Ubiquitylated proteins articles within Nature Communications

Featured

  • Article
    | Open Access

    Here, the authors describe BioE3, a biotin-based method to discriminate direct substrates of ubiquitin E3 ligases of interest from mere interactors using proximity proteomics. BioE3 responds to chemical treatments, and works with RING- and HECT-type E3s, as well as ubiquitin-likes (e.g., SUMO).

    • Orhi Barroso-Gomila
    • , Laura Merino-Cacho
    •  & James D. Sutherland

  • Article
    | Open Access

    The poly(ADP-ribosyl)transferases, tankyrase 1 and 2, are regulated by RNF146-mediated K48-linked polyubiquitylation and degradation. Here the authors show that this is opposed by K11-linked diubiquitylation by RING-UIM E3 ligases RNF114 and 166 and further impacted by several PAR-binding E3 ligases.

    • Jerome Perrard
    •  & Susan Smith

  • Article
    | Open Access

    Overexpression of human antigen R (HuR) correlates with high grade tumours and poor patient prognosis. Here, the authors engineer a TRIM21 biological PROTAC to demonstrate the benefit of a targeted protein degradation approach to deplete HuR, resulting in tumour growth inhibition in pre-clinical cancer models by altering the HuR-regulated proteome.

    • Alice Fletcher
    • , Dean Clift
    •  & James Hunt

  • Article
    | Open Access

    The colliding ribosomes are ubiquitinated by the sensor protein Hel2, leading to noncanonical subunit dissociation by the ribosome associated quality control trigger (RQT) complex. Here the authors reveal the decoding mechanism of the ribosome ubiquitin code by the RQT complex.

    • Yoshitaka Matsuo
    • , Takayuki Uchihashi
    •  & Toshifumi Inada

  • Article
    | Open Access

    This study describes how p97Ufd1-Npl4 and the UBA-UBX protein Ubxn7 disassemble vertebrate replisomes during replication termination, and it provides novel insights into how p97 complexes assemble with UBA-UBX proteins on ubiquitylated substrates

    • Olga V. Kochenova
    • , Sirisha Mukkavalli
    •  & Johannes C. Walter

  • Article
    | Open Access

    Cytokine signaling influences the differentiation of CD4+ T cells into varying functional subsets. Here the authors show that an E3 ubiquitin ligase Cul5 alters TH2 and TH9 development and absence of Cul5 in T cells results in higher levels of allergy-associated IL-4 and IL-9 secreting T cells.

    • Binod Kumar
    • , Natania S. Field
    •  & Paula M. Oliver

  • Article
    | Open Access

    The p97 unfoldase is an essential and abundant enzyme that segregates its substrates from macromolecular complexes and organelle membranes. Here, authors determined the structure of human p97 in the act of unfolding an authentic substrate.

    • Yang Xu
    • , Han Han
    •  & Peter S. Shen

  • Article
    | Open Access

    Tissue-specific transcriptional activity is silenced in mitotic cells. Here the authors reveal a general phosphorylation-dependent mechanism of recognition for the anaphase-promoting complex (APC) substrates, and show that the APC targets ID2 during the establishment of post-mitotic transcription.

    • Sang Bae Lee
    • , Luciano Garofano
    •  & Anna Lasorella

  • Article
    | Open Access

    The 20S particle is part of the 26S proteasome, but also exists as a free complex. Here, the authors outline signature activities of the 20S and combine chemical, structural, functional and proteomic assays to show that the 20S can degrade ubiquitin tags along with conjugated substrates.

    • Indrajit Sahu
    • , Sachitanand M. Mali
    •  & Michael H. Glickman

  • Article
    | Open Access

    OTULIN is a negative regulator of linear ubiquitination, and its deficiency in human causes multi-organ inflammations including the skin. Here the authors show, by combining various genetic tools with epidermis-specific Otulin knockout mice, that Otulin suppresses skin inflammation predominantly by inhibiting RIPK1-mediated keratinocytes necroptosis.

