bims-proteo Biomed News
on Proteostasis
Issue of 2022‒01‒23
38 papers selected by
Eric Chevet
INSERM
  1. Inositol Requiring Enzyme (IRE), a multiplayer in sensing endoplasmic reticulum stress.
  2. Disruption of the Nα-Acetyltransferase NatB Causes Sensitivity to Reductive Stress in Arabidopsis thaliana.
  3. A positive genetic selection for transmembrane domain mutations in HRD1 underscores the importance of Hrd1 complex integrity during ERAD.
  4. Role of systems biology and multi-omics analyses in delineating spatial interconnectivity and temporal dynamicity of ER stress mediated cellular responses.
  5. Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis.
  6. SURF4-induced tubular ERGIC selectively expedites ER-to-Golgi transport.
  7. The deubiquitinase Usp27x as a novel regulator of cFLIPL protein expression and sensitizer to death-receptor-induced apoptosis.
  8. Chemical regulation of the protein quality control E3 ubiquitin ligase C-terminus of Hsc70 interacting protein (CHIP).
  9. Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes.
  10. NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems.
  11. Regulation of Neurodegeneration-associated Protein Fragments by the N-degron Pathways.
  12. Reconstitution of the DTX3L-PARP9 complex reveals determinants for high affinity heterodimerization and multimeric assembly.
  13. Augmented ERAD (ER-associated degradation) activity in chondrocytes is necessary for cartilage development and maintenance.
  14. Identification of substrates for human deubiquitinating enzymes (DUBs): An up-to-date review and a case study for neurodevelopmental disorders.
  15. Selective localization of Mfn2 near PINK1 enables its preferential ubiquitination by Parkin on mitochondria.
  16. ER reductive stress caused by Ero1α S-nitrosation accelerates senescence.
  17. Unfolding by Cdc48/p97: different strokes for different folks.
  18. Branched ubiquitin code: from basic biology to targeted protein degradation.
  19. ER-GCaMP6f: An Endoplasmic Reticulum-Targeted Genetic Probe to Measure Calcium Activity in Astrocytic Processes.
  20. A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family.
  21. Chaperone mediated autophagy contributes to the newly synthesized histones H3 and H4 quality control.
  22. Host E3 ligase HUWE1 attenuates the pro-apoptotic activity of the MERS-CoV accessory protein ORF3 by promoting its ubiquitin-dependent degradation.
  23. TRIM21 suppresses CHK1 activation by preferentially targeting CLASPIN for K63-linked ubiquitination.
  24. Novel regulation mechanism of adrenal cortisol and DHEA biosynthesis via the endogen ERAD inhibitor small VCP-interacting protein.
  25. Optimized protocol to detect protein UFMylation in cells and in vitro via immunoblotting.
  26. Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons.
  27. MDM2-Driven Ubiquitination Rapidly Removes p53 from Its Cognate Promoters.
  28. GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites.
  29. Activation of E6AP/UBE3A-Mediated Protein Ubiquitination and Degradation Pathways by a Cyclic γ-AA Peptide.
  30. Location, location, location: subcellular protein partitioning in proteostasis and aging.
  31. Cellular architecture of human brain metastases.
  32. The immune-specific E3 ubiquitin ligase MARCH1 is upregulated during HCMV infection to regulate iron levels.
  33. A Selective Small-Molecule c-Myc Degrader Potently Regresses Lethal c-Myc Overexpressing Tumors.
  34. Targeted protein degradation: Emerging concepts and protein state-specific targeting principles.
  35. Associations of genetic variation in E3 SUMO-protein ligase CBX4 with noise-induced hearing loss.
  36. Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment.
  37. Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control.
  38. PROTAC targeted protein degraders: the past is prologue.
  1. Anim Cells Syst (Seoul). 2021 ;25(6): 347-357
    Inositol Requiring Enzyme (IRE), a multiplayer in sensing endoplasmic reticulum stress.
    Zhixin Zhou, Qian Wang, Marek Michalak.
      The endoplasmic reticulum (ER) can sense a wide variety of external and internal perturbations and responds by mounting stress coping responses, such as the unfolded protein response (UPR). The UPR is composed of three stress sensors, namely IRE1α, PERK, and ATF6 that are activated to re-establish ER homeostasis. IRE1α represents the most ancient branch of the UPR affecting many cellular processes in plant and animal cells. IRE1α is a type I transmembrane protein with kinase/nuclease activities in response to ER stress. Both the ER luminal and cytosolic IRE1α interactomes have been identified revealing a multifunctional role of the ER stress sensor. IRE1α is also associated with organellar membrane contacts to promote rapid communication between intracellular organelles under stress conditions.
    Keywords:  IRE1α; endoplasmic reticulum; stress sensor; unfolded protein response
    DOI:  https://doi.org/10.1080/19768354.2021.2020901
  2. Front Plant Sci. 2021 ;12 799954
    Disruption of the Nα-Acetyltransferase NatB Causes Sensitivity to Reductive Stress in Arabidopsis thaliana.
    Monika Huber, Laura Armbruster, Ross D Etherington, Carolina De La Torre, Malcolm J Hawkesford, Carsten Sticht, Daniel J Gibbs, Rüdiger Hell, Markus Wirtz.
      In Arabidopsis thaliana, the evolutionary conserved N-terminal acetyltransferase (Nat) complexes NatA and NatB co-translationally acetylate 60% of the proteome. Both have recently been implicated in the regulation of plant stress responses. While NatA mediates drought tolerance, NatB is required for pathogen resistance and the adaptation to high salinity and high osmolarity. Salt and osmotic stress impair protein folding and result in the accumulation of misfolded proteins in the endoplasmic reticulum (ER). The ER-membrane resident E3 ubiquitin ligase DOA10 targets misfolded proteins for degradation during ER stress and is conserved among eukaryotes. In yeast, DOA10 recognizes conditional degradation signals (Ac/N-degrons) created by NatA and NatB. Assuming that this mechanism is preserved in plants, the lack of Ac/N-degrons required for efficient removal of misfolded proteins might explain the sensitivity of NatB mutants to protein harming conditions. In this study, we investigate the response of NatB mutants to dithiothreitol (DTT) and tunicamycin (TM)-induced ER stress. We report that NatB mutants are hypersensitive to DTT but not TM, suggesting that the DTT hypersensitivity is caused by an over-reduction of the cytosol rather than an accumulation of unfolded proteins in the ER. In line with this hypothesis, the cytosol of NatB depleted plants is constitutively over-reduced and a global transcriptome analysis reveals that their reductive stress response is permanently activated. Moreover, we demonstrate that doa10 mutants are susceptible to neither DTT nor TM, ruling out a substantial role of DOA10 in ER-associated protein degradation (ERAD) in plants. Contrary to previous findings in yeast, our data indicate that N-terminal acetylation (NTA) does not inhibit ER targeting of a substantial amount of proteins in plants. In summary, we provide further evidence that NatB-mediated imprinting of the proteome is vital for the response to protein harming stress and rule out DOA10 as the sole recognin for substrates in the plant ERAD pathway, leaving the role of DOA10 in plants ambiguous.
    Keywords:  DOA10; ER-associated degradation; N-acetyltransferase NatB; N-degron; N-terminal acetylation; co-translational modification; proteostasis; reductive stress
    DOI:  https://doi.org/10.3389/fpls.2021.799954
  3. Curr Genet. 2022 Jan 18.
    A positive genetic selection for transmembrane domain mutations in HRD1 underscores the importance of Hrd1 complex integrity during ERAD.
    Kunio Nakatsukasa, Sylvia Wigge, Yuki Takano, Tomoyuki Kawarasaki, Takumi Kamura, Jeffrey L Brodsky.
