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  1. Article ; Online: The HisRS-like domain of GCN2 is a pseudoenzyme that can bind uncharged tRNA.

    Yin, Jay Z / Keszei, Alexander F A / Houliston, Scott / Filandr, Frantisek / Beenstock, Jonah / Daou, Salima / Kitaygorodsky, Julia / Schriemer, David C / Mazhab-Jafari, Mohammad T / Gingras, Anne-Claude / Sicheri, Frank

    Structure (London, England : 1993)

    2024  

    Abstract: GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated ... ...

    Abstract GCN2 is a stress response kinase that phosphorylates the translation initiation factor eIF2α to inhibit general protein synthesis when activated by uncharged tRNA and stalled ribosomes. The presence of a HisRS-like domain in GCN2, normally associated with tRNA aminoacylation, led to the hypothesis that eIF2α kinase activity is regulated by the direct binding of this domain to uncharged tRNA. Here we solved the structure of the HisRS-like domain in the context of full-length GCN2 by cryoEM. Structure and function analysis shows the HisRS-like domain of GCN2 has lost histidine and ATP binding but retains tRNA binding abilities. Hydrogen deuterium exchange mass spectrometry, site-directed mutagenesis and computational docking experiments support a tRNA binding model that is partially shifted from that employed by bona fide HisRS enzymes. These results demonstrate that the HisRS-like domain of GCN2 is a pseudoenzyme and advance our understanding of GCN2 regulation and function.
    Language English
    Publishing date 2024-03-22
    Publishing country United States
    Document type Journal Article
    ZDB-ID 1213087-4
    ISSN 1878-4186 ; 0969-2126
    ISSN (online) 1878-4186
    ISSN 0969-2126
    DOI 10.1016/j.str.2024.02.021
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes.

    Barbour, Haithem / Daou, Salima / Hendzel, Michael / Affar, El Bachir

    Nature communications

    2020  Volume 11, Issue 1, Page(s) 5947

    Abstract: Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the ... ...

    Abstract Histone posttranslational modifications are key regulators of chromatin-associated processes including gene expression, DNA replication and DNA repair. Monoubiquitinated histone H2A, H2Aub (K118 in Drosophila or K119 in vertebrates) is catalyzed by the Polycomb group (PcG) repressive complex 1 (PRC1) and reversed by the PcG-repressive deubiquitinase (PR-DUB)/BAP1 complex. Here we critically assess the current knowledge regarding H2Aub deposition and removal, its crosstalk with PcG repressive complex 2 (PRC2)-mediated histone H3K27 methylation, and the recent attempts toward discovering its readers and solving its enigmatic functions. We also discuss mounting evidence of the involvement of H2A ubiquitination in human pathologies including cancer, while highlighting some knowledge gaps that remain to be addressed.
    MeSH term(s) Animals ; Chromatin/metabolism ; Deubiquitinating Enzymes/metabolism ; Epigenesis, Genetic ; Histones/metabolism ; Humans ; Methylation ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Polycomb-Group Proteins/chemistry ; Polycomb-Group Proteins/genetics ; Polycomb-Group Proteins/metabolism ; Ubiquitination
    Chemical Substances Chromatin ; Histones ; Polycomb-Group Proteins ; Deubiquitinating Enzymes (EC 3.4.19.12)
    Language English
    Publishing date 2020-11-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-020-19722-9
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: Polycomb group-mediated histone H2A monoubiquitination in epigenome regulation and nuclear processes

    Haithem Barbour / Salima Daou / Michael Hendzel / El Bachir Affar

    Nature Communications, Vol 11, Iss 1, Pp 1-

    2020  Volume 16

    Abstract: Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and ... ...

    Abstract Histone H2A monoubiquitination on lysine 119 in vertebrate and lysine 118 in Drosophila (H2Aub) is an epigenomic mark usually associated with gene repression by Polycomb group factors. Here the authors review the current knowledge on the deposition and removal of H2Aub, its function in transcription and other DNA-associated processes as well as its relevance to human disease.
    Keywords Science ; Q
    Language English
    Publishing date 2020-11-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  4. Article ; Online: Vivid views of the PINK1 protein.

