410 lines
59 KiB
XML
410 lines
59 KiB
XML
<document id="6788491CF37163FDF569A09087842D54" ID-DOI="10.1016/j.phytochem.2015.12.001" ID-ISSN="1873-3700" ID-Zenodo-Dep="10485389" IM.bibliography_approvedBy="felipe" IM.illustrations_approvedBy="julia" IM.materialsCitations_approvedBy="julia" IM.metadata_approvedBy="julia" IM.tables_approvedBy="julia" IM.taxonomicNames_approvedBy="julia" IM.treatments_approvedBy="julia" checkinTime="1704944597226" checkinUser="felipe" docAuthor="Vylíčilová, Hana, Husičková, Alexandra, Spíchal, Lukáš, Srovnal, Josef, Doležal, Karel, Plíhal, Ondřej & Plíhalová, Lucie" docDate="2016" docId="03DA8788501F3F32FCFDFEAEFD58FC07" docLanguage="en" docName="Phytochemistry.122.22-33.pdf" docOrigin="Phytochemistry 122" docSource="http://dx.doi.org/10.1016/j.phytochem.2015.12.001" docStyle="DocumentStyle:9E596C34F4E94307D29315B03ACE1007.6:Phytochemistry.2014-2019.journal_article" docStyleId="9E596C34F4E94307D29315B03ACE1007" docStyleName="Phytochemistry.2014-2019.journal_article" docStyleVersion="6" docTitle="Arabidopsis leaves" docType="treatment" docVersion="4" lastPageNumber="28" masterDocId="FFE3FFF0501C3F34FFC2FFD5FFBDFFBD" masterDocTitle="C 2 - substituted aromatic cytokinin sugar conjugates delay the onset of senescence by maintaining the activity of the photosynthetic apparatus" masterLastPageNumber="33" masterPageNumber="22" pageNumber="25" updateTime="1705343994947" updateUser="julia">
|
||
<mods:mods id="FDABBC42FD5BCC2C9FD0CE69AAC7117D" xmlns:mods="http://www.loc.gov/mods/v3">
|
||
<mods:titleInfo id="22BB058E92025A3D9603964A4FB8D154">
|
||
<mods:title id="28491E0758E28AEA1E1F850F440ABFCB">C 2 - substituted aromatic cytokinin sugar conjugates delay the onset of senescence by maintaining the activity of the photosynthetic apparatus</mods:title>
|
||
</mods:titleInfo>
|
||
<mods:name id="17BFF82FE9B6ACC1A1E9681AFE8E5E5A" type="personal">
|
||
<mods:role id="D79101C67217D9FFD38986A4C43113AC">
|
||
<mods:roleTerm id="925440BDBCC138A7AA196D0971F564A4">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="689A78BB6CAA8564B9F0E4137E2241DC">Vylíčilová, Hana</mods:namePart>
|
||
<mods:affiliation id="FEA649E4A04E42D538EC258E092E64F2">Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Chemical Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ- 78371, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:name id="C73BE4BE9BC9A46013167EB5A5260A3F" type="personal">
|
||
<mods:role id="0528C2738AAA70A6D066583DD0968CCD">
|
||
<mods:roleTerm id="5D5ECBC7E49DA525B08B0B0100298BB3">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="7B9F7C78824F99BA4DF9FFAF7898491E">Husičková, Alexandra</mods:namePart>
|
||
<mods:affiliation id="BC1ADBEBFA2CC0044D9956E62896E4B1">Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Biophysics, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ- 78371, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:name id="048397566EDCDFD41CE2BE9E28C2EC14" type="personal">
|
||
<mods:role id="F78724CA939FDF37843D28E585E47DBE">
|
||
<mods:roleTerm id="759599CF4CEAB9C7DFF6CF317FF8E369">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="EE64CB74FDEA483A26194CD876BC1AB8">Spíchal, Lukáš</mods:namePart>
|
||
<mods:affiliation id="5EC1610345C8DE7D7C01A27C52D73BF3">Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Chemical Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ- 78371, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:name id="F673BDC0A9D993BB0275A36A58C80FF0" type="personal">
|
||
<mods:role id="4A47095E6C163D18AB9FA53DF9306F86">
|
||
<mods:roleTerm id="A6A42A169780C11F6238494F6026381C">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="8F1E36821E4F6F1385A3DEC13BADBA36">Srovnal, Josef</mods:namePart>
|
||
<mods:affiliation id="B7FCC0B1C014729CC2F22B226F7A881B">Institute of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University and University Hospital in Olomouc, Hněvotínská 5, CZ- 77900 Olomouc, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:name id="CEA35F19502A51919EF75F03329B73E2" type="personal">
|
||
<mods:role id="3649034DDF1F9EDE99DF9B0061B15D90">
|
||
<mods:roleTerm id="768901A93BE9B2A9B108B101A6D52B16">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="798E28563C21454F27F7BCD27654E54B">Doležal, Karel</mods:namePart>
|
||
<mods:affiliation id="E00EE7553C863FD6EDB7C63FC5D27E43">Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Chemical Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ- 78371, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:name id="A13E567C558EF1E5A7F9DE53D191368F" type="personal">
|
||
<mods:role id="E575D98CD1C5226F69C2108239DEF04D">
|
||
<mods:roleTerm id="8A353DC78E361D8D5F7F0FBC40E20021">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="06BE6FBA0F2EF74046C4BEC1F76B3564">Plíhal, Ondřej</mods:namePart>
|
||
<mods:affiliation id="787553193E0CB8235C1B9234B552E435">Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Molecular Biology, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ- 78371, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:name id="76ADD9E0F6E80E2A85A552455096B539" type="personal">
|
||
<mods:role id="EDAF3323C7536908E56BF0E8246CE029">
|
||
<mods:roleTerm id="A909CD2981731EDFAA9F00FE1FBD3F87">Author</mods:roleTerm>
|
||
</mods:role>
|
||
<mods:namePart id="6580F1D491325340ED3DD9DBC0D35D16">Plíhalová, Lucie</mods:namePart>
|
||
<mods:affiliation id="3B27F76B5353DFB09BBA9A111A4B2FEC">Centre of the Region Haná for Biotechnological and Agricultural Research, Department of Chemical Biology and Genetics, Faculty of Science, Palacký University, Šlechtitelů 27, Olomouc CZ- 78371, Czech Republic</mods:affiliation>
|
||
</mods:name>
|
||
<mods:typeOfResource id="F0825B3808A46A2D06B40B6EBB71C638">text</mods:typeOfResource>
|
||
<mods:relatedItem id="4FB69EA661902B6E62D7E1939C9E7E18" type="host">
|
||
<mods:titleInfo id="E71C6AC808D6A3D8AD6BEB94FE53C21F">
|
||
<mods:title id="B6D0516C0625A35FBC34987E80107750">Phytochemistry</mods:title>
|
||
</mods:titleInfo>
|
||
<mods:part id="2D0C7E324BE195D4E5A29DC1922A6BC4">
|
||
<mods:date id="7B50CD44454EFA4D9A7CA5D4CC2A1E43">2016</mods:date>
|
||
<mods:detail id="BEC8089AC4EB49B17E72AC8B9F6A2867" type="pubDate">
|
||
<mods:number id="AE66800244BA559B095B15FD53F96E38">2016-02-29</mods:number>
|
||
</mods:detail>
|
||
<mods:detail id="8192CB4104B056037EFA9BF93C10F741" type="volume">
|
||
<mods:number id="8A79490C35A5717F178FE5539084FE8B">122</mods:number>
|
||
</mods:detail>
|
||
<mods:extent id="8F57D8AF096688FE8799F994770F5810" unit="page">
|
||
<mods:start id="46435F9C32CF7544B185CAE44966C380">22</mods:start>
|
||