      Misfolded proteins in the endoplasmic reticulum (ER) are retrotranslocated to the cytosol for ubiquitination and degradation by the proteasome. During this process, known as ER-associated degradation (ERAD), the ER-embedded Hrd1 ubiquitin ligase plays a central role in recognizing, ubiquitinating, and retrotranslocating scores of lumenal and integral membrane proteins. To better define the mechanisms underlying Hrd1 function in Saccharomyces cerevisiae, several model substrates have been developed. One substrate is Sec61-2, a temperature sensitive allele of the Sec61 translocation channel. Cells expressing Sec61-2 grow at 25 °C because the protein is stable, but sec61-2 yeast are inviable at 38 °C because the mutated protein is degraded in a Hrd1-dependent manner. Therefore, deleting HRD1 stabilizes Sec61-2 and hence sec61-2hrd1∆ double mutants are viable at 38 °C. This unique phenotype allowed us to perform a non-biased screen for loss-of-function alleles in HRD1. Based on its importance in mediating substrate retrotranslocation, the screen was also developed to focus on mutations in sequences encoding Hrd1's transmembrane-rich domain. Ultimately, a group of recessive mutations was identified in HRD1, including an ensemble of destabilizing mutations that resulted in the delivery of Hrd1 to the ERAD pathway. A more stable mutant resided in a buried transmembrane domain, yet the Hrd1 complex was disrupted in yeast expressing this mutant. Together, these data confirm the importance of Hrd1 complex integrity during ERAD, suggest that allosteric interactions between transmembrane domains regulate Hrd1 complex formation, and provide the field with new tools to define the dynamic interactions between ERAD components during substrate retrotranslocation.
    Keywords:  Degradation; E3 ubiquitin ligase; ER quality control; Endoplasmic reticulum; Proteasome; Ubiquitination
    DOI:  https://doi.org/10.1007/s00294-022-01227-1
  4. Biochim Biophys Acta Mol Cell Res. 2022 Jan 12. pii: S0167-4889(22)00001-5. [Epub ahead of print] 119210
    Role of systems biology and multi-omics analyses in delineating spatial interconnectivity and temporal dynamicity of ER stress mediated cellular responses.
    Priyanka Mallick, Sebabrata Maity, Oishee Chakrabarti, Saikat Chakrabarti.
      The endoplasmic reticulum (ER) is a membranous organelle involved in calcium storage, lipid biosynthesis, protein folding and processing. Many patho-physiological conditions and pharmacological agents are known to perturb normal ER function and can lead to ER stress, which severely compromise protein folding mechanism and hence poses high risk of proteotoxicity. Upon sensing ER stress, the different stress signaling pathways interconnect with each other and work together to preserve cellular homeostasis. ER stress response is a part of the integrative stress response (ISR) and might play an important role in the pathogenesis of chronic neurodegenerative diseases, where misfolded protein accumulation and cell death are common. The initiation, manifestation and progression of ER stress mediated unfolded protein response (UPR) is a complex procedure involving multiple proteins, pathways and cellular organelles. To understand the cause and consequences of such complex processes, implementation of an integrative holistic approach is required to identify novel players and regulators of ER stress. As multi-omics data-based systems analyses have shown potential to unravel the underneath molecular mechanism of complex biological systems, it is important to emphasize the utility of this approach in understanding the ER stress biology. In this review we first discuss the ER stress signaling pathways and regulatory players, along with their inter-connectivity. We next highlight the importance of systems and network biology approaches using multi-omics data in understanding ER stress mediated cellular responses. This report would help advance our current understanding of the multivariate spatial interconnectivity and temporal dynamicity of ER stress.
    Keywords:  Endoplasmic reticulum stress; Multi-omics approaches; Stress sensing pathways; Unfolded protein response; meta-pathway network
    DOI:  https://doi.org/10.1016/j.bbamcr.2022.119210
  5. Nature. 2022 Jan 19.
    Ageing exacerbates ribosome pausing to disrupt cotranslational proteostasis.
    Kevin C Stein, Fabián Morales-Polanco, Joris van der Lienden, T Kelly Rainbolt, Judith Frydman.
      Ageing is accompanied by a decline in cellular proteostasis, which underlies many age-related protein misfolding diseases1,2. Yet, how ageing impairs proteostasis remains unclear. As nascent polypeptides represent a substantial burden on the proteostasis network3, we hypothesized that altered translational efficiency during ageing could help to drive the collapse of proteostasis. Here we show that ageing alters the kinetics of translation elongation in both Caenorhabditis elegans and Saccharomyces cerevisiae. Ribosome pausing was exacerbated at specific positions in aged yeast and worms, including polybasic stretches, leading to increased ribosome collisions known to trigger ribosome-associated quality control (RQC)4-6. Notably, aged yeast cells exhibited impaired clearance and increased aggregation of RQC substrates, indicating that ageing overwhelms this pathway. Indeed, long-lived yeast mutants reduced age-dependent ribosome pausing, and extended lifespan correlated with greater flux through the RQC pathway. Further linking altered translation to proteostasis collapse, we found that nascent polypeptides exhibiting age-dependent ribosome pausing in C. elegans were strongly enriched among age-dependent protein aggregates. Notably, ageing increased the pausing and aggregation of many components of proteostasis, which could initiate a cycle of proteostasis collapse. We propose that increased ribosome pausing, leading to RQC overload and nascent polypeptide aggregation, critically contributes to proteostasis impairment and systemic decline during ageing.
    DOI:  https://doi.org/10.1038/s41586-021-04295-4
  6. Dev Cell. 2022 Jan 11. pii: S1534-5807(21)01038-8. [Epub ahead of print]
    SURF4-induced tubular ERGIC selectively expedites ER-to-Golgi transport.
    Rui Yan, Kun Chen, Bowen Wang, Ke Xu.
      The endoplasmic reticulum (ER)-to-Golgi transport is critical to protein secretion and intracellular sorting. Here, we report a highly elongated tubular ER-Golgi intermediate compartment (t-ERGIC) that selectively expedites the ER-to-Golgi transport for soluble cargoes of the receptor SURF4. Lacking the canonical ERGIC marker ERGIC-53 yet positive for the small GTPases Rab1A/B, the t-ERGIC is further marked by its extraordinarily elongated and thinned shape. With its large surface-to-volume ratio, high intracellular traveling speeds, and ER-Golgi recycling capabilities, the t-ERGIC accelerates the trafficking of SURF4-bound cargoes. The biogenesis and cargo selectivity of t-ERGIC both depend on SURF4, which recognizes the N terminus of soluble cargoes and co-clusters with the selected cargoes to expand the ER-exit site. In the steady state, the t-ERGIC-mediated fast ER-to-Golgi transport is antagonized by the KDEL-mediated ER retrieval. Together, our results argue that specific cargo-receptor interactions give rise to distinct transport carriers that regulate the trafficking kinetics.
    Keywords:  ER-Golgi intermediate compartment; ER-exit site expansion; ER-to-Golgi transport; N-terminal selective binding; SURF4-KDELR antagonism; SURF4-cargo co-clustering; membrane vesicle trafficking; protein secretion kinetics; soluble cargo; tubular carrier
    DOI:  https://doi.org/10.1016/j.devcel.2021.12.018
  7. Apoptosis. 2022 Jan 19.
    The deubiquitinase Usp27x as a novel regulator of cFLIPL protein expression and sensitizer to death-receptor-induced apoptosis.
    Manuel Nico Dold, Xiulin Ng, Claudia Alber, Ian Edward Gentle, Georg Häcker, Arnim Weber.
      Death receptors are transmembrane proteins that can induce the activation of caspase-8 upon ligand binding, initiating apoptosis. Recent work has highlighted the great molecular complexity of death receptor signalling, in particular through ubiquitination/deubiquitination. We have earlier defined the deubiquitinase Ubiquitin-Specific Protease 27x (Usp27x) as an enzyme capable of stabilizing the pro-apoptotic Bcl-2 family member Bim. Here, we report that enhanced expression of Usp27x in human melanoma cells leads to the loss of cellular FLICE-like inhibitory protein (cFLIP) and sensitizes to Tumor necrosis factor receptor 1 (TNF-R1) or Toll-like receptor 3 (TLR3)-induced extrinsic apoptosis through enabling enhanced processing of caspase-8. The loss of cFLIPL upon overexpression of Usp27x was not due to reduced transcription, could be partially counteracted by blocking the ubiquitin proteasome system and was independent of the known cFLIPL destabilizing ubiquitin E3-ligases Itch and DTX1. Instead, Usp27x interacted with the E3-ligase TRIM28 and reduced ubiquitination of TRIM28. Reduction of cFLIPL protein levels by Usp27x-induction depended on TRIM28, which was also required for polyI:C-induced cell death. This work defines Usp27x as a novel regulator of cFLIPL protein expression and a deubiquitinase in fine tuning death receptor signalling pathways to execute apoptosis.
    Keywords:  Apoptosis; Caspase-8; TLR3; TNF; TRIM28; Usp27x
    DOI:  https://doi.org/10.1007/s10495-021-01706-9
  8. Chembiochem. 2022 Jan 21.
    Chemical regulation of the protein quality control E3 ubiquitin ligase C-terminus of Hsc70 interacting protein (CHIP).
