De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes
Identifieur interne : 000159 ( Pmc/Corpus ); précédent : 000158; suivant : 000160De Novo Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes
Auteurs : Yevgen Zolotarov ; Martina StrömvikSource :
- PLoS ONE [ 1932-6203 ] ; 2015.
Abstract
Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes,
Url:
DOI: 10.1371/journal.pone.0129016
PubMed: 26114291
PubMed Central: 4482647
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en"><italic>De Novo</italic> Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes</title><author><name sortKey="Zolotarov, Yevgen" sort="Zolotarov, Yevgen" uniqKey="Zolotarov Y" first="Yevgen" last="Zolotarov">Yevgen Zolotarov</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Stromvik, Martina" sort="Stromvik, Martina" uniqKey="Stromvik M" first="Martina" last="Strömvik">Martina Strömvik</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">26114291</idno><idno type="pmc">4482647</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4482647</idno><idno type="RBID">PMC:4482647</idno><idno type="doi">10.1371/journal.pone.0129016</idno><date when="2015">2015</date><idno type="wicri:Area/Pmc/Corpus">000159</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main"><italic>De Novo</italic> Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes</title><author><name sortKey="Zolotarov, Yevgen" sort="Zolotarov, Yevgen" uniqKey="Zolotarov Y" first="Yevgen" last="Zolotarov">Yevgen Zolotarov</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author><author><name sortKey="Stromvik, Martina" sort="Stromvik, Martina" uniqKey="Stromvik M" first="Martina" last="Strömvik">Martina Strömvik</name><affiliation><nlm:aff id="aff001"></nlm:aff></affiliation></author></analytic><series><title level="j">PLoS ONE</title><idno type="eISSN">1932-6203</idno><imprint><date when="2015">2015</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, <italic>de novo</italic> motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The K<sub>n</sub> dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a <monospace>GATA</monospace> core. SK<sub>n</sub> and Y<sub>n</sub>SK<sub>n</sub> dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. Y<sub>n</sub>K<sub>n</sub> dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Hannah, Ma" uniqKey="Hannah M">MA Hannah</name></author><author><name sortKey="Heyer, Ag" uniqKey="Heyer A">AG Heyer</name></author><author><name sortKey="Hincha, Dk" uniqKey="Hincha D">DK Hincha</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Maruyama, K" uniqKey="Maruyama K">K Maruyama</name></author><author><name sortKey="Takeda, M" uniqKey="Takeda M">M Takeda</name></author><author><name sortKey="Kidokoro, S" uniqKey="Kidokoro S">S Kidokoro</name></author><author><name sortKey="Yamada, K" uniqKey="Yamada K">K Yamada</name></author><author><name sortKey="Sakuma, Y" uniqKey="Sakuma Y">Y Sakuma</name></author><author><name sortKey="Urano, K" uniqKey="Urano K">K 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<front><journal-meta><journal-id journal-id-type="nlm-ta">PLoS One</journal-id><journal-id journal-id-type="iso-abbrev">PLoS ONE</journal-id><journal-id journal-id-type="publisher-id">plos</journal-id><journal-id journal-id-type="pmc">plosone</journal-id><journal-title-group><journal-title>PLoS ONE</journal-title></journal-title-group><issn pub-type="epub">1932-6203</issn><publisher><publisher-name>Public Library of Science</publisher-name><publisher-loc>San Francisco, CA USA</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">26114291</article-id><article-id pub-id-type="pmc">4482647</article-id><article-id pub-id-type="doi">10.1371/journal.pone.0129016</article-id><article-id pub-id-type="publisher-id">PONE-D-15-01354</article-id><article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject></subj-group></article-categories><title-group><article-title><italic>De Novo</italic> Regulatory Motif Discovery Identifies Significant Motifs in Promoters of Five Classes of Plant Dehydrin Genes</article-title><alt-title alt-title-type="running-head"><italic>De Novo</italic> Regulatory Motif Discovery in Plant Dehydrin Gene Promoters</alt-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Zolotarov</surname><given-names>Yevgen</given-names></name><xref ref-type="aff" rid="aff001"></xref></contrib><contrib contrib-type="author"><name><surname>Strömvik</surname><given-names>Martina</given-names></name><xref rid="cor001" ref-type="corresp">*</xref><xref ref-type="aff" rid="aff001"></xref></contrib></contrib-group><aff id="aff001"><addr-line>Department of Plant Science, Macdonald Campus, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada</addr-line></aff><contrib-group><contrib contrib-type="editor"><name><surname>Yang</surname><given-names>Haibing</given-names></name><role>Academic Editor</role><xref ref-type="aff" rid="edit1"></xref></contrib></contrib-group><aff id="edit1"><addr-line>Purdue University, UNITED STATES</addr-line></aff><author-notes><fn fn-type="conflict" id="coi001"><p><bold>Competing Interests: </bold>The authors have declared that no competing interests exist.</p></fn><fn fn-type="con" id="contrib001"><p>Conceived and designed the experiments: MS YZ. Performed the experiments: YZ. Analyzed the data: YZ. Contributed reagents/materials/analysis tools: MS. Wrote the paper: MS YZ.</p></fn><corresp id="cor001">* E-mail: <email>martina.stromvik@mcgill.ca</email></corresp></author-notes><pub-date pub-type="epub"><day>26</day><month>6</month><year>2015</year></pub-date><pub-date pub-type="collection"><year>2015</year></pub-date><volume>10</volume><issue>6</issue><elocation-id>e0129016</elocation-id><history><date date-type="received"><day>11</day><month>1</month><year>2015</year></date><date date-type="accepted"><day>4</day><month>5</month><year>2015</year></date></history><permissions><copyright-year>2015</copyright-year><copyright-holder>Zolotarov, Strömvik</copyright-holder><license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited</license-p></license></permissions><self-uri content-type="pdf" xlink:type="simple" xlink:href="pone.0129016.pdf"></self-uri><abstract><p>Plants accumulate dehydrins in response to osmotic stresses. Dehydrins are divided into five different classes, which are thought to be regulated in different manners. To better understand differences in transcriptional regulation of the five dehydrin classes, <italic>de novo</italic> motif discovery was performed on 350 dehydrin promoter sequences from a total of 51 plant genomes. Overrepresented motifs were identified in the promoters of five dehydrin classes. The K<sub>n</sub> dehydrin promoters contain motifs linked with meristem specific expression, as well as motifs linked with cold/dehydration and abscisic acid response. KS dehydrin promoters contain a motif with a <monospace>GATA</monospace> core. SK<sub>n</sub> and Y<sub>n</sub>SK<sub>n</sub> dehydrin promoters contain motifs that match elements connected with cold/dehydration, abscisic acid and light response. Y<sub>n</sub>K<sub>n</sub> dehydrin promoters contain motifs that match abscisic acid and light response elements, but not cold/dehydration response elements. Conserved promoter motifs are present in the dehydrin classes and across different plant lineages, indicating that dehydrin gene regulation is likely also conserved.</p></abstract><funding-group><funding-statement>This work was supported by a grant from Natural Sciences and Engineering Research Council of Canada (NSERC) (Grant no. 283303) to M.V.S.</funding-statement></funding-group><counts><fig-count count="0"></fig-count><table-count count="6"></table-count><page-count count="19"></page-count></counts><custom-meta-group><custom-meta id="data-availability"><meta-name>Data Availability</meta-name><meta-value>All relevant data are within the paper, its Supporting Information files, or via GitHub (<ext-link ext-link-type="uri" xlink:href="https://github.com/zolotarov/dehydrin_promoters">https://github.com/zolotarov/dehydrin_promoters</ext-link>).</meta-value></custom-meta></custom-meta-group></article-meta><notes><title>Data Availability</title><p>All relevant data are within the paper, its Supporting Information files, or via GitHub (<ext-link ext-link-type="uri" xlink:href="https://github.com/zolotarov/dehydrin_promoters">https://github.com/zolotarov/dehydrin_promoters</ext-link>).</p></notes></front><body><sec sec-type="intro" id="sec001"><title>Introduction</title><p>Plants have developed specific mechanisms that allow them to prepare for and survive drastic changes in their environment. One of the better-studied mechanisms is cold acclimation, which allows plants to develop freezing tolerance [<xref rid="pone.0129016.ref001" ref-type="bibr">1</xref>,<xref rid="pone.0129016.ref002" ref-type="bibr">2</xref>]. During exposure to low non-freezing temperatures gene expression is modulated and numerous solutes, known as osmoprotectants, and protective proteins accumulate in plant tissues. Dehydrins or dehydration proteins, (DHN) belong to group II LEA (late embryogenesis abundant) proteins. They are often found among those protective proteins and they are ubiquitous in transcriptomes of plants under osmotic stress, such as cold, drought and high salinity [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>–<xref rid="pone.0129016.ref007" ref-type="bibr">7</xref>]. All dehydrins contain a 15 amino acid K-segment, rich in lysine residues, represented by <monospace>EKKGIMDKIKEKLPG</monospace> conserved sequence [<xref rid="pone.0129016.ref008" ref-type="bibr">8</xref>]. The K-segment forms an amphipathic α-helix that allows dehydrins to stabilize plant membranes and proteins during dehydration stresses [<xref rid="pone.0129016.ref009" ref-type="bibr">9</xref>–<xref rid="pone.0129016.ref012" ref-type="bibr">12</xref>]. In addition to the K-segment, dehydrins can contain a Y-segment (T/VDEYGNP) and an S-segment (3+ serines) [<xref rid="pone.0129016.ref013" ref-type="bibr">13</xref>]. The S-segment is thought to be involved in ion binding and dehydrin phosphorylation, which induces a conformational change in dehydrins [<xref rid="pone.0129016.ref014" ref-type="bibr">14</xref>,<xref rid="pone.0129016.ref015" ref-type="bibr">15</xref>]. Currently, the function of the Y-segment is unknown. The dehydrins are categorized into 5 subclasses (K<sub>n</sub>, KS, SK<sub>n</sub>, Y<sub>n</sub>K<sub>n</sub> and Y<sub>n</sub>SK<sub>n</sub>) based on the presence and location of the 3 conserved segments [<xref rid="pone.0129016.ref013" ref-type="bibr">13</xref>]. Members of each subclass are expressed in response to a different set of stimuli. However, there is no clear link between subclass types and expression triggers [<xref rid="pone.0129016.ref016" ref-type="bibr">16</xref>].