689 lines
149 KiB
XML
689 lines
149 KiB
XML
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<mods:title id="A9C718DFD5F41DEBDDB3CE44B80CABCC">Suspension cell secretome of the grain legume Lathyrus sativus (grasspea) reveals roles in plant development and defense responses</mods:title>
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<mods:namePart id="E0E3D3E0F3629094115DB3432665889C">Rathi, Divya</mods:namePart>
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<mods:namePart id="AAFA1A1154A600A64C0F70373A96AAB7">Verma, Jitendra Kumar</mods:namePart>
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<mods:namePart id="0553A2636E8E013676428A44DCCA6336">Chakraborty, Subhra</mods:namePart>
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<mods:date id="656C689EACF445084EB6685CD97E0467">2022</mods:date>
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<paragraph id="003354622775536FA16ABD80FB058130" blockId="1.[818,1244,1012,1032]" box="[818,1244,1012,1032]" pageId="1" pageNumber="2">
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<heading id="5B7BE30E2775536FA16ABD80FB058130" bold="true" box="[818,1244,1012,1032]" fontSize="36" level="1" pageId="1" pageNumber="2" reason="1">
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<emphasis id="32F888702775536FA16ABD80FB058130" bold="true" box="[818,1244,1012,1032]" italics="true" pageId="1" pageNumber="2">
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2.1.
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<taxonomicName id="C78C2FE12775536FA13ABD81FC2A8130" authority="L." authorityName="L." box="[866,1011,1012,1032]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="subSpecies" species="sativus" subSpecies="suspension">Lathyrus sativus</taxonomicName>
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suspension culture system
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Dedifferentiated plant SCCs constitute a totipotent single cell-type homogenous system, which is more effective for investigating biological functions and regulatory mechanisms in the context of developmental stimuli than tissue-enriched multicellular systems. Among crops, legumes are an interesting set of plants that express unique secretory proteins, particularly in nodulation-induced root samples. Hence, we prepared the non-embryogenic calli of an orphan legume,
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<taxonomicName id="C78C2FE12775536FA70EBAA1FA7181DF" box="[1366,1448,1236,1255]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="1" pageNumber="2" phylum="Tracheophyta" rank="species" species="sativus">
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<emphasis id="32F888702775536FA70EBAA1FA7181DF" bold="true" box="[1366,1448,1236,1255]" italics="true" pageId="1" pageNumber="2">L. sativus</emphasis>
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, for generating totipotent cells and developed the reference secretome map. The overall research design and flow process are shown in
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<figureCitation id="98B748E72775536FA730BB79FA468027" box="[1384,1439,1292,1311]" captionStart="Fig" captionStartId="2.[100,130,1452,1469]" captionTargetBox="[108,766,152,1423]" captionTargetId="figure-838@2.[106,767,148,1424]" captionTargetPageId="2" captionText="Fig. 1. Schematic representation of the experimental design and workflow of the establishment of the grasspea suspension secretome (GSS). Proteomic profiling was accomplished by generating suspension culture and sequential assessment of physicochemical properties and protein identification." figureDoi="http://doi.org/10.5281/zenodo.8234551" httpUri="https://zenodo.org/record/8234551/files/figure.png" pageId="1" pageNumber="2">Fig. 1</figureCitation>
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. The resulted SCCs served as a defined set of grasspea secreted proteins, which were employed for the identification of species-specific “secretome markers”. Friable, non-embryogenic and cream colored calli were obtained using
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<quantity id="C774F9872775536FA19DBB0EFC2C80B6" box="[965,1013,1403,1422]" metricMagnitude="-6" metricUnit="kg" metricValue="1.0" pageId="1" pageNumber="2" unit="mg" value="1.0">1 mg</quantity>
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/mL picloram (
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<figureCitation id="98B748E72775536FA6DFBB0EFB1480B6" box="[1159,1229,1403,1422]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="1" pageNumber="2">Fig. 2A</figureCitation>
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) over other phytohormone combinations, which induced organogenesis (
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<bibRefCitation id="641D29932775536FA6BDBBE2FA4F8092" author="Rathi, D. & Gayali, S. & Pareek, A. & Chakraborty, S. & Chakraborty, N." box="[1253,1430,1431,1451]" pageId="1" pageNumber="2" pagination="839 - 855" refId="ref15223" refString="Rathi, D., Gayali, S., Pareek, A., Chakraborty, S., Chakraborty, N., 2019 a. Transcriptome profiling illustrates expression signatures of dehydration tolerance in developing grasspea seedlings. Planta 250, 839 - 855. https: // doi. org / 10.1007 / s 00425 - 018 - 03082 - 2." type="journal article" year="2019">Rathi et al., 2019a</bibRefCitation>
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). The calli so obtained ranged from
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<quantity id="C774F9872775536FA608BBC6FB5580FE" box="[1104,1164,1459,1478]" metricMagnitude="-5" metricUnit="kg" metricValue="2.0" pageId="1" pageNumber="2" unit="mg" value="20.0">20 mg</quantity>
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in 2nd week up to
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<quantity id="C774F9872775536FA71FBBC6FA5680FE" box="[1351,1423,1459,1478]" metricMagnitude="-4" metricUnit="kg" metricValue="1.0" pageId="1" pageNumber="2" unit="mg" value="100.0">100 mg</quantity>
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in 4th week of growth. Four-week-old calli were used to successfully establish SC. Live cells stained green with fluorescein diacetate (FDA), while the dead cells stained blue with Evans blue (
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<figureCitation id="98B748E72775536FA69EB872FAD78322" box="[1222,1294,1543,1562]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="1" pageNumber="2">Fig. 2B</figureCitation>
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). The SCCs were of different shapes, such as small round cells, large round cells, ellipsoids and elongated cells, conforming to the different growth stages of totipotent cells. Physiological assessments were performed after the second subculturing to determine the suitable stage for the application of stress (
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<figureCitation id="98B748E72775536FA162B8E7FC5A839D" box="[826,899,1682,1701]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="1" pageNumber="2">Fig. 2C</figureCitation>
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). While the total protein content was found to increase, the soluble sugars decreased in the SCCs, reflecting active growth (
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<figureCitation id="98B748E72775536FA727B8DBFA1C83F9" box="[1407,1477,1710,1729]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="1" pageNumber="2">Fig. 2C</figureCitation>
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). The biomass and viability of SCCs were increased until the 10th day, beyond which these parameters decreased (
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<figureCitation id="98B748E72775536FA687B893FAF083C1" box="[1247,1321,1766,1785]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="1" pageNumber="2">Fig. 2C</figureCitation>
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). The pH of suspension cultures stabilized at 4.2 after the 3rd day of subculturing, reflecting the active growth of SCCs (
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<figureCitation id="98B748E72775536FA6D1B96BFB178209" box="[1161,1230,1822,1841]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="1" pageNumber="2">Fig. 2C</figureCitation>
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). Therefore, the 10th day of culture was an ideal stage for harvesting the secretome.
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</paragraph>
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<paragraph id="003354622775536FA16AB906FB1882BE" blockId="1.[818,1217,1906,1926]" box="[818,1217,1906,1926]" pageId="1" pageNumber="2">
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<heading id="5B7BE30E2775536FA16AB906FB1882BE" bold="true" box="[818,1217,1906,1926]" fontSize="36" level="1" pageId="1" pageNumber="2" reason="1">
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<emphasis id="32F888702775536FA16AB906FB1882BE" bold="true" box="[818,1217,1906,1926]" italics="true" pageId="1" pageNumber="2">2.2. Purity and enrichment of the secretome</emphasis>
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</heading>
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</paragraph>
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<paragraph id="003354622775536CA109B9DEFD728278" blockId="1.[849,1488,1963,1982]" lastBlockId="2.[100,770,1586,1856]" lastPageId="2" lastPageNumber="3" pageId="1" pageNumber="2">
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The secretome samples from 3 biological replicates were pooled, concentrated, and visualized by CBB staining (
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<figureCitation id="98B748E72776536CA075B847FDA1837E" box="[557,632,1586,1606]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="2" pageNumber="3">Fig. 2D</figureCitation>
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). The
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<collectionCode id="669DCCA72776536CA0E0B846FD04837E" box="[696,733,1587,1606]" pageId="2" pageNumber="3">GSS</collectionCode>
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gel profile displayed a mixed proportion of moderate and low molecular weight proteins. Furthermore, the purity assessment of the
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<collectionCode id="669DCCA72776536CA0D6B81FFD6A8345" box="[654,691,1642,1661]" pageId="2" pageNumber="3">GSS</collectionCode>
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fraction revealed minimal contamination with cytosolic components (
|
||
<figureCitation id="98B748E72776536CA0C3B8F3FFAB838D" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="2" pageNumber="3">Fig. 2E and F</figureCitation>
|
||
; Supplementary
|
||
<figureCitation id="98B748E72776536CA34FB8D7FE82838D" box="[279,347,1698,1717]" captionStart="Fig" captionStartId="2.[100,130,1452,1469]" captionTargetBox="[108,766,152,1423]" captionTargetId="figure-838@2.[106,767,148,1424]" captionTargetPageId="2" captionText="Fig. 1. Schematic representation of the experimental design and workflow of the establishment of the grasspea suspension secretome (GSS). Proteomic profiling was accomplished by generating suspension culture and sequential assessment of physicochemical properties and protein identification." figureDoi="http://doi.org/10.5281/zenodo.8234551" httpUri="https://zenodo.org/record/8234551/files/figure.png" pageId="2" pageNumber="3">Fig. S1</figureCitation>
|
||
). The catalase activity was observed to be multifold higher in the total callus protein sample compared to
|
||
<collectionCode id="669DCCA72776536CA0E4B8CBFD3883E9" box="[700,737,1726,1745]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
(p-value
|
||
<emphasis id="32F888702776536CA2F9B8AFFF6883D5" box="[161,177,1754,1773]" italics="true" pageId="2" pageNumber="3"><</emphasis>
|
||
0.05) (
|
||
<figureCitation id="98B748E72776536CA2A7B8AFFE9183D5" box="[255,328,1754,1773]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="2" pageNumber="3">Fig. 2E</figureCitation>
|
||
). Immunoblot analysis using the chloroplastspecific RubisCo large subunit (RbCL) revealed a negligible presence of rbcL in
|
||
<collectionCode id="669DCCA72776536CA290B967FF34821D" box="[200,237,1810,1829]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
compared to callus samples (
|
||
<figureCitation id="98B748E72776536CA051B967FD97821D" box="[521,590,1810,1829]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="2" pageNumber="3">Fig. 2F</figureCitation>
|
||
). Overall,
|
||
<collectionCode id="669DCCA72776536CA0EAB967FD0E821D" box="[690,727,1810,1829]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
was essentially free from cytosolic and chloroplast contamination.
|
||
</paragraph>
|
||
<caption id="54F304EA2776536CA23CBBD9FD778331" ID-DOI="http://doi.org/10.5281/zenodo.8234551" ID-Zenodo-Dep="8234551" httpUri="https://zenodo.org/record/8234551/files/figure.png" pageId="2" pageNumber="3" startId="2.[100,130,1452,1469]" targetBox="[108,766,152,1423]" targetPageId="2" targetType="figure">
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<paragraph id="003354622776536CA23CBBD9FD778331" blockId="2.[100,770,1452,1545]" pageId="2" pageNumber="3">
|
||
<emphasis id="32F888702776536CA23CBBD9FF478085" bold="true" box="[100,158,1452,1469]" pageId="2" pageNumber="3">Fig. 1.</emphasis>
|
||
Schematic representation of the experimental design and workflow of the establishment of the grasspea suspension secretome (GSS). Proteomic profiling was accomplished by generating suspension culture and sequential assessment of physicochemical properties and protein identification.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="003354622776536CA23CB906FD7282BE" blockId="2.[100,683,1906,1926]" box="[100,683,1906,1926]" pageId="2" pageNumber="3">
|
||
<heading id="5B7BE30E2776536CA23CB906FD7282BE" bold="true" box="[100,683,1906,1926]" fontSize="36" level="1" pageId="2" pageNumber="3" reason="1">
|
||
<emphasis id="32F888702776536CA23CB906FD7282BE" bold="true" box="[100,683,1906,1926]" italics="true" pageId="2" pageNumber="3">2.3. Identification and predicted localization of secreted proteins</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph id="003354622776536CA2DCB9DEFC6787B9" blockId="2.[132,770,1963,1982]" lastBlockId="2.[818,1488,148,1980]" pageId="2" pageNumber="3">
|
||
The LC-MS/
|
||
<collectionCode id="669DCCA72776536CA2AFB9DEFECC8286" box="[247,277,1963,1982]" country="Italy" lsid="urn:lsid:biocol.org:col:14396" name="Herbarium Messanaensis, Università di Messina" pageId="2" pageNumber="3" type="Herbarium">MS</collectionCode>
|
||
analysis of
|
||
<collectionCode id="669DCCA72776536CA3D1B9DEFE778286" box="[393,430,1963,1982]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
yielded a nonredundant set of 741 proteins (
|
||
<figureCitation id="98B748E72776536CA1D5BEE1FBD6859F" box="[909,1039,148,167]" captionStart="Fig" captionStartId="4.[100,130,1237,1254]" captionTargetBox="[107,765,150,1208]" captionTargetId="figure-928@4.[106,767,148,1210]" captionTargetPageId="4" captionText="Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234555" httpUri="https://zenodo.org/record/8234555/files/figure.png" pageId="2" pageNumber="3">Fig. 3A and B</figureCitation>
|
||
; Supplementary Table
|
||
<collectionCode id="669DCCA72776536CA6B1BEE1FB2E859F" box="[1257,1271,148,167]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
1). Thirty-four proteins associated with plasmodesmata, physical mediators of cell–cell signaling in plants, were identified in our study, including the dual specificity protein kinase YAK1, germin-like proteins, nectarin-1, subtilisin-like protease SBT2.1, peroxidase 71, LRR receptor-like serine/ threonine-protein kinase At
|
||
<quantity id="C774F9872776536CA661BF6AFB95840A" box="[1081,1100,287,306]" metricMagnitude="-3" metricUnit="kg" metricValue="1.0" pageId="2" pageNumber="3" unit="g" value="1.0">1g</quantity>
|
||
14390, SUMO-activating enzyme subunit 2 and pinoresinol reductase 2, among others. Eighty-two cell wallassociated proteins were identified, including cellulose synthase-like protein D5 and catalytic subunits 11 and 4, reduced wall acetylation 4 and NAC domain-containing protein 10, among others. Although protein secretion is a tightly regulated process, we observed the secretion of intracellular proteins as reported previously (
|
||
<bibRefCitation id="641D29932776536CA684BFB2FA8084E2" author="Jeffery, C. J." box="[1244,1369,455,474]" pageId="2" pageNumber="3" pagination="19 - 24" refId="ref12682" refString="Jeffery, C. J., 2016. Protein species and moonlighting proteins: very small changes in a protein' s covalent structure can change its biochemical function. J. Proteomics 134, 19 - 24. https: // doi. org / 10.1016 / j. jprot. 2015.10.003." type="journal article" year="2016">Jeffery, 2016</bibRefCitation>
|
||
). One of the ENTH/VNT family proteins, clathrin interactor Epsin 2, which is known for intercellular membrane trafficking, was also found to be secreted into the grasspea extracellular space. Other examples include nucleotide binding proteins such as pumilio (APUM-5), FRS12 (FAR1-RELATED SEQUENCE12), DNA-directed RNA polymerase and ATP-dependent RNA helicases.
