Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis
Identifieur interne : 000A69 ( Ncbi/Merge ); précédent : 000A68; suivant : 000A70Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis
Auteurs : M. S. Krasnikova [Russie] ; I. A. Milyutina [Russie] ; V. K. Bobrova [Russie] ; L. V. Ozerova [Russie] ; A. V. Troitsky [Russie] ; A. G. Solovyev ; S. Y. Morozov [Russie]Source :
- Journal of Biomedicine and Biotechnology [ 1110-7243 ] ; 2009.
Abstract
TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in
Url:
DOI: 10.1155/2009/952304
PubMed: 19859540
PubMed Central: 2762245
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Milyutina</name><affiliation wicri:level="4"><nlm:aff id="I2">A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><orgName type="university">Université d'État de Moscou</orgName><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author><author><name sortKey="Bobrova, V K" sort="Bobrova, V K" uniqKey="Bobrova V" first="V. K." last="Bobrova">V. K. Bobrova</name><affiliation wicri:level="4"><nlm:aff id="I2">A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>A.N. 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Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><orgName type="university">Université d'État de Moscou</orgName><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">19859540</idno><idno type="pmc">2762245</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2762245</idno><idno type="RBID">PMC:2762245</idno><idno type="doi">10.1155/2009/952304</idno><date when="2009">2009</date><idno type="wicri:Area/Pmc/Corpus">001006</idno><idno type="wicri:Area/Pmc/Curation">001005</idno><idno type="wicri:Area/Pmc/Checkpoint">001008</idno><idno type="wicri:Area/Ncbi/Merge">000A69</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis</title><author><name sortKey="Krasnikova, M S" sort="Krasnikova, M S" uniqKey="Krasnikova M" first="M. S." last="Krasnikova">M. S. Krasnikova</name><affiliation wicri:level="1"><nlm:aff id="I1">Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskaya 42, 127550 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskaya 42, 127550 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author><author><name sortKey="Milyutina, I A" sort="Milyutina, I A" uniqKey="Milyutina I" first="I. A." last="Milyutina">I. A. Milyutina</name><affiliation wicri:level="4"><nlm:aff id="I2">A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><orgName type="university">Université d'État de Moscou</orgName><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author><author><name sortKey="Bobrova, V K" sort="Bobrova, V K" uniqKey="Bobrova V" first="V. K." last="Bobrova">V. K. Bobrova</name><affiliation wicri:level="4"><nlm:aff id="I2">A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><orgName type="university">Université d'État de Moscou</orgName><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author><author><name sortKey="Ozerova, L V" sort="Ozerova, L V" uniqKey="Ozerova L" first="L. V." last="Ozerova">L. V. Ozerova</name><affiliation wicri:level="1"><nlm:aff id="I3">Main Botanic Garden Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>Main Botanic Garden Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author><author><name sortKey="Troitsky, A V" sort="Troitsky, A V" uniqKey="Troitsky A" first="A. V." last="Troitsky">A. V. Troitsky</name><affiliation wicri:level="4"><nlm:aff id="I2">A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><orgName type="university">Université d'État de Moscou</orgName><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author><author><name sortKey="Solovyev, A G" sort="Solovyev, A G" uniqKey="Solovyev A" first="A. G." last="Solovyev">A. G. Solovyev</name><affiliation><nlm:aff>NONE</nlm:aff></affiliation><affiliation><nlm:aff>NONE</nlm:aff></affiliation></author><author><name sortKey="Morozov, S Y" sort="Morozov, S Y" uniqKey="Morozov S" first="S. Y." last="Morozov">S. Y. Morozov</name><affiliation wicri:level="4"><nlm:aff id="I2">A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</nlm:aff><country xml:lang="fr">Russie</country><wicri:regionArea>A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow</wicri:regionArea><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName><orgName type="university">Université d'État de Moscou</orgName><placeName><settlement type="city">Moscou</settlement><region>District fédéral central</region></placeName></affiliation></author></analytic><series><title level="j">Journal of Biomedicine and Biotechnology</title><idno type="ISSN">1110-7243</idno><idno type="eISSN">1110-7251</idno><imprint><date when="2009">2009</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in <italic>Arabidopsis thaliana</italic> is controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the 3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the 5′-terminal miR390 target site.