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Yakoub G, Choi YS, Wong RP, Strauch T, Ann KJ, Cohen RE, Ulrich HD. Avidity-based biosensors for ubiquitylated PCNA reveal choreography of DNA damage bypass. SCIENCE ADVANCES 2023; 9:eadf3041. [PMID: 37672592 PMCID: PMC10482348 DOI: 10.1126/sciadv.adf3041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
In eukaryotes, the posttranslational modifier ubiquitin is used to regulate the amounts, interactions, or activities of proteins in diverse pathways and signaling networks. Its effects are mediated by monoubiquitin or polyubiquitin chains of varying geometries. We describe the design, validation, and application of a series of avidity-based probes against the ubiquitylated forms of the DNA replication clamp, proliferating cell nuclear antigen (PCNA), in budding yeast. Directed against total ubiquitylated PCNA or specifically K63-polyubiquitylated PCNA, the probes are tunable in their activities and can be used either as biosensors or as inhibitors of the PCNA-dependent DNA damage bypass pathway. Used in live cells, the probes revealed the timing of PCNA ubiquitylation during damage bypass and a particular susceptibility of the ribosomal DNA locus to the activation of the pathway. Our approach is applicable to a wide range of ubiquitin-conjugated proteins, thus representing a generalizable strategy for the design of biosensors for specific (poly)ubiquitylated forms of individual substrates.
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Affiliation(s)
- George Yakoub
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Yun-Seok Choi
- Department of Biochemistry and Molecular Biology, Colorado State University, 273 MRB, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA
| | - Ronald P. Wong
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Tina Strauch
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Kezia J. Ann
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, 273 MRB, 1870 Campus Delivery, Fort Collins, CO 80523-1870, USA
| | - Helle D. Ulrich
- Institute of Molecular Biology gGmbH, Ackermannweg 4, D-55128 Mainz, Germany
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2
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Hepowit NL, Moon B, Ebert AC, Dickson RC, MacGurn JA. Art2 mediates selective endocytosis of methionine transporters during adaptation to sphingolipid depletion. J Cell Sci 2023; 136:jcs260675. [PMID: 37337792 PMCID: PMC10399987 DOI: 10.1242/jcs.260675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 06/01/2023] [Indexed: 06/21/2023] Open
Abstract
Accumulating evidence in several model organisms indicates that reduced sphingolipid biosynthesis promotes longevity, although underlying mechanisms remain unclear. In yeast, sphingolipid depletion induces a state resembling amino acid restriction, which we hypothesized might be due to altered stability of amino acid transporters at the plasma membrane. To test this, we measured surface abundance for a diverse panel of membrane proteins in the presence of myriocin, a sphingolipid biosynthesis inhibitor, in Saccharomyces cerevisiae. Unexpectedly, we found that surface levels of most proteins examined were either unaffected or increased during myriocin treatment, consistent with an observed decrease in bulk endocytosis. In contrast, sphingolipid depletion triggered selective endocytosis of the methionine transporter Mup1. Unlike methionine-induced Mup1 endocytosis, myriocin triggered Mup1 endocytosis that required the Rsp5 adaptor Art2, C-terminal lysine residues of Mup1 and the formation of K63-linked ubiquitin polymers. These findings reveal cellular adaptation to sphingolipid depletion by ubiquitin-mediated remodeling of nutrient transporter composition at the cell surface.
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Affiliation(s)
- Nathaniel L. Hepowit
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Bradley Moon
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Adam C. Ebert
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
| | - Robert C. Dickson
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA
| | - Jason A. MacGurn
- Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN 37240, USA
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3
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HECT ubiquitin ligases as accessory proteins of the plant proteasome. Essays Biochem 2022; 66:135-145. [PMID: 35635104 PMCID: PMC9400063 DOI: 10.1042/ebc20210064] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 04/21/2022] [Accepted: 04/29/2022] [Indexed: 12/31/2022]
Abstract
The proteasome plays vital roles in eukaryotic cells by orchestrating the regulated degradation of large repertoires of substrates involved in numerous biological processes. Proteasome dysfunction is associated with a wide variety of human pathologies and in plants severely affects growth, development and responses to stress. The activity of E3 ubiquitin ligases marks proteins fated for degradation with chains of the post-translational modifier, ubiquitin. Proteasomal processing of ubiquitinated substrates involves ubiquitin chain recognition, deubiquitination, ATP-mediated unfolding and translocation, and proteolytic digestion. This complex series of steps is made possible not only by the many specialised subunits of the 1.5 MDa proteasome complex but also by a range of accessory proteins that are recruited to the proteasome. A surprising class of accessory proteins are members of the HECT-type family of ubiquitin ligases that utilise a unique mechanism for post-translational attachment of ubiquitin to their substrates. So why do proteasomes that already contain all the necessary machinery to recognise ubiquitinated substrates, harbour HECT ligase activity? It is now clear that some ubiquitin ligases physically relay their substrates to proteasome-associated HECT ligases, which prevent substrate stalling at the proteasome. Moreover, HECT ligases ubiquitinate proteasome subunits, thereby modifying the proteasome's ability to recognise substrates. They may therefore enable proteasomes to be both non-specific and extraordinarily selective in a complex substrate environment. Understanding the relationship between the proteasome and accessory HECT ligases will reveal how the proteasome controls so many diverse plant developmental and stress responses.
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Du J, Babik S, Li Y, Deol KK, Eyles SJ, Fejzo J, Tonelli M, Strieter E. A cryptic K48 ubiquitin chain binding site on UCH37 is required for its role in proteasomal degradation. eLife 2022; 11:e76100. [PMID: 35451368 PMCID: PMC9033301 DOI: 10.7554/elife.76100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 04/07/2022] [Indexed: 11/16/2022] Open
Abstract
Degradation by the 26 S proteasome is an intricately regulated process fine tuned by the precise nature of ubiquitin modifications attached to a protein substrate. By debranching ubiquitin chains composed of K48 linkages, the proteasome-associated ubiquitin C-terminal hydrolase UCHL5/UCH37 serves as a positive regulator of protein degradation. How UCH37 achieves specificity for K48 chains is unclear. Here, we use a combination of hydrogen-deuterium mass spectrometry, chemical crosslinking, small-angle X-ray scattering, nuclear magnetic resonance (NMR), molecular docking, and targeted mutagenesis to uncover a cryptic K48 ubiquitin (Ub) chain-specific binding site on the opposite face of UCH37 relative to the canonical S1 (cS1) ubiquitin-binding site. Biochemical assays demonstrate the K48 chain-specific binding site is required for chain debranching and proteasome-mediated degradation of proteins modified with branched chains. Using quantitative proteomics, translation shutoff experiments, and linkage-specific affinity tools, we then identify specific proteins whose degradation depends on the debranching activity of UCH37. Our findings suggest that UCH37 and potentially other DUBs could use more than one S1 site to perform different biochemical functions.
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Affiliation(s)
- Jiale Du
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Sandor Babik
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Yanfeng Li
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Kirandeep K Deol
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
| | - Stephen J Eyles
- Mass Spectrometry Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Jasna Fejzo
- Biomolecular NMR Core Facility, Institute for Applied Life Sciences (IALS), University of Massachusetts AmherstAmherstUnited States
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison (NMRFAM), University of Wisconsin-MadisonMadisonUnited States
| | - Eric Strieter
- Department of Chemistry, University of Massachusetts AmherstAmherstUnited States
- Molecular & Cellular Biology Graduate Program, University of Massachusetts AmherstAmherstUnited States
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5
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Schoeffler AJ, Helgason E, Popovych N, Dueber EC. Diagnosing and mitigating method-based avidity artifacts that confound polyubiquitin-binding assays. BIOPHYSICAL REPORTS 2021; 1:100033. [PMID: 36425458 PMCID: PMC9680732 DOI: 10.1016/j.bpr.2021.100033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/09/2021] [Indexed: 06/16/2023]
Abstract
Polyubiquitination is a complex form of posttranslational modification responsible for the control of numerous cellular processes. Many ubiquitin-binding proteins recognize distinct polyubiquitin chain types, and these associations help drive ubiquitin-signaling pathways. There is considerable interest in understanding the specificity of ubiquitin-binding proteins; however, because of the multivalent nature of polyubiquitin, affinity measurements of these interactions that rely on affixing ubiquitin-binding proteins to a surface can display artifactual, method-dependent avidity, or "bridging." This artifact, which is distinct from biologically relevant, avid interactions with polyubiquitin, is commonplace in such polyubiquitin-binding measurements and can lead to dramatic overestimations of binding affinities for particular chain types, and thus, incorrect conclusions about specificity. Here, we use surface-based measurements of ubiquitin binding in three model systems to illustrate bridging and lay out practical ways of identifying and mitigating it. Specifically, we describe a simple fitting model that enables researchers to diagnose the severity of bridging artifacts, determine whether they can be minimized, and more accurately evaluate polyubiquitin-binding specificity.
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Affiliation(s)
- Allyn J. Schoeffler
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Elizabeth Helgason
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Nataliya Popovych
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
| | - Erin C. Dueber
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California
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6
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Whiteley AM, Prado MA, de Poot SAH, Paulo JA, Ashton M, Dominguez S, Weber M, Ngu H, Szpyt J, Jedrychowski MP, Easton A, Gygi SP, Kurz T, Monteiro MJ, Brown EJ, Finley D. Global proteomics of Ubqln2-based murine models of ALS. J Biol Chem 2020; 296:100153. [PMID: 33277362 PMCID: PMC7873701 DOI: 10.1074/jbc.ra120.015960] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 11/21/2020] [Accepted: 12/04/2020] [Indexed: 12/12/2022] Open
Abstract
Familial neurodegenerative diseases commonly involve mutations that result in either aberrant proteins or dysfunctional components of the proteolytic machinery that act on aberrant proteins. UBQLN2 is a ubiquitin receptor of the UBL/UBA family that binds the proteasome through its ubiquitin-like domain and is thought to deliver ubiquitinated proteins to proteasomes for degradation. UBQLN2 mutations result in familial amyotrophic lateral sclerosis (ALS)/frontotemporal dementia in humans through an unknown mechanism. Quantitative multiplexed proteomics was used to provide for the first time an unbiased and global analysis of the role of Ubqln2 in controlling the composition of the proteome. We studied several murine models of Ubqln2-linked ALS and also generated Ubqln2 null mutant mice. We identified impacts of Ubqln2 on diverse physiological pathways, most notably serotonergic signaling. Interestingly, we observed an upregulation of proteasome subunits, suggesting a compensatory response to diminished proteasome output. Among the specific proteins whose abundance is linked to UBQLN2 function, the strongest hits were the ubiquitin ligase TRIM32 and two retroelement-derived proteins, PEG10 and CXX1B. Cycloheximide chase studies using induced human neurons and HEK293 cells suggested that PEG10 and TRIM32 are direct clients. Although UBQLN2 directs the degradation of multiple proteins via the proteasome, it surprisingly conferred strong protection from degradation on the Gag-like protein CXX1B, which is expressed from the same family of retroelement genes as PEG10. In summary, this study charts the proteomic landscape of ALS-related Ubqln2 mutants and identifies candidate client proteins that are altered in vivo in disease models and whose degradation is promoted by UBQLN2.
