Interaction network containing conserved and essential protein complexes in Escherichia coli.
Identifieur interne : 001286 ( PubMed/Curation ); précédent : 001285; suivant : 001287Interaction network containing conserved and essential protein complexes in Escherichia coli.
Auteurs : Gareth Butland [Canada] ; José Manuel Peregrín-Alvarez ; Joyce Li ; Wehong Yang ; Xiaochun Yang ; Veronica Canadien ; Andrei Starostine ; Dawn Richards ; Bryan Beattie ; Nevan Krogan ; Michael Davey ; John Parkinson ; Jack Greenblatt ; Andrew EmiliSource :
- Nature [ 1476-4687 ] ; 2005.
English descriptors
- KwdEn :
- Alleles, Computational Biology, Conserved Sequence (genetics), Escherichia coli (genetics), Escherichia coli (metabolism), Escherichia coli Proteins (chemistry), Escherichia coli Proteins (genetics), Escherichia coli Proteins (isolation & purification), Escherichia coli Proteins (metabolism), Evolution, Molecular, Genes, Bacterial (genetics), Genes, Essential (genetics), Genomics, Mass Spectrometry, Multiprotein Complexes (chemistry), Multiprotein Complexes (genetics), Multiprotein Complexes (isolation & purification), Multiprotein Complexes (metabolism), Open Reading Frames (genetics), Phylogeny, Protein Binding, Recombinant Fusion Proteins (chemistry), Recombinant Fusion Proteins (genetics), Recombinant Fusion Proteins (isolation & purification), Recombinant Fusion Proteins (metabolism), Reproducibility of Results.
- MESH :
- chemical , chemistry : Escherichia coli Proteins, Multiprotein Complexes, Recombinant Fusion Proteins.
- genetics : Conserved Sequence, Escherichia coli, Escherichia coli Proteins, Genes, Bacterial, Genes, Essential, Multiprotein Complexes, Open Reading Frames, Recombinant Fusion Proteins.
- chemical , isolation & purification : Escherichia coli Proteins, Multiprotein Complexes, Recombinant Fusion Proteins.
- metabolism : Escherichia coli, Escherichia coli Proteins, Multiprotein Complexes, Recombinant Fusion Proteins.
- Alleles, Computational Biology, Evolution, Molecular, Genomics, Mass Spectrometry, Phylogeny, Protein Binding, Reproducibility of Results.
Abstract
Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.
DOI: 10.1038/nature03239
PubMed: 15690043
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xml:lang="en"><term>Alleles</term><term>Computational Biology</term><term>Conserved Sequence (genetics)</term><term>Escherichia coli (genetics)</term><term>Escherichia coli (metabolism)</term><term>Escherichia coli Proteins (chemistry)</term><term>Escherichia coli Proteins (genetics)</term><term>Escherichia coli Proteins (isolation & purification)</term><term>Escherichia coli Proteins (metabolism)</term><term>Evolution, Molecular</term><term>Genes, Bacterial (genetics)</term><term>Genes, Essential (genetics)</term><term>Genomics</term><term>Mass Spectrometry</term><term>Multiprotein Complexes (chemistry)</term><term>Multiprotein Complexes (genetics)</term><term>Multiprotein Complexes (isolation & purification)</term><term>Multiprotein Complexes (metabolism)</term><term>Open Reading Frames (genetics)</term><term>Phylogeny</term><term>Protein Binding</term><term>Recombinant Fusion Proteins (chemistry)</term><term>Recombinant Fusion Proteins (genetics)</term><term>Recombinant Fusion 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coli Proteins</term><term>Multiprotein Complexes</term><term>Recombinant Fusion Proteins</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Alleles</term><term>Computational Biology</term><term>Evolution, Molecular</term><term>Genomics</term><term>Mass Spectrometry</term><term>Phylogeny</term><term>Protein Binding</term><term>Reproducibility of Results</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Proteins often function as components of multi-subunit complexes. Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. 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Despite its long history as a model organism, no large-scale analysis of protein complexes in Escherichia coli has yet been reported. To this end, we have targeted DNA cassettes into the E. coli chromosome to create carboxy-terminal, affinity-tagged alleles of 1,000 open reading frames (approximately 23% of the genome). A total of 857 proteins, including 198 of the most highly conserved, soluble non-ribosomal proteins essential in at least one bacterial species, were tagged successfully, whereas 648 could be purified to homogeneity and their interacting protein partners identified by mass spectrometry. An interaction network of protein complexes involved in diverse biological processes was uncovered and validated by sequential rounds of tagging and purification. This network includes many new interactions as well as interactions predicted based solely on genomic inference or limited phenotypic data. This study provides insight into the function of previously uncharacterized bacterial proteins and the overall topology of a microbial interaction network, the core components of which are broadly conserved across Prokaryota.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Butland</LastName><ForeName>Gareth</ForeName><Initials>G</Initials><AffiliationInfo><Affiliation>Banting and Best Department of Medical Research, University of Toronto, 112 College Street, Toronto, Ontario M5G 1L6, Canada.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peregrín-Alvarez</LastName><ForeName>José Manuel</ForeName><Initials>JM</Initials></Author><Author ValidYN="Y"><LastName>Li</LastName><ForeName>Joyce</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Wehong</ForeName><Initials>W</Initials></Author><Author ValidYN="Y"><LastName>Yang</LastName><ForeName>Xiaochun</ForeName><Initials>X</Initials></Author><Author ValidYN="Y"><LastName>Canadien</LastName><ForeName>Veronica</ForeName><Initials>V</Initials></Author><Author ValidYN="Y"><LastName>Starostine</LastName><ForeName>Andrei</ForeName><Initials>A</Initials></Author><Author ValidYN="Y"><LastName>Richards</LastName><ForeName>Dawn</ForeName><Initials>D</Initials></Author><Author ValidYN="Y"><LastName>Beattie</LastName><ForeName>Bryan</ForeName><Initials>B</Initials></Author><Author ValidYN="Y"><LastName>Krogan</LastName><ForeName>Nevan</ForeName><Initials>N</Initials></Author><Author ValidYN="Y"><LastName>Davey</LastName><ForeName>Michael</ForeName><Initials>M</Initials></Author><Author ValidYN="Y"><LastName>Parkinson</LastName><ForeName>John</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Greenblatt</LastName><ForeName>Jack</ForeName><Initials>J</Initials></Author><Author 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MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005798" MajorTopicYN="N">Genes, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D020043" MajorTopicYN="Y">Genes, Essential</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D023281" MajorTopicYN="N">Genomics</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D013058" MajorTopicYN="N">Mass Spectrometry</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D046912" MajorTopicYN="N">Multiprotein Complexes</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="Y">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName><QualifierName UI="Q000378" MajorTopicYN="Y">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016366" MajorTopicYN="N">Open Reading Frames</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011485" MajorTopicYN="N">Protein Binding</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D011993" MajorTopicYN="N">Recombinant Fusion Proteins</DescriptorName><QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName><QualifierName UI="Q000302" MajorTopicYN="N">isolation & purification</QualifierName><QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D015203" MajorTopicYN="N">Reproducibility of Results</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2004</Year><Month>10</Month><Day>06</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2004</Year><Month>12</Month><Day>03</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2005</Year><Month>2</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2005</Year><Month>2</Month><Day>24</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2005</Year><Month>2</Month><Day>4</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">15690043</ArticleId><ArticleId IdType="pii">nature03239</ArticleId><ArticleId IdType="doi">10.1038/nature03239</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce 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