Relevant bibliographies by topics / Ubiquitin

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Ubiquitin'

Author: Grafiati
Published: 4 June 2021
Last updated: 5 April 2025

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Journal articles on the topic "Ubiquitin"

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Kama, Rachel, Galina Gabriely, Vydehi Kanneganti, and Jeffrey E. Gerst. "Cdc48 and ubiquilins confer selective anterograde protein sorting and entry into the multivesicular body in yeast." Molecular Biology of the Cell 29, no. 8 (April 15, 2018): 948–63. http://dx.doi.org/10.1091/mbc.e17-11-0652.

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Cdc48/p97 is known primarily for the retrotranslocation of misfolded proteins in endoplasmic reticulum (ER)-associated protein degradation (ERAD). Here we uncover a novel function for both Cdc48 and the conserved ubiquitin-associated/ubiquitin-like ubiquitin receptor (ubiquilin) proteins in yeast (e.g., Ddi1, Dsk2, and Rad23), which deliver ubiquitinated proteins to the proteasome for degradation. We show that Cdc48, its core adaptors Npl4 and Ufd1, and the ubiquilins confer the constitutive anterograde delivery of carboxypeptidase S (Cps1), a membranal hydrolase, to the multivesicular body (MVB) and vacuolar lumen. Cdc48 and Ddi1 act downstream of Rsp5-dependent Cps1 ubiquitination to facilitate the disassembly of insoluble Cps1 oligomers and upstream of ESCRT-0 to facilitate the entry of soluble protein into the MVB. Consequentially, detergent-insoluble Cps1 accumulates in cells bearing mutations in CDC48, DDI1, and all three ubiquilins (ddi1Δ, dsk2Δ, rad23Δ). Thus, Cdc48 and the ubiquilins have ERAD- and proteasome-independent functions in the anterograde delivery of specific proteins to the yeast vacuole for proteolytic activation. As Cdc48/p97 and the ubiquilins are major linkage groups associated with the onset of human neurodegenerative disease (e.g., amytrophic lateral sclerosis, Alzheimer’s, and Paget’s disease of the bone), there may be a connection between their involvement in anterograde protein sorting and disease pathogenesis.
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Lee, Dong Yun, and Eric J. Brown. "Ubiquilins in the crosstalk among proteolytic pathways." Biological Chemistry 393, no. 6 (June 1, 2012): 441–47. http://dx.doi.org/10.1515/hsz-2012-0120.

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Abstract Protein degradation occurs through several distinct proteolytic pathways for membrane and cytosolic proteins. There is evidence that these processes are linked and that crosstalk among these major protein degradation pathways occurs. Ubiquilins, a family of ubiquitin-binding proteins, are involved in all protein degradation pathways. This minireview provides an overview of ubiquilin function in protein degradation and contrasts it with sequestosome-1 (p62), a protein that also has been implicated in multiple proteolytic pathways.
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Jantrapirom, Salinee, Luca Lo Piccolo, Dumnoensun Pruksakorn, Saranyapin Potikanond, and Wutigri Nimlamool. "Ubiquilin Networking in Cancers." Cancers 12, no. 6 (June 15, 2020): 1586. http://dx.doi.org/10.3390/cancers12061586.

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Ubiquilins or UBQLNs, members of the ubiquitin-like and ubiquitin-associated domain (UBL-UBA) protein family, serve as adaptors to coordinate the degradation of specific substrates via both proteasome and autophagy pathways. The UBQLN substrates reveal great diversity and impact a wide range of cellular functions. For decades, researchers have been attempting to uncover a puzzle and understand the role of UBQLNs in human cancers, particularly in the modulation of oncogene’s stability and nucleotide excision repair. In this review, we summarize the UBQLNs’ genetic variants that are associated with the most common cancers and also discuss their reliability as a prognostic marker. Moreover, we provide an overview of the UBQLNs networks that are relevant to cancers in different ways, including cell cycle, apoptosis, epithelial-mesenchymal transition, DNA repairs and miRNAs. Finally, we include a future prospective on novel ubiquilin-based cancer therapies.
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Hill, Spencer, Joseph S. Harrison, Steven M. Lewis, Brian Kuhlman, and Gary Kleiger. "Mechanism of Lysine 48 Selectivity during Polyubiquitin Chain Formation by the Ube2R1/2 Ubiquitin-Conjugating Enzyme." Molecular and Cellular Biology 36, no. 11 (April 4, 2016): 1720–32. http://dx.doi.org/10.1128/mcb.00097-16.