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Affiliation(s)
| | - Miguel A Prado
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | | | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Marissa Ashton
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Sara Dominguez
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Martin Weber
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Hai Ngu
- Department of Pathology, Genentech Inc, South San Francisco, California, USA
| | - John Szpyt
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Mark P Jedrychowski
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Amy Easton
- Department of Neuroscience, Genentech Inc, South San Francisco, California, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA
| | - Thimo Kurz
- Henry Wellcome Lab of Cell Biology, College of Medical, Veterinary and Life Sciences, Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, United Kingdom
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland Medical School, Baltimore, Maryland, USA
| | - Eric J Brown
- Department of Immunology and Infectious Diseases, Genentech Inc, South San Francisco, California, USA
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts, USA.
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7
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Giovannone AJ, Reales E, Bhattaram P, Nackeeran S, Monahan AB, Syed R, Weimbs T. The H abc domain of syntaxin 3 is a ubiquitin binding domain. Sci Rep 2020; 10:21350. [PMID: 33288783 PMCID: PMC7721868 DOI: 10.1038/s41598-020-78412-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 11/24/2020] [Indexed: 11/08/2022] Open
Abstract
Syntaxins are a family of membrane-anchored SNARE proteins that are essential components required for membrane fusion in eukaryotic intracellular membrane trafficking pathways. Syntaxins contain an N-terminal regulatory domain, termed the Habc domain that is not highly conserved at the primary sequence level but folds into a three-helix bundle that is structurally conserved among family members. The syntaxin Habc domain has previously been found to be structurally very similar to the GAT domain present in GGA family members and related proteins that are otherwise completely unrelated to syntaxins. Because the GAT domain has been found to be a ubiquitin binding domain we hypothesized that the Habc domain of syntaxins may also bind to ubiquitin. Here, we report that the Habc domain of syntaxin 3 (Stx3) indeed binds to monomeric ubiquitin with low affinity. This domain binds efficiently to K63-linked poly-ubiquitin chains within a narrow range of chain lengths but not to K48-linked poly-ubiquitin chains. Other syntaxin family members also bind to K63-linked poly-ubiquitin chains but with different chain length specificities. Molecular modeling suggests that residues of the GGA3-GAT domain known to be important for ionic and hydrophobic interactions with ubiquitin may have equivalent, conserved residues within the Habc domain of Stx3. We conclude that the syntaxin Habc domain and the GAT domain are both structurally and functionally related, and likely share a common ancestry despite sequence divergence. Binding of Ubiquitin to the Habc domain may regulate the function of syntaxins in membrane fusion or may suggest additional functions of this protein family.
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Affiliation(s)
- Adrian J Giovannone
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
| | - Elena Reales
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
- Department of Organic Chemistry, School of Sciences, University of Cadiz, Cádiz, Spain
- Biomedical Research and Innovation Institute of Cadiz (INiBICA), Cádiz, Spain
| | - Pallavi Bhattaram
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
- Department of Orthopaedics, Emory University School of Medicine, Atlanta, 30322, USA
| | - Sirpi Nackeeran
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
| | - Adam B Monahan
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
| | - Rashid Syed
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA
- Department of Chemistry and Biochemistry, California State University Northridge, Northridge, CA, 91330-8262, USA
| | - Thomas Weimbs
- Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California Santa Barbara, Santa Barbara, CA, 93106-9625, USA.
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Moulinier-Anzola J, Schwihla M, De-Araújo L, Artner C, Jörg L, Konstantinova N, Luschnig C, Korbei B. TOLs Function as Ubiquitin Receptors in the Early Steps of the ESCRT Pathway in Higher Plants. MOLECULAR PLANT 2020; 13:717-731. [PMID: 32087370 DOI: 10.1016/j.molp.2020.02.012] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 01/17/2020] [Accepted: 02/13/2020] [Indexed: 05/21/2023]
Abstract
Protein abundance and localization at the plasma membrane (PM) shapes plant development and mediates adaptation to changing environmental conditions. It is regulated by ubiquitination, a post-translational modification crucial for the proper sorting of endocytosed PM proteins to the vacuole for subsequent degradation. To understand the significance and the variety of roles played by this reversible modification, the function of ubiquitin receptors, which translate the ubiquitin signature into a cellular response, needs to be elucidated. In this study, we show that TOL (TOM1-like) proteins function in plants as multivalent ubiquitin receptors, governing ubiquitinated cargo delivery to the vacuole via the conserved Endosomal Sorting Complex Required for Transport (ESCRT) pathway. TOL2 and TOL6 interact with components of the ESCRT machinery and bind to K63-linked ubiquitin via two tandemly arranged conserved ubiquitin-binding domains. Mutation of these domains results not only in a loss of ubiquitin binding but also altered localization, abolishing TOL6 ubiquitin receptor activity. Function and localization of TOL6 is itself regulated by ubiquitination, whereby TOL6 ubiquitination potentially modulates degradation of PM-localized cargoes, assisting in the fine-tuning of the delicate interplay between protein recycling and downregulation. Taken together, our findings demonstrate the function and regulation of a ubiquitin receptor that mediates vacuolar degradation of PM proteins in higher plants.
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Affiliation(s)
- Jeanette Moulinier-Anzola
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Maximilian Schwihla
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lucinda De-Araújo
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Christina Artner
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Lisa Jörg
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Nataliia Konstantinova
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Christian Luschnig
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria
| | - Barbara Korbei
- Institute of Molecular Plant Biology, Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna (BOKU), Muthgasse 18, 1190 Vienna, Austria.
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Abstract
Many proteins in the cell are tagged with a polyubiquitin chain, which serves as a recognition signal for degradation by the proteasome. Some tagged substrates bind directly to the proteasome, but others are delivered through shuttling factors. Yeast Ddi1 and its homologs in other eukaryotic cells have protein domains typical of shuttling factors, but they also contain a predicted protease domain that is related to those in retroviral proteases. This paper shows that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains. Ddi1 is the only known endoprotease besides the proteasome that cleaves polyubiquitinated substrates. Ddi1 might prevent the excessive accumulation of polyubiquitinated proteins in cells. The Saccharomyces cerevisiae protein Ddi1 and its homologs in higher eukaryotes have been proposed to serve as shuttling factors that deliver ubiquitinated substrates to the proteasome. Although Ddi1 contains both ubiquitin-interacting UBA and proteasome-interacting UBL domains, the UBL domain is atypical, as it binds ubiquitin. Furthermore, unlike other shuttling factors, Ddi1 and its homologs contain a conserved helical domain (helical domain of Ddi1, HDD) and a retroviral-like protease (RVP) domain. The RVP domain is probably responsible for cleavage of the precursor of the transcription factor Nrf1 in higher eukaryotes, which results in the up-regulation of proteasomal subunit genes. However, enzymatic activity of the RVP domain has not yet been demonstrated, and the function of Ddi1 remains poorly understood. Here, we show that Ddi1 is a ubiquitin-dependent protease, which cleaves substrate proteins only when they are tagged with long ubiquitin chains (longer than about eight ubiquitins). The RVP domain is inactive in isolation, in contrast to its retroviral counterpart. Proteolytic activity of Ddi1 requires the HDD domain and is stimulated by the UBL domain, which mediates high-affinity interaction with the polyubiquitin chain. Compromising the activity of Ddi1 in yeast cells results in the accumulation of polyubiquitinated proteins. Aside from the proteasome, Ddi1 is the only known endoprotease that acts on polyubiquitinated substrates. Ddi1 and its homologs likely cleave polyubiquitinated substrates under conditions where proteasome function is compromised.
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10
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Li Y, Lan Q, Gao Y, Xu C, Xu Z, Wang Y, Chang L, Wu J, Deng Z, He F, Finley D, Xu P. Ubiquitin Linkage Specificity of Deubiquitinases Determines Cyclophilin Nuclear Localization and Degradation. iScience 2020; 23:100984. [PMID: 32240951 PMCID: PMC7115106 DOI: 10.1016/j.isci.2020.100984] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 01/16/2020] [Accepted: 03/09/2020] [Indexed: 11/25/2022] Open
Abstract
Ubiquitin chain specificity has been described for some deubiquitinases (DUBs) but lacks a comprehensive profiling in vivo. We used quantitative proteomics to compare the seven lysine-linked ubiquitin chains between wild-type yeast and its 20 DUB-deletion strains, which may reflect the linkage specificity of DUBs in vivo. Utilizing the specificity and ubiquitination heterogeneity, we developed a method termed DUB-mediated identification of linkage-specific ubiquitinated substrates (DILUS) to screen the ubiquitinated lysine residues on substrates modified with certain chains and regulated by specific DUB. Then we were able to identify 166 Ubp2-regulating substrates with 244 sites potentially modified with K63-linked chains. Among these substrates, we further demonstrated that cyclophilin A (Cpr1) modified with K63-linked chain on K151 site was regulated by Ubp2 and mediated the nuclear translocation of zinc finger protein Zpr1. The K48-linked chains at non-K151 sites of Cpr1 were mainly regulated by Ubp3 and served as canonical signals for proteasome-mediated degradation.
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Affiliation(s)
- Yanchang Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Qiuyan Lan
- School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Yuan Gao
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Cong Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Zhongwei Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Yihao Wang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Lei Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Junzhu Wu
- School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zixin Deng
- School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Fuchu He
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China
| | - Daniel Finley
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Research Unit of Proteomics & Research and Development of New Drug of Chinese Academy of Medical Sciences, Beijing Institute of Lifeomics, 38 Science Park Road, Beijing 102206, China; School of Basic Medical Science, Key Laboratory of Combinatorial Biosynthesis and Drug Discovery of Ministry of Education, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; Guizhou University School of Medicine, Guiyang 550025, China; Second Clinical Medicine Collage, Guangzhou University Chinese Medicine, Guangzhou 510006, China.