|
||
</paragraph>
|
||
<paragraph id="003354622776536CA109BCFFFB7F8274" blockId="2.[818,1488,148,1980]" pageId="2" pageNumber="3">
|
||
The present repertoire of the grasspea secretome highlights the functional divergence of the plant secretome. The secreted proteins mediate signaling not only in actively growing regions of the plant body (
|
||
<bibRefCitation id="641D29932776536CA162BCABFC0987C9" author="Hu, X. L. & Lu, H. & Hassan, M. M. & Zhang, J. & Yuan, G. & Abraham, P. E. & Shrestha, H. K. & Solis, M. I. V. & Chen, J. G. & Tschaplinski, T. J. & Doktycz, M. J." box="[826,976,733,753]" pageId="2" pageNumber="3" pagination="1 - 14" refId="ref12457" refString="Hu, X. L., Lu, H., Hassan, M. M., Zhang, J., Yuan, G., Abraham, P. E., Shrestha, H. K., Solis, M. I. V., Chen, J. G., Tschaplinski, T. J., Doktycz, M. J., 2021. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. Hortic. Res. 8, 1 - 14. https: // doi. org / 10.1038 / s 41438 - 021 - 00570 - 7." type="journal article" year="2021">Hu et al., 2021</bibRefCitation>
|
||
) but also in processes related to plant reproduction (
|
||
<bibRefCitation id="641D29932776536CA162BC8CFBD98634" author="Chae, K. & Lord, E. M." box="[826,1024,761,780]" pageId="2" pageNumber="3" pagination="627 - 636" refId="ref10666" refString="Chae, K., Lord, E. M., 2011. Pollen tube growth and guidance: roles of small, secreted proteins. Ann. Bot. 108, 627 - 636. https: // doi. org / 10.1093 / aob / mcr 015." type="journal article" year="2011">Chae and Lord, 2011</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932776536CA655BC8CFB3A8634" author="Matthys-Rochon, E." box="[1037,1251,761,780]" pageId="2" pageNumber="3" pagination="23 - 29" refId="ref14094" refString="Matthys-Rochon, E., 2005. Secreted molecules and their role in embryo formation in plants: a min-review. Acta Biol. Cracov. Ser. Bot. 47, 23 - 29." type="journal article" year="2005">Matthys-Rochon, 2005</bibRefCitation>
|
||
). Significantly, a myriad of functional protein classes was identified in our study that have direct roles in conferring biotic (
|
||
<bibRefCitation id="641D29932776536CA66EBD47FACD867C" author="Haegeman, A. & Mantelin, S. & Jones, J. T. & Gheysen, G." box="[1078,1300,817,837]" pageId="2" pageNumber="3" pagination="19 - 31" refId="ref12150" refString="Haegeman, A., Mantelin, S., Jones, J. T., Gheysen, G., 2012. Functional roles of effectors of plant-parasitic nematodes. Gene 492, 19 - 31. https: // doi. org / 10.1016 / j. gene. 2011.10.040." type="journal article" year="2012">Haegeman et al., 2012</bibRefCitation>
|
||
) and abiotic stress responses (
|
||
<bibRefCitation id="641D29932776536CA1C1BD38FB598658" author="Nakaminami, K. & Matsui, A. & Shinozaki, K. & Seki, M." box="[921,1152,845,864]" pageId="2" pageNumber="3" pagination="149 - 153" refId="ref14478" refString="Nakaminami, K., Matsui, A., Shinozaki, K., Seki, M., 2012. RNA regulation in plant abiotic stress responses. Biochim. Biophys. Acta Gene Regul. Mech. 1819, 149 - 153. https: // doi. org / 10.1016 / j. bbagrm. 2011.07.015." type="journal article" year="2012">Nakaminami et al., 2012</bibRefCitation>
|
||
). Disease resistance proteins (
|
||
<collectionCode id="669DCCA72776536CA7C1BD38FA7F8658" box="[1433,1446,845,864]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
145,
|
||
<collectionCode id="669DCCA72776536CA16ABD1CFCE78644" box="[818,830,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
211,
|
||
<collectionCode id="669DCCA72776536CA12ABD1CFCA78644" box="[882,894,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
372,
|
||
<collectionCode id="669DCCA72776536CA1EABD1CFC678644" box="[946,958,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
412,
|
||
<collectionCode id="669DCCA72776536CA1AABD1CFC278644" box="[1010,1022,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
455,
|
||
<collectionCode id="669DCCA72776536CA66ABD1CFBE78644" box="[1074,1086,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
468,
|
||
<collectionCode id="669DCCA72776536CA62BBD1CFBA68644" box="[1139,1151,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
672,
|
||
<collectionCode id="669DCCA72776536CA6EBBD1CFB678644" box="[1203,1214,873,892]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="2" pageNumber="3" type="Herbarium">S</collectionCode>
|
||
704) were characteristically expressed in the
|
||
<collectionCode id="669DCCA72776536CA186BDF0FBDA86A0" box="[990,1027,901,920]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
samples and were previously identified to be effective against fungi, viruses and nematodes (
|
||
<bibRefCitation id="641D29932776536CA6AFBDD4FA10868C" author="McDowell, J. M. & Dhandaydham, M. & Long, T. A. & Aarts, M. G. & Goff, S. & Holub, E. B. & Dangl, J. L." box="[1271,1481,929,948]" pageId="2" pageNumber="3" pagination="1861 - 1874" refId="ref14130" refString="McDowell, J. M., Dhandaydham, M., Long, T. A., Aarts, M. G., Goff, S., Holub, E. B., Dangl, J. L., 1998. Intragenic recombination and diversifying selection contribute to the evolution of downy mildew resistance at the RPP 8 locus of Arabidopsis. Plant Cell 10, 1861 - 1874. https: // doi. org / 10.1105 / tpc. 10.11.1861." type="journal article" year="1998">McDowell et al., 1998</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932776536CA16ABDC8FC3786E8" author="Cooley, M. B. & Pathirana, S. & Wu, H. J. & Kachroo, P. & Klessig, D. F." box="[818,1006,957,976]" pageId="2" pageNumber="3" pagination="663 - 676" refId="ref10882" refString="Cooley, M. B., Pathirana, S., Wu, H. J., Kachroo, P., Klessig, D. F., 2000. Members of the Arabidopsis HRT / RPP 8 family of resistance genes confer resistance to both viral and oomycete pathogens. Plant Cell 12, 663 - 676. https: // doi. org / 10.1105 / tpc. 12.5.663." type="journal article" year="2000">Cooley et al., 2000</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932776536CA1A6BDC8FAD786E8" author="Zhang, X. C. & Gassmann, W." box="[1022,1294,957,976]" pageId="2" pageNumber="3" pagination="1577 - 1587" refId="ref18311" refString="Zhang, X. C., Gassmann, W., 2007. Alternative splicing and mRNA levels of the disease resistance gene RPS 4 are induced during defense responses. Plant Physiol. 145, 1577 - 1587. https: // doi. org / 10.1104 / pp. 107.108720." type="journal article" year="2007">Zhang and Gassmann, 2007</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932776536CA745BDC8FA1086E8" author="Yuan, L. & Zhang, S. & Wang, Y. & Li, Y. & Wang, X. & Yang, Q." box="[1309,1481,957,976]" pageId="2" pageNumber="3" refId="ref18076" refString="Yuan, L., Zhang, S., Wang, Y., Li, Y., Wang, X., Yang, Q., 2018. Surfactin inhibits membrane fusion during invasion of epithelial cells by enveloped viruses. J. Virol. 92, e 00809 - e 00818. https: // doi. org / 10.1128 / JVI. 00809 - 18." type="book" year="2018">Yuan et al., 2018</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932776536CA16ABDACFBC186D4" author="Warmerdam, S. & Sterken, M. G. & Sukarta, O. C. & Van Schaik, C. C. & Oortwijn, M. E. & Torres, J. L. & Bakker, J. & Smant, G. & Goverse, A." box="[818,1048,985,1004]" pageId="2" pageNumber="3" pagination="1 - 14" refId="ref17469" refString="Warmerdam, S., Sterken, M. G., Sukarta, O. C., Van Schaik, C. C., Oortwijn, M. E., Lozano- Torres, J. L., Bakker, J., Smant, G., Goverse, A., 2020. The TIR-NB-LRR pair DSC 1 and WRKY 19 contributes to basal immunity of Arabidopsis to the root-knot nematode Meloidogyne incognita. BMC Plant Biol. 20, 1 - 14. https: // doi. org / 10.1186 / s 12870 - 020 - 2285 - x." type="journal article" year="2020">Warmerdam et al., 2020</bibRefCitation>
|
||
). The disease resistance-like protein dominant suppressor of CAMTA3 (DSC1) plays a significant role in conferring basal immunity in
|
||
<taxonomicName id="C78C2FE12776536CA1B8BA65FA91811C" authority="(Warmerdam et al., 2020)" baseAuthorityName="Warmerdam" baseAuthorityYear="2020" box="[992,1352,1040,1060]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="2" pageNumber="3" phylum="Tracheophyta" rank="genus">
|
||
Arabidopsis (
|
||
<bibRefCitation id="641D29932776536CA604BA65FAE6811C" author="Warmerdam, S. & Sterken, M. G. & Sukarta, O. C. & Van Schaik, C. C. & Oortwijn, M. E. & Torres, J. L. & Bakker, J. & Smant, G. & Goverse, A." box="[1116,1343,1040,1060]" pageId="2" pageNumber="3" pagination="1 - 14" refId="ref17469" refString="Warmerdam, S., Sterken, M. G., Sukarta, O. C., Van Schaik, C. C., Oortwijn, M. E., Lozano- Torres, J. L., Bakker, J., Smant, G., Goverse, A., 2020. The TIR-NB-LRR pair DSC 1 and WRKY 19 contributes to basal immunity of Arabidopsis to the root-knot nematode Meloidogyne incognita. BMC Plant Biol. 20, 1 - 14. https: // doi. org / 10.1186 / s 12870 - 020 - 2285 - x." type="journal article" year="2020">Warmerdam et al., 2020</bibRefCitation>
|
||
)
|
||
</taxonomicName>
|
||
. The secretion of arginyl transferase 1 (ATE1) is particularly intriguing, since posttranslational arginylation of secreted signaling proteins is of immense significance across the varied kingdoms of life (
|
||
<bibRefCitation id="641D29932776536CA740BA11FCBB81AB" author="Saha, S. & Kashina, A." pageId="2" pageNumber="3" pagination="1 - 8" refId="ref15784" refString="Saha, S., Kashina, A., 2011. Posttranslational arginylation as a global biological regulator. Dev. Biol. 358, 1 - 8. https: // doi. org / 10.1016 / j. ydbio. 2011.06.043." type="journal article" year="2011">Saha and Kashina, 2011</bibRefCitation>
|
||
). ATE1 was even identified as a constituent of exosome-like vesicles in
|
||
<taxonomicName id="C78C2FE12776536CA120BAE9FB1F8197" authority="(Liang et al., 2019)" baseAuthorityName="Liang" baseAuthorityYear="2019" box="[888,1222,1180,1199]" class="Insecta" family="Scarabaeidae" genus="Taenia" kingdom="Animalia" order="Coleoptera" pageId="2" pageNumber="3" phylum="Arthropoda" rank="species" species="asiatica">
|
||
<emphasis id="32F888702776536CA120BAE9FBD88197" bold="true" box="[888,1025,1180,1199]" italics="true" pageId="2" pageNumber="3">Taenia asiatica</emphasis>
|
||
(
|
||
<bibRefCitation id="641D29932776536CA649BAE9FB658197" author="Liang, P. & Mao, L. & Zhang, S. & Guo, X. & Liu, G. & Wang, L. & Hou, J. & Zheng, Y. & Luo, X." box="[1041,1212,1180,1199]" pageId="2" pageNumber="3" pagination="105036" refId="ref13603" refString="Liang, P., Mao, L., Zhang, S., Guo, X., Liu, G., Wang, L., Hou, J., Zheng, Y., Luo, X., 2019. Identification and molecular characterization of exosome-like vesicles derived from the Taenia asiatica adult worm. Acta Trop. 198, 105036 https: // doi. org / 10.1016 / j. actatropica. 2019.05.027." type="journal article" year="2019">Liang et al., 2019</bibRefCitation>
|
||
)
|
||
</taxonomicName>
|
||
. Targeting fungal virulence factors is an effective plant defense strategy, and in the present study, we identified proteins of similar functionality, including Kiwellin-1 (
|
||
<bibRefCitation id="641D29932776536CA7FABAA1FC1E803B" author="Altegoer, F. & Weiland, P. & Giammarinaro, P. I. & Freibert, S. A. & Binnebesel, L. & Han, X. & Lepak, A. & Kahmann, R. & Lechner, M. & Bange, G." pageId="2" pageNumber="3" pagination="7816 - 7825" refId="ref9982" refString="Altegoer, F., Weiland, P., Giammarinaro, P. I., Freibert, S. A., Binnebesel, L., Han, X., Lepak, A., Kahmann, R., Lechner, M., Bange, G., 2020. The two paralogous kiwellin proteins KWL 1 and KWL 1 - b from maize are structurally related and have overlapping functions in plant defense. J. Biol. Chem. 295, 7816 - 7825. https: // doi. org / 10.1074 / jbc. RA 119.012207." type="journal article" year="2020">Altegoer et al., 2020</bibRefCitation>
|
||
). BOI-related
|
||
<collectionCode id="669DCCA72776536CA611BA85FB81803B" box="[1097,1112,1264,1283]" country="United Kingdom" lsid="urn:lsid:biocol.org:col:15670" name="Royal Botanic Garden Edinburgh" pageId="2" pageNumber="3" type="Herbarium">E</collectionCode>
|
||
3 ubiquitin-protein ligase, a crucial plant defense protein against biotic and abiotic stress, was also observed in the
|
||
<collectionCode id="669DCCA72776536CA16ABB52FC838002" box="[818,858,1319,1338]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
. The cell defense-related UBP1-associated protein 2
|
||
<collectionCode id="669DCCA72776536CA718BB52FA978002" box="[1344,1358,1319,1338]" country="Germany" lsid="urn:lsid:biocol.org:col:15534" name="Botanischer Garten und Botanisches Museum Berlin-Dahlem, Zentraleinrichtung der Freien Universitaet" pageId="2" pageNumber="3" type="Herbarium">B</collectionCode>
|
||
(UBA2) (
|
||
<bibRefCitation id="641D29932776536CA7F1BB52FC40806E" author="Kim, C. Y. & Bove, J. & Assmann, S. M." pageId="2" pageNumber="3" pagination="57 - 70" refId="ref12890" refString="Kim, C. Y., Bove, J., Assmann, S. M., 2008. Overexpression of wound-responsive RNAbinding proteins induces leaf senescence and hypersensitive-like cell death. New Phytol. 180, 57 - 70. https: // doi. org / 10.1111 / j. 1469 - 8137.2008.02557. x." type="journal article" year="2008">Kim et al., 2008</bibRefCitation>
|
||
) was secreted in
|
||
<collectionCode id="669DCCA72776536CA66FBB36FB85806E" box="[1079,1116,1347,1366]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
samples, raising questions about its role in the extracellular space, since its role in the nucleus is associated with mRNA stabilization (
|
||
<bibRefCitation id="641D29932776536CA1A4BB0EFB3C80B6" author="Lambermon, M. H. & Fu, Y. & Kirk, D. A. W. & Dupasquier, M. & Filipowicz, W. & Lorkovic, Z. J." box="[1020,1253,1403,1422]" pageId="2" pageNumber="3" pagination="4346 - 4357" refId="ref13193" refString="Lambermon, M. H., Fu, Y., Kirk, D. A. W., Dupasquier, M., Filipowicz, W., Lorkovic, Z. J., 2002. UBA 1 and UBA 2, two proteins that interact with UBP 1, a multifunctional effector of pre-mRNA maturation in plants. Mol. Cell Biol. 22, 4346 - 4357. https: // doi. org / 10.1128 / MCB. 22.12.4346 - 4357.2002." type="journal article" year="2002">Lambermon et al., 2002</bibRefCitation>
|
||
). Genes associated with abiotic stress tolerance included the SNARE-interacting proteins KEULE and syntaxin (
|
||
<bibRefCitation id="641D29932776536CA19BBBC6FBA380FE" author="Kwon, C. & Lee, J. H. & Yun, H. S." box="[963,1146,1459,1478]" pageId="2" pageNumber="3" pagination="501" refId="ref13143" refString="Kwon, C., Lee, J. H., Yun, H. S., 2020. SNAREs in plant biotic and abiotic stress responses. Mol. Cells 43, 501. https: // doi. org / 10.14348 / molcells. 2020.0007." type="journal article" year="2020">Kwon et al., 2020</bibRefCitation>
|
||
). One of the PERK family genes, proline-rich extensin-like receptor kinase 5 (AtPERK5), was also a constituent of the grasspea suspension secretome. PERKs have been indicated to be critical for not only abiotic stress tolerance but also plant growth and development (
|
||
<bibRefCitation id="641D29932776536CA66AB857FB34830D" author="Borassi, C. & Sede, A. R. & Mecchia, M. A. & Salgado Salter, J. D. & Marzol, E. & Muschietti, J. P. & Estevez, J. M." box="[1074,1261,1570,1590]" pageId="2" pageNumber="3" pagination="477 - 487" refId="ref10268" refString="Borassi, C., Sede, A. R., Mecchia, M. A., Salgado Salter, J. D., Marzol, E., Muschietti, J. P., Estevez, J. M., 2016. An update on cell surface proteins containing extensin-motifs. J. Exp. Bot. 67, 477 - 487. https: // doi. org / 10.1093 / jxb / erv 455." type="journal article" year="2016">Borassi et al., 2016</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932776536CA6A4B856FA18830D" author="Kesawat, M. S. & Kherawat, B. S. & Singh, A. & Dey, P. & Routray, S. & Mohapatra, C. & Saha, D. & Ram, C. & Siddique, K. H. & Kumar, A. & Gupta, R." box="[1276,1473,1570,1590]" pageId="2" pageNumber="3" pagination="496" refId="ref12736" refString="Kesawat, M. S., Kherawat, B. S., Singh, A., Dey, P., Routray, S., Mohapatra, C., Saha, D., Ram, C., Siddique, K. H., Kumar, A., Gupta, R., 2022. Genome-wide analysis and characterization of the proline-rich extensin-like receptor kinases (perks) gene family reveals their role in different developmental stages and stress conditions in wheat (Triticum aestivum L.). Plants 11, 496. https: // doi. org / 10.3390 / plants 11040496." type="journal article" year="2022">Kesawat et al., 2022</bibRefCitation>
|
||
). Two late embryogenesis abundant proteins (LEA14 and LEA76) were active constituents of the
|
||
<collectionCode id="669DCCA72776536CA647B82FFB9D8355" box="[1055,1092,1626,1645]" pageId="2" pageNumber="3">GSS</collectionCode>
|
||
profile, and LEA proteins have established roles in desiccation tolerance (
|
||
<bibRefCitation id="641D29932776536CA606B803FAC283B1" author="Candat, A. & Paszkiewicz, G. & Neveu, M. & Gautier, R. & Logan, D. C. & Avelange-Macherel, M. H. & Macherel, D." box="[1118,1307,1654,1673]" pageId="2" pageNumber="3" pagination="3148 - 3166" refId="ref10584" refString="Candat, A., Paszkiewicz, G., Neveu, M., Gautier, R., Logan, D. C., Avelange-Macherel, M. H., Macherel, D., 2014. The ubiquitous distribution of late embryogenesis abundant proteins across cell compartments in Arabidopsis offers tailored protection against abiotic stress. Plant Cell 26, 3148 - 3166. https: // doi. org / 10.1105 / tpc. 114.127316." type="journal article" year="2014">Candat et al., 2014</bibRefCitation>
|
||
). The secretion of auxin response factor 5 (Monopteros) is also intriguing, as previous studies have established its role in regulating mobile proteins (
|
||
<bibRefCitation id="641D29932776536CA72FB8DBFC7883E5" author="Schlereth, A. & Liu, W. & Kientz, M. & Flipse, J. & Rademacher, E. H. & Schmid, M. & Jurgens, G. & Weijers, D." pageId="2" pageNumber="3" pagination="913 - 916" refId="ref16014" refString="Schlereth, A., M ¨ oller, B., Liu, W., Kientz, M., Flipse, J., Rademacher, E. H., Schmid, M., Jurgens, G., Weijers, D., 2010. MONOPTEROS controls embryonic root initiation by regulating a mobile transcription factor. Nature 464, 913 - 916. https: // doi. org / 10.1038 / nature 08836." type="journal article" year="2010">Schlereth et al., 2010</bibRefCitation>
|
||
), but none have reported Monopteros to be extracellular. One of the water-deficit responsive transcription factors, bHLH45 (
|
||
<bibRefCitation id="641D29932776536CA7C1B893FC76822D" author="Wang, X. & Chung, K. P. & Lin, W. & Jiang, L." pageId="2" pageNumber="3" pagination="21 - 37" refId="ref17406" refString="Wang, X., Chung, K. P., Lin, W., Jiang, L., 2018. Protein secretion in plants: conventional and unconventional pathways and new techniques. J. Exp. Bot. 69, 21 - 37. https: // doi. org / 10.1093 / jxb / erx 262." type="journal article" year="2018">Wang et al., 2018</bibRefCitation>
|
||
), was also secreted in
|
||
<taxonomicName id="C78C2FE12776536CA6E9B977FAD7822C" box="[1201,1294,1793,1813]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="2" pageNumber="3" phylum="Tracheophyta" rank="species" species="sativus">
|
||
<emphasis id="32F888702776536CA6E9B977FAD7822C" bold="true" box="[1201,1294,1793,1813]" italics="true" pageId="2" pageNumber="3">L. sativus</emphasis>
|
||
</taxonomicName>
|
||
. An abiotic stress tolerance-promoting PLAT domain-containing protein (
|
||
<bibRefCitation id="641D29932776536CA70CB96BFCBB8274" author="Hyun, T. K. & van der Graaff, E. & Albacete, A. & Eom, S. H. & Grosskinsky, D. K. & Janschek, U. & Rim, Y. & Ali, W. W. & Kim, S. Y. & Roitsch, T." pageId="2" pageNumber="3" pagination="112946" refId="ref12575" refString="Hyun, T. K., van der Graaff, E., Albacete, A., Eom, S. H., Grosskinsky, D. K., B ¨ ohm, H., Janschek, U., Rim, Y., Ali, W. W., Kim, S. Y., Roitsch, T., 2014. The Arabidopsis PLAT domain protein 1 is critically involved in abiotic stress tolerance. PLoS One 9, e 112946. https: // doi. org / 10.1371 / journal. pone. 0112946." type="journal article" year="2014">Hyun et al., 2014</bibRefCitation>
|
||
), was also identified in our study.