    Daou, Salima / Sicheri, Frank

    Nature

    2015  Volume 552, Issue 7683, Page(s) 38–39

    MeSH term(s) Humans ; Mitochondria ; Parkinson Disease ; Protein Kinases ; Ubiquitin-Protein Ligases
    Chemical Substances Ubiquitin-Protein Ligases (EC 2.3.2.27) ; Protein Kinases (EC 2.7.-)
    Language English
    Publishing date 2015-11-03
    Publishing country England
    Document type Journal Article ; Comment
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/d41586-017-07691-x
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: An inventory of crosstalk between ubiquitination and other post-translational modifications in orchestrating cellular processes.

    Barbour, Haithem / Nkwe, Nadine Sen / Estavoyer, Benjamin / Messmer, Clémence / Gushul-Leclaire, Mila / Villot, Romain / Uriarte, Maxime / Boulay, Karine / Hlayhel, Sari / Farhat, Bassel / Milot, Eric / Mallette, Frédérick A / Daou, Salima / Affar, El Bachir

    iScience

    2023  Volume 26, Issue 5, Page(s) 106276

    Abstract: Ubiquitination is an important post-translational modification (PTM) that regulates a large spectrum of cellular processes in eukaryotes. Abnormalities in ubiquitin signaling underlie numerous human pathologies including cancer and neurodegeneration. ... ...

    Abstract Ubiquitination is an important post-translational modification (PTM) that regulates a large spectrum of cellular processes in eukaryotes. Abnormalities in ubiquitin signaling underlie numerous human pathologies including cancer and neurodegeneration. Much progress has been made during the last three decades in understanding how ubiquitin ligases recognize their substrates and how ubiquitination is orchestrated. Several mechanisms of regulation have evolved to prevent promiscuity including the assembly of ubiquitin ligases in multi-protein complexes with dedicated subunits and specific post-translational modifications of these enzymes and their co-factors. Here, we outline another layer of complexity involving the coordinated access of E3 ligases to substrates. We provide an extensive inventory of ubiquitination crosstalk with multiple PTMs including SUMOylation, phosphorylation, methylation, acetylation, hydroxylation, prolyl isomerization, PARylation, and O-GlcNAcylation. We discuss molecular mechanisms by which PTMs orchestrate ubiquitination, thus increasing its specificity as well as its crosstalk with other signaling pathways to ensure cell homeostasis.
    Language English
    Publishing date 2023-02-26
    Publishing country United States
    Document type Journal Article ; Review
    ISSN 2589-0042
    ISSN (online) 2589-0042
    DOI 10.1016/j.isci.2023.106276
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: In Vitro Ubiquitination and Deubiquitination Assays of Nucleosomal Histones.

    Masclef, Louis / Maxime, Uriarte / Ahmed, Oumaima / Sen Nkwe, Nadine / Barbour, Haithem / Iannantuono, Nicholas V G / Boubekeur, Amina / Daou, Salima / Affar, El Bachir

    Journal of visualized experiments : JoVE

    2019  , Issue 149

    Abstract: Ubiquitination is a post-translational modification that plays important roles in various signaling pathways and is notably involved in the coordination of chromatin function and DNA-associated processes. This modification involves a sequential action of ...