<mods:end id="7755E7451B0CB1A4302EBF1C525B2574">33</mods:end>
|
||
</mods:extent>
|
||
</mods:part>
|
||
</mods:relatedItem>
|
||
<mods:location id="313982EBD35FA4A39576786ADC94E96A">
|
||
<mods:url id="2C7EB84C951C548DAC501CFA9C9B001F">http://dx.doi.org/10.1016/j.phytochem.2015.12.001</mods:url>
|
||
</mods:location>
|
||
<mods:classification id="F233D95D73A45B32CA060475363C0726">journal article</mods:classification>
|
||
<mods:identifier id="9AA59874BE9F593D3E960167DB8227D7" type="DOI">10.1016/j.phytochem.2015.12.001</mods:identifier>
|
||
<mods:identifier id="0155239674BBFEE9406D73C8C9CE24E8" type="ISSN">1873-3700</mods:identifier>
|
||
<mods:identifier id="1B6B3EC611A6FD0D43DFF141B7C7DF53" type="Zenodo-Dep">10485389</mods:identifier>
|
||
</mods:mods>
|
||
<treatment id="03DA8788501F3F32FCFDFEAEFD58FC07" LSID="urn:lsid:plazi:treatment:03DA8788501F3F32FCFDFEAEFD58FC07" httpUri="http://treatment.plazi.org/id/03DA8788501F3F32FCFDFEAEFD58FC07" lastPageId="6" lastPageNumber="28" pageId="3" pageNumber="25">
|
||
<subSubSection id="C3696515501F3F37FCFDFEAEFA07FE32" box="[831,1466,379,399]" pageId="3" pageNumber="25" type="nomenclature">
|
||
<paragraph id="8BCC369E501F3F37FCFDFEAEFA07FE32" blockId="3.[831,1466,379,399]" box="[831,1466,379,399]" pageId="3" pageNumber="25">
|
||
<heading id="D08481F2501F3F37FCFDFEAEFA07FE32" box="[831,1466,379,399]" fontSize="36" level="2" pageId="3" pageNumber="25" reason="3">
|
||
<emphasis id="B907EA8C501F3F37FCFDFEAEFA07FE32" box="[831,1466,379,399]" italics="true" pageId="3" pageNumber="25">
|
||
2.4. Regulation of gene expression in senescent
|
||
<taxonomicName id="4C734D1D501F3F37FACBFEAEFAC5FE32" authority="Heynh." box="[1289,1400,379,399]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="3" pageNumber="25" phylum="Tracheophyta" rank="species" species="leaves">Arabidopsis</taxonomicName>
|
||
leaves
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
</subSubSection>
|
||
<subSubSection id="C3696515501F3F32FC9CFE61FD58FC07" lastPageId="6" lastPageNumber="28" pageId="3" pageNumber="25" type="description">
|
||
<paragraph id="8BCC369E501F3F37FC9CFE61FC23FC00" blockId="3.[831,1501,436,1487]" pageId="3" pageNumber="25">
|
||
Using BAP and DMSO treatments as references, we performed genome-wide expression profiling of senescent
|
||
<taxonomicName id="4C734D1D501F3F37FAEAFE1AFA2AFE5E" box="[1320,1431,463,483]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="3" pageNumber="25" phylum="Tracheophyta" rank="species" species="leaves">
|
||
<emphasis id="B907EA8C501F3F37FAEAFE1AFA2AFE5E" box="[1320,1431,463,483]" italics="true" pageId="3" pageNumber="25">Arabidopsis</emphasis>
|
||
</taxonomicName>
|
||
leaves treated with compounds
|
||
<emphasis id="B907EA8C501F3F37FB8BFE3EFBEBFE43" bold="true" box="[1097,1110,491,510]" pageId="3" pageNumber="25">3</emphasis>
|
||
and
|
||
<quantity id="4C8B9B7B501F3F37FB4DFE3EFB07FE43" box="[1167,1210,491,510]" metricMagnitude="-1" metricUnit="m" metricValue="1.524" pageId="3" pageNumber="25" unit="in" value="6.0">
|
||
<emphasis id="B907EA8C501F3F37FB4DFE3EFB21FE43" bold="true" box="[1167,1180,491,510]" pageId="3" pageNumber="25">6</emphasis>
|
||
in
|
||
</quantity>
|
||
order to better understand the regulation of senescence by ArCKs at the molecular level. Compounds
|
||
<emphasis id="B907EA8C501F3F37FC00FDF6FC72FD8B" bold="true" box="[962,975,547,566]" pageId="3" pageNumber="25">3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C501F3F37FBC9FDF6FBA5FD8B" bold="true" box="[1035,1048,547,566]" pageId="3" pageNumber="25">6</emphasis>
|
||
were selected because they exhibited the highest anti-senescence activity in the detached wheat leaf bioassay (
|
||
<tableCitation id="C6F10325501F3F37FCB1FD8EFC7FFDD3" box="[883,962,603,622]" captionStart="Table 2" captionStartId="2.[87,131,1480,1494]" captionTargetPageId="2" captionText="Table 2 The activity of the synthetic cytokinin derivatives in the tobacco callus and Amaranthus bioassays and the detached wheat leaf senescence bioassay relative to that of the control compound (BAP) at the optimal concentration (i.e. the concentration where the maximum positive effect of the tested compound was observed). All values were determined from two independent assays each performed in six technical replicates." pageId="3" pageNumber="25">Table 2</tableCitation>
|
||
). Expression changes were monitored in detached senescent
|
||
<taxonomicName id="4C734D1D501F3F37FC68FDA3FBA4FD37" box="[938,1049,630,650]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="3" pageNumber="25" phylum="Tracheophyta" rank="species" species="leaves">
|
||
<emphasis id="B907EA8C501F3F37FC68FDA3FBA4FD37" box="[938,1049,630,650]" italics="true" pageId="3" pageNumber="25">Arabidopsis</emphasis>
|
||
</taxonomicName>
|
||
leaves after 48 h of incubation in darkness with a 10 µM solution of one of the tested compounds or with DMSO alone; a complete list of DE genes from the three treatments (i.e. treatment with
|
||
<emphasis id="B907EA8C501F3F37FB97FD1FFBDFFD60" bold="true" box="[1109,1122,714,733]" pageId="3" pageNumber="25">3</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C501F3F37FBACFD1FFBC6FD60" bold="true" box="[1134,1147,714,733]" pageId="3" pageNumber="25">6</emphasis>
|
||
and BAP) is shown in the Supplementary
|
||
<tableCitation id="C6F10325501F3F37FC59FD32FC4DFD47" box="[923,1008,743,762]" captionStart="Table 1" captionStartId="2.[87,131,183,197]" captionTargetPageId="2" captionText="Table 1 Structures and abbreviations of the synthesised compounds." pageId="3" pageNumber="25">Table S1</tableCitation>
|
||
. Transcriptome profiling was performed using a standardized procedure developed for the detached leaf assay, which has previously been used to investigate the genetic effects of treatment with Kin derivatives that exhibit anti-senescent activity (
|
||
<bibRefCitation id="EFE24B6F501F3F37FC5BFC83FB85FCD4" author="Mik, V. & Szucova, L. & Smehilova, M. & Zatloukal, M. & Dolezal, K. & Nisler, J. & Gruz, J. & Galuszka, P. & Strnad, M. & Spichal, L." box="[921,1080,854,874]" pageId="3" pageNumber="25" pagination="821 - 831" refId="ref11942" refString="Mik, V., Szucova, L., Smehilova, M., Zatloukal, M., Dolezal, K., Nisler, J., Gruz, J., Galuszka, P., Strnad, M., Spichal, L., 2011. N 9 - substituted derivatives of kinetin: effective anti-senescence agents. Phytochemistry 72, 821 - 831." type="journal article" year="2011">Mik et al., 2011</bibRefCitation>
|
||
). While these Kin derivatives were effective anti-senescence agents under both light and constant dark conditions, their senescence-delaying activity was greatest in darkness.
