bims-proteo Biomed News
on Proteostasis
Issue of 2021‒08‒29
thirty-four papers selected by
Eric Chevet
INSERM
  1. The Targeting of Native Proteins to the Endoplasmic Reticulum-Associated Degradation (ERAD) Pathway: An Expanding Repertoire of Regulated Substrates.
  2. Inhibition of the SEC61 translocon by mycolactone induces a protective autophagic response controlled by EIF2S1-dependent translation that does not require ULK1 activity.
  3. Identification of a quality-control factor that monitors failures during proteasome assembly.
  4. Coordinated Regulation of Plant Immunity by Poly(ADP-ribosyl)ation and K63-Linked Ubiquitination.
  5. An in vitro vesicle formation assay reveals cargo clients and factors that mediate vesicular trafficking.
  6. The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis.
  7. Deletion of mFICD AMPylase alters cytokine secretion and affects visual short-term learning in vivo.
  8. Oligomerization of Selective Autophagy Receptors for the Targeting and Degradation of Protein Aggregates.
  9. CHIP/STUB1 Ubiquitin Ligase Functions as a Negative Regulator of ErbB2 by Promoting Its Early Post-Biosynthesis Degradation.
  10. Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation.
  11. Profiling CELMoD-Mediated Degradation of Cereblon Neosubstrates.
  12. Global Mass Spectrometry-Based Analysis of Protein Ubiquitination Using K-ε-GG Remnant Antibody Enrichment.
  13. Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1α kinase inhibitor KIRA6 through HSP60 targeting.
  14. The Link between VAPB Loss of Function and Amyotrophic Lateral Sclerosis.
  15. Kinetic Detection of E3:PROTAC:Target Ternary Complexes Using NanoBRET Technology in Live Cells.
  16. An In Vitro Pull-down Assay of the E3 Ligase:PROTAC:Substrate Ternary Complex to Identify Effective PROTACs.
  17. USP19 (ubiquitin specific peptidase 19) promotes TBK1 (TANK-binding kinase 1) degradation via chaperone-mediated autophagy.
  18. The chaperone HSPB1 prepares protein aggregates for resolubilization by HSP70.
  19. The mRNA decapping complex is buffered by nuclear localization.
  20. Mechanistic and Structural Features of PROTAC Ternary Complexes.
  21. Quality control of protein import into mitochondria.
  22. Determination of Proteasomal Unfolding Ability.
  23. Hypusinated eIF5A is required for the translation of collagen.
  24. RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery.
  25. The Unfolded Protein Response Is a Major Driver of LCN2 Expression in BCR-ABL- and JAK2V617F-Positive MPN.
  26. TREM2-dependent lipid droplet biogenesis in phagocytes is required for remyelination.
  27. Inducing Ubiquitylation and Protein Degradation as a Drug Development Strategy.
  28. Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation.
  29. Proteomics Mapping of the ISGylation Landscape in Innate Immunity.
  30. A cancer ubiquitome landscape identifies metabolic reprogramming as target of Parkin tumor suppression.
  31. Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors.
  32. Methods for Quantitative Assessment of Protein Degradation.
  33. The Anterior GRadient (AGR) family proteins in epithelial ovarian cancer.
  34. A global map of associations between types of protein posttranslational modifications and human genetic diseases.
  1. Biomolecules. 2021 Aug 11. pii: 1185. [Epub ahead of print]11(8):
    The Targeting of Native Proteins to the Endoplasmic Reticulum-Associated Degradation (ERAD) Pathway: An Expanding Repertoire of Regulated Substrates.
    Deepa Kumari, Jeffrey L Brodsky.
      All proteins are subject to quality control processes during or soon after their synthesis, and these cellular quality control pathways play critical roles in maintaining homeostasis in the cell and in organism health. Protein quality control is particularly vital for those polypeptides that enter the endoplasmic reticulum (ER). Approximately one-quarter to one-third of all proteins synthesized in eukaryotic cells access the ER because they are destined for transport to the extracellular space, because they represent integral membrane proteins, or because they reside within one of the many compartments of the secretory pathway. However, proteins that mature inefficiently are subject to ER-associated degradation (ERAD), a multi-step pathway involving the chaperone-mediated selection, ubiquitination, and extraction (or "retrotranslocation") of protein substrates from the ER. Ultimately, these substrates are degraded by the cytosolic proteasome. Interestingly, there is an increasing number of native enzymes and metabolite and solute transporters that are also targeted for ERAD. While some of these proteins may transiently misfold, the ERAD pathway also provides a route to rapidly and quantitatively downregulate the levels and thus the activities of a variety of proteins that mature or reside in the ER.
    Keywords:  ERAD; molecular chaperones; proteasome; protein quality control; ubiquitin
    DOI:  https://doi.org/10.3390/biom11081185
  2. Autophagy. 2021 Aug 23. 1-19
    Inhibition of the SEC61 translocon by mycolactone induces a protective autophagic response controlled by EIF2S1-dependent translation that does not require ULK1 activity.
    Belinda S Hall, Scott J Dos Santos, Louise Tzung-Harn Hsieh, Maria Manifava, Marie-Thérèse Ruf, Gerd Pluschke, Nicholas Ktistakis, Rachel E Simmonds.
      The Mycobacterium ulcerans exotoxin, mycolactone, is responsible for the immunosuppression and tissue necrosis that characterizes Buruli ulcer. Mycolactone inhibits SEC61-dependent co-translational translocation of proteins into the endoplasmic reticulum and the resultant cytosolic translation triggers degradation of mislocalized proteins by the ubiquitin-proteasome system. Inhibition of SEC61 by mycolactone also activates multiple EIF2S1/eIF2α kinases in the integrated stress response (ISR). Here we show mycolactone increased canonical markers of selective macroautophagy/autophagy LC3B-II, ubiquitin and SQSTM1/p62 in diverse disease-relevant primary cells and cell lines. Increased formation of puncta positive for the early autophagy markers WIPI2, RB1CC1/FIP200 and ATG16L1 indicates increased initiation of autophagy. The mycolactone response was SEC61A1-dependent and involved a pathway that required RB1CC1 but not ULK. Deletion of Sqstm1 reduced cell survival in the presence of mycolactone, suggesting this response protects against the increased cytosolic protein burden caused by the toxin. However, reconstitution of baseline SQSTM1 expression in cells lacking all autophagy receptor proteins could not rescue viability. Translational regulation by EIF2S1 in the ISR plays a key role in the autophagic response to mycolactone. Mycolactone-dependent induction of SQSTM1 was reduced in eif2ak3-/-/perk-/- cells while the p-EIF2S1 antagonist ISRIB reversed the upregulation of SQSTM1 and reduced RB1CC1, WIPI2 and LC3B puncta formation. Increased SQSTM1 staining could be seen in Buruli ulcer patient skin biopsy samples, reinforcing genetic data that suggests autophagy is relevant to disease pathology. Since selective autophagy and the ISR are both implicated in neurodegeneration, cancer and inflammation, the pathway uncovered here may have a broad relevance to human disease.Abbreviations: ATF4: activating transcription factor 4; ATG: autophagy related; BAF: bafilomycin A1; ATG16L1: autophagy related 16 like 1; BU: Buruli ulcer; CQ: chloroquine; EIF2AK3: eukaryotic translation initiation factor 2 alpha kinase 3; CALCOCO2: calcium binding and coiled-coil domain 2; DMSO: dimethyl sulfoxide; EIF2S1: eukaryotic translation initiation factor 2 subunit alpha; ER: endoplasmic reticulum; GFP: green fluorescent protein; HDMEC: human dermal microvascular endothelial cells; HFFF: human fetal foreskin fibroblasts; ISR: integrated stress response; ISRIB: integrated stress response inhibitor; MAP1LC3B/LC3B: microtubule associated protein 1 light chain 3 beta; MEF: mouse embryonic fibroblast; Myco: mycolactone; NBR1: NBR1 autophagy cargo receptor; NFE2L2: nuclear factor, erythroid 2 like 2; OPTN: optineurin; PFA: paraformaldehyde; PtdIns3P: phosphatidylinositol-3-phosphate; RB1CC1: RB1-inducible coiled coil 1; SQSTM1: sequestosome 1; TAX1BP1: Tax1 binding protein 1; ULK: unc-51 like autophagy activating kinase; UPS: ubiquitin-proteasome system; WIPI: WD repeat domain, phosphoinositide interacting; WT: wild type.
