Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
Identifieur interne : 001115 ( PubMed/Corpus ); précédent : 001114; suivant : 001116Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.
Auteurs : Ronish Gupta ; Bart Kus ; Christopher Fladd ; James Wasmuth ; Raffi Tonikian ; Sachdev Sidhu ; Nevan J. Krogan ; John Parkinson ; Daniela RotinSource :
- Molecular systems biology [ 1744-4292 ] ; 2007.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Ribosomal Proteins, Ubiquitin.
- chemical : Peptide Library, Proteome.
- metabolism : Saccharomyces cerevisiae.
- Amino Acid Motifs, Amino Acid Sequence, Molecular Sequence Data, Protein Array Analysis, Protein Binding, Reproducibility of Results, Substrate Specificity.
Abstract
Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets.
DOI: 10.1038/msb4100159
PubMed: 17551511
Links to Exploration step
pubmed:17551511Le document en format XML
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Krogan</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author><author><name sortKey="Rotin, Daniela" sort="Rotin, Daniela" uniqKey="Rotin D" first="Daniela" last="Rotin">Daniela Rotin</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2007">2007</date><idno type="RBID">pubmed:17551511</idno><idno type="pmid">17551511</idno><idno type="doi">10.1038/msb4100159</idno><idno type="wicri:Area/PubMed/Corpus">001115</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001115</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.</title><author><name sortKey="Gupta, Ronish" sort="Gupta, Ronish" uniqKey="Gupta R" first="Ronish" last="Gupta">Ronish Gupta</name><affiliation><nlm:affiliation>Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.</nlm:affiliation></affiliation></author><author><name sortKey="Kus, Bart" sort="Kus, Bart" uniqKey="Kus B" first="Bart" last="Kus">Bart Kus</name></author><author><name sortKey="Fladd, Christopher" sort="Fladd, Christopher" uniqKey="Fladd C" first="Christopher" last="Fladd">Christopher Fladd</name></author><author><name sortKey="Wasmuth, James" sort="Wasmuth, James" uniqKey="Wasmuth J" first="James" last="Wasmuth">James Wasmuth</name></author><author><name sortKey="Tonikian, Raffi" sort="Tonikian, Raffi" uniqKey="Tonikian R" first="Raffi" last="Tonikian">Raffi Tonikian</name></author><author><name sortKey="Sidhu, Sachdev" sort="Sidhu, Sachdev" uniqKey="Sidhu S" first="Sachdev" last="Sidhu">Sachdev Sidhu</name></author><author><name sortKey="Krogan, Nevan J" sort="Krogan, Nevan J" uniqKey="Krogan N" first="Nevan J" last="Krogan">Nevan J. Krogan</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author><author><name sortKey="Rotin, Daniela" sort="Rotin, Daniela" uniqKey="Rotin D" first="Daniela" last="Rotin">Daniela Rotin</name></author></analytic><series><title level="j">Molecular systems biology</title><idno type="eISSN">1744-4292</idno><imprint><date when="2007" type="published">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Amino Acid Motifs</term><term>Amino Acid Sequence</term><term>Molecular Sequence Data</term><term>Peptide Library</term><term>Protein Array Analysis</term><term>Protein Binding</term><term>Proteome</term><term>Reproducibility of Results</term><term>Ribosomal Proteins (metabolism)</term><term>Saccharomyces cerevisiae (metabolism)</term><term>Substrate Specificity</term><term>Ubiquitin (metabolism)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Ribosomal Proteins</term><term>Ubiquitin</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Peptide Library</term><term>Proteome</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Amino Acid Motifs</term><term>Amino Acid Sequence</term><term>Molecular Sequence Data</term><term>Protein Array Analysis</term><term>Protein Binding</term><term>Reproducibility of Results</term><term>Substrate Specificity</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">17551511</PMID><DateCreated><Year>2007</Year><Month>06</Month><Day>06</Day></DateCreated><DateCompleted><Year>2007</Year><Month>07</Month><Day>02</Day></DateCompleted><DateRevised><Year>2014</Year><Month>09</Month><Day>04</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1744-4292</ISSN><JournalIssue CitedMedium="Internet"><Volume>3</Volume><PubDate><Year>2007</Year></PubDate></JournalIssue><Title>Molecular systems biology</Title><ISOAbbreviation>Mol. Syst. Biol.</ISOAbbreviation></Journal><ArticleTitle>Ubiquitination screen using protein microarrays for comprehensive identification of Rsp5 substrates in yeast.