 22. 9(38): eadh8228

Temporal landscape of mitochondrial proteostasis governed by the UPRmt.

Louise Uoselis, Runa Lindblom, Wai Kit Lam, Catharina J Küng, Marvin Skulsuppaisarn, Grace Khuu, Thanh N Nguyen, Danielle L Rudler, Aleksandra Filipovska, Ralf B Schittenhelm, Michael Lazarou.

Breakdown of mitochondrial proteostasis activates quality control pathways including the mitochondrial unfolded protein response (UPRmt) and PINK1/Parkin mitophagy. However, beyond the up-regulation of chaperones and proteases, we have a limited understanding of how the UPRmt remodels and restores damaged mitochondrial proteomes. Here, we have developed a functional proteomics framework, termed MitoPQ (Mitochondrial Proteostasis Quantification), to dissect the UPRmt's role in maintaining proteostasis during stress. We find essential roles for the UPRmt in both protecting and repairing proteostasis, with oxidative phosphorylation metabolism being a central target of the UPRmt. Transcriptome analyses together with MitoPQ reveal that UPRmt transcription factors drive independent signaling arms that act in concert to maintain proteostasis. Unidirectional interplay between the UPRmt and PINK1/Parkin mitophagy was found to promote oxidative phosphorylation recovery when the UPRmt failed. Collectively, this study defines the network of proteostasis mediated by the UPRmt and highlights the value of functional proteomics in decoding stressed proteomes.

DOI: https://doi.org/10.1126/sciadv.adh8228
Nat Cell Biol. 2023 Sep 21.

Defining E3 ligase-substrate relationships through multiplex CRISPR screening.

Richard T Timms, Elijah L Mena, Yumei Leng, Mamie Z Li, Iva A Tchasovnikarova, Itay Koren, Stephen J Elledge.

Specificity within the ubiquitin-proteasome system is primarily achieved through E3 ubiquitin ligases, but for many E3s their substrates-and in particular the molecular features (degrons) that they recognize-remain largely unknown. Current approaches for assigning E3s to their cognate substrates are tedious and low throughput. Here we developed a multiplex CRISPR screening platform to assign E3 ligases to their cognate substrates at scale. A proof-of-principle multiplex screen successfully performed ~100 CRISPR screens in a single experiment, refining known C-degron pathways and identifying an additional pathway through which Cul2FEM1B targets C-terminal proline. Further, by identifying substrates for Cul1FBXO38, Cul2APPBP2, Cul3GAN, Cul3KLHL8, Cul3KLHL9/13 and Cul3KLHL15, we demonstrate that the approach is compatible with pools of full-length protein substrates of varying stabilities and, when combined with site-saturation mutagenesis, can assign E3 ligases to their cognate degron motifs. Thus, multiplex CRISPR screening will accelerate our understanding of how specificity is achieved within the ubiquitin-proteasome system.

DOI: https://doi.org/10.1038/s41556-023-01229-2
Mol Cell. 2023 Sep 21. pii: S1097-2765(23)00658-5. [Epub ahead of print]83(18): 3377-3392.e6

Elucidation of E3 ubiquitin ligase specificity through proteome-wide internal degron mapping.

Zhiqian Zhang, Brandon Sie, Aiquan Chang, Yumei Leng, Christopher Nardone, Richard T Timms, Stephen J Elledge.

  The ubiquitin-proteasome system plays a critical role in biology by regulating protein degradation. Despite their importance, precise recognition specificity is known for a few of the 600 E3s. Here, we establish a two-pronged strategy for identifying and mapping critical residues of internal degrons on a proteome-scale in HEK-293T cells. We employ global protein stability profiling combined with machine learning to identify 15,800 peptides likely to contain sequence-dependent degrons. We combine this with scanning mutagenesis to define critical residues for over 5,000 predicted degrons. Focusing on Cullin-RING ligase degrons, we generated mutational fingerprints for 219 degrons and developed DegronID, a computational algorithm enabling the clustering of degron peptides with similar motifs. CRISPR analysis enabled the discovery of E3-degron pairs, of which we uncovered 16 pairs that revealed extensive degron variability and structural determinants. We provide the visualization of these data on the public DegronID data browser as a resource for future exploration.