    Keywords:  Buruli ulcer; RB1CC1/FIP200; SQSTM1/p62; eif2s1/eIF2α; integrated stress response; mislocalized proteins; mycolactone; translocation inhibitor; ulk1
    DOI:  https://doi.org/10.1080/15548627.2021.1961067
  3. Science. 2021 Aug 27. 373(6558): 998-1004
    Identification of a quality-control factor that monitors failures during proteasome assembly.
    Eszter Zavodszky, Sew-Yeu Peak-Chew, Szymon Juszkiewicz, Ana J Narvaez, Ramanujan S Hegde.
      In eukaryotic cells, half of all proteins function as subunits within multiprotein complexes. Imbalanced synthesis of subunits leads to unassembled intermediates that must be degraded to minimize cellular toxicity. Here, we found that excess PSMC5, a subunit of the proteasome base, was targeted for degradation by the HERC1 ubiquitin ligase in mammalian cells. HERC1 identified unassembled PSMC5 by its cognate assembly chaperone PAAF1. Because PAAF1 only dissociates after assembly, HERC1 could also engage later assembly intermediates such as the PSMC4-PSMC5-PAAF1 complex. A missense mutant of HERC1 that causes neurodegeneration in mice was impaired in the recognition and ubiquitination of the PSMC5-PAAF1 complex. Thus, proteasome assembly factors can serve as adaptors for ubiquitin ligases to facilitate elimination of unassembled intermediates and maintain protein homeostasis.
    DOI:  https://doi.org/10.1126/science.abc6500
  4. Mol Plant. 2021 Aug 18. pii: S1674-2052(21)00326-9. [Epub ahead of print]
    Coordinated Regulation of Plant Immunity by Poly(ADP-ribosyl)ation and K63-Linked Ubiquitination.
    Dongsheng Yao, Marcus A Arguez, Ping He, Andrew F Bent, Junqi Song.
      Poly(ADP-ribosyl)ation (PARylation) is a post-translational modification reversibly catalyzed by poly(ADP-ribose) polymerases (PARPs) and poly(ADP-ribose) glycohydrolases (PARGs) and plays a key role in multiple cellular processes. The molecular mechanisms by which PARylation regulates innate immunity remain largely unknown. Here we show that Arabidopsis UBC13A and UBC13B, the major drivers of lysine 63 (K63)-linked polyubiquitination, directly interact with PARPs/PARGs. Activation of pathogen-associated molecular pattern (PAMP)-triggered immunity promotes these interactions and enhances PARylation of UBC13. Both parp1 parp2 and ubc13a ubc13b mutants are compromised in immune responses with an increase of total pathogenesis-related (PR) proteins but the decrease of secreted PR proteins. Protein disulfide-isomerases (PDIs), essential components of endoplasmic reticulum quality control (ERQC) to ensure proper folding and maturation of proteins destined for secretion, complex with PARPs/PARGs and are PARylated upon PAMP perception. Significantly, PARylation of UBC13 regulates K63-linked ubiquitination of PDIs, which may further promote their disulfide isomerase activities for correct protein folding and subsequent secretion. Our results indicate that plant immunity is coordinately regulated by PARylation and K63-linked ubiquitination.
    Keywords:  K63-linked ubiquitination; PAMP-triggered immunity; PARP1; PARP2; PDI; UBC13; poly(ADP-ribosyl)ation; secretory pathway; systemic acquired resistance
    DOI:  https://doi.org/10.1016/j.molp.2021.08.013
  5. Proc Natl Acad Sci U S A. 2021 Aug 31. pii: e2101287118. [Epub ahead of print]118(35):
    An in vitro vesicle formation assay reveals cargo clients and factors that mediate vesicular trafficking.
    Yan Huang, Haidi Yin, Baiying Li, Qian Wu, Yang Liu, Kristina Poljak, Julija Maldutyte, Xiao Tang, Mo Wang, Zhixiao Wu, Elizabeth A Miller, Liwen Jiang, Zhong-Ping Yao, Yusong Guo.
      The fidelity of protein transport in the secretory pathway relies on the accurate sorting of proteins to their correct destinations. To deepen our understanding of the underlying molecular mechanisms, it is important to develop a robust approach to systematically reveal cargo proteins that depend on specific sorting machinery to be enriched into transport vesicles. Here, we used an in vitro assay that reconstitutes packaging of human cargo proteins into vesicles to quantify cargo capture. Quantitative mass spectrometry (MS) analyses of the isolated vesicles revealed cytosolic proteins that are associated with vesicle membranes in a GTP-dependent manner. We found that two of them, FAM84B (also known as LRAT domain containing 2 or LRATD2) and PRRC1, contain proline-rich domains and regulate anterograde trafficking. Further analyses revealed that PRRC1 is recruited to endoplasmic reticulum (ER) exit sites, interacts with the inner COPII coat, and its absence increases membrane association of COPII. In addition, we uncovered cargo proteins that depend on GTP hydrolysis to be captured into vesicles. Comparing control cells with cells depleted of the cargo receptors, SURF4 or ERGIC53, we revealed specific clients of each of these two export adaptors. Our results indicate that the vesicle formation assay in combination with quantitative MS analysis is a robust and powerful tool to uncover novel factors that mediate vesicular trafficking and to uncover cargo clients of specific cellular factors.
    Keywords:  COPII; cargo receptor; cargo sorting; intracellular protein transport; secretory pathway
    DOI:  https://doi.org/10.1073/pnas.2101287118
  6. Plant Cell. 2021 Aug 26. pii: koab210. [Epub ahead of print]
    The F-box E3 ubiquitin ligase BAF1 mediates the degradation of the brassinosteroid-activated transcription factor BES1 through selective autophagy in Arabidopsis.
    Ping Wang, Trevor M Nolan, Natalie M Clark, Hao Jiang, Christian Montes-Serey, Hongqing Guo, Diane C Bassham, Justin W Walley, Yanhai Yin.
