246 lines
32 KiB
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246 lines
32 KiB
XML
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<mods:title id="313D743D2DCE6F341A84FED28C5E638D">Distribution and evolution of the serine / aspartate racemase family in plants</mods:title>
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<mods:namePart id="D8F049BA6D638BE1BECD984EFE64CA53">Uda, Kouji</mods:namePart>
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<mods:affiliation id="6123C40EB4B7D0A5B49E52AF10957168">Laboratory of Biochemistry, Faculty of Science and Technology, Kochi University, Kochi, 780 - 8520, Japan</mods:affiliation>
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<mods:namePart id="75BFA935D9186F5FAB897F3F52CFFDF3">Edashige, Yumika</mods:namePart>
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<mods:namePart id="E8AE91E4230EA7DC35556DE34D5140B6">Nishimura, Rie</mods:namePart>
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<mods:namePart id="C7426B2887EB6DEEB5C74BE41ECA42FF">Shikano, Yuuna</mods:namePart>
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<mods:namePart id="B94F2E501638AF739B5CD76423E26786">Matsui, Tohru</mods:namePart>
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<mods:namePart id="88D22CE2EB2941DF7F1330F691CD6693">Radkov, Atanas D.</mods:namePart>
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<mods:namePart id="2292E196C90D5CCA4D28823AC1D8A72B">Moe, Luke A.</mods:namePart>
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<mods:title id="8FC2C652CEC32174F6D9F975AE037538">Phytochemistry</mods:title>
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<mods:date id="9FB302EB5E671513A5866FF340783919">2020</mods:date>
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<mods:title id="68A0AF24D028AF532D2B9A2F1E8A94B5">112164</mods:title>
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<mods:number id="01347074D356317BFA9DE737199E8FD3">2020-01-31</mods:number>
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<mods:number id="401C2A39CF8E459DA4A462C6087FB1D9">169</mods:number>
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<mods:identifier id="049582D0302284688104630EEA8B97F1" type="CLB-Dataset">264478</mods:identifier>
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<mods:identifier id="70E9156179864B3C905C7FEC8B7ECB07" type="DOI">10.1016/j.phytochem.2019.112164</mods:identifier>
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<treatment id="039087E6FF93FF91FFAAFB7EFC0F9124" ID-DOI="http://doi.org/10.5281/zenodo.8301786" ID-Zenodo-Dep="8301786" LSID="urn:lsid:plazi:treatment:039087E6FF93FF91FFAAFB7EFC0F9124" httpUri="http://treatment.plazi.org/id/039087E6FF93FF91FFAAFB7EFC0F9124" lastPageNumber="4" pageId="3" pageNumber="4">
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<subSubSection id="C323657BFF93FF91FFAAFB7EFDF092E3" box="[100,557,1219,1238]" pageId="3" pageNumber="4" type="nomenclature">
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<paragraph id="8B8636F0FF93FF91FFAAFB7EFDF092E3" blockId="3.[100,557,1219,1238]" box="[100,557,1219,1238]" pageId="3" pageNumber="4">
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<heading id="D0CE819CFF93FF91FFAAFB7EFDF092E3" bold="true" box="[100,557,1219,1238]" fontSize="36" level="1" pageId="3" pageNumber="4" reason="1">
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<emphasis id="B94DEAE2FF93FF91FFAAFB7EFDF092E3" bold="true" box="[100,557,1219,1238]" italics="true" pageId="3" pageNumber="4">
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2.3. Evolution of the AspR gene in order
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<taxonomicName id="4C394D73FF93FF91FE17FB7EFDF092E3" ID-CoL="43W" authority="Juss. ex Bercht. & J.Presl, 1820" authorityName="Juss. ex Bercht. & J.Presl" authorityYear="1820" box="[473,557,1219,1238]" class="Magnoliopsida" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Solanales</taxonomicName>
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</emphasis>
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</heading>
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</paragraph>
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</subSubSection>
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<subSubSection id="C323657BFF93FF91FF4BFB46FE429010" pageId="3" pageNumber="4" type="description">