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11
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Mader J, Huber J, Bonn F, Dötsch V, Rogov VV, Bremm A. Oxygen-dependent asparagine hydroxylation of the ubiquitin-associated (UBA) domain in Cezanne regulates ubiquitin binding. J Biol Chem 2020; 295:2160-2174. [PMID: 31937588 DOI: 10.1074/jbc.ra119.010315] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 12/27/2019] [Indexed: 12/26/2022] Open
Abstract
Deubiquitinases (DUBs) are vital for the regulation of ubiquitin signals, and both catalytic activity of and target recruitment by DUBs need to be tightly controlled. Here, we identify asparagine hydroxylation as a novel posttranslational modification involved in the regulation of Cezanne (also known as OTU domain-containing protein 7B (OTUD7B)), a DUB that controls key cellular functions and signaling pathways. We demonstrate that Cezanne is a substrate for factor inhibiting HIF1 (FIH1)- and oxygen-dependent asparagine hydroxylation. We found that FIH1 modifies Asn35 within the uncharacterized N-terminal ubiquitin-associated (UBA)-like domain of Cezanne (UBACez), which lacks conserved UBA domain properties. We show that UBACez binds Lys11-, Lys48-, Lys63-, and Met1-linked ubiquitin chains in vitro, establishing UBACez as a functional ubiquitin-binding domain. Our findings also reveal that the interaction of UBACez with ubiquitin is mediated via a noncanonical surface and that hydroxylation of Asn35 inhibits ubiquitin binding. Recently, it has been suggested that Cezanne recruitment to specific target proteins depends on UBACez Our results indicate that UBACez can indeed fulfill this role as regulatory domain by binding various ubiquitin chain types. They also uncover that this interaction with ubiquitin, and thus with modified substrates, can be modulated by oxygen-dependent asparagine hydroxylation, suggesting that Cezanne is regulated by oxygen levels.
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Affiliation(s)
- Julia Mader
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Jessica Huber
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Florian Bonn
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Volker Dötsch
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Vladimir V Rogov
- Institute of Biophysical Chemistry and Center for Biomolecular Magnetic Resonance, Goethe University Frankfurt, Max-von-Laue Strasse 9, 60438 Frankfurt am Main, Germany
| | - Anja Bremm
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany.
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12
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Choi YS, Lian S, Cohen RE. Fluorescent Sensors That Enable a General Method To Quantify Affinities of Receptor Proteins for Polyubiquitin Ligands. ACS Sens 2019; 4:2908-2914. [PMID: 31599572 DOI: 10.1021/acssensors.9b01240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
In all eukaryotic cells, modifications of proteins by polymers of ubiquitin (polyUb) are signals used in diverse biological processes. To better understand how polyUb signals are read and promote their different functions, quantitative measurements of their interactions with receptor proteins are needed. However, affinities and selectivities of different forms of polyUb with various receptors have been difficult to determine because the availability of well-defined polyUb chains can be limiting and there is a lack of general, sensitive methods to assay their interactions. We have addressed this challenge by developing a series of fluorescent protein sensors for polyUb; by competition of the sensors against receptor proteins in vitro for limiting amounts of polyUb, receptor·polyUb affinities can be quantified. Due to the high affinities of the polyUb sensors (Kd ∼ 10-9 M), binding assays using this competition format require much less polyUb (<0.1%) than would be needed in direct titrations of the polyUb ligands. Furthermore, the high sensitivity and large dynamic range of the sensor fluorescence readout allow for precise measurements even for very tight interactions (i.e., nanomolar Kd). Importantly, as demonstrated here with Ub2 and Ub3 ligands, the assay does not require labeling of either the receptor protein or the polyUb, and it can be used with polyUb ligands composed of virtually any Ub-Ub linkage type.
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Affiliation(s)
- Yun-Seok Choi
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
- School of Natural Sciences, Black Hills State University, Spearfish, South Dakota 57799, United States
| | - Sharon Lian
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
| | - Robert E. Cohen
- Department of Biochemistry and Molecular Biology, Colorado State University, 1870 Campus Delivery, Fort Collins, Colorado 80523, United States
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13
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Haakonsen DL, Rape M. Branching Out: Improved Signaling by Heterotypic Ubiquitin Chains. Trends Cell Biol 2019; 29:704-716. [PMID: 31300189 DOI: 10.1016/j.tcb.2019.06.003] [Citation(s) in RCA: 94] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 06/06/2019] [Accepted: 06/11/2019] [Indexed: 02/08/2023]
Abstract
Ubiquitin chains of distinct topologies control the stability, interactions, or localization of many proteins in eukaryotic cells, and thus play an essential role in cellular information transfer. It has recently been found that ubiquitin chains can be combined to produce branched conjugates that are characterized by the presence of at least two linkages within the same polymer. Akin to their homotypic counterparts, branched chains elicit a wide array of biological outputs, further expanding the versatility, specificity, and efficiency of ubiquitin-dependent signaling. This review discusses emerging understanding of the synthesis and function of branched ubiquitin chains.
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Affiliation(s)
- Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.
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14
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Harman CA, Monteiro MJ. The specificity of ubiquitin binding to ubiquilin-1 is regulated by sequences besides its UBA domain. Biochim Biophys Acta Gen Subj 2019; 1863:1568-1574. [PMID: 31175912 DOI: 10.1016/j.bbagen.2019.06.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/24/2019] [Accepted: 06/03/2019] [Indexed: 12/12/2022]
Abstract
UBQLN proteins regulate proteostasis by facilitating clearance of misfolded proteins through the proteasome and autophagy degradation pathways. Consistent with its proteasomal function, UBQLN proteins contain both UBL and UBA domains, which bind subunits of the proteasome, including the S5a subunit, and ubiquitin chains, respectively. Conclusions regarding the binding properties of UBQLN proteins have been derived principally through studies of its individual domains, not the full-length (FL) proteins. Here we describe the in vitro binding properties of FL-UBQLN1 with the S5a subunit of the proteasome and two different lysine-linked (K48 or K63) ubiquitin chains. We show that in contrast to its isolated UBA domain, which binds almost equally well with both K48 and K63 ubiquitin chains, FL UBQLN1 binds preferentially with K63 chains. Furthermore, we show that deletion of the UBL domain from UBQLN1 abrogates ubiquitin binding. Taken together these results suggest that sequences outside of the UBA domain in UBQLN1 function to regulate the specificity and binding with different ubiquitin moieties. We also show that the UBL domain of UBQLN1 is required for S5a binding and that its binding to UBQLN1, in turn, enhances K48 ubiquitin chain binding to the complex. We discuss the implications of our findings with the known function of UBQLN proteins in protein degradation.
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Affiliation(s)
- Christine A Harman
- Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States.
| | - Mervyn J Monteiro
- Center for Biomedical Engineering and Technology, Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD, United States.
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15
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Abstract
As the endpoint for the ubiquitin-proteasome system, the 26S proteasome is the principal proteolytic machine responsible for regulated protein degradation in eukaryotic cells. The proteasome's cellular functions range from general protein homeostasis and stress response to the control of vital processes such as cell division and signal transduction. To reliably process all the proteins presented to it in the complex cellular environment, the proteasome must combine high promiscuity with exceptional substrate selectivity. Recent structural and biochemical studies have shed new light on the many steps involved in proteasomal substrate processing, including recognition, deubiquitination, and ATP-driven translocation and unfolding. In addition, these studies revealed a complex conformational landscape that ensures proper substrate selection before the proteasome commits to processive degradation. These advances in our understanding of the proteasome's intricate machinery set the stage for future studies on how the proteasome functions as a major regulator of the eukaryotic proteome.
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Affiliation(s)
- Jared A M Bard
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ellen A Goodall
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Eric R Greene
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
| | - Erik Jonsson
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
| | - Ken C Dong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
| | - Andreas Martin
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA;
- California Institute for Quantitative Biosciences, University of California at Berkeley, Berkeley, California 94720, USA
- Howard Hughes Medical Institute, University of California at Berkeley, Berkeley, California 94720, USA
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16
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Nyati S, Chaudhry N, Chatur A, Gregg BS, Kimmel L, Khare D, Basrur V, Ray D, Rehemtulla A. A novel reporter for real-time, quantitative imaging of AKT-directed K63-poly-ubiquitination in living cells. Oncotarget 2018. [PMID: 29541398 PMCID: PMC5834254 DOI: 10.18632/oncotarget.24323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Post-translational K63-linked poly-ubiquitination of AKT is required for its membrane recruitment and phosphorylation dependent activation in response to growth-factor stimulation. Current assays for target specific poly-ubiquitination involve cumbersome enzymatic preparations and semi-quantitative readouts. We have engineered a reporter that can quantitatively and in a target specific manner report on AKT-directed K63-polyubiquitination (K63UbR) in live cells. The reporter constitutes the AKT-derived poly-ubiquitination substrate peptide, a K63 poly-ubiquitin binding domain (UBD) as well as the split luciferase protein complementation domains. In cells, wherein signaling events upstream of AKT are activated (e.g. either EGFR or IGFR), poly-ubiquitination of the reporter leads to a stearic constraint that prevents luciferase complementation. However, upon inhibition of growth factor receptor signaling, loss of AKT poly-ubiquitination results in a decrease in interaction between the target peptide and the UBD, allowing for reconstitution of the split luciferase domains and therefore increased bioluminescence in a quantitative and dynamic manner. The K63UbR was confirmed to be suitable for high throughput screen (HTS), thus providing an excellent tool for small molecule or siRNA based HTS to discover new inhibitors or identify novel regulators of this key signaling node. Furthermore, the K63UbR platform could be adapted for non-invasive monitoring of additional target specific K63-polyubiquitination events in live cells.