      Brassinosteroids (BRs) regulate plant growth, development and stress responses by activating the core transcription factor BRI1-EMS-SUPPRESSOR1 (BES1), whose degradation occurs through the proteasome and autophagy pathways. The E3 ubiquitin ligase(s) that modify BES1 for autophagy-mediated degradation remain to be fully defined. Here, we identified an F-box family E3 ubiquitin ligase named BES1-ASSOCIATED F-BOX1 (BAF1) in Arabidopsis thaliana. BAF1 interacts with BES1 and mediates its ubiquitination and degradation. Our genetic data demonstrated that BAF1 inhibits BR signaling in a BES1-dependent manner. Moreover, BAF1 targets BES1 for autophagic degradation in a selective manner. BAF1-triggered selective autophagy of BES1 depends on the ubiquitin binding receptor DOMINANT SUPPRESSOR OF KAR2 (DSK2). Sucrose starvation-induced selective autophagy of BES1, but not bulk autophagy, was significantly compromised in baf1 mutant and BAF1-ΔF (BAF1 F-box decoy) overexpression plants, but clearly increased by BAF1 overexpression. The baf1 and BAF1-ΔF overexpression plants had increased BR-regulated growth but were sensitive to long-term sucrose starvation, while BAF1 overexpression plants had decreased BR-regulated growth but were highly tolerant of sucrose starvation. Our results not only established BAF1 as an E3 ubiquitin ligase that targets BES1 for degradation through selective autophagy pathway, but also revealed a mechanism for plants to reduce growth during sucrose starvation.
    Keywords:  BAF1; BES1 protein degradation; Brassinosteroids; selective autophagy; sucrose starvation; ubiquitination
    DOI:  https://doi.org/10.1093/plcell/koab210
  7. J Biol Chem. 2021 Aug 19. pii: S0021-9258(21)00793-6. [Epub ahead of print] 100991
    Deletion of mFICD AMPylase alters cytokine secretion and affects visual short-term learning in vivo.
    Nicholas McCaul, Corey M Porter, Anouk Becker, Chih-Hang Antony Tang, Charlotte Wijne, Bhaskar Chatterjee, Djenet Bousbaine, Angelina Bilate, Chih-Chi Andrew Hu, Hidde Ploegh, Matthias C Truttmann.
      Fic domain-containing AMP transferases (fic AMPylases) are conserved enzymes that catalyze the covalent transfer of AMP to proteins. This post-translational modification regulates the function of several proteins, including the ER-resident chaperone Grp78/BiP. Here we introduce a mouse FICD (mFICD) AMPylase knock-out mouse model to study fic AMPylase function in vertebrates. We find that mFICD deficiency is well-tolerated in unstressed mice. We also show that mFICD-deficient mouse embryonic fibroblasts are depleted of AMPylated proteins. mFICD deletion alters protein synthesis and secretion in splenocytes, including that of IgM, an antibody secreted early during infections, and the pro-inflammatory cytokine IL-1β, without affecting the unfolded protein response. Finally, we demonstrate that visual nonspatial short-term learning is stronger in old mFICD-/- mice than in wild-type controls while other measures of cognition, memory, and learning are unaffected. Together, our results suggest a role for mFICD in adaptive immunity and neuronal plasticity in vivo.
    Keywords:  AMPylation; BiP; FICD; HYPE; UPR; post-translational modification
    DOI:  https://doi.org/10.1016/j.jbc.2021.100991
  8. Cells. 2021 Aug 05. pii: 1989. [Epub ahead of print]10(8):
    Oligomerization of Selective Autophagy Receptors for the Targeting and Degradation of Protein Aggregates.
    Wenjun Chen, Tianyun Shen, Lijun Wang, Kefeng Lu.
      The selective targeting and disposal of solid protein aggregates are essential for cells to maintain protein homoeostasis. Autophagy receptors including p62, NBR1, Cue5/TOLLIP (CUET), and Tax1-binding protein 1 (TAX1BP1) proteins function in selective autophagy by targeting ubiquitinated aggregates through ubiquitin-binding domains. Here, we summarize previous beliefs and recent findings on selective receptors in aggregate autophagy. Since there are many reviews on selective autophagy receptors, we focus on their oligomerization, which enables receptors to function as pathway determinants and promotes phase separation.
    Keywords:  Cue5; Dsk2; TAX1BP1; autophagy; p62; proteasome; receptors; ubiquitin
    DOI:  https://doi.org/10.3390/cells10081989
  9. Cancers (Basel). 2021 Aug 04. pii: 3936. [Epub ahead of print]13(16):
    CHIP/STUB1 Ubiquitin Ligase Functions as a Negative Regulator of ErbB2 by Promoting Its Early Post-Biosynthesis Degradation.
    Haitao Luan, Tameka A Bailey, Robert J Clubb, Bhopal C Mohapatra, Aaqib M Bhat, Sukanya Chakraborty, Namista Islam, Insha Mushtaq, Matthew D Storck, Srikumar M Raja, Vimla Band, Hamid Band.
      Overexpression of the epidermal growth factor receptor (EGFR) family member ErbB2 (HER2) drives oncogenesis in up to 25% of invasive breast cancers. ErbB2 expression at the cell surface is required for oncogenesis but mechanisms that ensure the optimal cell surface display of overexpressed ErbB2 following its biosynthesis in the endoplasmic reticulum are poorly understood. ErbB2 is dependent on continuous association with HSP90 molecular chaperone for its stability and function as an oncogenic driver. Here, we use knockdown and overexpression studies to show that the HSP90/HSC70-interacting negative co-chaperone CHIP (C-terminus of HSC70-Interacting protein)/STUB1 (STIP1-homologous U-Box containing protein 1) targets the newly synthesized, HSP90/HSC70-associated, ErbB2 for ubiquitin/proteasome-dependent degradation in the endoplasmic reticulum and Golgi, thus identifying a novel mechanism that negatively regulates cell surface ErbB2 levels in breast cancer cells, consistent with frequent loss of CHIP expression previously reported in ErbB2-overexpressing breast cancers. ErbB2-overexpressing breast cancer cells with low CHIP expression exhibited higher endoplasmic reticulum stress inducibility. Accordingly, the endoplasmic reticulum stress-inducing anticancer drug Bortezomib combined with ErbB2-targeted humanized antibody Trastuzumab showed synergistic inhibition of ErbB2-overexpressing breast cancer cell proliferation. Our findings reveal new insights into mechanisms that control the surface expression of overexpressed ErbB2 and suggest that reduced CHIP expression may specify ErbB2-overexpressing breast cancers suitable for combined treatment with Trastuzumab and ER stress inducing agents.
    Keywords:  Bortezomib; CHIP/STUB1; E3; ErbB2; Golgi; Trastuzumab; breast cancer; degradation; endoplasmic reticulum; pulse-chase; ubiquitin; ubiquitin ligase
    DOI:  https://doi.org/10.3390/cancers13163936
  10. PLoS One. 2021 ;16(8): e0256640
    Interactome analysis of Bag-1 isoforms reveals novel interaction partners in endoplasmic reticulum-associated degradation.
    Nisan Denizce Can, Ezgi Basturk, Tugba Kizilboga, Izzet Mehmet Akcay, Baran Dingiloglu, Ozge Tatli, Sevilay Acar, Pelin Ozfiliz Kilbas, Efe Elbeyli, Serena Muratcioglu, Ayse Tarbin Jannuzzi, Attila Gursoy, Ozlem Keskin, Hamdi Levent Doganay, Betul Karademir Yilmaz, Gizem Dinler Doganay.