    Adam J Kanack, Michael D Olp, Oliver J Newsom, Jamie B Scaglione, David M Gooden, Kevin McMahon, Brian C Smith, Kenneth Scaglione.
      The ubiquitin ligase C-terminus of Hsc70 interacting protein (CHIP) is an important regulator of proteostasis. Despite playing an important role in maintaining proteostasis, little progress has been made in developing small molecules that regulate ubiquitin transfer by CHIP. Here we used differential scanning fluorimetry to identify compounds that bound CHIP. Compounds that bound CHIP were then analyzed by quantitative ubiquitination assays to identify those that altered CHIP function. One compound, MS.001, inhibited both the chaperone binding and ubiquitin ligase activity of CHIP at low micromolar concentrations. Interestingly, we found that MS.001 did not have activity against isolated U-box or tetratricopeptide (TPR) domains, but instead only inhibited full-length CHIP. Using  in silico  docking we identified a potential MS.001 binding site on the linker domain of CHIP and mutation of this site rendered CHIP resistant to MS.001. Together our data identify an inhibitor of the E3 ligase CHIP and provides insight into the development of compounds that regulate CHIP activity.
    Keywords:  ubiquitin, ubiquitin ligase, chaperone, neurodegeneration, protein folding, proteasome
    DOI:  https://doi.org/10.1002/cbic.202100633
  9. Adv Protein Chem Struct Biol. 2022 ;pii: S1876-1623(21)00063-8. [Epub ahead of print]128 163-198
    Ribosome-membrane crosstalk: Co-translational targeting pathways of proteins across membranes in prokaryotes and eukaryotes.
    Krishnamoorthi Srinivasan, Aneek Banerjee, Priya Baid, Ankit Dhur, Jayati Sengupta.
      Ribosomes are the molecular machine of living cells designed for decoding mRNA-encoded genetic information into protein. Being sophisticated machinery, both in design and function, the ribosome not only carries out protein synthesis, but also coordinates several other ribosome-associated cellular processes. One such process is the translocation of proteins across or into the membrane depending on their secretory or membrane-associated nature. These proteins comprise a large portion of a cell's proteome and act as key factors for cellular survival as well as several crucial functional pathways. Protein transport to extra- and intra-cytosolic compartments (across the eukaryotic endoplasmic reticulum (ER) or across the prokaryotic plasma membrane) or insertion into membranes majorly occurs through an evolutionarily conserved protein-conducting channel called translocon (eukaryotic Sec61 or prokaryotic SecYEG channels). Targeting proteins to the membrane-bound translocon may occur via post-translational or co-translational modes and it is often mediated by recognition of an N-terminal signal sequence in the newly synthesizes polypeptide chain. Co-translational translocation is coupled to protein synthesis where the ribosome-nascent chain complex (RNC) itself is targeted to the translocon. Here, in the light of recent advances in structural and functional studies, we discuss our current understanding of the mechanistic models of co-translational translocation, coordinated by the actively translating ribosomes, in prokaryotes and eukaryotes.
    Keywords:  Cryo-EM, cryo-ET; Lipid bilayer; SRP-SR, 3D structures; Sec61; SecYEG; Translocon
    DOI:  https://doi.org/10.1016/bs.apcsb.2021.07.003
  10. Mol Cell. 2022 Jan 12. pii: S1097-2765(21)01136-9. [Epub ahead of print]
    NudC guides client transfer between the Hsp40/70 and Hsp90 chaperone systems.
    Maximilian M Biebl, Florent Delhommel, Ofrah Faust, Krzysztof M Zak, Ganesh Agam, Xiaoyan Guo, Moritz Mühlhofer, Vinay Dahiya, Daniela Hillebrand, Grzegorz M Popowicz, Martin Kampmann, Don C Lamb, Rina Rosenzweig, Michael Sattler, Johannes Buchner.
      In the eukaryotic cytosol, the Hsp70 and the Hsp90 chaperone machines work in tandem with the maturation of a diverse array of client proteins. The transfer of nonnative clients between these systems is essential to the chaperoning process, but how it is regulated is still not clear. We discovered that NudC is an essential transfer factor with an unprecedented mode of action: NudC interacts with Hsp40 in Hsp40-Hsp70-client complexes and displaces Hsp70. Then, the interaction of NudC with Hsp90 allows the direct transfer of Hsp40-bound clients to Hsp90 for further processing. Consistent with this mechanism, NudC increases client activation in vitro as well as in cells and is essential for cellular viability. Together, our results show the complexity of the cooperation between the major chaperone machineries in the eukaryotic cytosol.
    Keywords:  Glucocorticoid receptor; Hsp40; Hsp70; Hsp90; NMR spectroscopy; NudC; co-chaperones; molecular chaperones; protein folding; spFRET
    DOI:  https://doi.org/10.1016/j.molcel.2021.12.031
  11. Neurotox Res. 2022 Jan 18.
    Regulation of Neurodegeneration-associated Protein Fragments by the N-degron Pathways.
    Mohamed A Eldeeb, Mohamed A Ragheb, Marwa H Soliman, Richard P Fahlman.
      Among the most salient features that underpin the development of aging-related neurodegenerative disorders are the accumulation of protein aggregates and the decrease in cellular degradation capacity. Mammalian cells have evolved sophisticated quality control mechanisms to repair or eliminate the otherwise abnormal or misfolded proteins. Chaperones identify unstable or abnormal conformations in proteins and often help them regain their correct conformation. However, if repair is not an option, abnormal proteins are selectively degraded to prevent undesired interactions with other proteins or oligomerization into toxic multimeric complexes. The autophagic-lysosomal system and the ubiquitin-proteasome system mediate the selective and targeted degradation of abnormal or aberrant protein fragments. Despite an increasing understanding regarding the molecular responses that counteract the formation and clearance of dysfunctional protein aggregates, the role of N-degrons in these processes is poorly understood. Previous work demonstrated that the Arg-N-end rule degradation pathway (Arg-N-degron pathway) mediates the degradation of neurodegeneration-associated proteins, thereby regulating crucial signaling hubs that modulate the progression of neurodegenerative diseases. Herein, we discuss the functional interconnection between N-degron pathways and proteins associated with neurodegenerative disorders, including Alzheimer's disease, amyotrophic lateral sclerosis, and Parkinson's disease. We also highlight some future prospects related to how the molecular insights gained from these processes will help unveil novel therapeutic approaches.
    Keywords:  N-degron; N-end rule; PINK1; Parkin; Parkinson’s disease; Proteasome; Protein degradation; Synucleinopathies; Aβ; Ubiquitin; Tau
    DOI:  https://doi.org/10.1007/s12640-021-00396-0
  12. Biochem J. 2022 Jan 17. pii: BCJ20210722. [Epub ahead of print]
    Reconstitution of the DTX3L-PARP9 complex reveals determinants for high affinity heterodimerization and multimeric assembly.
    Yashwanth Ashok, Carlos Vela-Rodríguez, Chun-Song Yang, Heli I Alanen, Fan Liu, Bryce M Paschal, Lari Lehtiö.
      Ubiquitination and ADP-ribosylation are post-translational modifications that play major roles in pathways including the DNA damage response and viral infection. The enzymes responsible for these modifications are therefore potential targets for therapeutic intervention. DTX3L is an E3 Ubiquitin ligase that forms a heterodimer with PARP9. In addition to its ubiquitin ligase activity, DTX3L-PARP9 also acts as an ADP-ribosyl transferase for Gly76 on the C-terminus of ubiquitin. NAD+-dependent ADP-ribosylation of ubiquitin by DTX3L-PARP9 prevents ubiquitin from conjugating to protein substrates. To gain insight into how DTX3L-PARP9 generates these post-translational modifications, we have generated recombinant forms of DTX3L and PARP9 and studied their physical interactions. We show the DTX3L D3 domain (230-510) mediates the interaction with PARP9 with nanomolar affinity and an apparent 1:1 stoichiometry. We also show that DTX3L and PARP9 assemble into a higher molecular weight oligomer, and that this is mediated by the DTX3L N-terminal region (1-200). Lastly, we show that ADP-ribosylation of ubiquitin at Gly76 is reversible in vitro by several Macrodomain-type hydrolases. Our study provides a framework to understand how DTX3L-PARP9 mediates ADP-ribosylation and ubiquitination through both intra- and inter-subunit interactions.