</p><p>As defined by Close, 1997, dehydrins must contain a K-segment. According to that definition, dehydrins are only found in plants. There are other proteins described as dehydrins, for example from <italic>Escherichia coli</italic> (GenBank: AAB18249.1), a fungus <italic>Pneumocystis carinii</italic> (GenBank: CAC43457.1) [<xref rid="pone.0129016.ref004" ref-type="bibr">4</xref>] or from whitish truffle <italic>Tuber borchii</italic> (GenBank: ABC33908.1) [<xref rid="pone.0129016.ref017" ref-type="bibr">17</xref>]. However, these proteins do not contain the K-segment or any of the other conserved dehydrin segments and therefore should not be considered to be proper dehydrins.</p><p>Stress response in plants can be regulated in an abscisic acid (ABA) dependent and/or independent manner [<xref rid="pone.0129016.ref018" ref-type="bibr">18</xref>]. Multiple transcription factors, such as C-repeat binding factor/dehydration responsive element binding protein (CBF/DREB) and ABA response element binding protein (AREB), participate in water stress response, by binding to <italic>cis</italic>-regulatory elements in the promoters of their respective regulons. The CBF1-3 are transcription factors that participate in ABA independent cold and dehydration induced gene expression [<xref rid="pone.0129016.ref019" ref-type="bibr">19</xref>] and they bind a C-repeat (CRT) <italic>cis</italic>-regulatory element core (CCGAC), also known as dehydration response element (DRE). Members of the CBF regulon include well-studied <italic>A</italic>. <italic>thaliana</italic> genes, such as LTI78/COR78 [<xref rid="pone.0129016.ref020" ref-type="bibr">20</xref>], COR15A and COR47 (an SK<sub>n</sub> dehydrin) [<xref rid="pone.0129016.ref021" ref-type="bibr">21</xref>]. However, not all members of the CBF regulon have the CRT <italic>cis</italic>-regulatory element in their promoters [<xref rid="pone.0129016.ref022" ref-type="bibr">22</xref>], hence there are yet undiscovered motifs that are involved in cold and drought response. Numerous transcription factors participate in the ABA dependent stress response and they bind several <italic>cis</italic>-regulatory elements with a <monospace>TACGTG</monospace> core [<xref rid="pone.0129016.ref023" ref-type="bibr">23</xref>]. Many members of the CBF regulon are also upregulated in response to drought and ABA exposure, demonstrating a cross-talk between stress-induced pathways [<xref rid="pone.0129016.ref024" ref-type="bibr">24</xref>]. For example, in barley (<italic>Hordeum vulgare</italic> L.), a K<sub>n</sub> dehydrin is strongly upregulated in response to cold, dehydration and ABA, and its promoter contains CRT and abscisic acid response elements (ABREs) <italic>cis</italic>-regulatory elements, whereas a barley SK<sub>n</sub> dehydrin, whose promoter contains multiple CRTs and no ABREs is only weakly upregulated in response to ABA, but shows a significant upregulation in response to cold [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>]. The expression of CBFs, and, in turn, their regulons, is modulated by photoperiod through phytochrome B and phytochrome-interacting factors [<xref rid="pone.0129016.ref025" ref-type="bibr">25</xref>,<xref rid="pone.0129016.ref026" ref-type="bibr">26</xref>].</p><p>In this study, we tested whether the different classes of dehydrin genes house specific and conserved <italic>cis</italic>-regulatory elements in their promoters that could contribute to gene characterization. <italic>De novo</italic> motif discovery, a computational approach to identify statistically overrepresented sequence motifs within a promoter sequence, was used to analyze a total of 350 dehydrin promoters. For each of the five dehydrin classes, statistically significant motifs were identified, and matched to experimentally validated <italic>cis</italic>-regulatory elements known from literature. Motifs linked to ABA-dependent and ABA-independent stress response pathways were detected in the promoters of dehydrin genes from various, distant plant lineages, which indicates that the stress response pathways regulating dehydrin expression are conserved.</p></sec><sec sec-type="materials|methods" id="sec002"><title>Methods</title><sec id="sec003"><title>Plant genomes used in the computational analyses</title><p>Permission to use data from genomes that are not published was obtained from members of sequencing consortia, where stated. In other cases, published data was used.</p><p>The following genome sequences were obtained from Phytozome v10 (<ext-link ext-link-type="uri" xlink:href="http://phytozome.jgi.doe.gov/">http://phytozome.jgi.doe.gov</ext-link>) [<xref rid="pone.0129016.ref027" ref-type="bibr">27</xref>] using BioMart [<xref rid="pone.0129016.ref028" ref-type="bibr">28</xref>]: <italic>Amborella trichopoda</italic> [<xref rid="pone.0129016.ref029" ref-type="bibr">29</xref>], <italic>Aquilegia coerulea</italic> (<italic>Aquilegia coerulea</italic> Genome Sequencing Project, <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/">http://www.phytozome.net/</ext-link>, permission obtained from Dr. Scott Hodges), <italic>Arabidopsis halleri</italic> (<italic>Arabidopsis halleri</italic> v1.1, DOE-JGI, <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/ahalleri">http://www.phytozome.net/ahalleri</ext-link>), <italic>Arabidopsis lyrata</italic> [<xref rid="pone.0129016.ref030" ref-type="bibr">30</xref>], <italic>Arabidopsis thaliana</italic> [<xref rid="pone.0129016.ref031" ref-type="bibr">31</xref>], <italic>Boechera stricta</italic> (<italic>Boechera stricta</italic> v1.2, DOE-JGI, <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/bstricta">http://www.phytozome.net/bstricta</ext-link>), <italic>Brachypodium distachyon</italic> [<xref rid="pone.0129016.ref032" ref-type="bibr">32</xref>], turnip mustard (<italic>Brassica rapa</italic> L.<italic>)</italic> [<xref rid="pone.0129016.ref033" ref-type="bibr">33</xref>,<xref rid="pone.0129016.ref034" ref-type="bibr">34</xref>], papaya (<italic>Carica papaya)</italic> [<xref rid="pone.0129016.ref035" ref-type="bibr">35</xref>], <italic>Capsella grandiflora</italic> and <italic>Capsella rubella</italic> [<xref rid="pone.0129016.ref036" ref-type="bibr">36</xref>], clementine (<italic>Citrus clementina)</italic> and, sweet orange (<italic>Citrus sinensis)</italic> [<xref rid="pone.0129016.ref037" ref-type="bibr">37</xref>], cucumber (<italic>Cucumis sativus)</italic> (permission obtained from Dr. Yiqun Weng), <italic>Eucalyptus grandis</italic> [<xref rid="pone.0129016.ref038" ref-type="bibr">38</xref>], <italic>Eutrema salsugineum</italic> (formerly <italic>Thellungiella halophila</italic>) [<xref rid="pone.0129016.ref039" ref-type="bibr">39</xref>], strawberry (<italic>Fragaria vesca)</italic> [<xref rid="pone.0129016.ref040" ref-type="bibr">40</xref>], soybean (<italic>Glycine max)</italic> [<xref rid="pone.0129016.ref041" ref-type="bibr">41</xref>], cotton (<italic>Gossypuim raimondii)</italic> [<xref rid="pone.0129016.ref042" ref-type="bibr">42</xref>], flax (<italic>Linum usitatissimum)</italic> [<xref rid="pone.0129016.ref043" ref-type="bibr">43</xref>], apple (<italic>Malus domestica)</italic> [<xref rid="pone.0129016.ref044" ref-type="bibr">44</xref>], cassava (<italic>Manihot esculenta)</italic> [<xref rid="pone.0129016.ref045" ref-type="bibr">45</xref>], barrel medic (<italic>Medicago truncatula</italic>) [<xref rid="pone.0129016.ref046" ref-type="bibr">46</xref>], monkey flower (<italic>Mimulus guttatus</italic>) [<xref rid="pone.0129016.ref047" ref-type="bibr">47</xref>], rice (<italic>Oryza sativa</italic>) [<xref rid="pone.0129016.ref048" ref-type="bibr">48</xref>], swtichgrass (<italic>Panicum virgatum v1</italic>.<italic>0</italic>, <italic>DOE-JGI</italic>, <ext-link ext-link-type="uri" xlink:href="http://www.phytozome.net/pvirgatum"><italic>http://www.phytozome.net/pvirgatum</italic></ext-link>), common bean (<italic>Phaseolus vulgaris</italic> L.<italic>)</italic> [<xref rid="pone.0129016.ref049" ref-type="bibr">49</xref>], moss (<italic>Physcomitrella patens)</italic> [<xref rid="pone.0129016.ref050" ref-type="bibr">50</xref>], peach (<italic>Prunus persica)</italic> [<xref rid="pone.0129016.ref051" ref-type="bibr">51</xref>], poplar (<italic>Populus trichocarpa)</italic> [<xref rid="pone.0129016.ref052" ref-type="bibr">52</xref>], castor bean (<italic>Ricinus communis)</italic> [<xref rid="pone.0129016.ref053" ref-type="bibr">53</xref>], foxtail millet (<italic>Setaria italica)</italic> [<xref rid="pone.0129016.ref054" ref-type="bibr">54</xref>], Shrub willow (<italic>Salix purpurea</italic> v1.0, DOE-JGI, <ext-link ext-link-type="uri" xlink:href="http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Spurpurea">http://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Spurpurea</ext-link>), tomato (<italic>Solanum lycopersicum)</italic> [<xref rid="pone.0129016.ref055" ref-type="bibr">55</xref>], potato (<italic>Solanum tuberosum)</italic> [<xref rid="pone.0129016.ref056" ref-type="bibr">56</xref>], greater duckweed (<italic>Spirodela polyrhiza</italic>) [<xref rid="pone.0129016.ref057" ref-type="bibr">57</xref>], cocoa (<italic>Theobroma cacao</italic>) [<xref rid="pone.0129016.ref058" ref-type="bibr">58</xref>], grape (<italic>Vitis vinifera)</italic> [<xref rid="pone.0129016.ref059" ref-type="bibr">59</xref>], maize (<italic>Zea mays)</italic> [<xref rid="pone.0129016.ref060" ref-type="bibr">60</xref>].