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Lysine selectivity is of critical importance during polyubiquitin chain formation because the identity of the lysine controls the biological outcome. Ubiquitins are covalently linked in polyubiquitin chains through one of seven lysine residues on its surface and the C terminus of adjacent protomers. Lys 48-linked polyubiquitin chains signal for protein degradation; however, the structural basis for Lys 48 selectivity remains largely unknown. The ubiquitin-conjugating enzyme Ube2R1/2 has exquisite specificity for Lys 48, and computational docking of Ube2R1/2 and ubiquitin predicts that Lys 48 is guided to the active site through a key electrostatic interaction between Arg 54 on ubiquitin and Asp 143 on Ube2R1/2. The validity of this interaction was confirmed through biochemical experiments. Since structural examples involving Arg 54 in protein-ubiquitin complexes are exceedingly rare, these results provide additional insight into how ubiquitin-protein complexes can be stabilized. We discuss how these findings relate to how other ubiquitin-conjugating enzymes direct the lysine specificity of polyubiquitin chains.
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Ford, Diana L., and Mervyn J. Monteiro. "Dimerization of ubiquilin is dependent upon the central region of the protein: evidence that the monomer, but not the dimer, is involved in binding presenilins." Biochemical Journal 399, no. 3 (October 13, 2006): 397–404. http://dx.doi.org/10.1042/bj20060441.

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Ubiquilin proteins have been shown to interact with a wide variety of other cellular proteins, often regulating the stability and degradation of the interacting protein. Ubiquilin contains a UBL (ubiquitin-like) domain at the N-terminus and a UBA (ubiquitin-associated) domain at the C-terminus, separated by a central region containing Sti1-like repeats. Little is known about regulation of the interaction of ubiquilin with other proteins. In the present study, we show that ubiquilin is capable of forming dimers, and that dimerization requires the central region of ubiquilin, but not its UBL or the UBA domains. Furthermore, we provide evidence suggesting that monomeric ubiquilin is likely to be the active form that is involved in binding presenilin proteins. Our results provide new insight into the regulatory mechanism underlying the interaction of ubiquilin with presenilins.
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Hurtley, Stella M. "One Ubiquitin, Two Ubiquitin, Three Ubiquitin, Four." Science's STKE 2007, no. 369 (January 16, 2007): tw26. http://dx.doi.org/10.1126/stke.3692007tw26.

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The role of protein ubiquitination is well known in promoting regulated protein degradation. Mukhopadhyay and Riezman review what is known about the contribution of protein ubiquitination in other cellular pathways, including intracellular signaling, endocytosis, and protein sorting.D. Mukhopadhyay, H. Riezman, Proteasome-independent functions of ubiquitin in endocytosis and signaling. Science315, 201-205 (2007). [Abstract][Full Text]
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Ivanova, K. A., A. A. Belogurov, and A. A. Kudriaeva. "Architectonics of Ubiquitin Chains." Биоорганическая химия 50, no. 4 (October 25, 2024): 379–97. http://dx.doi.org/10.31857/s0132342324040038.

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Ubiquitination, one of the most common posttranslational modifications of proteins, has a significant impact on its functions, such as stability, activity and cellular localization. Disorders in the processes of ubiquitination and deubiquitination are associated with various oncological and neurodegenerative diseases. The complexity of ubiquitin signaling – monoubiquitination and polyubiquitination with different lengths and types of interconnections between ubiquitins – determines their versatility and ability to regulate hundreds of different cellular processes. Advanced biochemical, mass spectrometric and computational methods are required for in-depth understanding of the mechanisms of assembly and disassembly, detection of ubiquitin chains and their signal transmission. Recent scientific achievements make it possible to identify the ubiquitination of proteins and the structure of ubiquitin chains, however, there are still a considerable number of unresolved issues in this area. Current review claims for a detailed analysis of the current understanding of the architectonics of the ubiquitin chains.
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Chatrin, Chatrin, Mads Gabrielsen, Lori Buetow, Mark A. Nakasone, Syed F. Ahmed, David Sumpton, Gary J. Sibbet, Brian O. Smith, and Danny T. Huang. "Structural insights into ADP-ribosylation of ubiquitin by Deltex family E3 ubiquitin ligases." Science Advances 6, no. 38 (September 2020): eabc0418. http://dx.doi.org/10.1126/sciadv.abc0418.

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Cellular cross-talk between ubiquitination and other posttranslational modifications contributes to the regulation of numerous processes. One example is ADP-ribosylation of the carboxyl terminus of ubiquitin by the E3 DTX3L/ADP-ribosyltransferase PARP9 heterodimer, but the mechanism remains elusive. Here, we show that independently of PARP9, the conserved carboxyl-terminal RING and DTC (Deltex carboxyl-terminal) domains of DTX3L and other human Deltex proteins (DTX1 to DTX4) catalyze ADP-ribosylation of ubiquitin’s Gly76. Structural studies reveal a hitherto unknown function of the DTC domain in binding NAD+. Deltex RING domain recruits E2 thioesterified with ubiquitin and juxtaposes it with NAD+ bound to the DTC domain to facilitate ADP-ribosylation of ubiquitin. This ubiquitin modification prevents its activation but is reversed by the linkage nonspecific deubiquitinases. Our study provides mechanistic insights into ADP-ribosylation of ubiquitin by Deltex E3s and will enable future studies directed at understanding the increasingly complex network of ubiquitin cross-talk.
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Seok Ko, Han, Takashi Uehara, Kazuhiro Tsuruma, and Yasuyuki Nomura. "Ubiquilin interacts with ubiquitylated proteins and proteasome through its ubiquitin-associated and ubiquitin-like domains." FEBS Letters 566, no. 1-3 (April 28, 2004): 110–14. http://dx.doi.org/10.1016/j.febslet.2004.04.031.