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Affiliation(s)
- Shyam Nyati
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Nauman Chaudhry
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Areeb Chatur
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Brandon S Gregg
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Lauren Kimmel
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Dheeraj Khare
- Life Sciences Institute, University of Michigan, Ann Arbor, MI-48109, USA
| | - Venkatesha Basrur
- UMCCC Proteomics Shared Resource, University of Michigan, Ann Arbor, MI-48109, USA.,Department of Pathology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Dipankar Ray
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
| | - Alnawaz Rehemtulla
- Department of Radiation Oncology, University of Michigan, Ann Arbor, MI-48109, USA
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17
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Romero-Barrios N, Vert G. Proteasome-independent functions of lysine-63 polyubiquitination in plants. THE NEW PHYTOLOGIST 2018; 217:995-1011. [PMID: 29194634 DOI: 10.1111/nph.14915] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2017] [Accepted: 10/12/2017] [Indexed: 05/21/2023]
Abstract
Contents Summary 995 I. Introduction 995 II. The plant Ub machinery 996 III. From Ub to Ub linkage types in plants 997 IV. Increasing analytical resolution for K63 polyUb in plants 998 V. How to build K63 polyUb chains? 998 VI. Cellular roles of K63 polyUb in plants 999 VII. Physiological roles of K63 polyUb in plants 1004 VIII. Future perspectives: towards the next level of the Ub code 1006 Acknowledgements 1006 References 1007 SUMMARY: Ubiquitination is a post-translational modification essential for the regulation of eukaryotic proteins, having an impact on protein fate, function, localization or activity. What originally appeared to be a simple system to regulate protein turnover by the 26S proteasome is now known to be the most intricate regulatory process cells have evolved. Ubiquitin can be arranged in countless chain assemblies, triggering various cellular outcomes. Polyubiquitin chains using lysine-63 from ubiquitin represent the second most abundant type of ubiquitin modification. Recent studies have exposed their common function in proteasome-independent functions in non-plant model organisms. The existence of lysine-63 polyubiquitination in plants is, however, only just emerging. In this review, we discuss the recent advances on the characterization of ubiquitin chains and the molecular mechanisms driving the formation of lysine-63-linked ubiquitin modifications. We provide an overview of the roles associated with lysine-63 polyubiquitination in plant cells in the light of what is known in non-plant models. Finally, we review the crucial roles of lysine-63 polyubiquitin-dependent processes in plant growth, development and responses to environmental conditions.
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Affiliation(s)
- Natali Romero-Barrios
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
| | - Grégory Vert
- Institute for Integrative Biology of the Cell (I2BC), CNRS/CEA/Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, 91198, France
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18
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Takahashi TS, Hirade Y, Toma A, Sato Y, Yamagata A, Goto-Ito S, Tomita A, Nakada S, Fukai S. Structural insights into two distinct binding modules for Lys63-linked polyubiquitin chains in RNF168. Nat Commun 2018; 9:170. [PMID: 29330428 PMCID: PMC5766498 DOI: 10.1038/s41467-017-02345-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 11/22/2017] [Indexed: 12/18/2022] Open
Abstract
The E3 ubiquitin (Ub) ligase RNF168 plays a critical role in the initiation of the DNA damage response to double-strand breaks (DSBs). The recruitment of RNF168 by ubiquitylated targets involves two distinct regions, Ub-dependent DSB recruitment module (UDM) 1 and UDM2. Here we report the crystal structures of the complex between UDM1 and Lys63-linked diUb (K63-Ub2) and that between the C-terminally truncated UDM2 (UDM2ΔC) and K63-Ub2. In both structures, UDM1 and UDM2ΔC fold as a single α-helix. Their simultaneous bindings to the distal and proximal Ub moieties provide specificity for Lys63-linked Ub chains. Structural and biochemical analyses of UDM1 elucidate an Ub-binding mechanism between UDM1 and polyubiquitylated targets. Mutations of Ub-interacting residues in UDM2 prevent the accumulation of RNF168 to DSB sites in U2OS cells, whereas those in UDM1 have little effect, suggesting that the interaction of UDM2 with ubiquitylated and polyubiquitylated targets mainly contributes to the RNF168 recruitment. E3 ubiquitin ligase RNF168 is important for the repair of DNA double-strand breaks and recognizes ubiquitylated targets through two Ub-dependent DSB recruitment modules UDM1 and UDM2. Here the authors combine crystallography, cell biology and biochemical experiments to reveal how UDM1 and UDM2 interact with polyubiquitin chains.
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Affiliation(s)
- Tomio S Takahashi
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Yoshihiro Hirade
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Aya Toma
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan
| | - Yusuke Sato
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan
| | - Atsushi Yamagata
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan.,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan
| | - Sakurako Goto-Ito
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan.,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan
| | - Akiko Tomita
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan
| | - Shinichiro Nakada
- Department of Bioregulation and Cellular Response, Graduate School of Medicine, Osaka University, Osaka, 565-0871, Japan. .,Institute for Advanced Co-Creation Studies, Osaka University, Osaka, 565-0871, Japan.
| | - Shuya Fukai
- Institute of Molecular and Cellular Biosciences, The University of Tokyo, Tokyo, 113-0032, Japan. .,Synchrotron Radiation Research Organization, The University of Tokyo, Tokyo, 113-0032, Japan. .,Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8501, Japan.
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19
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Abstract
Linear (head-to-tail linked) polyubiquitin chains play a key role in the regulation of NF-κB signaling. In this issue of Structure, Lin et al. (2017) shed light on how linear tri-ubiquitin binds to ABIN2, a molecule that shares ubiquitin-binding properties of NEMO, the key activator of NF-κB.
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20
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Systematic approaches to identify E3 ligase substrates. Biochem J 2017; 473:4083-4101. [PMID: 27834739 PMCID: PMC5103871 DOI: 10.1042/bcj20160719] [Citation(s) in RCA: 110] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Revised: 08/25/2016] [Accepted: 08/30/2016] [Indexed: 12/11/2022]
Abstract
Protein ubiquitylation is a widespread post-translational modification, regulating cellular signalling with many outcomes, such as protein degradation, endocytosis, cell cycle progression, DNA repair and transcription. E3 ligases are a critical component of the ubiquitin proteasome system (UPS), determining the substrate specificity of the cascade by the covalent attachment of ubiquitin to substrate proteins. Currently, there are over 600 putative E3 ligases, but many are poorly characterized, particularly with respect to individual protein substrates. Here, we highlight systematic approaches to identify and validate UPS targets and discuss how they are underpinning rapid advances in our understanding of the biochemistry and biology of the UPS. The integration of novel tools, model systems and methods for target identification is driving significant interest in drug development, targeting various aspects of UPS function and advancing the understanding of a diverse range of disease processes.
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21
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Munari F, Bortot A, Zanzoni S, D'Onofrio M, Fushman D, Assfalg M. Identification of primary and secondary UBA footprints on the surface of ubiquitin in cell-mimicking crowded solution. FEBS Lett 2017; 591:979-990. [PMID: 28267209 DOI: 10.1002/1873-3468.12615] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 02/24/2017] [Accepted: 02/24/2017] [Indexed: 01/09/2023]
Abstract
Despite significant advancements in our understanding of ubiquitin-mediated signaling, the influence of the intracellular environment on the formation of transient ubiquitin-partner complexes remains poorly explored. In our work, we introduce macromolecular crowding as a first level of complexity toward the imitation of a cellular environment in the study of such interactions. Using NMR spectroscopy, we find that the stereospecific complex of ubiquitin and the ubiquitin-associated domain (UBA) is minimally perturbed by the crowding agent Ficoll. However, in addition to the primary canonical recognition patch on ubiquitin, secondary patches are identified, indicating that in cell-mimicking crowded solution, UBA contacts ubiquitin at multiple sites.
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Affiliation(s)
| | - Andrea Bortot
- Department of Biotechnology, University of Verona, Italy
| | - Serena Zanzoni
- Department of Biotechnology, University of Verona, Italy
| | | | - David Fushman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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22
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Chojnacki M, Mansour W, Hameed DS, Singh RK, El Oualid F, Rosenzweig R, Nakasone MA, Yu Z, Glaser F, Kay LE, Fushman D, Ovaa H, Glickman MH. Polyubiquitin-Photoactivatable Crosslinking Reagents for Mapping Ubiquitin Interactome Identify Rpn1 as a Proteasome Ubiquitin-Associating Subunit. Cell Chem Biol 2017; 24:443-457.e6. [PMID: 28330605 DOI: 10.1016/j.chembiol.2017.02.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 12/29/2016] [Accepted: 02/23/2017] [Indexed: 01/05/2023]
Abstract
Ubiquitin (Ub) signaling is a diverse group of processes controlled by covalent attachment of small protein Ub and polyUb chains to a range of cellular protein targets. The best documented Ub signaling pathway is the one that delivers polyUb proteins to the 26S proteasome for degradation. However, studies of molecular interactions involved in this process have been hampered by the transient and hydrophobic nature of these interactions and the lack of tools to study them. Here, we develop Ub-phototrap (UbPT), a synthetic Ub variant containing a photoactivatable crosslinking side chain. Enzymatic polymerization into chains of defined lengths and linkage types provided a set of reagents that led to identification of Rpn1 as a third proteasome ubiquitin-associating subunit that coordinates docking of substrate shuttles, unloading of substrates, and anchoring of polyUb conjugates. Our work demonstrates the value of UbPT, and we expect that its future uses will help define and investigate the ubiquitin interactome.
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Affiliation(s)
- Michal Chojnacki
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel; Department of Medical Biochemistry, Medical University of Łódź, Łódź, Poland
| | - Wissam Mansour
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Dharjath S Hameed
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands
| | - Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
| | - Farid El Oualid
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands
| | - Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada; Department of Structural Biology, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Mark A Nakasone
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Zanlin Yu
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Fabian Glaser
- The Technion Bioinformatics Knowledge Unit (BKU) of the Lorry Lokey Interdisciplinary Center for Life Sciences and Engineering, Technion-Israel Institute of Technology, 32000 Haifa, Israel
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, The University of Toronto, Toronto, ON M5S 1A8, Canada
| | - David Fushman
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA.
| | - Huib Ovaa
- Division of Cell Biology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, the Netherlands; Department of Chemical Immunology, Leiden University Medical Center, Einthovenweg 20, 2333 ZC Leiden, the Netherlands.
| | - Michael H Glickman
- Department of Biology, Technion-Israel Institute of Technology, 32000 Haifa, Israel.
