Ubiquitins articles within Nature Communications

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  • Article
    | Open Access

    Most insights into deubiquitinase (DUB) substrate specificity originate from studies with isolated di-ubiquitins (diUb), but in cells diUbs with different linkage types coexist. Here, the authors develop a mass spectrometric DUB activity assay that can probe all diUbs simultaneously under substrate competition conditions.

    • Bianca D. M. van Tol
    • , Bjorn R. van Doodewaerd
    •  & Paul P. Geurink

  • Article
    | Open Access

    Ubiquitin is not only a posttranslational modifier but itself is subject to modifications, such as acetylation. Characterization of distinct acetylated ubiquitin variants reveals that each acetylation site has a particular impact on ubiquitin structure and its protein-protein interaction properties.

    • Simon Maria Kienle
    • , Tobias Schneider
    •  & Martin Scheffner

  • Article
    | Open Access

    The authors provide a litmus test for the recognition mechanism of transiently binding proteins based on nuclear magnetic resonance and find a conformational selection binding mechanism through concentration-dependent kinetics of ubiquitin and SH3.

    • Kalyan S. Chakrabarti
    • , Simon Olsson
    •  & Christian Griesinger

  • Article
    | Open Access

    Absence of regulatory T cells results in a severe inflammatory disease which leads to death in infancy in both human patients and in mouse models. Authors show here that in mice, conditional deletion of Rbx1, the RING component of Cullin-RING ligases in regulatory T cells causes a similar phenotype, due to the disrupted degradation of important regulatory proteins.

    • Di Wu
    • , Haomin Li
    •  & Yi Sun

  • Article
    | Open Access

    Ufmylation is a well-established ubiquitin-like protein modification, but its mechanism is largely unclear. Here, the authors present a crystal structure of the ufmylation-specific E1-E2 complex, revealing differences to the ubiquitination machinery and mechanistic details of the ufmylation process.

    • Manoj Kumar
    • , Prasanth Padala
    •  & Reuven Wiener

  • Article
    | Open Access

    Misfolded proteins are ubquitinated and subsequently condensed by cargo receptors for selective autophagy. Here, the authors use in vitro reconstitution to elegantly dissect how the receptors p62/SQSTM1, NBR1 and TAX1BP1 contribute to p62-ubiquitin condensate formation and degradation by autophagy.

    • Eleonora Turco
    • , Adriana Savova
    •  & Sascha Martens

  • Article
    | Open Access

    Sequestration of reactants in lipid vesicles is a strategy prevalent in biological systems to raise the rate and specificity of chemical reactions. Here, the authors show that micelle-assisted reactions facilitate native chemical ligation between a peptide-thioester and a Cys-peptide modified by a lipid-like moiety.

    • Shuaijiang Jin
    • , Roberto J. Brea
    •  & Neal K. Devaraj

  • Article
    | Open Access

    Many pathogens manipulate ubiquitin-mediated signaling to evade host cell defense. Here, the authors characterize the structure and enzymatic activity of a deubiquitylase domain from the causative pathogen of scrub typhus, providing evidence for a distinct mechanism of ubiquitin chain selectivity.

    • Jason M. Berk
    • , Christopher Lim
    •  & Mark Hochstrasser

  • 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

    The Lys48-linked polyubiquitin-mediated proteasomal degradation in yeast depends on Cdc48 and its cofactors Ufd1 and Npl4. Here, the authors present crystal structures of Npl4 bound to Lys48-linked diubiquitin and the Npl4-binding motif of Ufd1, providing insights into the reaction mechanism of the Cdc48- Ufd1/Npl4 complex.

    • Yusuke Sato
    • , Hikaru Tsuchiya
    •  & Shuya Fukai

  • Article
    | Open Access

    Ufmylation is a ubiquitylation-like protein modification but only a few ufmylation substrates and functions have been discovered so far. Here, the authors demonstrate ufmylation of histone H4 upon DNA damage and show that this modification is involved in the amplification of ATM activation.

    • Bo Qin
    • , Jia Yu
    •  & Zhenkun Lou

  • Article
    | Open Access

    Ubiquitin modification also occurs in archaea. Here, the authors characterize an archaeal ancestral ubiquitination system, present the crystal structure of the archaeal deubiquitinase Rpn11 from Caldiarchaeum subterraneum bound to ubiquitin and provide insights into evolutionary relationships.

    • Adrian C. D. Fuchs
    • , Lorena Maldoner
    •  & Jörg Martin

  • Article
    | Open Access

    Ubiquitin (Ub) receptors are responsible for the recognition of ubiquitylated proteins. Here the authors describe the crystal structure of the ubiquitylated form of the Ub-receptor Rpn10, which suggest that ubiquitylation of Rpn10 promotes its dissociation from the proteasome.

    • Tal Keren-Kaplan
    • , Lee Zeev Peters
    •  & Gali Prag

  • Article
    | Open Access

    mRNA deadenylation, the first step in regulated degradation, is mediated by the action of the CCR4-NOT and PAN2-PAN3 complexes. Here the authors show that the RNA-binding E3 ubiquitin-ligase MEX-3C associates with the CCR4-NOT complex and ubiquitinates the catalytic subunit CNOT7 to regulate its deadenylation activity.

    • Florencia Cano
    • , Radu Rapiteanu
    •  & Paul J. Lehner

  • Article
    | Open Access

    Phagocytes employ multiple bactericidal mechanisms to kill microorganisms, including the generation of toxic superoxide and other reactive oxygen species. Here the authors utilize a multi-omics approach to identify and characterize new regulatory nodes implicated in mucosal immunity that control phagocyte oxidative burst.

    • Daniel B. Graham
    • , Christine E. Becker
    •  & Ramnik J. Xavier

  • Article
    | Open Access

    Ubiquitin is a stable and soluble protein, but it is commonly found in inclusion bodies in neurodegenerative disorders and cancer. Here, Morimoto et al. report that increasing ubiquitin chain length leads to the formation of amyloid-like fibrils, which are degraded by an autophagy mechanism.

    • Daichi Morimoto
    • , Erik Walinda
    •  & Masahiro Shirakawa

  • Article
    | Open Access

    Posttranslational modification of proteins by small ubiquitin-related modifier is a response to stress signalling in plants. Here, theArabdiposisprotein SIZ1 is shown to cause SUMOylation of nitrate reductases 1 and 2 and to increase their activity, suggesting that SIZ1 controls nitrate uptake via SUMOylation.

    • Bong Soo Park
    • , Jong Tae Song
    •  & Hak Soo Seo

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