|
||
</paragraph>
|
||
<paragraph id="8BCC369E501F3F30FC9CFC13FF7EF9CE" blockId="3.[831,1501,436,1487]" lastBlockId="4.[87,757,1381,1986]" lastPageId="4" lastPageNumber="26" pageId="3" pageNumber="25">
|
||
Hierarchical clustering analysis of the resulting data sets revealed that the samples treated with specific cytokinins clustered together and exhibited low variability in their responses, as did the mock-treated wild
|
||
<typeStatus id="54C8883C501F3F37FB91FBCFFB3DFB90" box="[1107,1152,1050,1069]" pageId="3" pageNumber="25">type</typeStatus>
|
||
<taxonomicName id="4C734D1D501F3F37FB45FBCDFB4BFB91" box="[1159,1270,1048,1068]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="3" pageNumber="25" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="B907EA8C501F3F37FB45FBCDFB4BFB91" box="[1159,1270,1048,1068]" italics="true" pageId="3" pageNumber="25">Arabidopsis</emphasis>
|
||
</taxonomicName>
|
||
leaf samples (
|
||
<figureCitation id="13482A1B501F3F37FA4EFBCCFA6EFB91" box="[1420,1491,1049,1068]" captionStart="Fig" captionStartId="4.[87,113,1240,1254]" captionTargetBox="[359,1191,184,1211]" captionTargetId="figure-445@4.[359,1191,181,1211]" captionTargetPageId="4" captionText="Fig. 2. Transcriptome reprogramming mediated by cytokinin derivatives as revealed by DNA microarray analysis (Affymetrix). Hierarchical clustering was performed for all data sets, i.e. Arabidopsis leaves treated with BAP, compound 3, compound 6, and DMSO alone (A). Clustering analysis of genes exhibiting differential expression after treatment with BAP, compound 3 or compound 6 (B).Venn diagrams of genes regulated by 3 and genes regulated by 6, showing the substantial overlap of the two sets (C). GO classification of genes regulated by 3 and 6 (D); genes were categorized into groups according to their GO terms, based on their predicted or putative functions." figureDoi="http://doi.org/10.5281/zenodo.10485393" httpUri="https://zenodo.org/record/10485393/files/figure.png" pageId="3" pageNumber="25">Fig. 2A</figureCitation>
|
||
). Interestingly, the BAP-treated samples formed the most distinct group and had a gene expression profile that differed significantly from those for all of the other groups. In contrast, the gene expression profiles for the groups treated with
|
||
<emphasis id="B907EA8C501F3F37FB13FB5CFB63FB21" bold="true" box="[1233,1246,1161,1180]" pageId="3" pageNumber="25">3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C501F3F37FACCFB5CFAA6FB21" bold="true" box="[1294,1307,1161,1180]" pageId="3" pageNumber="25">6</emphasis>
|
||
were quite similar. This is readily apparent in the heat map shown in
|
||
<figureCitation id="13482A1B501F3F37FA8DFB70FA2EFB05" box="[1359,1427,1189,1208]" captionStart="Fig" captionStartId="4.[87,113,1240,1254]" captionTargetBox="[359,1191,184,1211]" captionTargetId="figure-445@4.[359,1191,181,1211]" captionTargetPageId="4" captionText="Fig. 2. Transcriptome reprogramming mediated by cytokinin derivatives as revealed by DNA microarray analysis (Affymetrix). Hierarchical clustering was performed for all data sets, i.e. Arabidopsis leaves treated with BAP, compound 3, compound 6, and DMSO alone (A). Clustering analysis of genes exhibiting differential expression after treatment with BAP, compound 3 or compound 6 (B).Venn diagrams of genes regulated by 3 and genes regulated by 6, showing the substantial overlap of the two sets (C). GO classification of genes regulated by 3 and 6 (D); genes were categorized into groups according to their GO terms, based on their predicted or putative functions." figureDoi="http://doi.org/10.5281/zenodo.10485393" httpUri="https://zenodo.org/record/10485393/files/figure.png" pageId="3" pageNumber="25">Fig. 2B</figureCitation>
|
||
, which presents data for 8659 genes whose expression changed significantly after treatment with
|
||
<emphasis id="B907EA8C501F3F37FB9CFB08FBD6FB4D" bold="true" box="[1118,1131,1245,1264]" pageId="3" pageNumber="25">3</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C501F3F37FBBAFB08FB38FB4D" bold="true" box="[1144,1157,1245,1264]" pageId="3" pageNumber="25">6</emphasis>
|
||
or
|
||
<collectionCode id="ED62AE5B501F3F37FB6BFB08FB6CFB4D" box="[1193,1233,1245,1264]" country="United Kingdom" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13830" lsid="urn:lsid:biocol.org:col:13830" name="Oxford Botanic Garden" pageId="3" pageNumber="25" type="Herbarium">BAP</collectionCode>
|
||
(
|
||
<emphasis id="B907EA8C501F3F37FB23FB09FB50FB4D" box="[1249,1261,1244,1264]" italics="true" pageId="3" pageNumber="25">
|
||
<collectionCode id="ED62AE5B501F3F37FB23FB09FB50FB4D" box="[1249,1261,1244,1264]" country="France" lsid="urn:lsid:biocol.org:col:15763" name="Museum National d' Histoire Naturelle, Paris (MNHN) - Vascular Plants" pageId="3" pageNumber="25" type="Herbarium">P</collectionCode>
|
||
</emphasis>
|
||
value
|
||
<emphasis id="B907EA8C501F3F37FAF0FB08FAFEFB4D" bold="true" box="[1330,1347,1245,1264]" pageId="3" pageNumber="25">
|
||
<collectionCode id="ED62AE5B501F3F37FAF0FB08FAFEFB4D" box="[1330,1347,1245,1264]" country="Denmark" name="University of Copenhagen" pageId="3" pageNumber="25" type="Herbarium">Ḉ</collectionCode>
|
||
</emphasis>
|
||
0.01 in at least one treatment). To limit the number of target genes, we adopted more stringent statistical criteria for identifying genes whose expression had changed significantly. Specifically, the data were
|
||
<collectionCode id="ED62AE5B501F3F37FCFDFA99FCD2FAE2" box="[831,879,1356,1375]" country="USA" httpUri="http://grbio.org/cool/2rcx-9912" name="R. M. Alden Research Lab" pageId="3" pageNumber="25">RMA</collectionCode>
|
||
normalized and genes were required to have a signal ratio change log
|
||
<subScript id="17F734DB501F3F37FC6CFAA4FC0AFAC0" attach="left" box="[942,951,1393,1405]" fontSize="5" pageId="3" pageNumber="25">2</subScript>
|
||
of
|
||
<emphasis id="B907EA8C501F3F37FC1FFABDFC4EFAC6" bold="true" box="[989,1011,1384,1403]" italics="true" pageId="3" pageNumber="25">
|
||
<collectionCode id="ED62AE5B501F3F37FC1FFABDFC4EFAC6" box="[989,1011,1384,1403]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="3" pageNumber="25" type="Herbarium">À</collectionCode>
|
||
</emphasis>
|
||
0.5 or
|
||
<emphasis id="B907EA8C501F3F37FBFAFABDFBF4FAC6" bold="true" box="[1080,1097,1384,1403]" pageId="3" pageNumber="25">
|
||
<collectionCode id="ED62AE5B501F3F37FBFAFABDFBF4FAC6" box="[1080,1097,1384,1403]" country="Denmark" name="University of Copenhagen" pageId="3" pageNumber="25" type="Herbarium">Ḉ</collectionCode>
|
||
</emphasis>
|
||
<emphasis id="B907EA8C501F3F37FB8BFABDFBE7FAC6" box="[1097,1114,1384,1403]" italics="true" pageId="3" pageNumber="25">—</emphasis>
|
||
0.5 in addition to a
|
||
<emphasis id="B907EA8C501F3F37FAEFFAB2FA84FAC6" box="[1325,1337,1383,1403]" italics="true" pageId="3" pageNumber="25">
|
||
<collectionCode id="ED62AE5B501F3F37FAEFFAB2FA84FAC6" box="[1325,1337,1383,1403]" country="France" lsid="urn:lsid:biocol.org:col:15763" name="Museum National d' Histoire Naturelle, Paris (MNHN) - Vascular Plants" pageId="3" pageNumber="25" type="Herbarium">P</collectionCode>