</p><p>The following genomes were obtained from other sources: kiwifruit (<italic>Actinidia chinensis</italic>) [<xref rid="pone.0129016.ref061" ref-type="bibr">61</xref>], sugar beet (<italic>Beta vulgaris</italic>) [<xref rid="pone.0129016.ref062" ref-type="bibr">62</xref>]; pigeonpea (<italic>Cajanus cajan</italic>) [<xref rid="pone.0129016.ref063" ref-type="bibr">63</xref>] <ext-link ext-link-type="uri" xlink:href="http://www.icrisat.org/gt-bt/iipg/genomedata.zip">http://www.icrisat.org/gt-bt/iipg/genomedata.zip</ext-link>; pepper (<italic>Capsicum annuum</italic>) [<xref rid="pone.0129016.ref064" ref-type="bibr">64</xref>]; chickpea (<italic>Cicer arietinum</italic>) [<xref rid="pone.0129016.ref065" ref-type="bibr">65</xref>] <ext-link ext-link-type="uri" xlink:href="http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip">http://www.icrisat.org/gt-bt/ICGGC/genomedata.zip</ext-link>; <italic>Lotus japonicus</italic> [<xref rid="pone.0129016.ref066" ref-type="bibr">66</xref>] <ext-link ext-link-type="uri" xlink:href="http://ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/">ftp://ftp.kazusa.or.jp/pub/lotus/lotus_r2.5/</ext-link>; banana (<italic>Musa acuminata</italic>) [<xref rid="pone.0129016.ref067" ref-type="bibr">67</xref>]; <italic>Oryza brachyantha</italic> [<xref rid="pone.0129016.ref068" ref-type="bibr">68</xref>]; date palm (<italic>Phoenix dactylifera</italic>, Draft Sequence Version 3) [<xref rid="pone.0129016.ref069" ref-type="bibr">69</xref>] <ext-link ext-link-type="uri" xlink:href="http://qatar-weill.cornell.edu/research/datepalmGenome/download.html">http://qatar-weill.cornell.edu/research/datepalmGenome/download.html</ext-link>; Norway spruce (<italic>Picea abies</italic>) [<xref rid="pone.0129016.ref070" ref-type="bibr">70</xref>]; loblolly pine (<italic>Pinus taeda</italic>) [<xref rid="pone.0129016.ref071" ref-type="bibr">71</xref>].</p></sec><sec id="sec004"><title>Identification of dehydrin genes</title><p>A custom solution was used to identify all dehydrin genes found in the plant genomes described above. Amino acid sequences of several known dehydrins were obtained from NCBI GenBank [<xref rid="pone.0129016.ref072" ref-type="bibr">72</xref>] and sequences of their K-segment were used to populate a seed FASTA file. A Python script was written that used Biopython [<xref rid="pone.0129016.ref073" ref-type="bibr">73</xref>] Motif module to scan all amino acid sequence for proteins containing a sequence similar to the K-segment, based on its position frequency matrix (PFM). After each round of search new K-segment sequences were added to the original FASTA file. The Y-segment sequence file was constructed in a similar manner using identified dehydrin protein sequences. Identified dehydrins were categorized based on the occurrence of conserved segments using either their PFMs (K- and Y-segments) or a regular expression that described a simpler S-segment. All identified dehydrins were divided into five categories: K<sub>n</sub>, KS, SK<sub>n</sub>, Y<sub>n</sub>K<sub>n</sub>, Y<sub>n</sub>SK<sub>n</sub> and 1000 bps upstream of the transcription start site (where data was available, otherwise upstream from the start site) were obtained from Phytozome BioMart or they were directly extracted from the genomes using custom scripts. <italic>Oxytropis arctobia</italic> and <italic>Oxytropis splendens</italic> KS dehydrin gene sequences were obtained from NCBI GenBank (accessions: AEV59613 and AEV59617, respectively [<xref rid="pone.0129016.ref006" ref-type="bibr">6</xref>]). 1000 bp of <italic>O</italic>. <italic>arctobia</italic> and <italic>O</italic>. <italic>splendens</italic> promoters were obtained by amplifying GenomeWalker libraries and sequencing PCR products (Zolotarov et. al., unpublished).</p><p>To validate that the identified genes can actually be considered dehydrins, phmmer, as implemented on the HMMER web server [<xref rid="pone.0129016.ref074" ref-type="bibr">74</xref>] was used to search sequences on UniProt Knowledgebase [<xref rid="pone.0129016.ref075" ref-type="bibr">75</xref>] that have a significant similarity to putative dehydrins discovered using our custom method. The top ten significant hits were taken for each putative dehydrin and their domain annotation was extracted. Additionally, Needleman-Wunsch [<xref rid="pone.0129016.ref076" ref-type="bibr">76</xref>] pairwise alignment was used to compare 15 putative KS dehydrin to a known <italic>Arabidopsis</italic> KS dehydrin (AT1G54410). The closest match to every putative dehydrin in the NCBI GenBank non-redundant database was searched for using BLAST [<xref rid="pone.0129016.ref077" ref-type="bibr">77</xref>].</p><p>All the scripts and sequence data used in this paper are available from <ext-link ext-link-type="uri" xlink:href="https://github.com/zolotarov/dehydrin_promoters">https://github.com/zolotarov/dehydrin_promoters</ext-link></p></sec><sec id="sec005"><title>Intrinsic disorder and hydrophilicity analysis</title><p>The identified dehydrin sequences were compared for intrinsic disorder and hydrophilicity with random plant protein sequences to assess the classification as a dehydrin. To calculate the grand average of hydrophilicity, Biopython ProtParam module was used. To calculate disorder proportion, IUPred [<xref rid="pone.0129016.ref078" ref-type="bibr">78</xref>] scores were calculated for each amino acid. The proportion of amino acids with the score above 0.5 (indicating disorder) was calculated. Statistical comparison was performed using t-test implemented in the scipy library [<xref rid="pone.0129016.ref079" ref-type="bibr">79</xref>,<xref rid="pone.0129016.ref080" ref-type="bibr">80</xref>]. The same number of random protein sequences was obtained for each species as the number of dehydrins used in this study. The sequences were downloaded using NCBI Entrez Direct E-utilities [<xref rid="pone.0129016.ref081" ref-type="bibr">81</xref>].</p></sec><sec id="sec006"><title>De novo motif discovery</title><p>Motifs were discovered using MEME v4.9.1 [<xref rid="pone.0129016.ref082" ref-type="bibr">82</xref>], Seeder v0.01 [<xref rid="pone.0129016.ref083" ref-type="bibr">83</xref>] and Weeder v1.4.2 [<xref rid="pone.0129016.ref084" ref-type="bibr">84</xref>], and using the five sets of sequences as separate input. Significant motifs were selected based on following parameters: E-value ≤ 0.05 for MEME, Q-value ≤ 0.01 for Seeder and the top 3 motifs recommended by Weeder adviser. All promoters that were available through Phytozome BioMart from all species included in the analyses, was used as a background set (a total of 1029220 promoters). A separate parser was written to extract significant PFMs from result files produced by each program. The PFMs produced for each dehydrin class were entered into the STAMP [<xref rid="pone.0129016.ref085" ref-type="bibr">85</xref>] website to group matrices by similarity and to identify significant (E-value ≤ 0.05) matches in PLACE [<xref rid="pone.0129016.ref023" ref-type="bibr">23</xref>]. A representative member from a tree node of matrices grouped by similarity was selected and its sequence logo was generated using WebLogo 3.3 [<xref rid="pone.0129016.ref086" ref-type="bibr">86</xref>].</p></sec></sec><sec id="sec007"><title>Results and Discussion</title><p>In order to further understand how different dehydrins are regulated in response to environmental stress, motifs corresponding to conserved <italic>cis</italic>-regulatory elements were detected in the upstream regions of dehydrin genes in all five subclasses. Dehydrin proteins are by nature unstructured, and a custom identification strategy was employed to retrieve as many dehydrin genes with up to 1000 bp upstream region as possible. In total, 340 dehydrin promoters of size 1000 bp and eight dehydrin promoters of shorter length were retrieved from 51 plant genome sequences. In addition, two promoters from dehydrin genes isolated from two <italic>Oxytropis</italic> species were also included (<xref rid="pone.0129016.t001" ref-type="table">Table 1</xref>, <xref rid="pone.0129016.s001" ref-type="supplementary-material">S1 Table</xref>). Out of the queried genomes, 10 were from monocotyledonous plants, 37 from dicotyledonous plants, one from a basal angiosperm (<italic>Amborella trichopoda</italic>), two from gymnosperms (<italic>Picea abies</italic> and <italic>Pinus taeda</italic>) and one from moss (<italic>Physcomitrella patens</italic>). The 350 sequences identified were confirmed to also match annotated dehydrins. For 330 out of 350 sequences, at least half of the top ten significant hits had “Dehydrin” as domain annotation. For the remaining 20 putative dehydrins, less than half of the top ten significant hits carried that annotation. Out of those, three were annotated as either a dehydrin or similar to dehydrin on NCBI GenBank and two were annotated as having a dehydrin domain on UniProtKB. The rest of the sequences were all short putative KS dehydrins. In these cases, all significant phmmer hits were analyzed. From 14.2% to 30.1% of significant hits had “Dehydrin” domain architecture, for sequences with lowest and highest number of significant hits with “Dehydrin” annotation, respectively. The rest of significant hits had no architecture annotation. When Needleman-Wunsch pairwise alignment was used to compare 15 putative KS dehydrin to a known <italic>Arabidopsis</italic> KS dehydrin (AT1G54410), sequence similarities ranged from 59.0% to 98.0%. This evidence supports the notion that the sequences extracted for the analyses can be classified as dehydrins.</p><table-wrap id="pone.0129016.t001" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0129016.t001</object-id><label>Table 1</label><caption><title>Number of analyzed dehydrin promoters per species.