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Morgan, Rachel E., Vijay Chudasama, Paul Moody, Mark E. B. Smith, and Stephen Caddick. "A novel synthetic chemistry approach to linkage-specific ubiquitin conjugation." Organic & Biomolecular Chemistry 13, no. 14 (2015): 4165–68. http://dx.doi.org/10.1039/c5ob00130g.

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Dissertations / Theses on the topic "Ubiquitin"

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Sekiyama, Naotaka. "STRUCTURAL ANALYSIS OF UBIQUITIN AND UBIQUITIN-LIKE PROTEIN RECEPTORS." 京都大学 (Kyoto University), 2010. http://hdl.handle.net/2433/120884.

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Braxton, Courtney N. "The progress on mapping ubiquitin signaling using photocrosslinking mono and di-ubiquitin probes and other ubiquitin moieties." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5382.

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Ubiquitin (Ub) is a small, 76 amino acid, and post-translational modification (PTM) protein in eukaryotes. Modification of a substrate protein via the covalent attachment of the C-terminal glycine of Ub to the ε-amino group of lysine residues in a substrate is termed ubiquitination. Unlike, other PTM proteins, Ub can form polyUb chains at one or more of its seven lysine residues. (K6, K11, K27, K29, K33, K48, and K68). The consequence of these different polymerization sites is altered biological response with different polyUb linkages conferring different fates to target proteins. Unfortunately, the study of these chains have been limited by the inability to generate homogeneous polyUbs chains linked at known lysine residues. Furthermore, a three step enzymatic cascade consisting of activating-enzymes (E1s), conjugating enzymes (E2s), and ligase enzymes (E3s) tightly controls this modification. In response, our laboratory has developed a system that creates polyUb chains through bacterial expression and "synthetic" building blocks. Now, the main questions are what do these chains interact with in the cell and how do these interactions mediate biological responses? In an attempt to answer these questions, this dissertation looks at different molecular techniques created to capture the transient interactions of monoUb and diUb probes with Ub substrates, such as, ubiquitin binding domains (UBDs) and conjugating E2 enzymes. One molecular technique focuses on the use of incorporating a genetically encoded, photo-crosslinker, p-Benzoyl-L-phenylalanine (pBpa) into diUb probes to capture their interaction with UBDs. This sets the foundation for understanding Ub’s cellular signaling recognition of UBDs. Another technique is creating diUb probes that contain lysine derivatives, Nε-L-Thiaprolyl-L-lysine (ThzK) or Nε-L-Cysteinyl-L-lysine (CysK), and can form a disulfide bonds with E2 enzymes to capture their complex, opening an opportunity to understand mechanistically the role E2 enzymes have with polyUb chain formation. Herein, these techniques are established to help unravel the complexity of Ub signaling.
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Haririnia, Aydin. "Molecular interactions of ubiquitin and polyubiquitin with ubiquitin binding domains." College Park, Md. : University of Maryland, 2007. http://hdl.handle.net/1903/7627.

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Thesis (Ph. D.)--University of Maryland, College Park, 2007.
Thesis research directed by: Dept. of Chemistry and Biochemistry. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Lange, Anja. "Structural characterization of the interaction of the Stam2's ubiquitin binding domains with ubiquitin chains by NMR : Cooperativity or not, that is the question !" Thesis, Lyon 1, 2010. http://www.theses.fr/2010LYO10308.