      Bag-1 is a multifunctional protein that regulates Hsp70 chaperone activity, apoptosis, and proliferation. The three major Bag-1 isoforms have different subcellular localizations and partly non-overlapping functions. To identify the detailed interaction network of each isoform, we utilized mass spectrometry-based proteomics and found that interactomes of Bag-1 isoforms contained many common proteins, with variations in their abundances. Bag-1 interactomes were enriched with proteins involved in protein processing and degradation pathways. Novel interaction partners included VCP/p97; a transitional ER ATPase, Rad23B; a shuttling factor for ubiquitinated proteins, proteasome components, and ER-resident proteins, suggesting a role for Bag-1 also in ER-associated protein degradation (ERAD). Bag-1 pull-down from cells and tissues from breast cancer patients validated these interactions and showed cancer-related prominence. Using in silico predictions we detected hotspot residues of Bag-1. Mutations of these residues caused loss of binding to protein quality control elements and impaired proteasomal activity in MCF-7 cells. Following CD147 glycosylation pattern, we showed that Bag-1 downregulated VCP/p97-dependent ERAD. Overall, our data extends the interaction map of Bag-1, and broadens its role in protein homeostasis. Targeting the interaction surfaces revealed in this study might be an effective strategy in the treatment of cancer.
    DOI:  https://doi.org/10.1371/journal.pone.0256640
  11. Methods Mol Biol. 2021 ;2365 283-300
    Profiling CELMoD-Mediated Degradation of Cereblon Neosubstrates.
    Joel W Thompson, Thomas Clayton, Gody Khambatta, Leslie A Bateman, Christopher W Carroll, Philip P Chamberlain, Mary E Matyskiela.
      Targeted protein degradation is garnering increased attention as a therapeutic modality due in part to its promise of modulating targets previously considered undruggable. Cereblon E3 Ligase Modulating Drugs (CELMoDs) are one of the most well-characterized therapeutics employing this modality. CELMoDs hijack Cereblon E3 ligase activity causing neosubstrates to be ubiquitinated and degraded in the proteasome. Here, we describe a suite of assays-cellular substrate degradation, confirmation of CELMoD mechanism of action, in vitro ubiquitination, and Cereblon binding-that can be used to characterize CELMoD-mediated degradation of Cereblon neosubstrates. While the assays presented herein can be run independently, when combined they provide a strong platform to support the discovery and optimization of CELMoDs and fuel validation of targets degraded by this drug modality.
    Keywords:  CELMoD; Cellular neosubstrate degradation; Cereblon; Cereblon binding; In vitro ubiquitination; Targeted protein degradation
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_15
  12. Methods Mol Biol. 2021 ;2365 203-216
    Global Mass Spectrometry-Based Analysis of Protein Ubiquitination Using K-ε-GG Remnant Antibody Enrichment.
    Alissa J Nelson, Yiying Zhu, Jian Min Ren, Matthew P Stokes.
      Ubiquitination is a post-translational modification that affects protein degradation as well as a variety of cellular processes. Methods that globally profile ubiquitination are powerful tools to better understand these processes. Here we describe an updated method for identification and quantification of thousands of sites of ubiquitination from cells, tissues, or other biological materials. The method involves cell lysis and digestion to peptides, immunoaffinity enrichment with an antibody recognizing di-glycine remnants left behind at ubiquitinated lysines, and liquid chromatography-tandem mass spectrometry analysis of the enriched peptides.
    Keywords:  LC-MS/MS; Mass spectrometry; PTMScan; Post-translational modification; Protein degradation; Proteomics; Ubiquitin; Ubiquitination
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_11
  13. Cell Death Differ. 2021 Aug 27.
    Stress-induced inflammation evoked by immunogenic cell death is blunted by the IRE1α kinase inhibitor KIRA6 through HSP60 targeting.
    Nicole Rufo, Dimitris Korovesis, Sofie Van Eygen, Rita Derua, Abhishek D Garg, Francesca Finotello, Monica Vara-Perez, Jan Rožanc, Michael Dewaele, Peter A de Witte, Leonidas G Alexopoulos, Sophie Janssens, Lasse Sinkkonen, Thomas Sauter, Steven H L Verhelst, Patrizia Agostinis.
      Mounting evidence indicates that immunogenic therapies engaging the unfolded protein response (UPR) following endoplasmic reticulum (ER) stress favor proficient cancer cell-immune interactions, by stimulating the release of immunomodulatory/proinflammatory factors by stressed or dying cancer cells. UPR-driven transcription of proinflammatory cytokines/chemokines exert beneficial or detrimental effects on tumor growth and antitumor immunity, but the cell-autonomous machinery governing the cancer cell inflammatory output in response to immunogenic therapies remains poorly defined. Here, we profiled the transcriptome of cancer cells responding to immunogenic or weakly immunogenic treatments. Bioinformatics-driven pathway analysis indicated that immunogenic treatments instigated a NF-κB/AP-1-inflammatory stress response, which dissociated from both cell death and UPR. This stress-induced inflammation was specifically abolished by the IRE1α-kinase inhibitor KIRA6. Supernatants from immunogenic chemotherapy and KIRA6 co-treated cancer cells were deprived of proinflammatory/chemoattractant factors and failed to mobilize neutrophils and induce dendritic cell maturation. Furthermore, KIRA6 significantly reduced the in vivo vaccination potential of dying cancer cells responding to immunogenic chemotherapy. Mechanistically, we found that the anti-inflammatory effect of KIRA6 was still effective in IRE1α-deficient cells, indicating a hitherto unknown off-target effector of this IRE1α-kinase inhibitor. Generation of a KIRA6-clickable photoaffinity probe, mass spectrometry, and co-immunoprecipitation analysis identified cytosolic HSP60 as a KIRA6 off-target in the IKK-driven NF-κB pathway. In sum, our study unravels that HSP60 is a KIRA6-inhibitable upstream regulator of the NF-κB/AP-1-inflammatory stress responses evoked by immunogenic treatments. It also urges caution when interpreting the anti-inflammatory action of IRE1α chemical inhibitors.
    DOI:  https://doi.org/10.1038/s41418-021-00853-5
  14. Cells. 2021 Jul 23. pii: 1865. [Epub ahead of print]10(8):
    The Link between VAPB Loss of Function and Amyotrophic Lateral Sclerosis.
    Nica Borgese, Nicola Iacomino, Sara Francesca Colombo, Francesca Navone.
      The VAP proteins are integral adaptor proteins of the endoplasmic reticulum (ER) membrane that recruit a myriad of interacting partners to the ER surface. Through these interactions, the VAPs mediate a large number of processes, notably the generation of membrane contact sites between the ER and essentially all other cellular membranes. In 2004, it was discovered that a mutation (p.P56S) in the VAPB paralogue causes a rare form of dominantly inherited familial amyotrophic lateral sclerosis (ALS8). The mutant protein is aggregation-prone, non-functional and unstable, and its expression from a single allele appears to be insufficient to support toxic gain-of-function effects within motor neurons. Instead, loss-of-function of the single wild-type allele is required for pathological effects, and VAPB haploinsufficiency may be the main driver of the disease. In this article, we review the studies on the effects of VAPB deficit in cellular and animal models. Several basic cell physiological processes are affected by downregulation or complete depletion of VAPB, impinging on phosphoinositide homeostasis, Ca2+ signalling, ion transport, neurite extension, and ER stress. In the future, the distinction between the roles of the two VAP paralogues (A and B), as well as studies on motor neurons generated from induced pluripotent stem cells (iPSC) of ALS8 patients will further elucidate the pathogenic basis of p.P56S familial ALS, as well as of other more common forms of the disease.
