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  1. Article ; Online: Ubiquitin-dependent regulation of transcription in development and disease.

    Mark, Kevin G / Rape, Michael

    EMBO reports

    2021  Volume 22, Issue 4, Page(s) e51078

    Abstract: Transcription is an elaborate process that is required to establish and maintain the identity of the more than two hundred cell types of a metazoan organism. Strict regulation of gene expression is therefore vital for tissue formation and homeostasis. An ...

    Abstract Transcription is an elaborate process that is required to establish and maintain the identity of the more than two hundred cell types of a metazoan organism. Strict regulation of gene expression is therefore vital for tissue formation and homeostasis. An accumulating body of work found that ubiquitylation of histones, transcription factors, or RNA polymerase II is crucial for ensuring that transcription occurs at the right time and place during development. Here, we will review principles of ubiquitin-dependent control of gene expression and discuss how breakdown of these regulatory circuits leads to a wide array of human diseases.
    MeSH term(s) Animals ; Histones/genetics ; Histones/metabolism ; Humans ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Transcription, Genetic ; Ubiquitin/genetics ; Ubiquitin/metabolism ; Ubiquitination
    Chemical Substances Histones ; Ubiquitin ; RNA Polymerase II (EC 2.7.7.-)
    Language English
    Publishing date 2021-03-28
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 2020896-0
    ISSN 1469-3178 ; 1469-221X
    ISSN (online) 1469-3178
    ISSN 1469-221X
    DOI 10.15252/embr.202051078
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  2. Article: Assembly and function of branched ubiquitin chains.

    Kolla, SriDurgaDevi / Ye, Mengchen / Mark, Kevin G / Rapé, Michael

    Trends in biochemical sciences

    2022  Volume 47, Issue 9, Page(s) 759–771

    Abstract: Post-translational modification with ubiquitin is required for cell division, differentiation, and survival in all eukaryotes. As part of an intricate signaling code, ubiquitin is attached to its targets as single molecules or polymeric chains, with the ... ...

    Abstract Post-translational modification with ubiquitin is required for cell division, differentiation, and survival in all eukaryotes. As part of an intricate signaling code, ubiquitin is attached to its targets as single molecules or polymeric chains, with the distinct modifications encoding a wide range of outcomes. After early work focused on homotypic ubiquitin chains, such as the K48-linked polymers that drive proteasomal degradation, recent studies noted abundant conjugates that contained ubiquitin molecules modified on two or more sites. Such branched ubiquitin chains are produced in response to specific signals and they exert functions that are critical for cellular and organismal homeostasis. In this review, we will discuss our rapidly evolving understanding of the assembly and function of branched ubiquitin chains.
    MeSH term(s) Cell Division ; Protein Processing, Post-Translational ; Signal Transduction ; Ubiquitin/metabolism ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemical Substances Ubiquitin ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2022-05-01
    Publishing country England
    Document type Journal Article ; Review ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 194216-5
    ISSN 1362-4326 ; 0968-0004 ; 0376-5067
    ISSN (online) 1362-4326
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.04.003
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  3. Article: Assembly and function of branched ubiquitin chains

    Kolla, SriDurgaDevi / Ye, Mengchen / Mark, Kevin G. / Rapé, Michael

    Trends in biochemical sciences. 2022,

    2022  

    Abstract: Posttranslational modification with ubiquitin is required for cell division, differentiation, and survival in all eukaryotes. As part of an intricate signaling code, ubiquitin is attached to its targets as single molecules or polymeric chains, with the ... ...

    Abstract Posttranslational modification with ubiquitin is required for cell division, differentiation, and survival in all eukaryotes. As part of an intricate signaling code, ubiquitin is attached to its targets as single molecules or polymeric chains, with the distinct modifications encoding a wide range of outcomes. After early work focused on homotypic ubiquitin chains, such as the K48-linked polymers that drive proteasomal degradation, recent studies noted abundant conjugates that contained ubiquitin molecules modified on two or more sites. Such branched ubiquitin chains are produced in response to specific signals, and they exert functions that are critical for cellular and organismal homeostasis. In this review, we will discuss our rapidly evolving understanding of the assembly and function of branched ubiquitin chains.
    Keywords cell division ; eukaryotic cells ; homeostasis ; polymers ; post-translational modification ; ubiquitin
    Language English
    Publishing place Elsevier Ltd
    Document type Article
    Note Pre-press version
    ZDB-ID 194220-7
    ISSN 0968-0004 ; 0376-5067
    ISSN 0968-0004 ; 0376-5067
    DOI 10.1016/j.tibs.2022.04.003
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  4. Article ; Online: Isolation of ubiquitinated substrates by tandem affinity purification of E3 ligase-polyubiquitin-binding domain fusions (ligase traps).