Keywords:  Alphafold2; CRL; Cullin-RING ligase; DegronID; E3 ubiquitin ligase; GPS; degron; global protein stability; protein degradation; ubiquitination

DOI:  https://doi.org/10.1016/j.molcel.2023.08.022
Nat Struct Mol Biol. 2023 Sep 21.

Time-resolved cryo-EM (TR-EM) analysis of substrate polyubiquitination by the RING E3 anaphase-promoting complex/cyclosome (APC/C).

Tatyana Bodrug, Kaeli A Welsh, Derek L Bolhuis, Ethan Paulаkonis, Raquel C Martinez-Chacin, Bei Liu, Nicholas Pinkin, Thomas Bonacci, Liying Cui, Pengning Xu, Olivia Roscow, Sascha Josef Amann, Irina Grishkovskaya, Michael J Emanuele, Joseph S Harrison, Joshua P Steimel, Klaus M Hahn, Wei Zhang, Ellen D Zhong, David Haselbach, Nicholas G Brown.

Substrate polyubiquitination drives a myriad of cellular processes, including the cell cycle, apoptosis and immune responses. Polyubiquitination is highly dynamic, and obtaining mechanistic insight has thus far required artificially trapped structures to stabilize specific steps along the enzymatic process. So far, how any ubiquitin ligase builds a proteasomal degradation signal, which is canonically regarded as four or more ubiquitins, remains unclear. Here we present time-resolved cryogenic electron microscopy studies of the 1.2 MDa E3 ubiquitin ligase, known as the anaphase-promoting complex/cyclosome (APC/C), and its E2 co-enzymes (UBE2C/UBCH10 and UBE2S) during substrate polyubiquitination. Using cryoDRGN (Deep Reconstructing Generative Networks), a neural network-based approach, we reconstruct the conformational changes undergone by the human APC/C during polyubiquitination, directly visualize an active E3-E2 pair modifying its substrate, and identify unexpected interactions between multiple ubiquitins with parts of the APC/C machinery, including its coactivator CDH1. Together, we demonstrate how modification of substrates with nascent ubiquitin chains helps to potentiate processive substrate polyubiquitination, allowing us to model how a ubiquitin ligase builds a proteasomal degradation signal.

DOI: https://doi.org/10.1038/s41594-023-01105-5
Autophagy. 2023 Sep 21.

ER stress elicits non-canonical CASP8 (caspase 8) activation on autophagosomal membranes to induce apoptosis.

Tatsuya Hattori, Kevin A Fundora, Kouta Hamamoto, David M Opozda, Xinwen Liang, Xiaoming Liu, Jiawen Zhang, Yasin Uzun, Yoshinori Takahashi, Hong-Gang Wang.

  The VPS37A gene encodes a subunit of the endosomal sorting complex required for transport (ESCRT)-I complex that is frequently lost in a wide variety of human solid cancers. We have previously demonstrated the role of VPS37A in directing the ESCRT membrane scission machinery to seal the phagophore for autophagosome completion. Here, we report that VPS37A-deficient cells exhibit an accumulation of the apoptotic initiator CASP8 (caspase 8) on the phagophore and are primed to undergo rapid apoptosis through the intracellular death-inducing signaling complex (iDISC)-mediated CASP8 activation upon exposure to endoplasmic reticulum (ER) stress. Using CRISPR-Cas9 gene editing and comparative transcriptome analysis, we identified the ATF4-mediated stress response pathway as a crucial mediator to elicit iDISC-mediated apoptosis following the inhibition of autophagosome closure. Notably, ATF4-mediated iDISC activation occurred independently of the death receptor TNFRSF10B/DR5 upregulation but required the pro-apoptotic transcriptional factor DDIT3/CHOP to enhance the mitochondrial amplification pathway for full-activation of CASP8 in VPS37A-deficient cells stimulated with ER stress inducers. Our analysis also revealed the upregulation of NFKB/NF-kB signaling as a potential mechanism responsible for restraining iDISC activation and promoting cell survival upon VPS37A depletion. These findings have important implications for the future development of new strategies to treat human cancers, especially those with VPS37A loss.