    Keywords:  FFAT motif; VAP proteins; endoplasmic reticulum; membrane contact sites; motor neurons; neurodegeneration; phosphoinositides
    DOI:  https://doi.org/10.3390/cells10081865
  15. Methods Mol Biol. 2021 ;2365 151-171
    Kinetic Detection of E3:PROTAC:Target Ternary Complexes Using NanoBRET Technology in Live Cells.
    Sarah D Mahan, Kristin M Riching, Marjeta Urh, Danette L Daniels.
      Heterobifunctional small-molecule degraders known as Proteolysis Targeting Chimeras (PROTACs) serve as a chemical bridge bringing into direct association a target protein with an active E3 ligase complex, called the ternary complex, to facilitate targeted protein degradation. This ternary complex formation is the first key mechanistic step in a cascade of events that results in ubiquitination and subsequent degradation of the target protein via the ubiquitin-proteasome pathway. The ternary complex, however, is a nonnative cellular complex; therefore, PROTAC compound design has many challenges to overcome to ensure successful formation, including achieving structural and electrostatic favorability among target and ligase. Due to these challenges, finding successful PROTACs typically requires testing of extensive libraries of heterobifunctional compounds with varying linkers and E3 handles. As PROTAC ternary complex formation is also critically dependent on cellular context, live cell assays and technologies for rapid and robust screening are highly enabling for triaging of early stage compounds. Here, we present cellular assays utilizing NanoBRET technology for the study of ternary complexes, showing examples with two most popular PROTAC E3 ligase components, VHL (von Hippel-Lindau disease tumor suppressor) and CRBN (Cereblon). These assays can be run in either endpoint or real-time kinetic formats, are compatible with high-throughput workflows, and provide insight into how altering the PROTAC chemical composition affects the formation and stability of the ternary complex in live cells.
    Keywords:  CRBN; Cellular ternary complex; E3 ligase components; Kinetic; NanoBRET; PROTACs; Protein degradation; Ubiquitination; VHL
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_8
  16. Methods Mol Biol. 2021 ;2365 135-150
    An In Vitro Pull-down Assay of the E3 Ligase:PROTAC:Substrate Ternary Complex to Identify Effective PROTACs.
    Daniel P Bondeson, Blake E Smith, Alexandru D Buhimschi.
      Assessing the specificity of PROTACs and confirming their proposed mechanism of action are critical for a robust targeted protein degradation program. Owing to their novel mechanism, new assays are needed to meet these goals. We and others have shown that a common explanation of PROTAC efficacy is the ability of the PROTAC to form a ternary complex between the E3 ubiquitin ligase and the target protein. In this chapter, we provide a simple in vitro method to quickly and inexpensively assess this property of PROTAC molecules. We provide detailed instructions for the purification of the specific E3 ubiquitin ligase VHL and then a generic protocol which can be adapted to any E3 ligase and substrate protein combination. This accessible method to study the ternary complex can strengthen any PROTAC-focused medicinal chemistry effort.
    Keywords:  Degrader; E3 ubiquitin ligase; PROTAC; Targeted protein degradation; Ternary complex; VHL
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_7
  17. Autophagy. 2021 Aug 26. 1-18
    USP19 (ubiquitin specific peptidase 19) promotes TBK1 (TANK-binding kinase 1) degradation via chaperone-mediated autophagy.
    Xibao Zhao, Qianqian Di, Juan Yu, Jiazheng Quan, Yue Xiao, Huihui Zhu, Hongrui Li, Jing Ling, Weilin Chen.
      TBK1 (TANK-binding kinase 1) is an essential receptor protein required for the innate immune response, but the mechanisms underlying TBK1 stability, especially those regulated via autophagy, remain poorly understood. Here, we demonstrate that USP19 (ubiquitin specific peptidase 19) interacts with and promotes TBK1 lysosomal degradation via chaperone-mediated autophagy (CMA). We observed that TBK1 had a canonical CMA motif, knocking down key proteins involved in CMA (HSPA8/HSC70 or LAMP2A) or inhibiting CMA-prevented USP19-mediated TBK1 degradation. Furthermore, USP19 deficiency in macrophages caused an elevation of TBK1 and the activation of the type-I interferon signaling pathway after vesicular stomatitis virus (VSV) infection. Consistently, macrophage-specific usp19 knockout in mice resulted in attenuated VSV replication and resistance to VSV infection in vivo. Altogether, our results suggest that USP19 is a key regulator of TBK1 and uncovers a previously uncharacterized role for USP19 in CMA-mediated TBK1 degradation and infectious diseases.
    Keywords:  Antiviral immunity; autophagic degradation; hspa8/hsc70; lamp2a; type i interferon
    DOI:  https://doi.org/10.1080/15548627.2021.1963155
  18. Sci Rep. 2021 Aug 24. 11(1): 17139
    The chaperone HSPB1 prepares protein aggregates for resolubilization by HSP70.
    Conrado C Gonçalves, Itai Sharon, T Martin Schmeing, Carlos H I Ramos, Jason C Young.
      In human cells under stress conditions, misfolded polypeptides can form potentially cytotoxic insoluble aggregates. To eliminate aggregates, the HSP70 chaperone machinery extracts and resolubilizes polypeptides for triage to refolding or degradation. Yeast and bacterial chaperones of the small heat-shock protein (sHSP) family can bind substrates at early stages of misfolding, during the aggregation process. The co-aggregated sHSPs then facilitate downstream disaggregation by HSP70. Because it is unknown whether a human sHSP has this activity, we investigated the disaggregation role of human HSPB1. HSPB1 co-aggregated with unfolded protein substrates, firefly luciferase and mammalian lactate dehydrogenase. The co-aggregates formed with HSPB1 were smaller and more regularly shaped than those formed in its absence. Importantly, co-aggregation promoted the efficient disaggregation and refolding of the substrates, led by HSP70. HSPB1 itself was also extracted during disaggregation, and its homo-oligomerization ability was not required. Therefore, we propose that a human sHSP is an integral part of the chaperone network for protein disaggregation.
    DOI:  https://doi.org/10.1038/s41598-021-96518-x
  19. J Cell Sci. 2021 Aug 26. pii: jcs.259156. [Epub ahead of print]
    The mRNA decapping complex is buffered by nuclear localization.
    Kiril Tishinov, Anne Spang.
      mRNA decay is a key step in regulating the cellular proteome. Processing bodies (P-bodies) are thought to be sites of mRNA decay and/or storage. P-body units assemble into P-body granules under stress conditions. How this assembly is regulated, however, remains poorly understood. Here, we show that the translational repressor Scd6 and the decapping stimulator Edc3 act partially redundantly in P-body assembly by sequestering the Dcp1/2 decapping complex in the cytoplasm and preventing it from becoming imported into the nucleus by the karyopherin ß Kap95. One of two nuclear localization signals in Dcp2 overlaps with the RNA binding site, suggesting an additional mechanism to regulate Dcp1/2 localization. Nuclear Dcp1/2 does not drive mRNA decay and might be stored there as a readily releasable pool, indicating a dynamic equilibrium between cytoplasmic and nuclear Dcp1/2. Cytoplasmic Dcp1/2 is linked to Dhh1 via Edc3. Functional P-bodies are present at the endoplasmic reticulum where Dcp2 potentially acts to increase the local concentration of Dhh1 through interaction with Edc3 to drive phase separation and hence P-body formation.