    Mark, Kevin G / Loveless, Theresa B / Toczyski, David P

    Nature protocols

    2016  Volume 11, Issue 2, Page(s) 291–301

    Abstract: Ubiquitination is an essential protein modification that influences eukaryotic processes ranging from substrate degradation to nonproteolytic pathway alterations, including DNA repair and endocytosis. Previous attempts to analyze substrates via physical ... ...

    Abstract Ubiquitination is an essential protein modification that influences eukaryotic processes ranging from substrate degradation to nonproteolytic pathway alterations, including DNA repair and endocytosis. Previous attempts to analyze substrates via physical association with their respective ubiquitin ligases have had some success. However, because of the transient nature of enzyme-substrate interactions and rapid protein degradation, detection of substrates remains a challenge. Ligase trapping is an affinity purification approach in which ubiquitin ligases are fused to a polyubiquitin-binding domain, which allows the isolation of ubiquitinated substrates. Immunoprecipitation is first used to enrich for proteins that are bound to the ligase trap. Subsequently, affinity purification is used under denaturing conditions to capture proteins conjugated with hexahistidine-tagged ubiquitin. By using this protocol, ubiquitinated substrates that are specific for a given ligase can be isolated for mass spectrometry or western blot analysis. After cells have been collected, the described protocol can be completed in 2-3 d.
    MeSH term(s) Chromatography, Affinity/methods ; Immunoprecipitation ; Polyubiquitin/genetics ; Polyubiquitin/metabolism ; Protein Binding ; Proteins/isolation & purification ; Proteins/metabolism ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemical Substances Proteins ; Polyubiquitin (120904-94-1) ; Ubiquitin-Protein Ligases (EC 2.3.2.27)
    Language English
    Publishing date 2016-01-14
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 2244966-8
    ISSN 1750-2799 ; 1754-2189
    ISSN (online) 1750-2799
    ISSN 1754-2189
    DOI 10.1038/nprot.2016.008
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  5. Article ; Online: Orphan quality control shapes network dynamics and gene expression.

    Mark, Kevin G / Kolla, SriDurgaDevi / Aguirre, Jacob D / Garshott, Danielle M / Schmitt, Stefan / Haakonsen, Diane L / Xu, Christina / Kater, Lukas / Kempf, Georg / Martínez-González, Brenda / Akopian, David / See, Stephanie K / Thomä, Nicolas H / Rapé, Michael

    Cell

    2023  Volume 186, Issue 19, Page(s) 4252–4253

    Language English
    Publishing date 2023-09-15
    Publishing country United States
    Document type Published Erratum
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.08.006
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    Zs.A 1167: Show issues Location:
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  6. Article ; Online: Orphan quality control shapes network dynamics and gene expression.

    Mark, Kevin G / Kolla, SriDurgaDevi / Aguirre, Jacob D / Garshott, Danielle M / Schmitt, Stefan / Haakonsen, Diane L / Xu, Christina / Kater, Lukas / Kempf, Georg / Martínez-González, Brenda / Akopian, David / See, Stephanie K / Thomä, Nicolas H / Rapé, Michael

    Cell

    2023  Volume 186, Issue 16, Page(s) 3460–3475.e23

    Abstract: All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of ... ...

    Abstract All eukaryotes require intricate protein networks to translate developmental signals into accurate cell fate decisions. Mutations that disturb interactions between network components often result in disease, but how the composition and dynamics of complex networks are established remains poorly understood. Here, we identify the E3 ligase UBR5 as a signaling hub that helps degrade unpaired subunits of multiple transcriptional regulators that act within a network centered on the c-Myc oncoprotein. Biochemical and structural analyses show that UBR5 binds motifs that only become available upon complex dissociation. By rapidly turning over unpaired transcription factor subunits, UBR5 establishes dynamic interactions between transcriptional regulators that allow cells to effectively execute gene expression while remaining receptive to environmental signals. We conclude that orphan quality control plays an essential role in establishing dynamic protein networks, which may explain the conserved need for protein degradation during transcription and offers opportunities to modulate gene expression in disease.
    MeSH term(s) Humans ; Gene Expression ; HEK293 Cells ; HeLa Cells ; Mutation ; Signal Transduction ; Transcription Factors/metabolism ; Ubiquitin-Protein Ligases/metabolism
    Chemical Substances Transcription Factors ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; MYC protein, human
    Language English
    Publishing date 2023-07-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
    ZDB-ID 187009-9
    ISSN 1097-4172 ; 0092-8674
    ISSN (online) 1097-4172
    ISSN 0092-8674
    DOI 10.1016/j.cell.2023.06.015
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  7. Article ; Online: Ndd1 turnover by SCF(Grr1) is inhibited by the DNA damage checkpoint in Saccharomyces cerevisiae.