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Résumé en anglais uniquement
From the discovery of ubiquitin and its function as signal for proteasomal degradation over 20 years ago to this days, it became evident that ubiquitin is a universal signal in eukaryotic cells. Ubiquitin in its different forms is involved in many versatile cellular processes. Knowing that the ubiquitin signal is differently translated, depending on its occurrences as mono-ubiquitin or poly-ubiquitin, raises the question: how do cells distinguish between the different occurrences of ubiquitin and translate it into the proper response? Proteins interacting with ubiquitin contain so called ubiquitin binding domains (UBDs), whereas the affinities to ubiquitin vary from a few _M to mM. So far only three (K63, K48 and linear chains) out of the eight possible chain-linkages can be produced in sufficient amounts to characterize their interaction with UBDs. K48- and K63- linked ubiquitin chains regulate different cellular events and need to be recognized by different proteins. Thus, it is of prime importance to characterize the binding of different UBDs to these two kinds of ubiquitin chains, as it can give important clues related to the general mechanism of chain discrimination by ubiquitin adapter proteins. Some isolated UBDs exhibit a preference for one chain linkage type over the other, whereas others do not discriminate between mono-ubiquitin or K63- and K48-linked chains. Interestingly, many ubiquitin adapter proteins harbor more than one UBD. STAM2 is a ubiquitin adapter protein, that is involved in endosomal receptor sorting and supposed to preferentially bind mono-ubiquitin and K63- over K48-linked ubiquitin. STAM2 contains two UBDs (a VHS and UIM domain) that were shown to bind to ubiquitin . The current manuscript shows that STAM2’s SH3 domain binds ubiquitin as well. To understand the function of the sequential arrangement of three UBDs in one protein, first binding of the individual VHS and UIM domains to monoubiquitin as well as K48- and K63-linked di-ubiquitin was investigated. This work shows, that the VHS domain displays a different mode of binding for K63- and K48-linked diubiquitin. In spite of the fact, that the apparent Kd for both chains is the same, only one VHS domain can bind to K48-linked di-ubiquitin chains (with a preference for the distal domain), whereas K63-linked di-ubiquitin can accommodate two VHS domains at a time. Since no conclusion can be drawn with respect to the apparent Kds, the different binding modes might gain more impact in consideration of the ensemble of three UBDs. Results presented in this manuscript, based on a construct containing the VHS and UIM domain, show that binding to K63- but not K48-linked di-ubiquitin is cooperative
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Pirim, Ibrahim. "Ubiquitin and neurogenerative diseases." Thesis, University of Nottingham, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.335277.

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Deschutter, Julie. "Identification de la monoubiquitination de la protéine SHIP2 et caractérisation des mécanismes régulateurs associés." Doctoral thesis, Universite Libre de Bruxelles, 2009. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/241308.

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Depaux, Arnaud. "Régulation des complexes d'ubiquitinylation et de sumoylation par la ligase E3 hSIAH2." Paris 7, 2006. http://www.theses.fr/2006PA077094.

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Les modifications post-traductionnelles des protéines (phosphorylation, l'acétylation ou l'ubiquitinylation) permettent de réguler leur activité, stabilité, localisation ou interactions avec d'autres facteurs. Les complexes permettant la modification par l'ubiquitine ou Sumo bien que d'organisation similaire sont composés de protéines différentes : une ligase El qui active le résidu, une ligase E2 permettant le transfert de l'ubiquitine sur le substrat et une ligase E3 qui assure la spécificité de reconnaissance du substrat. Plusieurs familles de ligases E3 ont été décrites mais seule la famille de protéines à domaine RING Finger présente des membres impliqués dans les complexes de la sumoylation et de l'ubiquitinylation. Afin de caractériser de nouveaux partenaires des ligases à domaine RING Finger hSIAHl et hSIAH2 (human Seven In Absentia homolog), nous avons développé une expérience de double-hybride chez la levure en utilisant hSIAH2 pour appât. La caractérisation des partenaires ainsi isolés a fait l'objet de mon projet de thèse. J'ai mis en évidence des protéines impliquées dans l'ubiquitinylation (Ubiquitine, Ubc5 ou hSIAH) et la sumoylation (PIAS, SUMO et Ubc9). J'ai ainsi démontré que hSIAH2 est capable de former des homodimères et des hétérodimères avec hSIAH et que cette dimérisation permet de réguler la propre stabilité des deux protéines. D'autre part, j'ai montré que hSIAH2 catalyse l'ubiquitinylation de PIAS et sa dégradation par le protéasome. L'ensemble de ce travail a mis en évidence le rôle spécifique de hSIAH2 dans la régulation de la stabilité d'intermédiaires essentiels, à la fois, aux complexes d'ubiquitinylation et de sumoylation
After synthesis, proteins are targeted to post-translational modifications such as acetylation, phosphorylation or ubiquitination. These mechanisms regulate their function, stability, localization or interaction with partners. Modification process by ubiquitin or sumo named ubiquitination or sumoylation respectively involve complexes with similar organization but compose of different enzymes. Their organization relies on Sumo or ubiquitin activating El enzyme, transferring E2-ligase and E3-ligase or sub-complex conferring the substrate specific récognition. El-ligase is unique for each complex, whereas E2 and E3-ligases are multiple. Among E3-ligase families, RING Finger protein family only has been involved in both modifications complexes. Two human homologs of Drosophila Seven In Absentia (hSIAHl et hSIAH2), belong to RING Finger E3-ligase family. In a yeast two hybrid assay, we have identified new SIAH interacting proteins. Their characterization has been the purpose of my PhD project. We have characterized partners implicated in both ubiquitination (ubiquitin, Ubc5 or hSIAH) and sumoylation (Sumo, Ubc9 and PIAS) pathways. In a first attempt, I have demonstrated that hSIAH proteins can form homo- or hetero-dimers. Dimerization régulates their stability via a proteasome dependent degradation. I have also demonstrated that hSIAH2 catalyzes the proteasome dependent degradation of PIAS1, a sumo E3-ligase. Altogether this study evidences an important rôle for hSIAH2 in the regulation of the stability of ubiquitination and sumolation complexes
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Bazirgan, Omar Al-Kasim. "Functional analysis of the ubiquitin ligase Hrd1p with the ubiquitin-conjugating enzyme Ubc7p." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3246079.