|
||
</paragraph>
|
||
<paragraph id="003354622776536DA109B920FE67821A" blockId="2.[818,1488,148,1980]" lastBlockId="3.[100,771,1277,1965]" lastPageId="3" lastPageNumber="4" pageId="2" pageNumber="3">
|
||
The secreted proteins were sequentially subjected to localization prediction analysis using 7 different programs. SignalP and SecretomeP predicted the presence of signal peptides in 147 and 183 proteins, respectively, and 38 were exclusively predicted by the latter. SecretomeP also predicted 123 proteins to be secreted through the
|
||
<collectionCode id="669DCCA72777536DA08DBA88FD268028" box="[725,767,1277,1296]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
. We found an additional increase in the prediction of secreted proteins using OutCyte, wherein 139, 133 and 75 were categorized as
|
||
<collectionCode id="669DCCA72777536DA0F2BB41FD08807F" box="[682,721,1332,1351]" country="0" httpUri="http://grbio.org/cool/xgvw-ide6" name="Wyoming-Colorado Paleontological Society" pageId="3" pageNumber="4">CPS</collectionCode>
|
||
,
|
||
<collectionCode id="669DCCA72777536DA083BB41FCDB807F" box="[731,770,1332,1351]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
and
|
||
<collectionCode id="669DCCA72777536DA2D7BB24FF68805C" box="[143,177,1361,1380]" country="Germany" name="Teylers Museum, Paleontologische" pageId="3" pageNumber="4">TM</collectionCode>
|
||
, respectively. Interestingly, two proteins (
|
||
<collectionCode id="669DCCA72777536DA01FBB25FD8A805B" box="[583,595,1360,1379]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="3" pageNumber="4" type="Herbarium">S</collectionCode>
|
||
468, probable disease resistance protein and
|
||
<collectionCode id="669DCCA72777536DA339BB19FEB48047" box="[353,365,1388,1407]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="3" pageNumber="4" type="Herbarium">S</collectionCode>
|
||
687, cytochrome f) were predicted to follow
|
||
<collectionCode id="669DCCA72777536DA23CBBFDFF5280A3" box="[100,139,1416,1435]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
by OutCyte but
|
||
<collectionCode id="669DCCA72777536DA37FBBFDFE9580A3" box="[295,332,1416,1435]" country="0" httpUri="http://grbio.org/cool/xgvw-ide6" name="Wyoming-Colorado Paleontological Society" pageId="3" pageNumber="4">CPS</collectionCode>
|
||
by SecretomeP. While ApoplastP predicted 69 proteins as bona fide
|
||
<collectionCode id="669DCCA72777536DA368BBD1FE85808F" box="[304,348,1444,1463]" country="China" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13249" lsid="urn:lsid:biocol.org:col:13249" name="Hubei College of Traditional Chinese Medicine" pageId="3" pageNumber="4" type="Herbarium">ECM</collectionCode>
|
||
constituents,
|
||
<collectionCode id="669DCCA72777536DA3B8BBD1FDFA808F" box="[480,547,1444,1463]" pageId="3" pageNumber="4">BUSCA</collectionCode>
|
||
and DeepLoc predicted 140 and 112 proteins as
|
||
<collectionCode id="669DCCA72777536DA314BBB5FEA180EB" box="[332,376,1472,1491]" country="China" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13249" lsid="urn:lsid:biocol.org:col:13249" name="Hubei College of Traditional Chinese Medicine" pageId="3" pageNumber="4" type="Herbarium">ECM</collectionCode>
|
||
residents, respectively.
|
||
<collectionCode id="669DCCA72777536DA002BBB5FDA080EB" box="[602,633,1472,1491]" country="Germany" name="Teylers Museum, Paleontologische" pageId="3" pageNumber="4">TM</collectionCode>
|
||
domains were predicted in 152
|
||
<collectionCode id="669DCCA72777536DA356BBA9FEEA80D7" box="[270,307,1500,1519]" pageId="3" pageNumber="4">GSS</collectionCode>
|
||
proteins by
|
||
<collectionCode id="669DCCA72777536DA3EABBA9FDD380D7" box="[434,522,1500,1519]" pageId="3" pageNumber="4">TMHMM</collectionCode>
|
||
. Furthermore, organellardefined predictions were made by DeepLoc and
|
||
<collectionCode id="669DCCA72777536DA01EBB8DFD558333" box="[582,652,1528,1547]" pageId="3" pageNumber="4">BUSCA</collectionCode>
|
||
, which predicted 43 and 46 proteins to be PM residents, respectively. ApoplastP and SignalP predicted a redundant set of
|
||
<collectionCode id="669DCCA72777536DA3A1B85AFDC7837A" box="[505,542,1583,1602]" pageId="3" pageNumber="4">GSS</collectionCode>
|
||
proteins to be secreted compared to other programs. Only 117
|
||
<collectionCode id="669DCCA72777536DA3BFB83EFDD58366" box="[487,524,1611,1630]" pageId="3" pageNumber="4">GSS</collectionCode>
|
||
proteins were commonly predicted by
|
||
<collectionCode id="669DCCA72777536DA2B2B812FEE98342" box="[234,304,1639,1658]" pageId="3" pageNumber="4">BUSCA</collectionCode>
|
||
, DeepLOC, OutCyte and SecretomeP (
|
||
<figureCitation id="98B748E72777536DA0F5B812FD2E8342" box="[685,759,1639,1658]" captionStart="Fig" captionStartId="4.[100,130,1237,1254]" captionTargetBox="[107,765,150,1208]" captionTargetId="figure-928@4.[106,767,148,1210]" captionTargetPageId="4" captionText="Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234555" httpUri="https://zenodo.org/record/8234555/files/figure.png" pageId="3" pageNumber="4">Fig. 3C</figureCitation>
|
||
). Approximately 60% of the proteins were predicted to be secreted, as projected with the variable softwares. Furthermore, ~25% of proteins were predicted to follow
|
||
<collectionCode id="669DCCA72777536DA308B8CEFEAE83F6" box="[336,375,1723,1742]" country="0" httpUri="http://grbio.org/cool/xgvw-ide6" name="Wyoming-Colorado Paleontological Society" pageId="3" pageNumber="4">CPS</collectionCode>
|
||
, and ~29% were predicted to follow
|
||
<collectionCode id="669DCCA72777536DA08DB8CEFD2683F6" box="[725,767,1723,1742]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
. Since OutCyte, SecretomeP and
|
||
<collectionCode id="669DCCA72777536DA3D6B8A2FE0883D2" box="[398,465,1751,1770]" pageId="3" pageNumber="4">BUSCA</collectionCode>
|
||
predicted the maximum number of secreted proteins, we utilized these programs in the study of crop secretomes in a conjunctive manner.
|
||
</paragraph>
|
||
<caption id="54F304EA2777536DA23CBA36FC6D81EB" ID-DOI="http://doi.org/10.5281/zenodo.8234553" ID-Zenodo-Dep="8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="3" pageNumber="4" startId="3.[100,130,1091,1108]" targetBox="[208,1380,149,1062]" targetPageId="3" targetType="figure">
|
||
<paragraph id="003354622777536DA23CBA36FC6D81EB" blockId="3.[100,1487,1091,1236]" pageId="3" pageNumber="4">
|
||
<emphasis id="32F888702777536DA23CBA36FF45816C" bold="true" box="[100,156,1091,1108]" pageId="3" pageNumber="4">Fig. 2.</emphasis>
|
||
Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="003354622777536DA2DCB95FFC2082A9" blockId="3.[100,771,1277,1965]" lastBlockId="3.[818,1488,1277,1937]" pageId="3" pageNumber="4">
|
||
Although there is recent evidence for the secretion of cytoplasmic constituents to the cell surface to assume different biological functions (
|
||
<bibRefCitation id="641D29932777536DA234B917FEF3824D" author="Zininga, T. & Ramatsui, L. & Shonhai, A." box="[108,298,1890,1910]" pageId="3" pageNumber="4" pagination="2846" refId="ref18501" refString="Zininga, T., Ramatsui, L., Shonhai, A., 2018. Heat shock proteins as immunomodulants. Molecules 23, 2846. https: // doi. org / 10.3390 / molecules 23112846." type="journal article" year="2018">Zininga et al., 2018</bibRefCitation>
|
||
), this field of study demands more experimental evidence, even more so in the case of plants. Since the dawn of the plant secretome, plasma membrane proteins have been frequently identified in the outermost fraction, presumably owing to their functionality as cell surface-associated proteins (
|
||
<bibRefCitation id="641D29932777536DA663BB6CFB2F8013" author="Tanveer, T. & Shaheen, K. & Parveen, S. & Kazi, A. G. & Ahmad, P." box="[1083,1270,1304,1324]" pageId="3" pageNumber="4" pagination="29426" refId="ref16631" refString="Tanveer, T., Shaheen, K., Parveen, S., Kazi, A. G., Ahmad, P., 2014. Plant secretomics: identification, isolation, and biological significance under environmental stress. Plant Signal. Behav. 9, e 29426 https: // doi. org / 10.4161 / psb. 29426." type="journal article" year="2014">Tanveer et al., 2014</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA759BB6DFCBB807F" author="Nogueira-Lopez, G. & Greenwood, D. R. & Middleditch, M. & Winefield, C. & Eaton, C. & Steyaert, J. M. & Mendoza-Mendoza, A." pageId="3" pageNumber="4" pagination="409" refId="ref14646" refString="Nogueira-Lopez, G., Greenwood, D. R., Middleditch, M., Winefield, C., Eaton, C., Steyaert, J. M., Mendoza-Mendoza, A., 2018. The apoplastic secretome of Trichoderma virens during interaction with maize roots shows an inhibition of plant defence and scavenging oxidative stress secreted proteins. Front. Plant Sci. 9, 409. https: // doi. org / 10.3389 / fpls. 2018.00409." type="journal article" year="2018">Nogueira-Lopez et al., 2018</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA136BB41FB98807F" author="Ramulifho, E. & Goche, T. & Van As, J. & Tsilo, T. J. & Chivasa, S. & Ngara, R." box="[878,1089,1332,1352]" pageId="3" pageNumber="4" pagination="218" refId="ref15085" refString="Ramulifho, E., Goche, T., Van As, J., Tsilo, T. J., Chivasa, S., Ngara, R., 2019. Establishment and characterization of callus and cell suspension cultures of selected Sorghum bicolor (L.) Moench varieties: a resource for gene discovery in plant stress biology. Agronomy 9, 218. https: // doi. org / 10.3390 / agronomy 9050218." type="journal article" year="2019">Ramulifho et al., 2019</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA615BB41FA91807F" author="Flores-Tornero, M. & Wang, L. & Hafidh, S. & Vogler, F. & Honys, D. & Sprunck, S. & Dresselhaus, T." box="[1101,1352,1332,1352]" pageId="3" pageNumber="4" pagination="47 - 60" refId="ref11761" refString="Flores-Tornero, M., Wang, L., Poteˇˇsil, D., Hafidh, S., Vogler, F., Zdr´ahal, Z., Honys, D., Sprunck, S., Dresselhaus, T., 2021. Comparative analyses of angiosperm secretomes identify apoplastic pollen tube functions and novel secreted peptides. Plant Reprod. 34, 47 - 60. https: // doi. org / 10.1007 / s 00497 - 020 - 00399 - 5." type="journal article" year="2021">Flores-Tornero et al., 2021</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA70CBB41FCBB805B" author="Ngcala, M. G. & Goche, T. & Brown, A. P. & Chivasa, S. & Ngara, R." pageId="3" pageNumber="4" pagination="29" refId="ref14582" refString="Ngcala, M. G., Goche, T., Brown, A. P., Chivasa, S., Ngara, R., 2020. Heat stress triggers differential protein accumulation in the extracellular matrix of sorghum cell suspension cultures. Proteomes 8, 29. https: // doi. org / 10.3390 / proteomes 8040029." type="journal article" year="2020">Ngcala et al., 2020</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA135BB25FBFF805B" author="Vincent, D. & Rafiqi, M. & Job, D." box="[877,1062,1360,1380]" pageId="3" pageNumber="4" pagination="1626" refId="ref17193" refString="Vincent, D., Rafiqi, M., Job, D., 2020. The multiple facets of plant-fungal interactions revealed through plant and fungal secretomics. Front. Plant Sci. 10, 1626. https: // doi. org / 10.3389 / fpls. 2019.01626." type="journal article" year="2020">Vincent et al., 2020</bibRefCitation>
|
||
). Membrane proteins often contain a defined signal peptide but are secreted through the
|
||
<collectionCode id="669DCCA72777536DA694BB19FB2C8047" box="[1228,1269,1388,1407]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
, as in the case of cystic fibrosis transmembrane conductance regulator (CFTR) (
|
||
<bibRefCitation id="641D29932777536DA73ABBFDFCBB808F" author="Gee, H. Y. & Noh, S. H. & Tang, B. L. & Kim, K. H. & Lee, M. G." pageId="3" pageNumber="4" pagination="746 - 760" refId="ref11907" refString="Gee, H. Y., Noh, S. H., Tang, B. L., Kim, K. H., Lee, M. G., 2011. Rescue of ΔF 508 - CFTR trafficking via a GRASP-dependent unconventional secretion pathway. Cell 146, 746 - 760. https: // doi. org / 10.1016 / j. cell. 2011.07.021." type="journal article" year="2011">Gee et al., 2011</bibRefCitation>
|
||
). Experimental evidence of non-classically secreted plasma membrane proteins has yet to be ascertained in plants (
|
||
<bibRefCitation id="641D29932777536DA6A6BBB5FA1880EB" author="Robinson, D. G. & Ding, Y. & Jiang, L." box="[1278,1473,1472,1491]" pageId="3" pageNumber="4" pagination="31 - 43" refId="ref15681" refString="Robinson, D. G., Ding, Y., Jiang, L., 2016. Unconventional protein secretion in plants: a critical assessment. Protoplasma 253, 31 - 43. https: // doi. org / 10.1007 / s 00709 - 015 - 0887 - 1." type="journal article" year="2016">Robinson et al., 2016</bibRefCitation>
|
||
). Additionally, the localization of
|
||
<collectionCode id="669DCCA72777536DA604BBA9FBA280D7" box="[1116,1147,1500,1519]" country="Germany" name="Teylers Museum, Paleontologische" pageId="3" pageNumber="4">TM</collectionCode>
|
||
domain-containing transporters and ion channels is frequently determined by active processes of exocytosis and endocytosis, which is reflected in the dynamic composition of the eukaryotic secretome. Moreover, the
|
||
<collectionCode id="669DCCA72777536DA6D6B85AFB6C837A" box="[1166,1205,1583,1602]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
pathway attributes functional divergence to known cytoplasmic proteins, for instance, the Hsps (
|
||
<bibRefCitation id="641D29932777536DA162B812FBC68342" author="Campanella, C. & Bavisotto, C. C. & Gammazza, A. M. & Nikolic, D. & Rappa, F. & David, S. & Cappello, F. & Bucchieri, F. & Fais, S." box="[826,1055,1639,1658]" pageId="3" pageNumber="4" pagination="4" refId="ref10500" refString="Campanella, C., Bavisotto, C. C., Gammazza, A. M., Nikolic, D., Rappa, F., David, S., Cappello, F., Bucchieri, F., Fais, S., 2014. Exosomal heat shock proteins as new players in tumour cell-to-cell communication. J. Circ. Biomark. 3, 4. https: // doi. org / 10.5772 / 58721." type="journal article" year="2014">Campanella et al., 2014</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA675B812FB068342" author="Reddy, V. S. & Madala, S. K. & Trinath, J. & Reddy, G. B." box="[1069,1247,1639,1658]" pageId="3" pageNumber="4" pagination="441 - 454" refId="ref15489" refString="Reddy, V. S., Madala, S. K., Trinath, J., Reddy, G. B., 2018. Extracellular small heat shock proteins: exosomal biogenesis and function. Cell Stress Chaperones 23, 441 - 454. https: // doi. org / 10.1007 / s 12192 - 017 - 0856 - z." type="journal article" year="2018">Reddy et al., 2018</bibRefCitation>
|
||
). This family of proteins functions as chaperones intracellularly but behaves more as signaling proteins extracellularly. The possible routes of
|
||
<collectionCode id="669DCCA72777536DA6ADB8EAFAC5838A" box="[1269,1308,1695,1714]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
have not yet been completely elucidated (
|
||