    Edenberg, Ellen R / Mark, Kevin G / Toczyski, David P

    PLoS genetics

    2015  Volume 11, Issue 4, Page(s) e1005162

    Abstract: In Saccharomyces cerevisiae, Ndd1 is the dedicated transcriptional activator of the mitotic gene cluster, which includes thirty-three genes that encode key mitotic regulators, making Ndd1 a hub for the control of mitosis. Previous work has shown that ... ...

    Abstract In Saccharomyces cerevisiae, Ndd1 is the dedicated transcriptional activator of the mitotic gene cluster, which includes thirty-three genes that encode key mitotic regulators, making Ndd1 a hub for the control of mitosis. Previous work has shown that multiple kinases, including cyclin-dependent kinase (Cdk1), phosphorylate Ndd1 to regulate its activity during the cell cycle. Previously, we showed that Ndd1 was inhibited by phosphorylation in response to DNA damage. Here, we show that Ndd1 is also subject to regulation by protein turnover during the mitotic cell cycle: Ndd1 is unstable during an unperturbed cell cycle, but is strongly stabilized in response to DNA damage. We find that Ndd1 turnover in metaphase requires Cdk1 activity and the ubiquitin ligase SCF(Grr1). In response to DNA damage, Ndd1 stabilization requires the checkpoint kinases Mec1/Tel1 and Swe1, the S. cerevisiae homolog of the Wee1 kinase. In both humans and yeast, the checkpoint promotes Wee1-dependent inhibitory phosphorylation of Cdk1 following exposure to DNA damage. While this is critical for checkpoint-induced arrest in most organisms, this is not true in budding yeast, where the function of damage-induced inhibitory phosphorylation is less well understood. We propose that the DNA damage checkpoint stabilizes Ndd1 by inhibiting Cdk1, which we show is required for targeting Ndd1 for destruction.
    MeSH term(s) CDC2 Protein Kinase/biosynthesis ; CDC2 Protein Kinase/genetics ; Cell Cycle/genetics ; Cell Cycle Proteins/biosynthesis ; Cell Cycle Proteins/genetics ; DNA Damage/genetics ; F-Box Proteins/biosynthesis ; F-Box Proteins/genetics ; Gene Expression Regulation, Fungal ; Humans ; Intracellular Signaling Peptides and Proteins ; Mitosis/genetics ; Saccharomyces cerevisiae ; Saccharomyces cerevisiae Proteins/biosynthesis ; Saccharomyces cerevisiae Proteins/genetics ; Transcription Factors/biosynthesis ; Transcription Factors/genetics ; Ubiquitin-Protein Ligases/biosynthesis ; Ubiquitin-Protein Ligases/genetics
    Chemical Substances Cell Cycle Proteins ; F-Box Proteins ; Intracellular Signaling Peptides and Proteins ; NDD1 protein, S cerevisiae ; RAD24 protein, S cerevisiae ; Saccharomyces cerevisiae Proteins ; Transcription Factors ; GRR1 protein, S cerevisiae (143550-97-4) ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; CDC2 Protein Kinase (EC 2.7.11.22)
    Language English
    Publishing date 2015-04-20
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 2186725-2
    ISSN 1553-7404 ; 1553-7390
    ISSN (online) 1553-7404
    ISSN 1553-7390
    DOI 10.1371/journal.pgen.1005162
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  8. Article ; Online: EMI1 switches from being a substrate to an inhibitor of APC/C

    Cappell, Steven D / Mark, Kevin G / Garbett, Damien / Pack, Lindsey R / Rape, Michael / Meyer, Tobias

    Nature

    2018  Volume 558, Issue 7709, Page(s) 313–317

    Abstract: Mammalian cells integrate mitogen and stress signalling before the end of G1 phase to determine whether or not they enter the cell ... ...