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Thesis (Ph. D.)--University of California, San Diego, 2007.
Title from first page of PDF file (viewed March 9, 2007). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references.
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Wakeford, Emmrich. "L’inhibition de la dégradation protéasomale causée par l’altération du bon fonctionnement du processus d’ubiquitination influe négativement sur la propagation du norovirus murin." Electronic Thesis or Diss., Université de Lille (2022-....), 2024. http://www.theses.fr/2024ULILS084.

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Le norovirus, un virus non-enveloppé à ARN simple brin positif (+) de la famille des Caliciviridae est très contagieux et résistant. Un important effort de recherche est mené pour comprendre les mécanismes de la pathogenèse norovirale. Le système immunitaire inné est principalement activé lors des infections à norovirus. L'ubiquitination est un processus post-traductionnel ATP-dépendant, qui régule de nombreuses étapes de cette réponse immunitaire en catalysant l’ajout de différents types de chaînes de polyubiquitine sur certains résidus lysine de protéines cibles de manière à réguler leur sort.Il est à noter que des niveaux accrus de polyubiquitination peuvent être mesurés dans des cultures de macrophages après infection avec la souche de norovirus murin S99 (MNoV_S99). Dans une première étude, nous avons évalué comment l'altération de la formation des chaînes de polyubiquitine pouvait affecter le cycle de vie de MNoV_S99. En utilisant la lignée cellulaire de macrophage Raw264.7, plusieurs lignées cellulaires stables ont été générées en surexprimant les constructions YFP-Ubiquitin_WT, _K29R, _K48R ou_K63R. Toutes les constructions non-WT codent une protéine de fusion d'ubiquitine dont une lysine a été mutée en un résidu arginine, empêchant ainsi la formation des chaînes de polyubiquitine correspondantes. Une expression significativement réduite de plusieurs marqueurs viraux ainsi qu’une diminution significative des titres viraux a pu être mesurée seulement dans les cellules K48R. Cette régulation négative n’était pas liée à une entrée virale perturbée, mais plutôt par une hypersécrétion constitutive de la cytokine pro-inflammatoire TNF générant ainsi un environnement hostile à la propagation du MNoV_S99. L’ajout de chaînes de polyubiquitine K48 sur un substrat entraîne généralement celui-ci vers la dégradation protéasomale. Nos données sont les premières à suggérer que le MNoV_S99 bénéficie de la régulation à la baisse d’un ou plusieurs composants cytosoliques anti-viraux, encore non identifiés, vraisemblablement sensibles à la dégradation protéasomale. Les E3-ubiquitine ligases jouent un rôle central dans le processus d'ubiquitination en sélectionnant les substrats à ubiquitiner. Il a été démontré que SMURF1, une ubiquitine ligase à domaine HECT, atténue la demi-vie de plusieurs agents pathogènes par le biais de l'ubiquitination K48.Dans la seconde étude présentée dans ce manuscrit, nous avons analysé le rôle joué par SMURF1 dans la propagation du MNoV_S99. Tout d’abord, nous avons identifié l’interaction de SMURF1 avec la principale protéine de capside norovirale VP1. Mais cette interaction n'est pas associée à l'ubiquitination de la capside virale, ce qui suggère que le virus lui-même n'est pas ciblé par la dégradation protéasomale. En effet, lorsque des macrophages dérivés de la moelle osseuse (BMDM), de souris, où Smurf1 est inactivé par rapport à des souris sauvages, ont été infectés par le MNoV_S99, nous avons mesuré une diminution significative de l'expression de plusieurs marqueurs viraux. De même, les titres viraux dans les cultures Smurf1-/-étaient significativement inférieurs à ceux des BMDM WT. Ceci suggère un rôle bénéfique de SMURF1 et de l'ubiquitination K48-dépendante dans le cycle de vie des norovirus. Ceci a été confirmé par le fait que les BMDM WT traités avec l'inhibiteur de protéasome MG132 ont montré une production de MNoV_S99 significativement réduite.Dans l'ensemble, nos données permettent de mettre en lumière un rôle bénéfique de l'activité protéasomale dans le maintien d'un environnement permissif dans la propagation de la souche S99 du norovirus murin
The Norovirus, a small non-enveloped single stranded positive-sense RNA virus, that belongs to the Caliciviridae family, is highly contagious and resistant and is a major causal agent of viral gastroenteritis resulting in a high human and socioeconomic cost. Due to a lack of approved therapy options, intensive research effort is on going to better understand the mechanisms of noroviral pathogenesis.Viral entry is known to trigger signals that activate the innate immune system in order to neutralize the pathogen. Ubiquitination is an ATP-dependent multistep posttranslational process, involved in the regulation of the immune response, in which a ubiquitin moiety is added to a substrate. Interestingly, we have measured increased levels of polyubiquitination following mouse norovirus (MNoV) infection in macrophages. Different types of polyubiquitin chains can be formed on a given target’s lysine residue which determines the fate of those proteins. In a first study we have evaluated how the alteration of polyubiquitin chain formation could affect the noroviral life cycle. Using the macrophage cell line Raw264.7, several stable cell lines were generated by overexpressing YFP-Ubiquitin_WT, _K29R, _K48Ror_K63R constructs. All non-WT constructs encode a ubiquitin fusion protein with one lysine mutated into an arginine residue, thus preventing the formation of their respective polyubiquitin chains. Upon infection with the murine norovirus S99 (MNoV_S99) strain, we measured a significantly reduced expression of the viral markers VP1, NS5 and double-stranded RNA in cells where the formation of polyubiquitin chains via lysine 48 was abrogated. The TCID50 titration method further confirmed the drop of norovirus production in these cells. This negative regulation could not be explained by perturbed viral entry, however, a constitutive hypersecretion of the pro-inflammatory cytokine TNF and downstream upregulation of IκBαphosphorylation followed by NF-κB nuclear translocation was found which could potentially impose a non-permissive environment for MNoV_S99 replication and propagation.Additionally, since K48-polyubiquitin chain formation is well described to target proteins toward proteasomal degradation, our data are the first to suggest that the MNoV_S99benefits from the down regulation of unidentified cytosolic component(s) that are cleared via the proteasome.E3-ubiquitin ligases play a central role in the ubiquitination process by selecting which substrates go through ubiquitination. SMURF1, a HECT domain ubiquitin ligase, wasshown to mitigate, via K48-ubiquitination, the half-life of several pathogens. In the second study presented in this manuscript, we have investigated the role played bySMURF1 in MNoV_S99 propagation. Interestingly, we have identified that SMURF1 can bind to the main noroviral capsid protein Vp1. But this interaction was not associated with ubiquitination of the viral capsid, suggesting that the virus itself is not targeted towards proteasomal degradation. Indeed, when bone marrow derived macrophages (BMDM), established from Smurf1 knock-out mice in comparison with WT mice, were infected with MNoV_S99 we measured significantly decreased expression of several viral markers. Similarly, viral titres in Smurf1-/- cultures were significantly lower than WT BMDMs. This hints at a beneficial role of SMURF1 and K48-dependent ubiquitination in the noroviral lifecycle. This was further confirmed when WT BMDMs treated with the proteasome inhibitor MG132 showed significantly reduced MNoV_S99 production.Taken together, our data shed light on a beneficial role of the proteasomal activity in maintaining a permissive environment for the propagation of the S99 mouse norovirus strain
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Rumsby, Ellen Louise. "Regulation of the cell division cycle by ubiquitin and ubiquitin-like modifications in yeast." Thesis, University of Newcastle upon Tyne, 2015. http://hdl.handle.net/10443/2938.

