The Modular Organization of Protein Interactions in Escherichia coli.
Identifieur interne : 001D66 ( Main/Exploration ); précédent : 001D65; suivant : 001D67The Modular Organization of Protein Interactions in Escherichia coli.
Auteurs : José M. Peregrín-Alvarez [Canada] ; Xuejian Xiong ; Chong Su ; John ParkinsonSource :
- PLoS computational biology [ 1553-7358 ] ; 2009.
English descriptors
- KwdEn :
- MESH :
- chemical , metabolism : Escherichia coli Proteins, Multienzyme Complexes.
- metabolism : Escherichia coli.
- methods : Protein Interaction Mapping.
- physiology : Signal Transduction.
- Computer Simulation, Models, Biological.
Abstract
Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks.
DOI: 10.1371/journal.pcbi.1000523
PubMed: 19798435
Affiliations:
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Peregrín-Alvarez</name><affiliation wicri:level="1"><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada. peregrin@ebi.ac.uk</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation></author><author><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name></author><author><name sortKey="Su, Chong" sort="Su, Chong" uniqKey="Su C" first="Chong" last="Su">Chong Su</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2009">2009</date><idno type="RBID">pubmed:19798435</idno><idno type="pmid">19798435</idno><idno type="doi">10.1371/journal.pcbi.1000523</idno><idno type="wicri:Area/PubMed/Corpus">000E37</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">000E37</idno><idno type="wicri:Area/PubMed/Curation">000E37</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">000E37</idno><idno type="wicri:Area/PubMed/Checkpoint">000E37</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">000E37</idno><idno type="wicri:Area/Ncbi/Merge">000B59</idno><idno type="wicri:Area/Ncbi/Curation">000B59</idno><idno type="wicri:Area/Ncbi/Checkpoint">000B59</idno><idno type="wicri:Area/Main/Merge">001F13</idno><idno type="wicri:Area/Main/Curation">001D66</idno><idno type="wicri:Area/Main/Exploration">001D66</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">The Modular Organization of Protein Interactions in Escherichia coli.</title><author><name sortKey="Peregrin Alvarez, Jose M" sort="Peregrin Alvarez, Jose M" uniqKey="Peregrin Alvarez J" first="José M" last="Peregrín-Alvarez">José M. Peregrín-Alvarez</name><affiliation wicri:level="1"><nlm:affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario, Canada. peregrin@ebi.ac.uk</nlm:affiliation><country xml:lang="fr">Canada</country><wicri:regionArea>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario</wicri:regionArea><wicri:noRegion>Ontario</wicri:noRegion></affiliation></author><author><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name></author><author><name sortKey="Su, Chong" sort="Su, Chong" uniqKey="Su C" first="Chong" last="Su">Chong Su</name></author><author><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name></author></analytic><series><title level="j">PLoS computational biology</title><idno type="eISSN">1553-7358</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computer Simulation</term><term>Escherichia coli (metabolism)</term><term>Escherichia coli Proteins (metabolism)</term><term>Models, Biological</term><term>Multienzyme Complexes (metabolism)</term><term>Protein Interaction Mapping (methods)</term><term>Signal Transduction (physiology)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="metabolism" xml:lang="en"><term>Escherichia coli Proteins</term><term>Multienzyme Complexes</term></keywords><keywords scheme="MESH" qualifier="metabolism" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Protein Interaction Mapping</term></keywords><keywords scheme="MESH" qualifier="physiology" xml:lang="en"><term>Signal Transduction</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computer Simulation</term><term>Models, Biological</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Escherichia coli serves as an excellent model for the study of fundamental cellular processes such as metabolism, signalling and gene expression. Understanding the function and organization of proteins within these processes is an important step towards a 'systems' view of E. coli. Integrating experimental and computational interaction data, we present a reliable network of 3,989 functional interactions between 1,941 E. coli proteins ( approximately 45% of its proteome). These were combined with a recently generated set of 3,888 high-quality physical interactions between 918 proteins and clustered to reveal 316 discrete modules. In addition to known protein complexes (e.g., RNA and DNA polymerases), we identified modules that represent biochemical pathways (e.g., nitrate regulation and cell wall biosynthesis) as well as batteries of functionally and evolutionarily related processes. To aid the interpretation of modular relationships, several case examples are presented, including both well characterized and novel biochemical systems. Together these data provide a global view of the modular organization of the E. coli proteome and yield unique insights into structural and evolutionary relationships in bacterial networks.</div></front></TEI><affiliations><list><country><li>Canada</li></country></list><tree><noCountry><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Su, Chong" sort="Su, Chong" uniqKey="Su C" first="Chong" last="Su">Chong Su</name><name sortKey="Xiong, Xuejian" sort="Xiong, Xuejian" uniqKey="Xiong X" first="Xuejian" last="Xiong">Xuejian Xiong</name></noCountry><country name="Canada"><noRegion><name sortKey="Peregrin Alvarez, Jose M" sort="Peregrin Alvarez, Jose M" uniqKey="Peregrin Alvarez J" first="José M" last="Peregrín-Alvarez">José M. Peregrín-Alvarez</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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