|
||
</emphasis>
|
||
-value of <0.01; see the Methods section for details. In this way we defined a group of 1128 genes whose expression changed after treatment with
|
||
<emphasis id="B907EA8C501F3F37FA6DFA75FA01FA0E" bold="true" box="[1455,1468,1440,1459]" pageId="3" pageNumber="25">3</emphasis>
|
||
(of which 510 were upregulated and 618 downregulated), and 944 genes whose expression changed upon treatment with
|
||
<emphasis id="B907EA8C50183F30FD6CFAB0FD06FAC5" bold="true" box="[686,699,1381,1400]" pageId="4" pageNumber="26">6</emphasis>
|
||
(548 upregulated, 396 downregulated). These two groups overlapped extensively: there were 671 genes common to both (
|
||
<figureCitation id="13482A1B50183F30FD69FA48FD4CFA0D" box="[683,753,1437,1456]" captionStart="Fig" captionStartId="4.[87,113,1240,1254]" captionTargetBox="[359,1191,184,1211]" captionTargetId="figure-445@4.[359,1191,181,1211]" captionTargetPageId="4" captionText="Fig. 2. Transcriptome reprogramming mediated by cytokinin derivatives as revealed by DNA microarray analysis (Affymetrix). Hierarchical clustering was performed for all data sets, i.e. Arabidopsis leaves treated with BAP, compound 3, compound 6, and DMSO alone (A). Clustering analysis of genes exhibiting differential expression after treatment with BAP, compound 3 or compound 6 (B).Venn diagrams of genes regulated by 3 and genes regulated by 6, showing the substantial overlap of the two sets (C). GO classification of genes regulated by 3 and 6 (D); genes were categorized into groups according to their GO terms, based on their predicted or putative functions." figureDoi="http://doi.org/10.5281/zenodo.10485393" httpUri="https://zenodo.org/record/10485393/files/figure.png" pageId="4" pageNumber="26">Fig. 2C</figureCitation>
|
||
;
|
||
<tableCitation id="C6F1032550183F30FF95FA6CFF11FA71" box="[87,172,1465,1484]" captionStart="Table 2" captionStartId="2.[87,131,1480,1494]" captionTargetPageId="2" captionText="Table 2 The activity of the synthetic cytokinin derivatives in the tobacco callus and Amaranthus bioassays and the detached wheat leaf senescence bioassay relative to that of the control compound (BAP) at the optimal concentration (i.e. the concentration where the maximum positive effect of the tested compound was observed). All values were determined from two independent assays each performed in six technical replicates." pageId="4" pageNumber="26">Table S2</tableCitation>
|
||
, Supplementary data). To better understand the molecular functions of these genes, we categorized the transcripts in both groups according to their
|
||
<collectionCode id="ED62AE5B50183F30FE9DFA24FEC3F9B9" box="[351,382,1521,1540]" country="United Kingdom" lsid="urn:lsid:biocol.org:col:13862" name="Philosophical Society" pageId="4" pageNumber="26" type="Herbarium">GO</collectionCode>
|
||
terms (
|
||
<bibRefCitation id="EFE24B6F50183F30FE0DFA24FD12F9B9" author="Ashburner, M. & Ball, C. A. & Blake, J. A. & Botstein, D. & Butler, H. & Cherry, J. M. & Davis, A. P. & Dolinski, K. & Dwight, S. S. & Eppig, J. T. & Harris, M. A. & Hill, D. P. & Issel-Tarver, L. & Kasarskis, A. & Lewis, S. & Matese, J. C. & Richardson, J. E. & Ringwald, M. & Rubin, G. M. & Sherlock, G." box="[463,687,1521,1540]" pageId="4" pageNumber="26" pagination="25 - 29" refId="ref10360" refString="Ashburner, M., Ball, C. A., Blake, J. A., Botstein, D., Butler, H., Cherry, J. M., Davis, A. P., Dolinski, K., Dwight, S. S., Eppig, J. T., Harris, M. A., Hill, D. P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J. C., Richardson, J. E., Ringwald, M., Rubin, G. M., Sherlock, G., 2000. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat. Genet. 25, 25 - 29." type="journal article" year="2000">Ashburner et al., 2000</bibRefCitation>
|
||
) using categories such as ‘transcription factor activity’, ‘DNA or RNA binding’, and ‘protein binding’ (
|
||
<figureCitation id="13482A1B50183F30FEA4F9FDFE10F981" box="[358,429,1576,1596]" captionStart="Fig" captionStartId="4.[87,113,1240,1254]" captionTargetBox="[359,1191,184,1211]" captionTargetId="figure-445@4.[359,1191,181,1211]" captionTargetPageId="4" captionText="Fig. 2. Transcriptome reprogramming mediated by cytokinin derivatives as revealed by DNA microarray analysis (Affymetrix). Hierarchical clustering was performed for all data sets, i.e. Arabidopsis leaves treated with BAP, compound 3, compound 6, and DMSO alone (A). Clustering analysis of genes exhibiting differential expression after treatment with BAP, compound 3 or compound 6 (B).Venn diagrams of genes regulated by 3 and genes regulated by 6, showing the substantial overlap of the two sets (C). GO classification of genes regulated by 3 and 6 (D); genes were categorized into groups according to their GO terms, based on their predicted or putative functions." figureDoi="http://doi.org/10.5281/zenodo.10485393" httpUri="https://zenodo.org/record/10485393/files/figure.png" pageId="4" pageNumber="26">Fig. 2D</figureCitation>
|
||
). This analysis indicated that the affected genes were rather evenly distributed over the defined categories.
|
||
</paragraph>
|
||
<caption id="DF0C6616501F3F37FFB3F874FB80F860" ID-DOI="http://doi.org/10.5281/zenodo.10485391" ID-Zenodo-Dep="10485391" httpUri="https://zenodo.org/record/10485391/files/figure.png" pageId="3" pageNumber="25" startId="3.[113,139,1953,1967]" targetBox="[144,1467,1528,1924]" targetPageId="3" targetType="figure">
|
||
<paragraph id="8BCC369E501F3F37FFB3F874FB80F860" blockId="3.[113,1500,1952,2014]" pageId="3" pageNumber="25">
|
||
<emphasis id="B907EA8C501F3F37FFB3F874FF19F812" bold="true" box="[113,164,1953,1967]" pageId="3" pageNumber="25">Fig. 1.</emphasis>
|
||
Cytokinin-dependent expression of
|
||
<emphasis id="B907EA8C501F3F37FE0CF877FE65F80D" box="[462,472,1954,1968]" italics="true" pageId="3" pageNumber="25">β</emphasis>
|
||
-galactosidase in
|
||
<taxonomicName id="4C734D1D501F3F37FDA7F874FD29F80D" authorityName="Castellani & Chalmers" authorityYear="1919" baseAuthorityName="Migula" baseAuthorityYear="1895" box="[613,660,1953,1968]" class="Gammaproteobacteria" family="Enterobacteriaceae" genus="Escherichia" kingdom="Bacteria" order="Enterobacteriales" pageId="3" pageNumber="25" phylum="Proteobacteria" rank="species" species="coli">
|
||
<emphasis id="B907EA8C501F3F37FDA7F874FD29F80D" box="[613,660,1953,1968]" italics="true" pageId="3" pageNumber="25">E. coli</emphasis>
|
||
</taxonomicName>
|
||
(ΔrcsC,
|
||
<emphasis id="B907EA8C501F3F37FD1BF874FCA1F80D" box="[729,796,1953,1968]" italics="true" pageId="3" pageNumber="25">cps::lacZ</emphasis>
|
||
) expressing ZmHK1 (A) and ZmHK3a (B). tZ was used as a positive control; error bars show SD values for three replicates. Relative upregulation of GUS expression is shown in comparison to a DMSO-treated control (C); error bars show SD values for three replicates. Three-day-old transgenic seedlings were incubated with the tested compounds at a concentration of 10 µM.
