The origins of apicomplexan sequence innovation.
Identifieur interne : 000A59 ( Ncbi/Merge ); précédent : 000A58; suivant : 000A60The origins of apicomplexan sequence innovation.
Auteurs : James Wasmuth [Canada] ; Jennifer Daub ; José Manuel Peregrín-Alvarez ; Constance A M. Finney ; John ParkinsonSource :
- Genome research [ 1088-9051 ] ; 2009.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : Protozoan Proteins.
- genetics : Apicomplexa.
- Animals, Evolution, Molecular, Humans, Phylogeny, Protein Structure, Tertiary.
Abstract
The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.
DOI: 10.1101/gr.083386.108
PubMed: 19363216
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pubmed:19363216Le document en format XML
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Finney</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">Genome research</title><idno type="ISSN">1088-9051</idno><imprint><date when="2009" type="published">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Apicomplexa (genetics)</term><term>Evolution, Molecular</term><term>Humans</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term><term>Protozoan Proteins (genetics)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>Protozoan Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Apicomplexa</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Evolution, Molecular</term><term>Humans</term><term>Phylogeny</term><term>Protein Structure, Tertiary</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">19363216</PMID><DateCreated><Year>2009</Year><Month>07</Month><Day>02</Day></DateCreated><DateCompleted><Year>2009</Year><Month>09</Month><Day>04</Day></DateCompleted><DateRevised><Year>2016</Year><Month>10</Month><Day>19</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Print">1088-9051</ISSN><JournalIssue CitedMedium="Print"><Volume>19</Volume><Issue>7</Issue><PubDate><Year>2009</Year><Month>Jul</Month></PubDate></JournalIssue><Title>Genome research</Title><ISOAbbreviation>Genome Res.</ISOAbbreviation></Journal><ArticleTitle>The origins of apicomplexan sequence innovation.</ArticleTitle><Pagination><MedlinePgn>1202-13</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1101/gr.083386.108</ELocationID><Abstract><AbstractText>The Apicomplexa are a group of phylogenetically related parasitic protists that include Plasmodium, Cryptosporidium, and Toxoplasma. Together they are a major global burden on human health and economics. To meet this challenge, several international consortia have generated vast amounts of sequence data for many of these parasites. Here, we exploit these data to perform a systematic analysis of protein family and domain incidence across the phylum. A total of 87,736 protein sequences were collected from 15 apicomplexan species. These were compared with three protein databases, including the partial genome database, PartiGeneDB, which increases the breadth of taxonomic coverage. From these searches we constructed taxonomic profiles that reveal the extent of apicomplexan sequence diversity. Sequences without a significant match outside the phylum were denoted as apicomplexan specialized. These were collated into 9134 discrete protein families and placed in the context of the apicomplexan phylogeny, identifying the putative origin of each family. Most apicomplexan families were associated with an individual genus or species. Interestingly, many genera-specific innovations were associated with specialized host cell invasion and/or parasite survival processes. Contrastingly, those families reflecting more ancestral relationships were enriched in generalized housekeeping functions such as translation and transcription, which have diverged within the apicomplexan lineage. Protein domain searches revealed 192 domains not previously reported in apicomplexans together with a number of novel domain combinations. We highlight domains that may be important to parasite survival.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Wasmuth</LastName><ForeName>James</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, Ontario M5G 2L3, Canada. jwasmuth@sickkids.ca</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Daub</LastName><ForeName>Jennifer</ForeName><Initials>J</Initials></Author><Author ValidYN="Y"><LastName>Peregrín-Alvarez</LastName><ForeName>José Manuel</ForeName><Initials>JM</Initials></Author><Author ValidYN="Y"><LastName>Finney</LastName><ForeName>Constance A M</ForeName><Initials>CA</Initials></Author><Author ValidYN="Y"><LastName>Parkinson</LastName><ForeName>John</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>Medical Research Council</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2009</Year><Month>04</Month><Day>10</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>Genome Res</MedlineTA><NlmUniqueID>9518021</NlmUniqueID><ISSNLinking>1088-9051</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D015800">Protozoan Proteins</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><CommentsCorrectionsList><CommentsCorrections RefType="Cites"><RefSource>J Infect Dis. 2002 Jun 1;185(11):1637-43</RefSource><PMID Version="1">12023770</PMID></CommentsCorrections><CommentsCorrections RefType="Cites"><RefSource>Lancet. 2002 Jun 22;359(9324):2188-94</RefSource><PMID 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UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D019143" MajorTopicYN="N">Evolution, Molecular</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D006801" MajorTopicYN="N">Humans</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D010802" MajorTopicYN="N">Phylogeny</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D017434" MajorTopicYN="N">Protein Structure, Tertiary</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D015800" MajorTopicYN="N">Protozoan Proteins</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading></MeshHeadingList><OtherID Source="NLM">PMC2704437</OtherID></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2009</Year><Month>4</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2009</Year><Month>4</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2009</Year><Month>9</Month><Day>5</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">19363216</ArticleId><ArticleId IdType="pii">gr.083386.108</ArticleId><ArticleId IdType="doi">10.1101/gr.083386.108</ArticleId><ArticleId IdType="pmc">PMC2704437</ArticleId></ArticleIdList></PubmedData></pubmed><affiliations><list><country><li>Canada</li></country></list><tree><noCountry><name sortKey="Daub, Jennifer" sort="Daub, Jennifer" uniqKey="Daub J" first="Jennifer" last="Daub">Jennifer Daub</name><name sortKey="Finney, Constance A M" sort="Finney, Constance A M" uniqKey="Finney C" first="Constance A M" last="Finney">Constance A M. Finney</name><name sortKey="Parkinson, John" sort="Parkinson, John" uniqKey="Parkinson J" first="John" last="Parkinson">John Parkinson</name><name sortKey="Peregrin Alvarez, Jose Manuel" sort="Peregrin Alvarez, Jose Manuel" uniqKey="Peregrin Alvarez J" first="José Manuel" last="Peregrín-Alvarez">José Manuel Peregrín-Alvarez</name></noCountry><country name="Canada"><noRegion><name sortKey="Wasmuth, James" sort="Wasmuth, James" uniqKey="Wasmuth J" first="James" last="Wasmuth">James Wasmuth</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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