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The ability of a cell to regulate its cell cycle in response to external stimuli, such as oxidative stress, is important to maintain viability by preventing damage and allowing time for repair. However, the underlying sensing and signalling mechanisms behind cell cycle regulation in response to oxidative stress remain largely unclear. Ubiquitin and ubiquitin-like (Ubl) proteins are a family of highly conserved protein modifiers with a role in many cellular processes including cell cycle regulation. The use of catalytic cysteine residues in the conjugation pathways of ubiquitin and Ubls suggest a mechanism by which these modifiers can be redox-regulated. Thus the aim of this project was to investigate the regulation of the cell division cycle by ubiquitin and Ubls in response to two conditions previously observed to lead to G1 phase cell cycle arrest in S. cerevisiae, treatment with the oxidising agent diamide and glutathione depletion. We find that in response to diamide the ubiquitin E2, Cdc34 is particularly sensitive to oxidation compared to the other E2s examined. Oxidation of Cdc34 was shown to lead to an increase in the stability of the Cdc34 substrate Sic1, coincident with G1 phase arrest. We also find that the Rub1 Ubl modifier is essential for regulation of the cell cycle in response to diamide. Interestingly, we find that Rub1 is also required to prevent budding in response to glutathione depletion. Importantly, here we reveal that SIC1 is essential to maintain viability by preventing replication-induced DNA damage following glutathione depletion. Our studies demonstrate that G1 phase cell cycle arrest in response to diamide and glutathione depletion is multifaceted, involving many of the same proteins but that these proteins are regulated differently in response to the two conditions.
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Books on the topic "Ubiquitin"

1

Conaway, Joan, and Ray DeShaies. Abstracts of papers presented at the 2005 meeting on the ubiquitin family: April 27-May 1, 2005. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 2005.