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<paragraph id="8B8636F0FF93FF91FF4BFB46FE429010" blockId="3.[100,770,1275,1992]" pageId="3" pageNumber="4">
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To verify our hypothesis that
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<taxonomicName id="4C394D73FF93FF91FE68FB46FDB3933B" box="[422,622,1275,1294]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">
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<emphasis id="B94DEAE2FF93FF91FE68FB46FDB3933B" bold="true" box="[422,622,1275,1294]" italics="true" pageId="3" pageNumber="4">Solanum lycopersicum</emphasis>
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</taxonomicName>
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AspR gene has evolved from SerR by gene duplication and amino acid substitutions, the gene loci of the SerR and AspR genes were compared among seven plants of the order
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<taxonomicName id="4C394D73FF93FF91FED0FAF2FEAB9357" box="[286,374,1359,1378]" class="Magnoliopsida" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Solanales</taxonomicName>
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and
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<taxonomicName id="4C394D73FF93FF91FE66FAF3FDF19354" box="[424,556,1358,1377]" class="Magnoliopsida" family="Rubiaceae" genus="Coffea" kingdom="Plantae" order="Gentianales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="arabica">
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<emphasis id="B94DEAE2FF93FF91FE66FAF3FDF19354" bold="true" box="[424,556,1358,1377]" italics="true" pageId="3" pageNumber="4">Coffea arabica</emphasis>
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</taxonomicName>
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, order
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<taxonomicName id="4C394D73FF93FF91FDBDFAF2FD3E9357" box="[627,739,1359,1378]" class="Magnoliopsida" kingdom="Plantae" order="Gentianales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Gentianales</taxonomicName>
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, as an outgroup (
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<figureCitation id="13022A75FF93FF91FF3CFAD7FEF0934B" box="[242,301,1386,1406]" captionStart="Fig" captionStartId="4.[1151,1181,152,169]" captionTargetBox="[100,1151,151,1058]" captionTargetId="graphics-749@4.[111,967,473,1009]" captionTargetPageId="4" captionText="Fig. 2. Chromosomal gene arrangement around SerR homologous genes (a) and phylogenetic tree based on the nucleotide sequence of SerR homologous genes (b) from Solanales species. (a) The arrows indicate the direction of transcription. The genome sequences were obtained from GenBank and the accession numbers are as follows: CP025656, Ipomoea trifida; NW_015850497, Nicotiana tabacum; CM008450, Capsicum baccatum; NC_015445, Solanum lycopersicum; NC_028644, Solanum pennellii; NW_006239070, Solanum tuberosum; FYAA01000154, Solanum verrucosum; NC_039913, Coffea arabica. Each SerR homologous gene was predicted as AspR or SerR based on the amino acid sequence of the triple serine loop region. AHL5, AT-hook motif nuclear-localized protein 5; FTIP1, FT-interacting protein 1; NOB1, RNA-binding protein NOB1; LOR, LURP-one-related. (b) The nucleotide sequence of SerR homologous genes was obtained from genome sequences. The ML tree was constructed using the MEGA 7 (Kumar et al., 2016) and the ML bootstrap values are shown at the branching point. The symbols (A) to (D) before sequence name correspond to the gene arrangement shown in (a)." figureDoi="http://doi.org/10.5281/zenodo.8293822" httpUri="https://zenodo.org/record/8293822/files/figure.png" pageId="3" pageNumber="4">Fig. 2</figureCitation>
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). Each plant genome sequence obtained from GenBank contained one to three SerR homologous genes. These SerR homologous genes were separated into
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<specimenCount id="9D3FFD79FF93FF91FE29FA1EFD959383" box="[487,584,1443,1462]" pageId="3" pageNumber="4" type="generic" typeStatus="types">two types</specimenCount>
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: one with HPN residues at positions 150 to 152 and one with PSS residues at the same positions, and we assumed the former to be a SerR and the latter to be an AspR according to the prediction of enzyme activity mentioned above (triple serine loop region).