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23
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Rao T, Gao R, Takada S, Al Abo M, Chen X, Walters KJ, Pommier Y, Aihara H. Novel TDP2-ubiquitin interactions and their importance for the repair of topoisomerase II-mediated DNA damage. Nucleic Acids Res 2016; 44:10201-10215. [PMID: 27543075 PMCID: PMC5137425 DOI: 10.1093/nar/gkw719] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 07/30/2016] [Accepted: 08/08/2016] [Indexed: 12/22/2022] Open
Abstract
Tyrosyl DNA phosphodiesterase 2 (TDP2) is a multifunctional protein implicated in DNA repair, signal transduction and transcriptional regulation. In its DNA repair role, TDP2 safeguards genome integrity by hydrolyzing 5′-tyrosyl DNA adducts formed by abortive topoisomerase II (Top2) cleavage complexes to allow error-free repair of DNA double-strand breaks, thereby conferring cellular resistance against Top2 poisons. TDP2 consists of a C-terminal catalytic domain responsible for its phosphodiesterase activity, and a functionally uncharacterized N-terminal region. Here, we demonstrate that this N-terminal region contains a ubiquitin (Ub)-associated (UBA) domain capable of binding multiple forms of Ub with distinct modes of interactions and preference for either K48- or K63-linked polyUbs over monoUb. The structure of TDP2 UBA bound to monoUb shows a canonical mode of UBA-Ub interaction. However, the absence of the highly conserved MGF motif and the presence of a fourth α-helix make TDP2 UBA distinct from other known UBAs. Mutations in the TDP2 UBA-Ub binding interface do not affect nuclear import of TDP2, but severely compromise its ability to repair Top2-mediated DNA damage, thus establishing the importance of the TDP2 UBA–Ub interaction in DNA repair. The differential binding to multiple Ub forms could be important for responding to DNA damage signals under different contexts or to support the multi-functionality of TDP2.
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Affiliation(s)
- Timsi Rao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Rui Gao
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Saeko Takada
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
| | - Muthana Al Abo
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Xiang Chen
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Kylie J Walters
- Protein Processing Section, Structural Biophysics Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Yves Pommier
- Laboratory of Molecular Pharmacology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, Minneapolis, MN 55455, USA
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Lan G, Tu Y. Information processing in bacteria: memory, computation, and statistical physics: a key issues review. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2016; 79:052601. [PMID: 27058315 PMCID: PMC4955840 DOI: 10.1088/0034-4885/79/5/052601] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Living systems have to constantly sense their external environment and adjust their internal state in order to survive and reproduce. Biological systems, from as complex as the brain to a single E. coli cell, have to process these data in order to make appropriate decisions. How do biological systems sense external signals? How do they process the information? How do they respond to signals? Through years of intense study by biologists, many key molecular players and their interactions have been identified in different biological machineries that carry out these signaling functions. However, an integrated, quantitative understanding of the whole system is still lacking for most cellular signaling pathways, not to say the more complicated neural circuits. To study signaling processes in biology, the key thing to measure is the input-output relationship. The input is the signal itself, such as chemical concentration, external temperature, light (intensity and frequency), and more complex signals such as the face of a cat. The output can be protein conformational changes and covalent modifications (phosphorylation, methylation, etc), gene expression, cell growth and motility, as well as more complex output such as neuron firing patterns and behaviors of higher animals. Due to the inherent noise in biological systems, the measured input-output dependence is often noisy. These noisy data can be analysed by using powerful tools and concepts from information theory such as mutual information, channel capacity, and the maximum entropy hypothesis. This information theory approach has been successfully used to reveal the underlying correlations between key components of biological networks, to set bounds for network performance, and to understand possible network architecture in generating observed correlations. Although the information theory approach provides a general tool in analysing noisy biological data and may be used to suggest possible network architectures in preserving information, it does not reveal the underlying mechanism that leads to the observed input-output relationship, nor does it tell us much about which information is important for the organism and how biological systems use information to carry out specific functions. To do that, we need to develop models of the biological machineries, e.g. biochemical networks and neural networks, to understand the dynamics of biological information processes. This is a much more difficult task. It requires deep knowledge of the underlying biological network-the main players (nodes) and their interactions (links)-in sufficient detail to build a model with predictive power, as well as quantitative input-output measurements of the system under different perturbations (both genetic variations and different external conditions) to test the model predictions to guide further development of the model. Due to the recent growth of biological knowledge thanks in part to high throughput methods (sequencing, gene expression microarray, etc) and development of quantitative in vivo techniques such as various florescence technology, these requirements are starting to be realized in different biological systems. The possible close interaction between quantitative experimentation and theoretical modeling has made systems biology an attractive field for physicists interested in quantitative biology. In this review, we describe some of the recent work in developing a quantitative predictive model of bacterial chemotaxis, which can be considered as the hydrogen atom of systems biology. Using statistical physics approaches, such as the Ising model and Langevin equation, we study how bacteria, such as E. coli, sense and amplify external signals, how they keep a working memory of the stimuli, and how they use these data to compute the chemical gradient. In particular, we will describe how E. coli cells avoid cross-talk in a heterogeneous receptor cluster to keep a ligand-specific memory. We will also study the thermodynamic costs of adaptation for cells to maintain an accurate memory. The statistical physics based approach described here should be useful in understanding design principles for cellular biochemical circuits in general.
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Affiliation(s)
- Ganhui Lan
- George Washington University, Washington DC 20052, USA
| | - Yuhai Tu
- IBM T. J. Watson Research Center, Yorktown Heights, NY 10598, USA
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25
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Isolation of ubiquitinated substrates by tandem affinity purification of E3 ligase-polyubiquitin-binding domain fusions (ligase traps). Nat Protoc 2016; 11:291-301. [PMID: 26766115 DOI: 10.1038/nprot.2016.008] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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.
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26
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Emmerich CH, Cohen P. Optimising methods for the preservation, capture and identification of ubiquitin chains and ubiquitylated proteins by immunoblotting. Biochem Biophys Res Commun 2015; 466:1-14. [PMID: 26325464 PMCID: PMC4709362 DOI: 10.1016/j.bbrc.2015.08.109] [Citation(s) in RCA: 88] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 08/24/2015] [Indexed: 12/31/2022]
Abstract
Immunoblotting is a powerful technique for the semi-quantitative analysis of ubiquitylation events, and remains the most commonly used method to study this process due to its high specificity, speed, sensitivity and relatively low cost. However, the ubiquitylation of proteins is complex and, when the analysis is performed in an inappropriate manner, it can lead to the misinterpretation of results and to erroneous conclusions being reached. Here we discuss the advantages and disadvantages of the methods currently in use to analyse ubiquitin chains and protein ubiquitylation, and describe the procedures that we have found to be most useful for optimising the quality and reliability of the data that we have generated. We also highlight commonly encountered problems and the pitfalls inherent in some of these methods. Finally, we introduce a set of recommendations to help researchers obtain high quality data, especially those new to the field of ubiquitin signalling. The specific topics addressed in this article include sample preparation, the separation, detection and identification of particular ubiquitin chains by immunoblotting, and the analysis of ubiquitin chain topology through the combined use of ubiquitin-binding proteins and ubiquitin linkage-specific deubiquitylases.
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Affiliation(s)
- Christoph H Emmerich
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom.
| | - Philip Cohen
- Medical Research Council Protein Phosphorylation and Ubiquitylation Unit, Sir James Black Centre, University of Dundee, Dundee DD1 5EH, Scotland, United Kingdom
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27
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Girard JR, Tenthorey JL, Morgan DO. An E2 accessory domain increases affinity for the anaphase-promoting complex and ensures E2 competition. J Biol Chem 2015; 290:24614-25. [PMID: 26306044 DOI: 10.1074/jbc.m115.678193] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Indexed: 11/06/2022] Open
Abstract
The anaphase-promoting complex/cyclosome (APC/C) is a member of the RING family of E3 ubiquitin ligases, which promote ubiquitin transfer from an E2 ubiquitin-conjugating enzyme to a substrate. In budding yeast, the APC/C collaborates with two E2s, Ubc4 and Ubc1, to promote the initiation and elongation, respectively, of polyubiquitin chains on the substrate. Ubc4 and Ubc1 are thought to compete for the same site on the APC/C, but it is not clear how their affinities are balanced. Here, we demonstrate that a C-terminal ubiquitin-associated (UBA) domain enhances the affinity of Ubc1 for the APC/C. Deletion of the UBA domain reduced apparent APC/C affinity for Ubc1 and decreased polyubiquitin chain length. Surprisingly, the positive effect of the UBA domain was not due to an interaction with the acceptor ubiquitin attached to the APC/C substrate or the donor ubiquitin attached to Ubc1 itself. Instead, our evidence suggests that the UBA domain binds to a site on the APC/C core, thereby increasing Ubc1 affinity and enhancing its ability to compete with Ubc4. The UBA domain is required for normal Ubc1 function and E2 competition in vivo. Thus, the UBA domain of Ubc1 ensures efficient polyubiquitination of substrate by balancing Ubc1 affinity with that of Ubc4.
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Affiliation(s)
- Juliet R Girard
- From the Departments of Physiology and Biochemistry and Biophysics and Tetrad Graduate Program, University of California, San Francisco, California 94143
| | | | - David O Morgan
- From the Departments of Physiology and Biochemistry and Biophysics and Tetrad Graduate Program, University of California, San Francisco, California 94143
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28
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Job F, Settele F, Lorey S, Rundfeldt C, Baumann L, Beck-Sickinger AG, Haupts U, Lilie H, Bosse-Doenecke E. Ubiquitin is a versatile scaffold protein for the generation of molecules with de novo binding and advantageous drug-like properties. FEBS Open Bio 2015; 5:579-93. [PMID: 26258013 PMCID: PMC4522466 DOI: 10.1016/j.fob.2015.07.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 01/17/2023] Open
Abstract
In the search for effective therapeutic strategies, protein-based biologicals are under intense development. While monoclonal antibodies represent the majority of these drugs, other innovative approaches are exploring the use of scaffold proteins for the creation of binding molecules with tailor-made properties. Ubiquitin is especially suited for this strategy due to several key characteristics. Ubiquitin is a natural serum protein, 100% conserved across the mammalian class and possesses high thermal, structural and proteolytic stability. Because of its small size and lack of posttranslational modifications, it can be easily produced in Escherichia coli. In this work we provide evidence that ubiquitin is safe as tested experimentally in vivo. In contrast to previously published results, we show that, in our hands, ubiquitin does not act as a functional ligand of the chemokine receptor CXCR4. Cellular assays based on different signaling pathways of the receptor were conducted with the natural agonist SDF-1 as a benchmark. In none of the assays could a response to ubiquitin treatment be elicited. Furthermore, intravenous application to mice at high concentrations did not induce any detectable effect on cytokine levels or hematological parameters.
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Affiliation(s)
- Florian Job
- Institute for Biochemistry and Biotechnology/Technical Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Florian Settele
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Susan Lorey
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Chris Rundfeldt
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Lars Baumann
- Institute of Biochemistry, University of Leipzig, Brüderstraße 34, D-04103 Leipzig, Germany
| | | | - Ulrich Haupts
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
| | - Hauke Lilie
- Institute for Biochemistry and Biotechnology/Technical Biochemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Straße 3, D-06120 Halle (Saale), Germany
| | - Eva Bosse-Doenecke
- Scil Proteins GmbH, Heinrich-Damerow-Straße 1, D-06120 Halle (Saale), Germany
- Corresponding author. Tel.: +49 345 4780 365; fax: +49 345 27996 332.