<bibRefCitation id="641D29932777536DA64AB8CEFB6C83F6" author="Ding, Y. & Robinson, D. G. & Jiang, L." box="[1042,1205,1723,1742]" pageId="3" pageNumber="4" pagination="107 - 115" refId="ref11045" refString="Ding, Y., Robinson, D. G., Jiang, L., 2014. Unconventional protein secretion (UPS) pathways in plants. Curr. Opin. Cell Biol. 29, 107 - 115. https: // doi. org / 10.1016 / j. ceb. 2014.05.008." type="journal article" year="2014">Ding et al., 2014</bibRefCitation>
|
||
), except for dissection of the exosome pathway and compositional modulation in response to environmental constraints (
|
||
<bibRefCitation id="641D29932777536DA657B886FB64823E" author="Woith, E. & Guerriero, G. & Hausman, J. F. & Renaut, J. & Leclercq, C. C. & Weise, C. & Legay, S. & Weng, A. & Melzig, M. F." box="[1039,1213,1779,1798]" pageId="3" pageNumber="4" pagination="3719" refId="ref17716" refString="Woith, E., Guerriero, G., Hausman, J. F., Renaut, J., Leclercq, C. C., Weise, C., Legay, S., Weng, A., Melzig, M. F., 2021. Plant extracellular vesicles and nanovesicles: focus on secondary metabolites, proteins, and lipids with perspectives on their potential and sources. Int. J. Mol. Sci. 22, 3719. https: // doi. org / 10.3390 / ijms 22073719." type="journal article" year="2021">Woith et al., 2021</bibRefCitation>
|
||
). Also, synaptotagmin mediated
|
||
<collectionCode id="669DCCA72777536DA107B97AFC5F821A" box="[863,902,1807,1826]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="3" pageNumber="4" type="Herbarium">UPS</collectionCode>
|
||
as well as intercellular communication has been established in plants (
|
||
<bibRefCitation id="641D29932777536DA122B95FFBF08206" author="Zhang, H. & Zhang, L. & Gao, B. & Fan, H. & Jin, J. & Botella, M. A. & Jiang, L. & Lin, J." box="[890,1065,1834,1854]" pageId="3" pageNumber="4" pagination="26477" refId="ref18232" refString="Zhang, H., Zhang, L., Gao, B., Fan, H., Jin, J., Botella, M. A., Jiang, L., Lin, J., 2011. Golgi apparatus-localized synaptotagmin 2 is required for unconventional secretion in Arabidopsis. PLoS One 6, e 26477. https: // doi. org / 10.1007 / s 10265019 - 01130 - w." type="journal article" year="2011">Zhang et al., 2011</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932777536DA66EB95FFAD38206" author="Uchiyama, A. & Shimada-Beltran, H. & Levy, A. & Zheng, J. Y. & Javia, P. A. & Lazarowitz, S. G." box="[1078,1290,1834,1854]" pageId="3" pageNumber="4" pagination="584" refId="ref16865" refString="Uchiyama, A., Shimada-Beltran, H., Levy, A., Zheng, J. Y., Javia, P. A., Lazarowitz, S. G., 2014. The Arabidopsis synaptotagmin SYTA regulates the cell-to-cell movement of diverse plant viruses. Front. Plant Sci. 5, 584. https: // doi. org / 10.3389 / fpls. 2014.00584." type="journal article" year="2014">Uchiyama et al., 2014</bibRefCitation>
|
||
)
|
||
<collectionCode id="669DCCA72777536DA741B95EFAFE8206" box="[1305,1319,1835,1854]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="3" pageNumber="4" type="Herbarium">A</collectionCode>
|
||
cytosolic cellular signaling protein, translationally controlled tumour protein (TCTP), was found to be secreted in
|
||
<taxonomicName id="C78C2FE12777536DA65FB917FB81824D" box="[1031,1112,1890,1909]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="3" pageNumber="4" phylum="Tracheophyta" rank="species" species="sativus">
|
||
<emphasis id="32F888702777536DA65FB917FB81824D" bold="true" box="[1031,1112,1890,1909]" italics="true" pageId="3" pageNumber="4">L. sativus</emphasis>
|
||
</taxonomicName>
|
||
, like its homolog in tobacco pollen tubes (
|
||
<bibRefCitation id="641D29932777536DA162B90BFC3582A9" author="Hafidh, S. & Fila, J. & Honys, D." box="[826,1004,1918,1937]" pageId="3" pageNumber="4" pagination="1 - 29" refId="ref12204" refString="Hafidh, S., Poteˇˇsil, D., Fila, J., Capkov ˇ´a, V., Zdr´ahal, Z., Honys, D., 2016. Quantitative proteomics of the tobacco pollen tube secretome identifies novel pollen tube guidance proteins important for fertilization. Genome Biol. 17, 1 - 29. https: // doi. org / 10.1186 / s 13059 - 016 - 0928 - x." type="journal article" year="2016">Hafidh et al., 2016</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
<caption id="54F304EA2770536AA23CBAA0FE7080A1" ID-DOI="http://doi.org/10.5281/zenodo.8234555" ID-Zenodo-Dep="8234555" httpUri="https://zenodo.org/record/8234555/files/figure.png" pageId="4" pageNumber="5" startId="4.[100,130,1237,1254]" targetBox="[107,765,150,1208]" targetPageId="4" targetType="figure">
|
||
<paragraph id="003354622770536AA23CBAA0FE7080A1" blockId="4.[100,771,1237,1433]" pageId="4" pageNumber="5">
|
||
<emphasis id="32F888702770536AA23CBAA0FF7B81DE" bold="true" box="[100,162,1237,1254]" pageId="4" pageNumber="5">Fig. 3.</emphasis>
|
||
Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total
|
||
<emphasis id="32F888702770536AA0ABBB7DFF51800B" bold="true" italics="true" pageId="4" pageNumber="5">in vitro</emphasis>
|
||
secretome (IVS) and
|
||
<emphasis id="32F888702770536AA366BB57FE5D800A" bold="true" box="[318,388,1313,1331]" italics="true" pageId="4" pageNumber="5">in planta</emphasis>
|
||
secretome (IPS) and second (D) compared to the
|
||
<emphasis id="32F888702770536AA2D0BB4EFF1C8074" bold="true" box="[136,197,1339,1356]" italics="true" pageId="4" pageNumber="5">in vitro</emphasis>
|
||
suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome).
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="003354622770536AA23CBBB7FD6B80ED" blockId="4.[100,690,1473,1493]" box="[100,690,1473,1493]" pageId="4" pageNumber="5">
|
||
<heading id="5B7BE30E2770536AA23CBBB7FD6B80ED" bold="true" box="[100,690,1473,1493]" fontSize="36" level="1" pageId="4" pageNumber="5" reason="1">
|
||
<emphasis id="32F888702770536AA23CBBB7FD6B80ED" bold="true" box="[100,690,1473,1493]" italics="true" pageId="4" pageNumber="5">
|
||
2.4. Novel and known domains of the
|
||
<taxonomicName id="C78C2FE12770536AA39DBBB4FD8F80ED" box="[453,598,1473,1493]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="subSpecies" species="sativus" subSpecies="secretome">Lathyrus sativus</taxonomicName>
|
||
secretome
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph id="003354622770536AA2DCBB8FFA77875D" blockId="4.[100,770,1530,1967]" lastBlockId="4.[818,1488,148,1450]" pageId="4" pageNumber="5">
|
||
We conducted an in-depth analysis of the identified proteins, highlighting the presence of both known and novel domains in GSS (Supplementary Table S1; Supplementary
|
||
<figureCitation id="98B748E72770536AA39AB844FDD8837D" box="[450,513,1585,1605]" captionStart="Fig" captionStartId="3.[100,130,1091,1108]" captionTargetBox="[208,1380,149,1062]" captionTargetId="figure-541@3.[206,1381,148,1063]" captionTargetPageId="3" captionText="Fig. 2. Generation of grasspea calli, establishment of suspension culture and isolation of the grasspea suspension secretome (GSS). (A) Root-cut and shoot-cut embryo axes were employed for the generation of 4-week-old calli, which were bulked together in a suspension culture. (B) Microscopic examination of suspension cells and viability assessment using Evans blue (left panel) and FDA (right panel). (C) Quantitative analysis of physicochemical properties including changes in pH in the suspension culture, fresh weight (FW), dry weight (DW), soluble sugars and total protein. (D) Protein SDS-PAGE profile of the grasspea secretome. Lane 1 represents the molecular weight marker (MW). Purity evaluation of grasspea secreted fraction using (E) catalase activity and (F) western blotting with anti-RbcL (Supplementary Fig. S1). Relative catalase activities are presented as mean ± SE of triplicate experiments." figureDoi="http://doi.org/10.5281/zenodo.8234553" httpUri="https://zenodo.org/record/8234553/files/figure.png" pageId="4" pageNumber="5">Fig. S2</figureCitation>
|
||
). The 14-3-3 proteins (S33, S61) were identified in GSS, corroborating their indispensable presence in the plant secretome (
|
||
<bibRefCitation id="641D29932770536AA31EB81FFE3A8344" author="Wen, F. & VanEtten, H. D. & Tsaprailis, G. & Hawes, M. C." box="[326,483,1641,1661]" pageId="4" pageNumber="5" pagination="773 - 783" refId="ref17577" refString="Wen, F., VanEtten, H. D., Tsaprailis, G., Hawes, M. C., 2007. Extracellular proteins in pea root tip and border cell exudates. Plant Physiol. 143, 773 - 783. https: // doi. org / 10.1104 / pp. 106.091637." type="journal article" year="2007">Wen et al., 2007</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA3A8B81CFD428344" author="Gupta, S. & Wardhan, V. & Verma, S. & Gayali, S. & Rajamani, U. & Datta, A. & Chakraborty, S. & Chakraborty, N." box="[496,667,1641,1661]" pageId="4" pageNumber="5" pagination="5006 - 5015" refId="ref12065" refString="Gupta, S., Wardhan, V., Verma, S., Gayali, S., Rajamani, U., Datta, A., Chakraborty, S., Chakraborty, N., 2011. Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins. J. Proteome Res. 10, 5006 - 5015. https: // doi. org / 10.1021 / pr 200493 d." type="journal article" year="2011">Gupta et al., 2011</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA0F0B81CFF4D83A0" author="Liu, J. J. & Sturrock, R. N. & Sniezko, R. A. & Williams, H. & Benton, R. & Zamany, A." pageId="4" pageNumber="5" pagination="1 - 16" refId="ref13784" refString="Liu, J. J., Sturrock, R. N., Sniezko, R. A., Williams, H., Benton, R., Zamany, A., 2015. Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors. BMC Genom. 16, 1 - 16. https: // doi. org / 10.1186 / s 12864 - 015 - 1861 - 1." type="journal article" year="2015">Liu et al., 2015</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA2F8B8F0FEB883A0" author="Ves-Urai, P. & Krobthong, S. & Thongsuk, K. & Roytrakul, S. & Yokthongwattana, C." box="[160,353,1669,1688]" pageId="4" pageNumber="5" pagination="1 - 17" refId="ref17130" refString="Ves-Urai, P., Krobthong, S., Thongsuk, K., Roytrakul, S., Yokthongwattana, C., 2021. Comparative secretome analysis between salinity-tolerant and control Chlamydomonas reinhardtii strains. Planta 253, 1 - 17. https: // doi. org / 10.1007 / s 00425 - 021 - 03583 - 7." type="journal article" year="2021">Ves-Urai et al., 2021</bibRefCitation>
|
||
). Hydroxyacid dehydrogenases identified in GSS were previously reported to be a part of fungal (
|
||
<bibRefCitation id="641D29932770536AA028B8D4FF4D83E8" author="Severino, V. & Farina, A. & Fleischmann, F. & Dalio, R. J. & Di Maro, A. & Scognamiglio, M. & Fiorentino, A. & Parente, A. & Osswald, W. & Chambery, A." pageId="4" pageNumber="5" pagination="112317" refId="ref16145" refString="Severino, V., Farina, A., Fleischmann, F., Dalio, R. J., Di Maro, A., Scognamiglio, M., Fiorentino, A., Parente, A., Osswald, W., Chambery, A., 2014. Molecular profiling of the Phytophthora plurivora secretome: a step towards understanding the cross-talk between plant pathogenic oomycetes and their hosts. PLoS One 9, e 112317. https: // doi. org / 10.1371 / journal. pone. 0112317." type="journal article" year="2014">Severino et al., 2014</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA2F8B8C8FEE483E8" author="Fang, K. & Zhou, J. & Chen, L. & Li, Y. X. & Yang, A. L. & Dong, X. F. & Zhang, H. B." box="[160,317,1725,1744]" pageId="4" pageNumber="5" pagination="1009769" refId="ref11613" refString="Fang, K., Zhou, J., Chen, L., Li, Y. X., Yang, A. L., Dong, X. F., Zhang, H. B., 2021. Virulence and community dynamics of fungal species with vertical and horizontal transmission on a plant with multiple infections. PLoS Pathog. 17, e 1009769 https: // doi. org / 10.1371 / journal. ppat. 1009769." type="journal article" year="2021">Fang et al., 2021</bibRefCitation>
|
||
) and microbial secretomes (
|
||
<bibRefCitation id="641D29932770536AA01FB8C8FF4D83D4" author="Mastronunzio, J. E. & Huang, Y. & Benson, D. R." pageId="4" pageNumber="5" pagination="6721 - 6728" refId="ref14035" refString="Mastronunzio, J. E., Huang, Y., Benson, D. R., 2009. Diminished exoproteome of Frankia spp. in culture and symbiosis. Appl. Environ. Microbiol. 75, 6721 - 6728. https: // doi. org / 10.1128 / AEM. 01559 - 09." type="journal article" year="2009">Mastronunzio et al., 2009</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA2C7B8ACFE8983D4" author="Komeil, D. & Padilla-Reynaud, R. & Lerat, S. & Simao-Beaunoir, A. M. & Beaulieu, C." box="[159,336,1753,1772]" pageId="4" pageNumber="5" pagination="1 - 16" refId="ref12950" refString="Komeil, D., Padilla-Reynaud, R., Lerat, S., Simao-Beaunoir, A. M., Beaulieu, C., 2014. Comparative secretome analysis of Streptomyces scabiei during growth in the presence or absence of potato suberin. Proteome Sci. 12, 1 - 16. https: // doi. org / 10.1186 / 1477 - 5956 - 12 - 35." type="journal article" year="2014">Komeil et al., 2014</bibRefCitation>
|
||
). Eight AAA domain-containing proteins (S19, S171, S197, S360, S384, S542, S583, and S600) were identified in the GSS, like the secretomes of sunflower (
|
||
<bibRefCitation id="641D29932770536AA381B964FD57821C" author="Pinedo, M. & Regente, M. & Elizalde, M. & Quiroga, I., A & Pagnussat, L. & Jorrin-Novo, J. & Maldonado, A. & de la Canal, L." box="[473,654,1809,1828]" pageId="4" pageNumber="5" pagination="270 - 276" refId="ref14903" refString="Pinedo, M., Regente, M., Elizalde, M., Y Quiroga, I., A Pagnussat, L., Jorrin-Novo, J., Maldonado, A., de la Canal, L., 2012. Extracellular sunflower proteins: evidence on non-classical secretion of a jacalin-related lectin. Protein Pept. Lett. 19, 270 - 276. https: // doi. org / 10.2174 / 092986612799363163." type="journal article" year="2012">Pinedo et al., 2012</bibRefCitation>
|
||
) and model moss species (
|
||
<bibRefCitation id="641D29932770536AA2A9B959FE1C8207" author="Lehtonen, M. T. & Takikawa, Y. & Ronnholm, G. & Akita, M. & Kalkkinen, N. & Iivarinen, E. & Somervuo, P. & Varjosalo, M. & Valkonen, J. P." box="[241,453,1836,1856]" pageId="4" pageNumber="5" pagination="447 - 459" refId="ref13400" refString="Lehtonen, M. T., Takikawa, Y., Ronnholm, G., Akita, M., Kalkkinen, N., Ahola- Iivarinen, E., Somervuo, P., Varjosalo, M., Valkonen, J. P., 2014. Protein secretome of moss plants (Physcomitrella patens) with emphasis on changes induced by a fungal elicitor. J. Proteome Res. 13, 447 - 459. https: // doi. org / 10.1021 / pr 400827 a." type="journal article" year="2014">Lehtonen et al., 2014</bibRefCitation>
|
||
), and these are associated with ATPase-associated cellular activities. Abhydrolase domain-containing proteins comprised 2-hydroxyisoflavanone dehydratase, auxin response 4 and methylesterase 4, and these were observed to follow CPS and UPS. These proteins were previously reported to be a part of insect and fungal secretomes (
|
||
