Response to long-term NaHCO3-derived alkalinity in model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: transcriptomic profiling and physiological characterization
The current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation...
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| creator | Babuin, María Florencia Campestre, María Paula Rocco, Rubén Bordenave, Cesar D Escaray, Francisco J Antonelli, Cristian Calzadilla, Pablo Gárriz, Andrés Serna, Eva Carrasco, Pedro Ruiz, Oscar A Menendez, Ana B |
| description | The current knowledge regarding transcriptomic changes induced by alkalinity on plants is scarce and limited to studies where plants were subjected to the alkaline salt for periods not longer than 48 h, so there is no information available regarding the regulation of genes involved in the generation of a new homeostatic cellular condition after long-term alkaline stress. Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. Our results provided a set of selected, differentially expressed genes deserving further investigation and suggested that the L. japonicus ecotypes could constitute a useful model to search for common and distinct tolerance mechanisms to long-term alkaline stress response in plants. |
| doi_str_mv | 10.1371/journal.pone.0097106 |
| format | Article |
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Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. Our results provided a set of selected, differentially expressed genes deserving further investigation and suggested that the L. japonicus ecotypes could constitute a useful model to search for common and distinct tolerance mechanisms to long-term alkaline stress response in plants.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0097106</identifier><identifier>PMID: 24835559</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Abiotic stress ; Alkalinity ; Antacids - pharmacology ; Arabidopsis ; Biology and Life Sciences ; Chlorophyll ; Chlorophyll - analysis ; Ecotypes ; Fluorescence ; Gas exchange ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Plant - drug effects ; Gene regulation ; Genes ; Genomes ; Genomics ; Gluconeogenesis ; Glycolysis ; Iron ; Iron - analysis ; Legumes ; Lotus - drug effects ; Lotus - metabolism ; Lotus japonicus ; Medicine and Health Sciences ; Oligonucleotide Array Sequence Analysis ; Oxidative stress ; Physiology ; Plant growth ; Plant Roots - metabolism ; Plant Shoots - metabolism ; Plant Transpiration - physiology ; Proteins ; Real-Time Polymerase Chain Reaction ; Research and Analysis Methods ; Salinity ; Salts ; Senescence ; Shoots ; Signal transduction ; Sodium bicarbonate ; Sodium Bicarbonate - pharmacology ; Species Specificity ; Stress response ; Stresses ; Studies ; Transcription factors ; Zinc ; Zinc - analysis</subject><ispartof>PloS one, 2014-05, Vol.9 (5), p.e97106</ispartof><rights>2014 Babuin et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. 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Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. Gifu B-129 and MG-20 also differed in their regulation of genes that could play important roles in the generation of a new Fe/Zn homeostatic cellular condition, synthesis of plant compounds involved in stress response, protein-degradation, damage repair and root senescence, as well as in glycolysis, gluconeogenesis and TCA. In addition, there were differences between both ecotypes in the expression patterns of putative transcription factors that could determine distinct arrangements of flavonoid and isoflavonoid compounds. 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drug effects</subject><subject>Lotus - metabolism</subject><subject>Lotus japonicus</subject><subject>Medicine and Health Sciences</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Oxidative stress</subject><subject>Physiology</subject><subject>Plant growth</subject><subject>Plant Roots - metabolism</subject><subject>Plant Shoots - metabolism</subject><subject>Plant Transpiration - physiology</subject><subject>Proteins</subject><subject>Real-Time Polymerase Chain Reaction</subject><subject>Research and Analysis Methods</subject><subject>Salinity</subject><subject>Salts</subject><subject>Senescence</subject><subject>Shoots</subject><subject>Signal transduction</subject><subject>Sodium bicarbonate</subject><subject>Sodium Bicarbonate - pharmacology</subject><subject>Species Specificity</subject><subject>Stress response</subject><subject>Stresses</subject><subject>Studies</subject><subject>Transcription factors</subject><subject>Zinc</subject><subject>Zinc - analysis</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2014</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>BENPR</sourceid><sourceid>DOA</sourceid><recordid>eNp1ks1uEzEUhUcIREvhDRBYYj3B_5NhgQRRSSulVEKwtjz-SZw648F2Kg0P1Wes20yrdsHKV_Y5372-OlX1HsEZIg36vA372Es_G0JvZhC2DYL8RXWMWoJrjiF5-aQ-qt6ktIWQkTnnr6sjTOeEMdYeVze_TCqEZEAOwId-XWcTd-CnPFtcklqb6K6NBtJfSe96l0fgerAL2niwCnmfwFYWt1OlOlUhj4NJYOnsHnyvEW6B7DW4cKO8Clu3k-BiWWP4BeQo-6SiG3LYOQWGGKwr9PW9fNiMyQUf1k5JD9RGRqnKSO6fzC70b6tXVvpk3k3nSfXnx-nvxVm9ulyeL76tasUwz3XTIETbxljFldUIN4pS2GgpDeekJdQqRQni2mrDsUVMS9Jx3krKSAcN1uSk-njgDj4kMa06CcQwIxRzRovi_KDQQW7FEMv_4iiCdOL-IsS1kDE75Y1oG6zmnepMay1VlncGNtRyyLhVtGNdYX2duu27ndHK9GVF_hn0-UvvNmIdrgWFmEIEC-DTBIjh796k_J-R6UGlYkgpGvvYAUFxl6kHl7jLlJgyVWwfnk73aHoIEbkFADbOqw</recordid><startdate>20140516</startdate><enddate>20140516</enddate><creator>Babuin, María Florencia</creator><creator>Campestre, María Paula</creator><creator>Rocco, Rubén</creator><creator>Bordenave, Cesar D</creator><creator>Escaray, Francisco J</creator><creator>Antonelli, Cristian</creator><creator>Calzadilla, Pablo</creator><creator>Gárriz, Andrés</creator><creator>Serna, Eva</creator><creator>Carrasco, Pedro</creator><creator>Ruiz, Oscar A</creator><creator>Menendez, Ana B</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20140516</creationdate><title>Response to long-term NaHCO3-derived alkalinity in model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: transcriptomic profiling and physiological characterization</title><author>Babuin, María Florencia ; Campestre, María Paula ; Rocco, Rubén ; Bordenave, Cesar D ; Escaray, Francisco J ; Antonelli, Cristian ; Calzadilla, Pablo ; Gárriz, Andrés ; Serna, Eva ; Carrasco, Pedro ; Ruiz, Oscar A ; Menendez, Ana B</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c526t-7711497efc6cfd127c4407daae663934fcc4316dfde62f15da3b669a453b0e2d3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2014</creationdate><topic>Abiotic stress</topic><topic>Alkalinity</topic><topic>Antacids - 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Lotus japonicus is a model legume broadly used to study many important physiological processes including biotic interactions and biotic and abiotic stresses. In the present study, we characterized phenotipically the response to alkaline stress of the most widely used L. japonicus ecotypes, Gifu B-129 and MG-20, and analyzed global transcriptome of plants subjected to 10 mM NaHCO3 during 21 days, by using the Affymetrix Lotus japonicus GeneChip®. Plant growth assessment, gas exchange parameters, chlorophyll a fluorescence transient (OJIP) analysis and metal accumulation supported the notion that MG-20 plants displayed a higher tolerance level to alkaline stress than Gifu B-129. Overall, 407 and 459 probe sets were regulated in MG-20 and Gifu B-129, respectively. The number of probe sets differentially expressed in roots was higher than that of shoots, regardless the ecotype. 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| ispartof | PloS one, 2014-05, Vol.9 (5), p.e97106 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_1525342654 |
| source | Public Library of Science (PLoS) Journals Open Access; MEDLINE; DOAJ Directory of Open Access Journals; PubMed Central; Free Full-Text Journals in Chemistry; EZB Electronic Journals Library |
| subjects | Abiotic stress Alkalinity Antacids - pharmacology Arabidopsis Biology and Life Sciences Chlorophyll Chlorophyll - analysis Ecotypes Fluorescence Gas exchange Gene expression Gene Expression Profiling Gene Expression Regulation, Plant - drug effects Gene regulation Genes Genomes Genomics Gluconeogenesis Glycolysis Iron Iron - analysis Legumes Lotus - drug effects Lotus - metabolism Lotus japonicus Medicine and Health Sciences Oligonucleotide Array Sequence Analysis Oxidative stress Physiology Plant growth Plant Roots - metabolism Plant Shoots - metabolism Plant Transpiration - physiology Proteins Real-Time Polymerase Chain Reaction Research and Analysis Methods Salinity Salts Senescence Shoots Signal transduction Sodium bicarbonate Sodium Bicarbonate - pharmacology Species Specificity Stress response Stresses Studies Transcription factors Zinc Zinc - analysis |
| title | Response to long-term NaHCO3-derived alkalinity in model Lotus japonicus Ecotypes Gifu B-129 and Miyakojima MG-20: transcriptomic profiling and physiological characterization |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-02-07T19%3A23%3A02IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Response%20to%20long-term%20NaHCO3-derived%20alkalinity%20in%20model%20Lotus%20japonicus%20Ecotypes%20Gifu%20B-129%20and%20Miyakojima%20MG-20:%20transcriptomic%20profiling%20and%20physiological%20characterization&rft.jtitle=PloS%20one&rft.au=Babuin,%20Mar%C3%ADa%20Florencia&rft.date=2014-05-16&rft.volume=9&rft.issue=5&rft.spage=e97106&rft.pages=e97106-&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0097106&rft_dat=%3Cproquest_plos_%3E3305984321%3C/proquest_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=1525342654&rft_id=info:pmid/24835559&rft_doaj_id=oai_doaj_org_article_972c8bcbe9ff4cf6be074f6056fc4b5b&rfr_iscdi=true |