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29
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Budhidarmo R, Day CL. IAPs: Modular regulators of cell signalling. Semin Cell Dev Biol 2014; 39:80-90. [PMID: 25542341 DOI: 10.1016/j.semcdb.2014.12.002] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 12/17/2014] [Indexed: 01/30/2023]
Abstract
Members of the inhibitor of apoptosis (IAP) family are characterised by the presence of at least one baculoviral IAP repeat (BIR) domain. However, during the course of evolution, other globular modules have been adopted to perform distinct functions. Consequently, the IAP family is now recognised as consisting of members that perform critical functions in different aspects of cellular regulation. In this review, the structural diversity present within the IAP protein family is presented. Known structures of individual domains are discussed and their properties are described in light of recent data. In particular the plasticity of BIR domains and their ability to accommodate different binding partners is highlighted, as well as the importance of communication between the domains in regulating the covalent attachment of ubiquitin.
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Affiliation(s)
- Rhesa Budhidarmo
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand.
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30
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Hopper JTS, Robinson CV. Mass spectrometry quantifies protein interactions--from molecular chaperones to membrane porins. Angew Chem Int Ed Engl 2014; 53:14002-15. [PMID: 25354304 DOI: 10.1002/anie.201403741] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Indexed: 12/16/2022]
Abstract
Proteins possess an intimate relationship between their structure and function, with folded protein structures generating recognition motifs for the binding of ligands and other proteins. Mass spectrometry (MS) can provide information on a number of levels of protein structure, from the primary amino acid sequence to its three-dimensional fold and quaternary interactions. Given that MS is a gas-phase technique, with its foundations in analytical chemistry, it is perhaps counter-intuitive to use it to study the structure and non-covalent interactions of proteins that form in solution. Herein we show, however, that MS can go beyond simply preserving protein interactions in the gas phase by providing new insight into dynamic interaction networks, dissociation mechanisms, and the cooperativity of ligand binding. We consider potential pitfalls in data interpretation and place particular emphasis on recent studies that revealed quantitative information about dynamic protein interactions, in both soluble and membrane-embedded assemblies.
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Affiliation(s)
- Jonathan T S Hopper
- Physical and Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ (UK)
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31
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Erpapazoglou Z, Walker O, Haguenauer-Tsapis R. Versatile roles of k63-linked ubiquitin chains in trafficking. Cells 2014; 3:1027-88. [PMID: 25396681 PMCID: PMC4276913 DOI: 10.3390/cells3041027] [Citation(s) in RCA: 131] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 10/14/2014] [Accepted: 10/21/2014] [Indexed: 12/11/2022] Open
Abstract
Modification by Lys63-linked ubiquitin (UbK63) chains is the second most abundant form of ubiquitylation. In addition to their role in DNA repair or kinase activation, UbK63 chains interfere with multiple steps of intracellular trafficking. UbK63 chains decorate many plasma membrane proteins, providing a signal that is often, but not always, required for their internalization. In yeast, plants, worms and mammals, this same modification appears to be critical for efficient sorting to multivesicular bodies and subsequent lysosomal degradation. UbK63 chains are also one of the modifications involved in various forms of autophagy (mitophagy, xenophagy, or aggrephagy). Here, in the context of trafficking, we report recent structural studies investigating UbK63 chains assembly by various E2/E3 pairs, disassembly by deubiquitylases, and specifically recognition as sorting signals by receptors carrying Ub-binding domains, often acting in tandem. In addition, we address emerging and unanticipated roles of UbK63 chains in various recycling pathways that function by activating nucleators required for actin polymerization, as well as in the transient recruitment of signaling molecules at the plasma or ER membrane. In this review, we describe recent advances that converge to elucidate the mechanisms underlying the wealth of trafficking functions of UbK63 chains.
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Affiliation(s)
- Zoi Erpapazoglou
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
| | - Olivier Walker
- Institut des Sciences Analytiques, UMR5280, Université de Lyon/Université Lyon 1, 69100 Villeurbanne, France.
| | - Rosine Haguenauer-Tsapis
- Institut Jacques Monod-CNRS, UMR 7592, Université-Paris Diderot, Sorbonne Paris Cité, F-75205 Paris, France.
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32
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Hopper JTS, Robinson CV. Massenspektrometrie zur Quantifizierung von Wechselwirkungen zwischen Proteinen - von molekularen Chaperonen zu Membranporinen. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201403741] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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33
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Budhidarmo R, Day CL. The ubiquitin-associated domain of cellular inhibitor of apoptosis proteins facilitates ubiquitylation. J Biol Chem 2014; 289:25721-36. [PMID: 25065467 DOI: 10.1074/jbc.m113.545475] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
The cellular inhibitor of apoptosis (cIAP) proteins are essential RING E3 ubiquitin ligases that regulate apoptosis and inflammatory responses. cIAPs contain a ubiquitin-associated (UBA) domain that binds ubiquitin and is implicated in the regulation of cell survival and proteasomal degradation. Here we show that mutation of the MGF and LL motifs in the UBA domain of cIAP1 caused unfolding and increased cIAP1 multimonoubiquitylation. By developing a UBA mutant that disrupted ubiquitin binding but not the structure of the UBA domain, we found that the UBA domain enhances cIAP1 and cIAP2 ubiquitylation. We demonstrate that the UBA domain binds to the UbcH5b∼Ub conjugate, and this promotes RING domain-dependent monoubiquitylation. This study establishes ubiquitin-binding modules, such as the UBA domain, as important regulatory modules that can fine tune the activity of E3 ligases.
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Affiliation(s)
- Rhesa Budhidarmo
- From the Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Catherine L Day
- From the Department of Biochemistry, Otago School of Medical Sciences, University of Otago, Dunedin 9054, New Zealand
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34
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Kinase and channel activity of TRPM6 are co-ordinated by a dimerization motif and pocket interaction. Biochem J 2014; 460:165-75. [PMID: 24650431 PMCID: PMC4019984 DOI: 10.1042/bj20131639] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mutations in the gene that encodes the atypical channel-kinase TRPM6 (transient receptor potential melastatin 6) cause HSH (hypomagnesaemia with secondary hypocalcaemia), a disorder characterized by defective intestinal Mg2+ transport and impaired renal Mg2+ reabsorption. TRPM6, together with its homologue TRPM7, are unique proteins as they combine an ion channel domain with a C-terminally fused protein kinase domain. How TRPM6 channel and kinase activity are linked is unknown. Previous structural analysis revealed that TRPM7 possesses a non-catalytic dimerization motif preceding the kinase domain. This interacts with a dimerization pocket lying within the kinase domain. In the present study, we provide evidence that the dimerization motif in TRPM6 plays a critical role in regulating kinase activity as well as ion channel activity. We identify mutations within the TRPM6 dimerization motif (Leu1718 and Leu1721) or dimerization pocket (L1743A, Q1832K, A1836N, L1840A and L1919Q) that abolish dimerization and establish that these mutations inhibit protein kinase activity. We also demonstrate that kinase activity of a dimerization motif mutant can be restored by addition of a peptide encompassing the dimerization motif. Moreover, we observe that mutations that disrupt the dimerization motif and dimerization pocket interaction greatly diminish TRPM6 ion channel activity, in a manner that is independent of kinase activity. Finally, we analyse the impact on kinase activity of ten disease-causing missense mutations that lie outwith the protein kinase domain of TRPM6. This revealed that one mutation lying nearby the dimerization motif (S1754N), found previously to inhibit channel activity, abolished kinase activity. These results provide the first evidence that there is structural co-ordination between channel and kinase activity, which is mediated by the dimerization motif and pocket interaction. We discuss that modulation of this interaction could comprise a major regulatory mechanism by which TRPM6 function is controlled. We show that TRPM6 kinase activity is linked to channel activity. This occurs through a kinase-independent mechanism involving the dimerization motif binding to a pocket within the kinase domain. A disease-causing mutation (S1754N) lying nearby the dimerization pocket inactivates kinase activity.
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35
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Walinda E, Morimoto D, Sugase K, Konuma T, Tochio H, Shirakawa M. Solution structure of the ubiquitin-associated (UBA) domain of human autophagy receptor NBR1 and its interaction with ubiquitin and polyubiquitin. J Biol Chem 2014; 289:13890-902. [PMID: 24692539 DOI: 10.1074/jbc.m114.555441] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
NBR1 (neighbor of BRCA1 gene 1) is a protein commonly found in ubiquitin-positive inclusions in neurodegenerative diseases. Due to its high architectural similarity to the well studied autophagy receptor protein p62/SQSTM1, NBR1 has been thought to analogously bind to ubiquitin-marked autophagic substrates via its C-terminal ubiquitin-associated (UBA) domain and deliver them to autophagosomes for degradation. Unexpectedly, we find that NBR1 differs from p62 in its UBA structure and accordingly in its interaction with ubiquitin. Structural differences are observed on helix α-3, which is tilted farther from helix α-2 and extended by approximately one turn in NBR1. This results not only in inhibition of a p62-type self-dimerization of NBR1 UBA but also in a significantly higher affinity for monoubiquitin as compared with p62 UBA. Importantly, the NBR1 UBA-ubiquitin complex structure shows that the negative charge of the side chain in front of the conserved MGF motif in the UBA plays an integral role in the recognition of ubiquitin. In addition, NMR and isothermal titration calorimetry experiments show that NBR1 UBA binds to each monomeric unit of polyubiquitin with similar affinity and by the same surface used for binding to monoubiquitin. This indicates that NBR1 lacks polyubiquitin linkage-type specificity, in good agreement with the nonspecific linkages observed in intracellular ubiquitin-positive inclusions. Consequently, our results demonstrate that the structural differences between NBR1 UBA and p62 UBA result in a much higher affinity of NBR1 for ubiquitin, which in turn suggests that NBR1 may form intracellular inclusions with ubiquitylated autophagic substrates more efficiently than p62.