    Abstract Ubiquitination is a post-translational modification that plays important roles in various signaling pathways and is notably involved in the coordination of chromatin function and DNA-associated processes. This modification involves a sequential action of several enzymes including E1 ubiquitin-activating, E2 ubiquitin-conjugating and E3 ubiquitin-ligase and is reversed by deubiquitinases (DUBs). Ubiquitination induces degradation of proteins or alteration of protein function including modulation of enzymatic activity, protein-protein interaction and subcellular localization. A critical step in demonstrating protein ubiquitination or deubiquitination is to perform in vitro reactions with purified components. Effective ubiquitination and deubiquitination reactions could be greatly impacted by the different components used, enzyme co-factors, buffer conditions, and the nature of the substrate.  Here, we provide step-by-step protocols for conducting ubiquitination and deubiquitination reactions. We illustrate these reactions using minimal components of the mouse Polycomb Repressive Complex 1 (PRC1), BMI1, and RING1B, an E3 ubiquitin ligase that monoubiquitinates histone H2A on lysine 119. Deubiquitination of nucleosomal H2A is performed using a minimal Polycomb Repressive Deubiquitinase (PR-DUB) complex formed by the human deubiquitinase BAP1 and the DEUBiquitinase ADaptor (DEUBAD) domain of its co-factor ASXL2. These ubiquitination/deubiquitination assays can be conducted in the context of either recombinant nucleosomes reconstituted with bacteria-purified proteins or native nucleosomes purified from mammalian cells. We highlight the intricacies that can have a significant impact on these reactions and we propose that the general principles of these protocols can be swiftly adapted to other E3 ubiquitin ligases and deubiquitinases.
    MeSH term(s) Animals ; HEK293 Cells ; Histones/metabolism ; Humans ; Mice ; Nucleosomes/chemistry ; Ubiquitination
    Chemical Substances Histones ; Nucleosomes
    Language English
    Publishing date 2019-07-25
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Video-Audio Media
    ZDB-ID 2259946-0
    ISSN 1940-087X ; 1940-087X
    ISSN (online) 1940-087X
    ISSN 1940-087X
    DOI 10.3791/59385
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Electron transfer dissociation (ETD): the mass spectrometric breakthrough essential for O-GlcNAc protein site assignments-a study of the O-GlcNAcylated protein host cell factor C1.

    Myers, Samuel A / Daou, Salima / Affar, El Bachir / Burlingame, Al

    Proteomics

    2013  Volume 13, Issue 6, Page(s) 982–991

    Abstract: The development of electron-based, unimolecular dissociation MS, i.e. electron capture and electron transfer dissociation (ECD and ETD, respectively), has greatly increased the speed and reliability of labile PTM site assignment. The field of ... ...

    Abstract The development of electron-based, unimolecular dissociation MS, i.e. electron capture and electron transfer dissociation (ECD and ETD, respectively), has greatly increased the speed and reliability of labile PTM site assignment. The field of intracellular O-GlcNAc (O-linked N-acetylglucosamine) signaling has especially advanced with the advent of ETD MS. Only within the last five years have proteomic-scale experiments utilizing ETD allowed the assignment of hundreds of O-GlcNAc sites within cells and subcellular structures. Our ability to identify and unambiguously assign the site of O-GlcNAc modifications using ETD is rapidly increasing our understanding of this regulatory glycosylation and its potential interaction with other PTMs. Here, we discuss the advantages of using ETD, complimented with collisional-activation MS, in a study of the extensively O-GlcNAcylated protein Host Cell Factor C1 (HCF-1). HCF-1 is a transcriptional coregulator that forms a stable complex with O-GlcNAc transferase and controls cell cycle progression. ETD, along with higher energy collisional dissociation (HCD) MS, was employed to assign the PTMs of the HCF-1 protein isolated from HEK293T cells. These include 19 sites of O-GlcNAcylation, two sites of phosphorylation, and two sites bearing dimethylarginine, and showcase the residue-specific, PTM complexity of this regulator of cell proliferation.
    MeSH term(s) Amino Acid Sequence ; Animals ; Chromatography, High Pressure Liquid ; Glycopeptides/chemistry ; Glycopeptides/isolation & purification ; Glycosylation ; HEK293 Cells ; Host Cell Factor C1/chemistry ; Host Cell Factor C1/isolation & purification ; Host Cell Factor C1/metabolism ; Humans ; Mice ; Molecular Sequence Data ; Peptide Fragments/chemistry ; Peptide Fragments/isolation & purification ; Protein Processing, Post-Translational ; Spectrometry, Mass, Electrospray Ionization/methods ; Tandem Mass Spectrometry/methods
    Chemical Substances Glycopeptides ; HCFC1 protein, human ; Host Cell Factor C1 ; Peptide Fragments
    Language English
    Publishing date 2013-01-18
    Publishing country Germany
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2032093-0
    ISSN 1615-9861 ; 1615-9853
    ISSN (online) 1615-9861
    ISSN 1615-9853
    DOI 10.1002/pmic.201200332
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: A potent nuclear export mechanism imposes USP16 cytoplasmic localization during interphase.