</title></caption><alternatives><graphic id="pone.0129016.t001g" xlink:href="pone.0129016.t001"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1">Species</th><th align="left" rowspan="1" colspan="1">K<sub>n</sub></th><th align="left" rowspan="1" colspan="1">KS</th><th align="left" rowspan="1" colspan="1">SK<sub>n</sub></th><th align="left" rowspan="1" colspan="1">Y<sub>n</sub>K<sub>n</sub></th><th align="left" rowspan="1" colspan="1">Y<sub>n</sub>SK<sub>n</sub></th><th align="left" rowspan="1" colspan="1">Total</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1"><italic>Actinidia chinensis</italic></td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Amborella trichopoda</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Aquilegia coerulea</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis halleri</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis lyrata</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Arabidopsis thaliana</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Beta vulgaris</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Boechera stricta</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Brachypodium distachyon</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Brassica rapa</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">11</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Cajanus cajan</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Capsella grandiflora</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Capsella rubella</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Capsicum annuum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Carica papaya</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Cicer arietinum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Citrus clementina</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Citrus sinensis</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Cucumis sativus</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Eucalyptus grandis</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Eutrema salsugineum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Fragaria vesca</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Glycine max</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Gossypium raimondii</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">8</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Linum usitatissimum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">11</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Lotus japonicus</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Malus domestica</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">9</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Manihot esculenta</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Medicago truncatula</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Mimulus guttatus</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Musa acuminata</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Oryza brachyantha</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">7</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Oryza sativa</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">6</td><td align="left" rowspan="1" colspan="1">8</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Panicum virgatum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Phaseolus vulgaris</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Phoenix dactylifera</italic></td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Physcomitrella patens</italic></td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">4</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Picea abies</italic></td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">9</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">13</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Pinus taeda</italic></td><td align="left" rowspan="1" colspan="1">8</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">10</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">18</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Populus trichocarpa</italic></td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">7</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Prunus persica</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">6</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Ricinus communis</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Salix purpurea</italic></td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">10</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Setaria italica</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">5</td><td align="left" rowspan="1" colspan="1">7</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Solanum lycopersicum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">4</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Solanum tuberosum</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Sorghum bicolor</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Spirodela polyrhiza</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Theobroma cacao</italic></td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">5</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Vitis vinifera</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Zea mays</italic></td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">2</td><td align="left" rowspan="1" colspan="1">0</td><td align="left" rowspan="1" colspan="1">3</td><td align="left" rowspan="1" colspan="1">7</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Oxytropis splendens</italic><xref rid="t001fn001" ref-type="table-fn">*</xref></td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1"><italic>Oxytropis arctobia</italic><xref rid="t001fn001" ref-type="table-fn">*</xref></td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">1</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">–</td><td align="left" rowspan="1" colspan="1">1</td></tr><tr><td align="left" rowspan="1" colspan="1"><bold>Total</bold></td><td align="left" rowspan="1" colspan="1">39</td><td align="left" rowspan="1" colspan="1">47</td><td align="left" rowspan="1" colspan="1">120</td><td align="left" rowspan="1" colspan="1">21</td><td align="left" rowspan="1" colspan="1">123</td><td align="left" rowspan="1" colspan="1">350</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t001fn001"><p>* Only one promoter was obtained per species, using genome walking.</p></fn></table-wrap-foot></table-wrap><sec id="sec008"><title>Biochemical properties of dehydrins</title><p>Dehydrins are known to be intrinsically disordered and hydrophilic [<xref rid="pone.0129016.ref087" ref-type="bibr">87</xref>], making it difficult, if not impossible, to identify them by overall sequence homology. These properties are, however, important for their hypothesized function in protein stabilization through interaction with water molecules, as well as for their subcellular location in the cytosol and the nucleus and not within membranes [<xref rid="pone.0129016.ref087" ref-type="bibr">87</xref>,<xref rid="pone.0129016.ref088" ref-type="bibr">88</xref>]. To assess the identification of the dehydrins included in this study, the grand average of hydropathicity (GRAVY, [<xref rid="pone.0129016.ref089" ref-type="bibr">89</xref>]) and the proportions of amino acids in the disordered regions were compared between dehydrins and random plant proteins. It was found that the 350 dehydrin amino acid sequences analyzed, were significantly more hydrophilic than 350 random plant protein sequences (GRAVY -1.3470 for dehydrins, -0.2938 for random plant proteins, p-value < 0.001). The level of structural disorder indicated that in the dehydrins analyzed, the average proportion of amino acid sequences in the state of disorder was 99.32% compared to 15.95% in random plant proteins (p-value < 0.001).</p></sec><sec id="sec009"><title>Promoters of KS dehydrins have one conserved GATA motif</title><p>In total, 47 KS dehydrin promoters were included in the <italic>de novo</italic> motif discovery (<xref rid="pone.0129016.t001" ref-type="table">Table 1</xref>). Using the <italic>de novo</italic> motif discovery tool Seeder [<xref rid="pone.0129016.ref083" ref-type="bibr">83</xref>,<xref rid="pone.0129016.ref090" ref-type="bibr">90</xref>], one single putative conserved regulatory motif was discovered in all 47 promoter sequences (Motif 1, <xref rid="pone.0129016.t002" ref-type="table">Table 2</xref>, <xref rid="pone.0129016.s002" ref-type="supplementary-material">S2 Table</xref>). A similar motif was also discovered with Weeder [<xref rid="pone.0129016.ref084" ref-type="bibr">84</xref>]. The KS dehydrins are known to be expressed in response to cold and dehydration, as well as being constitutively expressed [<xref rid="pone.0129016.ref006" ref-type="bibr">6</xref>,<xref rid="pone.0129016.ref091" ref-type="bibr">91</xref>–<xref rid="pone.0129016.ref093" ref-type="bibr">93</xref>]. Although the single identified overrepresented motif in KS dehydrin promoters does not directly match any typical cold or dehydration-related <italic>cis</italic>-regulatory elements in the PLACE database [<xref rid="pone.0129016.ref023" ref-type="bibr">23</xref>], it does match two motifs involved in light regulation and one involved in sugar regulation (<xref rid="pone.0129016.t002" ref-type="table">Table 2</xref>): IBOXCORENT (I-box core) [<xref rid="pone.0129016.ref094" ref-type="bibr">94</xref>], REBETALGLHCB21 [<xref rid="pone.0129016.ref095" ref-type="bibr">95</xref>] and SREATMSD [<xref rid="pone.0129016.ref096" ref-type="bibr">96</xref>], respectively. These three experimentally validated motifs share four nucleotides (GATA).</p><table-wrap id="pone.0129016.t002" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0129016.t002</object-id><label>Table 2</label><caption><title>Selected <italic>de novo</italic> motifs found in KS dehydrin promoters and their putative function identified through PLACE database.