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Affiliation(s)
- Erik Walinda
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
| | - Daichi Morimoto
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
| | - Kenji Sugase
- the Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
| | - Tsuyoshi Konuma
- the Bioorganic Research Institute, Suntory Foundation for Life Sciences, Osaka 618-8503, Japan
| | - Hidehito Tochio
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
| | - Masahiro Shirakawa
- From the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan and
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36
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Mark KG, Simonetta M, Maiolica A, Seller CA, Toczyski DP. Ubiquitin ligase trapping identifies an SCF(Saf1) pathway targeting unprocessed vacuolar/lysosomal proteins. Mol Cell 2014; 53:148-61. [PMID: 24389104 DOI: 10.1016/j.molcel.2013.12.003] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Revised: 11/15/2013] [Accepted: 11/26/2013] [Indexed: 12/31/2022]
Abstract
We have developed a technique, called Ubiquitin Ligase Substrate Trapping, for the isolation of ubiquitinated substrates in complex with their ubiquitin ligase (E3). By fusing a ubiquitin-associated (UBA) domain to an E3 ligase, we were able to selectively purify the polyubiquitinated forms of E3 substrates. Using ligase traps of eight different F box proteins (SCF specificity factors) coupled with mass spectrometry, we identified known, as well as previously unreported, substrates. Polyubiquitinated forms of candidate substrates associated with their cognate F box partner, but not other ligase traps. Interestingly, the four most abundant candidate substrates identified for the F box protein Saf1 were all vacuolar/lysosomal proteins. Analysis of one of these substrates, Prb1, showed that Saf1 selectively promotes ubiquitination of the unprocessed form of the zymogen. This suggests that Saf1 is part of a pathway that targets protein precursors for proteasomal degradation.
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Affiliation(s)
- Kevin G Mark
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Marco Simonetta
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - Alessio Maiolica
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich CH-8093, Switzerland
| | - Charles A Seller
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA
| | - David P Toczyski
- Department of Biochemistry and Biophysics, Helen Diller Family Comprehensive Cancer Center, San Francisco, CA 94158, USA.
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37
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Middleton AJ, Budhidarmo R, Day CL. Use of E2~Ubiquitin Conjugates for the Characterization of Ubiquitin Transfer by RING E3 Ligases Such as the Inhibitor of Apoptosis Proteins. Methods Enzymol 2014; 545:243-63. [DOI: 10.1016/b978-0-12-801430-1.00010-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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38
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Ngadjeua F, Chiaravalli J, Traincard F, Raynal B, Fontan E, Agou F. Two-sided ubiquitin binding of NF-κB essential modulator (NEMO) zinc finger unveiled by a mutation associated with anhidrotic ectodermal dysplasia with immunodeficiency syndrome. J Biol Chem 2013; 288:33722-33737. [PMID: 24100029 DOI: 10.1074/jbc.m113.483305] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Hypomorphic mutations in the X-linked human NEMO gene result in various forms of anhidrotic ectodermal dysplasia with immunodeficiency. NEMO function is mediated by two distal ubiquitin binding domains located in the regulatory C-terminal domain of the protein: the coiled-coil 2-leucine zipper (CC2-LZ) domain and the zinc finger (ZF) domain. Here, we investigated the effect of the D406V mutation found in the NEMO ZF of an ectodermal dysplasia with immunodeficiency patients. This point mutation does not impair the folding of NEMO ZF or mono-ubiquitin binding but is sufficient to alter NEMO function, as NEMO-deficient fibroblasts and Jurkat T lymphocytes reconstituted with full-length D406V NEMO lead to partial and strong defects in NF-κB activation, respectively. To further characterize the ubiquitin binding properties of NEMO ZF, we employed di-ubiquitin (di-Ub) chains composed of several different linkages (Lys-48, Lys-63, and linear (Met-1-linked)). We showed that the pathogenic mutation preferentially impairs the interaction with Lys-63 and Met-1-linked di-Ub, which correlates with its ubiquitin binding defect in vivo. Furthermore, sedimentation velocity and gel filtration showed that NEMO ZF, like other NEMO related-ZFs, binds mono-Ub and di-Ub with distinct stoichiometries, indicating the presence of a new Ub site within the NEMO ZF. Extensive mutagenesis was then performed on NEMO ZF and characterization of mutants allowed the proposal of a structural model of NEMO ZF in interaction with a Lys-63 di-Ub chain.
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Affiliation(s)
- Flora Ngadjeua
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France; Université Pierre et Marie Curie, Cellule Pasteur UPMC, rue du Dr. Roux 75015 Paris, France
| | - Jeanne Chiaravalli
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - François Traincard
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Bertrand Raynal
- Plateforme de Biophysique des Macromolécules et de leurs Interactions, Institut Pasteur, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Elisabeth Fontan
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France
| | - Fabrice Agou
- Institut Pasteur, Unité de Biochimie Structurale et Cellulaire, Department of Structural Biology and Chemistry, CNRS, UMR 3528, 25/28 rue du Dr. Roux 75724 Paris cedex 15, France.
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Ehlinger A, Walters KJ. Structural insights into proteasome activation by the 19S regulatory particle. Biochemistry 2013; 52:3618-28. [PMID: 23672618 DOI: 10.1021/bi400417a] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Since its discovery in the late 1970s, the ubiquitin-proteasome system (UPS) has become recognized as the major pathway for regulated cellular proteolysis. Processes such as cell cycle control, pathogen resistance, and protein quality control rely on selective protein degradation at the proteasome for homeostatic function. Perhaps as a consequence of the importance of this pathway, and the genesis of severe diseases upon its dysregulation, protein degradation by the UPS is highly controlled from the level of substrate recognition to proteolysis. Technological advances over the past decade have created an explosion of structural and mechanistic information that has underscored the complexity of the proteasome and its upstream regulatory factors. Significant insights have come from the study of the 19S proteasome regulatory particle (RP) responsible for recognition and processing of ubiquitinated substrates destined for proteolysis. Established as a highly dynamic proteasome activator, the RP has a large number of both permanent and transient components with specialized functional roles that are critical for proteasome function. In this review, we highlight recent mechanistic developments in the study of proteasome activation by the RP and how they provide context to our current understanding of the UPS.
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Affiliation(s)
- Aaron Ehlinger
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota , Minneapolis, Minnesota 55455, United States
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Dimerization and ubiquitin mediated recruitment of A20, a complex deubiquitinating enzyme. Immunity 2013; 38:896-905. [PMID: 23602765 DOI: 10.1016/j.immuni.2013.03.008] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 03/27/2013] [Indexed: 01/10/2023]
Abstract
A20 is an anti-inflammatory protein linked to multiple human autoimmune diseases and lymphomas. A20 possesses a deubiquitinating motif and a zinc finger, ZF4, that binds ubiquitin and supports its E3 ubiquitin ligase activity. To understand how these activities mediate A20's physiological functions, we generated two lines of gene-targeted mice, abrogating either A20's deubiquitinating activity (Tnfaip3(OTU) mice) or A20's ZF4 (Tnfaip3(ZF4) mice). Both Tnfaip3(OTU) and Tnfaip3(ZF4) mice exhibited increased responses to TNF and sensitivity to colitis. A20's C103 deubiquitinating motif restricted both K48- and K63-linked ubiquitination of receptor interacting protein 1 (RIP1). A20's ZF4 was required for recruiting A20 to ubiquitinated RIP1. A20(OTU) proteins and A20(ZF4) proteins complemented each other to regulate RIP1 ubiquitination and NFκB signaling normally in compound mutant Tnfaip3(OTU/ZF4) cells. This complementation involved homodimerization of A20 proteins, and we have defined an extensive dimerization interface in A20. These studies reveal how A20 proteins collaborate to restrict TNF signaling.
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41
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De Biasio A, Blanco FJ. Proliferating Cell Nuclear Antigen Structure and Interactions. PROTEIN-NUCLEIC ACIDS INTERACTIONS 2013; 91:1-36. [DOI: 10.1016/b978-0-12-411637-5.00001-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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42
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Proliferating cell nuclear antigen (PCNA) interactions in solution studied by NMR. PLoS One 2012; 7:e48390. [PMID: 23139781 PMCID: PMC3491057 DOI: 10.1371/journal.pone.0048390] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Accepted: 09/24/2012] [Indexed: 01/25/2023] Open
Abstract
PCNA is an essential factor for DNA replication and repair. It forms a ring shaped structure of 86 kDa by the symmetric association of three identical protomers. The ring encircles the DNA and acts as a docking platform for other proteins, most of them containing the PCNA Interaction Protein sequence (PIP-box). We have used NMR to characterize the interactions of PCNA with several other proteins and fragments in solution. The binding of the PIP-box peptide of the cell cycle inhibitor p21 to PCNA is consistent with the crystal structure of the complex. A shorter p21 peptide binds with reduced affinity but retains most of the molecular recognition determinants. However the binding of the corresponding peptide of the tumor suppressor ING1 is extremely weak, indicating that slight deviations from the consensus PIP-box sequence dramatically reduce the affinity for PCNA, in contrast with a proposed less stringent PIP-box sequence requirement. We could not detect any binding between PCNA and the MCL-1 or the CDK2 protein, reported to interact with PCNA in biochemical assays. This suggests that they do not bind directly to PCNA, or they do but very weakly, with additional unidentified factors stabilizing the interactions in the cell. Backbone dynamics measurements show three PCNA regions with high relative flexibility, including the interdomain connector loop (IDCL) and the C-terminus, both of them involved in the interaction with the PIP-box. Our work provides the basis for high resolution studies of direct ligand binding to PCNA in solution.
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Singh RK, Zerath S, Kleifeld O, Scheffner M, Glickman MH, Fushman D. Recognition and cleavage of related to ubiquitin 1 (Rub1) and Rub1-ubiquitin chains by components of the ubiquitin-proteasome system. Mol Cell Proteomics 2012; 11:1595-611. [PMID: 23105008 DOI: 10.1074/mcp.m112.022467] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Of all ubiquitin-like proteins, Rub1 (Nedd8 in mammals) is the closest kin of ubiquitin. We show via NMR that structurally, Rub1 and ubiquitin are fundamentally similar as well. Despite these profound similarities, the prevalence of Rub1/Nedd8 and of ubiquitin as modifiers of the proteome is starkly different, and their attachments to specific substrates perform different functions. Recently, some proteins, including p53, p73, EGFR, caspase-7, and Parkin, have been shown to be modified by both Rub1/Nedd8 and ubiquitin within cells. To understand whether and how it might be possible to distinguish among the same target protein modified by Rub1 or ubiquitin or both, we examined whether ubiquitin receptors can differentiate between Rub1 and ubiquitin. Surprisingly, Rub1 interacts with proteasome ubiquitin-shuttle proteins comparably to ubiquitin but binds more weakly to a proteasomal ubiquitin receptor Rpn10. We identified Rub1-ubiquitin heteromers in yeast and Nedd8-Ub heteromers in human cells. We validate that in human cells and in vitro, human Rub1 (Nedd8) forms chains with ubiquitin where it acts as a chain terminator. Interestingly, enzymatically assembled K48-linked Rub1-ubiquitin heterodimers are recognized by various proteasomal ubiquitin shuttles and receptors comparably to K48-linked ubiquitin homodimers. Furthermore, these heterologous chains are cleaved by COP9 signalosome or 26S proteasome. A derubylation function of the proteasome expands the repertoire of its enzymatic activities. In contrast, Rub1 conjugates may be somewhat resilient to the actions of other canonical deubiquitinating enzymes. Taken together, these findings suggest that once Rub1/Nedd8 is channeled into ubiquitin pathways, it is recognized essentially like ubiquitin.