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</paragraph>
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</subSubSection>
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<subSubSection id="C323657BFF93FF91FF4BF993FC0F9124" pageId="3" pageNumber="4" type="discussion">
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<paragraph id="8B8636F0FF93FF91FF4BF993FC0F9124" blockId="3.[100,770,1275,1992]" lastBlockId="3.[818,1488,1121,1809]" pageId="3" pageNumber="4">
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The
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<taxonomicName id="4C394D73FF93FF91FF7CF993FE839075" box="[178,350,1581,1601]" class="Magnoliopsida" family="Solanaceae" genus="Nicotiana" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="tabacum">
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<emphasis id="B94DEAE2FF93FF91FF7CF993FE839075" bold="true" box="[178,350,1581,1601]" italics="true" pageId="3" pageNumber="4">Nicotiana tabacum</emphasis>
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</taxonomicName>
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(
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<taxonomicName id="4C394D73FF93FF91FEA0F993FE179074" box="[366,458,1582,1601]" class="Magnoliopsida" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Solanales</taxonomicName>
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,
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<taxonomicName id="4C394D73FF93FF91FE18F993FD9D9074" box="[470,576,1582,1601]" class="Magnoliopsida" family="Solanaceae" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="family">Solanaceae</taxonomicName>
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) and
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<taxonomicName id="4C394D73FF93FF91FDB2F990FCDF9075" box="[636,770,1581,1600]" class="Magnoliopsida" family="Rubiaceae" genus="Coffea" kingdom="Plantae" order="Gentianales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="arabica">
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<emphasis id="B94DEAE2FF93FF91FDB2F990FCDF9075" bold="true" box="[636,770,1581,1600]" italics="true" pageId="3" pageNumber="4">Coffea arabica</emphasis>
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</taxonomicName>
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(
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<taxonomicName id="4C394D73FF93FF91FFA5F9F7FF019068" box="[107,220,1610,1629]" class="Magnoliopsida" kingdom="Plantae" order="Gentianales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Gentianales</taxonomicName>
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) genomes have only one SerR gene. The chromosomal gene arrangement around the SerR gene is shown as gene arrangement (B) in
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<figureCitation id="13022A75FF93FF91FF6FF93CFF3990A0" box="[161,228,1665,1685]" captionStart="Fig" captionStartId="4.[1151,1181,152,169]" captionTargetBox="[100,1151,151,1058]" captionTargetId="graphics-749@4.[111,967,473,1009]" captionTargetPageId="4" captionText="Fig. 2. Chromosomal gene arrangement around SerR homologous genes (a) and phylogenetic tree based on the nucleotide sequence of SerR homologous genes (b) from Solanales species. (a) The arrows indicate the direction of transcription. The genome sequences were obtained from GenBank and the accession numbers are as follows: CP025656, Ipomoea trifida; NW_015850497, Nicotiana tabacum; CM008450, Capsicum baccatum; NC_015445, Solanum lycopersicum; NC_028644, Solanum pennellii; NW_006239070, Solanum tuberosum; FYAA01000154, Solanum verrucosum; NC_039913, Coffea