    Keywords:  adenosine diphosphate ribose; post translational modification; protein-protein interactions; ubiquitin ligases
    DOI:  https://doi.org/10.1042/BCJ20210722
  13. Sci Adv. 2022 Jan 21. 8(3): eabl4222
    Augmented ERAD (ER-associated degradation) activity in chondrocytes is necessary for cartilage development and maintenance.
    Hyo Jung Sim, Chanmi Cho, Ha Eun Kim, Ju Yeon Hong, Eun Kyung Song, Keun Yeong Kwon, Dong Gil Jang, Seok-Jung Kim, Hyun-Shik Lee, Changwook Lee, Taejoon Kwon, Siyoung Yang, Tae Joo Park.
      Chondrocytes secrete massive extracellular matrix (ECM) molecules that are produced, folded, and modified in the endoplasmic reticulum (ER). Thus, the ER-associated degradation (ERAD) complex-which removes misfolded and unfolded proteins to maintain proteostasis in the ER- plays an indispensable role in building and maintaining cartilage. Here, we examined the necessity of the ERAD complex in chondrocytes for cartilage formation and maintenance. We show that ERAD gene expression is exponentially increased during chondrogenesis, and disruption of ERAD function causes severe chondrodysplasia in developing embryos and loss of adult articular cartilage. ERAD complex malfunction also causes abnormal accumulation of cartilage ECM molecules and subsequent chondrodysplasia. ERAD gene expression is decreased in damaged cartilage from patients with osteoarthritis (OA), and disruption of ERAD function in articular cartilage leads to cartilage destruction in a mouse OA model.
    DOI:  https://doi.org/10.1126/sciadv.abl4222
  14. Semin Cell Dev Biol. 2022 Jan 15. pii: S1084-9521(22)00003-9. [Epub ahead of print]
    Identification of substrates for human deubiquitinating enzymes (DUBs): An up-to-date review and a case study for neurodevelopmental disorders.
    Nagore Elu, Nerea Osinalde, Juanma Ramirez, Natalia Presa, Jose Antonio Rodriguez, Gorka Prieto, Ugo Mayor.
      Similar to the reversal of kinase-mediated protein phosphorylation by phosphatases, deubiquitinating enzymes (DUBs) oppose the action of E3 ubiquitin ligases and reverse the ubiquitination of proteins. A total of 99 human DUBs, classified in 7 families, allow in this way for a precise control of cellular function and homeostasis. Ubiquitination regulates a myriad of cellular processes, and is altered in many pathological conditions. Thus, ubiquitination-regulating enzymes are increasingly regarded as potential candidates for therapeutic intervention. In this context, given the predicted easier pharmacological control of DUBs relative to E3 ligases, a significant effort is now being directed to better understand the processes and substrates regulated by each DUB. Classical studies have identified specific DUB substrate candidates by traditional molecular biology techniques in a case-by-case manner. Lately, single experiments can identify thousands of ubiquitinated proteins at a specific cellular context and narrow down which of those are regulated by a given DUB, thanks to the development of new strategies to isolate and enrich ubiquitinated material and to improvements in mass spectrometry detection capabilities. Here we present an overview of both types of studies, discussing the criteria that, in our view, need to be fulfilled for a protein to be considered as a high-confidence substrate of a given DUB. Applying these criteria, we have manually reviewed the relevant literature currently available in a systematic manner, and identified 650 high-confidence substrates of human DUBs. We make this information easily accessible to the research community through an updated version of the DUBase website (https://ehubio.ehu.eus/dubase/). Finally, in order to illustrate how this information can contribute to a better understanding of the physiopathological role of DUBs, we place a special emphasis on a subset of these enzymes that have been associated with neurodevelopmental disorders.
    DOI:  https://doi.org/10.1016/j.semcdb.2022.01.001
  15. Open Biol. 2022 Jan;12(1): 210255
    Selective localization of Mfn2 near PINK1 enables its preferential ubiquitination by Parkin on mitochondria.
    Marta Vranas, Yang Lu, Shafqat Rasool, Nathalie Croteau, Jonathan D Krett, Véronique Sauvé, Kalle Gehring, Edward A Fon, Thomas M Durcan, Jean-François Trempe.
      Mutations in Parkin and PINK1 cause early-onset familial Parkinson's disease. Parkin is a RING-In-Between-RING E3 ligase that transfers ubiquitin from an E2 enzyme to a substrate in two steps: (i) thioester intermediate formation on Parkin and (ii) acyl transfer to a substrate lysine. The process is triggered by PINK1, which phosphorylates ubiquitin on damaged mitochondria, which in turn recruits and activates Parkin. This leads to the ubiquitination of outer mitochondrial membrane proteins and clearance of the organelle. While the targets of Parkin on mitochondria are known, the factors determining substrate selectivity remain unclear. To investigate this, we examined how Parkin catalyses ubiquitin transfer to substrates. We found that His433 in the RING2 domain contributes to the catalysis of acyl transfer. In cells, the mutation of His433 impairs mitophagy. In vitro ubiquitination assays with isolated mitochondria show that Mfn2 is a kinetically preferred substrate. Using proximity-ligation assays, we show that Mfn2 specifically co-localizes with PINK1 and phospho-ubiquitin (pUb) in U2OS cells upon mitochondrial depolarization. We propose a model whereby ubiquitination of Mfn2 is efficient by virtue of its localization near PINK1, which leads to the recruitment and activation of Parkin via pUb at these sites.
    Keywords:  Mfn2; PINK1; Parkin; mitochondria; ubiquitin
    DOI:  https://doi.org/10.1098/rsob.210255
  16. Free Radic Biol Med. 2022 Jan 13. pii: S0891-5849(22)00017-X. [Epub ahead of print]
    ER reductive stress caused by Ero1α S-nitrosation accelerates senescence.
    Xinhua Qiao, Yingmin Zhang, Aojun Ye, Yini Zhang, Ting Xie, Zhenyu Lv, Cang Shi, Dongli Wu, Boyu Chu, Xun Wu, Weiqi Zhang, Ping Wang, Guang-Hui Liu, Chih-Chen Wang, Lei Wang, Chang Chen.
      Oxidative stress in aging has attracted much attention; however, the role of reductive stress in aging remains largely unknown. Here, we report that the endoplasmic reticulum (ER) undergoes reductive stress during replicative senescence, as shown by specific glutathione and H2O2 fluorescent probes. We constructed an ER-specific reductive stress cell model by ER-specific catalase overexpression and observed accelerated senescent phenotypes accompanied by disrupted proteostasis and a compromised ER unfolded protein response (UPR). Mechanistically, S-nitrosation of the pivotal ER sulfhydryl oxidase Ero1α led to decreased activity, therefore resulting in reductive stress in the ER. Inhibition of inducible nitric oxide synthase decreased the level of Ero1α S-nitrosation and decreased cellular senescence. Moreover, the expression of constitutively active Ero1α restored an oxidizing state in the ER and successfully rescued the senescent phenotypes. Our results uncover a new mechanism of senescence promoted by ER reductive stress and provide proof-of-concept that maintaining the oxidizing power of the ER and organelle-specific precision redox regulation could be valuable future geroprotective strategies.
    Keywords:  Aging; Endoplasmic reticulum (ER); Ero1α; Proteostasis; Reductive stress; S-Nitrosation/S-nitrosylation; Senescence; Unfolded protein response (UPR)
    DOI:  https://doi.org/10.1016/j.freeradbiomed.2022.01.006
  17. Trends Cell Biol. 2022 Jan 17. pii: S0962-8924(22)00002-2. [Epub ahead of print]
    Unfolding by Cdc48/p97: different strokes for different folks.
    Alexander Buchberger.
      The protein unfoldase Cdc48/p97 targets a wide variety of cellular substrates, but the molecular basis of substrate turnover remains incompletely understood. Two recent reports, by Ji et al. and van den Boom et al., provide detailed insights into the unfolding process and reveal pronounced flexibility of substrate handling by Cdc48/p97.
    Keywords:  AAA ATPase; protein phosphatase 1; proteinopathy; proteolysis; ubiquitin
    DOI:  https://doi.org/10.1016/j.tcb.2022.01.001
  18. J Biochem. 2022 Jan 14. pii: mvac002. [Epub ahead of print]
    Branched ubiquitin code: from basic biology to targeted protein degradation.
    Fumiaki Ohtake.