    Keywords:  Endoplasmic reticulum; MRNA; Membrane-less granules; Nucleo-cytoplasmic transport; Phase separation; Processing bodies
    DOI:  https://doi.org/10.1242/jcs.259156
  20. Methods Mol Biol. 2021 ;2365 79-113
    Mechanistic and Structural Features of PROTAC Ternary Complexes.
    Ryan Casement, Adam Bond, Conner Craigon, Alessio Ciulli.
      The rapid and ever-growing advancements from within the field of proteolysis-targeting chimeras (PROTAC)-induced protein degradation have driven considerable development to gain a deeper understanding of their mode of action. The ternary complex formed by PROTACs with their target protein and E3 ubiquitin ligase is the key species in their substoichiometric catalytic mechanism. Here, we describe the theoretical framework that underpins ternary complexes, including a current understanding of the three-component binding model, cooperativity, hook effect and structural considerations. We discuss in detail the biophysical methods used to interrogate ternary complex formation in vitro, including X-ray crystallography, AlphaLISA, FRET, FP, ITC and SPR. Finally, we provide detailed ITC methods and discuss approaches to assess binary and ternary target engagement, target ubiquitination and degradation that can be used to obtain a more holistic understanding of the mode of action within a cellular environment.
    Keywords:  Biophysical methods, crystal structures; Cooperativity; E3 ubiquitin ligase; Hook effect; Protein ubiquitination; Target engagement; Targeted protein degradation (TPD); Ternary complex; proteolysis-targeting chimeras (PROTACs)
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_5
  21. Biochem J. 2021 Aug 27. 478(16): 3125-3143
    Quality control of protein import into mitochondria.
    Fabian den Brave, Jeannine Engelke, Thomas Becker.
      Mitochondria import about 1000 proteins that are produced as precursors on cytosolic ribosomes. Defects in mitochondrial protein import result in the accumulation of non-imported precursor proteins and proteotoxic stress. The cell is equipped with different quality control mechanisms to monitor protein transport into mitochondria. First, molecular chaperones guide unfolded proteins to mitochondria and deliver non-imported proteins to proteasomal degradation. Second, quality control factors remove translocation stalled precursor proteins from protein translocases. Third, protein translocases monitor protein sorting to mitochondrial subcompartments. Fourth, AAA proteases of the mitochondrial subcompartments remove mislocalized or unassembled proteins. Finally, impaired efficiency of protein transport is an important sensor for mitochondrial dysfunction and causes the induction of cellular stress responses, which could eventually result in the removal of the defective mitochondria by mitophagy. In this review, we summarize our current understanding of quality control mechanisms that govern mitochondrial protein transport.
    Keywords:  TIM23 complex; TOM complex; mitochondria; protein sorting; protein transport
    DOI:  https://doi.org/10.1042/BCJ20190584
  22. Methods Mol Biol. 2021 ;2365 217-244
    Determination of Proteasomal Unfolding Ability.
    Christina M Hurley, Daniel A Kraut.
      We use an in vitro degradation assay with a model substrate to assess proteasomal unfolding ability. Our substrate has an unstructured region that is the site of ubiquitination, followed by an easy-to-unfold domain and a difficult-to-unfold domain. Degradation proceeds through the unstructured and easy-to-unfold domains, but the difficult-to-unfold domain can be degraded completely or, if the proteasome stalls, can be released as a partially degraded fragment. The ratio between these two possible outcomes allows us to quantify the unfolding ability and determine how processively the proteasome degrades its substrates.
    Keywords:  ATP-dependent protease; Proteasome; Protein Degradation; Protein Unfolding; Ubiquitin-proteasome system
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_12
  23. J Cell Sci. 2021 Aug 27. pii: jcs.258643. [Epub ahead of print]
    Hypusinated eIF5A is required for the translation of collagen.
    Marina Barba-Aliaga, Adriana Mena, Vanessa Espinoza, Nadezda Apostolova, Mercedes Costell, Paula Alepuz.
      Translation of mRNAs that encode peptide sequences with consecutive prolines (polyproline) requires the conserved and essential elongation factor eIF5A to facilitate the formation of peptide bonds. It has been shown that upon eIF5A depletion, yeast ribosomes stall in polyproline motifs, but also in tripeptide sequences that combine proline with glycine and charged amino acids. Mammalian collagens are enriched in putative eIF5A-dependent Pro-Gly-containing tripeptides. Here we show that depletion of active eIF5A in mouse fibroblasts reduced collagen 1 (Col1a1) content, which concentrated around the nuclei. Moreover, it provoked the up-regulation of endoplasmic reticulum (ER)-stress markers suggesting retention of partially synthesized Col1 in the ER. We confirmed that eIF5A is needed for heterologous collagen synthesis in yeast, and using a double luciferase reporter system we showed that eIF5A depletion interrupts translation at Pro-Gly-collagenic motifs. A dramatically lower level of Col1α1 protein was also observed in functional eIF5A-depleted human hepatic stellate cells treated with the profibrotic cytokine TGF-β1. In sum, our results show that collagen expression requires eIF5A and imply its potential as a target for regulating collagen production in fibrotic diseases.
    Keywords:  Collagen; EIF5A; ER stress; Fibrosis; Translation
    DOI:  https://doi.org/10.1242/jcs.258643
  24. Mol Biol Cell. 2021 Aug 25. mbcE21060295
    RUSC2 and WDR47 oppositely regulate kinesin-1-dependent distribution of ATG9A to the cell periphery.
    Carlos M Guardia, Akansha Jain, Rafael Mattera, Alex Friefeld, Yan Li, Juan S Bonifacino.
      Autophagy-related protein 9 (ATG9) is a transmembrane protein component of the autophagy machinery that cycles between the trans-Golgi network (TGN) in the perinuclear area and other compartments in the peripheral area of the cell. In mammalian cells, export of the ATG9A isoform from the TGN into ATG9A-containing vesicles is mediated by the adaptor protein 4 (AP-4) complex. However, the mechanisms responsible for the subsequent distribution of these vesicles to the cell periphery is unclear. Herein we show that the AP-4-accessory protein RUSC2 couples ATG9A-containing vesicles to the plus-end-directed microtubule motor kinesin-1 via an interaction between a disordered region of RUSC2 and the kinesin-1 light chain (KLC). This interaction is counteracted by the microtubule-associated WD40-repeat domain 47 protein (WDR47). These findings uncover a mechanism for the peripheral distribution of ATG9A-containing vesicles, involving the function of RUSC2 as a kinesin-1 adaptor and WDR47 as a negative regulator of this function.
    DOI:  https://doi.org/10.1091/mbc.E21-06-0295
  25. Cancers (Basel). 2021 Aug 21. pii: 4210. [Epub ahead of print]13(16):
    The Unfolded Protein Response Is a Major Driver of LCN2 Expression in BCR-ABL- and JAK2V617F-Positive MPN.