</title></caption><alternatives><graphic id="pone.0129016.t002g" xlink:href="pone.0129016.t002"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1"></th><th colspan="4" align="center" rowspan="1">Match in PLACE<xref rid="t002fn005" ref-type="table-fn"><sup>5</sup></xref></th></tr><tr><th align="left" rowspan="1" colspan="1"><italic>De novo</italic> motif</th><th align="left" rowspan="1" colspan="1">Sequence</th><th align="left" rowspan="1" colspan="1">Name</th><th align="left" rowspan="1" colspan="1">E-value<xref rid="t002fn006" ref-type="table-fn"><sup>6</sup></xref></th><th align="left" rowspan="1" colspan="1">Function</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">1. Seeder<xref rid="t002fn001" ref-type="table-fn"><sup>1</sup></xref> AWTCGGATAA<xref rid="t002fn002" ref-type="table-fn"><sup><bold>2</bold></sup></xref> (47/47<xref rid="t002fn003" ref-type="table-fn"><sup><bold>3</bold></sup></xref>, 8.8e-07<xref rid="t002fn004" ref-type="table-fn"><sup>4</sup></xref>)</td><td align="left" rowspan="1" colspan="1"><monospace>GATAAGR</monospace></td><td align="left" rowspan="1" colspan="1">IBOXCORENT</td><td align="left" rowspan="1" colspan="1">1.4e-08</td><td align="left" rowspan="1" colspan="1">Found in light-responsive conserved DNA modular arrays</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TTATCC</monospace></td><td align="left" rowspan="1" colspan="1">SREATMSD</td><td align="left" rowspan="1" colspan="1">1.2e-07</td><td align="left" rowspan="1" colspan="1">Sugar-repressive element (SRE) found in genes down-regulated after main stem decapitation</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CGGATA</monospace></td><td align="left" rowspan="1" colspan="1">REBETALGLHCB21</td><td align="left" rowspan="1" colspan="1">1.8e-07</td><td align="left" rowspan="1" colspan="1">Required for phytochrome regulation</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t002fn001"><p><sup>1</sup>Number of the motif and the <italic>de novo</italic> discovery software that was used to locate that motif.</p></fn><fn id="t002fn002"><p><sup>2</sup>Motif consensus sequence in IUPAC nucleotide code.</p></fn><fn id="t002fn003"><p><sup>3</sup>Occurrence is the number of promoters containing a <italic>de novo</italic> motif out of the total number of promoters analyzed for a specific dehydrin class, presented in the parentheses.</p></fn><fn id="t002fn004"><p><sup>4</sup>Siginificance of the motif, E-value calculated by MEME, Q-value calculated by Seeder, presented in the parentheses.</p></fn><fn id="t002fn005"><p><sup>5</sup>PLACE matches were identified using STAMP, only significant matches with E-value < 0.05 are presented.</p></fn><fn id="t002fn006"><p><sup>6</sup>E-value of the match with PLACE motif.</p></fn></table-wrap-foot></table-wrap><p>One of these motifs, the I-box (<monospace>GATAAGR</monospace>) can form a light-responsive conserved DNA modular array (CMA) together with a G-box (<monospace>CACGTGGC</monospace>) when located in close proximity to one another. In transgenic Arabidopsis and tobacco (<italic>Nicotiana tabacum</italic>) plants, the presence of this CMA in a promoter, drives GUS reporter gene expression when exposed to light. Interestingly, this expression seems to be mediated by phytochrome and cryptochrome photoreceptors [<xref rid="pone.0129016.ref094" ref-type="bibr">94</xref>].</p><p>Another of the motifs matching the motif discovered in the KS dehydrin promoters, the REBETALGLHCB21, also called REβ (<monospace>CGGATA</monospace>), was first identified in gibbous duckweed (<italic>Lemna gibba</italic>) [<xref rid="pone.0129016.ref095" ref-type="bibr">95</xref>]. It is involved in phytochrome-mediated repression of promoter activity in darkness, when located in close proximity with REα (<monospace>AACCAA</monospace>). Although REα was not identified as a significantly overrepresented motif, it is found in 26 out of the 47 KS dehydrin promoters analyzed. The <monospace>GATA</monospace> part of the REβ was shown to be absolutely necessary for darkness-induced repression [<xref rid="pone.0129016.ref095" ref-type="bibr">95</xref>]. Furthermore, in Arabidopsis, C-repeat (<monospace>CCGAC</monospace>, CRT)-linked cold and dehydration induced gene expression is mediated by phytochrome [<xref rid="pone.0129016.ref025" ref-type="bibr">25</xref>]. While CRT was not found to be significantly overrepresented within the set of KS dehydrin promoters, it is noteworthy that 27 out of the 47 KS dehydrin promoters contain one or more copies of CRT or its reverse complement. Sixteen of the promoters contain both REα and REβ.</p><p>The motif discovered in the KS dehydrin promoters also matched a sugar-repressive element, SREATMSD (<monospace>TTATCC</monospace>, SRE), shown to be involved in sugar mediated gene repression in Arabidopsis [<xref rid="pone.0129016.ref096" ref-type="bibr">96</xref>]. Sugars are known osmoprotectants that are produced by plants in response to cold [<xref rid="pone.0129016.ref097" ref-type="bibr">97</xref>]. One of the suggested roles of dehydrins is in the stabilization of protein conformation. Sugars, such as sucrose and trehalose, can replace water molecules on the surface of a protein and can thus conserve its conformation. This allows cells to restore their function after rehydration [<xref rid="pone.0129016.ref098" ref-type="bibr">98</xref>].</p></sec><sec id="sec010"><title>Motifs discovered in promoters of K<sub>n</sub> match abscisic acid and low temperature response elements</title><p>A total of 39 K<sub>n</sub> dehydrin promoters were included in the <italic>de novo</italic> regulatory motif discovery analysis (<xref rid="pone.0129016.t001" ref-type="table">Table 1</xref>). The K<sub>n</sub> dehydrins are expressed in response to high salinity, abscisic acid (ABA), cold and dehydration [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>,<xref rid="pone.0129016.ref005" ref-type="bibr">5</xref>,<xref rid="pone.0129016.ref099" ref-type="bibr">99</xref>,<xref rid="pone.0129016.ref100" ref-type="bibr">100</xref>]. A total of three putative regulatory motifs were identified in this set of promoters (<xref rid="pone.0129016.t003" ref-type="table">Table 3</xref>, <xref rid="pone.0129016.s002" ref-type="supplementary-material">S2 Table</xref>)—two were discovered using MEME (Motif 2: <monospace>GGCAGGAC/GTGGTGCC</monospace>; and Motif 3: <monospace>ATGTCGGC/GCCGACAT</monospace>) and one using Seeder (Motif 4: <monospace>TCGCCGACAT/ATGTCGGCGA</monospace>). Motif 2 (<monospace>GGCAGGAC</monospace>) has a significant match to the SITEIIBOSPCNA (<monospace>TGGTCCCAC</monospace>) motif in the PLACE database. This motif is linked with meristematic tissue-specific gene expression in rice (<italic>Oryza sativa</italic>) [<xref rid="pone.0129016.ref101" ref-type="bibr">101</xref>] and it was found in 31 out of the 39 promoters. Motifs 3 and 4, found in all analyzed K<sub>n</sub> dehydrin promoters, match DREDR1ATRD29AB motif (<monospace>TACCGACAT</monospace>) [<xref rid="pone.0129016.ref102" ref-type="bibr">102</xref>] and LTREATLTI78 (<monospace>ACCGACA</monospace>) [<xref rid="pone.0129016.ref103" ref-type="bibr">103</xref>], two low temperature response elements (LTREs) involved in cold response in <italic>A</italic>. <italic>thaliana</italic>. Additionally, Motif 3 matches an ABRE found in wheat and rice- ABREOSRAB21 (<monospace>ACGTSSSC</monospace>) [<xref rid="pone.0129016.ref104" ref-type="bibr">104</xref>]. The presence of both LTREs and an ABRE indicates that K<sub>n</sub> dehydrins, similarly to SK<sub>n</sub> and Y<sub>n</sub>SK<sub>n</sub> dehydrins, could be expressed in ABA-dependent and independent manner in response to osmotic stresses.</p><table-wrap id="pone.0129016.t003" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0129016.t003</object-id><label>Table 3</label><caption><title>Selected <italic>de novo</italic> motifs found in K<sub>n</sub> dehydrin promoters and their putative function identified through PLACE database.</title></caption><alternatives><graphic id="pone.0129016.t003g" xlink:href="pone.0129016.t003"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1"></th><th colspan="4" align="center" rowspan="1">Match in PLACE<xref rid="t003fn005" ref-type="table-fn"><sup>5</sup></xref></th></tr><tr><th align="left" rowspan="1" colspan="1"><italic>De novo</italic> motif</th><th align="left" rowspan="1" colspan="1">Sequence</th><th align="left" rowspan="1" colspan="1">Name</th><th align="left" rowspan="1" colspan="1">E-value<xref rid="t003fn006" ref-type="table-fn"><sup>6</sup></xref></th><th align="left" rowspan="1" colspan="1">Function</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">2. MEME<xref rid="t003fn001" ref-type="table-fn"><sup>1</sup></xref> GGCMCCAC<xref rid="t003fn002" ref-type="table-fn"><sup><bold>2</bold></sup></xref> (31/39<xref rid="t003fn003" ref-type="table-fn"><sup>3</sup></xref>, 1.2e-06<xref rid="t003fn004" ref-type="table-fn"><sup>4</sup></xref>)</td><td align="left" rowspan="1" colspan="1"><monospace>TGGTCCCAC</monospace></td><td align="left" rowspan="1" colspan="1">SITEIIBOSPCNA</td><td align="left" rowspan="1" colspan="1">4.3e-07</td><td align="left" rowspan="1" colspan="1">Involved for meristematic tissue-specific expression in rice</td></tr><tr><td align="left" rowspan="1" colspan="1">3. MEME AYGTCGGY (39/39, 3.7e-05)</td><td align="left" rowspan="1" colspan="1"><monospace>TACCGACAT</monospace></td><td align="left" rowspan="1" colspan="1">DREDR1ATRD29AB</td><td align="left" rowspan="1" colspan="1">6.4e-11</td><td align="left" rowspan="1" colspan="1">Response to drought, low temperature and high salinity. Bound by CBF1 in <italic>Arabidopsis</italic></td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>ACCGACA</monospace></td><td align="left" rowspan="1" colspan="1">LTREATLTI78</td><td align="left" rowspan="1" colspan="1">5.5e-09</td><td align="left" rowspan="1" colspan="1">LTRE</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>ACGTSSSC</monospace></td><td align="left" rowspan="1" colspan="1">ABREOSRAB21</td><td align="left" rowspan="1" colspan="1">3.3e-05</td><td align="left" rowspan="1" colspan="1">ABRE found in wheat and rice</td></tr><tr><td align="left" rowspan="1" colspan="1">4. Seeder WNRCCGACAT (39/39, 2.1e-05)</td><td align="left" rowspan="1" colspan="1"><monospace>ACCGACA</monospace></td><td align="left" rowspan="1" colspan="1">LTREATLTI78</td><td align="left" rowspan="1" colspan="1">3.7e-07</td><td align="left" rowspan="1" colspan="1">LTRE</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TACCGACAT</monospace></td><td align="left" rowspan="1" colspan="1">DREDR1ATRD29AB</td><td align="left" rowspan="1" colspan="1">4.9e-08</td><td align="left" rowspan="1" colspan="1">Response to drought, low temperature and high salinity. Bound by CBF1 in <italic>Arabidopsis</italic></td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t003fn001"><p><sup>1</sup>Number of the motif and the <italic>de novo</italic> discovery software that was used to locate that motif.</p></fn><fn id="t003fn002"><p><sup>2</sup>Motif consensus sequence in IUPAC nucleotide code.