</ArticleTitle><Pagination><MedlinePgn>116</MedlinePgn></Pagination><Abstract><AbstractText>Ubiquitin-protein ligases (E3s) are responsible for target recognition and regulate stability, localization or function of their substrates. However, the substrates of most E3 enzymes remain unknown. Here, we describe the development of a novel proteomic in vitro ubiquitination screen using a protein microarray platform that can be utilized for the discovery of substrates for E3 ligases on a global scale. Using the yeast E3 Rsp5 as a test system to identify its substrates on a yeast protein microarray that covers most of the yeast (Saccharomyces cerevisiae) proteome, we identified numerous known and novel ubiquitinated substrates of this E3 ligase. Our enzymatic approach was complemented by a parallel protein microarray protein interaction study. Examination of the substrates identified in the analysis combined with phage display screening allowed exploration of binding mechanisms and substrate specificity of Rsp5. The development of a platform for global discovery of E3 substrates is invaluable for understanding the cellular pathways in which they participate, and could be utilized for the identification of drug targets.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Gupta</LastName><ForeName>Ronish</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Program in Cell Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kus</LastName><ForeName>Bart</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Fladd</LastName><ForeName>Christopher</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Wasmuth</LastName><ForeName>James</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Tonikian</LastName><ForeName>Raffi</ForeName><Initials>R</Initials></Author><Author ValidYN="Y"><LastName>Sidhu</LastName><ForeName>Sachdev</ForeName><Initials>S</Initials></Author><Author ValidYN="Y"><LastName>Krogan</LastName><ForeName>Nevan J</ForeName><Initials>NJ</Initials></Author><Author ValidYN="Y"><LastName>Parkinson</LastName><ForeName>John</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Rotin</LastName><ForeName>Daniela</ForeName><Initials>D</Initials></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2007</Year><Month>06</Month><Day>05</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Mol Syst Biol</MedlineTA><NlmUniqueID>101235389</NlmUniqueID><ISSNLinking>1744-4292</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D019151">Peptide Library</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D020543">Proteome</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D012269">Ribosomal Proteins</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D025801">Ubiquitin</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="C030831">ribosomal protein S5</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>Trends Genet. 2000 Jun;16(6):276-7</RefSource><PMID Version="1">10827456</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>J Membr Biol. 2000 Jul 1;176(1):1-17</RefSource><PMID Version="1">10882424</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Cell. 2000 Sep 1;102(5):577-86</RefSource><PMID 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UI="D000595" MajorTopicYN="N">Amino Acid Sequence</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D008969" MajorTopicYN="N">Molecular Sequence Data</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D019151" MajorTopicYN="N">Peptide Library</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D040081" MajorTopicYN="Y">Protein Array Analysis</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D020543" MajorTopicYN="N">Proteome</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D012269" MajorTopicYN="N">Ribosomal Proteins</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012441" MajorTopicYN="N">Saccharomyces cerevisiae</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D013379" MajorTopicYN="N">Substrate Specificity</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D025801" MajorTopicYN="N">Ubiquitin</DescriptorName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC1911201</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2007</Year><Month>03</Month><Day>14</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2007</Year><Month>04</Month><Day>24</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2007</Year><Month>6</Month><Day>7</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2007</Year><Month>7</Month><Day>3</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate 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