    Sen Nkwe, Nadine / Daou, Salima / Uriarte, Maxime / Gagnon, Jessica / Iannantuono, Nicholas Victor / Barbour, Haithem / Yu, Helen / Masclef, Louis / Fernández, Erlinda / Zamorano Cuervo, Natalia / Mashtalir, Nazar / Binan, Loïc / Sergeev, Mikhail / Bélanger, François / Drobetsky, Elliot / Milot, Eric / Wurtele, Hugo / Costantino, Santiago / Affar, El Bachir

    Journal of cell science

    2020  Volume 133, Issue 4

    Abstract: USP16 (also known as UBP-M) has emerged as a histone H2AK119 deubiquitylase (DUB) implicated in the regulation of chromatin-associated processes and cell cycle progression. Despite this, available evidence suggests that this DUB is also present in the ... ...

    Abstract USP16 (also known as UBP-M) has emerged as a histone H2AK119 deubiquitylase (DUB) implicated in the regulation of chromatin-associated processes and cell cycle progression. Despite this, available evidence suggests that this DUB is also present in the cytoplasm. How the nucleo-cytoplasmic transport of USP16, and hence its function, is regulated has remained elusive. Here, we show that USP16 is predominantly cytoplasmic in all cell cycle phases. We identified the nuclear export signal (NES) responsible for maintaining USP16 in the cytoplasm. We found that USP16 is only transiently retained in the nucleus following mitosis and then rapidly exported from this compartment. We also defined a non-canonical nuclear localization signal (NLS) sequence that plays a minimal role in directing USP16 into the nucleus. We further established that this DUB does not accumulate in the nucleus following DNA damage. Instead, only enforced nuclear localization of USP16 abolishes DNA double-strand break (DSB) repair, possibly due to unrestrained DUB activity. Thus, in contrast to the prevailing view, our data indicate that USP16 is actively excluded from the nucleus and that this DUB might indirectly regulate DSB repair.This article has an associated First Person interview with the first author of the paper.
    MeSH term(s) Active Transport, Cell Nucleus ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cytoplasm/genetics ; Cytoplasm/metabolism ; Interphase ; Nuclear Export Signals/genetics ; Nuclear Localization Signals/genetics ; Nuclear Localization Signals/metabolism
    Chemical Substances Nuclear Export Signals ; Nuclear Localization Signals
    Language English
    Publishing date 2020-02-24
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2993-2
    ISSN 1477-9137 ; 0021-9533
    ISSN (online) 1477-9137
    ISSN 0021-9533
    DOI 10.1242/jcs.239236
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: A phenolic small molecule inhibitor of RNase L prevents cell death from ADAR1 deficiency.

    Daou, Salima / Talukdar, Manisha / Tang, Jinle / Dong, Beihua / Banerjee, Shuvojit / Li, Yize / Duffy, Nicole M / Ogunjimi, Abiodun A / Gaughan, Christina / Jha, Babal K / Gish, Gerald / Tavernier, Nicolas / Mao, Daniel / Weiss, Susan R / Huang, Hao / Silverman, Robert H / Sicheri, Frank

    Proceedings of the National Academy of Sciences of the United States of America

    2020  Volume 117, Issue 40, Page(s) 24802–24812

    Abstract: The oligoadenylate synthetase (OAS)-RNase L system is an IFN-inducible antiviral pathway activated by viral infection. Viral double-stranded (ds) RNA activates OAS isoforms that synthesize the second messenger 2-5A, which binds and activates the ... ...