</p></fn><fn id="t003fn003"><p><sup>3</sup>Occurrence is the number of promoters containing a <italic>de novo</italic> motif out of the total number of promoters analyzed for a specific dehydrin class, presented in the parentheses.</p></fn><fn id="t003fn004"><p><sup>4</sup>Siginificance of the motif, E-value calculated by MEME, Q-value calculated by Seeder, presented in the parentheses.</p></fn><fn id="t003fn005"><p><sup>5</sup>PLACE matches were identified using STAMP, only significant matches with E-value < 0.05 are presented.</p></fn><fn id="t003fn006"><p><sup>6</sup>E-value of the match with PLACE motif.</p></fn></table-wrap-foot></table-wrap></sec><sec id="sec011"><title>SK<sub>n</sub> dehydrins contain multiple cold/dehydration, abscisic acid and light regulated response elements</title><p>A total of 120 SK<sub>n</sub> dehydrin promoters were analyzed (<xref rid="pone.0129016.t001" ref-type="table">Table 1</xref>). Six <italic>de novo</italic> discovered putative regulatory motifs are presented in <xref rid="pone.0129016.t004" ref-type="table">Table 4</xref> and <xref rid="pone.0129016.s002" ref-type="supplementary-material">S2 Table</xref>. MEME and Seeder each discovered three motifs. The SK<sub>n</sub> dehydrins are known to be expressed in response to cold, ABA, dehydration and salt [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>,<xref rid="pone.0129016.ref005" ref-type="bibr">5</xref>,<xref rid="pone.0129016.ref014" ref-type="bibr">14</xref>,<xref rid="pone.0129016.ref105" ref-type="bibr">105</xref>]. Three out of six motifs (motifs 5–7) have matches in PLACE that are known ABREs. Motif 5 (<monospace>CCACGTGTC/GACACGTGG</monospace>) matches ABREs from wheat (<italic>Triticum aestivum</italic>) [<xref rid="pone.0129016.ref103" ref-type="bibr">103</xref>] and canola (<italic>Brassica napus</italic>) [<xref rid="pone.0129016.ref106" ref-type="bibr">106</xref>]. Motif 6 (<monospace>CCGACGCG/CGCGTCGG</monospace>) matches ABREs from maize [<xref rid="pone.0129016.ref107" ref-type="bibr">107</xref>], and rice [<xref rid="pone.0129016.ref108" ref-type="bibr">108</xref>]. Motif 7 (<monospace>CCAACGCG/CGCGTTGG</monospace>) matches an ABRE from barley [<xref rid="pone.0129016.ref109" ref-type="bibr">109</xref>] and rice [<xref rid="pone.0129016.ref107" ref-type="bibr">107</xref>]. Motifs 6, 8 (<monospace>CACCGACC/GGTCGGTG</monospace>) and 9 (<monospace>TGGTCGGT/ACCGACCA</monospace>) match low temperature response elements known as C-repeats (CRT, consensus sequence: <monospace>RCCGAC</monospace>), found in numerous species [<xref rid="pone.0129016.ref110" ref-type="bibr">110</xref>–<xref rid="pone.0129016.ref112" ref-type="bibr">112</xref>].</p><table-wrap id="pone.0129016.t004" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0129016.t004</object-id><label>Table 4</label><caption><title>Selected <italic>de novo</italic> motifs found in SK<sub>n</sub> dehydrin promoters and their putative function identified through PLACE database.</title></caption><alternatives><graphic id="pone.0129016.t004g" xlink:href="pone.0129016.t004"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1"></th><th colspan="4" align="center" rowspan="1">Match in PLACE<xref rid="t004fn005" ref-type="table-fn"><sup>5</sup></xref></th></tr><tr><th align="left" rowspan="1" colspan="1"><italic>De novo</italic> motif</th><th align="left" rowspan="1" colspan="1">Sequence</th><th align="left" rowspan="1" colspan="1">Name</th><th align="left" rowspan="1" colspan="1">E-value<xref rid="t004fn006" ref-type="table-fn"><sup>6</sup></xref></th><th align="left" rowspan="1" colspan="1">Function</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">5. Seeder<xref rid="t004fn001" ref-type="table-fn"><sup>1</sup></xref> MCACGTGTC<xref rid="t004fn002" ref-type="table-fn"><sup><bold>2</bold></sup></xref> (120/120<xref rid="t004fn003" ref-type="table-fn"><sup>3</sup></xref>, 9.2e-19<xref rid="t004fn004" ref-type="table-fn"><sup>4</sup></xref>)</td><td align="left" rowspan="1" colspan="1"><monospace>GGACACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABRETAEM</td><td align="left" rowspan="1" colspan="1">6.5e-13</td><td align="left" rowspan="1" colspan="1">ABRE found in wheat</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TGACACGTGGCA</monospace></td><td align="left" rowspan="1" colspan="1">HY5AT</td><td align="left" rowspan="1" colspan="1">2.4e-12</td><td align="left" rowspan="1" colspan="1">Bound by HY5, involved in light regulation of transcriptional activity</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TCCACGTGTC</monospace></td><td align="left" rowspan="1" colspan="1">SGBFGMGMAUX28</td><td align="left" rowspan="1" colspan="1">1.1e-13</td><td align="left" rowspan="1" colspan="1">Recognized by G-box binding factors in soybean. Found in auxin-responsive genes</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>MCACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">GBOXLERBCS</td><td align="left" rowspan="1" colspan="1">8.1e-12</td><td align="left" rowspan="1" colspan="1">Sequence found in promoters of light-regulated genes</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CGCCACGTGTCC</monospace></td><td align="left" rowspan="1" colspan="1">ABREBNNAPA</td><td align="left" rowspan="1" colspan="1">2.4e-21</td><td align="left" rowspan="1" colspan="1">ABRE found in <italic>Brassica napus</italic></td></tr><tr><td align="left" rowspan="1" colspan="1">6. MEME CCGACGCG (120/120, 1.2e-50)</td><td align="left" rowspan="1" colspan="1"><monospace>CCCACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABREAZMRAB28</td><td align="left" rowspan="1" colspan="1">3.0e-05</td><td align="left" rowspan="1" colspan="1">ABRE, ABA and water-stress responses. Binding site of CBF2.</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>GCCGCGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABREMOTIFIIIOSRAB16B</td><td align="left" rowspan="1" colspan="1">4.0e-05</td><td align="left" rowspan="1" colspan="1">ABRE Motif III found in rice</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CCACGTGGCC</monospace></td><td align="left" rowspan="1" colspan="1">LTRECOREATCOR15</td><td align="left" rowspan="1" colspan="1">5.3e-06</td><td align="left" rowspan="1" colspan="1">LTRE</td></tr><tr><td align="left" rowspan="1" colspan="1">7. Seeder SCAACGCG (120/120, 2.0e-10)</td><td align="left" rowspan="1" colspan="1"><monospace>TCCACGTCTC</monospace></td><td align="left" rowspan="1" colspan="1">ABRE3HVA1</td><td align="left" rowspan="1" colspan="1">2.3e-05</td><td align="left" rowspan="1" colspan="1">ABRE found in barley</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>GCCGCGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABREMOTIFIIIOSRAB16B</td><td align="left" rowspan="1" colspan="1">6.0e-05</td><td align="left" rowspan="1" colspan="1">ABRE Motif III found in rice</td></tr><tr><td align="left" rowspan="1" colspan="1">8. MEME CACCGACC (119/120, 3.8e-59)</td><td align="left" rowspan="1" colspan="1"><monospace>RCCGAC</monospace></td><td align="left" rowspan="1" colspan="1">DRECRTCOREAT</td><td align="left" rowspan="1" colspan="1">1.9e-08</td><td align="left" rowspan="1" colspan="1">DRE/CRT found in genes expressed in response to cold and dehydration</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CCCACCTACC</monospace></td><td align="left" rowspan="1" colspan="1">ACIPVPAL2</td><td align="left" rowspan="1" colspan="1">3.8e-07</td><td align="left" rowspan="1" colspan="1">Required for vascular specific expression</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>ACCGACA</monospace></td><td align="left" rowspan="1" colspan="1">LTREATLTI78</td><td align="left" rowspan="1" colspan="1">3.1e-07</td><td align="left" rowspan="1" colspan="1">LTRE</td></tr><tr><td align="left" rowspan="1" colspan="1">9. Seeder KKGTCGGY (120/120, 4.9e-07)</td><td align="left" rowspan="1" colspan="1"><monospace>ACCGACA</monospace></td><td align="left" rowspan="1" colspan="1">LTREATLTI78</td><td align="left" rowspan="1" colspan="1">8.4e-07</td><td align="left" rowspan="1" colspan="1">LTRE</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>RCCGAC</monospace></td><td align="left" rowspan="1" colspan="1">DRECRTCOREAT</td><td align="left" rowspan="1" colspan="1">2.4e-08</td><td align="left" rowspan="1" colspan="1">DRE/CRT found in genes expressed in response to cold and dehydration</td></tr><tr><td align="left" rowspan="1" colspan="1">10. MEME GTGGGVCC (61/120, 2.5e-22)</td><td align="left" rowspan="1" colspan="1"><monospace>GGTCCCAT</monospace></td><td align="left" rowspan="1" colspan="1">GGTCCCATGMSAUR</td><td align="left" rowspan="1" colspan="1">8.3e-09</td><td align="left" rowspan="1" colspan="1">Auxin RE found in soybean</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CTCCCAC</monospace></td><td align="left" rowspan="1" colspan="1">BOXCPSAS1</td><td align="left" rowspan="1" colspan="1">3.9e-06</td><td align="left" rowspan="1" colspan="1">Involved in light-induced repression</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t004fn001"><p><sup>1</sup>Number of the motif and the <italic>de novo</italic> discovery software that was used to locate that motif.</p></fn><fn id="t004fn002"><p><sup>2</sup>Motif consensus sequence in IUPAC nucleotide code.</p></fn><fn id="t004fn003"><p><sup>3</sup>Occurrence is the number of promoters containing a <italic>de novo</italic> motif out of the total number of promoters analyzed for a specific dehydrin class, presented in the parentheses.</p></fn><fn id="t004fn004"><p><sup>4</sup>Siginificance of the motif, E-value calculated by MEME, Q-value calculated by Seeder, presented in the parentheses.</p></fn><fn id="t004fn005"><p><sup>5</sup>PLACE matches were identified using STAMP, only significant matches with E-value < 0.05 are presented.</p></fn><fn id="t004fn006"><p><sup>6</sup>E-value of the match with PLACE motif.</p></fn></table-wrap-foot></table-wrap><p>In addition, motif 5 matches an element from tomato and Arabidopsis light-regulated genes [<xref rid="pone.0129016.ref113" ref-type="bibr">113</xref>,<xref rid="pone.0129016.ref114" ref-type="bibr">114</xref>] and motif 10 (GTGGGACC) matches an element from pea involved in light-induced repression [<xref rid="pone.0129016.ref115" ref-type="bibr">115</xref>].