arabica. Each SerR homologous gene was predicted as AspR or SerR based on the amino acid sequence of the triple serine loop region. AHL5, AT-hook motif nuclear-localized protein 5; FTIP1, FT-interacting protein 1; NOB1, RNA-binding protein NOB1; LOR, LURP-one-related. (b) The nucleotide sequence of SerR homologous genes was obtained from genome sequences. The ML tree was constructed using the MEGA 7 (Kumar et al., 2016) and the ML bootstrap values are shown at the branching point. The symbols (A) to (D) before sequence name correspond to the gene arrangement shown in (a)." figureDoi="http://doi.org/10.5281/zenodo.8293822" httpUri="https://zenodo.org/record/8293822/files/figure.png" pageId="3" pageNumber="4">Fig. 2a</figureCitation>
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. The
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<taxonomicName id="4C394D73FF93FF91FED7F93FFE7F90A1" box="[281,418,1665,1685]" class="Magnoliopsida" family="Convolvulaceae" genus="Ipomoea" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="trifida">
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<emphasis id="B94DEAE2FF93FF91FED7F93FFE7F90A1" bold="true" box="[281,418,1665,1685]" italics="true" pageId="3" pageNumber="4">Ipomoea trifida</emphasis>
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</taxonomicName>
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(
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<taxonomicName id="4C394D73FF93FF91FE61F93CFDD690A1" box="[431,523,1665,1684]" class="Magnoliopsida" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Solanales</taxonomicName>
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,
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<taxonomicName id="4C394D73FF93FF91FDDBF93CFD7690A1" box="[533,683,1665,1684]" class="Magnoliopsida" family="Convolvulaceae" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="family">Convolvulaceae</taxonomicName>
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) genome lacks the NOB1 gene compared to
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<typeStatus id="54828852FF93FF91FE7BF923FE039084" box="[437,478,1694,1713]" pageId="3" pageNumber="4">type</typeStatus>
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(B) and has
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<typeStatus id="54828852FF93FF91FD93F923FD5B9084" box="[605,646,1694,1713]" pageId="3" pageNumber="4">type</typeStatus>
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(A) gene arrangement (
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<figureCitation id="13022A75FF93FF91FF18F904FEC590F9" box="[214,280,1721,1740]" captionStart="Fig" captionStartId="4.[1151,1181,152,169]" captionTargetBox="[100,1151,151,1058]" captionTargetId="graphics-749@4.[111,967,473,1009]" captionTargetPageId="4" captionText="Fig. 2. Chromosomal gene arrangement around SerR homologous genes (a) and phylogenetic tree based on the nucleotide sequence of SerR homologous genes (b) from Solanales species. (a) The arrows indicate the direction of transcription. The genome sequences were obtained from GenBank and the accession numbers are as follows: CP025656, Ipomoea trifida; NW_015850497, Nicotiana tabacum; CM008450, Capsicum baccatum; NC_015445, Solanum lycopersicum; NC_028644, Solanum pennellii; NW_006239070, Solanum tuberosum; FYAA01000154, Solanum verrucosum; NC_039913, Coffea arabica. Each SerR homologous gene was predicted as AspR or SerR based on the amino acid sequence of the triple serine loop region. AHL5, AT-hook motif nuclear-localized protein 5; FTIP1, FT-interacting protein 1; NOB1, RNA-binding protein NOB1; LOR, LURP-one-related. (b) The nucleotide sequence of SerR homologous genes was obtained from genome sequences. The ML tree was constructed using the MEGA 7 (Kumar et al., 2016) and the ML bootstrap values are shown at the branching point. The symbols (A) to (D) before sequence name correspond to the gene arrangement shown in (a)." figureDoi="http://doi.org/10.5281/zenodo.8293822" httpUri="https://zenodo.org/record/8293822/files/figure.png" pageId="3" pageNumber="4">Fig. 2a</figureCitation>