|
||
</paragraph>
|
||
</caption>
|
||
<caption id="DF0C661650183F30FF95FB0DFACEFA96" ID-DOI="http://doi.org/10.5281/zenodo.10485393" ID-Zenodo-Dep="10485393" httpUri="https://zenodo.org/record/10485393/files/figure.png" pageId="4" pageNumber="26" startId="4.[87,113,1240,1254]" targetBox="[359,1191,184,1211]" targetPageId="4" targetType="figure">
|
||
<paragraph id="8BCC369E50183F30FF95FB0DFACEFA96" blockId="4.[87,1474,1240,1323]" pageId="4" pageNumber="26">
|
||
<emphasis id="B907EA8C50183F30FF95FB0DFF34FB5B" bold="true" box="[87,137,1240,1254]" pageId="4" pageNumber="26">Fig. 2.</emphasis>
|
||
Transcriptome reprogramming mediated by cytokinin derivatives as revealed by DNA microarray analysis (Affymetrix). Hierarchical clustering was performed for all data sets, i.e.
|
||
<taxonomicName id="4C734D1D50183F30FF08FB3BFEE1FB40" box="[202,348,1262,1277]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="4" pageNumber="25" phylum="Tracheophyta" rank="species" species="leaves">
|
||
<emphasis id="B907EA8C50183F30FF08FB3BFE9EFB40" box="[202,291,1262,1277]" italics="true" pageId="4" pageNumber="26">Arabidopsis</emphasis>
|
||
leaves
|
||
</taxonomicName>
|
||
treated with BAP, compound 3, compound 6, and DMSO alone (A). Clustering analysis of genes exhibiting differential expression after treatment with BAP, compound 3 or compound 6 (B). Venn diagrams of genes regulated by 3 and genes regulated by 6, showing the substantial overlap of the two sets (C). GO classification of genes regulated by 3 and 6 (D); genes were categorized into groups according to their GO terms, based on their predicted or putative functions.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="8BCC369E50183F30FFB4F9A8FB08FA28" blockId="4.[87,757,1381,1986]" lastBlockId="4.[805,1475,1380,1986]" pageId="4" pageNumber="26">
|
||
We then examined the genes whose expression changed significantly in the three datasets (i.e. in senescent leaves treated with
|
||
<emphasis id="B907EA8C50183F30FD21F94DFD4DF916" bold="true" box="[739,752,1688,1707]" pageId="4" pageNumber="26">3</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FF95F961FFD9F97A" bold="true" box="[87,100,1716,1735]" pageId="4" pageNumber="26">6</emphasis>
|
||
or BAP) in more detail. This analysis revealed that the cytokinin derivatives had distinct modes of action to those observed for the parent free bases. In keeping with previous reports (
|
||
<bibRefCitation id="EFE24B6F50183F30FDB5F939FEB1F8A6" author="Brandstatter, I. & Kieber, J. J." pageId="4" pageNumber="26" pagination="1009 - 1019" refId="ref10571" refString="Brandstatter, I., Kieber, J. J., 1998. Two genes with similarity to bacterial response regulators are rapidly and specifically induced by cytokinin in Arabidopsis. Plant Cell 10, 1009 - 1019." type="journal article" year="1998">Brandstatter and Kieber, 1998</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="EFE24B6F50183F30FEDBF8DDFE53F8A6" author="Rashotte, A. M. & Carson, S. D. & To, J. P. & Kieber, J. J." box="[281,494,1800,1819]" pageId="4" pageNumber="26" pagination="1998 - 2011" refId="ref12329" refString="Rashotte, A. M., Carson, S. D., To, J. P., Kieber, J. J., 2003. Expression profiling of cytokinin action in Arabidopsis. Plant Physiol. 132, 1998 - 2011." type="journal article" year="2003">Rashotte et al., 2003</bibRefCitation>
|
||
), many cytokinin-related genes were upregulated in the BAP-treated leaves (
|
||
<figureCitation id="13482A1B50183F30FD6EF8F6FD50F88A" box="[684,749,1827,1847]" captionStart="Fig" captionStartId="5.[113,139,1445,1459]" captionTargetBox="[272,1330,181,1415]" captionTargetId="figure-293@5.[272,1331,181,1416]" captionTargetPageId="5" captionText="Fig. 3. Selected genes identified in differential expression analyses of detached Arabidopsis leaves treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM 3, 6, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log2-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the P <0.01 level and log2 fold change values of À1 or Ḉ—1 for at least one treatment are shown." figureDoi="http://doi.org/10.5281/zenodo.10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="4" pageNumber="26">Fig. 3</figureCitation>
|
||
;
|
||
<tableCitation id="C6F1032550183F30FF95F8EAFF0FF8EE" box="[87,178,1855,1875]" captionStart="Table 2" captionStartId="2.[87,131,1480,1494]" captionTargetPageId="2" captionText="Table 2 The activity of the synthetic cytokinin derivatives in the tobacco callus and Amaranthus bioassays and the detached wheat leaf senescence bioassay relative to that of the control compound (BAP) at the optimal concentration (i.e. the concentration where the maximum positive effect of the tested compound was observed). All values were determined from two independent assays each performed in six technical replicates." pageId="4" pageNumber="26">Table S2</tableCitation>
|
||
, Supplementary data). Importantly, these included the cytokinin response regulators
|
||
<emphasis id="B907EA8C50183F30FE52F88FFE7EF8D3" box="[400,451,1882,1902]" italics="true" pageId="4" pageNumber="26">ARR7</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FE13F88FFDB9F8D3" box="[465,516,1882,1902]" italics="true" pageId="4" pageNumber="26">ARR9</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FDD0F88FFDF8F8D3" box="[530,581,1882,1902]" italics="true" pageId="4" pageNumber="26">ARR5</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FD91F88FFD38F8D3" box="[595,645,1882,1902]" italics="true" pageId="4" pageNumber="26">ARR6</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50183F30FD7FF88FFD4DF8D3" box="[701,752,1882,1902]" italics="true" pageId="4" pageNumber="26">ARR4</emphasis>
|
||
. Exposure to high concentrations of BAP also prompted the induction of several cytokinin dehydrogenase genes including
|
||
<emphasis id="B907EA8C50183F30FD7FF847FD52F81B" box="[701,751,1938,1958]" italics="true" pageId="4" pageNumber="26">CKX1</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FF95F87BFF37F87F" box="[87,138,1966,1986]" italics="true" pageId="4" pageNumber="26">CKX2</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FF54F87BFF75F87F" box="[150,200,1966,1986]" italics="true" pageId="4" pageNumber="26">CKX3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50183F30FF39F87BFE90F87F" box="[251,301,1966,1986]" italics="true" pageId="4" pageNumber="26">CKX4</emphasis>
|
||
. Upregulation of response regulators, several
|
||
<emphasis id="B907EA8C50183F30FCE7FAB1FCF1FAC5" box="[805,844,1380,1400]" italics="true" pageId="4" pageNumber="26">CKX</emphasis>
|
||
genes, and other cytokinin response genes was also observed in senescent leaves treated with
|
||
<emphasis id="B907EA8C50183F30FBB1FA54FB3DFA29" bold="true" box="[1139,1152,1409,1428]" pageId="4" pageNumber="26">3</emphasis>
|
||
or
|
||
<emphasis id="B907EA8C50183F30FB61FA54FB0DFA29" bold="true" box="[1187,1200,1409,1428]" pageId="4" pageNumber="26">6</emphasis>
|
||
.
