Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).
Identifieur interne : 000026 ( PubMed/Corpus ); précédent : 000025; suivant : 000027Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).
Auteurs : Upendra N. Dwivedi ; Sameeksha Tiwari ; Pragya Prasanna ; Manika Awasthi ; Swati Singh ; Veda P. PandeySource :
- Omics : a journal of integrative biology [ 1557-8100 ] ; 2016.
Abstract
Citrus are among the economically most important fruit tree crops in the world. Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa infection, is a serious disease limiting citrus production at a global scale. With availability of citrus genomic resources, it is now possible to compare citrus expressed sequence tag (EST) data sets and identify single-nucleotide polymorphisms (SNPs) within and among different citrus cultivars that can be exploited for citrus resistance to infections, citrus breeding, among others. We report here, for the first time, SNPs in the EST data sets of X. fastidiosa-infected Citrus sinensis (sweet orange) and their functional annotation that revealed the involvement of eight C. sinensis candidate genes in CVC pathogenesis. Among these genes were xyloglucan endotransglycosylase, myo-inositol-1-phosphate synthase, and peroxidase were found to be involved in plant cell wall metabolism. These have been further investigated by molecular modeling for their role in CVC infection and defense. Molecular docking analyses of the wild and the mutant (SNP containing) types of the selected three enzymes with their respective substrates revealed a significant decrease in the binding affinity of substrates for the mutant enzymes, thus suggesting a decrease in the catalytic efficiency of these enzymes during infection, thereby facilitating a favorable condition for infection by the pathogen. These findings offer novel agrigenomics insights in developing future molecular targets and strategies for citrus fruit cultivation in ways that are resistant to X. fastidiosa infection, and by extension, with greater harvesting efficiency and economic value.
DOI: 10.1089/omi.2016.0062
PubMed: 27447755
Links to Exploration step
pubmed:27447755Le document en format XML
<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).</title><author><name sortKey="Dwivedi, Upendra N" sort="Dwivedi, Upendra N" uniqKey="Dwivedi U" first="Upendra N" last="Dwivedi">Upendra N. Dwivedi</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Tiwari, Sameeksha" sort="Tiwari, Sameeksha" uniqKey="Tiwari S" first="Sameeksha" last="Tiwari">Sameeksha Tiwari</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Prasanna, Pragya" sort="Prasanna, Pragya" uniqKey="Prasanna P" first="Pragya" last="Prasanna">Pragya Prasanna</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Awasthi, Manika" sort="Awasthi, Manika" uniqKey="Awasthi M" first="Manika" last="Awasthi">Manika Awasthi</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Singh, Swati" sort="Singh, Swati" uniqKey="Singh S" first="Swati" last="Singh">Swati Singh</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Pandey, Veda P" sort="Pandey, Veda P" uniqKey="Pandey V" first="Veda P" last="Pandey">Veda P. Pandey</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2016">2016</date><idno type="RBID">pubmed:27447755</idno><idno type="pmid">27447755</idno><idno type="doi">10.1089/omi.2016.0062</idno><idno type="wicri:Area/PubMed/Corpus">000026</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).</title><author><name sortKey="Dwivedi, Upendra N" sort="Dwivedi, Upendra N" uniqKey="Dwivedi U" first="Upendra N" last="Dwivedi">Upendra N. Dwivedi</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Tiwari, Sameeksha" sort="Tiwari, Sameeksha" uniqKey="Tiwari S" first="Sameeksha" last="Tiwari">Sameeksha Tiwari</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Prasanna, Pragya" sort="Prasanna, Pragya" uniqKey="Prasanna P" first="Pragya" last="Prasanna">Pragya Prasanna</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Awasthi, Manika" sort="Awasthi, Manika" uniqKey="Awasthi M" first="Manika" last="Awasthi">Manika Awasthi</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Singh, Swati" sort="Singh, Swati" uniqKey="Singh S" first="Swati" last="Singh">Swati Singh</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author><author><name sortKey="Pandey, Veda P" sort="Pandey, Veda P" uniqKey="Pandey V" first="Veda P" last="Pandey">Veda P. Pandey</name><affiliation><nlm:affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</nlm:affiliation></affiliation></author></analytic><series><title level="j">Omics : a journal of integrative biology</title><idno type="eISSN">1557-8100</idno><imprint><date when="2016" type="published">2016</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Citrus are among the economically most important fruit tree crops in the world. Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa infection, is a serious disease limiting citrus production at a global scale. With availability of citrus genomic resources, it is now possible to compare citrus expressed sequence tag (EST) data sets and identify single-nucleotide polymorphisms (SNPs) within and among different citrus cultivars that can be exploited for citrus resistance to infections, citrus breeding, among others. We report here, for the first time, SNPs in the EST data sets of X. fastidiosa-infected Citrus sinensis (sweet orange) and their functional annotation that revealed the involvement of eight C. sinensis candidate genes in CVC pathogenesis. Among these genes were xyloglucan endotransglycosylase, myo-inositol-1-phosphate synthase, and peroxidase were found to be involved in plant cell wall metabolism. These have been further investigated by molecular modeling for their role in CVC infection and defense. Molecular docking analyses of the wild and the mutant (SNP containing) types of the selected three enzymes with their respective substrates revealed a significant decrease in the binding affinity of substrates for the mutant enzymes, thus suggesting a decrease in the catalytic efficiency of these enzymes during infection, thereby facilitating a favorable condition for infection by the pathogen. These findings offer novel agrigenomics insights in developing future molecular targets and strategies for citrus fruit cultivation in ways that are resistant to X. fastidiosa infection, and by extension, with greater harvesting efficiency and economic value.</div></front></TEI><pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">27447755</PMID><DateCreated><Year>2016</Year><Month>8</Month><Day>9</Day></DateCreated><DateRevised><Year>2016</Year><Month>8</Month><Day>9</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1557-8100</ISSN><JournalIssue CitedMedium="Internet"><Volume>20</Volume><Issue>8</Issue><PubDate><Year>2016</Year><Month>Aug</Month></PubDate></JournalIssue><Title>Omics : a journal of integrative biology</Title><ISOAbbreviation>OMICS</ISOAbbreviation></Journal><ArticleTitle>Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).</ArticleTitle><Pagination><MedlinePgn>485-90</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1089/omi.2016.0062</ELocationID><Abstract><AbstractText>Citrus are among the economically most important fruit tree crops in the world. Citrus variegated chlorosis (CVC), caused by Xylella fastidiosa infection, is a serious disease limiting citrus production at a global scale. With availability of citrus genomic resources, it is now possible to compare citrus expressed sequence tag (EST) data sets and identify single-nucleotide polymorphisms (SNPs) within and among different citrus cultivars that can be exploited for citrus resistance to infections, citrus breeding, among others. We report here, for the first time, SNPs in the EST data sets of X. fastidiosa-infected Citrus sinensis (sweet orange) and their functional annotation that revealed the involvement of eight C. sinensis candidate genes in CVC pathogenesis. Among these genes were xyloglucan endotransglycosylase, myo-inositol-1-phosphate synthase, and peroxidase were found to be involved in plant cell wall metabolism. These have been further investigated by molecular modeling for their role in CVC infection and defense. Molecular docking analyses of the wild and the mutant (SNP containing) types of the selected three enzymes with their respective substrates revealed a significant decrease in the binding affinity of substrates for the mutant enzymes, thus suggesting a decrease in the catalytic efficiency of these enzymes during infection, thereby facilitating a favorable condition for infection by the pathogen. These findings offer novel agrigenomics insights in developing future molecular targets and strategies for citrus fruit cultivation in ways that are resistant to X. fastidiosa infection, and by extension, with greater harvesting efficiency and economic value.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Dwivedi</LastName><ForeName>Upendra N</ForeName><Initials>UN</Initials><AffiliationInfo><Affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Tiwari</LastName><ForeName>Sameeksha</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Prasanna</LastName><ForeName>Pragya</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Awasthi</LastName><ForeName>Manika</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Singh</LastName><ForeName>Swati</ForeName><Initials>S</Initials><AffiliationInfo><Affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Pandey</LastName><ForeName>Veda P</ForeName><Initials>VP</Initials><AffiliationInfo><Affiliation>Bioinformatics Infrastructure Facility, Centre of Excellence in Bioinformatics, Department of Biochemistry, University of Lucknow , Lucknow, India .</Affiliation></AffiliationInfo></Author></AuthorList><Language>ENG</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2016</Year><Month>Jul</Month><Day>22</Day></ArticleDate></Article><MedlineJournalInfo><Country>United States</Country><MedlineTA>OMICS</MedlineTA><NlmUniqueID>101131135</NlmUniqueID><ISSNLinking>1536-2310</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2016</Year><Month>7</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2016</Year><Month>7</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2016</Year><Month>7</Month><Day>23</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">27447755</ArticleId><ArticleId IdType="doi">10.1089/omi.2016.0062</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Wicri/Bois/explor/OrangerV1/Data/PubMed/Corpus
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000026 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd -nk 000026 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien
|wiki= Wicri/Bois
|area= OrangerV1
|flux= PubMed
|étape= Corpus
|type= RBID
|clé= pubmed:27447755
|texte= Citrus Functional Genomics and Molecular Modeling in Relation to Citrus sinensis (Sweet Orange) Infection with Xylella fastidiosa (Citrus Variegated Chlorosis).
}}
Pour générer des pages wiki
HfdIndexSelect -h $EXPLOR_AREA/Data/PubMed/Corpus/RBID.i -Sk "pubmed:27447755" \
| HfdSelect -Kh $EXPLOR_AREA/Data/PubMed/Corpus/biblio.hfd \
| NlmPubMed2Wicri -a OrangerV1
| This area was generated with Dilib version V0.6.25. |  |