Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.
Identifieur interne : 001825 ( PubMed/Curation ); précédent : 001824; suivant : 001826Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.
Auteurs : Claudia Bragalini [France] ; Céline Ribière [France] ; Nicolas Parisot [France] ; Laurent Vallon [France] ; Elsa Prudent [France] ; Eric Peyretaillade [France] ; Mariangela Girlanda [Italie] ; Pierre Peyret [France] ; Roland Marmeisse [France] ; Patricia Luis [France]Source :
- DNA research : an international journal for rapid publication of reports on genes and genomes [ 1756-1663 ] ; 2014.
Descripteurs français
- KwdFr :
- ADN complémentaire (), ADN complémentaire (génétique), ADN complémentaire (isolement et purification), ARN messager (), ARN messager (génétique), ARN messager (isolement et purification), Bases de données d'acides nucléiques, Cellules eucaryotes, Microbiologie du sol, Métagénome, Saccharomyces cerevisiae (génétique), Sol ().
- MESH :
- génétique : ADN complémentaire, ARN messager, Saccharomyces cerevisiae.
- isolement et purification : ADN complémentaire, ARN messager.
- ADN complémentaire, ARN messager, Bases de données d'acides nucléiques, Cellules eucaryotes, Microbiologie du sol, Métagénome, Sol.
English descriptors
- KwdEn :
- DNA, Complementary (chemistry), DNA, Complementary (genetics), DNA, Complementary (isolation & purification), Databases, Nucleic Acid, Eukaryotic Cells, Metagenome, RNA, Messenger (chemistry), RNA, Messenger (genetics), RNA, Messenger (isolation & purification), Saccharomyces cerevisiae (genetics), Soil (chemistry), Soil Microbiology.
- MESH :
- chemical , chemistry : DNA, Complementary, RNA, Messenger, Soil.
- chemical , genetics : DNA, Complementary, RNA, Messenger.
- chemical , isolation & purification : DNA, Complementary, RNA, Messenger.
- genetics : Saccharomyces cerevisiae.
- Databases, Nucleic Acid, Eukaryotic Cells, Metagenome, Soil Microbiology.
Abstract
Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment.
DOI: 10.1093/dnares/dsu030
PubMed: 25281543
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uniqKey="Bragalini C" first="Claudia" last="Bragalini">Claudia Bragalini</name><affiliation wicri:level="1"><nlm:affiliation>Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622</wicri:regionArea></affiliation></author><author><name sortKey="Ribiere, Celine" sort="Ribiere, Celine" uniqKey="Ribiere C" first="Céline" last="Ribière">Céline Ribière</name><affiliation wicri:level="1"><nlm:affiliation>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France.</nlm:affiliation><country 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Université d'Auvergne, Clermont-Ferrand F-63001, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001</wicri:regionArea></affiliation></author><author><name sortKey="Girlanda, Mariangela" sort="Girlanda, Mariangela" uniqKey="Girlanda M" first="Mariangela" last="Girlanda">Mariangela Girlanda</name><affiliation wicri:level="1"><nlm:affiliation>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, Viale Mattioli 25, Turin 10125, Italy.</nlm:affiliation><country xml:lang="fr">Italie</country><wicri:regionArea>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, Viale Mattioli 25, Turin 10125</wicri:regionArea></affiliation></author><author><name sortKey="Peyret, Pierre" sort="Peyret, Pierre" uniqKey="Peyret P" first="Pierre" last="Peyret">Pierre Peyret</name><affiliation wicri:level="1"><nlm:affiliation>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001</wicri:regionArea></affiliation></author><author><name sortKey="Marmeisse, Roland" sort="Marmeisse, Roland" uniqKey="Marmeisse R" first="Roland" last="Marmeisse">Roland Marmeisse</name><affiliation wicri:level="1"><nlm:affiliation>Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France.</nlm:affiliation><country xml:lang="fr">France</country><wicri:regionArea>Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622</wicri:regionArea></affiliation></author><author><name sortKey="Luis, Patricia" sort="Luis, Patricia" uniqKey="Luis P" first="Patricia" last="Luis">Patricia Luis</name><affiliation wicri:level="1"><nlm:affiliation>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France patricia.luis@univ-lyon1.fr.