|
||
</paragraph>
|
||
<paragraph id="8BCC369E50183F30FC86FA48FB5DF87F" blockId="4.[805,1475,1380,1986]" pageId="4" pageNumber="26">
|
||
It is interesting to compare our results to those of a recent meta-analysis of microarray data reported by various laboratories, which identified a core list of cytokinin response genes (
|
||
<bibRefCitation id="EFE24B6F50183F30FAB0FA00FC24F9B9" author="Brenner, W. G. & Ramireddy, E. & Heyl, A. & Schmulling, T." pageId="4" pageNumber="26" pagination="8" refId="ref10611" refString="Brenner, W. G., Ramireddy, E., Heyl, A., Schmulling, T., 2012. Gene regulation by cytokinin in Arabidopsis. Front. Plant Sci. 3, 8." type="journal article" year="2012">Brenner et al., 2012</bibRefCitation>
|
||
). The results of both this meta-analysis and a search of the Genevestigator database (https://genevestigator.com/gv/) conducted by ourselves indicate that tZ treatment leads to rapid reprogramming of gene expression in
|
||
<taxonomicName id="4C734D1D50183F30FB08F996FA84F9EA" box="[1226,1337,1603,1623]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="4" pageNumber="26" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="B907EA8C50183F30FB08F996FA84F9EA" box="[1226,1337,1603,1623]" italics="true" pageId="4" pageNumber="26">Arabidopsis</emphasis>
|
||
</taxonomicName>
|
||
. Specifically, cytokinin response regulators such as
|
||
<emphasis id="B907EA8C50183F30FB70F98AFB4DF9CE" box="[1202,1264,1631,1651]" italics="true" pageId="4" pageNumber="26">ARR15</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FB3CF98AFA8CF9CE" box="[1278,1329,1631,1651]" italics="true" pageId="4" pageNumber="26">ARR5</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FAFCF98AFAC0F9CE" box="[1342,1405,1631,1651]" italics="true" pageId="4" pageNumber="26">ARR16</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FA48F98AFA00F9CE" box="[1418,1469,1631,1651]" italics="true" pageId="4" pageNumber="26">ARR7</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FCE7F9AEFCEAF932" box="[805,855,1659,1679]" italics="true" pageId="4" pageNumber="26">ARR4</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FCA1F9AEFC2BF932" box="[867,918,1659,1679]" italics="true" pageId="4" pageNumber="26">ARR6</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50183F30FC0BF9AEFC41F932" box="[969,1020,1659,1679]" italics="true" pageId="4" pageNumber="26">ARR9</emphasis>
|
||
were strongly upregulated in response to tZ treatment. Other cytokinin-responsive genes identified in the meta-analysis and database search include
|
||
<emphasis id="B907EA8C50183F30FB1EF966FAB2F97A" box="[1244,1295,1715,1735]" italics="true" pageId="4" pageNumber="26">CKX4</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50183F30FA80F966FAC8F97A" box="[1346,1397,1715,1735]" italics="true" pageId="4" pageNumber="26">CKX5</emphasis>
|
||
(which code for two cytokinin dehydrogenase isoforms),
|
||
<emphasis id="B907EA8C50183F30FADFF91AFAEEF95E" box="[1309,1363,1743,1763]" italics="true" pageId="4" pageNumber="26">AHK4</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50183F30FA45F91AFA00F95E" box="[1415,1469,1743,1763]" italics="true" pageId="4" pageNumber="26">AHK1</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FCE7F93EFCE9F942" box="[805,852,1771,1791]" italics="true" pageId="4" pageNumber="26">CRF5</emphasis>
|
||
or
|
||
<emphasis id="B907EA8C50183F30FC43F93EFC5EF942" box="[897,995,1771,1791]" italics="true" pageId="4" pageNumber="26">CYP735A2</emphasis>
|
||
, and
|
||
<emphasis id="B907EA8C50183F30FBE7F93EFBC5F942" box="[1061,1144,1771,1791]" italics="true" pageId="4" pageNumber="26">CYP82F1</emphasis>
|
||
. This group of core cytokinin-responsive genes clearly overlaps extensively with the list of genes whose expression was altered significantly following treatment with
|
||
<emphasis id="B907EA8C50183F30FC99F8EAFCD5F8EF" bold="true" box="[859,872,1855,1874]" pageId="4" pageNumber="26">3</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50183F30FCB4F8EAFC3EF8EF" bold="true" box="[886,899,1855,1874]" pageId="4" pageNumber="26">6</emphasis>
|
||
, or BAP (
|
||
<figureCitation id="13482A1B50183F30FC24F8EAFBA3F8EE" box="[998,1054,1855,1875]" captionStart="Fig" captionStartId="5.[113,139,1445,1459]" captionTargetBox="[272,1330,181,1415]" captionTargetId="figure-293@5.[272,1331,181,1416]" captionTargetPageId="5" captionText="Fig. 3. Selected genes identified in differential expression analyses of detached Arabidopsis leaves treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM 3, 6, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log2-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the P <0.01 level and log2 fold change values of À1 or Ḉ—1 for at least one treatment are shown." figureDoi="http://doi.org/10.5281/zenodo.10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="4" pageNumber="26">Fig. 3</figureCitation>
|
||
). It is also consistent with the cytokinin bioassay results presented in the preceding section and thus confirms that the halogenated aromatic cytokinin derivatives considered in this work are indeed active cytokinins whose signaling effects partially mirror those of BAP and tZ.
|
||
</paragraph>
|
||
<caption id="DF0C661650193F31FFB3FA70FDEEF998" ID-DOI="http://doi.org/10.5281/zenodo.10485395" ID-Zenodo-Dep="10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="5" pageNumber="27" startId="5.[113,139,1445,1459]" targetBox="[272,1330,181,1415]" targetPageId="5" targetType="figure">
|
||
<paragraph id="8BCC369E50193F31FFB3FA70FDEEF998" blockId="5.[113,1502,1444,1574]" pageId="5" pageNumber="27">
|
||
<emphasis id="B907EA8C50193F31FFB3FA70FF19FA0E" bold="true" box="[113,164,1445,1459]" pageId="5" pageNumber="27">Fig. 3.</emphasis>
|
||
Selected genes identified in differential expression analyses of detached
|
||
<taxonomicName id="4C734D1D50193F31FCC3FA71FC2FFA0E" box="[769,914,1444,1459]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="5" pageNumber="25" phylum="Tracheophyta" rank="species" species="leaves">
|
||
<emphasis id="B907EA8C50193F31FCC3FA71FCE7FA0E" box="[769,858,1444,1459]" italics="true" pageId="5" pageNumber="27">Arabidopsis</emphasis>
|
||
leaves
|
||
</taxonomicName>
|
||
treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM
|
||
<emphasis id="B907EA8C50193F31FDD3FA69FDA6FA77" bold="true" box="[529,539,1468,1482]" pageId="5" pageNumber="27">3</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50193F31FDE6FA69FD93FA77" bold="true" box="[548,558,1468,1482]" pageId="5" pageNumber="27">6</emphasis>
|
||
, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log
|
||
<subScript id="17F734DB50193F31FE28FA0CFE4CFA5E" attach="left" box="[490,497,1497,1507]" fontSize="4" pageId="5" pageNumber="27">2</subScript>
|
||
-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the
|
||
<emphasis id="B907EA8C50193F31FB04F9D5FB72F9B2" box="[1222,1231,1536,1551]" italics="true" pageId="5" pageNumber="27">P</emphasis>
|
||
<0.01 level and log
|
||
<subScript id="17F734DB50193F31FAB3F9D2FAC5F9AC" attach="left" box="[1393,1400,1543,1553]" fontSize="4" pageId="5" pageNumber="27">2</subScript>
|
||
fold change values of
|
||
<emphasis id="B907EA8C50193F31FF02F9C2FF6CF99B" bold="true" box="[192,209,1559,1574]" italics="true" pageId="5" pageNumber="27">À</emphasis>
|
||
1 or
|
||
<emphasis id="B907EA8C50193F31FF35F9C2FEB8F99B" bold="true" box="[247,261,1559,1574]" pageId="5" pageNumber="27">Ḉ</emphasis>
|
||
<emphasis id="B907EA8C50193F31FEC7F9C2FEAFF99B" box="[261,274,1559,1574]" italics="true" pageId="5" pageNumber="27">—</emphasis>
|
||
1 for at least one treatment are shown.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="8BCC369E50193F32FF53F9B5FDF0FECC" blockId="5.[113,783,1632,2014]" lastBlockId="6.[87,757,182,955]" lastPageId="6" lastPageNumber="28" pageId="5" pageNumber="27">
|
||
Our analysis also revealed some genes that were only affected by treatment with
|
||
<emphasis id="B907EA8C50193F31FEF5F9A9FEF9F932" bold="true" box="[311,324,1660,1679]" pageId="5" pageNumber="27">3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50193F31FEB8F9A9FE3AF932" bold="true" box="[378,391,1660,1679]" pageId="5" pageNumber="27">6</emphasis>
|
||
, most of which were directly or indirectly linked to photosynthesis. Some of these genes are listed in
|
||
