Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling
Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of e...
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| Veröffentlicht in: | Molecular cell 2017-10, Vol.68 (1), p.233-246.e5 |
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| creator | Michel, Martin A. Swatek, Kirby N. Hospenthal, Manuela K. Komander, David |
| description | Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific “affimer” reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
[Display omitted]
•Respective linkage-specific affimers recognize K6- or K33-/K11-linked chains•Structures of affimer:diUb complexes reveal mechanisms of linkage specificity•Improved affimers can be used in western blotting, confocal microscopy, and pull-downs•Pull-downs with K6-specific affimers reveal HUWE1 to be a major K6 ligase in cells
Michel et al. describe linkage-specific tools for the study of atypical K6 and K33/K11 ubiquitin linkages. Affimers have applications in western blotting, confocal microscopy, and pull-downs. Using a K6-specific affimer, they reveal that HUWE1 is a major source of cellular K6 chains and decorates Mfn2 with K6 chains. |
| doi_str_mv | 10.1016/j.molcel.2017.08.020 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_5640506</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><els_id>S1097276517306172</els_id><sourcerecordid>2067276796</sourcerecordid><originalsourceid>FETCH-LOGICAL-c496t-bdb9e9586d2bc1887014bbd30637719019d1a837626159297b40d38861eec4693</originalsourceid><addsrcrecordid>eNqFUU1v1DAQtRCIloV_gFCOXBJsx_HHBamqClSshEQpV8uxJ-ksibO1syvx78lqlxYucJqR5r03M-8R8prRilEm322qcRo8DBWnTFVUV5TTJ-ScUaNKwaR4euq5ks0ZeZHzhlImGm2ekzOujahrxs_J99sW73c4YyzWGH-4HsqbLXjs0BcXXYcjpFx8hT24obiOGfu7ORcY56n4LMsDA0LxKHGDfXQDxv4leda5IcOrU12R2w9X3y4_lesvH68vL9alF0bOZRtaA6bRMvDWM63VcmHbhprKWilmKDOBOV0rySVrDDeqFTTUWksG4IU09Yq8P-pud-0IwUOckxvsNuHo0k87ObR_TyLe2X7a20YK2ixrVuTtSSBN9zvIsx0xL64OLsK0y5ZTqRYHlfk_lBnBFaO8PkDFEerTlHOC7uEiRu0hPbuxx_TsIT1LtV3SW2hv_vzmgfQ7rsd3YfF0j5Bs9gjRQ8AEfrZhwn9v-AXvVKzK</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>1942710236</pqid></control><display><type>article</type><title>Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling</title><source>MEDLINE</source><source>Cell Press Free Archives</source><source>Elsevier ScienceDirect Journals</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Free Full-Text Journals in Chemistry</source><creator>Michel, Martin A. ; Swatek, Kirby N. ; Hospenthal, Manuela K. ; Komander, David</creator><creatorcontrib>Michel, Martin A. ; Swatek, Kirby N. ; Hospenthal, Manuela K. ; Komander, David</creatorcontrib><description>Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific “affimer” reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
[Display omitted]
•Respective linkage-specific affimers recognize K6- or K33-/K11-linked chains•Structures of affimer:diUb complexes reveal mechanisms of linkage specificity•Improved affimers can be used in western blotting, confocal microscopy, and pull-downs•Pull-downs with K6-specific affimers reveal HUWE1 to be a major K6 ligase in cells
Michel et al. describe linkage-specific tools for the study of atypical K6 and K33/K11 ubiquitin linkages. Affimers have applications in western blotting, confocal microscopy, and pull-downs. Using a K6-specific affimer, they reveal that HUWE1 is a major source of cellular K6 chains and decorates Mfn2 with K6 chains.</description><identifier>ISSN: 1097-2765</identifier><identifier>EISSN: 1097-4164</identifier><identifier>DOI: 10.1016/j.molcel.2017.08.020</identifier><identifier>PMID: 28943312</identifier><language>eng</language><publisher>United States: Elsevier Inc</publisher><subject>affimer ; Amino Acid Motifs ; antibodies ; Binding Sites ; Carrier Proteins - chemistry ; Carrier Proteins - genetics ; Carrier Proteins - metabolism ; Cell Line, Tumor ; Cloning, Molecular ; cross reaction ; crystal structure ; Crystallography, X-Ray ; Escherichia coli - genetics ; Escherichia coli - metabolism ; fluorescence microscopy ; Gene Expression ; GTP Phosphohydrolases - chemistry ; GTP Phosphohydrolases - genetics ; GTP Phosphohydrolases - metabolism ; HEK293 Cells ; HeLa Cells ; Humans ; HUWE1 ; Kinetics ; Lys6-linked ubiquitin chains ; Lysine - chemistry ; Lysine - metabolism ; Mfn2 ; microscale thermophoresis ; Mitochondrial Proteins - chemistry ; Mitochondrial Proteins - genetics ; Mitochondrial Proteins - metabolism ; mitophagy ; Models, Molecular ; Molecular Probes - chemistry ; Parkin ; post-translational modification ; Protein Binding ; Protein Interaction Domains and Motifs ; Protein Processing, Post-Translational ; Protein Structure, Secondary ; Recombinant Proteins - chemistry ; Recombinant Proteins - genetics ; Recombinant Proteins - metabolism ; Signal Transduction ; Substrate Specificity ; Tumor Suppressor Proteins ; ubiquitin ; Ubiquitin - chemistry ; Ubiquitin - genetics ; Ubiquitin - metabolism ; ubiquitin-protein ligase ; Ubiquitin-Protein Ligases - chemistry ; Ubiquitin-Protein Ligases - genetics ; Ubiquitin-Protein Ligases - metabolism ; Ubiquitination ; Western blotting ; X-ray crystallography</subject><ispartof>Molecular cell, 2017-10, Vol.68 (1), p.233-246.e5</ispartof><rights>2017 The Authors</rights><rights>Copyright © 2017 The Authors. Published by Elsevier Inc. All rights reserved.</rights><rights>2017 The Authors 2017</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c496t-bdb9e9586d2bc1887014bbd30637719019d1a837626159297b40d38861eec4693</citedby><cites>FETCH-LOGICAL-c496t-bdb9e9586d2bc1887014bbd30637719019d1a837626159297b40d38861eec4693</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.molcel.2017.08.020$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>230,314,777,781,882,3537,27905,27906,45976</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/28943312$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Michel, Martin A.</creatorcontrib><creatorcontrib>Swatek, Kirby N.</creatorcontrib><creatorcontrib>Hospenthal, Manuela K.</creatorcontrib><creatorcontrib>Komander, David</creatorcontrib><title>Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling</title><title>Molecular cell</title><addtitle>Mol Cell</addtitle><description>Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific “affimer” reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
[Display omitted]
•Respective linkage-specific affimers recognize K6- or K33-/K11-linked chains•Structures of affimer:diUb complexes reveal mechanisms of linkage specificity•Improved affimers can be used in western blotting, confocal microscopy, and pull-downs•Pull-downs with K6-specific affimers reveal HUWE1 to be a major K6 ligase in cells
Michel et al. describe linkage-specific tools for the study of atypical K6 and K33/K11 ubiquitin linkages. Affimers have applications in western blotting, confocal microscopy, and pull-downs. Using a K6-specific affimer, they reveal that HUWE1 is a major source of cellular K6 chains and decorates Mfn2 with K6 chains.</description><subject>affimer</subject><subject>Amino Acid Motifs</subject><subject>antibodies</subject><subject>Binding Sites</subject><subject>Carrier Proteins - chemistry</subject><subject>Carrier Proteins - genetics</subject><subject>Carrier Proteins - metabolism</subject><subject>Cell Line, Tumor</subject><subject>Cloning, Molecular</subject><subject>cross reaction</subject><subject>crystal structure</subject><subject>Crystallography, X-Ray</subject><subject>Escherichia coli - genetics</subject><subject>Escherichia coli - metabolism</subject><subject>fluorescence microscopy</subject><subject>Gene Expression</subject><subject>GTP Phosphohydrolases - chemistry</subject><subject>GTP Phosphohydrolases - genetics</subject><subject>GTP Phosphohydrolases - metabolism</subject><subject>HEK293 Cells</subject><subject>HeLa Cells</subject><subject>Humans</subject><subject>HUWE1</subject><subject>Kinetics</subject><subject>Lys6-linked ubiquitin chains</subject><subject>Lysine - chemistry</subject><subject>Lysine - metabolism</subject><subject>Mfn2</subject><subject>microscale thermophoresis</subject><subject>Mitochondrial Proteins - chemistry</subject><subject>Mitochondrial Proteins - genetics</subject><subject>Mitochondrial Proteins - metabolism</subject><subject>mitophagy</subject><subject>Models, Molecular</subject><subject>Molecular Probes - chemistry</subject><subject>Parkin</subject><subject>post-translational modification</subject><subject>Protein Binding</subject><subject>Protein Interaction Domains and Motifs</subject><subject>Protein Processing, Post-Translational</subject><subject>Protein