      Protein ubiquitylation regulates numerous pathways, and the diverse information encoded by various forms of ubiquitylation is known as the ubiquitin code. Recent studies revealed that branched ubiquitin chains are abundant in mammalian cells and regulate important pathways. They include proteasomal degradation of misfolded and disease-causing proteins, regulation of NF-B signaling, and apoptotic cell fate decisions. Targeted protein degradation through chemical degraders emerged as a transformative therapeutic paradigm aimed at inducing the disappearance of unwanted cellular proteins. To further improve the efficacy of target degradation and expand its applications, understanding the molecular mechanism of degraders' action from the view of ubiquitin code biology is required. In this review, I discuss the roles of the ubiquitin code in biological pathways and in chemically induced targeted protein degradation by focusing on the branched ubiquitin codes that we have characterized.
    Keywords:  PROTAC; mass spectrometry; proteasome; targeted protein degradation; ubiquitin
    DOI:  https://doi.org/10.1093/jb/mvac002
  19. Anal Chem. 2022 Jan 21.
    ER-GCaMP6f: An Endoplasmic Reticulum-Targeted Genetic Probe to Measure Calcium Activity in Astrocytic Processes.
    Surya P Aryal, Mengfan Xia, Ebubechi Adindu, Caroline Davis, Pavel I Ortinski, Christopher I Richards.
      Ca2+ is a major second messenger involved in cellular and subcellular signaling in a wide range of cells, including astrocytes, which use calcium ions to communicate with other cells in the brain. Even though a variety of genetically encoded Ca2+ indicators have been developed to study astrocyte calcium signaling, understanding the dynamics of endoplasmic reticulum calcium signaling is greatly limited by the currently available tools. To address this, we developed an endoplasmic reticulum-targeted calcium indicator, ER-GCaMP6f, which is anchored to the cytosolic side of the organelle and measures signaling that occurs in close proximity to the endoplasmic reticulum of astrocytes. Using a combination of confocal and super-resolution microscopy techniques, we demonstrate the localization of the indicator in the endoplasmic reticulum in both cell soma and processes of astrocytes. Combining ER-GCaMP6f with total internal reflection fluorescence microscopy, we show that Ca2+ fluctuations in small astrocytic processes can be detected, which are otherwise not observable with existing indicators and standard wide-field and confocal techniques. We also compared the ER-GCaMP6f indicator against currently used plasma membrane-tethered and cytosolic GCaMP6f indicators. ER-GCaMP6f identifies dynamics in calcium signaling of endoplasmic reticulum resident receptors that are missed by plasma membrane-anchored indicators. We also generated an adeno-associated virus (AAV5) and demonstrate that ER-GCaMP6f can be expressed in vivo and by measured calcium activity in brain slices. ER-GCaMP6f provides a powerful tool to study calcium signaling in close proximity to the endoplasmic reticulum in astrocyte cell soma and processes both in culture and in brain slices.
    DOI:  https://doi.org/10.1021/acs.analchem.1c04321
  20. Nat Commun. 2022 Jan 20. 13(1): 401
    A structural basis for the diverse linkage specificities within the ZUFSP deubiquitinase family.
    Thomas Hermanns, Christian Pichlo, Ulrich Baumann, Kay Hofmann.
      Eukaryotic deubiquitinases are important regulators of ubiquitin signaling and can be subdivided into several structurally distinct classes. The ZUFSP family, with ZUP1 as its sole human member, has a modular architecture with a core catalytic domain highly active against the ubiquitin-derived peptide RLRGG, but not against ubiquitin itself. Ubiquitin recognition is conferred by additional non-catalytic domains, making full-length ZUP1 active against long K63-linked chains. However, non-mammalian ZUFSP family members contain different ubiquitin-binding domains in their N-terminal regions, despite their high conservation within the catalytic domain. Here, by working with representative ZUFSP family members from insects, fungi and plants, we show that different N-terminal domains are associated with different linkage preferences. Biochemical and structural studies suggest that the acquisition of two family-specific proximal domains have changed the default K48 preference of the ZUFSP family to the K63 preference observed in ZUP1 and its insect homolog. Additional N-terminal zinc finger domains promote chain cleavage without changing linkage-specificity.
    DOI:  https://doi.org/10.1038/s41467-022-28049-6
  21. Nucleic Acids Res. 2022 Jan 17. pii: gkab1296. [Epub ahead of print]
    Chaperone mediated autophagy contributes to the newly synthesized histones H3 and H4 quality control.
    Juan Hormazabal, Francisco Saavedra, Claudia Espinoza-Arratia, Nicolas W Martinez, Tatiana Cruces, Iván E Alfaro, Alejandra Loyola.
      Although there are several pathways to ensure that proteins are folded properly in the cell, little is known about the molecular mechanisms regulating histone folding and proteostasis. In this work, we identified that chaperone-mediated autophagy (CMA) is the main pathway involved in the degradation of newly synthesized histones H3 and H4. This degradation is finely regulated by the interplay between HSC70 and tNASP, two histone interacting proteins. tNASP stabilizes histone H3 levels by blocking the direct transport of histone H3 into lysosomes. We further demonstrate that CMA degrades unfolded histone H3. Thus, we reveal that CMA is the main degradation pathway involved in the quality control of histone biogenesis, evidencing an additional mechanism in the intricate network of histone cellular proteostasis.
    DOI:  https://doi.org/10.1093/nar/gkab1296
  22. J Biol Chem. 2022 Jan 12. pii: S0021-9258(22)00024-2. [Epub ahead of print] 101584
    Host E3 ligase HUWE1 attenuates the pro-apoptotic activity of the MERS-CoV accessory protein ORF3 by promoting its ubiquitin-dependent degradation.
    Yuzheng Zhou, Rong Zheng, Sixu Liu, Cyrollah Disoma, Ashuai Du, Shiqin Li, Zongpeng Chen, Zijun Dong, Yongxing Zhang, Sijia Li, Pinjia Liu, Aroona Razzaq, Xuan Chen, Yujie Liao, Siyi Tao, Yuxin Liu, Lunan Xu, Qianjun Zhang, Jian Peng, Xu Deng, Shanni Li, Taijiao Jiang, Zanxian Xia.
      With the outbreak of SARS-CoV-2, coronaviruses have begun to attract great attention across the world. Of the known human coronaviruses, however, MERS-CoV is the most lethal. Coronavirus proteins can be divided into three groups: nonstructural proteins, structural proteins, and accessory proteins. While the number of each of these proteins varies greatly among different coronaviruses, accessory proteins are most closely related to the pathogenicity of the virus. We found for the first time that the ORF3 accessory protein of MERS-CoV, which closely resembles the ORF3a proteins of SARS-CoV and SARS-CoV-2, has the ability to induce apoptosis in cells in a dose-dependent manner. Although the functions of these three proteins are similar, the amino acid sequences and structures differ. Through bioinformatics analysis and validation, we revealed that ORF3 is an unstable protein, and has a shorter half-life in cells compared to that of SARS-CoV and SARS-CoV-2 ORF3a proteins. After screening, we identified a host E3 ligase, HUWE1, that specifically induces MERS-CoV ORF3 protein ubiquitination and degradation through the ubiquitin proteasome system. This results in the diminished ability of ORF3 to induce apoptosis, which might partially explain the lower spread of MERS-CoV compared to other coronaviruses. In summary, this study reveals a pathological function of MERS-CoV ORF3 protein and identifies a potential host antiviral protein, HUWE1, with an ability to antagonize MERS-CoV pathogenesis by inducing ORF3 degradation, thus enriching our knowledge of the pathogenesis of MERS-CoV and suggesting new targets and strategies for clinical development of drugs for MERS-CoV treatment.
    Keywords:  HUWE1; MERS-CoV; ORF3; apoptosis; degradation; ubiquitination
    DOI:  https://doi.org/10.1016/j.jbc.2022.101584
  23. Nucleic Acids Res. 2022 Jan 20. pii: gkac011. [Epub ahead of print]
    TRIM21 suppresses CHK1 activation by preferentially targeting CLASPIN for K63-linked ubiquitination.
    Xuefei Zhu, Jingwei Xue, Xing Jiang, Yamin Gong, Congwen Gao, Ting Cao, Qian Li, Lulu Bai, Yuwei Li, Gaixia Xu, Bin Peng, Xingzhi Xu.