<figureCitation id="13482A1B50193F31FFB3F961FF15F97A" box="[113,168,1716,1735]" captionStart="Fig" captionStartId="5.[113,139,1445,1459]" captionTargetBox="[272,1330,181,1415]" captionTargetId="figure-293@5.[272,1331,181,1416]" captionTargetPageId="5" captionText="Fig. 3. Selected genes identified in differential expression analyses of detached Arabidopsis leaves treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM 3, 6, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log2-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the P <0.01 level and log2 fold change values of À1 or Ḉ—1 for at least one treatment are shown." figureDoi="http://doi.org/10.5281/zenodo.10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="5" pageNumber="27">Fig. 3</figureCitation>
|
||
, in which the most significant hits are categorized according to their function in cytokinin signaling and metabolism or photosynthesis and related categories. Importantly, genes encoding components of the photosystem II light harvesting complex (LHCII), namely At
|
||
<quantity id="4C8B9B7B50193F31FEFAF8F6FEF2F88B" box="[312,335,1827,1846]" metricMagnitude="-3" metricUnit="kg" metricValue="2.0" pageId="5" pageNumber="27" unit="g" value="2.0">2g</quantity>
|
||
05070, At
|
||
<quantity id="4C8B9B7B50193F31FE75F8F6FE70F88B" box="[439,461,1827,1846]" metricMagnitude="-3" metricUnit="kg" metricValue="5.0" pageId="5" pageNumber="27" unit="g" value="5.0">5g</quantity>
|
||
54270, At
|
||
<quantity id="4C8B9B7B50193F31FDF5F8F6FDF6F88B" box="[567,587,1827,1846]" metricMagnitude="-3" metricUnit="kg" metricValue="1.0" pageId="5" pageNumber="27" unit="g" value="1.0">1g</quantity>
|
||
44575, At
|
||
<quantity id="4C8B9B7B50193F31FD74F8F6FD71F88B" box="[694,716,1827,1846]" metricMagnitude="-3" metricUnit="kg" metricValue="3.0" pageId="5" pageNumber="27" unit="g" value="3.0">3g</quantity>
|
||
01440, At
|
||
<quantity id="4C8B9B7B50193F31FF49F8EAFF1DF8EF" box="[139,160,1855,1874]" metricMagnitude="-3" metricUnit="kg" metricValue="3.0" pageId="5" pageNumber="27" unit="g" value="3.0">3g</quantity>
|
||
55330 and At
|
||
<quantity id="4C8B9B7B50193F31FEF3F8EAFEFAF8EF" box="[305,327,1855,1874]" metricMagnitude="-3" metricUnit="kg" metricValue="2.0" pageId="5" pageNumber="27" unit="g" value="2.0">2g</quantity>
|
||
39470, were upregulated by treatment with
|
||
<emphasis id="B907EA8C50193F31FFB3F88EFFC3F8D3" bold="true" box="[113,126,1883,1902]" pageId="5" pageNumber="27">3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50193F31FF76F88EFF7CF8D3" bold="true" box="[180,193,1883,1902]" pageId="5" pageNumber="27">6</emphasis>
|
||
. In contrast, BAP treatment had mostly negligible effects on these genes. In addition, our
|
||
<emphasis id="B907EA8C50193F31FE01F8A3FDB3F837" box="[451,526,1910,1930]" italics="true" pageId="5" pageNumber="27">in silico</emphasis>
|
||
analyses using the Genevestigator database confirmed that these genes are probably not affected by tZ treatment in
|
||
<taxonomicName id="4C734D1D50193F31FE48F878FE44F87C" box="[394,505,1965,1985]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="5" pageNumber="27" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="B907EA8C50193F31FE48F878FE44F87C" box="[394,505,1965,1985]" italics="true" pageId="5" pageNumber="27">Arabidopsis</emphasis>
|
||
</taxonomicName>
|
||
seedlings: treatments with 1 µm tZ solution for 30 min, 1 h, or 3 h had almost no measurable effects on the expression of any photosystem II-related gene. As mentioned above, the different modes of action of
|
||
<emphasis id="B907EA8C50193F31FA97F9A9FADFF932" bold="true" box="[1365,1378,1660,1679]" pageId="5" pageNumber="27">3</emphasis>
|
||
,
|
||
<emphasis id="B907EA8C50193F31FAB2F9A9FAC0F932" bold="true" box="[1392,1405,1660,1679]" pageId="5" pageNumber="27">6</emphasis>
|
||
and BAP may not be directly attributable to differential activation of cytokinin response regulators because all three of these ligands upregulated most of the
|
||
<emphasis id="B907EA8C50193F31FC2EF91BFBAEF95F" box="[1004,1043,1742,1762]" italics="true" pageId="5" pageNumber="27">ARR</emphasis>
|
||
genes to a similar degree. However,
|
||
<emphasis id="B907EA8C50193F31FABDF91BFA0CF95F" box="[1407,1457,1742,1762]" italics="true" pageId="5" pageNumber="27">ARR8</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C50193F31FCFDF93FFCC3F943" box="[831,894,1770,1790]" italics="true" pageId="5" pageNumber="27">ARR15</emphasis>
|
||
were found to be less upregulated in samples treated with BAP than those treated with
|
||
<emphasis id="B907EA8C50193F31FBA0F8D2FBD2F8A7" bold="true" box="[1122,1135,1799,1818]" pageId="5" pageNumber="27">3</emphasis>
|
||
or
|
||
<emphasis id="B907EA8C50193F31FB53F8D2FB23F8A7" bold="true" box="[1169,1182,1799,1818]" pageId="5" pageNumber="27">6</emphasis>
|
||
(
|
||
<figureCitation id="13482A1B50193F31FB6EF8D2FB5FF8A7" box="[1196,1250,1799,1818]" captionStart="Fig" captionStartId="5.[113,139,1445,1459]" captionTargetBox="[272,1330,181,1415]" captionTargetId="figure-293@5.[272,1331,181,1416]" captionTargetPageId="5" captionText="Fig. 3. Selected genes identified in differential expression analyses of detached Arabidopsis leaves treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM 3, 6, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log2-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the P <0.01 level and log2 fold change values of À1 or Ḉ—1 for at least one treatment are shown." figureDoi="http://doi.org/10.5281/zenodo.10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="5" pageNumber="27">Fig. 3</figureCitation>
|
||
). This may be important because
|
||
<emphasis id="B907EA8C50193F31FC57F8F7FC69F88B" box="[917,980,1826,1846]" italics="true" pageId="5" pageNumber="27">ARR15</emphasis>
|
||
is a negative regulator of AHK4-mediated cytokinin signal transduction whose expression is particularly strong in roots (
|
||
<bibRefCitation id="EFE24B6F50193F31FC85F88EFC51F8D3" author="Kiba, T. & Yamada, H. & Sato, S. & Kato, T. & Tabata, S. & Yamashino, T. & Mizuno, T." box="[839,1004,1883,1902]" pageId="5" pageNumber="27" pagination="868 - 874" refId="ref11417" refString="Kiba, T., Yamada, H., Sato, S., Kato, T., Tabata, S., Yamashino, T., Mizuno, T., 2003. The type-A response regulator, ARR 15, acts as a negative regulator in the cytokinin-mediated signal transduction in Arabidopsis thaliana. Plant Cell Physiol. 44, 868 - 874." type="journal article" year="2003">Kiba et al., 2003</bibRefCitation>
|
||
). Therefore, negative regulation of the cytokinin signaling machinery may diminish some of the negative effects associated with exogenous cytokinin treatment at higher concentrations. However, we cannot exclude the possibility that the tested cytokinin derivatives may activate multiple signaling pathway(s) simultaneously, some of which may be closely related to the cytokinin pathway. One of these may be the auxin signaling pathway: we found several auxin-related genes that were differentially regulated by treatment with
|
||
<emphasis id="B907EA8C501A3F32FE73FEDFFE03FEA0" bold="true" box="[433,446,266,285]" pageId="6" pageNumber="28">3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C501A3F32FE2CFEDFFDBDFEA0" bold="true" box="[494,512,266,285]" pageId="6" pageNumber="28">6,</emphasis>
|
||
including
|
||
<emphasis id="B907EA8C501A3F32FDABFEDCFD2AFEA0" box="[617,663,265,285]" italics="true" pageId="6" pageNumber="28">PIN3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C501A3F32FD05FEDCFD48FEA0" box="[711,757,265,285]" italics="true" pageId="6" pageNumber="28">PIN5</emphasis>
|
||
(
|
||
<figureCitation id="13482A1B501A3F32FF9DFEF3FF2AFE84" box="[95,151,294,313]" captionStart="Fig" captionStartId="5.[113,139,1445,1459]" captionTargetBox="[272,1330,181,1415]" captionTargetId="figure-293@5.[272,1331,181,1416]" captionTargetPageId="5" captionText="Fig. 3. Selected genes identified in differential expression analyses of detached Arabidopsis leaves treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM 3, 6, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log2-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the P <0.01 level and log2 fold change values of À1 or Ḉ—1 for at least one treatment are shown." figureDoi="http://doi.org/10.5281/zenodo.10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="6" pageNumber="28">Fig. 3</figureCitation>
|
||
). Another example is downregulation of the auxin-responsive gene At
|
||
<quantity id="4C8B9B7B501A3F32FF17FE97FF51FEE8" box="[213,236,322,341]" metricMagnitude="-3" metricUnit="kg" metricValue="2.0" pageId="6" pageNumber="28" unit="g" value="2.0">2g</quantity>
|
||
45210, which codes for senescence-associated gene 201 (SAG201), a positive regulator of senescence.