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). Gene arrangement (C) in which the SerR and AspR genes are arranged in tandem, is found in
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<taxonomicName id="4C394D73FF93FF91FE3EF968FD7490DD" box="[496,681,1749,1768]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="verrucosum">
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<emphasis id="B94DEAE2FF93FF91FE3EF968FD7490DD" bold="true" box="[496,681,1749,1768]" italics="true" pageId="3" pageNumber="4">Solanum verrucosum</emphasis>
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</taxonomicName>
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, S
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<emphasis id="B94DEAE2FF93FF91FD71F968FF1D9131" bold="true" italics="true" pageId="3" pageNumber="4">
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olanum
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<taxonomicName id="4C394D73FF93FF91FFAAF94CFF1D9131" box="[100,192,1777,1796]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="tuberosum">tuberosum</taxonomicName>
|
|
</emphasis>
|
|
and
|
|
<taxonomicName id="4C394D73FF93FF91FF35F94CFE6C9131" box="[251,433,1777,1796]" class="Magnoliopsida" family="Solanaceae" genus="Capsicum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="baccatum">
|
|
<emphasis id="B94DEAE2FF93FF91FF35F94CFE6C9131" bold="true" box="[251,433,1777,1796]" italics="true" pageId="3" pageNumber="4">Capsicum baccatum</emphasis>
|
|
</taxonomicName>
|
|
. Moreover,
|
|
<taxonomicName id="4C394D73FF93FF91FDE1F94CFD0E9131" box="[559,723,1777,1796]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="pennellii">
|
|
<emphasis id="B94DEAE2FF93FF91FDE1F94CFD0E9131" bold="true" box="[559,723,1777,1796]" italics="true" pageId="3" pageNumber="4">Solanum pennellii</emphasis>
|
|
</taxonomicName>
|
|
and
|
|
<taxonomicName id="4C394D73FF93FF91FFAAF8B0FEF39115" box="[100,302,1805,1824]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">
|
|
<emphasis id="B94DEAE2FF93FF91FFAAF8B0FEF39115" bold="true" box="[100,302,1805,1824]" italics="true" pageId="3" pageNumber="4">Solanum lycopersicum</emphasis>
|
|
</taxonomicName>
|
|
genomes contain one more tandem duplicated AspR gene and have
|
|
<typeStatus id="54828852FF93FF91FEFEF894FE849109" box="[304,345,1833,1852]" pageId="3" pageNumber="4">type</typeStatus>
|
|
(D) gene arrangement (
|
|
<figureCitation id="13022A75FF93FF91FD8DF894FD5A9109" box="[579,647,1833,1852]" captionStart="Fig" captionStartId="4.[1151,1181,152,169]" captionTargetBox="[100,1151,151,1058]" captionTargetId="graphics-749@4.[111,967,473,1009]" captionTargetPageId="4" captionText="Fig. 2. Chromosomal gene arrangement around SerR homologous genes (a) and phylogenetic tree based on the nucleotide sequence of SerR homologous genes (b) from Solanales species. (a) The arrows indicate the direction of transcription. The genome sequences were obtained from GenBank and the accession numbers are as follows: CP025656, Ipomoea trifida; NW_015850497, Nicotiana tabacum; CM008450, Capsicum baccatum; NC_015445, Solanum lycopersicum; NC_028644, Solanum pennellii; NW_006239070, Solanum tuberosum; FYAA01000154, Solanum verrucosum; NC_039913, Coffea