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RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases

Identifieur interne : 000051 ( Pmc/Checkpoint ); précédent : 000050; suivant : 000052

RNA-dependent RNA polymerase 1 in potato (Solanum tuberosum) and its relationship to other plant RNA-dependent RNA polymerases

Auteurs : Lydia J. R. Hunter [Royaume-Uni] ; Samuel F. Brockington [Royaume-Uni] ; Alex M. Murphy [Royaume-Uni] ; Adrienne E. Pate [Royaume-Uni] ; Kristina Gruden [Slovénie] ; Stuart A. Macfarlane [Royaume-Uni] ; Peter Palukaitis [Royaume-Uni, Corée du Sud] ; John P. Carr [Royaume-Uni]

Source :

RBID : PMC:4793286

Abstract

Cellular RNA-dependent RNA polymerases (RDRs) catalyze synthesis of double-stranded RNAs that can serve to initiate or amplify RNA silencing. Arabidopsis thaliana has six RDR genes; RDRs 1, 2 and 6 have roles in anti-viral RNA silencing. RDR6 is constitutively expressed but RDR1 expression is elevated following plant treatment with defensive phytohormones. RDR1 also contributes to basal virus resistance. RDR1 has been studied in several species including A. thaliana, tobacco (Nicotiana tabacum), N. benthamiana, N. attenuata and tomato (Solanum lycopersicum) but not to our knowledge in potato (S. tuberosum). StRDR1 was identified and shown to be salicylic acid-responsive. StRDR1 transcript accumulation decreased in transgenic potato plants constitutively expressing a hairpin construct and these plants were challenged with three viruses: potato virus Y, potato virus X, and tobacco mosaic virus. Suppression of StRDR1 gene expression did not increase the susceptibility of potato to these viruses. Phylogenetic analysis of RDR genes present in potato and in a range of other plant species identified a new RDR gene family, not present in potato and found only in Rosids (but apparently lost in the Rosid A. thaliana) for which we propose the name RDR7.


Url:
DOI: 10.1038/srep23082
PubMed: 26979928
PubMed Central: 4793286


Affiliations:


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PMC:4793286

Le document en format XML

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<title xml:lang="en" level="a" type="main">RNA-dependent RNA polymerase 1 in potato (
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) and its relationship to other plant RNA-dependent RNA polymerases</title>
<author>
<name sortKey="Hunter, Lydia J R" sort="Hunter, Lydia J R" uniqKey="Hunter L" first="Lydia J. R." last="Hunter">Lydia J. R. Hunter</name>
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<institution>Department of Plant Sciences, University of Cambridge</institution>
, Cambridge CB2 3EA,
<country>UK</country>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<nlm:aff id="a2">
<institution>The James Hutton Institute</institution>
, Invergowrie, Dundee DD2 5DA,
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<name sortKey="Brockington, Samuel F" sort="Brockington, Samuel F" uniqKey="Brockington S" first="Samuel F." last="Brockington">Samuel F. Brockington</name>
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<institution>Department of Plant Sciences, University of Cambridge</institution>
, Cambridge CB2 3EA,
<country>UK</country>
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<country xml:lang="fr">Royaume-Uni</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<country>UK</country>
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<name sortKey="Pate, Adrienne E" sort="Pate, Adrienne E" uniqKey="Pate A" first="Adrienne E." last="Pate">Adrienne E. Pate</name>
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<name sortKey="Gruden, Kristina" sort="Gruden, Kristina" uniqKey="Gruden K" first="Kristina" last="Gruden">Kristina Gruden</name>
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, Večna pot 111, 1000 Ljubljana,
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<div type="abstract" xml:lang="en">
<p>Cellular RNA-dependent RNA polymerases (RDRs) catalyze synthesis of double-stranded RNAs that can serve to initiate or amplify RNA silencing.
<italic>Arabidopsis thaliana</italic>
has six
<italic>RDR</italic>
genes;
<italic>RDRs 1</italic>
,
<italic>2</italic>
and
<italic>6</italic>
have roles in anti-viral RNA silencing.
<italic>RDR6</italic>
is constitutively expressed but
<italic>RDR1</italic>
expression is elevated following plant treatment with defensive phytohormones. RDR1 also contributes to basal virus resistance. RDR1 has been studied in several species including
<italic>A. thaliana</italic>
, tobacco (
<italic>Nicotiana tabacum</italic>
),
<italic>N. benthamiana</italic>
,
<italic>N. attenuata</italic>
and tomato (
<italic>Solanum lycopersicum</italic>
) but not to our knowledge in potato (
<italic>S. tuberosum</italic>
).
<italic>StRDR1</italic>
was identified and shown to be salicylic acid-responsive.
<italic>StRDR1</italic>
transcript accumulation decreased in transgenic potato plants constitutively expressing a hairpin construct and these plants were challenged with three viruses: potato virus Y, potato virus X, and tobacco mosaic virus. Suppression of
<italic>StRDR1</italic>
gene expression did not increase the susceptibility of potato to these viruses. Phylogenetic analysis of
<italic>RDR</italic>
genes present in potato and in a range of other plant species identified a new
<italic>RDR</italic>
gene family, not present in potato and found only in Rosids (but apparently lost in the Rosid
<italic>A. thaliana</italic>
) for which we propose the name
<italic>RDR7</italic>
.</p>
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</TEI>
<pmc article-type="research-article">
<pmc-dir>properties open_access</pmc-dir>
<front>
<journal-meta>
<journal-id journal-id-type="nlm-ta">Sci Rep</journal-id>
<journal-id journal-id-type="iso-abbrev">Sci Rep</journal-id>
<journal-title-group>
<journal-title>Scientific Reports</journal-title>
</journal-title-group>
<issn pub-type="epub">2045-2322</issn>
<publisher>
<publisher-name>Nature Publishing Group</publisher-name>
</publisher>
</journal-meta>
<article-meta>
<article-id pub-id-type="pmid">26979928</article-id>
<article-id pub-id-type="pmc">4793286</article-id>
<article-id pub-id-type="pii">srep23082</article-id>
<article-id pub-id-type="doi">10.1038/srep23082</article-id>
<article-categories>
<subj-group subj-group-type="heading">
<subject>Article</subject>
</subj-group>
</article-categories>
<title-group>
<article-title>RNA-dependent RNA polymerase 1 in potato (
<italic>Solanum tuberosum</italic>
) and its relationship to other plant RNA-dependent RNA polymerases</article-title>
</title-group>
<contrib-group>
<contrib contrib-type="author">
<name>
<surname>Hunter</surname>
<given-names>Lydia J. R.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
<xref ref-type="aff" rid="a2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Brockington</surname>
<given-names>Samuel F.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Murphy</surname>
<given-names>Alex M.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Pate</surname>
<given-names>Adrienne E.</given-names>
</name>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Gruden</surname>
<given-names>Kristina</given-names>
</name>