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Affiliation(s)
- Rajesh K Singh
- Department of Chemistry and Biochemistry, Center for Biomolecular Structure and Organization, University of Maryland, College Park, MD 20742, USA
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44
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Structural insights into specificity and diversity in mechanisms of ubiquitin recognition by ubiquitin-binding domains. Biochem Soc Trans 2012; 40:404-8. [PMID: 22435820 DOI: 10.1042/bst20110729] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
UBDs [Ub (ubiquitin)-binding domains], which are typically small protein motifs of <50 residues, are used by receptor proteins to transduce post-translational Ub modifications in a wide range of biological processes, including NF-κB (nuclear factor κB) signalling and proteasomal degradation pathways. More than 20 families of UBDs have now been characterized in structural detail and, although many recognize the canonical Ile44/Val70-binding patch on Ub, a smaller number have alternative Ub-recognition sites. The A20 Znf (A20-like zinc finger) of the ZNF216 protein is one of the latter and binds with high affinity to a polar site on Ub centred around Asp58/Gln62. ZNF216 shares some biological function with p62, with both linked to NF-κB signal activation and as shuttle proteins in proteasomal degradation pathways. The UBA domain (Ub-associated domain) of p62, although binding to Ub through the Ile44/Val70 patch, is unique in forming a stable dimer that negatively regulates Ub recognition. We show that the A20 Znf and UBA domain are able to form a ternary complex through independent interactions with a single Ub molecule, supporting functional models for Ub as a 'hub' for mediating multi-protein complex assembly and for enhancing signalling specificity.
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Agromayor M, Soler N, Caballe A, Kueck T, Freund SM, Allen MD, Bycroft M, Perisic O, Ye Y, McDonald B, Scheel H, Hofmann K, Neil SJD, Martin-Serrano J, Williams RL. The UBAP1 subunit of ESCRT-I interacts with ubiquitin via a SOUBA domain. Structure 2012; 20:414-28. [PMID: 22405001 PMCID: PMC3314968 DOI: 10.1016/j.str.2011.12.013] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 12/13/2011] [Accepted: 12/30/2011] [Indexed: 11/23/2022]
Abstract
The endosomal sorting complexes required for transport (ESCRTs) facilitate endosomal sorting of ubiquitinated cargo, MVB biogenesis, late stages of cytokinesis, and retroviral budding. Here we show that ubiquitin associated protein 1 (UBAP1), a subunit of human ESCRT-I, coassembles in a stable 1:1:1:1 complex with Vps23/TSG101, VPS28, and VPS37. The X-ray crystal structure of the C-terminal region of UBAP1 reveals a domain that we describe as a solenoid of overlapping UBAs (SOUBA). NMR analysis shows that each of the three rigidly arranged overlapping UBAs making up the SOUBA interact with ubiquitin. We demonstrate that UBAP1-containing ESCRT-I is essential for degradation of antiviral cell-surface proteins, such as tetherin (BST-2/CD317), by viral countermeasures, namely, the HIV-1 accessory protein Vpu and the Kaposi sarcoma-associated herpesvirus (KSHV) ubiquitin ligase K5.
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Affiliation(s)
- Monica Agromayor
- Department of Infectious Diseases, King's College London School of Medicine, London SE1 9RT, UK
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Lai MY, Zhang D, Laronde-Leblanc N, Fushman D. Structural and biochemical studies of the open state of Lys48-linked diubiquitin. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2012; 1823:2046-56. [PMID: 22542781 DOI: 10.1016/j.bbamcr.2012.04.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Revised: 04/10/2012] [Accepted: 04/11/2012] [Indexed: 01/05/2023]
Abstract
Ubiquitin (Ub) is a small protein highly conserved among eukaryotes and involved in practically all aspects of eukaryotic cell biology. Polymeric chains assembled from covalently-linked Ub monomers function as molecular signals in the regulation of a host of cellular processes. Our previous studies have shown that the predominant state of Lys48-linked di- and tetra-Ub chains at near-physiological conditions is a closed conformation, in which the Ub-Ub interface is formed by the hydrophobic surface residues of the adjacent Ub units. Because these very residues are involved in (poly)Ub interactions with the majority of Ub-binding proteins, their sequestration at the Ub-Ub interface renders the closed conformation of polyUb binding incompetent. Thus the existence of open conformation(s) and the interdomain motions opening and closing the Ub-Ub interface is critical for the recognition of Lys48-linked polyUb by its receptors. Knowledge of the conformational properties of a polyUb signal is essential for our understanding of its specific recognition by various Ub-receptors. Despite their functional importance, open states of Lys48-linked chains are poorly characterized. Here we report a crystal structure of the open state of Lys48-linked di-Ub. Moreover, using NMR, we examined interactions of the open state of this chain (at pH4.5) with a Lys48-linkage-selective receptor, the UBA2 domain of a shuttle protein hHR23a. Our results show that di-Ub binds UBA2 in the same mode and with comparable affinity as the closed state. Our data suggest a mechanism for polyUb signal recognition, whereby Ub-binding proteins select specific conformations out of the available ensemble of polyUb chain conformations. This article is part of a Special Issue entitled: Ubiquitin Drug Discovery and Diagnostics.
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Affiliation(s)
- Ming-Yih Lai
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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47
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Abstract
The posttranslational modification with ubiquitin, a process referred to as ubiquitylation, controls almost every process in cells. Ubiquitin can be attached to substrate proteins as a single moiety or in the form of polymeric chains in which successive ubiquitin molecules are connected through specific isopeptide bonds. Reminiscent of a code, the various ubiquitin modifications adopt distinct conformations and lead to different outcomes in cells. Here, we discuss the structure, assembly, and function of this ubiquitin code.
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Affiliation(s)
- David Komander
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, CB2 0QH, United Kingdom.
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48
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Husnjak K, Dikic I. Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu Rev Biochem 2012; 81:291-322. [PMID: 22482907 DOI: 10.1146/annurev-biochem-051810-094654] [Citation(s) in RCA: 569] [Impact Index Per Article: 47.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ubiquitin acts as a versatile cellular signal that controls a wide range of biological processes including protein degradation, DNA repair, endocytosis, autophagy, transcription, immunity, and inflammation. The specificity of ubiquitin signaling is achieved by alternative conjugation signals (monoubiquitin and ubiquitin chains) and interactions with ubiquitin-binding proteins (known as ubiquitin receptors) that decode ubiquitinated target signals into biochemical cascades in the cell. Herein, we review the current knowledge pertaining to the structural and functional features of ubiquitin-binding proteins and the mechanisms by which they recognize various types of ubiquitin topologies. The combinatorial use of diverse ubiquitin-binding domains (UBDs) in full-length proteins, selective recognition of chains with distinct linkages and length, and posttranslational modifications of ubiquitin receptors or multivalent interactions within protein complexes illustrate a few mechanisms by which a circuitry of signaling networks can be rewired by ubiquitin-binding proteins to control cellular functions in vivo.
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Affiliation(s)
- Koraljka Husnjak
- Institute of Biochemistry II, School of Medicine, Goethe University, 60590 Frankfurt am Main, Germany.
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49
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Sokratous K, Roach LV, Channing D, Strachan J, Long J, Searle MS, Layfield R, Oldham NJ. Probing Affinity and Ubiquitin Linkage Selectivity of Ubiquitin-Binding Domains Using Mass Spectrometry. J Am Chem Soc 2012; 134:6416-24. [DOI: 10.1021/ja300749d] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Kleitos Sokratous
- School of Chemistry, University of Nottingham, University Park NG7 2RD,
U.K
| | - Lucy V. Roach
- School of Chemistry, University of Nottingham, University Park NG7 2RD,
U.K
| | - Debora Channing
- School of Biomedical
Sciences,
Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
| | - Joanna Strachan
- School of Biomedical
Sciences,
Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
| | - Jed Long
- Centre for Biomolecular Sciences,
School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Mark S. Searle
- Centre for Biomolecular Sciences,
School of Chemistry, University Park, University of Nottingham, Nottingham NG7 2RD, U.K
| | - Robert Layfield
- School of Biomedical
Sciences,
Queen’s Medical Centre, University of Nottingham, Nottingham NG7 2UH, U.K
| | - Neil J. Oldham
- School of Chemistry, University of Nottingham, University Park NG7 2RD,
U.K
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50
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Sims JJ, Scavone F, Cooper EM, Kane LA, Youle RJ, Boeke JD, Cohen RE. Polyubiquitin-sensor proteins reveal localization and linkage-type dependence of cellular ubiquitin signaling. Nat Methods 2012; 9:303-9. [PMID: 22306808 PMCID: PMC3438894 DOI: 10.1038/nmeth.1888] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 01/03/2012] [Indexed: 11/25/2022]
Abstract
Polyubiquitin (polyUb) chain topology is thought to direct modified substrates to specific fates, but this function-topology relationship is poorly understood, as are the dynamics and subcellular locations of specific polyUb signals. Experimental access to these questions has been limited because linkage-specific inhibitors and in vivo sensors have been unavailable. Here we present a general strategy to track linkage-specific polyUb signals in yeast and mammalian cells, and to probe their functions. We designed several high-affinity lysine-63-polyUb-binding proteins and demonstrate their specificity both in vitro and in cells. We apply these tools as competitive inhibitors to dissect the polyUb-linkage dependence of NF-κB activation in several cell types, inferring the essential role of lysine-63-polyUb for signaling via the IL-1β and TNF-related weak inducer of apoptosis (TWEAK) but not TNF-α receptors. We anticipate live-cell imaging, proteomic, and biochemical applications for these tools, and extension of the design strategy to other polymeric ubiquitin-like protein modifications.
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Affiliation(s)
- Joshua J Sims
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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