Keywords:  ATF4-mediated ER stress response; Autophagy; ESCRT-mediated phagophore closure; NFKB/NF-kB signaling; VPS37A-deficient cancer; iDISC-mediated apoptosis

DOI:  https://doi.org/10.1080/15548627.2023.2258701
J Med Chem. 2023 Sep 22.

Unlocking DCAFs To Catalyze Degrader Development: An Arena for Innovative Approaches.

Qi Miao, Vilas D Kadam, Ayan Mukherjee, Zhi Tan, Mingxing Teng.

Chemically induced proximity-based targeted protein degradation (TPD) has become a prominent paradigm in drug discovery. With the clinical benefit demonstrated by certain small-molecule protein degraders that target the cullin-RING E3 ubiquitin ligases (CRLs), the field has proactively strategized to tackle anticipated drug resistance by harnessing additional E3 ubiquitin ligases to enrich the arsenal of this therapeutic approach. Here, we endeavor to explore the collaborative efforts involved in unlocking a broad range of CRL4DCAF for degrader drug development. Throughout the discussion, we also highlight how both conventional and innovative approaches in drug discovery can be taken to realize this objective. Moving ahead, we expect a greater allocation of resources in TPD to pursue these high-hanging fruits.

DOI: https://doi.org/10.1021/acs.jmedchem.3c01209
FEBS Lett. 2023 Sep 16.

Changing the guard - nuclear pore complex quality control.

Annemiek C Veldsink, Paola Gallardo, C Patrick Lusk, Liesbeth M Veenhoff.

  The integrity of the nuclear envelope (NE) depends on the function of nuclear pore complexes (NPCs), transport channels that control macromolecular traffic between the nucleus and cytosol. The central importance of NPCs suggests the existence of quality control (QC) mechanisms that oversee their assembly and function. In this perspective, we emphasize the challenges associated with NPC assembly and the need for QC mechanisms that operate at various stages of an NPC's life. This includes cytosolic pre-assembly QC that helps enforce key nucleoporin-nucleoporin interactions and their ultimate stoichiometry in the NPC in addition to mechanisms that monitor aberrant fusion of the inner and outer nuclear membranes. Furthermore, we discuss if and how these QC mechanisms may operate to sense faulty mature NPCs to facilitate their repair or removal. The so far uncovered mechanisms for NPC QC provide fertile ground for future research that not only benefits a better understanding of the vital role that NPCs play in cellular physiology but also how loss of NPC function and/or these QC mechanisms might be an input to ageing and disease.

Keywords:  ESCRT; Nuclear pore complex; ageing; autophagy; membrane fusion; nuclear envelope; nuclear pore complex assembly; nuclear transport; proteostasis; quality control

DOI:  https://doi.org/10.1002/1873-3468.14739
Mol Cell. 2023 Sep 21. pii: S1097-2765(23)00652-4. [Epub ahead of print]83(18): 3333-3346.e5

Regulation of nucleo-cytosolic 26S proteasome translocation by aromatic amino acids via mTOR is essential for cell survival under stress.

Ido Livneh, Victoria Cohen-Kaplan, Bertrand Fabre, Ifat Abramovitch, Chen Lulu, Nishanth Belugali Nataraj, Ikrame Lazar, Tamar Ziv, Yosef Yarden, Yaniv Zohar, Eyal Gottlieb, Aaron Ciechanover.

  The proteasome is responsible for removal of ubiquitinated proteins. Although several aspects of its regulation (e.g., assembly, composition, and post-translational modifications) have been unraveled, studying its adaptive compartmentalization in response to stress is just starting to emerge. We found that following amino acid starvation, the proteasome is translocated from its large nuclear pool to the cytoplasm-a response regulated by newly identified mTOR-agonistic amino acids-Tyr, Trp, and Phe (YWF). YWF relay their signal upstream of mTOR through Sestrin3 by disrupting its interaction with the GATOR2 complex. The triad activates mTOR toward its downstream substrates p62 and transcription factor EB (TFEB), affecting both proteasomal and autophagic activities. Proteasome translocation stimulates cytosolic proteolysis which replenishes amino acids, thus enabling cell survival. In contrast, nuclear sequestration of the proteasome following mTOR activation by YWF inhibits this proteolytic adaptive mechanism, leading to cell death, which establishes this newly identified pathway as a key stress-coping mechanism.