<bibRefCitation id="641D29932770536AA655BEE1FB66859F" author="Pandey, V. & Singh, M. & Pandey, D. & Marla, S. & Kumar, A." box="[1037,1215,148,167]" pageId="4" pageNumber="5" pagination="1700473" refId="ref14835" refString="Pandey, V., Singh, M., Pandey, D., Marla, S., Kumar, A., 2018. Secretome analysis identifies potential pathogenicity / virulence factors of Tilletia indica, a quarantined fungal pathogen inciting Karnal bunt disease in wheat. Proteomics 18, 1700473. https: // doi. org / 10.1002 / pmic. 201700473." type="journal article" year="2018">Pandey et al., 2018</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA692BEE1FA82859F" author="Zhu, J. & Zhu, K. & Li, L. & Li, Z. & Qin, W. & Park, Y. & He, Y." box="[1226,1371,148,167]" pageId="4" pageNumber="5" pagination="582" refId="ref18421" refString="Zhu, J., Zhu, K., Li, L., Li, Z., Qin, W., Park, Y., He, Y., 2020. Proteomics of the honeydew from the brown planthopper and green rice leafhopper reveal they are rich in proteins from insects, rice plant and bacteria. Insects 11, 582. https: // doi. org / 10.3390 / insects 11090582." type="journal article" year="2020">Zhu et al., 2020</bibRefCitation>
|
||
) and known to function in a UPS-dependent manner (
|
||
<bibRefCitation id="641D29932770536AA692BEC5FA1885FB" author="Garcia-Ceron, D. & Bleackley, M. R. & Anderson, M. A." box="[1226,1473,176,195]" pageId="4" pageNumber="5" pagination="151 - 177" refId="ref11850" refString="Garcia-Ceron, D., Bleackley, M. R., Anderson, M. A., 2021. Fungal extracellular vesicles in pathophysiology. Sub Cell. Biochem. 97, 151 - 177. https: // doi. org / 10.1007 / 978 - 3 - 030 - 67171 - 6." type="journal article" year="2021">Garcia-Ceron et al., 2021</bibRefCitation>
|
||
). Aminotransferases (
|
||
<bibRefCitation id="641D29932770536AA1A9BEBEFB7085E7" author="Cheng, F. Y. & Blackburn, K. & Lin, Y. M. & Goshe, M. B. & Williamson, J. D." box="[1009,1193,203,223]" pageId="4" pageNumber="5" pagination="82 - 93" refId="ref10805" refString="Cheng, F. Y., Blackburn, K., Lin, Y. M., Goshe, M. B., Williamson, J. D., 2009. Absolute protein quantification by LC / MSE for global analysis of salicylic acid-induced plant protein secretion responses. J. Proteome Res. 8, 82 - 93. https: // doi. org / 10.1021 / pr 800649 s." type="journal article" year="2009">Cheng et al., 2009</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA6E1BEB9FAB585E7" author="Wang, G. X. & Zhao, X. Y. & Meng, Z. X. & Kern, M. & Dietrich, A. & Chen, Z. & Cozacov, Z. & Zhou, D. & Okunade, A. L. & Su, X. & Li, S." box="[1209,1388,203,223]" pageId="4" pageNumber="5" pagination="1436 - 1443" refId="ref17302" refString="Wang, G. X., Zhao, X. Y., Meng, Z. X., Kern, M., Dietrich, A., Chen, Z., Cozacov, Z., Zhou, D., Okunade, A. L., Su, X., Li, S., 2014. The brown fat-enriched secreted factor Nrg 4 preserves metabolic homeostasis through attenuation of hepatic lipogenesis. Nat. Med. 20, 1436 - 1443. https: // doi. org / 10.1038 / nm. 3713." type="journal article" year="2014">Wang et al., 2014</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA724BEBEFC7A85C3" author="Williams, F. & Tew, H. A. & Paul, C. E. & Adams, J. C." pageId="4" pageNumber="5" pagination="60 - 68" refId="ref17636" refString="Williams, F., Tew, H. A., Paul, C. E., Adams, J. C., 2014. The predicted secretomes of Monosiga brevicollis and Capsaspora owczarzaki, close unicellular relatives of metazoans, reveal new insights into the evolution of the metazoan extracellular matrix. Matrix Biol. 37, 60 - 68. https: // doi. org / 10.1016 / j. matbio. 2014.02.002." type="journal article" year="2014">Williams et al., 2014</bibRefCitation>
|
||
) and ATP-synthase domain-containing proteins (
|
||
<bibRefCitation id="641D29932770536AA7D9BE92FC79842E" author="Agrawal, G. K. & Jwa, N. S. & Lebrun, M. H. & Job, D. & Rakwal, R." pageId="4" pageNumber="5" pagination="799 - 827" refId="ref9710" refString="Agrawal, G. K., Jwa, N. S., Lebrun, M. H., Job, D., Rakwal, R., 2010. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 10, 799 - 827. https: // doi. org / 10.1002 / pmic. 200900514." type="journal article" year="2010">Agrawal et al., 2010</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA1F5BF76FBBB842E" author="Espino, J. J. & Brito, N. & Shah, P. & Orlando, R." box="[941,1122,259,279]" pageId="4" pageNumber="5" pagination="3020 - 3034" refId="ref11485" refString="Espino, J. J., Guti´errez-S´anchez, G., Brito, N., Shah, P., Orlando, R., Gonz´alez, C., 2010. The Botrytis cinerea early secretome. Proteomics 10, 3020 - 3034. https: // doi. org / 10.1002 / pmic. 201000037." type="journal article" year="2010">Espino et al., 2010</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA628BF76FAF7842E" author="Vincent, D. & Rafiqi, M. & Job, D." box="[1136,1326,259,279]" pageId="4" pageNumber="5" pagination="1626" refId="ref17193" refString="Vincent, D., Rafiqi, M., Job, D., 2020. The multiple facets of plant-fungal interactions revealed through plant and fungal secretomics. Front. Plant Sci. 10, 1626. https: // doi. org / 10.3389 / fpls. 2019.01626." type="journal article" year="2020">Vincent et al., 2020</bibRefCitation>
|
||
) have long been known to be part of global eukaryotic secretomes. Further, the cysteine-rich secretory proteins (CAP superfamily) play crucial roles in biomolecular interactions in the extracellular space (
|
||
<bibRefCitation id="641D29932770536AA777BF22FC7C84BE" author="Schneiter, R. & Di Pietro, A." pageId="4" pageNumber="5" pagination="519 - 525" refId="ref16096" refString="Schneiter, R., Di Pietro, A., 2013. The CAP protein superfamily: function in sterol export and fungal virulence. Biomol. Concepts 4, 519 - 525. https: // doi. org / 10.1515 / bmc- 2013 - 0021." type="journal article" year="2013">Schneiter and Di Pietro, 2013</bibRefCitation>
|
||
), and four of these proteins were identified, including three PR-1s and a P14A. Copper oxidases (S305, S500, S555) are crucial components of eukaryotic secretomes, as they aid in conferring mechanical stiffness to the ECM (
|
||
<bibRefCitation id="641D29932770536AA605BFB2FAC684E2" author="Lum, G. & Min, X. J." box="[1117,1311,455,474]" pageId="4" pageNumber="5" pagination="114 - 119" refId="ref13933" refString="Lum, G., Min, X. J., 2011. Plant secretomes: current status and future perspectives. Plant Omics 4, 114 - 119." type="journal article" year="2011">Lum and Min, 2011</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA776BFB2FC7184CE" author="Ricard-Blum, S. & Vallet, S. D." pageId="4" pageNumber="5" pagination="170 - 189" refId="ref15630" refString="Ricard-Blum, S., Vallet, S. D., 2019. Fragments generated upon extracellular matrix remodeling: biological regulators and potential drugs. Matrix Biol. 75, 170 - 189. https: // doi. org / 10.1016 / j. matbio. 2017.11.005." type="journal article" year="2019">Ricard-Blum and Vallet, 2019</bibRefCitation>
|
||
). Interestingly, cupin superfamily proteins were particularly abundant (30 proteins) in the GSS, in accordance with previous plant secretome reports. Cupins are relevant in the ECM and/or secretome owing to their functions in the modification of mannose and rhamnose residues in higher plant cell walls (
|
||
<bibRefCitation id="641D29932770536AA6B8BC27FA79875D" author="Dunwell, J. M. & Culham, A. & Carter, C. E. & Sosa-Aguirre, C. R. & Goodenough, P. W." box="[1248,1440,594,613]" pageId="4" pageNumber="5" pagination="740 - 746" refId="ref11219" refString="Dunwell, J. M., Culham, A., Carter, C. E., Sosa-Aguirre, C. R., Goodenough, P. W., 2001. Evolution of functional diversity in the cupin superfamily. Trends Biochem. Sci. 26, 740 - 746. https: // doi. org / 10.1016 / S 0968 - 0004 (01) 01981 - 8." type="journal article" year="2001">Dunwell et al., 2001</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph id="003354622770536AA109BC1BFC2B8092" blockId="4.[818,1488,148,1450]" pageId="4" pageNumber="5">
|
||
DEAD-box helicases (S198, S446, S618) were identified in GSS despite their nucleus-specific functions. Interestingly, these proteins have also previously reported in insect (
|
||
<bibRefCitation id="641D29932770536AA6F2BCD3FA848781" author="Etebari, K. & Lindsay, K. R. & Ward, A. L. & Furlong, M. J." box="[1194,1373,678,697]" pageId="4" pageNumber="5" pagination="708 - 720" refId="ref11545" refString="Etebari, K., Lindsay, K. R., Ward, A. L., Furlong, M. J., 2020. Australian sugarcane soldier fly' s salivary gland transcriptome in response to starvation and feeding on sugarcane crops. Insect Sci. 27, 708 - 720. https: // doi. org / 10.1111 / 1744 - 7917.12676." type="journal article" year="2020">Etebari et al., 2020</bibRefCitation>
|
||
) and fungal secretomes (
|
||
<bibRefCitation id="641D29932770536AA1ECBCB7FBB387EC" author="Liu, J. J. & Sturrock, R. N. & Sniezko, R. A. & Williams, H. & Benton, R. & Zamany, A." box="[948,1130,705,725]" pageId="4" pageNumber="5" pagination="1 - 16" refId="ref13784" refString="Liu, J. J., Sturrock, R. N., Sniezko, R. A., Williams, H., Benton, R., Zamany, A., 2015. Transcriptome analysis of the white pine blister rust pathogen Cronartium ribicola: de novo assembly, expression profiling, and identification of candidate effectors. BMC Genom. 16, 1 - 16. https: // doi. org / 10.1186 / s 12864 - 015 - 1861 - 1." type="journal article" year="2015">Liu et al., 2015</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA6DBBCB7FAB887ED" author="Dussert, Y. & Mazet, I. D. & Couture, C. & Gouzy, J. & Piron, M. C. & Kuchly, C. & Bouchez, O. & Rispe, C. & Mestre, P. & Delmotte, F." box="[1155,1377,706,725]" pageId="4" pageNumber="5" pagination="954 - 969" refId="ref11294" refString="Dussert, Y., Mazet, I. D., Couture, C., Gouzy, J., Piron, M. C., Kuchly, C., Bouchez, O., Rispe, C., Mestre, P., Delmotte, F., 2019. A high-quality grapevine downy mildew genome assembly reveals rapidly evolving and lineage-specific putative host adaptation genes. Genome Biol. Evol. 11, 954 - 969. https: // doi. org / 10.1093 / gbe / evz 048." type="journal article" year="2019">Dussert et al., 2019</bibRefCitation>
|
||
). Dirigent domain-containing proteins (S211, S294, S391) indicated their function as abiotic (
|
||
<bibRefCitation id="641D29932770536AA1F0BC8CFBF28634" author="Ngcala, M. G." box="[936,1067,761,780]" pageId="4" pageNumber="5" refId="ref14539" refString="Ngcala, M. G., 2018. Molecular responses of sorghum cell suspension cultures to high temperature stress. QwaQwa: University of the Free State. http: // hdl. handle. net / 11 660 / 10130." type="url" year="2018">Ngcala, 2018</bibRefCitation>
|
||
) and biotic stress-responsive constituents (
|
||
<bibRefCitation id="641D29932770536AA162BD63FC248610" author="Regente, M. & Pinedo, M. & San Clemente, H. & Balliau, T. & Jamet, E. & De La Canal, L." box="[826,1021,789,809]" pageId="4" pageNumber="5" pagination="5485 - 5495" refId="ref15555" refString="Regente, M., Pinedo, M., San Clemente, H., Balliau, T., Jamet, E., De La Canal, L., 2017. Plant extracellular vesicles are incorporated by a fungal pathogen and inhibit its growth. J. Exp. Bot. 68, 5485 - 5495. https: // doi. org / 10.1093 / jxb / erx 355." type="journal article" year="2017">Regente et al., 2017</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA653BD60FB1F8610" author="Haseeb, H. A. & Zhang, J. & Guo, Y. & Gao, M. & Wei, G." box="[1035,1222,789,809]" pageId="4" pageNumber="5" pagination="446 - 459" refId="ref12382" refString="Haseeb, H. A., Zhang, J., Guo, Y., Gao, M., Wei, G., 2021. Proteomic analysis of pathogenresponsive proteins from maize stem apoplast triggered by Fusarium verticillioides. J. Integr. Agric. 21, 446 - 459. https: // doi. org / 10.1016 / S 2095 - 3119 (21) 63657 - 2." type="journal article" year="2021">Haseeb et al., 2021</bibRefCitation>
|
||
) of the extracellular space. Proteins harboring domains of unknown function (DUF1604, DUF296, DUF677, DUF4378, DUF825, DUF295, DUF825, DUF1744, DUF1298, DUF588) appeared to be predominant constituents of the grasspea secretome (Supplementary Table S1). Among these, DUF296 was previously reported to be differentially regulated in the cell wall of wheat endosperm (
|
||
<bibRefCitation id="641D29932770536AA1F2BDC8FBB886E8" author="Mehdi, C. & Virginie, L. & Audrey, G. & Axelle, B. & Colette, L. & Elisabeth, J. & Fabienne, G. & Mathilde, F. A." box="[938,1121,957,976]" pageId="4" pageNumber="5" pagination="239" refId="ref14219" refString="Mehdi, C., Virginie, L., Audrey, G., Axelle, B., Colette, L., H´el`ene, R., Elisabeth, J., Fabienne, G., Mathilde, F. A., 2020. Cell wall proteome of wheat grain endosperm and outer layers at two key stages of early development. Int. J. Mol. Sci. 21, 239. https: // doi. org / 10.3390 / ijms 21010239." type="journal article" year="2020">Mehdi et al., 2020</bibRefCitation>
|
||
). Hsps have now been recognized as ‘moonlighting proteins’ in the extracellular space, especially Hsp70 and Hsp90, which are mostly secreted through the UPS (
|
||
<bibRefCitation id="641D29932770536AA766BD81FCBB811C" author="Agrawal, G. K. & Jwa, N. S. & Lebrun, M. H. & Job, D. & Rakwal, R." pageId="4" pageNumber="5" pagination="799 - 827" refId="ref9710" refString="Agrawal, G. K., Jwa, N. S., Lebrun, M. H., Job, D., Rakwal, R., 2010. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 10, 799 - 827. https: // doi. org / 10.1002 / pmic. 200900514." type="journal article" year="2010">Agrawal et al., 2010</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA136BA65FBDD811C" author="Rabouille, C." box="[878,1028,1040,1060]" pageId="4" pageNumber="5" pagination="230 - 240" refId="ref15047" refString="Rabouille, C., 2017. Pathways of unconventional protein secretion. Trends Cell Biol. 27, 230 - 240. https: // doi. org / 10.1016 / j. tcb. 2016.11.007." type="journal article" year="2017">Rabouille, 2017</bibRefCitation>
|
||
). GDSL lipases have previously been reported in
|
||
<taxonomicName id="C78C2FE12770536AA16ABA59FC5E8107" box="[818,903,1068,1087]" class="Magnoliopsida" family="Fabaceae" genus="Medicago" kingdom="Plantae" order="Fabales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="32F888702770536AA16ABA59FC5E8107" bold="true" box="[818,903,1068,1087]" italics="true" pageId="4" pageNumber="5">Medicago</emphasis>
|
||
</taxonomicName>
|
||
and
|
||
<taxonomicName id="C78C2FE12770536AA1EABA59FBC08107" box="[946,1049,1068,1087]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="genus">
|
||
<emphasis id="32F888702770536AA1EABA59FBC08107" bold="true" box="[946,1049,1068,1087]" italics="true" pageId="4" pageNumber="5">Arabidopsis</emphasis>
|
||
</taxonomicName>
|
||
secretomes (
|
||
<bibRefCitation id="641D29932770536AA6CABA59FAC08107" author="Oh, I. S. & Park, A. R. & Bae, M. S. & Kwon, S. J. & Kim, Y. S. & Lee, J. E. & Kang, N. Y. & Lee, S. & Cheong, H. & Park, O. K." box="[1170,1305,1068,1088]" pageId="4" pageNumber="5" pagination="2832 - 2847" refId="ref14733" refString="Oh, I. S., Park, A. R., Bae, M. S., Kwon, S. J., Kim, Y. S., Lee, J. E., Kang, N. Y., Lee, S., Cheong, H., Park, O. K., 2005. Secretome analysis reveals an Arabidopsis lipase involved in defense against Alternaria brassicicola. Plant Cell 17, 2832 - 2847. https: // doi. org / 10.1105 / tpc. 105.034819." type="journal article" year="2005">Oh et al., 2005</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA77BBA59FCBB8163" author="Kusumawati, L. & Imin, N. & Djordjevic, M. A." pageId="4" pageNumber="5" pagination="4508 - 4520" refId="ref13082" refString="Kusumawati, L., Imin, N., Djordjevic, M. A., 2008. Characterization of the secretome of suspension cultures of Medicago species reveals proteins important for defense and development. J. Proteome Res. 7, 4508 - 4520. https: // doi. org / 10.1021 / pr 800291 z." type="journal article" year="2008">Kusumawati et al., 2008</bibRefCitation>