      Expression of the E3 ligase TRIM21 is increased in a broad spectrum of cancers; however, the functionally relevant molecular pathway targeted by TRIM21 overexpression remains largely unknown. Here, we show that TRIM21 directly interacts with and ubiquitinates CLASPIN, a mediator for ATR-dependent CHK1 activation. TRIM21-mediated K63-linked ubiquitination of CLASPIN counteracts the K6-linked ubiquitination of CLASPIN which is essential for its interaction with TIPIN and subsequent chromatin loading. We further show that overexpression of TRIM21, but not a TRIM21 catalytically inactive mutant, compromises CHK1 activation, leading to replication fork instability and tumorigenesis. Our findings demonstrate that TRIM21 suppresses CHK1 activation by preferentially targeting CLASPIN for K63-linked ubiquitination, providing a potential target for cancer therapy.
    DOI:  https://doi.org/10.1093/nar/gkac011
  24. Sci Rep. 2022 Jan 18. 12(1): 869
    Novel regulation mechanism of adrenal cortisol and DHEA biosynthesis via the endogen ERAD inhibitor small VCP-interacting protein.
    Recep Ilhan, Göklem Üner, Sinem Yilmaz, Esra Atalay Sahar, Sevil Cayli, Yalcin Erzurumlu, Oguz Gozen, Petek Ballar Kirmizibayrak.
      Endoplasmic reticulum-associated degradation (ERAD) is a well-characterized mechanism of protein quality control by removal of misfolded or unfolded proteins. The tight regulation of ERAD is critical for protein homeostasis as well as lipid metabolism. Although the mechanism is complex, all ERAD branches converge on p97/VCP, a key protein in the retrotranslocation step. The multifunctionality of p97/VCP relies on its multiple binding partners, one of which is the endogenous ERAD inhibitor, SVIP (small VCP-interacting protein). As SVIP is a promising target for the regulation of ERAD, we aimed to assess its novel physiological roles. We revealed that SVIP is highly expressed in the rat adrenal gland, especially in the cortex region, at a consistently high level during postnatal development, unlike the gradual increase in expression seen in developing nerves. Steroidogenic stimulators caused a decrease in SVIP mRNA expression and increase in SVIP protein degradation in human adrenocortical H295R cells. Interestingly, silencing of SVIP diminished cortisol secretion along with downregulation of steroidogenic enzymes and proteins involved in cholesterol uptake and cholesterol biosynthesis. A certain degree of SVIP overexpression mainly increased the biosynthesis of cortisol as well as DHEA by enhancing the expression of key steroidogenic proteins, whereas exaggerated overexpression led to apoptosis, phosphorylation of eIF2α, and diminished adrenal steroid hormone biosynthesis. In conclusion, SVIP is a novel regulator of adrenal cortisol and DHEA biosynthesis, suggesting that alterations in SVIP expression levels may be involved in the deregulation of steroidogenic stimulator signaling and abnormal adrenal hormone secretion.
    DOI:  https://doi.org/10.1038/s41598-022-04821-y
  25. STAR Protoc. 2022 Mar 18. 3(1): 101074
    Optimized protocol to detect protein UFMylation in cells and in vitro via immunoblotting.
    Junzhi Zhou, Qian Liang, Maogong Dong, Xiaohe Ma, Yaqi Jin, Di Guan, Jiang Liu, Miao Wang, Yu-Sheng Cong.
      Ubiquitin-fold modifier 1 (UFM1) system is a recently identified ubiquitin-like modification with essential biological functions. Similar to ubiquitination, the covalent conjugation of UFM1 (UFMylation) to target proteins involves a three-step enzymatic cascade catalyzed sequentially by UFM1-activating enzyme 5 (UBA5, E1), UFM1-conjugating enzyme 1 (UFC1, E2), and UFM1-specific ligase 1 (UFL1, E3). Here, we provide an optimized protocol adapted to previously reported methods for detecting the UFMylation of target protein in human cells and in vitro assays, respectively, with high reliability and reproducibility. For complete details on the use and execution of this protocol, please refer to Liu et al. (2020).
    Keywords:  Cell Biology; Molecular Biology; Protein Biochemistry
    DOI:  https://doi.org/10.1016/j.xpro.2021.101074
  26. Neuron. 2022 Jan 13. pii: S0896-6273(21)01046-1. [Epub ahead of print]
    Brain-derived autophagosome profiling reveals the engulfment of nucleoid-enriched mitochondrial fragments by basal autophagy in neurons.
    Juliet Goldsmith, Alban Ordureau, J Wade Harper, Erika L F Holzbaur.
      Neurons depend on autophagy to maintain cellular homeostasis, and defects in autophagy are pathological hallmarks of neurodegenerative disease. To probe the role of basal autophagy in the maintenance of neuronal health, we isolated autophagic vesicles from mouse brain tissue and used proteomics to identify the major cargos engulfed within autophagosomes, validating our findings in rodent primary and human iPSC-derived neurons. Mitochondrial proteins were identified as a major cargo in the absence of mitophagy adaptors such as OPTN. We found that nucleoid-associated proteins are enriched compared with other mitochondrial components. In the axon, autophagic engulfment of nucleoid-enriched mitochondrial fragments requires the mitochondrial fission machinery Drp1. We proposed that localized Drp1-dependent fission of nucleoid-enriched fragments in proximity to the sites of autophagosome biogenesis enhances their capture. The resulting efficient autophagic turnover of nucleoids may prevent accumulation of mitochondrial DNA in the neuron, thus mitigating activation of proinflammatory pathways that contribute to neurodegeneration.
    Keywords:  Drp1; TFAM; autophagy; mitochondria; mitochondrial division; mitochondrial nucleoids; mitophagy; neurodegeneration; neuronal homeostasis
    DOI:  https://doi.org/10.1016/j.neuron.2021.12.029
  27. Biomolecules. 2021 Dec 24. pii: 22. [Epub ahead of print]12(1):
    MDM2-Driven Ubiquitination Rapidly Removes p53 from Its Cognate Promoters.
    Kester Mo Henningsen, Valentina Manzini, Anna Magerhans, Sabrina Gerber, Matthias Dobbelstein.
      MDM2 is the principal antagonist of the tumor suppressor p53. p53 binds to its cognate DNA element within promoters and activates the transcription of adjacent genes. These target genes include MDM2. Upon induction by p53, the MDM2 protein binds and ubiquitinates p53, triggering its proteasomal degradation and providing negative feedback. This raises the question whether MDM2 can also remove p53 from its target promoters, and whether this also involves ubiquitination. In the present paper, we employ the MDM2-targeted small molecule Nutlin-3a (Nutlin) to disrupt the interaction of MDM2 and p53 in three different cancer cell lines: SJSA-1 (osteosarcoma), 93T449 (liposarcoma; both carrying amplified MDM2), and MCF7 (breast adenocarcinoma). Remarkably, removing Nutlin from the culture medium for less than five minutes not only triggered p53 ubiquitination, but also dissociated most p53 from its chromatin binding sites, as revealed by chromatin immunoprecipitation. This also resulted in reduced p53-responsive transcription, and it occurred much earlier than the degradation of p53 by the proteasome, arguing that MDM2 removes p53 from promoters prior to and thus independent of degradation. Accordingly, the short-term pharmacological inhibition of the proteasome did not alter the removal of p53 from promoters by Nutlin washout. However, when the proteasome inhibitor was applied for several hours, depleting non-conjugated ubiquitin prior to eliminating Nutlin, this compromised the removal of DNA-bound p53, as did an E1 ubiquitin ligase inhibitor. This suggests that the ubiquitination of p53 by MDM2 is necessary for its clearance from promoters. Depleting the MDM2 cofactor MDM4 in SJSA cells did not alter the velocity by that p53 was removed from promoters upon Nutlin washout. We conclude that MDM2 antagonizes p53 not only by covering its transactivation domain and by destabilization, but also by the rapid, ubiquitin-dependent termination of p53-chromatin interactions.
    Keywords:  DNA binding; MDM2; MDMX; Nutlin; p53; ubiquitination
    DOI:  https://doi.org/10.3390/biom12010022
  28. Brief Bioinform. 2022 Jan 17. pii: bbab574. [Epub ahead of print]
    GPS-Uber: a hybrid-learning framework for prediction of general and E3-specific lysine ubiquitination sites.
    Chenwei Wang, Xiaodan Tan, Dachao Tang, Yujie Gou, Cheng Han, Wanshan Ning, Shaofeng Lin, Weizhi Zhang, Miaomiao Chen, Di Peng, Yu Xue.