arabica. Each SerR homologous gene was predicted as AspR or SerR based on the amino acid sequence of the triple serine loop region. AHL5, AT-hook motif nuclear-localized protein 5; FTIP1, FT-interacting protein 1; NOB1, RNA-binding protein NOB1; LOR, LURP-one-related. (b) The nucleotide sequence of SerR homologous genes was obtained from genome sequences. The ML tree was constructed using the MEGA 7 (Kumar et al., 2016) and the ML bootstrap values are shown at the branching point. The symbols (A) to (D) before sequence name correspond to the gene arrangement shown in (a)." figureDoi="http://doi.org/10.5281/zenodo.8293822" httpUri="https://zenodo.org/record/8293822/files/figure.png" pageId="3" pageNumber="4">Fig. 2a</figureCitation>
|
|
). The phylogenetic tree constructed from the nucleotide sequences of SerR and AspR genes (
|
|
<figureCitation id="13022A75FF93FF91FF11F8DCFEFE9141" box="[223,291,1889,1908]" captionStart="Fig" captionStartId="4.[1151,1181,152,169]" captionTargetBox="[100,1151,151,1058]" captionTargetId="graphics-749@4.[111,967,473,1009]" captionTargetPageId="4" captionText="Fig. 2. Chromosomal gene arrangement around SerR homologous genes (a) and phylogenetic tree based on the nucleotide sequence of SerR homologous genes (b) from Solanales species. (a) The arrows indicate the direction of transcription. The genome sequences were obtained from GenBank and the accession numbers are as follows: CP025656, Ipomoea trifida; NW_015850497, Nicotiana tabacum; CM008450, Capsicum baccatum; NC_015445, Solanum lycopersicum; NC_028644, Solanum pennellii; NW_006239070, Solanum tuberosum; FYAA01000154, Solanum verrucosum; NC_039913, Coffea arabica. Each SerR homologous gene was predicted as AspR or SerR based on the amino acid sequence of the triple serine loop region. AHL5, AT-hook motif nuclear-localized protein 5; FTIP1, FT-interacting protein 1; NOB1, RNA-binding protein NOB1; LOR, LURP-one-related. (b) The nucleotide sequence of SerR homologous genes was obtained from genome sequences. The ML tree was constructed using the MEGA 7 (Kumar et al., 2016) and the ML bootstrap values are shown at the branching point. The symbols (A) to (D) before sequence name correspond to the gene arrangement shown in (a)." figureDoi="http://doi.org/10.5281/zenodo.8293822" httpUri="https://zenodo.org/record/8293822/files/figure.png" pageId="3" pageNumber="4">Fig. 2b</figureCitation>
|
|
), and the comparison between gene arrangements (A to D) have revealed the following findings. Gene arrangement (B), which has one SerR gene, is considered to be an ancestral arrangement
|
|
<typeStatus id="54828852FF93FF91FFAAF808FF5091FD" box="[100,141,1973,1992]" pageId="3" pageNumber="4">type</typeStatus>
|
|
in
|
|
<taxonomicName id="4C394D73FF93FF91FF7FF809FED491F2" box="[177,265,1972,1991]" class="Magnoliopsida" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Solanales</taxonomicName>
|
|
species since
|
|
<typeStatus id="54828852FF93FF91FE5AF808FE6091FD" box="[404,445,1973,1992]" pageId="3" pageNumber="4">type</typeStatus>
|
|
(B) is conserved in the outgroup species of
|
|
<taxonomicName id="4C394D73FF93FF91FC56FBDCFBC29241" box="[920,1055,1121,1140]" class="Magnoliopsida" family="Rubiaceae" genus="Coffea" kingdom="Plantae" order="Gentianales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="arabica">
|
|
<emphasis id="B94DEAE2FF93FF91FC56FBDCFBC29241" bold="true" box="[920,1055,1121,1140]" italics="true" pageId="3" pageNumber="4">Coffea arabica</emphasis>
|
|
</taxonomicName>
|
|
(
|
|
<taxonomicName id="4C394D73FF93FF91FBE0FBDCFB7F9241" box="[1070,1186,1121,1140]" class="Magnoliopsida" kingdom="Plantae" order="Gentianales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="order">Gentianales</taxonomicName>