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Rechsteiner, Martin, ed. Ubiquitin. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2.

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Martin, Rechsteiner, ed. Ubiquitin. New York: Plenum Press, 1988.

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1961-, Deshaies Raymond Joseph, ed. Ubiquitin and protein degradation. Amsterdam: Elsevier Academic Press, 2005.

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S, Jentsch, and Haendler B, eds. The ubiquitin system in health and disease. Berlin: Springer, 2009.

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Patterson, Cam, and Douglas M. Cyr. Ubiquitin-Proteasome Protocols. New Jersey: Humana Press, 2005. http://dx.doi.org/10.1385/1592598951.

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Rodriguez, Manuel S., and Rosa Barrio, eds. The Ubiquitin Code. New York, NY: Springer US, 2023. http://dx.doi.org/10.1007/978-1-0716-2859-1.

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Cam, Patterson, and Cyr Douglas M, eds. Ubiquitin-proteasome protocols. Totowa, N.J: Humana Press, 2005.

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Argilés, Josep M. Ubiquitin and disease. Austin, Tex., U.S.A: R.G. Landes, 1998.

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J, Schlesinger Milton, Hershko Avram, and Cold Spring Harbor Laboratory, eds. The Ubiquitin system. Cold Spring Harbor, N.Y: Cold Spring Harbor Laboratory, 1988.

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Book chapters on the topic "Ubiquitin"

1

Rechsteiner, Martin. "Introduction." In Ubiquitin, 1–4. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_1.

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Siegelman, Mark, and Irving L. Weissman. "Lymphocyte Homing Receptors, Ubiquitin, and Cell Surface Proteins." In Ubiquitin, 239–69. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_10.

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Ciechanover, Aaron. "Role of Transfer RNA in the Degradation of Selective Substrates of the Ubiquitin- and ATP-Dependent Proteolytic System." In Ubiquitin, 271–86. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_11.

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Varshavsky, Alexander, Andreas Bachmair, Daniel Finley, David Gonda, and Ingrid Wünning. "The N-End Rule of Selective Protein Turnover." In Ubiquitin, 287–324. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_12.

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Hershko, Avram. "Selectivity of Ubiquitin-Mediated Protein Breakdown." In Ubiquitin, 325–32. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_13.

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Wilkinson, Keith D. "Purification and Structural Properties of Ubiquitin." In Ubiquitin, 5–38. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_2.

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Finley, Daniel, Engin Özkaynak, Stefan Jentsch, John P. McGrath, Bonnie Bartel, Michael Pazin, Robert M. Snapka, and Alexander Varshavsky. "Molecular Genetics of the Ubiquitin System." In Ubiquitin, 39–75. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_3.

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Pickart, Cecile M. "Ubiquitin Activation and Ligation." In Ubiquitin, 77–99. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_4.

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Hough, Ronald F., Gregory W. Pratt, and Martin Rechsteiner. "Ubiquitin/ATP-Dependent Protease." In Ubiquitin, 101–34. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_5.

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Rose, Irwin A. "Ubiquitin Carboxyl-Terminal Hydrolases." In Ubiquitin, 135–55. Boston, MA: Springer US, 1988. http://dx.doi.org/10.1007/978-1-4899-2049-2_6.

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Conference papers on the topic "Ubiquitin"

1

Zhi, Xu, Dong Zhao, Zhongmei Zhou, and Ceshi Chen. "Abstract 213: RNF126 E3 ubiquitin ligase targets p21cipfor ubiquitin-mediated degradation." In Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL. American Association for Cancer Research, 2012. http://dx.doi.org/10.1158/1538-7445.am2012-213.

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Song, Chengcheng, Vyacheslav Akimov, Peter Foote, Xiaolong Lu, Blagoy Blagoev, and Rajesh Singh. "Abstract B074: Ubiquitin proteomics: profiling the landscape of ubiquitin modification by ubisite-omics." In Abstracts: AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; October 26-30, 2017; Philadelphia, PA. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1535-7163.targ-17-b074.

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Qin, Haoran, Yilin Zhong, and Shuning Liu. "Ubiquitin-proteasome pathway in disease." In Third International Conference on Biological Engineering and Medical Science (ICBioMed2023), edited by Alan Wang. SPIE, 2024. http://dx.doi.org/10.1117/12.3021667.

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Yao, Eric, Shenshen Lai, and Jun Yan. "Abstract 3862: Empowering research on ubiquitin and ubiquitin-like protein modification cascade using recombinant enzyme systems." In Proceedings: AACR Annual Meeting 2018; April 14-18, 2018; Chicago, IL. American Association for Cancer Research, 2018. http://dx.doi.org/10.1158/1538-7445.am2018-3862.