Keywords:  UPS; aromatic amino acids; mTOR; proteasome dynamics; protein quality control; proteolysis; stress response

DOI:  https://doi.org/10.1016/j.molcel.2023.08.016
Comput Struct Biotechnol J. 2023 ;21 4478-4487

Featured interactome of homocysteine-inducible endoplasmic reticulum protein uncovers novel binding partners in response to ER stress.

Rui Su, Jialing Yin, Xiaolan Ruan, Yanxi Chen, Pin Wan, Zhen Luo.

  Homocysteine-inducible endoplasmic reticulum protein (HERP) is an endoplasmic reticulum (ER)-resident protein and important for the adaptation of cellular protein homeostasis by ER-associated degradation (ERAD) system. HERP interactors are critical for cellular viability and the reaction to ER stress. To explore the exact mechanisms by which HERP performed the biological functions, we conducted an interaction analysis of HERP protein in HeLa cells by co-immunoprecipitation (Co-IP) and liquid chromatography-mass spectrometer (LC-MS)/MS coupled with label-free quantification (LFQ). Among the interactome results, 123 proteins significantly interacted with HERP, which leads to numerous biological processes including protein import into nucleus, ubiquitin-dependent ERAD pathway, negative regulation of apoptotic process, and protein transport from ER, along with multiple pathways including several diseases, protein processing in ER, fatty acid metabolism, and steroid biosynthesis. Furthermore, we selected several prey proteins from the interactome data and confirmed that HERP interacted with ancient ubiquitous protein 1 (AUP1), Fas-associated factor family member 2 (FAF2), tripartite motif containing 47 (TRIM47), acyl-CoA synthetase long-chain family member 3 (ACSL3), sequestosome 1 (SQSTM1), and poly(rC) binding protein 2 (PCBP2) by Co-IP and confocal microscopy experiments, respectively. Moreover, the expression and location of several interacted proteins were obviously altered in response to ER stress induced by Thapsigargin stimulation and Enterovirus 71 infection. In conclusion, our findings revealed that the vital proteins interacted with HERP to mediate signaling transduction, thus providing novel clues for the mechanisms of HERP associated with ERAD and metabolism in response to ER stress under physiological and pathological conditions.

Keywords:  Bioinformatic analysis; ER stress; HERP; Protein interactome

DOI:  https://doi.org/10.1016/j.csbj.2023.09.006
Mol Biol Cell. 2023 Sep 20. mbcE23060248

Exploring The "Misfolding Problem" by Systematic Discovery and Analysis of Functional-But-Degraded Proteins.

Matthew P Flagg, Breanna Lam, Darren K Lam, Tiffany M Le, Andy Kao, Yousif I Slaiwa, Randolph Y Hampton.

In both health and disease, the ubiquitin-proteasome system (UPS) degrades point mutants that retain partial function but have decreased stability compared to their wild-type counterparts. This class of UPS substrate includes routine translational errors and numerous human disease alleles, such as the most common cause of cystic fibrosis, ΔF508-CFTR. Yet, there is no systematic way to discover novel examples of these "minimally misfolded" substrates. To address that shortcoming, we designed a genetic screen to isolate functional-but-degraded point mutants, and we used the screen to study soluble, monomeric proteins with known structures. These simple parent proteins yielded diverse substrates, allowing us to investigate the structural features, cytotoxicity, and small-molecule regulation of minimal misfolding. Our screen can support numerous lines of inquiry, and it provides broad access to a class of poorly understood but biomedically critical quality-control substrates.

DOI: https://doi.org/10.1091/mbc.E23-06-0248
Autophagy. 2023 Sep 21.

Ksp1 is an autophagic receptor protein for the Snx4-assisted autophagy of Ssn2/Med13.

Sara E Hanley, Stephen D Willis, Steven J Doyle, Randy Strich, Katrina F Cooper.