|
|
). Hence, the lack of the NOB1 gene in arrangement (A) is considered to have occurred after the divergence of
|
|
<taxonomicName id="4C394D73FF93FF91FC67FB24FBCC9299" box="[937,1041,1177,1196]" class="Magnoliopsida" family="Solanaceae" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="family">Solanaceae</taxonomicName>
|
|
and the
|
|
<taxonomicName id="4C394D73FF93FF91FBA5FB24FADF9299" box="[1131,1282,1177,1196]" class="Magnoliopsida" family="Convolvulaceae" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="family">Convolvulaceae</taxonomicName>
|
|
. It became clear that the AspR gene was obtained by tandem duplication of the SerR gene and subsequent amino acid substitution. We thought that this event occurred for the first time in the common ancestor species of genus
|
|
<taxonomicName id="4C394D73FF93FF91FCFCFAB5FC5A932E" box="[818,903,1288,1307]" class="Magnoliopsida" family="Solanaceae" genus="Capsicum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="genus">
|
|
<emphasis id="B94DEAE2FF93FF91FCFCFAB5FC5A932E" bold="true" box="[818,903,1288,1307]" italics="true" pageId="3" pageNumber="4">Capsicum</emphasis>
|
|
</taxonomicName>
|
|
and genus
|
|
<taxonomicName id="4C394D73FF93FF91FC35FAB5FB95932E" box="[1019,1096,1288,1307]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="genus">
|
|
<emphasis id="B94DEAE2FF93FF91FC35FAB5FB95932E" bold="true" box="[1019,1096,1288,1307]" italics="true" pageId="3" pageNumber="4">Solanum</emphasis>
|
|
</taxonomicName>
|
|
without genus
|
|
<taxonomicName id="4C394D73FF93FF91FB2DFAB5FAE4932E" box="[1251,1337,1288,1307]" class="Magnoliopsida" family="Solanaceae" genus="Nicotiana" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="genus">
|
|
<emphasis id="B94DEAE2FF93FF91FB2DFAB5FAE4932E" bold="true" box="[1251,1337,1288,1307]" italics="true" pageId="3" pageNumber="4">Nicotiana</emphasis>
|
|
</taxonomicName>
|
|
. Moreover, the SerR and AspR genes were also arranged in tandem in the
|
|
<taxonomicName id="4C394D73FF93FF91FAABFA99FCAF9366" class="Magnoliopsida" family="Euphorbiaceae" genus="Manihot" kingdom="Plantae" order="Malpighiales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="esculenta">
|
|
<emphasis id="B94DEAE2FF93FF91FAABFA99FCAF9366" bold="true" italics="true" pageId="3" pageNumber="4">Manihot esculenta</emphasis>
|
|
</taxonomicName>
|
|
genome, suggesting that the
|
|
<taxonomicName id="4C394D73FF93FF91FB57FAFDFAE29366" box="[1177,1343,1344,1363]" class="Magnoliopsida" family="Euphorbiaceae" genus="Manihot" kingdom="Plantae" order="Malpighiales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="esculenta">
|
|
<emphasis id="B94DEAE2FF93FF91FB57FAFDFAE29366" bold="true" box="[1177,1343,1344,1363]" italics="true" pageId="3" pageNumber="4">Manihot esculenta</emphasis>
|
|
</taxonomicName>
|
|
AspR was obtained by a similar evolutionary process. The second AspR gene was obtained by tandem duplication of the AspR gene after the divergence of the genus
|
|
<taxonomicName id="4C394D73FF93FF91FC7AFA2EFBDC9393" box="[948,1025,1427,1446]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="genus">
|
|
<emphasis id="B94DEAE2FF93FF91FC7AFA2EFBDC9393" bold="true" box="[948,1025,1427,1446]" italics="true" pageId="3" pageNumber="4">Solanum</emphasis>
|
|
</taxonomicName>
|
|
. Considering the phylogenetic tree, the second tandem duplication event occurred in the ancestral species of four
|
|
<taxonomicName id="4C394D73FF93FF91FA7CFA0DFC6B93EB" pageId="3" pageNumber="4">
|
|
<emphasis id="B94DEAE2FF93FF91FA7CFA0DFCB793EB" bold="true" italics="true" pageId="3" pageNumber="4">Solanum</emphasis>