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Baulcombe, D" uniqKey="Baulcombe D">D Baulcombe</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vazquez, F" uniqKey="Vazquez F">F Vazquez</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vaucheret, H" uniqKey="Vaucheret H">H Vaucheret</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Vaucheret, H" uniqKey="Vaucheret H">H Vaucheret</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bonnet, E" uniqKey="Bonnet E">E Bonnet</name></author><author><name sortKey="Van De 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<front><journal-meta><journal-id journal-id-type="nlm-ta">J Biomed Biotechnol</journal-id><journal-id journal-id-type="publisher-id">JBB</journal-id><journal-title-group><journal-title>Journal of Biomedicine and Biotechnology</journal-title></journal-title-group><issn pub-type="ppub">1110-7243</issn><issn pub-type="epub">1110-7251</issn><publisher><publisher-name>Hindawi Publishing Corporation</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">19859540</article-id><article-id pub-id-type="pmc">2762245</article-id><article-id pub-id-type="doi">10.1155/2009/952304</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title>Novel miR390-Dependent Transacting siRNA Precursors in Plants Revealed by a PCR-Based Experimental Approach and Database Analysis</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Krasnikova</surname><given-names>M. S.</given-names></name><xref ref-type="aff" rid="I1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Milyutina</surname><given-names>I. A.</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Bobrova</surname><given-names>V. K.</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Ozerova</surname><given-names>L. V.</given-names></name><xref ref-type="aff" rid="I3"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Troitsky</surname><given-names>A. V.</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>Solovyev</surname><given-names>A. G.</given-names></name><xref ref-type="aff" rid="I1"><sup>1, 2</sup></xref><xref ref-type="aff" rid="I2"></xref></contrib><contrib contrib-type="author"><name><surname>Morozov</surname><given-names>S. Y.</given-names></name><xref ref-type="aff" rid="I2"><sup>2</sup></xref><xref ref-type="corresp" rid="cor1">*</xref></contrib></contrib-group><aff id="I1"><sup>1</sup>Institute of Agricultural Biotechnology, Russian Academy of Agricultural Sciences, Timiryazevskaya 42, 127550 Moscow, Russia</aff><aff id="I2"><sup>2</sup>A.N. Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119992 Moscow, Russia</aff><aff id="I3"><sup>3</sup>Main Botanic Garden Russian Academy of Sciences, Botanicheskaya 4, 127276 Moscow, Russia</aff><author-notes><corresp id="cor1">*S. Y. Morozov: <email>morozov@genebee.msu.su</email></corresp><fn fn-type="other"><p>Recommended by Zhumur Ghosh</p></fn></author-notes><pub-date pub-type="ppub"><year>2009</year></pub-date><pub-date pub-type="epub"><day>13</day><month>10</month><year>2009</year></pub-date><volume>2009</volume><elocation-id>952304</elocation-id><history><date date-type="received"><day>28</day><month>2</month><year>2009</year></date><date date-type="accepted"><day>31</day><month>7</month><year>2009</year></date></history><permissions><copyright-statement>Copyright © 2009 M. S. Krasnikova et al.</copyright-statement><copyright-year>2009</copyright-year><license license-type="open-access"><license-p>This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>TAS loci in plant genomes encode transacting small interfering RNAs (ta-siRNAs) that regulate expression of a number of genes. The function of TAS3 precursor in <italic>Arabidopsis thaliana</italic> is controlled by two miR390 target sites flanking two ta-siARF sequences targeting mRNAs of ARF transcription factors. Cleavage of the 3′-miR390-site initiates ta-siRNAs biogenesis. Here we describe the new method for identification of plant ta-siRNA precursors based on PCR with oligodeoxyribonucleotide primers mimicking miR390. The method was found to be efficient for dicotiledonous plants, cycads, and mosses. Based on sequences of amplified loci and a database analysis, a novel type of miR390-dependent TAS sequences was identified in dicots. These TAS loci are characterized by a smaller distance between miR390 sites compared to TAS3, a single copy of ta-siARF, and a sequence conservation pattern pointing to the possibility that processing of novel TAS-like locus is initiated by cleavage of the 5′-terminal miR390 target site.