  Ksp1 is a casein II-like kinase whose activity prevents aberrant macroautophagy/autophagy induction in nutrient-rich conditions in yeast. Here, we describe a kinase-independent role of Ksp1 as a novel autophagic receptor protein for Ssn2/Med13, a known cargo of Snx4-assisted autophagy of transcription factors. In this pathway, a subset of conserved transcriptional regulators, Ssn2/Med13, Rim15, and Msn2, are selectively targeted for vacuolar proteolysis following nitrogen starvation, assisted by the sorting nexin heterodimer Snx4-Atg20. Here we show that phagophores also engulf Ksp1 alongside its cargo for vacuolar proteolysis. Ksp1 directly associates with Atg8 following nitrogen starvation at the interface of an Atg8-family interacting motif (AIM)/LC3-interacting region (LIR) in Ksp1 and the LIR/AIM docking site (LDS) in Atg8. Mutating the LDS site prevents the autophagic degradation of Ksp1. However, deletion of the C terminal canonical AIM still permitted Ssn2/Med13 proteolysis, suggesting that additional non-canonical AIMs may mediate the Ksp1-Atg8 interaction. Ksp1 is recruited to the perivacuolar phagophore assembly site by Atg29, a member of the trimeric scaffold complex. This interaction is independent of Atg8 and Snx4, suggesting that Ksp1 is recruited early to phagophores, with Snx4 delivering Ssn2/Med13 thereafter. Finally, normal cell survival following prolonged nitrogen starvation requires Ksp1. Together, these studies define a kinase-independent role for Ksp1 as an autophagic receptor protein mediating Ssn2/Med13 degradation. They also suggest that phagophores built by the trimeric scaffold complex are capable of receptor-mediated autophagy. These results demonstrate the dual functionality of Ksp1, whose kinase activity prevents autophagy while it plays a scaffolding role supporting autophagic degradation.

Keywords:  Atg8; Ksp1; Ssn2/Med13; phagophore assembly site (PAS); receptor proteins; trimeric scaffold complex (17C); vacuolar degradation

DOI:  https://doi.org/10.1080/15548627.2023.2259708
Nat Commun. 2023 09 19. 14(1): 5815

A mechanism that ensures non-selective cytoplasm degradation by autophagy.

Tetsuya Kotani, Yuji Sakai, Hiromi Kirisako, Chika Kakuta, Soichiro Kakuta, Yoshinori Ohsumi, Hitoshi Nakatogawa.

In autophagy, a membrane cisterna called the isolation membrane expands, bends, becomes spherical, and closes to sequester cytoplasmic constituents into the resulting double-membrane vesicle autophagosome for lysosomal/vacuolar degradation. Here, we discover a mechanism that allows the isolation membrane to expand with a large opening to ensure non-selective cytoplasm sequestration within the autophagosome. A sorting nexin complex that localizes to the opening edge of the isolation membrane plays a critical role in this process. Without the complex, the isolation membrane expands with a small opening that prevents the entry of particles larger than about 25 nm, including ribosomes and proteasomes, although autophagosomes of nearly normal size eventually form. This study sheds light on membrane morphogenesis during autophagosome formation and selectivity in autophagic degradation.

DOI: https://doi.org/10.1038/s41467-023-41525-x
Elife. 2023 Sep 22. pii: e86367. [Epub ahead of print]12

PerTurboID, A targeted in situ method reveals the impact of kinase deletion on its local protein environment in the cytoadhesion complex of malaria causing parasites.

Heledd Davies, Hugo Belda, Malgorzata Broncel, Jill Dalimot, Moritz Treeck.

  Reverse genetics is key to understanding protein function, but the mechanistic connection between a gene of interest and the observed phenotype is not always clear. Here we describe the use of proximity labeling using TurboID and site-specific quantification of biotinylated peptides to measure changes to the local protein environment of selected targets upon perturbation. We apply this technique, which we call PerTurboID, to understand how the P. falciparum exported kinase, FIKK4.1, regulates the function of the major virulence factor of the malaria causing parasite, PfEMP1. We generated independent TurboID fusions of 2 proteins that are predicted substrates of FIKK4.1 in a FIKK4.1 conditional KO parasite line. Comparing the abundance of site-specific biotinylated peptides between wildtype and kinase deletion lines reveals the differential accessibility of proteins to biotinylation, indicating changes to localization, protein-protein interactions, or protein structure which are mediated by FIKK4.1 activity. We further show that FIKK4.1 is likely the only FIKK kinase that controls surface levels of PfEMP1, but not other surface antigens, on the infected red blood cell under standard culture conditions. We believe PerTurboID is broadly applicable to study the impact of genetic or environmental perturbation on a selected cellular niche.