</p><p>The presence of these significantly overrepresented motifs indicates that the SK<sub>n</sub> dehydrins are regulated at the transcriptional level and their expression is modulated in response to cold and ABA. SK<sub>n</sub> dehydrins should also be expressed in response to drought, since CRT, which is also called dehydration responsive element [<xref rid="pone.0129016.ref116" ref-type="bibr">116</xref>], is found in their promoters. The circadian clock controls cold induction of C-repeat binding factors (CBFs), which in turn bind CRT/DRE elements [<xref rid="pone.0129016.ref117" ref-type="bibr">117</xref>]. Phytochrome and cryptochrome genes are also regulated by a circadian clock in Arabidopsis [<xref rid="pone.0129016.ref118" ref-type="bibr">118</xref>]. COR27, a cold-induced gene, is regulated by circadian clock related evening elements (EE) [<xref rid="pone.0129016.ref119" ref-type="bibr">119</xref>]. In addition to EE, the COR27 promoter also contains multiple ABREs and G-boxes, to which motifs 5 and 6 also match. The core EE (<monospace>AATATCT</monospace>) [<xref rid="pone.0129016.ref120" ref-type="bibr">120</xref>] is found in 18 out of 73 SK<sub>n</sub> gene promoters analyzed. Motifs involved in light-induced regulation of gene expression found in the promoters of SK<sub>n</sub> genes could participate in modulation of these genes by the circadian clock. It has been shown previously, using bioinformatics methods, that the promoters of cold-regulated genes contain CRTs and ABREs [<xref rid="pone.0129016.ref112" ref-type="bibr">112</xref>,<xref rid="pone.0129016.ref121" ref-type="bibr">121</xref>] and our data also support those findings.</p><p>Motifs 5 and 10 match an auxin response element found in soybean GmAux28 [<xref rid="pone.0129016.ref122" ref-type="bibr">122</xref>] and SAUR15A promoter, respectively [<xref rid="pone.0129016.ref123" ref-type="bibr">123</xref>]. It has been shown previously that numerous genes related to auxin response in Arabidopsis are modulated in response to cold, such as auxin response factor ARF7 or the PINOID-binding protein 1 that is involved in hormone signaling and stress response [<xref rid="pone.0129016.ref124" ref-type="bibr">124</xref>].</p></sec><sec id="sec012"><title>Y<sub>n</sub>SK<sub>n</sub> dehydrins promoters contain multiple ABREs, light REs and a CRT</title><p>Y<sub>n</sub>SK<sub>n</sub> dehydrins represent the largest subclass out of the five dehydrin classes analyzed. A total of 123 Y<sub>n</sub>SK<sub>n</sub> gene promoters were analyzed (<xref rid="pone.0129016.t001" ref-type="table">Table 1</xref>). The Y<sub>n</sub>SK<sub>n</sub> dehydrins are expressed in response to ABA, dehydration and high salinity [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>,<xref rid="pone.0129016.ref005" ref-type="bibr">5</xref>,<xref rid="pone.0129016.ref100" ref-type="bibr">100</xref>]. The two motifs presented in <xref rid="pone.0129016.t005" ref-type="table">Table 5</xref> and <xref rid="pone.0129016.s002" ref-type="supplementary-material">S2 Table</xref> (Motifs 11 and 12) match numerous elements in the PLACE database and both were discovered using a Seeder. Motif 11 (<monospace>GACACGTGGC</monospace>) is very similar to Motif 5 (<monospace>GACACGTGT</monospace>), found in the SK<sub>n</sub> dehydrin promoters and they both match several of the same motifs in PLACE database, namely ABREs, G-box and light response elements. Motif 13 (<monospace>CACCGAC</monospace>) is almost identical to Motif 8 (<monospace>CACCGACC</monospace>) discovered in the SK<sub>n</sub> dehydrin promoters, which matches CRT/DRE necessary for CBF mediated cold and dehydration response [<xref rid="pone.0129016.ref116" ref-type="bibr">116</xref>]. Overall, motifs found Y<sub>n</sub>SK<sub>n</sub> dehydrin promoters are very similar to those found in SK<sub>n</sub> dehydrin promoters indicating that they possibly have a similar function, and that these two classes may have diverged more recently than the other classes. While the function of the Y-segment in the gene products of Y<sub>n</sub>SK<sub>n</sub> and Y<sub>n</sub>K<sub>n</sub> dehydrins is not known, it shows similarity to the nucleotide binding domain of plant chaperones [<xref rid="pone.0129016.ref125" ref-type="bibr">125</xref>]. The gene products of the other dehydrin classes do not have any such domains. In addition, there are evolutive constraints on the Y-segment in a dehydrin from arctic <italic>Oxytropis</italic> species compared with temperate species [<xref rid="pone.0129016.ref126" ref-type="bibr">126</xref>], suggesting that the Y-segment might carry an important function that differentiates Y<sub>n</sub>SK<sub>n</sub> from SK<sub>n</sub> dehydrins. Some of the published data shows that Y<sub>n</sub>SK<sub>n</sub> dehydrins are not expressed in response to cold [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>,<xref rid="pone.0129016.ref005" ref-type="bibr">5</xref>], however there is evidence that after a period of acclimation they do accumulate in Red-Osier Dogwood (<italic>Cornus sericea</italic> L.) [<xref rid="pone.0129016.ref127" ref-type="bibr">127</xref>] and apple trees [<xref rid="pone.0129016.ref128" ref-type="bibr">128</xref>]. It is possible that cold-induced Y<sub>n</sub>SK<sub>n</sub> dehydrin expression was not detected in some data sets due to a limited time of exposure to low temperature.</p><table-wrap id="pone.0129016.t005" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0129016.t005</object-id><label>Table 5</label><caption><title>Selected <italic>de novo</italic> motifs found in Y<sub>n</sub>SK<sub>n</sub> dehydrin promoters and their putative function identified through PLACE database.</title></caption><alternatives><graphic id="pone.0129016.t005g" xlink:href="pone.0129016.t005"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1"></th><th colspan="4" align="center" rowspan="1">Match in PLACE<xref rid="t005fn005" ref-type="table-fn"><sup>5</sup></xref></th></tr><tr><th align="left" rowspan="1" colspan="1"><italic>De novo</italic> motif</th><th align="left" rowspan="1" colspan="1">Sequence</th><th align="left" rowspan="1" colspan="1">Name</th><th align="left" rowspan="1" colspan="1">E-value<xref rid="t005fn006" ref-type="table-fn"><sup>6</sup></xref></th><th align="left" rowspan="1" colspan="1">Function</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">11. Seeder<xref rid="t005fn001" ref-type="table-fn"><sup><bold>1</bold></sup></xref> SACACGTGG<xref rid="t005fn002" ref-type="table-fn"><sup><bold>2</bold></sup></xref> (123/123<xref rid="t005fn003" ref-type="table-fn"><sup>3</sup></xref>, 4.8e-38<xref rid="t005fn004" ref-type="table-fn"><sup>4</sup></xref>)</td><td align="left" rowspan="1" colspan="1"><monospace>GGACACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABRETAEM</td><td align="left" rowspan="1" colspan="1">1.1e-16</td><td align="left" rowspan="1" colspan="1">ABRE found in wheat</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TCCACGTGTC</monospace></td><td align="left" rowspan="1" colspan="1">SGBFGMGMAUX28</td><td align="left" rowspan="1" colspan="1">2.5e-13</td><td align="left" rowspan="1" colspan="1">Recognized by G-box binding factors in soybean. Found in auxin-responsive genes</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CGCCACGTGTCC</monospace></td><td align="left" rowspan="1" colspan="1">ABREBNNAPA</td><td align="left" rowspan="1" colspan="1">6.7e-16</td><td align="left" rowspan="1" colspan="1">ABRE found in rapeseed</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TGACACGTGGCA</monospace></td><td align="left" rowspan="1" colspan="1">HY5AT</td><td align="left" rowspan="1" colspan="1">6.7e-16</td><td align="left" rowspan="1" colspan="1">Bound by HY5, involved in light regulation of transcriptional activity</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>MCACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">GBOXLERBCS</td><td align="left" rowspan="1" colspan="1">7.3e-14</td><td align="left" rowspan="1" colspan="1">Sequence found in promoters of light-regulated genes</td></tr><tr><td align="left" rowspan="1" colspan="1">12. Seeder CRCCGAC (123/123, 3.1e-11)</td><td align="left" rowspan="1" colspan="1"><monospace>RCCGAC</monospace></td><td align="left" rowspan="1" colspan="1">DRECRTCOREAT</td><td align="left" rowspan="1" colspan="1">2.3e-09</td><td align="left" rowspan="1" colspan="1">DRE/CRT found in gene expressed in response to cold and dehydration</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>RYCGAC</monospace></td><td align="left" rowspan="1" colspan="1">CBFHV</td><td align="left" rowspan="1" colspan="1">1.4e-07</td><td align="left" rowspan="1" colspan="1">CRT found in barley (<italic>Hordeum vulgare</italic>)</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t005fn001"><p><sup>1</sup>Number of the motif and the <italic>de novo</italic> discovery software that was used to locate that motif.</p></fn><fn id="t005fn002"><p><sup>2</sup>Motif consensus sequence in IUPAC nucleotide code.</p></fn><fn id="t005fn003"><p><sup>3</sup>Occurrence is the number of promoters containing a <italic>de novo</italic> motif out of the total number of promoters analyzed for a specific dehydrin class, presented in the parentheses.</p></fn><fn id="t005fn004"><p><sup>4</sup>Siginificance of the motif, E-value calculated by MEME, Q-value calculated by Seeder, presented in the parentheses.</p></fn><fn id="t005fn005"><p><sup>5</sup>PLACE matches were identified using STAMP, only significant matches with E-value < 0.05 are presented.</p></fn><fn id="t005fn006"><p><sup>6</sup>E-value of the match with PLACE motif.