    Stefan Tillmann, Kathrin Olschok, Sarah K Schröder, Marlena Bütow, Julian Baumeister, Milena Kalmer, Vera Preußger, Barbora Weinbergerova, Kim Kricheldorf, Jiri Mayer, Blanka Kubesova, Zdenek Racil, Martina Wessiepe, Jörg Eschweiler, Susanne Isfort, Tim H Brümmendorf, Walter Becker, Mirle Schemionek, Ralf Weiskirchen, Steffen Koschmieder, Nicolas Chatain.
      Lipocalin 2 (LCN2), a proinflammatory mediator, is involved in the pathogenesis of myeloproliferative neoplasms (MPN). Here, we investigated the molecular mechanisms of LCN2 overexpression in MPN. LCN2 mRNA expression was 20-fold upregulated in peripheral blood (PB) mononuclear cells of chronic myeloid leukemia (CML) and myelofibrosis (MF) patients vs. healthy controls. In addition, LCN2 serum levels were significantly increased in polycythemia vera (PV) and MF and positively correlated with JAK2V617F and mutated CALR allele burden and neutrophil counts. Mechanistically, we identified endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) as a main driver of LCN2 expression in BCR-ABL- and JAK2V617F-positive 32D cells. The UPR inducer thapsigargin increased LCN2 expression >100-fold, and this was not affected by kinase inhibition of BCR-ABL or JAK2V617F. Interestingly, inhibition of the UPR regulators inositol-requiring enzyme 1 (IRE1) and c-Jun N-terminal kinase (JNK) significantly reduced thapsigargin-induced LCN2 RNA and protein expression, and luciferase promoter assays identified nuclear factor kappa B (NF-κB) and CCAAT binding protein (C/EBP) as critical regulators of mLCN2 transcription. In conclusion, the IRE1-JNK-NF-κB-C/EBP axis is a major driver of LCN2 expression in MPN, and targeting UPR and LCN2 may represent a promising novel therapeutic approach in MPN.
    Keywords:  BCR-ABL; ER stress; IRE1; JAK2V617F; Lipocalin 2 (LCN2); MPN; NGAL; UPR
    DOI:  https://doi.org/10.3390/cancers13164210
  26. J Exp Med. 2021 Oct 04. pii: e20210227. [Epub ahead of print]218(10):
    TREM2-dependent lipid droplet biogenesis in phagocytes is required for remyelination.
    Garyfallia Gouna, Christian Klose, Mar Bosch-Queralt, Lu Liu, Ozgun Gokce, Martina Schifferer, Ludovico Cantuti-Castelvetri, Mikael Simons.
      Upon demyelinating injury, microglia orchestrate a regenerative response that promotes myelin repair, thereby restoring rapid signal propagation and protecting axons from further damage. Whereas the essential phagocytic function of microglia for remyelination is well known, the underlying metabolic pathways required for myelin debris clearance are poorly understood. Here, we show that cholesterol esterification in male mouse microglia/macrophages is a necessary adaptive response to myelin debris uptake and required for the generation of lipid droplets upon demyelinating injury. When lipid droplet biogenesis is defective, innate immune cells do not resolve, and the regenerative response fails. We found that triggering receptor expressed on myeloid cells 2 (TREM2)-deficient mice are unable to adapt to excess cholesterol exposure, form fewer lipid droplets, and build up endoplasmic reticulum (ER) stress. Alleviating ER stress in TREM2-deficient mice restores lipid droplet biogenesis and resolves the innate immune response. Thus, we conclude that TREM2-dependent formation of lipid droplets constitute a protective response required for remyelination to occur.
    DOI:  https://doi.org/10.1084/jem.20210227
  27. Methods Mol Biol. 2021 ;2365 175-184
    Inducing Ubiquitylation and Protein Degradation as a Drug Development Strategy.
    Kamaldeep S Dhami, XiaoDong Huang.
      A new drug discovery strategy by inducing the degradation of oncoproteins through ubiquitin-proteasome system (UPS) has gained a lot of traction in the last decade (Verma et al. Mol Cell 77(3):446-460, 2020; Huang, Dixit. Cell Res 26:484, 2016). Multiple degrader platforms, such as IMiDs (Kronke et al. Science 343:301-305, 2014; Lu et al. Science 343:305-309; 2014), PROTAC (proteolysis targeting chimera) (Winter et al. Science 348:1376-1381, 2015), and molecular glues (Tan et al. Nature 446:640-645, 2007), have been approved or currently being developed in clinical trials. Compared to conventional drug inhibitors, degraders have a lot of advantages, such as catalytic mechanisms of action (MOA), no requirement of high-affinity ligands with targets, and potentially more sustained efficacy (Verma et al. Mol Cell 77(3):446-460, 2020; Huang, Dixit. Cell Res 26:484, 2016; Bondeson et al. Nat Chem Biol 11:611-617). Here, we describe protocols that measure intrinsic protein ubiquitination, degrader-induced target protein degradation, and cancer cell proliferation evaluation, as these protocols can help evaluate the potential of a drug target using a degrader platform.
    Keywords:  Degrader; Inhibitor; PROTAC; Proteasome; Ubiquitin
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_9
  28. Cell. 2021 Aug 20. pii: S0092-8674(21)00943-0. [Epub ahead of print]
    Dual film-like organelles enable spatial separation of orthogonal eukaryotic translation.
    Christopher D Reinkemeier, Edward A Lemke.
      Engineering new functionality into living eukaryotic systems by enzyme evolution or de novo protein design is a formidable challenge. Cells do not rely exclusively on DNA-based evolution to generate new functionality but often utilize membrane encapsulation or formation of membraneless organelles to separate distinct molecular processes that execute complex operations. Applying this principle and the concept of two-dimensional phase separation, we develop film-like synthetic organelles that support protein translation on the surfaces of various cellular membranes. These sub-resolution synthetic films provide a path to make functionally distinct enzymes within the same cell. We use these film-like organelles to equip eukaryotic cells with dual orthogonal expanded genetic codes that enable the specific reprogramming of distinct translational machineries with single-residue precision. The ability to spatially tune the output of translation within tens of nanometers is not only important for synthetic biology but has implications for understanding the function of membrane-associated protein condensation in cells.
    Keywords:  2D phase separation; enzyme engineering; genetic code expansion; membrane signaling; orthogonal translation; synthetic biology; synthetic biomolecular condensates
    DOI:  https://doi.org/10.1016/j.cell.2021.08.001
  29. Front Immunol. 2021 ;12 720765
    Proteomics Mapping of the ISGylation Landscape in Innate Immunity.
    Fabien Thery, Denzel Eggermont, Francis Impens.
      During infection, pathogen sensing and cytokine signaling by the host induce expression of antimicrobial proteins and specialized post-translational modifications. One such protein is ISG15, a ubiquitin-like protein (UBL) conserved among vertebrates. Similar to ubiquitin, ISG15 covalently conjugates to lysine residues in substrate proteins in a process called ISGylation. Mice deficient for ISGylation or lacking ISG15 are strongly susceptible to many viral pathogens and several intracellular bacterial pathogens. Although ISG15 was the first UBL discovered after ubiquitin, the mechanisms behind its protective activity are poorly understood. Largely, this stems from a lack of knowledge on the ISG15 substrate repertoire. To unravel the antiviral activity of ISG15, early studies used mass spectrometry-based proteomics in combination with ISG15 pulldown. Despite reporting hundreds of ISG15 substrates, these studies were unable to identify the exact sites of modification, impeding a clear understanding of the molecular consequences of protein ISGylation. More recently, a peptide-based enrichment approach revolutionized the study of ubiquitin allowing untargeted discovery of ubiquitin substrates, including knowledge of their exact modification sites. Shared molecular determinants between ISG15 and ubiquitin allowed to take advantage of this technology for proteome-wide mapping of ISG15 substrates and modification sites. In this review, we provide a comprehensive overview of mass spectrometry-based proteomics studies on protein ISGylation. We critically discuss the relevant literature, compare reported substrates and sites and make suggestions for future research.