Keywords:  P. falciparum; cell biology; infectious disease; microbiology

DOI:  https://doi.org/10.7554/eLife.86367
iScience. 2023 Oct 20. 26(10): 107819

Dynamic association of the intramembrane proteases SPPL2a/b and their substrates with tetraspanin-enriched microdomains.

Nadja Leinung, Torben Mentrup, Mehul Patel, Tom Gallagher, Bernd Schröder.

  Signal peptide peptidase-like 2a and b (SPPL2a/b) are aspartyl intramembrane proteases and cleave tail-anchored proteins as well as N-terminal fragments (NTFs) derived from type II-oriented transmembrane proteins. How these proteases recruit substrates and cleavage is regulated, is still incompletely understood. We found that SPPL2a/b localize to detergent-resistant membrane (DRM) domains with the characteristics of tetraspanin-enriched microdomains (TEMs). Based on this, association with several tetraspanins was evaluated. We demonstrate that not only SPPL2a/b but also their substrates tumor necrosis factor (TNF) and CD74 associate with tetraspanins like CD9, CD81, and CD82 and/or TEMs and analyze the stability of these complexes in different detergents. CD9 and CD81 deficiency has protease- and substrate-selective effects on SPPL2a/b function. Our findings suggest that reciprocal interactions with tetraspanins may assist protease-substrate encounters of SPPL2a/b within the membrane. Beyond SPP/SPPL proteases, this supports previous concepts that tetraspanins facilitate membrane-embedded proteolytic processes.

Keywords:  Biological sciences; Molecular biology; Molecular interaction

DOI:  https://doi.org/10.1016/j.isci.2023.107819
STAR Protoc. 2023 Sep 19. pii: S2666-1667(23)00541-5. [Epub ahead of print]4(4): 102574

Protocol for quantifying the in vivo rate of protein degradation in mice using a pulse-chase technique.

Jamie E Hibbert, Kent W Jorgenson, Wenyuan G Zhu, Nathaniel D Steinert, Troy A Hornberger.

  The ability to measure the in vivo rate of protein degradation is a major limitation in numerous fields of biology. Here, we present a protocol for quantifying this rate in mice using a pulse-chase technique that utilizes an azide-bearing non-canonical amino acid called azidohomoalanine (AHA). We describe steps for using chow containing AHA to pulse-label the animal's proteome. We then detail the quantification of AHA-labeled proteins in whole-tissue lysates or histological sections using a copper-catalyzed azide-alkyne cycloaddition 'click' reaction. For complete details on the use and execution of this protocol, please refer to Steinert et al. (2023).1.

Keywords:  Cell Biology; Metabolism; Molecular Biology; Protein Biochemistry

DOI:  https://doi.org/10.1016/j.xpro.2023.102574
mBio. 2023 Sep 21. e0093423

PKR-mediated stress response enhances dengue and Zika virus replication.

Taissa Ricciardi-Jorge, Edroaldo Lummertz da Rocha, Edgar Gonzalez-Kozlova, Gabriela Flavia Rodrigues-Luiz, Brian J Ferguson, Trevor Sweeney, Nerea Irigoyen, Daniel Santos Mansur.