|
||
), and noticeably, lipases were also identified in the GSS. Similarly, maturase K (7 GSS proteins) has been reported in the extracellular space of pitcher plant (
|
||
<bibRefCitation id="641D29932770536AA18ABAF5FB5381AB" author="Zakaria, W. N. A. W. & Aizat, W. M. & Goh, H. H. & Noor, N. M." box="[978,1162,1152,1171]" pageId="4" pageNumber="5" pagination="681 - 694" refId="ref18148" refString="Zakaria, W. N. A. W., Aizat, W. M., Goh, H. H., Noor, N. M., 2019. Protein replenishment in pitcher fluids of Nepenthes x ventrata revealed by quantitative proteomics (SWATH- MS) informed by transcriptomics. J. Plant Res. 132, 681 - 694. https: // doi. org / 10.1007 / s 10265 - 019 - 01130 - w." type="journal article" year="2019">Zakaria et al., 2019</bibRefCitation>
|
||
), sea buckthorn (
|
||
<bibRefCitation id="641D29932770536AA769BAF5FC768197" author="Sougrakpam, Y. & Deswal, R." pageId="4" pageNumber="5" pagination="473 - 484" refId="ref16456" refString="Sougrakpam, Y., Deswal, R., 2016. Hippophae rhamnoides N-glycoproteome analysis: a small step towards sea buckthorn proteome mining. Physiol. Mol. Biol. Plants 22, 473 - 484. https: // doi. org / 10.1007 / s 12298 - 016 - 0390 - y." type="journal article" year="2016">Sougrakpam and Deswal, 2016</bibRefCitation>
|
||
), sunflower (
|
||
<bibRefCitation id="641D29932770536AA672BAE9FB0E8197" author="Pinedo, M. & Regente, M. & Elizalde, M. & Quiroga, I., A & Pagnussat, L. & Jorrin-Novo, J. & Maldonado, A. & de la Canal, L." box="[1066,1239,1180,1199]" pageId="4" pageNumber="5" pagination="270 - 276" refId="ref14903" refString="Pinedo, M., Regente, M., Elizalde, M., Y Quiroga, I., A Pagnussat, L., Jorrin-Novo, J., Maldonado, A., de la Canal, L., 2012. Extracellular sunflower proteins: evidence on non-classical secretion of a jacalin-related lectin. Protein Pept. Lett. 19, 270 - 276. https: // doi. org / 10.2174 / 092986612799363163." type="journal article" year="2012">Pinedo et al., 2012</bibRefCitation>
|
||
) and tobacco (
|
||
<bibRefCitation id="641D29932770536AA707BAE9FCBB81F3" author="Millar, D. J. & Whitelegge, J. P. & Bindschedler, L. V. & Rayon, C. & Boudet, A. M. & Rossignol, M. & Borderies, G. & Bolwell, G. P." pageId="4" pageNumber="5" pagination="2355 - 2372" refId="ref14310" refString="Millar, D. J., Whitelegge, J. P., Bindschedler, L. V., Rayon, C., Boudet, A. M., Rossignol, M., Borderies, G., Bolwell, G. P., 2009. The cell wall and secretory proteome of a tobacco cell line synthesising secondary wall. Proteomics 9, 2355 - 2372. https: // doi. org / 10.1002 / pmic. 200800721." type="journal article" year="2009">Millar et al., 2009</bibRefCitation>
|
||
). Also, p450 (11), peroxidases (17), protein kinase (24), pentatricopeptide repeat (PPR) domain-containing proteins (14), thaumatin (4), thioredoxin (4), U-box (5) and WD40 (7) were abundantly represented in the GSS, in accordance with previous reports on the plant secretome (
|
||
<bibRefCitation id="641D29932770536AA1C5BB52FB8E8002" author="Agrawal, G. K. & Jwa, N. S. & Lebrun, M. H. & Job, D. & Rakwal, R." box="[925,1111,1319,1339]" pageId="4" pageNumber="5" pagination="799 - 827" refId="ref9710" refString="Agrawal, G. K., Jwa, N. S., Lebrun, M. H., Job, D., Rakwal, R., 2010. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 10, 799 - 827. https: // doi. org / 10.1002 / pmic. 200900514." type="journal article" year="2010">Agrawal et al., 2010</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA63ABB52FAC38002" author="Shinano, T. & Komatsu, S. & Yoshimura, T. & Tokutake, S. & Kong, F. J. & Watanabe, T. & Wasaki, J. & Osaki, M." box="[1122,1306,1319,1339]" pageId="4" pageNumber="5" pagination="312 - 320" refId="ref16303" refString="Shinano, T., Komatsu, S., Yoshimura, T., Tokutake, S., Kong, F. J., Watanabe, T., Wasaki, J., Osaki, M., 2011. Proteomic analysis of secreted proteins from aseptically grown rice. Phytochemistry 72, 312 - 320. https: // doi. org / 10.1016 / j. phytochem. 2010.12.006." type="journal article" year="2011">Shinano et al., 2011</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA77CBB52FA108002" author="Gupta, S. & Wardhan, V. & Verma, S. & Gayali, S. & Rajamani, U. & Datta, A. & Chakraborty, S. & Chakraborty, N." box="[1316,1481,1319,1339]" pageId="4" pageNumber="5" pagination="5006 - 5015" refId="ref12065" refString="Gupta, S., Wardhan, V., Verma, S., Gayali, S., Rajamani, U., Datta, A., Chakraborty, S., Chakraborty, N., 2011. Characterization of the secretome of chickpea suspension culture reveals pathway abundance and the expected and unexpected secreted proteins. J. Proteome Res. 10, 5006 - 5015. https: // doi. org / 10.1021 / pr 200493 d." type="journal article" year="2011">Gupta et al., 2011</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA16ABB31FC31806E" author="Krause, C. & Richter, S. & Jurgens, G." box="[818,1000,1347,1367]" pageId="4" pageNumber="5" pagination="2429 - 2441" refId="ref13022" refString="Krause, C., Richter, S., Knoll ¨, C., Jurgens, G., 2013. Plant secretome-from cellular process to biological activity. Biochim. Biophys. Acta, Proteins Proteomics 1834, 2429 - 2441. https: // doi. org / 10.1016 / j. bbapap. 2013.03.024." type="journal article" year="2013">Krause et al., 2013</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA1ADBB31FB4C806E" author="Lum, G. & Meinken, J. & Orr, J. & Frazier, S. & Min, X. J." box="[1013,1173,1347,1367]" pageId="4" pageNumber="5" refId="ref13874" refString="Lum, G., Meinken, J., Orr, J., Frazier, S., Min, X. J., 2014. PlantSecKB: the plant secretome and subcellular proteome knowledgebase. Comput. Mol. Biol. 4 https: // doi. org / 10.5376 / CMB. 2014.04.0001." type="book" year="2014">Lum et al., 2014</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA6FABB36FAF3806E" author="Li, W. & Ahn, I. P. & Ning, Y. & Park, C. H. & Zeng, L. & Whitehill, J. G. & Lu, H. & Zhao, Q. & Ding, B. & Xie, Q. & Zhou, J. M." box="[1186,1322,1347,1367]" pageId="4" pageNumber="5" pagination="239 - 250" refId="ref13495" refString="Li, W., Ahn, I. P., Ning, Y., Park, C. H., Zeng, L., Whitehill, J. G., Lu, H., Zhao, Q., Ding, B., Xie, Q., Zhou, J. M., 2012. The U-Box / ARM E 3 ligase PUB 13 regulates cell death, defense, and flowering time in Arabidopsis. Plant Physiol. 159, 239 - 250. https: // doi. org / 10.1104 / pp. 111.192617." type="journal article" year="2012">Li et al., 2012</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA760BB36FA10806E" author="Ali, A. & Alexandersson, E. & Sandin, M. & Lenman, M. & Hedley, P. & Levander, F. & Andreasson, E." box="[1336,1481,1347,1367]" pageId="4" pageNumber="5" pagination="1 - 18" refId="ref9823" refString="Ali, A., Alexandersson, E., Sandin, M., Resj ¨ o, S., Lenman, M., Hedley, P., Levander, F., Andreasson, E., 2014. Quantitative proteomics and transcriptomics of potato in response to Phytophthora infestans in compatible and incompatible interactions. BMC Genom. 15, 1 - 18. https: // doi. org / 10.1186 / 1471 - 2164 - 15 - 497." type="journal article" year="2014">Ali et al., 2014</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932770536AA16ABB2AFC26804A" author="Ves-Urai, P. & Krobthong, S. & Thongsuk, K. & Roytrakul, S. & Yokthongwattana, C." box="[818,1023,1375,1395]" pageId="4" pageNumber="5" pagination="1 - 17" refId="ref17130" refString="Ves-Urai, P., Krobthong, S., Thongsuk, K., Roytrakul, S., Yokthongwattana, C., 2021. Comparative secretome analysis between salinity-tolerant and control Chlamydomonas reinhardtii strains. Planta 253, 1 - 17. https: // doi. org / 10.1007 / s 00425 - 021 - 03583 - 7." type="journal article" year="2021">Ves-Urai et al., 2021</bibRefCitation>
|
||
). GSS-resident BET domain-containing proteins (S304, S489) have previously been observed in the chickpea secretome (
|
||
<bibRefCitation id="641D29932770536AA162BBE2FC3D8092" author="Gupta, S. & Wardhan, V. & Kumar, A. & Rathi, D. & Pandey, A. & Chakraborty, S. & Chakraborty, N." box="[826,996,1431,1450]" pageId="4" pageNumber="5" pagination="1 - 14" refId="ref11980" refString="Gupta, S., Wardhan, V., Kumar, A., Rathi, D., Pandey, A., Chakraborty, S., Chakraborty, N., 2015. Secretome analysis of chickpea reveals dynamic extracellular remodeling and identifies a Bet v 1 - like protein, CaRRP 1 that participates in stress response. Sci. Rep. 5, 1 - 14. https: // doi. org / 10.1038 / srep 18427." type="journal article" year="2015">Gupta et al., 2015</bibRefCitation>
|
||
).
|
||
</paragraph>
|
||
<paragraph id="003354622770536AA16ABBA5FB7880DB" blockId="4.[818,1185,1488,1507]" box="[818,1185,1488,1507]" pageId="4" pageNumber="5">
|
||
<heading id="5B7BE30E2770536AA16ABBA5FB7880DB" bold="true" box="[818,1185,1488,1507]" fontSize="36" level="1" pageId="4" pageNumber="5" reason="1">
|
||
<emphasis id="32F888702770536AA16ABBA5FB7880DB" bold="true" box="[818,1185,1488,1507]" italics="true" pageId="4" pageNumber="5">
|
||
2.5. Distinct and shared features of
|
||
<collectionCode id="669DCCA72770536AA624BBA5FB7880DB" box="[1148,1185,1488,1507]" pageId="4" pageNumber="5">GSS</collectionCode>
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph id="003354622770536BA109B87DFF7D840A" blockId="4.[818,1488,1544,1982]" lastBlockId="5.[100,770,148,1450]" lastPageId="5" lastPageNumber="6" pageId="4" pageNumber="5">
|
||
Prior to this report, several research groups have identified proteins secreted from crop and model species using
|
||
<emphasis id="32F888702770536AA6AEB851FAE2830F" bold="true" box="[1270,1339,1572,1591]" italics="true" pageId="4" pageNumber="5">in vitro</emphasis>
|
||
setup of SCCs (Supplementary Table
|
||
<collectionCode id="669DCCA72770536AA654B835FBC1836B" box="[1036,1048,1600,1619]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="4" pageNumber="5" type="Herbarium">S</collectionCode>
|
||
2). We manually curated a database of the
|
||
<emphasis id="32F888702770536AA7E6B835FC828357" bold="true" italics="true" pageId="4" pageNumber="5">in vitro</emphasis>
|
||
secretome of plants and obtained a set of 5410 sequences. These in turn yielded a set of 3276 nonredundant sequences, which were employed for further downstream comparisons.
|
||
<taxonomicName id="C78C2FE12770536AA6AEB8E1FA90839F" box="[1270,1353,1684,1703]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="species" species="sativus">
|
||
<emphasis id="32F888702770536AA6AEB8E1FA90839F" bold="true" box="[1270,1353,1684,1703]" italics="true" pageId="4" pageNumber="5">L. sativus</emphasis>
|
||
</taxonomicName>
|
||
shared ~23% of the sequences with previous reports (
|
||
<figureCitation id="98B748E72770536AA6E9B8DAFB2283FB" box="[1201,1275,1711,1731]" captionStart="Fig" captionStartId="4.[100,130,1237,1254]" captionTargetBox="[107,765,150,1208]" captionTargetId="figure-928@4.[106,767,148,1210]" captionTargetPageId="4" captionText="Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234555" httpUri="https://zenodo.org/record/8234555/files/figure.png" pageId="4" pageNumber="5">Fig. 3D</figureCitation>
|
||
). The unique grasspea secretome sequences were subsequently queried for
|
||
<collectionCode id="669DCCA72770536AA713B8B9FA5B83E7" box="[1355,1410,1740,1759]" pageId="4" pageNumber="5">KEGG</collectionCode>
|
||
(Kyoto Encyclopedia of Genes and Genomes) pathway analysis, which revealed 23 signal transduction pathways, 7 of which were specific to phytohormone signaling.
|
||
<collectionCode id="669DCCA72770536AA1B7B96AFC24820A" box="[1007,1021,1823,1842]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="4" pageNumber="5" type="Herbarium">A</collectionCode>
|
||
species-specific comparison of grasspea was performed with
|
||
<taxonomicName id="C78C2FE12770536AA1E3B94EFBF08276" box="[955,1065,1851,1870]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="4" pageNumber="5" phylum="Tracheophyta" rank="genus">Arabidopsis</taxonomicName>
|
||
(326 proteins), chickpea (462 proteins), sorghum (287 proteins) and rice (315 proteins) (Supplementary
|
||
<figureCitation id="98B748E72770536AA7D2B922FA108252" box="[1418,1481,1879,1898]" captionStart="Fig" captionStartId="4.[100,130,1237,1254]" captionTargetBox="[107,765,150,1208]" captionTargetId="figure-928@4.[106,767,148,1210]" captionTargetPageId="4" captionText="Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234555" httpUri="https://zenodo.org/record/8234555/files/figure.png" pageId="4" pageNumber="5">Fig. S3</figureCitation>
|
||
; grouped from reports in Supplementary Tables
|
||
<collectionCode id="669DCCA72770536AA6ABB906FB2782BE" box="[1267,1278,1907,1926]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="4" pageNumber="5" type="Herbarium">S</collectionCode>
|
||
2
|
||
<collectionCode id="669DCCA72770536AA750B906FAC182BE" box="[1288,1304,1907,1926]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="4" pageNumber="5" type="Herbarium">A</collectionCode>
|
||
and
|
||
<collectionCode id="669DCCA72770536AA711B906FA8D82BE" box="[1353,1364,1907,1926]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="4" pageNumber="5" type="Herbarium">S</collectionCode>
|
||
2
|
||
<collectionCode id="669DCCA72770536AA707B906FAB482BE" box="[1375,1389,1907,1926]" country="Germany" lsid="urn:lsid:biocol.org:col:15534" name="Botanischer Garten und Botanisches Museum Berlin-Dahlem, Zentraleinrichtung der Freien Universitaet" pageId="4" pageNumber="5" type="Herbarium">B</collectionCode>
|
||
; sequence IDs provided in Supplementary Table
|
||
<collectionCode id="669DCCA72770536AA6C4B9FAFB7E829A" box="[1180,1191,1935,1954]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="4" pageNumber="5" type="Herbarium">S</collectionCode>
|
||
3
|
||
<collectionCode id="669DCCA72770536AA6E9B9FAFB1B829A" box="[1201,1218,1935,1954]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="4" pageNumber="5" type="Herbarium">A</collectionCode>
|
||
). Chickpea, being a leguminous crop, shared the maximum similarity with grasspea (72), highlighting the evolutionary conserved patterns of gene expression in plant families. However, chickpea and grasspea shared a miniscule number of secreted proteins with other plant families. Unique sequences reported for
|
||
<taxonomicName id="C78C2FE12771536BA282BE92FE9185C2" box="[218,328,231,250]" class="Magnoliopsida" family="Brassicaceae" genus="Arabidopsis" kingdom="Plantae" order="Brassicales" pageId="5" pageNumber="6" phylum="Tracheophyta" rank="genus">Arabidopsis</taxonomicName>
|
||
(174), chickpea (294), sorghum (152) and rice (176), highlight the significance of crop-specific organelle proteomes of plants.