<xref ref-type="aff" rid="a3">3</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>MacFarlane</surname>
<given-names>Stuart A.</given-names>
</name>
<xref ref-type="aff" rid="a2">2</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Palukaitis</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="a2">2</xref>
<xref ref-type="aff" rid="a4">4</xref>
</contrib>
<contrib contrib-type="author">
<name>
<surname>Carr</surname>
<given-names>John P.</given-names>
</name>
<xref ref-type="corresp" rid="c1">a</xref>
<xref ref-type="aff" rid="a1">1</xref>
</contrib>
<aff id="a1">
<label>1</label>
<institution>Department of Plant Sciences, University of Cambridge</institution>
, Cambridge CB2 3EA,
<country>UK</country>
</aff>
<aff id="a2">
<label>2</label>
<institution>The James Hutton Institute</institution>
, Invergowrie, Dundee DD2 5DA,
<country>UK</country>
</aff>
<aff id="a3">
<label>3</label>
<institution>National Institute of Biology</institution>
, Večna pot 111, 1000 Ljubljana,
<country>Slovenia</country>
</aff>
<aff id="a4">
<label>4</label>
<institution>Division of Environmental and Life Sciences, Seoul Women’s University</institution>
, Seoul,
<country>Republic of Korea</country>
</aff>
</contrib-group>
<author-notes>
<corresp id="c1">
<label>a</label>
<email>jpc1005@hermes.cam.ac.uk</email>
</corresp>
</author-notes>
<pub-date pub-type="epub">
<day>16</day>
<month>03</month>
<year>2016</year>
</pub-date>
<pub-date pub-type="collection">
<year>2016</year>
</pub-date>
<volume>6</volume>
<elocation-id>23082</elocation-id>
<history>
<date date-type="received">
<day>02</day>
<month>11</month>
<year>2015</year>
</date>
<date date-type="accepted">
<day>22</day>
<month>02</month>
<year>2016</year>
</date>
</history>
<permissions>
<copyright-statement>Copyright © 2016, Macmillan Publishers Limited</copyright-statement>
<copyright-year>2016</copyright-year>
<copyright-holder>Macmillan Publishers Limited</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/4.0/">
<pmc-comment>author-paid</pmc-comment>
<license-p>This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit
<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>
</license-p>
</license>
</permissions>
<abstract>
<p>Cellular RNA-dependent RNA polymerases (RDRs) catalyze synthesis of double-stranded RNAs that can serve to initiate or amplify RNA silencing.
<italic>Arabidopsis thaliana</italic>
has six
<italic>RDR</italic>
genes;
<italic>RDRs 1</italic>
,
<italic>2</italic>
and
<italic>6</italic>
have roles in anti-viral RNA silencing.
<italic>RDR6</italic>
is constitutively expressed but
<italic>RDR1</italic>
expression is elevated following plant treatment with defensive phytohormones. RDR1 also contributes to basal virus resistance. RDR1 has been studied in several species including
<italic>A. thaliana</italic>
, tobacco (
<italic>Nicotiana tabacum</italic>
),
<italic>N. benthamiana</italic>
,
<italic>N. attenuata</italic>
and tomato (
<italic>Solanum lycopersicum</italic>
) but not to our knowledge in potato (
<italic>S. tuberosum</italic>
).
<italic>StRDR1</italic>
was identified and shown to be salicylic acid-responsive.
<italic>StRDR1</italic>
transcript accumulation decreased in transgenic potato plants constitutively expressing a hairpin construct and these plants were challenged with three viruses: potato virus Y, potato virus X, and tobacco mosaic virus. Suppression of
<italic>StRDR1</italic>
gene expression did not increase the susceptibility of potato to these viruses. Phylogenetic analysis of
<italic>RDR</italic>
genes present in potato and in a range of other plant species identified a new
<italic>RDR</italic>
gene family, not present in potato and found only in Rosids (but apparently lost in the Rosid
<italic>A. thaliana</italic>
) for which we propose the name
<italic>RDR7</italic>
.</p>
</abstract>
</article-meta>
</front>
<floats-group>
<fig id="f1">
<label>Figure 1</label>
<caption>
<title>Phylogenetic analysis of plant
<italic>RDR</italic>
genes.</title>
<p>(
<bold>a</bold>
) Phylogeny of the potato
<italic>RDR</italic>
genes with other plant
<italic>RDR</italic>
s. White open circles are clade names, black circles are inferred gene duplications, red boxes are
<italic>Solanum tuberosum</italic>
sequences and grey boxes are
<italic>Arabidopsis thaliana</italic>
sequences. The
<italic>S. tuberosum RDR</italic>
sequences found on the Potato Genome Sequencing Consortium (PGSC) database are accompanied by their PGSC coding-sequence number. (
<bold>b</bold>
) Rosid-specific
<italic>RDR7</italic>
phylogeny. This enlarged section of (
<bold>a</bold>
) shows the Rosid species that possess
<italic>RDR7</italic>
gene sequences.</p>
</caption>
<graphic xlink:href="srep23082-f1"></graphic>
</fig>
<fig id="f2">
<label>Figure 2</label>
<caption>
<title>RTqPCR analysis of
<italic>StRDR1</italic>
expression after salicylic acid (SA) treatment of Pentland Dell potato plants.</title>
<p>Samples were taken at 0 hours (immediately before treatment), 24 hours and 48 hours after SA or control (water) treatment. Control-treated Pentland Dell plants were sprayed with water and the control sample at 0 hours was used as the reference. Cyclophilin was used as the reference gene for the RTqPCR analysis. Significant increases in