  The mechanisms by which flaviviruses use non-canonical translation to support their replication in host cells are largely unknown. Here, we investigated how the integrated stress response (ISR), which promotes translational arrest by eIF2ɑ phosphorylation (p-eIF2ɑ), regulates flavivirus replication. During dengue virus (DENV) and Zika virus (ZIKV) infection, eIF2ɑ phosphorylation peaked at 24 hours post-infection and was dependent on protein kinase RNA-activated (PKR) but not type I interferon. The ISR is activated downstream of p-eIF2α during infection with either virus, but translation arrest only occurred following DENV4 infection. Despite this difference, both DENV4 and ZIKV replications were impaired in cells lacking PKR, independent of type I interferon/NF-kB signaling or cell viability. By using a ZIKV 5'-untranslated region (UTR) reporter system as a model, we found that this region of the genome is sufficient to promote an enhancement of viral mRNA translation in the presence of an active ISR. Together, we provide evidence that flaviviruses escape ISR translational arrest and co-opt this response to increase viral replication. IMPORTANCE One of the fundamental features that make viruses intracellular parasites is the necessity to use cellular translational machinery. Hence, this is a crucial checkpoint for controlling infections. Here, we show that dengue and Zika viruses, responsible for nearly 400 million infections every year worldwide, explore such control for optimal replication. Using immunocompetent cells, we demonstrate that arrest of protein translations happens after sensing of dsRNA and that the information required to avoid this blocking is contained in viral 5'-UTR. Our work, therefore, suggests that the non-canonical translation described for these viruses is engaged when the intracellular stress response is activated.

Keywords:  PKR; Zika virus; dengue virus; innate immunity; protein translation

DOI:  https://doi.org/10.1128/mbio.00934-23
Nat Commun. 2023 Sep 21. 14(1): 5867

Regulation of cellular cholesterol distribution via non-vesicular lipid transport at ER-Golgi contact sites.

Tomoki Naito, Haoning Yang, Dylan Hong Zheng Koh, Divyanshu Mahajan, Lei Lu, Yasunori Saheki.

Abnormal distribution of cellular cholesterol is associated with numerous diseases, including cardiovascular and neurodegenerative diseases. Regulated transport of cholesterol is critical for maintaining its proper distribution in the cell, yet the underlying mechanisms remain unclear. Here, we show that lipid transfer proteins, namely ORP9, OSBP, and GRAMD1s/Asters (GRAMD1a/GRAMD1b/GRAMD1c), control non-vesicular cholesterol transport at points of contact between the ER and the trans-Golgi network (TGN), thereby maintaining cellular cholesterol distribution. ORP9 localizes to the TGN via interaction between its tandem α-helices and ORP10/ORP11. ORP9 extracts PI4P from the TGN to prevent its overaccumulation and suppresses OSBP-mediated PI4P-driven cholesterol transport to the Golgi. By contrast, GRAMD1s transport excess cholesterol from the Golgi to the ER, thereby preventing its build-up. Cells lacking ORP9 exhibit accumulation of cholesterol at the Golgi, which is further enhanced by additional depletion of GRAMD1s with major accumulation in the plasma membrane. This is accompanied by chronic activation of the SREBP-2 signalling pathway. Our findings reveal the importance of regulated lipid transport at ER-Golgi contacts for maintaining cellular cholesterol distribution and homeostasis.

DOI: https://doi.org/10.1038/s41467-023-41213-w
Am J Physiol Endocrinol Metab. 2023 Sep 20.

Endoplasmic Reticulum Stress in Pancreatic β-Cells Induces Incretin Desensitization and β-Cell Dysfunction via ATF4-Mediated PDE4D Expression.

Ji-Hye Lee, Hanguk Ryu, Hyejin Lee, Hye Ram Yu, Yurong Gao, Kyeong-Min Lee, Young-Joon Kim, Jaemin Lee.

  Pancreatic β-cell dysfunction and eventual loss are key steps in the progression of type 2 diabetes (T2D). Endoplasmic reticulum (ER) stress responses, especially those mediated by the PERK-ATF4 pathway, have been implicated in promoting these β-cell pathologies. However, the exact molecular events surrounding the role of the PERK-ATF4 pathway in β-cell dysfunction remain unknown. Here, we report our discovery that ATF4 promotes the expression of PDE4D, which disrupts β-cell function via a downregulation of cAMP signaling. We found that β-cell-specific transgenic expression of ATF4 led to early β-cell dysfunction and loss, a phenotype that resembles accelerated T2D. Expression of ATF4, rather than CHOP, promoted PDE4D expression, reduced cAMP signaling, and attenuated responses to incretins and elevated glucose. Furthermore, we found that β-cells of leptin receptor-deficient diabetic (db/db) mice had elevated nuclear localization of ATF4 and PDE4D expression, accompanied by impaired β-cell function. Accordingly, pharmacological inhibition of the ATF4 pathway attenuated PDE4D expression in the islets and promoted incretin-simulated glucose tolerance and insulin secretion in db/db mice. Finally, we found that inhibiting PDE4 activity with selective pharmacological inhibitors improved β-cell function in both db/db mice and β-cell-specific ATF4 transgenic mice. In summary, our results indicate that ER stress causes β-cell failure via ATF4-mediated PDE4D production, suggesting the ATF4-PDE4D pathway could be a therapeutic target for protecting β-cell function during the progression of T2D.