|
||
</paragraph>
|
||
<paragraph id="003354622771536BA2DCBF4EFE5B87B9" blockId="5.[100,770,148,1450]" pageId="5" pageNumber="6">
|
||
Next, we performed systematic analysis of
|
||
<collectionCode id="669DCCA72771536BA002BF4EFDA68476" box="[602,639,315,334]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
constituents compared to those of dicots, monocots, and lower plants (
|
||
<figureCitation id="98B748E72771536BA0EBBF22FD278452" box="[691,766,343,362]" captionStart="Fig" captionStartId="4.[100,130,1237,1254]" captionTargetBox="[107,765,150,1208]" captionTargetId="figure-928@4.[106,767,148,1210]" captionTargetPageId="4" captionText="Fig. 3. Overview of total grasspea suspension secreted (GSS) proteins and prediction of mode of secretion and (A) localization using multiple tools (B). Comparison of shared and distinct GSS proteins, first (C) with respect to total in vitro secretome (IVS) and in planta secretome (IPS) and second (D) compared to the in vitro suspension culture secretome reported in monocots, dicots, and lower plants, abbreviated as MSS, DSS and LSS, respectively (MSS corresponds to monocot suspension secretome, DSS to dicot suspension secretome and LSS to lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234555" httpUri="https://zenodo.org/record/8234555/files/figure.png" pageId="5" pageNumber="6">Fig. 3D</figureCitation>
|
||
; grouped from reports in Supplementary Table
|
||
<collectionCode id="669DCCA72771536BA048BF06FDC584BE" box="[528,540,371,390]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="5" pageNumber="6" type="Herbarium">S</collectionCode>
|
||
2; sequence IDs provided in Supplementary Table
|
||
<collectionCode id="669DCCA72771536BA315BFFAFE81849A" box="[333,344,399,418]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="5" pageNumber="6" type="Herbarium">S</collectionCode>
|
||
3
|
||
<collectionCode id="669DCCA72771536BA33ABFFAFEAA849A" box="[354,371,399,418]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="5" pageNumber="6" type="Herbarium">A</collectionCode>
|
||
). As expected,
|
||
<collectionCode id="669DCCA72771536BA05DBFFAFDF3849A" box="[517,554,399,418]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
shared maximum proteins with dicots (41), followed by monocots (29) and nonvascular plants (17). The 39 proteins shared by all 4 plant groups included GAPDH, dihydrolipoyl dehydrogenase 1, peroxidase 72, cysteine proteinase RD21
|
||
<collectionCode id="669DCCA72771536BA2BFBF8BFF218729" box="[231,248,510,529]" country="USA" lsid="urn:lsid:biocol.org:col:15406" name="Harvard University - Arnold Arboretum" pageId="5" pageNumber="6" type="Herbarium">A</collectionCode>
|
||
, 5-methyltetrahydropteroyltriglutamate homocysteine methyltransferase 1, pectinesterase/pectinesterase inhibitor 18 and glucan endo-1,3-beta-glucosidase, among others. Grasspea exhibited a unique set of sequences (561), establishing it as a suitable model system to investigate legume biology.
|
||
</paragraph>
|
||
<paragraph id="003354622771536BA2DCBCFFFDB88092" blockId="5.[100,770,148,1450]" pageId="5" pageNumber="6">
|
||
The examination of
|
||
<collectionCode id="669DCCA72771536BA30DBCFFFEA387A5" box="[341,378,650,669]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
revealed marked similarity to that of nonvascular plants, monocots, and dicots in the context of physicochemical properties. The isoelectric points of the secreted proteins exhibited an extremely broad range, from 3.5 to 11.5 (
|
||
<figureCitation id="98B748E72771536BA02EBCA8FD6687C9" box="[630,703,733,753]" captionStart="Fig" captionStartId="5.[818,848,1362,1379]" captionTargetBox="[824,1481,150,1334]" captionTargetId="figure-811@5.[823,1483,148,1335]" captionTargetPageId="5" captionText="Fig. 4. Physicochemical assessment of the grasspea suspension secretome (GSS), including pI (A), molecular weight (in kDa) (B), and hydrophilicity (C), with respect to MSS, DSS and LSS (MSS corresponds to the monocot suspension secretome, DSS to the dicot suspension secretome and LSS to the lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234557" httpUri="https://zenodo.org/record/8234557/files/figure.png" pageId="5" pageNumber="6">Fig. 4A</figureCitation>
|
||
). Similarly, the molecular weights of
|
||
<collectionCode id="669DCCA72771536BA3C9BC8CFE6F8634" box="[401,438,761,780]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
constituents were as low as 1 kDa and as high as 500 kDa (
|
||
<figureCitation id="98B748E72771536BA30ABD60FE418610" box="[338,408,789,808]" captionStart="Fig" captionStartId="5.[818,848,1362,1379]" captionTargetBox="[824,1481,150,1334]" captionTargetId="figure-811@5.[823,1483,148,1335]" captionTargetPageId="5" captionText="Fig. 4. Physicochemical assessment of the grasspea suspension secretome (GSS), including pI (A), molecular weight (in kDa) (B), and hydrophilicity (C), with respect to MSS, DSS and LSS (MSS corresponds to the monocot suspension secretome, DSS to the dicot suspension secretome and LSS to the lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234557" httpUri="https://zenodo.org/record/8234557/files/figure.png" pageId="5" pageNumber="6">Fig. 4B</figureCitation>
|
||
). Moreover,
|
||
<collectionCode id="669DCCA72771536BA049BD60FDEF8610" box="[529,566,789,808]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
proteins were mildly hydrophobic overall, ranging from 1.25 to 0.75 (
|
||
<figureCitation id="98B748E72771536BA01EBD44FD54867C" box="[582,653,817,836]" captionStart="Fig" captionStartId="5.[818,848,1362,1379]" captionTargetBox="[824,1481,150,1334]" captionTargetId="figure-811@5.[823,1483,148,1335]" captionTargetPageId="5" captionText="Fig. 4. Physicochemical assessment of the grasspea suspension secretome (GSS), including pI (A), molecular weight (in kDa) (B), and hydrophilicity (C), with respect to MSS, DSS and LSS (MSS corresponds to the monocot suspension secretome, DSS to the dicot suspension secretome and LSS to the lower plant suspension secretome)." figureDoi="http://doi.org/10.5281/zenodo.8234557" httpUri="https://zenodo.org/record/8234557/files/figure.png" pageId="5" pageNumber="6">Fig. 4C</figureCitation>
|
||
). The physicochemical properties of
|
||
<collectionCode id="669DCCA72771536BA314BD38FEA88658" box="[332,369,845,864]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
proteins are generally indicative of a broad functional range of secretomes. The secretome biomarkers are family specific, as exemplified by the unique proteins identified using
|
||
<collectionCode id="669DCCA72771536BA0E5BDF0FD0486A0" box="[701,733,901,920]" pageId="5" pageNumber="6">IVS</collectionCode>
|
||
approaches of monocots, dicots and nonvascular plants. While the characteristically low isoelectric points of
|
||
<collectionCode id="669DCCA72771536BA394BDC8FE2886E8" box="[460,497,957,976]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
proteins might be related to their easy secretion into the extracellular space (
|
||
<bibRefCitation id="641D29932771536BA077BDACFD0986D4" author="Byun, H. & Park, J. & Kim, S. C. & Ahn, J. H." box="[559,720,985,1004]" pageId="5" pageNumber="6" pagination="19782 - 19791" refId="ref10351" refString="Byun, H., Park, J., Kim, S. C., Ahn, J. H., 2017. A lower isoelectric point increases signal sequence-mediated secretion of recombinant proteins through a bacterial ABC transporter. J. Biol. Chem. 292, 19782 - 19791. https: // doi. org / 10.1074 / jbc. M 117.786749." type="journal article" year="2017">Byun et al., 2017</bibRefCitation>
|
||
), the higher isoelectric points might contribute to a specific functional advantage for the plant secretome. Notably, the neutral to slightly alkaline pI proteins (7–9) are relatively more abundant in monocots and non-vascular plants as compared to the dicots. The high molecular weight plant secretome components might be related to the function of anchorage as integral components of the
|
||
<collectionCode id="669DCCA72771536BA05EBAF5FDEB81AB" box="[518,562,1152,1171]" country="China" httpUri="http://biocol.org/urn:lsid:biocol.org:col:13249" lsid="urn:lsid:biocol.org:col:13249" name="Hubei College of Traditional Chinese Medicine" pageId="5" pageNumber="6" type="Herbarium">ECM</collectionCode>
|
||
(
|
||
<bibRefCitation id="641D29932771536BA01EBAF5FF4D8197" author="Marinkovich, M. P. & Lunstrum, G. P. & Burgeson, R. E." pageId="5" pageNumber="6" pagination="17900 - 17906" refId="ref13964" refString="Marinkovich, M. P., Lunstrum, G. P., Burgeson, R. E., 1992. The anchoring filament protein kalinin is synthesized and secreted as a high molecular weight precursor. J. Biol. Chem. 267, 17900 - 17906. https: // doi. org / 10.1016 / S 0021 - 9258 (19) 37127 - 3." type="journal article" year="1992">Marinkovich et al., 1992</bibRefCitation>
|
||
). Also, the high molecular weight proteins may be selectively exported to the extracellular space through
|
||
<collectionCode id="669DCCA72771536BA3AEBACDFDC681F3" box="[502,543,1208,1227]" country="Sweden" httpUri="http://biocol.org/urn:lsid:biocol.org:col:15542" lsid="urn:lsid:biocol.org:col:15542" name="Uppsala University, Museum of Evolution, Botany Section (Fytoteket)" pageId="5" pageNumber="6" type="Herbarium">UPS</collectionCode>
|
||
, either as constituents of exosomes or multi-vesicular bodies or other Golgi bypass routes. The low molecular weight
|
||
<collectionCode id="669DCCA72771536BA30EBA85FEA2803B" box="[342,379,1264,1283]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
constituents encompass the essential signaling components in developing regions of plants (
|
||
<bibRefCitation id="641D29932771536BA007BB7EFD258026" author="Stahl, U. & Lee, M. & Archer, D. & Cellini, F. & Ek, B. & Iannacone, R. & MacKenzie, D. & Semeraro, L. & Tramontano, E. & Stymme, S." box="[607,764,1291,1311]" pageId="5" pageNumber="6" pagination="481 - 490" refId="ref16513" refString="Stahl, U., Lee, M., Sjodahl ¨, S., Archer, D., Cellini, F., Ek, B., Iannacone, R., MacKenzie, D., Semeraro, L., Tramontano, E., Stymme, S., 1999. Plant low-molecular-weight phospholipase A 2 s (PLA 2 s) are structurally related to the animal secretory PLA 2 s and are present as a family of isoforms in rice (Oryza sativa). Plant Mol. Biol. 41, 481 - 490. https: // doi. org / 10.1023 / A: 1006323405788." type="journal article" year="1999">Stahl et al., 1999</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932771536BA23CBB5DFF238002" author="Lee, D. K. & Ahn, J. H. & Song, S. K. & Choi, Y. D. & Lee, J. S." box="[100,250,1319,1339]" pageId="5" pageNumber="6" pagination="985 - 997" refId="ref13328" refString="Lee, D. K., Ahn, J. H., Song, S. K., Choi, Y. D., Lee, J. S., 2003. Expression of an expansin gene is correlated with root elongation in soybean. Plant Physiol. 131, 985 - 997. https: // doi. org / 10.1104 / pp. 009902." type="journal article" year="2003">Lee et al., 2003</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932771536BA35FBB52FE678002" author="Yokota, E. & Ohmori, T. & Muto, S. & Shimmen, T." box="[263,446,1319,1339]" pageId="5" pageNumber="6" pagination="1008 - 1018" refId="ref17885" refString="Yokota, E., Ohmori, T., Muto, S., Shimmen, T., 2004. 21 - kDa polypeptide, a low-molecular-weight cyclophilin, is released from pollen of higher plants into the extracellular medium in vitro. Planta 218, 1008 - 1018. https: // doi. org / 10.1007 / s 00425 - 003 - 1177 - 2." type="journal article" year="2004">Yokota et al., 2004</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932771536BA394BB5DFD848002" author="Hu, X. L. & Lu, H. & Hassan, M. M. & Zhang, J. & Yuan, G. & Abraham, P. E. & Shrestha, H. K. & Solis, M. I. V. & Chen, J. G. & Tschaplinski, T. J. & Doktycz, M. J." box="[460,605,1319,1339]" pageId="5" pageNumber="6" pagination="1 - 14" refId="ref12457" refString="Hu, X. L., Lu, H., Hassan, M. M., Zhang, J., Yuan, G., Abraham, P. E., Shrestha, H. K., Solis, M. I. V., Chen, J. G., Tschaplinski, T. J., Doktycz, M. J., 2021. Advances and perspectives in discovery and functional analysis of small secreted proteins in plants. Hortic. Res. 8, 1 - 14. https: // doi. org / 10.1038 / s 41438 - 021 - 00570 - 7." type="journal article" year="2021">Hu et al., 2021</bibRefCitation>
|
||
) as well as plant immunity modules (
|
||
<bibRefCitation id="641D29932771536BA371BB31FDFC806E" author="Van de Velde, W. & Zehirov, G. & Szatmari, A. & Debreczeny, M. & Ishihara, H. & Kevei, Z. & Farkas, A. & Mikulass, K. & Nagy, A. & Tiricz, H. & Satiat-Jeunemaitre, B." box="[297,549,1347,1367]" pageId="5" pageNumber="6" pagination="1122 - 1126" refId="ref16938" refString="Van de Velde, W., Zehirov, G., Szatmari, A., Debreczeny, M., Ishihara, H., Kevei, Z., Farkas, A., Mikulass, K., Nagy, A., Tiricz, H., Satiat-Jeunemaitre, B., 2010. Plant peptides govern terminal differentiation of bacteria in symbiosis. Science 327, 1122 - 1126. https: // doi. org / 10.1126 / science. 1184057." type="journal article" year="2010">Van de Velde et al., 2010</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932771536BA06CBB31FD11806E" author="Yu, G. & Xian, L. & Zhuang, H. & Macho, A. P." box="[564,712,1347,1367]" pageId="5" pageNumber="6" pagination="145 - 150" refId="ref17955" refString="Yu, G., Xian, L., Zhuang, H., Macho, A. P., 2021. SGT 1 is not required for plant LRR-RLKmediated immunity. Mol. Plant Pathol. 22, 145 - 150. https: // doi. org / 10.1111 / mpp. 13012." type="journal article" year="2021">Yu et al., 2021</bibRefCitation>
|
||
). The mildly hydrophobic nature of
|
||
<collectionCode id="669DCCA72771536BA3DBBB2AFE71804A" box="[387,424,1375,1394]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
proteins might be due to their transient association with plant membranes and even biomolecules of hydrophobic nature or proteins with hydrophobic cores.
|
||
</paragraph>
|
||
<caption id="54F304EA2771536BA16ABB27FC2E80F1" ID-DOI="http://doi.org/10.5281/zenodo.8234557" ID-Zenodo-Dep="8234557" httpUri="https://zenodo.org/record/8234557/files/figure.png" pageId="5" pageNumber="6" startId="5.[818,848,1362,1379]" targetBox="[824,1481,150,1334]" targetPageId="5" targetType="figure">
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<paragraph id="003354622771536BA16ABB27FC2E80F1" blockId="5.[818,1488,1362,1481]" pageId="5" pageNumber="6">
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||
<emphasis id="32F888702771536BA16ABB27FCA8805B" bold="true" box="[818,881,1362,1379]" pageId="5" pageNumber="6">Fig. 4.</emphasis>
|
||
Physicochemical assessment of the grasspea suspension secretome (GSS), including pI (A), molecular weight (in kDa) (B), and hydrophilicity (C), with respect to MSS, DSS and LSS (MSS corresponds to the monocot suspension secretome, DSS to the dicot suspension secretome and LSS to the lower plant suspension secretome).