      As an important post-translational modification, lysine ubiquitination participates in numerous biological processes and is involved in human diseases, whereas the site specificity of ubiquitination is mainly decided by ubiquitin-protein ligases (E3s). Although numerous ubiquitination predictors have been developed, computational prediction of E3-specific ubiquitination sites is still a great challenge. Here, we carefully reviewed the existing tools for the prediction of general ubiquitination sites. Also, we developed a tool named GPS-Uber for the prediction of general and E3-specific ubiquitination sites. From the literature, we manually collected 1311 experimentally identified site-specific E3-substrate relations, which were classified into different clusters based on corresponding E3s at different levels. To predict general ubiquitination sites, we integrated 10 types of sequence and structure features, as well as three types of algorithms including penalized logistic regression, deep neural network and convolutional neural network. Compared with other existing tools, the general model in GPS-Uber exhibited a highly competitive accuracy, with an area under curve values of 0.7649. Then, transfer learning was adopted for each E3 cluster to construct E3-specific models, and in total 112 individual E3-specific predictors were implemented. Using GPS-Uber, we conducted a systematic prediction of human cancer-associated ubiquitination events, which could be helpful for further experimental consideration. GPS-Uber will be regularly updated, and its online service is free for academic research at http://gpsuber.biocuckoo.cn/.
    Keywords:  Post-translational modification; deep learning; lysine ubiquitination; site-specific E3-substrate relation; ubiquitin-protein ligase
    DOI:  https://doi.org/10.1093/bib/bbab574
  29. J Med Chem. 2022 Jan 19.
    Activation of E6AP/UBE3A-Mediated Protein Ubiquitination and Degradation Pathways by a Cyclic γ-AA Peptide.
    Bo Huang, Li Zhou, Ruochuan Liu, Lei Wang, Songyi Xue, Yan Shi, Geon Ho Jeong, In Ho Jeong, Sihao Li, Jun Yin, Jianfeng Cai.
      Manipulating the activities of E3 ubiquitin ligases with chemical ligands holds promise for correcting E3 malfunctions and repurposing the E3s for induced protein degradation in the cell. Herein, we report an alternative strategy to proteolysis-targeting chimeras (PROTACs) and molecular glues to induce protein degradation by constructing and screening a γ-AA peptide library for cyclic peptidomimetics binding to the HECT domain of E6AP, an E3 ubiquitinating p53 coerced by the human papillomavirus and regulating pathways implicated in neurodevelopmental disorders such as Angelman syndrome. We found that a γ-AA peptide P6, discovered from the affinity-based screening with the E6AP HECT domain, can significantly stimulate the ubiquitin ligase activity of E6AP to ubiquitinate its substrate proteins UbxD8, HHR23A, and β-catenin in reconstituted reactions and HEK293T cells. Furthermore, P6 can accelerate the degradation of E6AP substrates in the cell by enhancing the catalytic activities of E6AP. Our work demonstrates the feasibility of using synthetic ligands to stimulate E3 activities in the cell. The E3 stimulators could be developed alongside E3 inhibitors and substrate recruiters such as PROTACs and molecular glues to leverage the full potential of protein ubiquitination pathways for drug development.
    DOI:  https://doi.org/10.1021/acs.jmedchem.1c01922
  30. Biophys Rev. 2021 Dec;13(6): 931-941
    Location, location, location: subcellular protein partitioning in proteostasis and aging.
    Anita V Kumar, Louis R Lapierre.
      Somatic maintenance and cell survival rely on proper protein homeostasis to ensure reliable functions across the cell and to prevent proteome collapse. Maintaining protein folding and solubility is central to proteostasis and is coordinated by protein synthesis, chaperoning, and degradation capacities. An emerging aspect that influences proteostasis is the dynamic protein partitioning across different subcellular structures and compartments. Here, we review recent literature related to nucleocytoplasmic partitioning of proteins, nuclear and cytoplasmic quality control mechanisms, and their impact on the development of age-related diseases. We also highlight new points of entry to modulate spatially-regulated proteostatic mechanisms to delay aging.
    Keywords:  C. elegans; Nucleocytoplasmic partitioning; Proteostasis
    DOI:  https://doi.org/10.1007/s12551-021-00890-x
  31. Cell. 2022 Jan 12. pii: S0092-8674(21)01565-8. [Epub ahead of print]
    Cellular architecture of human brain metastases.
    Hugo Gonzalez, Wenbin Mei, Isabella Robles, Catharina Hagerling, Breanna M Allen, Trine Line Hauge Okholm, Ankitha Nanjaraj, Tamara Verbeek, Sandhya Kalavacherla, Merel van Gogh, Stephen Georgiou, Mariza Daras, Joanna J Phillips, Matthew H Spitzer, Jeroen P Roose, Zena Werb.
      Brain metastasis (BrM) is the most common form of brain cancer, characterized by neurologic disability and an abysmal prognosis. Unfortunately, our understanding of the biology underlying human BrMs remains rudimentary. Here, we present an integrative analysis of >100,000 malignant and non-malignant cells from 15 human parenchymal BrMs, generated by single-cell transcriptomics, mass cytometry, and complemented with mouse model- and in silico approaches. We interrogated the composition of BrM niches, molecularly defined the blood-tumor interface, and revealed stromal immunosuppressive states enriched with infiltrated T cells and macrophages. Specific single-cell interrogation of metastatic tumor cells provides a framework of 8 functional cell programs that coexist or anticorrelate. Collectively, these programs delineate two functional BrM archetypes, one proliferative and the other inflammatory, that are evidently shaped through tumor-immune interactions. Our resource provides a foundation to understand the molecular basis of BrM in patients with tumor cell-intrinsic and host environmental traits.
    Keywords:  CyTOF; blood tumor barrier; human metastasis; metastasis-associated macrophages; metastasis-infiltrated T cells; metastatic niche; metastatic program; metastatic tumor cells; metastatic tumors; single cell
    DOI:  https://doi.org/10.1016/j.cell.2021.12.043
  32. J Virol. 2022 Jan 19. jvi0180621
    The immune-specific E3 ubiquitin ligase MARCH1 is upregulated during HCMV infection to regulate iron levels.
    Madison Martin, Praneet Sandhu, Rinki Kumar, Nicholas J Buchkovich.
      Human cytomegalovirus (HCMV) modulates numerous cellular pathways to facilitate infection. Iron is essential to many cellular processes and is often incorporated into proteins and enzymes involved in oxidative phosphorylation and DNA synthesis and repair, among others. Despite its prominent role in the cell, little is known about the regulation of iron metabolism during HCMV infection. Herein, we observe modulation of the transferrin receptor (TfR) during infection and a corresponding change in the cellular labile iron pool. TfR and the iron pool are increased early during infection and then return to mock levels at the late stages of infection. We identified the cellular ubiquitin ligase MARCH1 as an important regulator of TfR. MARCH1 plays a proviral role during infection, as its knockdown leads to a decrease in infectious titers. Knockdown of MARCH1 also leads to an increase in ROS, lipid peroxidation and mitochondrial dysfunction. Inhibiting an early increase in TfR expression during infection also decreases virus production. These findings indicate the importance of tightly regulating iron metabolism during HCMV infection to facilitate efficient virus production. Importance Iron is essential for cells, playing important roles in energy generation, DNA replication, and gene expression. During infection, HCMV alters many cellular processes to aid its replication. We found that iron levels are tightly regulated during infection and that dysregulation of iron levels alters the ability to produce infectious virions. We also found that HCMV inactivates many of the cellular safeguards put in place to deal with excess iron. Thus, infected cells become more susceptible to variations in iron levels, which could be exploited as a therapeutic strategy for dealing with HCMV infections.
    DOI:  https://doi.org/10.1128/jvi.01806-21
  33. Adv Sci (Weinh). 2022 Jan 20. e2104344
    A Selective Small-Molecule c-Myc Degrader Potently Regresses Lethal c-Myc Overexpressing Tumors.
    Ying Xu, Qingfeng Yu, Ping Wang, Zhaoxing Wu, Lei Zhang, Shuigao Wu, Mengyuan Li, Bowen Wu, Hongzhi Li, Haifeng Zhuang, Xuzhao Zhang, Yu Huang, Xiaoxian Gan, Rongzhen Xu.