|
|
species
|
|
</taxonomicName>
|
|
, and then ancestral species of
|
|
<taxonomicName id="4C394D73FF93FF91FB29FA76FA7E93EA" box="[1255,1443,1483,1503]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="verrucosum">
|
|
<emphasis id="B94DEAE2FF93FF91FB29FA76FA7E93EA" bold="true" box="[1255,1443,1483,1503]" italics="true" pageId="3" pageNumber="4">Solanum verrucosum</emphasis>
|
|
</taxonomicName>
|
|
and
|
|
<taxonomicName id="4C394D73FF93FF91FCFCFA5AFC3893CF" box="[818,997,1511,1530]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="tuberosum">
|
|
<emphasis id="B94DEAE2FF93FF91FCFCFA5AFC3893CF" bold="true" box="[818,997,1511,1530]" italics="true" pageId="3" pageNumber="4">Solanum tuberosum</emphasis>
|
|
</taxonomicName>
|
|
lost one AspR gene. These findings indicate that
|
|
<taxonomicName id="4C394D73FF93FF91FCFCF9BEFBE39023" authority="AspRs" authorityName="AspRs" box="[818,1086,1539,1558]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">
|
|
<emphasis id="B94DEAE2FF93FF91FCFCF9BEFC269023" bold="true" box="[818,1019,1539,1558]" italics="true" pageId="3" pageNumber="4">Solanum lycopersicum</emphasis>
|
|
AspRs
|
|
</taxonomicName>
|
|
(AspR1 and AspR2) genes have evolved from SerR by gene tandem duplication and amino acid substitutions. The hypothesis that AspR evolved from SerR would be supported by that plant SerRs isolated in this study and many animal SerRs showed weak but distinct racemase activity toward aspartate (
|
|
<bibRefCitation id="EFA84B01FF93FF91FAF4F9CEFA1490B3" author="Ito, T. & Hayashida, M. & Kobayashi, S. & Muto, N. & Hayashi, A. & Yoshimura, T. & Mori, H." box="[1338,1481,1651,1670]" pageId="3" pageNumber="4" pagination="345 - 353" refId="ref8680" refString="Ito, T., Hayashida, M., Kobayashi, S., Muto, N., Hayashi, A., Yoshimura, T., Mori, H., 2016. Serine racemase is involved in d-aspartate biosynthesis. J. Biochem. 160, 345 - 353. https: // doi. org / 10.1093 / jb / mvw 043." type="journal article" year="2016">Ito et al., 2016</bibRefCitation>
|
|
;
|
|
<bibRefCitation id="EFA84B01FF93FF91FCFCF932FC109097" author="Uda, K. & Abe, K. & Dehara, Y. & Mizobata, K. & Sogawa, N. & Akagi, Y. & Saigan, M. & Radkov, A. D. & Moe, L. A." box="[818,973,1679,1698]" pageId="3" pageNumber="4" pagination="387 - 402" refId="ref9739" refString="Uda, K., Abe, K., Dehara, Y., Mizobata, K., Sogawa, N., Akagi, Y., Saigan, M., Radkov, A. D., Moe, L. A., 2016. Distribution and evolution of the serine / aspartate racemase family in invertebrates. Amino Acids 48, 387 - 402. https: // doi. org / 10.1007 / s 00726 - 015 - 2092 - 0." type="journal article" year="2016">Uda et al., 2016</bibRefCitation>
|
|
). We isolated and characterized only the AspR1 gene from
|
|
<taxonomicName id="4C394D73FF93FF91FCAAF917FBF59088" box="[868,1064,1706,1725]" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">
|
|
<emphasis id="B94DEAE2FF93FF91FCAAF917FBF59088" bold="true" box="[868,1064,1706,1725]" italics="true" pageId="3" pageNumber="4">Solanum lycopersicum</emphasis>
|
|
</taxonomicName>
|
|
and called it AspR in this study. The
|
|
<taxonomicName id="4C394D73FF93FF91FA4CF917FC7990EC" class="Magnoliopsida" family="Solanaceae" genus="Solanum" kingdom="Plantae" order="Solanales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="lycopersicum">
|
|
<emphasis id="B94DEAE2FF93FF91FA4CF917FC7990EC" bold="true" italics="true" pageId="3" pageNumber="4">Solanum lycopersicum</emphasis>
|
|
</taxonomicName>
|
|
AspR1 and AspR2 have 97% amino acid sequence identity and the expression level of the AspR2 gene was too low to isolate as described below.
|
|
</paragraph>
|
|
</subSubSection>
|
|
</treatment>
|
|
</document> |