Keywords:  ATF4; ER stress; PDE4D; beta cell dysfunction; incretin resistance

DOI:  https://doi.org/10.1152/ajpendo.00156.2023
bioRxiv. 2023 Sep 19. pii: 2023.09.04.556280. [Epub ahead of print]

UBC13-mediated template switching promotes replication stress resistance in FBH1-deficient cells.

Alexandra L Hawks, Amy Bergmann, Tyler McCraw, Jennifer M Mason.

The proper resolution of DNA damage during replication is essential for genome stability. FBH1, a UvrD, helicase plays crucial roles in the DNA damage response. FBH1 promotes double strand break formation and signaling in response to prolonged replication stress to initiate apoptosis. Human FBH1 regulates RAD51 to inhibit homologous recombination. A previous study suggested that mis-regulation of RAD51 may contribute to replication stress resistance in FBH1-deficient cells, but the underlying mechanism remains unknown. Here, we provide direct evidence that RAD51 promotes replication stress resistance in FBH1-deficient cells. We demonstrate inhibition of RAD51 using the small molecule, B02, partially rescues double strand break signaling in FBH1-deficient cells. We show that inhibition of only the strand exchange activity of RAD51 rescues double strand break signaling in FBH1 knockout cells. Finally, we show that depletion of UBC13, a E2 protein that promotes RAD51-dependent template switching, rescues double strand break formation and signaling sensitizing FBH1-deficient cells to replication stress. Our results suggest FBH1 regulates template switching to promote replication stress sensitivity.

DOI: https://doi.org/10.1101/2023.09.04.556280
FASEB J. 2023 Oct;37(10): e23217

E3 ubiquitin ligase RNF187 promotes growth of spermatogonia via lysine 48-linked polyubiquitination-mediated degradation of KRT36/KRT84.

Xiangling Yu, Bingya Xu, Tingting Gao, Xu Fu, Bing Jiang, Nianchao Zhou, Wenxin Gao, Tiantian Wu, Cong Shen, Xiaoyan Huang, Yibo Wu, Bo Zheng.

  Ubiquitination is the most common post-translational modification and is essential for various cellular regulatory processes. RNF187, which is known as RING domain AP1 coactivator-1, is a member of the RING finger family. RNF187 can promote the proliferation and migration of various tumor cells. However, whether it has a similar role in regulating spermatogonia is not clear. This study explored the role and molecular mechanism of RNF187 in a mouse spermatogonia cell line (GC-1). We found that RNF187 knockdown reduced the proliferation and migration of GC-1 cells and promoted their apoptosis. RNF187 overexpression significantly increased the proliferation and migration of GC-1 cells. In addition, we identified Keratin36/Keratin84 (KRT36/KRT84) as interactors with RNF187 by co-immunoprecipitation and mass spectrometry analyses. RNF187 promoted GC-1 cell growth by degrading KRT36/KRT84 via lysine 48-linked polyubiquitination. Subsequently, we found that KRT36 or KRT84 overexpression significantly attenuated proliferation and migration of RNF187-overexpressing GC-1 cells. In summary, our study explored the involvement of RNF187 in regulating the growth of spermatogonia via lysine 48-linked polyubiquitination-mediated degradation of KRT36/KRT84. This may provide a promising new strategy for treating infertility caused by abnormal spermatogonia development.

Keywords:  KRT36; KRT84; RNF187; polyubiquitination; spermatogonia

DOI:  https://doi.org/10.1096/fj.202301120R