    • Hannah Schünke
    • , Ulrike Göbel
    •  & Manolis Pasparakis

  • Article
    | Open Access

    The conserved SAM motif of Polycomb Repressive Complex 1 subunit Ph has been shown to play an important role in chromatin organization. Here, the authors study the effect of Ph SAM on chromatin in vitro, showing that it induces the formation of concentrated, phase-separated condensates, which enhance the ubiquitin ligase activity of PRC1.

    • Elias Seif
    • , Jin Joo Kang
    •  & Nicole J. Francis

  • Article
    | Open Access

    Ubiquitin pseudogenes are present in many organisms but whether they encode functional proteins has remained unclear. Here, the authors show that human UBB pseudogene 4 produces ubiquitin variants with amino acid compositions and cellular functions that are distinct from canonical ubiquitin.

    • Marie-Line Dubois
    • , Anna Meller
    •  & François-Michel Boisvert

  • Article
    | Open Access

    Ubiquitination of histone H2A can occur on distinct lysine residues, but how each site is recognised by the specific E3 ligase remains poorly understood. Here the authors demonstrate that the E3 ligase RNF168 binds the acidic patch on the nucleosome surface, directing the E2 to the target lysine K13/K15.

    • Velten Horn
    • , Michael Uckelmann
    •  & Hugo van Ingen

  • Article
    | Open Access

    Oncoprotein E6 facilitates the E6AP-catalyzed ubiquitination of p53. Here, the authors study the structural basis of this process by qualitative and quantitative cross-linking mass spectrometry, providing insights into E6AP-E6-p53 complex assembly and the conformational dynamics that enable p53 ubiquitination.

    • Carolin Sailer
    • , Fabian Offensperger
    •  & Florian Stengel

  • Article
    | Open Access

    The phytohormone auxin is sensed by SCFTIR1-AUX/IAA receptors leading to AUX/IAA repressor ubiquitylation and turnover. Here the authors show that IAA6 and IAA19 differ in their ubiquitylation and turnover dynamics, differentially contributing to auxin sensing and enabling discrimination of auxin concentrations.

    • Martin Winkler
    • , Michael Niemeyer
    •  & Luz Irina A. Calderón Villalobos

  • Article
    | Open Access

    Ubiquitylation and SUMOylation are two important related post-translational modifications. Here the authors present an approach for the simultaneous identification and quantification of protein-wide SUMO and ubiquitin sites from a single sample, uncovering widespread crosstalk between the two modifications.

    • Frédéric Lamoliatte
    • , Francis P. McManus
    •  & Pierre Thibault

  • Article
    | Open Access

    Multivesicular bodies (MVB) are endosomal compartments that can either fuse with the plasma membrane for the secretion of exosomes, or fuse with the lysosome and be degraded along with their contents. Here, the authors show that ISGylation of the MVB protein TSG101 impairs exosome secretion and acts as a regulator of MVB fate.

    • Carolina Villarroya-Beltri
    • , Francesc Baixauli
    •  & Francisco Sánchez-Madrid

  • Article
    | Open Access

    The proteasome plays a key role in proteostasis by mediating the degradation of ubiquitinated substrates. Here the authors show that an open-gate mutant of the proteasome is hyperactive towards a subset of substrates and can effectively delay the accumulation of toxic protein aggregates.

    • Won Hoon Choi
    • , Stefanie A. H. de Poot
    •  & Min Jae Lee

  • Article |

    Mutations in the gene encoding DJ-1 are associated with early-onset familial forms of Parkinson’s disease, and several different molecular functions have been attributed to this protein. Moscovitz et al.show that DJ-1 physically binds the 20S proteasome and inhibits its degradation activity.

    • Oren Moscovitz
    • , Gili Ben-Nissan
    •  & Michal Sharon

  • Article |

    Rad23 accompanies ubiquitinated substrates to the proteasome for destruction but manages to avoid degradation. In this study, Fishbainet al.show that Rad23 escapes because it lacks an effective initiation region; therefore, the proteasome is unable to engage the protein and unfold it.

    • Susan Fishbain
    • , Sumit Prakash
    •  & Andreas Matouschek

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