</nlm:affiliation><country wicri:rule="url">France</country><wicri:regionArea>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622</wicri:regionArea></affiliation></author></analytic><series><title level="j">DNA research : an international journal for rapid publication of reports on genes and genomes</title><idno type="eISSN">1756-1663</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>DNA, Complementary (chemistry)</term><term>DNA, Complementary (genetics)</term><term>DNA, Complementary (isolation & purification)</term><term>Databases, Nucleic Acid</term><term>Eukaryotic Cells</term><term>Metagenome</term><term>RNA, Messenger (chemistry)</term><term>RNA, Messenger (genetics)</term><term>RNA, Messenger (isolation & purification)</term><term>Saccharomyces cerevisiae (genetics)</term><term>Soil (chemistry)</term><term>Soil Microbiology</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN complémentaire ()</term><term>ADN complémentaire (génétique)</term><term>ADN complémentaire (isolement et purification)</term><term>ARN messager ()</term><term>ARN messager (génétique)</term><term>ARN messager (isolement et purification)</term><term>Bases de données d'acides nucléiques</term><term>Cellules eucaryotes</term><term>Microbiologie du sol</term><term>Métagénome</term><term>Saccharomyces cerevisiae (génétique)</term><term>Sol ()</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>DNA, Complementary</term><term>RNA, Messenger</term><term>Soil</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Complementary</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" type="chemical" qualifier="isolation & purification" xml:lang="en"><term>DNA, Complementary</term><term>RNA, Messenger</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN complémentaire</term><term>ARN messager</term><term>Saccharomyces cerevisiae</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>ADN complémentaire</term><term>ARN messager</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Databases, Nucleic Acid</term><term>Eukaryotic Cells</term><term>Metagenome</term><term>Soil Microbiology</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>ADN complémentaire</term><term>ARN messager</term><term>Bases de données d'acides nucléiques</term><term>Cellules eucaryotes</term><term>Microbiologie du sol</term><term>Métagénome</term><term>Sol</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment. </div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">25281543</PMID><DateCompleted><Year>2015</Year><Month>07</Month><Day>10</Day></DateCompleted><DateRevised><Year>2018</Year><Month>11</Month><Day>13</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1756-1663</ISSN><JournalIssue CitedMedium="Internet"><Volume>21</Volume><Issue>6</Issue><PubDate><Year>2014</Year><Month>Dec</Month></PubDate></JournalIssue><Title>DNA research : an international journal for rapid publication of reports on genes and genomes</Title><ISOAbbreviation>DNA Res.</ISOAbbreviation></Journal><ArticleTitle>Solution hybrid selection capture for the recovery of functional full-length eukaryotic cDNAs from complex environmental samples.</ArticleTitle><Pagination><MedlinePgn>685-94</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/dnares/dsu030</ELocationID><Abstract><AbstractText>Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment. </AbstractText><CopyrightInformation>© The Author 2014. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Bragalini</LastName><ForeName>Claudia</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ribière</LastName><ForeName>Céline</ForeName><Initials>C</Initials><AffiliationInfo><Affiliation>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parisot</LastName><ForeName>Nicolas</ForeName><Initials>N</Initials><AffiliationInfo><Affiliation>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Vallon</LastName><ForeName>Laurent</ForeName><Initials>L</Initials><AffiliationInfo><Affiliation>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Prudent</LastName><ForeName>Elsa</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peyretaillade</LastName><ForeName>Eric</ForeName><Initials>E</Initials><AffiliationInfo><Affiliation>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Girlanda</LastName><ForeName>Mariangela</ForeName><Initials>M</Initials><AffiliationInfo><Affiliation>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France Istituto per la Protezione Sostenibile delle Piante (IPSP), Consiglio Nazionale delle Ricerche, Viale Mattioli 25, Turin 10125, Italy.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Peyret</LastName><ForeName>Pierre</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>EA 4678 CIDAM, BP 10448, Clermont Université, Université d'Auvergne, Clermont-Ferrand F-63001, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Marmeisse</LastName><ForeName>Roland</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Department of Life Sciences and Systems Biology, University of Turin, viale Mattioli 25, Turin 10125, Italy Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Luis</LastName><ForeName>Patricia</ForeName><Initials>P</Initials><AffiliationInfo><Affiliation>Ecologie Microbienne, UMR CNRS 5557, USC INRA 1364, Université de Lyon, Université Lyon 1, Villeurbanne 69622, France patricia.luis@univ-lyon1.fr.</Affiliation></AffiliationInfo></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>2014</Year><Month>10</Month><Day>03</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>DNA Res</MedlineTA><NlmUniqueID>9423827</NlmUniqueID><ISSNLinking>1340-2838</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D018076">DNA, 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