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Hong, Huang Chun, Hu Tian, Wu Xin Yin, Jie Ke Ming, Yan Nian long, and Ying Mu Ying. "Structure and function of ubiquitin-conjugating enzymes." In International conference on Human Health and Medical Engineering. Southampton, UK: WIT Press, 2014. http://dx.doi.org/10.2495/hhme130411.

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Urschbach, Moritz, Susanne Huhmann, Luca Ferrari, Dominik Vogl, Dominik Appel, Sascha Martens, and Christian F. W. Becker. "Modular Access to Structurally Defined Ubiquitin Chains." In 37th European Peptide Symposium, 2029. The European Peptide Society, 2024. http://dx.doi.org/10.17952/37eps.2024.p2029.

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Wang, Zehua, Arun Seth, and Ceshi Chen. "Abstract 509: RNF115/BCA2 E3 ubiquitin ligase promotes breast cancer cell proliferation through targeting p21Waf1/Cip1for ubiquitin-mediated degradation ." In Proceedings: AACR 104th Annual Meeting 2013; Apr 6-10, 2013; Washington, DC. American Association for Cancer Research, 2013. http://dx.doi.org/10.1158/1538-7445.am2013-509.

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Ruiz-Agudo, Cristina, Lutz Joachim, King Michael, Marx Andreas, and Gebauer Denis. "Designer Ubiquitin Proteins Towards Controlling Calcium Carbonate Crystallization." In Goldschmidt2020. Geochemical Society, 2020. http://dx.doi.org/10.46427/gold2020.2242.

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Yoshida, Yukiko, Koji Matsuoka, Tomoki Chiba, Toshiaki Suzuki, Keiji Tanaka, and Tadashi Tai. "N-GLYCANS ARE RECOGNIZED BY E3 UBIQUITIN-LIGASE." In XXIst International Carbohydrate Symposium 2002. TheScientificWorld Ltd, 2002. http://dx.doi.org/10.1100/tsw.2002.430.

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Ma, Ke, Philip Ryan, Rachel Klevit, and Stanley Lipkowitz. "Abstract 4965: Multiple ubiquitin-conjugating enzymes modulate the ubiquitination and downregulation of the EGFR by the Cbl RING finger ubiquitin ligase." In Proceedings: AACR 106th Annual Meeting 2015; April 18-22, 2015; Philadelphia, PA. American Association for Cancer Research, 2015. http://dx.doi.org/10.1158/1538-7445.am2015-4965.

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Reports on the topic "Ubiquitin"

1

Royer, Lacey. Cul3 Ubiquitin Ligase and Ctb73 Protein Interactions. Portland State University Library, January 2014. http://dx.doi.org/10.15760/honors.48.

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Whitehead, Ian P. A Role for Ubiquitin Binding in Bcr-Abl Transformation. Fort Belvoir, VA: Defense Technical Information Center, June 2008. http://dx.doi.org/10.21236/ada487390.

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Vierstra, R. D. Mechanism for the selective conjugation of ubiquitin to phytochrome. Office of Scientific and Technical Information (OSTI), January 1990. http://dx.doi.org/10.2172/5229610.

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Whitehead, Ian P. A Role for Ubiquitin Binding in Bcr-Abl Transformation. Fort Belvoir, VA: Defense Technical Information Center, June 2009. http://dx.doi.org/10.21236/ada510762.

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Zhang, Hui. The Role of Ubiquitin E3 Ligase SCFSKP2 in Prostate Cancer Development. Fort Belvoir, VA: Defense Technical Information Center, February 2005. http://dx.doi.org/10.21236/ada435854.

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Spruck, Charles H. Identification of Substances for Ubiquitin-Dependent Proteolysis During Breast Tumor Progression. Fort Belvoir, VA: Defense Technical Information Center, October 2008. http://dx.doi.org/10.21236/ada510763.

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Schultz, David C. Analysis BAP-1 as a Ubiquitin Hydrolase in the BRCA1 Pathway. Fort Belvoir, VA: Defense Technical Information Center, October 1999. http://dx.doi.org/10.21236/ada392104.

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Schultz, David C. Analysis BAP-1 as a Ubiquitin Hydrolase in the BRCA1 Pathway. Fort Belvoir, VA: Defense Technical Information Center, October 2000. http://dx.doi.org/10.21236/ada392881.

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Davidge, Brittney. The Cul3 Ubiquitin Ligase: An Essential Regulator of Diverse Cellular Processes. Portland State University Library, January 2000. http://dx.doi.org/10.15760/etd.5666.

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Srikanth, Appikonda. The Role of Ubiquitin-Mediated Proteolysis of Cyclin D in Breast Cancer. Fort Belvoir, VA: Defense Technical Information Center, April 2005. http://dx.doi.org/10.21236/ada455151.

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