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="003354622771536BA23CBBA5FE5880DB" blockId="5.[100,385,1488,1507]" box="[100,385,1488,1507]" pageId="5" pageNumber="6">
|
||
<heading id="5B7BE30E2771536BA23CBBA5FE5880DB" bold="true" box="[100,385,1488,1507]" fontSize="36" level="1" pageId="5" pageNumber="6" reason="1">
|
||
<emphasis id="32F888702771536BA23CBBA5FE5880DB" bold="true" box="[100,385,1488,1507]" italics="true" pageId="5" pageNumber="6">
|
||
2.6.
|
||
<collectionCode id="669DCCA72771536BA2CDBBA5FF6380DB" box="[149,186,1488,1507]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
functional annotation
|
||
</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph id="003354622771536BA2DCB87DFAA483F0" blockId="5.[100,771,1544,1982]" lastBlockId="5.[818,1487,1522,1736]" pageId="5" pageNumber="6">
|
||
The
|
||
<collectionCode id="669DCCA72771536BA2E8B87DFF0C8323" box="[176,213,1544,1563]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
was sequentially subjected to Gene Ontology (
|
||
<collectionCode id="669DCCA72771536BA0C4B87DFD678323" box="[668,702,1544,1563]" country="United Kingdom" lsid="urn:lsid:biocol.org:col:13862" name="Philosophical Society" pageId="5" pageNumber="6" type="Herbarium">GO</collectionCode>
|
||
) annotation, wherein each protein possesses multiple
|
||
<collectionCode id="669DCCA72771536BA044B851FDE3830F" box="[540,570,1572,1591]" country="United Kingdom" lsid="urn:lsid:biocol.org:col:13862" name="Philosophical Society" pageId="5" pageNumber="6" type="Herbarium">GO</collectionCode>
|
||
terms. The biological processes were dominated by metabolic, biosynthetic and transportrelated proteins (
|
||
<figureCitation id="98B748E72771536BA352B829FE8A8357" box="[266,339,1628,1647]" captionStart="Fig" captionStartId="6.[100,130,1184,1201]" captionTargetBox="[340,1246,149,1156]" captionTargetId="figure-466@6.[338,1248,148,1157]" captionTargetPageId="6" captionText="Fig. 5. Functional annotation of the grasspea suspension secretome. (A) GO classification of proteins reveals the abundance of proteins associated with (B) response to abiotic stress, (C) response to biotic stress and (D) phytohormone signaling." figureDoi="http://doi.org/10.5281/zenodo.8234559" httpUri="https://zenodo.org/record/8234559/files/figure.png" pageId="5" pageNumber="6">Fig. 5A</figureCitation>
|
||
). Interestingly, 59 proteins were found to be associated with defense response, while 113 with abiotic stress response. The cellular component category revealed an abundance of membrane-associated proteins (
|
||
<figureCitation id="98B748E72771536BA37EB8DAFEB483FB" box="[294,365,1711,1731]" captionStart="Fig" captionStartId="6.[100,130,1184,1201]" captionTargetBox="[340,1246,149,1156]" captionTargetId="figure-466@6.[338,1248,148,1157]" captionTargetPageId="6" captionText="Fig. 5. Functional annotation of the grasspea suspension secretome. (A) GO classification of proteins reveals the abundance of proteins associated with (B) response to abiotic stress, (C) response to biotic stress and (D) phytohormone signaling." figureDoi="http://doi.org/10.5281/zenodo.8234559" httpUri="https://zenodo.org/record/8234559/files/figure.png" pageId="5" pageNumber="6">Fig. 5A</figureCitation>
|
||
, Supplementary Table
|
||
<collectionCode id="669DCCA72771536BA01FB8C5FD8C83FB" box="[583,597,1712,1731]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="5" pageNumber="6" type="Herbarium">S</collectionCode>
|
||
1). The three most abundant
|
||
<collectionCode id="669DCCA72771536BA295B8B9FF2B83E7" box="[205,242,1740,1759]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
functional categories were abiotic stress response (
|
||
<figureCitation id="98B748E72771536BA234B892FF6A83C2" box="[108,179,1767,1786]" captionStart="Fig" captionStartId="6.[100,130,1184,1201]" captionTargetBox="[340,1246,149,1156]" captionTargetId="figure-466@6.[338,1248,148,1157]" captionTargetPageId="6" captionText="Fig. 5. Functional annotation of the grasspea suspension secretome. (A) GO classification of proteins reveals the abundance of proteins associated with (B) response to abiotic stress, (C) response to biotic stress and (D) phytohormone signaling." figureDoi="http://doi.org/10.5281/zenodo.8234559" httpUri="https://zenodo.org/record/8234559/files/figure.png" pageId="5" pageNumber="6">Fig. 5B</figureCitation>
|
||
), biotic stress response (
|
||
<figureCitation id="98B748E72771536BA3C6B892FE3A83C2" box="[414,483,1767,1786]" captionStart="Fig" captionStartId="6.[100,130,1184,1201]" captionTargetBox="[340,1246,149,1156]" captionTargetId="figure-466@6.[338,1248,148,1157]" captionTargetPageId="6" captionText="Fig. 5. Functional annotation of the grasspea suspension secretome. (A) GO classification of proteins reveals the abundance of proteins associated with (B) response to abiotic stress, (C) response to biotic stress and (D) phytohormone signaling." figureDoi="http://doi.org/10.5281/zenodo.8234559" httpUri="https://zenodo.org/record/8234559/files/figure.png" pageId="5" pageNumber="6">Fig. 5C</figureCitation>
|
||
) and phytohormone signaling (
|
||
<figureCitation id="98B748E72771536BA234B976FF6C822E" box="[108,181,1795,1814]" captionStart="Fig" captionStartId="6.[100,130,1184,1201]" captionTargetBox="[340,1246,149,1156]" captionTargetId="figure-466@6.[338,1248,148,1157]" captionTargetPageId="6" captionText="Fig. 5. Functional annotation of the grasspea suspension secretome. (A) GO classification of proteins reveals the abundance of proteins associated with (B) response to abiotic stress, (C) response to biotic stress and (D) phytohormone signaling." figureDoi="http://doi.org/10.5281/zenodo.8234559" httpUri="https://zenodo.org/record/8234559/files/figure.png" pageId="5" pageNumber="6">Fig. 5D</figureCitation>
|
||
). Molecular function was mostly related to nucleotide and ion binding, and a significant number of proteins were associated with transferase activity, particularly phosphorus-containing groups. We identified rare proteins associated with exocytosis as well as endocytosis. Since the secretome constituents overlap with those of the cell wall, we identified several primary and secondary cell wall biosynthesis and modifying enzymes in addition to cuticle synthesis-related proteins (eceriferum 3 isoforms). Plant developmental proteins critical for root (12 proteins), leaf (5), seed (5), embryo (12) and flower (16) development were well represented in the secretome. Since totipotent cells were used for generating the
|
||
<emphasis id="32F888702771536BA64FB833FB818361" bold="true" box="[1047,1112,1606,1625]" italics="true" pageId="5" pageNumber="6">in vitro</emphasis>
|
||
secretome, it was comprised of several crucial proteins (24) related to cell growth, shape, and division. The cell–cell signaling-associated secreted proteins could be classified into transporters, symporters, antiporters, membrane-associated receptors and signaling proteins and plasmodesmata-inhabited proteins.
|
||
</paragraph>
|
||
<paragraph id="003354622771536BA16AB976FB0B822E" blockId="5.[818,1234,1795,1814]" box="[818,1234,1795,1814]" pageId="5" pageNumber="6">
|
||
<heading id="5B7BE30E2771536BA16AB976FB0B822E" bold="true" box="[818,1234,1795,1814]" fontSize="36" level="1" pageId="5" pageNumber="6" reason="1">
|
||
<emphasis id="32F888702771536BA16AB976FB0B822E" bold="true" box="[818,1234,1795,1814]" italics="true" pageId="5" pageNumber="6">2.7. Subcellular localization of target proteins</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph id="0033546227715368A109B94EFCDA80DE" blockId="5.[818,1487,1851,1982]" lastBlockId="6.[100,771,1268,1511]" lastPageId="6" lastPageNumber="7" pageId="5" pageNumber="6">
|
||
We selected two proteins, endochitinase (
|
||
<collectionCode id="669DCCA72771536BA68FB94EFB3A8276" box="[1239,1251,1851,1870]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="5" pageNumber="6" type="Herbarium">S</collectionCode>
|
||
597) and G-type lectin Sreceptor-like serine threonine kinase (
|
||
<collectionCode id="669DCCA72771536BA6CFB922FB7A8252" box="[1175,1187,1879,1898]" country="Sweden" lsid="urn:lsid:biocol.org:col:15668" name="Department of Botany, Swedish Museum of Natural History" pageId="5" pageNumber="6" type="Herbarium">S</collectionCode>
|
||
718), predicted to be functional constituents of
|
||
<collectionCode id="669DCCA72771536BA19AB906FC3382BE" box="[962,1002,1907,1926]" pageId="5" pageNumber="6">GSS</collectionCode>
|
||
, to investigate the
|
||
<emphasis id="32F888702771536BA6C6B906FB3782BD" bold="true" box="[1182,1262,1906,1926]" italics="true" pageId="5" pageNumber="6">in planta</emphasis>
|
||
localization. Endochitinases are integral components of the plant secretome due to their function as antifungal proteins (
|
||
<bibRefCitation id="641D29932771536BA601B9DEFACA8286" author="Agrawal, G. K. & Jwa, N. S. & Lebrun, M. H. & Job, D. & Rakwal, R." box="[1113,1299,1963,1982]" pageId="5" pageNumber="6" pagination="799 - 827" refId="ref9710" refString="Agrawal, G. K., Jwa, N. S., Lebrun, M. H., Job, D., Rakwal, R., 2010. Plant secretome: unlocking secrets of the secreted proteins. Proteomics 10, 799 - 827. https: // doi. org / 10.1002 / pmic. 200900514." type="journal article" year="2010">Agrawal et al., 2010</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D29932771536BA746B9DEFA108286" author="Krause, C. & Richter, S. & Jurgens, G." box="[1310,1481,1963,1982]" pageId="5" pageNumber="6" pagination="2429 - 2441" refId="ref13022" refString="Krause, C., Richter, S., Knoll ¨, C., Jurgens, G., 2013. Plant secretome-from cellular process to biological activity. Biochim. Biophys. Acta, Proteins Proteomics 1834, 2429 - 2441. https: // doi. org / 10.1016 / j. bbapap. 2013.03.024." type="journal article" year="2013">Krause et al., 2013</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D299327725368A23CBA81FEC1803F" author="Yadav, N. & Khurana, S. P. & Yadav, D. K." box="[100,280,1268,1288]" pageId="6" pageNumber="7" pagination="357 - 384" refId="ref17816" refString="Yadav, N., Khurana, S. P., Yadav, D. K., 2015. Plant secretomics: unique initiatives. In: PlantOmics: the Omics of Plant Science. Springer, New Delhi, pp. 357 - 384. https: // doi. org / 10.1007 / 978 - 81 - 322 - 2172 - 2 _ 12." type="book chapter" year="2015">Yadav et al., 2015</bibRefCitation>
|
||
). On the other hand, G-type lectin S-receptor-like serine threonine kinases are crucial for cell surface signaling and have been reported to be plasma membrane-associated proteins (
|
||
<bibRefCitation id="641D299327725368A09ABB59FF4D8063" author="Khoza, T. G." pageId="6" pageNumber="7" refId="ref12850" refString="Khoza, T. G., 2017. Identification of the ergosterol-interacting proteins in the Arabidopsis thaliana plasma membrane. University of Johannesburg, Johannesburg. http: // hdl. handle. net / 102000 / 0002." type="url" year="2017">Khoza, 2017</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D299327725368A2FEBB3DFE7D8063" author="von Aderkas, P. & Prior, N. A. & Little, S. A." box="[166,420,1352,1371]" pageId="6" pageNumber="7" pagination="1844" refId="ref17245" refString="von Aderkas, P., Prior, N. A., Little, S. A., 2018. The evolution of sexual fluids in gymnosperms from pollination drops to nectar. Front. Plant Sci. 9, 1844. https: // doi. org / 10.3389 / fpls. 2018.01844." type="journal article" year="2018">von Aderkas et al., 2018</bibRefCitation>
|
||
;
|
||
<bibRefCitation id="641D299327725368A3EEBB3DFD1C8063" author="Schellenberger, R. & Touchard, M. & Baillieul, F. & Cordelier, S. & Crouzet, J. & Dorey, S." box="[438,709,1352,1371]" pageId="6" pageNumber="7" pagination="1602 - 1616" refId="ref15939" refString="Schellenberger, R., Touchard, M., Cl´ement, C., Baillieul, F., Cordelier, S., Crouzet, J., Dorey, S., 2019. Apoplastic invasion patterns triggering plant immunity: plasma membrane sensing at the frontline. Mol. Plant Pathol. 20, 1602 - 1616. https: // doi. org / 10.1111 / mpp. 12857." type="journal article" year="2019">Schellenberger et al., 2019</bibRefCitation>
|
||
). The localization of target proteins was restricted to the cell surface, as revealed by plasmolyzed protoplasts, especially for endochitinase (
|
||
<figureCitation id="98B748E727725368A234BBE9FF2C8097" box="[108,245,1436,1455]" captionStart="Fig" captionStartId="7.[100,130,1754,1771]" captionTargetBox="[341,1247,150,1725]" captionTargetId="figure-86@7.[338,1249,148,1727]" captionTargetPageId="7" captionText="Fig. 6. Localization validation of endochitinase (S597) and G-type lectin S-receptor-like serine threonine kinase (S718). The panels include (A) expression of YFPtagged S597 in onion epidermal cells, (B) plasmolysis of S597-transformed onion peel (C), expression of YFP-tagged S718 in onion peel cells and (D) plasmolyzed onion peel cells expressing YFP-tagged S718. A pSITE3CA empty vector control was also monitored besides the target genes (E)." figureDoi="http://doi.org/10.5281/zenodo.8234561" httpUri="https://zenodo.org/record/8234561/files/figure.png" pageId="6" pageNumber="7">Fig. 6A and B</figureCitation>
|
||
). However, in the case of G-type lectin S-receptor-like serine threonine kinase, diffuse expression of the tagged protein was also observed in the cytoplasm, in addition to the cell surface (
|
||
<figureCitation id="98B748E727725368A021BBA6FD2180DE" box="[633,760,1491,1510]" captionStart="Fig" captionStartId="7.[100,130,1754,1771]" captionTargetBox="[341,1247,150,1725]" captionTargetId="figure-86@7.[338,1249,148,1727]" captionTargetPageId="7" captionText="Fig. 6. Localization validation of endochitinase (S597) and G-type lectin S-receptor-like serine threonine kinase (S718). The panels include (A) expression of YFPtagged S597 in onion epidermal cells, (B) plasmolysis of S597-transformed onion peel (C), expression of YFP-tagged S718 in onion peel cells and (D) plasmolyzed onion peel cells expressing YFP-tagged S718. A pSITE3CA empty vector control was also monitored besides the target genes (E)." figureDoi="http://doi.org/10.5281/zenodo.8234561" httpUri="https://zenodo.org/record/8234561/files/figure.png" pageId="6" pageNumber="7">Fig. 6C and D</figureCitation>
|
||
).
|
||
</paragraph>
|
||
<caption id="54F304EA27725368A23CBAD5FCDF81F3" ID-DOI="http://doi.org/10.5281/zenodo.8234559" ID-Zenodo-Dep="8234559" httpUri="https://zenodo.org/record/8234559/files/figure.png" pageId="6" pageNumber="7" startId="6.[100,130,1184,1201]" targetBox="[340,1246,149,1156]" targetPageId="6" targetType="figure">
|
||
<paragraph id="0033546227725368A23CBAD5FCDF81F3" blockId="6.[100,1487,1184,1227]" pageId="6" pageNumber="7">
|
||
<emphasis id="32F8887027725368A23CBAD5FF448189" bold="true" box="[100,157,1184,1201]" pageId="6" pageNumber="7">Fig. 5.</emphasis>
|
||
Functional annotation of the grasspea suspension secretome. (A) GO classification of proteins reveals the abundance of proteins associated with (B) response to abiotic stress, (C) response to biotic stress and (D) phytohormone signaling.
|
||
</paragraph>
|
||
</caption>
|
||
<paragraph id="0033546227725368A23CB87EFF268326" blockId="6.[100,255,1547,1566]" box="[100,255,1547,1566]" pageId="6" pageNumber="7">
|
||
<heading id="5B7BE30E27725368A23CB87EFF268326" bold="true" box="[100,255,1547,1566]" fontSize="36" level="1" pageId="6" pageNumber="7" reason="1">
|
||
<emphasis id="32F8887027725368A23CB87EFF268326" bold="true" box="[100,255,1547,1566]" pageId="6" pageNumber="7">3. Conclusions</emphasis>
|
||
</heading>
|
||
</paragraph>
|
||
<paragraph id="0033546227725368A2DCB836FC378063" blockId="6.[100,770,1603,1957]" lastBlockId="6.[818,1488,1268,1371]" pageId="6" pageNumber="7">
|
||
In the present study, we attempted to decode the secretome of an orphan legume species known for its unique agricultural traits. Cell-to-cell communication, signaling and extracellular space modifying enzymes were abundantly represented in the
|
||
<collectionCode id="669DCCA727725368A051B8E2FDE88392" box="[521,561,1687,1706]" pageId="6" pageNumber="7">GSS</collectionCode>
|
||
. Our findings suggest that totipotent SCCs have the potential to redifferentiate into tissues and organs, depending on the environmental cues. We observed that
|
||
<taxonomicName id="C78C2FE127725368A23CB89EFF6183C5" box="[100,184,1770,1790]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="species" species="sativus">
|
||
<emphasis id="32F8887027725368A23CB89EFF6183C5" bold="true" box="[100,184,1770,1790]" italics="true" pageId="6" pageNumber="7">L. sativus</emphasis>
|
||
</taxonomicName>
|
||
cells are capable of secreting proteins related to key developmental cues and phytohormone-associated pathways. The evolutionary conservation of secretory proteins is evident in the species-specific comparison, more so in the case of plant families. These proteins can be established as “plant secretome markers”. The transient localization analysis of key signaling proteins validated their secretion from the cell surface in nature. Overall,
|
||
<taxonomicName id="C78C2FE127725368A33BB9E7FE6E829D" box="[355,439,1938,1957]" class="Magnoliopsida" family="Fabaceae" genus="Lathyrus" kingdom="Plantae" order="Fabales" pageId="6" pageNumber="7" phylum="Tracheophyta" rank="species" species="sativus">
|
||
<emphasis id="32F8887027725368A33BB9E7FE6E829D" bold="true" box="[355,439,1938,1957]" italics="true" pageId="6" pageNumber="7">L. sativus</emphasis>
|
||
</taxonomicName>
|
||
exhibited both shared and distinct components of the cell surface, some of which were hitherto undiscovered. Conclusively, the proteome landscape portrayed not only the plant-specific secreted protein markers but also novel constituents of the grasspea secretome.
|
||
</paragraph>
|
||
</subSubSection>
|
||
</treatment>
|
||
</document> |