    Abstract The oligoadenylate synthetase (OAS)-RNase L system is an IFN-inducible antiviral pathway activated by viral infection. Viral double-stranded (ds) RNA activates OAS isoforms that synthesize the second messenger 2-5A, which binds and activates the pseudokinase-endoribonuclease RNase L. In cells, OAS activation is tamped down by ADAR1, an adenosine deaminase that destabilizes dsRNA. Mutation of
    MeSH term(s) 2',5'-Oligoadenylate Synthetase/genetics ; 2',5'-Oligoadenylate Synthetase/metabolism ; Adenine Nucleotides/metabolism ; Adenosine Deaminase/deficiency ; Adenosine Deaminase/genetics ; Autoimmune Diseases of the Nervous System/enzymology ; Autoimmune Diseases of the Nervous System/genetics ; Autoimmune Diseases of the Nervous System/physiopathology ; Cell Death/drug effects ; Endoribonucleases/antagonists & inhibitors ; Endoribonucleases/genetics ; Endoribonucleases/metabolism ; Enzyme Inhibitors/chemistry ; Enzyme Inhibitors/pharmacology ; Humans ; Nervous System Malformations/enzymology ; Nervous System Malformations/genetics ; Nervous System Malformations/physiopathology ; Oligoribonucleotides/metabolism ; Phenol/chemistry ; Phenol/pharmacology ; RNA-Binding Proteins/genetics
    Chemical Substances Adenine Nucleotides ; Enzyme Inhibitors ; Oligoribonucleotides ; RNA-Binding Proteins ; Phenol (339NCG44TV) ; 2',5'-oligoadenylate (61172-40-5) ; 2',5'-Oligoadenylate Synthetase (EC 2.7.7.84) ; Endoribonucleases (EC 3.1.-) ; 2-5A-dependent ribonuclease (EC 3.1.26.-) ; ADAR protein, human (EC 3.5.4.37) ; Adenosine Deaminase (EC 3.5.4.4)
    Keywords covid19
    Language English
    Publishing date 2020-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 209104-5
    ISSN 1091-6490 ; 0027-8424
    ISSN (online) 1091-6490
    ISSN 0027-8424
    DOI 10.1073/pnas.2006883117
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article: In vitro ubiquitination and deubiquitination assays of nucleosomal histones

    Masclef, Louis / Affar, El Bachir / Ahmed, Oumaima / Barbour, Haithem / Boubekeur, Amina / Daou, Salima / Iannantuono, Nicholas V.G / Maxime, Uriarte / Sen Nkwe, Nadine

    Journal of visualized experiments. 2019 July 25, , no. 149

    2019  

    Abstract: Ubiquitination is a post-translational modification that plays important roles in various signaling pathways and is notably involved in the coordination of chromatin function and DNA-associated processes. This modification involves a sequential action of ...

    Abstract Ubiquitination is a post-translational modification that plays important roles in various signaling pathways and is notably involved in the coordination of chromatin function and DNA-associated processes. This modification involves a sequential action of several enzymes including E1 ubiquitin-activating, E2 ubiquitin-conjugating and E3 ubiquitin-ligase and is reversed by deubiquitinases (DUBs). Ubiquitination induces degradation of proteins or alteration of protein function including modulation of enzymatic activity, protein-protein interaction and subcellular localization. A critical step in demonstrating protein ubiquitination or deubiquitination is to perform in vitro reactions with purified components. Effective ubiquitination and deubiquitination reactions could be greatly impacted by the different components used, enzyme co-factors, buffer conditions, and the nature of the substrate. Here, we provide step-by-step protocols for conducting ubiquitination and deubiquitination reactions. We illustrate these reactions using minimal components of the mouse Polycomb Repressive Complex 1 (PRC1), BMI1, and RING1B, an E3 ubiquitin ligase that monoubiquitinates histone H2A on lysine 119. Deubiquitination of nucleosomal H2A is performed using a minimal Polycomb Repressive Deubiquitinase (PR-DUB) complex formed by the human deubiquitinase BAP1 and the DEUBiquitinase ADaptor (DEUBAD) domain of its co-factor ASXL2. These ubiquitination/deubiquitination assays can be conducted in the context of either recombinant nucleosomes reconstituted with bacteria-purified proteins or native nucleosomes purified from mammalian cells. We highlight the intricacies that can have a significant impact on these reactions and we propose that the general principles of these protocols can be swiftly adapted to other E3 ubiquitin ligases and deubiquitinases.
    Keywords enzyme activity ; histones ; humans ; lysine ; mice ; nucleosomes ; protein-protein interactions ; signal transduction ; ubiquitination ; ubiquitin-protein ligase ; ubiquitinyl hydrolase 1
    Language English
    Dates of publication 2019-0725
    Size p. e59385.
    Publishing place Journal of Visualized Experiments
    Document type Article
    ZDB-ID 2259946-0
    ISSN 1940-087X
    ISSN 1940-087X
    DOI 10.3791/59385
    Database NAL-Catalogue (AGRICOLA)

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