Structure, Secondary</subject><subject>Recombinant Proteins - chemistry</subject><subject>Recombinant Proteins - genetics</subject><subject>Recombinant Proteins - metabolism</subject><subject>Signal Transduction</subject><subject>Substrate Specificity</subject><subject>Tumor Suppressor Proteins</subject><subject>ubiquitin</subject><subject>Ubiquitin - chemistry</subject><subject>Ubiquitin - genetics</subject><subject>Ubiquitin - metabolism</subject><subject>ubiquitin-protein ligase</subject><subject>Ubiquitin-Protein Ligases - chemistry</subject><subject>Ubiquitin-Protein Ligases - genetics</subject><subject>Ubiquitin-Protein Ligases - metabolism</subject><subject>Ubiquitination</subject><subject>Western blotting</subject><subject>X-ray crystallography</subject><issn>1097-2765</issn><issn>1097-4164</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2017</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFUU1v1DAQtRCIloV_gFCOXBJsx_HHBamqClSshEQpV8uxJ-ksibO1syvx78lqlxYucJqR5r03M-8R8prRilEm322qcRo8DBWnTFVUV5TTJ-ScUaNKwaR4euq5ks0ZeZHzhlImGm2ekzOujahrxs_J99sW73c4YyzWGH-4HsqbLXjs0BcXXYcjpFx8hT24obiOGfu7ORcY56n4LMsDA0LxKHGDfXQDxv4leda5IcOrU12R2w9X3y4_lesvH68vL9alF0bOZRtaA6bRMvDWM63VcmHbhprKWilmKDOBOV0rySVrDDeqFTTUWksG4IU09Yq8P-pud-0IwUOckxvsNuHo0k87ObR_TyLe2X7a20YK2ixrVuTtSSBN9zvIsx0xL64OLsK0y5ZTqRYHlfk_lBnBFaO8PkDFEerTlHOC7uEiRu0hPbuxx_TsIT1LtV3SW2hv_vzmgfQ7rsd3YfF0j5Bs9gjRQ8AEfrZhwn9v-AXvVKzK</recordid><startdate>20171005</startdate><enddate>20171005</enddate><creator>Michel, Martin A.</creator><creator>Swatek, Kirby N.</creator><creator>Hospenthal, Manuela K.</creator><creator>Komander, David</creator><general>Elsevier Inc</general><general>Cell Press</general><scope>6I.</scope><scope>AAFTH</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>7S9</scope><scope>L.6</scope><scope>5PM</scope></search><sort><creationdate>20171005</creationdate><title>Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling</title><author>Michel, Martin A. ; Swatek, Kirby N. ; Hospenthal, Manuela K. ; Komander, David</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c496t-bdb9e9586d2bc1887014bbd30637719019d1a837626159297b40d38861eec4693</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2017</creationdate><topic>affimer</topic><topic>Amino Acid Motifs</topic><topic>antibodies</topic><topic>Binding Sites</topic><topic>Carrier Proteins - chemistry</topic><topic>Carrier Proteins - genetics</topic><topic>Carrier Proteins - metabolism</topic><topic>Cell Line, Tumor</topic><topic>Cloning, Molecular</topic><topic>cross reaction</topic><topic>crystal structure</topic><topic>Crystallography, X-Ray</topic><topic>Escherichia coli - genetics</topic><topic>Escherichia coli - metabolism</topic><topic>fluorescence microscopy</topic><topic>Gene Expression</topic><topic>GTP Phosphohydrolases - chemistry</topic><topic>GTP Phosphohydrolases - genetics</topic><topic>GTP Phosphohydrolases - metabolism</topic><topic>HEK293 Cells</topic><topic>HeLa Cells</topic><topic>Humans</topic><topic>HUWE1</topic><topic>Kinetics</topic><topic>Lys6-linked ubiquitin chains</topic><topic>Lysine - chemistry</topic><topic>Lysine - metabolism</topic><topic>Mfn2</topic><topic>microscale thermophoresis</topic><topic>Mitochondrial Proteins - chemistry</topic><topic>Mitochondrial Proteins - genetics</topic><topic>Mitochondrial Proteins - metabolism</topic><topic>mitophagy</topic><topic>Models, Molecular</topic><topic>Molecular Probes - chemistry</topic><topic>Parkin</topic><topic>post-translational modification</topic><topic>Protein Binding</topic><topic>Protein Interaction Domains and Motifs</topic><topic>Protein Processing, Post-Translational</topic><topic>Protein Structure, Secondary</topic><topic>Recombinant Proteins - chemistry</topic><topic>Recombinant Proteins - genetics</topic><topic>Recombinant Proteins - metabolism</topic><topic>Signal Transduction</topic><topic>Substrate Specificity</topic><topic>Tumor Suppressor Proteins</topic><topic>ubiquitin</topic><topic>Ubiquitin - chemistry</topic><topic>Ubiquitin - genetics</topic><topic>Ubiquitin - metabolism</topic><topic>ubiquitin-protein ligase</topic><topic>Ubiquitin-Protein Ligases - chemistry</topic><topic>Ubiquitin-Protein Ligases - genetics</topic><topic>Ubiquitin-Protein Ligases - metabolism</topic><topic>Ubiquitination</topic><topic>Western blotting</topic><topic>X-ray crystallography</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Michel, Martin A.