    Keywords:  ISG15; infection; interferon; mass spectrometry; ubiquitin-like modification
    DOI:  https://doi.org/10.3389/fimmu.2021.720765
  30. Sci Adv. 2021 Aug;pii: eabg7287. [Epub ahead of print]7(35):
    A cancer ubiquitome landscape identifies metabolic reprogramming as target of Parkin tumor suppression.
    Ekta Agarwal, Aaron R Goldman, Hsin-Yao Tang, Andrew V Kossenkov, Jagadish C Ghosh, Lucia R Languino, Valentina Vaira, David W Speicher, Dario C Altieri.
      Changes in metabolism that affect mitochondrial and glycolytic networks are hallmarks of cancer, but their impact in disease is still elusive. Using global proteomics and ubiquitome screens, we now show that Parkin, an E3 ubiquitin ligase and key effector of mitophagy altered in Parkinson's disease, shuts off mitochondrial dynamics and inhibits the non-oxidative phase of the pentose phosphate pathway. This blocks tumor cell movements, creates metabolic and oxidative stress, and inhibits primary and metastatic tumor growth. Uniformly down-regulated in cancer patients, Parkin tumor suppression requires its E3 ligase function, is reversed by antioxidants, and is independent of mitophagy. These data demonstrate that cancer metabolic networks are potent oncogenes directly targeted by endogenous tumor suppression.
    DOI:  https://doi.org/10.1126/sciadv.abg7287
  31. Cell Rep. 2021 Aug 24. pii: S2211-1247(21)01002-0. [Epub ahead of print]36(8): 109568
    Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors.
    Camilla Calandrini, Sander R van Hooff, Irene Paassen, Dilara Ayyildiz, Sepide Derakhshan, M Emmy M Dolman, Karin P S Langenberg, Marieke van de Ven, Cecilia de Heus, Nalan Liv, Marcel Kool, Ronald R de Krijger, Godelieve A M Tytgat, Marry M van den Heuvel-Eibrink, Jan J Molenaar, Jarno Drost.
      Malignant rhabdoid tumors (MRTs) represent one of the most aggressive childhood malignancies. No effective treatment options are available, and prognosis is, therefore, dismal. Previous studies have demonstrated that tumor organoids capture the heterogeneity of patient tumors and can be used to predict patient response to therapy. Here, we perform drug screening on patient-derived normal and tumor organoids to identify MRT-specific therapeutic vulnerabilities. We identify neddylation inhibitor MLN4924 as a potential therapeutic agent. Mechanistically, we find increased neddylation in MRT organoids and tissues and show that MLN4924 induces a cytotoxic response via upregulation of the unfolded protein response. Lastly, we demonstrate in vivo efficacy in an MRT PDX mouse model, in which single-agent MLN4924 treatment significantly extends survival. Our study demonstrates that organoids can be used to find drugs selectively targeting tumor cells while leaving healthy cells unharmed and proposes neddylation inhibition as a therapeutic strategy in MRT.
    Keywords:  MLN4924; drug screening; malignant rhabdoid tumors; neddylation; organoids; targeted therapy
    DOI:  https://doi.org/10.1016/j.celrep.2021.109568
  32. Methods Mol Biol. 2021 ;2365 247-263
    Methods for Quantitative Assessment of Protein Degradation.
    Radosław P Nowak, Hong Yue, Emily Y Park, Eric S Fischer.
      Assessment of small molecules that promote selective protein degradation (degraders) requires detailed characterization and measurement of protein levels in cells. Here we describe ratio-metric methods based on a dual fluorescent GFP/mCherry reporter system to quantify cellular protein levels. We further develop a kinetic framework for the analysis of such data. We describe two methods of generating the stable GFP-protein of interest (POI)/mCherry reporter cell lines, alternative readout methods by FACS and Laser Scanning Cytometry as well as the corresponding tools used for processing and analysis of such data. Finally, we show that the commonly used half-maximal degradation constant (DC50) or maximum degradation efficacy (Dmax) metrics are time-dependent and propose a time-invariant Michaelis-Menten-like analysis of degradation kinetics with analogous key parameters Km app and Vmax app.
    Keywords:  CRBN; DC50; Degradation kinetics; IMiD; PROTAC; Targeted protein degradation; VHL
    DOI:  https://doi.org/10.1007/978-1-0716-1665-9_13
  33. J Exp Clin Cancer Res. 2021 Aug 27. 40(1): 271
    The Anterior GRadient (AGR) family proteins in epithelial ovarian cancer.
    Delphine Fessart, Jacques Robert, Cecile Hartog, Eric Chevet, Frederic Delom, Guillaume Babin.
      Epithelial ovarian cancer (EOC) is the most common gynecologic disorder. Even with the recent progresses made towards the use of new therapeutics, it still represents the most lethal gynecologic malignancy in women from developed countries.The discovery of the anterior gradient proteins AGR2 and AGR3, which are highly related members belonging to the protein disulfide isomerase (PDI) family, attracted researchers' attention due to their putative involvement in adenocarcinoma development. This review compiles the current knowledge on the role of the AGR family and the expression of its members in EOC and discusses the potential clinical relevance of AGR2 and AGR3 for EOC diagnosis, prognosis, and therapeutics.A better understanding of the role of the AGR family may thus provide new handling avenues for EOC patients.
    Keywords:  AGR2; AGR3; Endoplasmic reticulum proteins; Epithelial ovarian Cancer
    DOI:  https://doi.org/10.1186/s13046-021-02060-z
  34. iScience. 2021 Aug 20. 24(8): 102917
    A global map of associations between types of protein posttranslational modifications and human genetic diseases.
    Perceval Vellosillo, Pablo Minguez.
      There are >200 types of protein posttranslational modifications (PTMs) described in eukaryotes, each with unique proteome coverage and functions. We hypothesized that some genetic diseases may be caused by the removal of a specific type of PTMs by genomic variants and the consequent deregulation of particular functions. We collected >320,000 human PTMs representing 59 types and crossed them with >4M nonsynonymous DNA variants annotated with predicted pathogenicity and disease associations. We report >1.74M PTM-variant co-occurrences that an enrichment analysis distributed into 215 pairwise associations between 18 PTM types and 148 genetic diseases. Of them, 42% were not previously described. Removal of lysine acetylation exerts the most pronounced effect, and less studied PTM types such as S-glutathionylation or S-nitrosylation show relevance. Using pathogenicity predictions, we identified PTM sites that may produce particular diseases if prevented. Our results provide evidence of a substantial impact of PTM-specific removal on the pathogenesis of genetic diseases and phenotypes.
    Keywords:  Omics; Proteomics; Systems Biology
    DOI:  https://doi.org/10.1016/j.isci.2021.102917
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