|
||
</paragraph>
|
||
<paragraph id="8BCC369E501A3F32FFB4FEAFFE35FCAE" blockId="6.[87,757,182,955]" pageId="6" pageNumber="28">
|
||
We also found a group of genes involved in chlorophyll degradation that were downregulated in response to treatment with
|
||
<emphasis id="B907EA8C501A3F32FD2AFE40FD48FE15" bold="true" box="[744,757,405,424]" pageId="6" pageNumber="28">3</emphasis>
|
||
and
|
||
<emphasis id="B907EA8C501A3F32FF40FE64FF32FE79" bold="true" box="[130,143,433,452]" pageId="6" pageNumber="28">6</emphasis>
|
||
(
|
||
<figureCitation id="13482A1B501A3F32FF5EFE64FF6CFE79" box="[156,209,433,452]" captionStart="Fig" captionStartId="5.[113,139,1445,1459]" captionTargetBox="[272,1330,181,1415]" captionTargetId="figure-293@5.[272,1331,181,1416]" captionTargetPageId="5" captionText="Fig. 3. Selected genes identified in differential expression analyses of detached Arabidopsis leaves treated with cytokinin derivatives. Senescent leaves were incubated in darkness for 48 h in MS medium containing 10 µM 3, 6, or BAP and their gene expression profiles were compared to those for DMSO-treated control leaves of the same age. Gene expression values were calculated as log2-ratios of the signals for the treated samples relative to those for the control leaves. The heat map is color-coded using the scheme presented in the figure; genes shown in gray were not significantly affected. Only genes related to photosynthesis (specifically those related to photosystem I/II, the Calvin cycle, and chlorophyll/LHCII catabolism) and cytokinin/other plant hormone signaling, with expression changes significant at the P <0.01 level and log2 fold change values of À1 or Ḉ—1 for at least one treatment are shown." figureDoi="http://doi.org/10.5281/zenodo.10485395" httpUri="https://zenodo.org/record/10485395/files/figure.png" pageId="6" pageNumber="28">Fig. 3</figureCitation>
|
||
;
|
||
<tableCitation id="C6F10325501A3F32FF1CFE64FE8EFE79" box="[222,307,433,452]" captionStart="Table 2" captionStartId="2.[87,131,1480,1494]" captionTargetPageId="2" captionText="Table 2 The activity of the synthetic cytokinin derivatives in the tobacco callus and Amaranthus bioassays and the detached wheat leaf senescence bioassay relative to that of the control compound (BAP) at the optimal concentration (i.e. the concentration where the maximum positive effect of the tested compound was observed). All values were determined from two independent assays each performed in six technical replicates." pageId="6" pageNumber="28">Table S2</tableCitation>
|
||
, Supplementary data). Several of these genes were previously described as leaf anti-senescent markers that respond to auxin, cytokinin and some other molecules that regulate leaf senescence (
|
||
<bibRefCitation id="EFE24B6F501A3F32FE8CFDD0FE4AFDA5" author="Li, Z. & Peng, J. & Wen, X. & Guo, H." box="[334,503,517,536]" pageId="6" pageNumber="28" pagination="526 - 539" refId="ref11695" refString="Li, Z., Peng, J., Wen, X., Guo, H., 2012. Gene network analysis and functional studies of senescence-associated genes reveal novel regulators of Arabidopsis leaf senescence. J. Integr. Plant Biol. 54, 526 - 539." type="journal article" year="2012">Li et al., 2012</bibRefCitation>
|
||
). This group included At
|
||
<quantity id="4C8B9B7B501A3F32FFB3FDF4FF34FD89" box="[113,137,545,564]" metricMagnitude="-3" metricUnit="kg" metricValue="4.0" pageId="6" pageNumber="28" unit="g" value="4.0">4g</quantity>
|
||
13250, which codes for a protein that is involved in LHCII degradation in rice, non-yellow coloring protein 1 (NYC1) (
|
||
<bibRefCitation id="EFE24B6F501A3F32FF9DFD8CFEA1FDD1" author="Kusaba, M. & Ito, H. & Morita, R. & Iida, S. & Sato, Y. & Fujimoto, M. & Kawasaki, S. & Tanaka, R. & Hirochika, H. & Nishimura, M. & Tanaka, A." box="[95,284,601,620]" pageId="6" pageNumber="28" pagination="1362 - 1375" refId="ref11613" refString="Kusaba, M., Ito, H., Morita, R., Iida, S., Sato, Y., Fujimoto, M., Kawasaki, S., Tanaka, R., Hirochika, H., Nishimura, M., Tanaka, A., 2007. Rice NON-YELLOW COLORING 1 is involved in light-harvesting complex II and grana degradation during leaf senescence. Plant Cell 19, 1362 - 1375." type="journal article" year="2007">Kusaba et al., 2007</bibRefCitation>
|
||
). It also included genes encoding other chlorophyll/LHCII catabolic reductases such as At
|
||
<quantity id="4C8B9B7B501A3F32FDD6FDA0FD96FD35" box="[532,555,629,648]" metricMagnitude="-3" metricUnit="kg" metricValue="4.0" pageId="6" pageNumber="28" unit="g" value="4.0">4g</quantity>
|
||
22920, which codes for non-yellowing protein 1 (NYE1), and At
|
||
<quantity id="4C8B9B7B501A3F32FDD7FD44FD90FD19" box="[533,557,657,676]" metricMagnitude="-3" metricUnit="kg" metricValue="4.0" pageId="6" pageNumber="28" unit="g" value="4.0">4g</quantity>
|
||
11910, which codes for non-yellowing protein 2 (NYE2). The latter gene was also downregulated in response to BAP treatment together with At
|
||
<quantity id="4C8B9B7B501A3F32FFB3FD31FF3AFD4A" box="[113,135,740,759]" metricMagnitude="-3" metricUnit="kg" metricValue="3.0" pageId="6" pageNumber="28" unit="g" value="3.0">3g</quantity>
|
||
44880, which codes for Pheophorbide A oxygenase/accelerated cell death 1 (PAO/ACD1).
|
||
</paragraph>
|
||
<paragraph id="8BCC369E501A3F32FFB4FCC9FD58FC07" blockId="6.[87,757,182,955]" pageId="6" pageNumber="28">In conclusion, we have collected evidence that selected cytokinin derivatives have similar signaling outputs to their parent free bases in general but also exhibit selectively modulated anti-senescence activity. This modulation is primarily due to upregulation of genes coding for the subunits of LHCII and LHCI and downregulation of genes that are responsible for LHCII and chlorophyll degradation.</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |