Ubiquitylation articles within Nature

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  • Article
    | Open Access

    The E3 ligase SIFI is identified as a dedicated silencing factor of the integrated stress response, a finding that has implications for the development of therapeutics for neurodegenerative diseases caused by mitochondrial protein import stress.

    • Diane L. Haakonsen
    • , Michael Heider
    •  & Michael Rapé

  • Article
    | Open Access

    The membrane-shaping protein ARL6IP1 is involved in the selective degradation of the endoplasmic reticulum, and this process depends on its ubiquitination and interaction with other membrane-shaping proteins such as FAM134B.

    • Hector Foronda
    • , Yangxue Fu
    •  & Christian A. Hübner

  • Article |

    Structures of Ubr1 in complex with Ubc2, ubiquitin and two N-degron peptides reveal a Ubc2-binding region and an acceptor ubiquitin-binding loop on Ubr1, providing mechanistic insights into the initiation and elongation steps of ubiquitination catalysed by Ubr1.

    • Man Pan
    • , Qingyun Zheng
    •  & Minglei Zhao

  • Article |

    Upon Salmonella invasion of the mammalian cytosol, ubiquitylation of a non-proteinaceous substrate—the lipid A moiety of bacterial lipopolysaccharide—by the E3 ubiquitin ligase RNF213 marks the bacteria as cargo for antibacterial autophagy.

    • Elsje G. Otten
    • , Emma Werner
    •  & Felix Randow

  • Article |

    Structural studies of the dimerization quality control E3 ubiquitin ligase SCF–FBXL17 indicate that its selectivity for aberrant complex formation is based on recognizing both shape and complementarity of interacting domains.

    • Elijah L. Mena
    • , Predrag Jevtić
    •  & Michael Rape

  • Article |

    The detection of microorganism-associated ligands by plant cells activates a signalling cascade in which the kinase BIK1 is monoubiquinated, released from the FLS2–BAK1 complex, and internalized by endocytosis.

    • Xiyu Ma
    • , Lucas A. N. Claus
    •  & Libo Shan

  • Article |

    Hyperosmotic stress leads to a phase separation of the proteasome, triggered by interactions between RAD23B and ubiquitylated proteins, which bring together p97 and proteasome-associated proteins into nuclear proteolytic foci.

    • Sayaka Yasuda
    • , Hikaru Tsuchiya
    •  & Yasushi Saeki

  • Article |

    Mycobacterium tuberculosis suppresses the production of inflammatory cytokines by host cells through the host-mediated ubiquitination of a mycobacterial protein, enhancing the interaction of a host signalling inhibitor with another signalling molecule.

    • Lin Wang
    • , Juehui Wu
    •  & Baoxue Ge

  • Article |

    The structure of the multiprotein Fanconi anaemia core complex, determined using cryo-electron microscopy and mass spectrometry, shows that the complex adopts an extended asymmetric structure and highlights the structural and functional asymmetry of the RING finger domains.

    • Shabih Shakeel
    • , Eeson Rajendra
    •  & Lori A. Passmore

  • Letter |

    Enzymatic cleavage within ubiquitin molecules followed by quantitative mass-spectrometry simplifies complex ubiquitin chains and enables mapping of polyubiquitin architectures.

    • Kirby N. Swatek
    • , Joanne L. Usher
    •  & David Komander

  • Letter |

    Hypoxia in the shoot meristem of Arabidopsis links the regulation of metabolic activity to development by inhibiting proteolysis of a substrate of the N-degron pathway, which controls class-III homeodomain-leucine zipper transcription factors.

    • Daan A. Weits
    • , Alicja B. Kunkowska
    •  & Francesco Licausi

  • Letter |

    OTULIN, which removes ubiquitin chains deposited by LUBAC, promotes LUBAC activity by preventing its auto-ubiquitination, thereby supporting normal mouse embryo development and preventing pro-inflammatory cell death in adult mice.

    • Klaus Heger
    • , Katherine E. Wickliffe
    •  & Vishva M. Dixit

  • Letter |

    Structural mass spectrometry of full-length human parkin and a structure of the activated parkin core reveal large-scale domain rearrangements involved in activation of parkin by PINK1.

    • Christina Gladkova
    • , Sarah L. Maslen
    •  & David Komander

  • Article |

    Stabilization of a transient protein kinase–substrate complex using a nanobody provides molecular details about how the Parkinson’s disease-linked protein kinase PINK1 phosphorylates ubiquitin, and suggests new pharmacological strategies.

    • Alexander F. Schubert
    • , Christina Gladkova
    •  & David Komander

  • Letter |

    The development of selective ubiquitin-specific protease-7 (USP7) inhibitors GNE-6640 and GNE-6776, which induce tumour cell death and reveal differential kinetics of Lys-48 and Lys-63-linked ubiquitin chain depolymerization by USP7.

    • Lorna Kategaya
    • , Paola Di Lello
    •  & Ingrid E. Wertz

  • Article |

    This paper reports the identification of a new cereblon-modulating agent, CC-885, which targets the translation termination factor GSPT1 and demonstrates anti-tumour activity in patient-derived tumour cells; the crystal structure of the cereblon–DDB1–GSPT1–CC-885 complex reveals a common motif for cereblon-substrate recruitment.

    • Mary E. Matyskiela
    • , Gang Lu
    •  & Philip P. Chamberlain

  • Article |

    Much of the intracellular protein degradation in eukaryotes is controlled by cullin–RING ubiquitin ligases (CRLs), a vast class of enzymes which are regulated by the COP9 signalosome (CSN); structural characterization of CSN–N8CRL4A complexes by cryo-electron microscopy reveals an induced-fit mechanism of CSN activation triggered only by catalytically activated CRLs without bound substrate, explaining how CSN acts as a global regulator of CRLs.

    • Simone Cavadini
    • , Eric S. Fischer
    •  & Nicolas H. Thomä

  • Letter |

    Thalidomide and its derivative lenalidomide bind the CRL4CRBN E3 ubiquitin ligase and target protein substrates for degradation; structural and functional data determined here show that casein kinase 1α and the lymphoid transcription factor Ikaros, the efficacy targets of lenalidomide in two different blood cancers, interact with the CRBN–lenalidomide interface through a β-hairpin destruction motif.

    • Georg Petzold
    • , Eric S. Fischer
    •  & Nicolas H. Thomä

  • Letter |

    The first structure of fully active HOIP of the RBR family of RING-type E3 ligases in its transfer complex with an E2~ubiquitin conjugate provides insights into its mechanism of action, including the ideal alignment of the E2 and E3 catalytic centres for ubiquitin transfer and the allosteric regulation of the RBR family.

    • Bernhard C. Lechtenberg
    • , Akhil Rajput
    •  & Stefan J. Riedl

  • Letter |

    This study shows that a vertebrate-specific ubiquitin ligase modulates neural crest specification in Xenopus development and human embryonic stem-cell differentiation; a proteomics approach reveals that the CUL3KBTBD8 ligase modulates translation by targeting the modulators of ribosomes production NOLC1 and its paralogue TCOF1, which is mutated in a neural-crest-associated syndrome.

    • Achim Werner
    • , Shintaro Iwasaki
    •  & Michael Rape

  • Article |

    The PINK1 ubiquitin kinase is shown to recruit the two autophagy receptors NDP52 and OPTN to mitochondria to activate mitophagy directly, independently of the ubiquitin ligase parkin; once recruited to mitochondria, NDP52 and OPTN recruit autophagy initiation components, and parkin may amplify the phospho-ubiquitin signal generated by PINK1, resulting in robust autophagy induction.

    • Michael Lazarou
    • , Danielle A. Sliter
    •  & Richard J. Youle

  • Letter |

    This study provides insights into conformational changes that lead to phospho-ubiquitin-induced PARKIN activation and how PARKIN is recruited to phospho-ubiquitin chains on mitochondria; the crystal structure of PARKIN in complex with phospho-ubiquitin also indicates that the pocket within PARKIN where phospho-ubiquitin binds carries amino acid residues that are mutated in patients with autosomal-recessive juvenile Parkinsonism.

    • Tobias Wauer
    • , Michal Simicek
    •  & David Komander

  • Letter |

    RIG-I protein recognizes viral duplex RNA with a 5′-triphosphate group, activating innate immune responses; a crystal structure of its tetrameric CARD signalling domain reveals that non-covalently linked ubiquitin chains stabilize the tetramer in a ‘lock-washer’ structure that serves as a signalling platform for the recruitment and activation of MAVS.

    • Alys Peisley
    • , Bin Wu
    •  & Sun Hur

  • Article |

    This study shows that 53BP1 recruitment to sites of DNA damage involves dual recognition of H4K20me2 and H2AK15 histone ubiquitination; the ubiquitin mark and the surrounding epitope on H2A are read by a region of 53BP1 designated the ubiquitination-dependent recruitment motif.

    • Amélie Fradet-Turcotte
    • , Marella D. Canny
    •  & Daniel Durocher

  • Article |

    The size of COPII vesicles is shown to be controlled by monoubiquitylation, with potential implications for cranio-lenticulo-sutural dysplasia and chylomicron retention disease.

    • Lingyan Jin
    • , Kanika Bajaj Pahuja
    •  & Michael Rape

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