      MYC oncogene is involved in the majority of human cancers and is often associated with poor outcomes, rendering it an extraordinarily desirable target, but therapeutic targeting of c-Myc protein has been a challenge for >30 years. Here, WBC100, a novel oral active molecule glue that selectively degrades c-Myc protein over other proteins and potently kills c-Myc overexpressing cancer cells is reported. WBC100 targets the nuclear localization signal 1 (NLS1)-Basic-nuclear localization signal 2 (NLS2) region of c-Myc and induces c-Myc protein degradation through ubiquitin E3 ligase CHIP mediated 26S proteasome pathway, leading to apoptosis of cancer cells. In vivo, WBC100 potently regresses multiple lethal c-Myc overexpressing tumors such as acute myeloid leukemia, pancreatic, and gastric cancers with good tolerability in multiple xenograft mouse models. Identification of the NLS1-Basic-NLS2 region as a druggable pocket for targeting the "undruggable" c-Myc protein and that single-agent WBC100 potently regresses c-Myc overexpressing tumors through selective c-Myc proteolysis opens new perspectives for pharmacologically intervening c-Myc in human cancers.
    Keywords:  WBC100; c-Myc oncoprotein; cancer; proteolysis targeting molecule; targeted therapy
    DOI:  https://doi.org/10.1002/advs.202104344
  34. Curr Opin Chem Biol. 2022 Jan 15. pii: S1367-5931(21)00159-9. [Epub ahead of print]67 102114
    Targeted protein degradation: Emerging concepts and protein state-specific targeting principles.
    Andrew J Tao, Gillian E Gadbois, Stanley A Buczynski, Fleur M Ferguson.
      Targeted protein degraders are heterobifunctional small molecules that link a target ligand or bait to an E3-ligase binder via a chemical spacer. Upon entering the cell, these ligands trigger the formation of a ternary complex between the target protein, degrader and E3-ligase, which leads to target polyubiquitination and proteasomal degradation. In recent years, TPD has expanded rapidly as a field, becoming the modality of choice in drug discovery and chemical probe development. This has been driven by the unique pharmacology of these molecules, which allows for fast and reversible knockdown of the target protein. Recent studies have demonstrated that degraders with specificity for a defined subpopulation of a protein-of-interest can be developed, giving rise to the emerging concept of protein state-specific targeting. In this article, we review advances towards developing degraders that differentiate between target protein subpopulations based on their; activation state, oligomerization state, cellular localization state, and cell type.
    Keywords:  Degraders; Molecular glues; PROTACs; Targeted protein degradation
    DOI:  https://doi.org/10.1016/j.cbpa.2021.102114
  35. Hum Mol Genet. 2022 Jan 17. pii: ddac006. [Epub ahead of print]
    Associations of genetic variation in E3 SUMO-protein ligase CBX4 with noise-induced hearing loss.
    Boshen Wang, Liu Wan, Peng Sun, Ludi Zhang, Lei Han, Hengdong Zhang, Juan Zhang, Yuepu Pu, Baoli Zhu.
      Noise-induced hearing loss (NIHL) is a multifactorial disease caused by environmental, genetic, and epigenetic variables. SUMOylation is a post-translational modification that regulates biological processes. The objective of this study was to determine the link between genetic variation in the CBX4 and the risk of NIHL. This study applied a case-control design with 588 cases and 582 controls, and the sample was predominantly male (93.76%). The T allele of CBX4 rs1285250 was found to be significantly linked with NIHL (p = 0.002) and showed strong associations in both the codominant and recessive models (TT vs CC, p = 0.005; TT/TC vs CC, p = 0.009). By constructing a mouse model of hearing loss due to noise exposure, changes in hearing thresholds were observed in noise-exposed mice, along with a decrease in the number of cochlear hair cells. Furthermore, noise promotes cochlear hair cell apoptosis by inducing SP1/CBX4 pathway activation. Further functional studies demonstrated that SP1 has an influence on the promoter activity of the CBX4 rs1285250 intron, with the promoter activity of the T allele being higher than that of the C allele. Knockdown of transcription factor SP1 reduced the expression of CBX4 expression and simultaneously reduced apoptosis in HEI-OC1 cells. Together, our findings have shown that CBX4 genetic polymorphism rs1285250 T-allele was associated with increased risk of NIHL and might be used as biomarkers for male workers exposed to noise. Furthermore, we speculate that the CBX4 of rs1285250 T-allele leads to a stronger potential enhancer activity from a predicted gain of stronger SP1 binding.
    Keywords:  CBX4; Noise-induced hearing loss; SP1; SUMOylation
    DOI:  https://doi.org/10.1093/hmg/ddac006
  36. J Proteome Res. 2022 Jan 19.
    Interrogating Kinase-Substrate Relationships with Proximity Labeling and Phosphorylation Enrichment.
    Tian Zhang, Anne Fassl, Laura P Vaites, Sipei Fu, Piotr Sicinski, Joao A Paulo, Steven P Gygi.
      Kinases govern many cellular responses through the reversible transfer of a phosphate moiety to their substrates. However, pairing a substrate with a kinase is challenging. In proximity labeling experiments, proteins proximal to a target protein are marked by biotinylation, and mass spectrometry can be used for their identification. Here, we combine ascorbate peroxidase (APEX) proximity labeling and a phosphorylation enrichment-based workflow, Phospho-APEX (pAPEX), to rapidly identify phosphorylated and biotinylated neighbor proteins which can be considered for candidate substrates. The pAPEX strategy enriches and quantifies differences in proximity for proteins and phosphorylation sites proximal to an APEX2-tagged kinase under the kinase "ON" and kinase "OFF" conditions. As a proof of concept, we identified candidate substrates of MAPK1 in HEK293T and HCT116 cells and candidate substrates of PKA in HEK293T cells. In addition to many known substrates, C15orf39 was identified and confirmed as a novel MAPK1 substrate. In all, we adapted the proximity labeling-based platform to accommodate phosphorylation analysis for kinase substrate identification.
    Keywords:  MAPK1; PKA; kinases; phosphopeptide enrichment; proximity labeling; substrates identification
    DOI:  https://doi.org/10.1021/acs.jproteome.1c00865
  37. EMBO J. 2022 Jan 18. e109256
    Ribosome slowdown triggers codon-mediated mRNA decay independently of ribosome quality control.
    Yuichiro Mishima, Peixun Han, Kota Ishibashi, Seisuke Kimura, Shintaro Iwasaki.
      The control of mRNA stability plays a central role in regulating gene expression patterns. Recent studies have revealed that codon composition in the open reading frame determines mRNA stability in multiple organisms. Based on genome-wide correlation approaches, this previously unrecognized role for the genetic code is attributable to the kinetics of the codon-decoding process by the ribosome. However, complementary experimental analyses are required to clarify the codon effects on mRNA stability and the related cotranslational mRNA decay pathways, for example, those triggered by aberrant ribosome stalling. In the current study, we performed a set of reporter-based analyses to define codon-mediated mRNA decay and ribosome stall-dependent mRNA decay in zebrafish embryos. Our analysis showed that the effect of codons on mRNA stability stems from the decoding process, independent of the ribosome quality control factor Znf598 and stalling-dependent mRNA decay. We propose that codon-mediated mRNA decay is rather triggered by transiently slowed ribosomes engaging in a productive translation cycle in zebrafish embryos.
    Keywords:  codons; mRNA degradation; ribosome; tRNA; zebrafish
    DOI:  https://doi.org/10.15252/embj.2021109256
  38. Nat Rev Drug Discov. 2022 Jan 18.
    PROTAC targeted protein degraders: the past is prologue.
    Miklós Békés, David R Langley, Craig M Crews.
      Targeted protein degradation (TPD) is an emerging therapeutic modality with the potential to tackle disease-causing proteins that have historically been highly challenging to target with conventional small molecules. In the 20 years since the concept of a proteolysis-targeting chimera (PROTAC) molecule harnessing the ubiquitin-proteasome system to degrade a target protein was reported, TPD has moved from academia to industry, where numerous companies have disclosed programmes in preclinical and early clinical development. With clinical proof-of-concept for PROTAC molecules against two well-established cancer targets provided in 2020, the field is poised to pursue targets that were previously considered 'undruggable'. In this Review, we summarize the first two decades of PROTAC discovery and assess the current landscape, with a focus on industry activity. We then discuss key areas for the future of TPD, including establishing the target classes for which TPD is most suitable, expanding the use of ubiquitin ligases to enable precision medicine and extending the modality beyond oncology.
    DOI:  https://doi.org/10.1038/s41573-021-00371-6
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