<italic>StRDR1</italic>
transcript accumulation were seen at 24 hours and 48 hours after SA treatment (p < 0.005; *). Error bars represent standard error of the mean.</p>
</caption>
<graphic xlink:href="srep23082-f2"></graphic>
</fig>
<fig id="f3">
<label>Figure 3</label>
<caption>
<title>Generation of
<italic>StRDR1</italic>
-depleted transgenic potato lines.</title>
<p>PCR of plant genomic DNA to verify the presence of the
<italic>StRDR1</italic>
-specific hairpin constructs RNAi1 (
<bold>a</bold>
) or RNAi2 (
<bold>b</bold>
) in the transformed potato lines. PCR used a primer complementary to a sequence located in the 35S promoter of the T-DNA insert and primers specific to either RNAi 1 and 2, to amplify regions of 535 bp and 550 bp, respectively. DNA from non-transformed (NT) plants and a no template PCR control (negative: -ve) were included in the analysis and control PCR reactions were carried out using primers specific for β-tubulin (expected product of 480 bp). (
<bold>c</bold>
)
<italic>StRDR1</italic>
accumulation is efficiently decreased in a potato lines expressing the RNAi1 (Line 1.3) and RNAi2 construct (Line 2.5) (for other examples see
<xref ref-type="supplementary-material" rid="S1">Supplementary Fig. S3</xref>
). Accumulation levels of transcripts of
<italic>StRDR2</italic>
(
<bold>d</bold>
) and
<italic>StRDR6</italic>
(
<bold>e</bold>
) were not diminished in plants of transgenic lines expressing either RNAi1 or RNAi2 to inhibit StRDR1 expression. Error bars represent standard error of the mean.</p>
</caption>
<graphic xlink:href="srep23082-f3"></graphic>
</fig>
<fig id="f4">
<label>Figure 4</label>
<caption>
<title>TMV infection and
<italic>StRDR1</italic>
transcript accumulation in
<italic>StRDR1</italic>
-depleted transgenic potato plants.</title>
<p>(
<bold>a</bold>
) RTqPCR was used to determine the relative level of TMV coat protein (
<italic>CP</italic>
) RNA (
<bold>a</bold>
) in inoculated leaves of non-transformed (NT) and transgenic Line 1.3 plants at 7 days post-inoculation (dpi). RNA was also extracted from mock-inoculated leaves. In each of three independent experiments, TMV
<italic>CP</italic>
RNA accumulation in transgenic samples was normalized to that in the non-transformed control. In only one experiment was any significant increase in CP accumulation noted (p = 0.007: *) (
<bold>b</bold>
) RTqPCR was used to measure accumulation, relative to that mock-inoculated non-transformed plant, of
<italic>RDR1</italic>
in mock-inoculated and TMV-inoculated plants at 7 dpi in inoculated, mock-inoculated leaves and upper non-inoculated leaves. Error bars represent standard error of the mean.</p>
</caption>
<graphic xlink:href="srep23082-f4"></graphic>
</fig>
<fig id="f5">
<label>Figure 5</label>
<caption>
<title>Accumulation of PVX and PVY
<sup>O</sup>
RNA in
<italic>StRDR1</italic>
-depleted transgenic potato plants.</title>
<p>RTqPCR was used to determine the relative levels of PVX (
<bold>a</bold>
) and PVY
<sup>O</sup>
(
<bold>b</bold>
) RNA in inoculated leaves of non-transformed (NT) and transgenic Line 1.3 plants at 7 and 10 days post-inoculation, respectively. RNA was also extracted from mock-inoculated leaves. In each of three independent experiments, viral RNA accumulation in transgenic samples was normalized to that in the non-transformed control. Error bars represent standard error of the mean.</p>
</caption>
<graphic xlink:href="srep23082-f5"></graphic>
</fig>
</floats-group>
</pmc>
<affiliations>
<list>
<country>
<li>Corée du Sud</li>
<li>Royaume-Uni</li>
<li>Slovénie</li>
</country>
</list>
<tree>
<country name="Royaume-Uni">
<noRegion>
<name sortKey="Hunter, Lydia J R" sort="Hunter, Lydia J R" uniqKey="Hunter L" first="Lydia J. R." last="Hunter">Lydia J. R. Hunter</name>
</noRegion>
<name sortKey="Brockington, Samuel F" sort="Brockington, Samuel F" uniqKey="Brockington S" first="Samuel F." last="Brockington">Samuel F. Brockington</name>
<name sortKey="Carr, John P" sort="Carr, John P" uniqKey="Carr J" first="John P." last="Carr">John P. Carr</name>
<name sortKey="Hunter, Lydia J R" sort="Hunter, Lydia J R" uniqKey="Hunter L" first="Lydia J. R." last="Hunter">Lydia J. R. Hunter</name>
<name sortKey="Macfarlane, Stuart A" sort="Macfarlane, Stuart A" uniqKey="Macfarlane S" first="Stuart A." last="Macfarlane">Stuart A. Macfarlane</name>
<name sortKey="Murphy, Alex M" sort="Murphy, Alex M" uniqKey="Murphy A" first="Alex M." last="Murphy">Alex M. Murphy</name>
<name sortKey="Palukaitis, Peter" sort="Palukaitis, Peter" uniqKey="Palukaitis P" first="Peter" last="Palukaitis">Peter Palukaitis</name>
<name sortKey="Pate, Adrienne E" sort="Pate, Adrienne E" uniqKey="Pate A" first="Adrienne E." last="Pate">Adrienne E. Pate</name>
</country>
<country name="Slovénie">
<noRegion>
<name sortKey="Gruden, Kristina" sort="Gruden, Kristina" uniqKey="Gruden K" first="Kristina" last="Gruden">Kristina Gruden</name>
</noRegion>
</country>
<country name="Corée du Sud">
<noRegion>
<name sortKey="Palukaitis, Peter" sort="Palukaitis, Peter" uniqKey="Palukaitis P" first="Peter" last="Palukaitis">Peter Palukaitis</name>
</noRegion>
</country>
</tree>
</affiliations>
</record>

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