In Silico Identification, Phylogenetic and Bioinformatic Analysis of Argonaute Genes in Plants
Identifieur interne : 000C36 ( Main/Exploration ); précédent : 000C35; suivant : 000C37In Silico Identification, Phylogenetic and Bioinformatic Analysis of Argonaute Genes in Plants
Auteurs : Khaled Mirzaei [Iran] ; Bahman Bahramnejad [Iran] ; Mohammad Hasan Shamsifard [Iran] ; Wahid Zamani [France]Source :
- International Journal of Genomics [ 2314-436X ] ; 2014.
Abstract
Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.
Url:
DOI: 10.1155/2014/967461
PubMed: 25309901
PubMed Central: 4181786
Affiliations:
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University of Kurdistan, Sanandaj 66177-15175</wicri:regionArea><wicri:noRegion>Sanandaj 66177-15175</wicri:noRegion></affiliation></author><author><name sortKey="Bahramnejad, Bahman" sort="Bahramnejad, Bahman" uniqKey="Bahramnejad B" first="Bahman" last="Bahramnejad">Bahman Bahramnejad</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural Biotechnology, Faculty of Agriculture, University of Kurdistan, Sanandaj 66177-15175, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agricultural Biotechnology, Faculty of Agriculture, University of Kurdistan, Sanandaj 66177-15175</wicri:regionArea><wicri:noRegion>Sanandaj 66177-15175</wicri:noRegion></affiliation></author><author><name sortKey="Shamsifard, Mohammad Hasan" sort="Shamsifard, Mohammad Hasan" uniqKey="Shamsifard M" first="Mohammad Hasan" last="Shamsifard">Mohammad Hasan Shamsifard</name><affiliation wicri:level="1"><nlm:aff id="I1">Department of Agricultural Biotechnology, Faculty of Agriculture, University of Kurdistan, Sanandaj 66177-15175, Iran</nlm:aff><country xml:lang="fr">Iran</country><wicri:regionArea>Department of Agricultural Biotechnology, Faculty of Agriculture, University of Kurdistan, Sanandaj 66177-15175</wicri:regionArea><wicri:noRegion>Sanandaj 66177-15175</wicri:noRegion></affiliation></author><author><name sortKey="Zamani, Wahid" sort="Zamani, Wahid" uniqKey="Zamani W" first="Wahid" last="Zamani">Wahid Zamani</name><affiliation wicri:level="3"><nlm:aff id="I2">Laboratory of Alpine Ecology, Joseph Fourier University, 38041 Grenoble, France</nlm:aff><country xml:lang="fr">France</country><wicri:regionArea>Laboratory of Alpine Ecology, Joseph Fourier University, 38041 Grenoble</wicri:regionArea><placeName><region type="region" nuts="2">Auvergne-Rhône-Alpes</region><region type="old region" nuts="2">Rhône-Alpes</region><settlement type="city">Grenoble</settlement></placeName></affiliation></author></analytic><series><title level="j">International Journal of Genomics</title><idno type="ISSN">2314-436X</idno><idno type="eISSN">2314-4378</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Argonaute protein family is the key players in pathways of gene silencing and small regulatory RNAs in different organisms. Argonaute proteins can bind small noncoding RNAs and control protein synthesis, affect messenger RNA stability, and even participate in the production of new forms of small RNAs. The aim of this study was to characterize and perform bioinformatic analysis of Argonaute proteins in 32 plant species that their genome was sequenced. A total of 437 Argonaute genes were identified and were analyzed based on lengths, gene structure, and protein structure. Results showed that Argonaute proteins were highly conserved across plant kingdom. Phylogenic analysis divided plant Argonautes into three classes. Argonaute proteins have three conserved domains PAZ, MID and PIWI. In addition to three conserved domains namely, PAZ, MID, and PIWI, we identified few more domains in AGO of some plant species. Expression profile analysis of Argonaute proteins showed that expression of these genes varies in most of tissues, which means that these proteins are involved in regulation of most pathways of the plant system. Numbers of alternative transcripts of Argonaute genes were highly variable among the plants. A thorough analysis of large number of putative Argonaute genes revealed several interesting aspects associated with this protein and brought novel information with promising usefulness for both basic and biotechnological applications.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hannon, Gj" uniqKey="Hannon G">GJ Hannon</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Filipowicz, W" uniqKey="Filipowicz W">W Filipowicz</name></author><author><name sortKey="Jaskiewicz, L" uniqKey="Jaskiewicz L">L Jaskiewicz</name></author><author><name sortKey="Kolb, Fa" uniqKey="Kolb F">FA Kolb</name></author><author><name sortKey="Pillai, Rs" uniqKey="Pillai R">RS Pillai</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Borges, F" uniqKey="Borges F">F Borges</name></author><author><name sortKey="Pereira, Pa" uniqKey="Pereira P">PA Pereira</name></author><author><name 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Jeanneau</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Pejchal, R" uniqKey="Pejchal R">R Pejchal</name></author><author><name sortKey="Ludwig, Ml" uniqKey="Ludwig M">ML Ludwig</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>France</li><li>Iran</li></country><region><li>Auvergne-Rhône-Alpes</li><li>Rhône-Alpes</li></region><settlement><li>Grenoble</li></settlement></list><tree><country name="Iran"><noRegion><name sortKey="Mirzaei, Khaled" sort="Mirzaei, Khaled" uniqKey="Mirzaei K" first="Khaled" last="Mirzaei">Khaled Mirzaei</name></noRegion><name sortKey="Bahramnejad, Bahman" sort="Bahramnejad, Bahman" uniqKey="Bahramnejad B" first="Bahman" last="Bahramnejad">Bahman Bahramnejad</name><name sortKey="Shamsifard, Mohammad Hasan" sort="Shamsifard, Mohammad Hasan" uniqKey="Shamsifard M" first="Mohammad Hasan" last="Shamsifard">Mohammad Hasan Shamsifard</name></country><country name="France"><region name="Auvergne-Rhône-Alpes"><name sortKey="Zamani, Wahid" sort="Zamani, Wahid" uniqKey="Zamani W" first="Wahid" last="Zamani">Wahid Zamani</name></region></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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