</p></abstract></article-meta></front><floats-group><fig id="fig1" position="float"><label>Figure 1</label><caption><p>Agarose gel analysis of PCR products. (a) Amplification of genomic DNA sequences flanked by miR390 sites. PCR products were obtained on <italic>Nicotiana tabacum</italic> genomic DNA with primers P-Tas3 and M-Tas3/caa (Lane 1), on <italic>N. tabacum</italic> genomic DNA with primers P-Tas3 and M-Tas3/aca (Lane 2), on <italic>Arabidopsis thaliana</italic> genomic DNA with primers P-Tas3 and M-Tas3/caa (Lane 3), and on <italic>A. thaliana</italic> genomic DNA with primers P-Tas3 and M-Tas3/aca (Lane 4). Arrow points to the 170-nt PCR product. M is DNA size markers. Marker fragment sizes in base pairs are indicated on the left. (b) Amplification of <italic>N. tabacum</italic> genomic DNA and cDNA preparation. PCR products were obtained on <italic>N. tabacum</italic> genomic DNA with primers P-Tas3 and M-Tas3/caa (Lane 1), on <italic>N. tabacum</italic> cDNA with primers P-Tas3 and M-Tas3/caa (Lane 2), and on <italic>N. tabacum</italic> cDNA with primers P-Tas3 and M-Tas3/aca (Lane 3). M is DNA size markers. Marker fragment sizes in base pairs are indicated on the left.</p></caption><graphic xlink:href="JBB2009-952304.001"></graphic></fig><fig id="fig2" position="float"><label>Figure 2</label><caption><p>Nucleotide sequence alignment of “280-nt-long” ta-siARF loci of dicot plants. Sequences of <italic>Nicotiana tabacum</italic> and <italic>Nicotiana benthamiana</italic> (undelined) were determined in this study, the others were from GeneBank. Boxes indicate miR390 complementary sites and ta-siARF-encoding sequence regions. The length of nonconserved sequence between the 5′-miR390 complementary site and ta-siARF sequence not included in the alignment is indicated. Shading shows residues identical for the given position in most sequences. Sequences of <italic>N. tabacum</italic> and <italic>N. benthamiana</italic> miR390 complementary sites originate from primers used for the amplification of ta-siARF loci. GeneBank accession numbers of the sequences included in the alignment are as follows: <italic>Nicotiana tabacum</italic>, FJ804751; <italic>Nicotiana benthamiana</italic>, FJ804742; <italic>Arabidopsis thaliana</italic>, BX838290; <italic>Glycine max</italic>, BE330988; <italic>Manihot esculenta</italic>, CK652751; <italic>Malus domestica</italic>, CN490861; <italic>Vitis vinifera</italic>, DT025007; <italic>Populus trichocarpa</italic>, DT498974; <italic>Lycopersicon esculentum</italic>, DV105041.</p></caption><graphic xlink:href="JBB2009-952304.002"></graphic></fig><fig id="fig3" position="float"><label>Figure 3</label><caption><p>Nucleotide sequence alignment of “170-nt-long” ta-siARF loci of dicot plants. Sequences of <italic>Nicotiana tabacum, Datura stramonium</italic>, <italic>Solanum demissum,</italic> and <italic>Physalis longifolia</italic> (undelined) were determined in this study the others were from GeneBank. Boxes indicate miR390 complementary sites and ta-siARF-encoding sequence regions. The length of nonconserved sequence between the ta-siARF sequence and 3′-miR390 complementary site not included in the alignment is indicated. Dashes in the sequences of <italic>Cichorium endivia</italic>, <italic>Citrus aurantium</italic>, <italic>Citrus sinensis,</italic> and <italic>Populus tremula</italic> indicate the sequence region lacking the 3′-miR390 complementary site that could not be aligned with other sequences. Shading shows residues identical for the given position in most sequences. Sequences of <italic>N. tabacum, D. stramonium</italic>, <italic>S. demissum,</italic> and <italic>P. longifolia</italic> miR390 complementary sites originate from primers used for the amplification of ta-siARF loci. GeneBank accession numbers of the sequences included in the alignment are as follows: <italic>Nicotiana tabacum</italic>, FJ804743; <italic>Datura stramonium</italic>, FJ804744; <italic>Solanum demissum</italic>, FJ804745; <italic>Physalis