    Abstract Mammalian cells integrate mitogen and stress signalling before the end of G1 phase to determine whether or not they enter the cell cycle
    MeSH term(s) Cdh1 Proteins/antagonists & inhibitors ; Cdh1 Proteins/metabolism ; Cell Cycle/physiology ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Cyclin E/metabolism ; Cyclin-Dependent Kinase 2/metabolism ; F-Box Proteins/genetics ; F-Box Proteins/metabolism ; Feedback, Physiological ; G1 Phase ; HeLa Cells ; Humans ; S Phase
    Chemical Substances Cdh1 Proteins ; Cell Cycle Proteins ; Cyclin E ; F-Box Proteins ; FBXO5 protein, human ; FZR1 protein, human ; CDK2 protein, human (EC 2.7.11.22) ; Cyclin-Dependent Kinase 2 (EC 2.7.11.22)
    Language English
    Publishing date 2018-06-06
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, N.I.H., Intramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-018-0199-7
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  9. Article ; Online: Gene expression and cell identity controlled by anaphase-promoting complex.

    Oh, Eugene / Mark, Kevin G / Mocciaro, Annamaria / Watson, Edmond R / Prabu, J Rajan / Cha, Denny D / Kampmann, Martin / Gamarra, Nathan / Zhou, Coral Y / Rape, Michael

    Nature

    2020  Volume 579, Issue 7797, Page(s) 136–140

    Abstract: Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional ... ...

    Abstract Metazoan development requires the robust proliferation of progenitor cells, the identities of which are established by tightly controlled transcriptional networks
    MeSH term(s) Anaphase ; Anaphase-Promoting Complex-Cyclosome/metabolism ; Cell Differentiation/genetics ; Cell Division ; Gene Expression Regulation ; HEK293 Cells ; HeLa Cells ; Histones/chemistry ; Histones/metabolism ; Human Embryonic Stem Cells/cytology ; Human Embryonic Stem Cells/metabolism ; Humans ; Interphase ; Intracellular Signaling Peptides and Proteins/metabolism ; Mitosis ; Multiprotein Complexes/metabolism ; Organophosphates/metabolism ; Polyubiquitin/metabolism ; Proteasome Endopeptidase Complex/metabolism ; Transcription Initiation Site ; Ubiquitin/metabolism ; Ubiquitination
    Chemical Substances Histones ; Intracellular Signaling Peptides and Proteins ; Multiprotein Complexes ; Organophosphates ; Ubiquitin ; WDR5 protein, human ; Polyubiquitin (120904-94-1) ; tributyl phosphate (95UAS8YAF5) ; Anaphase-Promoting Complex-Cyclosome (EC 2.3.2.27) ; Proteasome Endopeptidase Complex (EC 3.4.25.1)
    Language English
    Publishing date 2020-02-19
    Publishing country England
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 120714-3
    ISSN 1476-4687 ; 0028-0836
    ISSN (online) 1476-4687
    ISSN 0028-0836
    DOI 10.1038/s41586-020-2034-1
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  10. Article: Prb1 Protease Activity Is Required for Its Recognition by the F-Box Protein Saf1

    Mark, Kevin G / Meza-Gutierrez Fernando / Johnson Jeffrey R / Newton Billy W / Krogan Nevan J / Toczyski David P

    Biochemistry. 2015 July 28, v. 54, no. 29

    2015  

    Abstract: The SCF ubiquitin ligase associates with substrates through its F-box protein adaptor. Substrates are typically recognized through a defined phosphodegron. Here, we characterize the interaction of the F-box protein Saf1 with Prb1, one of its vacuolar ... ...

    Abstract The SCF ubiquitin ligase associates with substrates through its F-box protein adaptor. Substrates are typically recognized through a defined phosphodegron. Here, we characterize the interaction of the F-box protein Saf1 with Prb1, one of its vacuolar protease substrates. We show that Saf1 binds the mature protein but ubiquitinates only the zymogen precursor. The ubiquitinated lysine was found to be in a peptide eliminated from the mature protein. Mutations that eliminate the catalytic activity of Prb1, or the related substrate Prc1, block Saf1 targeting of the zymogen precursor. Our data suggest that Saf1 does not require a conventional degron as do other F-box proteins but instead recognizes the catalytic site itself.
    Keywords F-box proteins ; active sites ; catalytic activity ; enzyme activity ; lysine ; mutation ; proteinases ; ubiquitin-protein ligase ; vacuoles
    Language English
    Dates of publication 2015-0728
    Size p. 4423-4426.
    Publishing place American Chemical Society
    Document type Article
    ZDB-ID 1108-3
    ISSN 1520-4995 ; 0006-2960
    ISSN (online) 1520-4995
    ISSN 0006-2960
    DOI 10.1021%2Facs.biochem.5b00504
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