</p></fn></table-wrap-foot></table-wrap></sec><sec id="sec013"><title>Y<sub>n</sub>K<sub>n</sub> dehydrins promoters contain ABREs and light REs</title><p>Y<sub>n</sub>K<sub>n</sub> dehydrins represent the smallest subgroup, with only 21 members found in 51 plant genomes (<xref rid="pone.0129016.t001" ref-type="table">Table 1</xref>). Y<sub>n</sub>K<sub>n</sub> dehydrins are known to be expressed in response to cold [<xref rid="pone.0129016.ref129" ref-type="bibr">129</xref>,<xref rid="pone.0129016.ref130" ref-type="bibr">130</xref>], and two motifs were detected in their promoters (<xref rid="pone.0129016.t006" ref-type="table">Table 6</xref>, <xref rid="pone.0129016.s002" ref-type="supplementary-material">S2 Table</xref>). One was identified using Seeder and the other using MEME. Both motifs match several ABREs and light REs in the PLACE database. Motif 13 (<monospace>TA<underline>ACACGTG</underline>TC/GACACGTGTTA</monospace>) is similar to motif 11 (<monospace>G<underline>ACACGTG</underline>GC/GCCACGTGTC</monospace>) identified in Y<sub>n</sub>SK<sub>n</sub> dehydrins and it matches the some of the same motifs in PLACE. Motif 14 (<monospace><underline>ACGTGGC</underline>A/TGCCACGT</monospace>) is similar to motif 11 (<monospace>GAC<underline>ACGTGGC</underline></monospace>) found in Y<sub>n</sub>SK<sub>n</sub> dehydrin. The lack of CRTs in the promoters of Y<sub>n</sub>K<sub>n</sub> dehydrins suggests that they might be expressed in response to cold in ABA-dependent manner, not linked with the CBF transcription factors [<xref rid="pone.0129016.ref018" ref-type="bibr">18</xref>].</p><table-wrap id="pone.0129016.t006" orientation="portrait" position="float"><object-id pub-id-type="doi">10.1371/journal.pone.0129016.t006</object-id><label>Table 6</label><caption><title>Selected <italic>de novo</italic> motifs found in Y<sub>n</sub>K<sub>n</sub> dehydrin promoters and their putative function identified through PLACE database.</title></caption><alternatives><graphic id="pone.0129016.t006g" xlink:href="pone.0129016.t006"></graphic><table frame="hsides" rules="groups"><colgroup span="1"><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col><col align="left" valign="middle" span="1"></col></colgroup><thead><tr><th align="left" rowspan="1" colspan="1"></th><th colspan="4" align="center" rowspan="1">Match in PLACE<xref rid="t006fn005" ref-type="table-fn"><sup>5</sup></xref></th></tr><tr><th align="left" rowspan="1" colspan="1"><italic>De novo</italic> motif</th><th align="left" rowspan="1" colspan="1">Sequence</th><th align="left" rowspan="1" colspan="1">Name</th><th align="left" rowspan="1" colspan="1">E-value<xref rid="t006fn006" ref-type="table-fn"><sup>6</sup></xref></th><th align="left" rowspan="1" colspan="1">Function</th></tr></thead><tbody><tr><td align="left" rowspan="1" colspan="1">13. Seeder<xref rid="t006fn001" ref-type="table-fn"><sup>1</sup></xref> YRACACGTGTCC<xref rid="t006fn002" ref-type="table-fn"><sup>2</sup></xref> (21/21<xref rid="t006fn003" ref-type="table-fn"><sup>3</sup></xref>, 1.5e-09<xref rid="t006fn004" ref-type="table-fn"><sup>4</sup></xref>)</td><td align="left" rowspan="1" colspan="1"><monospace>GGACACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABRETAEM</td><td align="left" rowspan="1" colspan="1">4.1-e11</td><td align="left" rowspan="1" colspan="1">ABRE found in wheat</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CGCCACGTGTCC</monospace></td><td align="left" rowspan="1" colspan="1">ABREBNNAPA</td><td align="left" rowspan="1" colspan="1">7.8e-11</td><td align="left" rowspan="1" colspan="1">ABRE found in rapeseed</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>CGCACGTGTC</monospace></td><td align="left" rowspan="1" colspan="1">ABRE2HVA22</td><td align="left" rowspan="1" colspan="1">6.3e-09</td><td align="left" rowspan="1" colspan="1">ABRE2 found in barley HVA22 gene</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TCCACGTGTC</monospace></td><td align="left" rowspan="1" colspan="1">SGBFGMGMAUX28</td><td align="left" rowspan="1" colspan="1">6.3e-09</td><td align="left" rowspan="1" colspan="1">Recognized by G-box binding factors in soybean. Found in auxin-responsive genes</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>AACGCGTGTC</monospace></td><td align="left" rowspan="1" colspan="1">CE3OSOSEM</td><td align="left" rowspan="1" colspan="1">1.1e-10</td><td align="left" rowspan="1" colspan="1">Coupling element 3 found in rice, required for ABA induced expression</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>TGACACGTGGCA</monospace></td><td align="left" rowspan="1" colspan="1">HY5AT</td><td align="left" rowspan="1" colspan="1">7.5e-09</td><td align="left" rowspan="1" colspan="1">Bound by HY5, involved in light regulation of transcriptional activity</td></tr><tr><td align="left" rowspan="1" colspan="1">14. MEME ACGTGKCA (21/21, 8.3e-05)</td><td align="left" rowspan="1" colspan="1"><monospace>ACGTGKC</monospace></td><td align="left" rowspan="1" colspan="1">ACGTABREMOTIFA2OSEM</td><td align="left" rowspan="1" colspan="1">1.3e-11</td><td align="left" rowspan="1" colspan="1">Core of ABRE in rice</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>ACGTGGCA</monospace></td><td align="left" rowspan="1" colspan="1">LRENPCABE</td><td align="left" rowspan="1" colspan="1">5.7e-13</td><td align="left" rowspan="1" colspan="1">Positive light RE in tobacco</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>YACGTGGC</monospace></td><td align="left" rowspan="1" colspan="1">ABREATCONSENSUS</td><td align="left" rowspan="1" colspan="1">7.4e-09</td><td align="left" rowspan="1" colspan="1">ABRE found in Arabidopsis</td></tr><tr><td align="left" rowspan="1" colspan="1"></td><td align="left" rowspan="1" colspan="1"><monospace>RTACGTGGCR</monospace></td><td align="left" rowspan="1" colspan="1">ABADESI1</td><td align="left" rowspan="1" colspan="1">2.0e-11</td><td align="left" rowspan="1" colspan="1">ABRE and desiccation response in rice</td></tr></tbody></table></alternatives><table-wrap-foot><fn id="t006fn001"><p><sup>1</sup>Number of the motif and the <italic>de novo</italic> discovery software that was used to locate that motif.</p></fn><fn id="t006fn002"><p><sup>2</sup>Motif consensus sequence in IUPAC nucleotide code.</p></fn><fn id="t006fn003"><p><sup>3</sup>Occurrence is the number of promoters containing a <italic>de novo</italic> motif out of the total number of promoters analyzed for a specific dehydrin class, presented in the parentheses.</p></fn><fn id="t006fn004"><p><sup>4</sup>Siginificance of the motif, E-value calculated by MEME, Q-value calculated by Seeder, presented in the parentheses.</p></fn><fn id="t006fn005"><p><sup>5</sup>PLACE matches were identified using STAMP, only significant matches with E-value < 0.05 are presented.</p></fn><fn id="t006fn006"><p><sup>6</sup>E-value of the match with PLACE motif.</p></fn></table-wrap-foot></table-wrap></sec></sec><sec sec-type="conclusions" id="sec014"><title>Conclusions</title><p>Numerous dehydrins were identified in 51 plant genomes, many of which are not found in protein databases such as InterPro or PROSITE, or they are not annotated in Phytozome. The identified dehydrins were categorized into five subclasses based on the occurrence of conserved protein segments. Three <italic>de novo</italic> motif discovery software tools were used to find statistically significant overrepresented motifs in the promoters of each group of dehydrins. These motifs were matched to known <italic>cis</italic>-regulatory elements in the PLACE database to help explain the regulation of dehydrin expression in response to different environmental stimuli.</p><p>Dehydrins are expressed in response to multiple stress stimuli. Although there is overlap in expression triggers between dehydrin subclasses, there are differences in the pattern of expression. Some of the dehydrins are expressed constitutively in all tissues [<xref rid="pone.0129016.ref003" ref-type="bibr">3</xref>,<xref rid="pone.0129016.ref005" ref-type="bibr">5</xref>] and more specifically in seeds [<xref rid="pone.0129016.ref131" ref-type="bibr">131</xref>,<xref rid="pone.0129016.ref132" ref-type="bibr">132</xref>]. The presence of ABREs, CRTs and light REs in the promoters of Y<sub>n</sub>SK<sub>n</sub> and SK<sub>n</sub> dehydrins indicates that they could be expressed in response to dehydration and cold in both ABA-dependent and independent pathway and that this expression is modulated by light.</p><p>While Y<sub>n</sub>SK<sub>n</sub> and SK<sub>n</sub> dehydrin are found in most species, often in several copies, the other three subclasses are encountered less often. It is probable that they either have specialized functions or they are expressed together with Y<sub>n</sub>SK<sub>n</sub> and SK<sub>n</sub> dehydrins to increase the overall protective effect against dehydration. It is important to note that the number of discovered dehydrins is probably an underestimation due to incompleteness of genome assembly and errors inherent in sequencing.</p><p>Dehydrins play an important role in the survival of plants facing various stresses. Motifs matching <italic>cis</italic>-regulatory elements linked to both ABA-dependent and independent stress response pathways, as well as light response pathways were detected in dehydrins from many different plant families. The implication of this finding is that the regulation of dehydrins is conserved in the plant lineages included in this study and that stress-linked selection pressure preserved <italic>cis</italic>-regulatory elements in the promoters of dehydrins through stabilizing selection.</p></sec><sec sec-type="supplementary-material" id="sec015"><title>Supporting Information</title><supplementary-material content-type="local-data" id="pone.0129016.s001"><label>S1 Table</label><caption><title>Annotation and meta-data about the dehydrins included in the study.</title><p>Each identified dehydrin was further analyzed by BLAST to find the closest match at NCBI GenBank non-reduntant database. The fields are 1. Species; 2. Gene; 3. Dehydrin subgroup; 4. BLAST top hit e-value; 5. BLAST top hit accession; 6. BLAST top hit description; 7. K-segment location; 8. Y-segment location; 9. S-segment location.</p><p>(CSV)</p></caption><media xlink:href="pone.0129016.s001.csv"><caption><p>Click here for additional data file.</p></caption></media></supplementary-material><supplementary-material content-type="local-data" id="pone.0129016.s002"><label>S2 Table</label><caption><title>Motif logos of motifs discovered in dehydrin promoters.</title><p>Weblogos were made for each of the motifs identified by <italic>de novo</italic> motif discovery algorithms in five classes of dehydrin genes. 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