longifolia</italic>, FJ804746; <italic>Nicotiana tabacum</italic>, AM791738; <italic>Solanum lycopersicum</italic>, BE459870; <italic>Vitis vinifera</italic>, CU775162; <italic>Beta vulgaris</italic>, CV301446; <italic>Manihot esculenta</italic>, DV447689; <italic>Gossypium hirsutum</italic>, DW502659; <italic>Helianthus exilis</italic> 1, EE630512; <italic>Helianthus exilis</italic> 2, EE657417; <italic>Cyamopsis tetragonoloba</italic>, EG977206; <italic>Vigna unguiculata</italic>, FG922881; <italic>Cynara scolymus</italic>, GE588140; <italic>Cichorium endivia</italic>, EL348656; <italic>Citrus aurantium,</italic> EY848024; <italic>Citrus sinensis</italic>, CK935773; <italic>Populus tremula</italic>, DN500355.</p></caption><graphic xlink:href="JBB2009-952304.003"></graphic></fig><fig id="fig4" position="float"><label>Figure 4</label><caption><p>Nucleotide sequence alignment of “short” ta-siARF loci of cycad and conifer plants. The sequence of <italic>Cycas revoluta</italic> (undelined) was determined in this study, the others were taken from GeneBank. Boxes indicate miR390 complementary sites and ta-siARF sequence regions. Shading shows residues identical for the given position in most sequences. Sequences of <italic>C. revoluta</italic> miR390 complementary sites originate from primers used for the amplification of ta-siARF loci. GeneBank accession numbers of the sequences included in the alignment are as follows: <italic>Cycas revoluta</italic>, FJ804750; <italic>Picea sitchensis</italic>, EF086492; <italic>Pinus pinaster</italic>, BX682439; <italic>Pinus taeda</italic>, CV034496; <italic>Picea sitchensis</italic>, CO220369; <italic>Zamia fischeri</italic>, DY034932; <italic>Cryptomeria japonica</italic>, DC432705.</p></caption><graphic xlink:href="JBB2009-952304.004"></graphic></fig><fig id="fig5" position="float"><label>Figure 5</label><caption><p>Nucleotide sequence alignment of ta-siARF loci of mosses. (a) Alignment of <italic>Brachythecium latifolium</italic> clone 50 Br sequence and <italic>Physcomitrella patens</italic> TAS3d. (b) Alignment of <italic>B. latifolium</italic> clone 47 Br sequence and <italic>Hookeria lucens</italic> with <italic>P. patens</italic> TAS3b and TAS3c. Sequences of <italic>B. latifolium</italic> and <italic>H. lucens</italic> (undelined) were determined in this study, the others were from GeneBank. Boxes indicate miR390 complementary sites, ta-siARF sequence regions and ta-siAP2 regions. Shading shows residues identical for the given position in most sequences. Sequences of <italic>B. latifolium</italic> and <italic>H. lucens</italic> miR390 complementary sites originate from primers used for the amplification of ta-siARF loci. GeneBank accession numbers of the sequences included in the alignment are as follows: <italic>Brachythecium latifolium</italic> clone 50 Br, FJ804747; <italic>Brachythecium latifolium</italic> clone 47 Br, FJ804748; <italic>Hookeria lucens</italic>, FJ804749; <italic>Physcomitrella patens</italic> TAS3d, BK005828; <italic>P. patens</italic> TAS3b, BK005826; <italic>P. patens</italic> TAS3c, BK005827.</p></caption><graphic xlink:href="JBB2009-952304.005"></graphic></fig></floats-group></pmc><affiliations><list><country><li>Russie</li></country><region><li>District fédéral central</li></region><settlement><li>Moscou</li></settlement><orgName><li>Université d'État de Moscou</li></orgName></list><tree><noCountry><name sortKey="Solovyev, A G" sort="Solovyev, A G" uniqKey="Solovyev A" first="A. G." last="Solovyev">A. G. Solovyev</name></noCountry><country name="Russie"><region name="District fédéral central"><name sortKey="Krasnikova, M S" sort="Krasnikova, M S" uniqKey="Krasnikova M" first="M. S." last="Krasnikova">M. S. Krasnikova</name></region><name sortKey="Bobrova, V K" sort="Bobrova, V K" uniqKey="Bobrova V" first="V. K." last="Bobrova">V. K. Bobrova</name><name sortKey="Milyutina, I A" sort="Milyutina, I A" uniqKey="Milyutina I" first="I. A." last="Milyutina">I. A. Milyutina</name><name sortKey="Morozov, S Y" sort="Morozov, S Y" uniqKey="Morozov S" first="S. Y." last="Morozov">S. Y. Morozov</name><name sortKey="Ozerova, L V" sort="Ozerova, L V" uniqKey="Ozerova L" first="L. V." last="Ozerova">L. V. Ozerova</name><name sortKey="Troitsky, A V" sort="Troitsky, A V" uniqKey="Troitsky A" first="A. V." last="Troitsky">A. V. Troitsky</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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