</creatorcontrib><creatorcontrib>Swatek, Kirby N.</creatorcontrib><creatorcontrib>Hospenthal, Manuela K.</creatorcontrib><creatorcontrib>Komander, David</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>AGRICOLA</collection><collection>AGRICOLA - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular cell</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Michel, Martin A.</au><au>Swatek, Kirby N.</au><au>Hospenthal, Manuela K.</au><au>Komander, David</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling</atitle><jtitle>Molecular cell</jtitle><addtitle>Mol Cell</addtitle><date>2017-10-05</date><risdate>2017</risdate><volume>68</volume><issue>1</issue><spage>233</spage><epage>246.e5</epage><pages>233-246.e5</pages><issn>1097-2765</issn><eissn>1097-4164</eissn><abstract>Several ubiquitin chain types have remained unstudied, mainly because tools and techniques to detect these posttranslational modifications are scarce. Linkage-specific antibodies have shaped our understanding of the roles and dynamics of polyubiquitin signals but are available for only five out of eight linkage types. We here characterize K6- and K33-linkage-specific “affimer” reagents as high-affinity ubiquitin interactors. Crystal structures of affimers bound to their cognate chain types reveal mechanisms of specificity and a K11 cross-reactivity in the K33 affimer. Structure-guided improvements yield superior affinity reagents suitable for western blotting, confocal fluorescence microscopy and pull-down applications. This allowed us to identify RNF144A and RNF144B as E3 ligases that assemble K6-, K11-, and K48-linked polyubiquitin in vitro. A protocol to enrich K6-ubiquitinated proteins from cells identifies HUWE1 as a main E3 ligase for this chain type, and we show that mitofusin-2 is modified with K6-linked polyubiquitin in a HUWE1-dependent manner.
[Display omitted]
•Respective linkage-specific affimers recognize K6- or K33-/K11-linked chains•Structures of affimer:diUb complexes reveal mechanisms of linkage specificity•Improved affimers can be used in western blotting, confocal microscopy, and pull-downs•Pull-downs with K6-specific affimers reveal HUWE1 to be a major K6 ligase in cells
Michel et al. describe linkage-specific tools for the study of atypical K6 and K33/K11 ubiquitin linkages. Affimers have applications in western blotting, confocal microscopy, and pull-downs. Using a K6-specific affimer, they reveal that HUWE1 is a major source of cellular K6 chains and decorates Mfn2 with K6 chains.</abstract><cop>United States</cop><pub>Elsevier Inc</pub><pmid>28943312</pmid><doi>10.1016/j.molcel.2017.08.020</doi><tpages>14</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | affimer Amino Acid Motifs antibodies Binding Sites Carrier Proteins - chemistry Carrier Proteins - genetics Carrier Proteins - metabolism Cell Line, Tumor Cloning, Molecular cross reaction crystal structure Crystallography, X-Ray Escherichia coli - genetics Escherichia coli - metabolism fluorescence microscopy Gene Expression GTP Phosphohydrolases - chemistry GTP Phosphohydrolases - genetics GTP Phosphohydrolases - metabolism HEK293 Cells HeLa Cells Humans HUWE1 Kinetics Lys6-linked ubiquitin chains Lysine - chemistry Lysine - metabolism Mfn2 microscale thermophoresis Mitochondrial Proteins - chemistry Mitochondrial Proteins - genetics Mitochondrial Proteins - metabolism mitophagy Models, Molecular Molecular Probes - chemistry Parkin post-translational modification Protein Binding Protein Interaction Domains and Motifs Protein Processing, Post-Translational Protein Structure, Secondary Recombinant Proteins - chemistry Recombinant Proteins - genetics Recombinant Proteins - metabolism Signal Transduction Substrate Specificity Tumor Suppressor Proteins ubiquitin Ubiquitin - chemistry Ubiquitin - genetics Ubiquitin - metabolism ubiquitin-protein ligase Ubiquitin-Protein Ligases - chemistry Ubiquitin-Protein Ligases - genetics Ubiquitin-Protein Ligases - metabolism Ubiquitination Western blotting X-ray crystallography |
| title | Ubiquitin Linkage-Specific Affimers Reveal Insights into K6-Linked Ubiquitin Signaling |
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