Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it>
<p>Abstract</p> <p>Background</p> <p>Rhizotoxic ions in problem soils inhibit nutrient and water acquisition by roots, which in turn leads to reduced crop yields. Previous studies on the effects of rhizotoxic ions on root growth and physiological functions suggested tha...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2009-03-01
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| Series: | BMC Plant Biology |
| Online Access: | http://www.biomedcentral.com/1471-2229/9/32 |
| _version_ | 1818960695546347520 |
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| author | Sakurai Nozomu Sato Shigeru Hibino Takashi Suzuki Yuji Kobayashi Yuriko Sawaki Yoshiharu Ikka Takashi Zhao Cheng-Ri Shibata Daisuke Koyama Hiroyuki |
| author_facet | Sakurai Nozomu Sato Shigeru Hibino Takashi Suzuki Yuji Kobayashi Yuriko Sawaki Yoshiharu Ikka Takashi Zhao Cheng-Ri Shibata Daisuke Koyama Hiroyuki |
| author_sort | Sakurai Nozomu |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Rhizotoxic ions in problem soils inhibit nutrient and water acquisition by roots, which in turn leads to reduced crop yields. Previous studies on the effects of rhizotoxic ions on root growth and physiological functions suggested that some mechanisms were common to all rhizotoxins, while others were more specific. To understand this complex system, we performed comparative transcriptomic analysis with various rhizotoxic ions, followed by bioinformatics analysis, in the model plant <it>Arabidopsis thaliana</it>.</p> <p>Results</p> <p>Roots of <it>Arabidopsis </it>were treated with the major rhizotoxic stressors, aluminum (Al) ions, cadmium (Cd) ions, copper (Cu) ions and sodium (NaCl) chloride, and the gene expression responses were analyzed by DNA array technology. The top 2.5% of genes whose expression was most increased by each stressor were compared with identify common and specific gene expression responses induced by these stressors. A number of genes encoding glutathione-S-transferases, peroxidases, Ca-binding proteins and a trehalose-synthesizing enzyme were induced by all stressors. In contrast, gene ontological categorization identified sets of genes uniquely induced by each stressor, with distinct patterns of biological processes and molecular function. These contained known resistance genes for each stressor, such as <it>AtALMT1 </it>(encoding Al-activated malate transporter) in the Al-specific group and <it>DREB </it>(encoding dehydration responsive element binding protein) in the NaCl-specific group. These gene groups are likely to reflect the common and differential cellular responses and the induction of defense systems in response to each ion. We also identified co-expressed gene groups specific to rhizotoxic ions, which might aid further detailed investigation of the response mechanisms.</p> <p>Conclusion</p> <p>In order to understand the complex responses of roots to rhizotoxic ions, we performed comparative transcriptomic analysis followed by bioinformatics characterization. Our analyses revealed that both general and specific genes were induced in <it>Arabidopsis </it>roots exposed to various rhizotoxic ions. Several defense systems, such as the production of reactive oxygen species and disturbance of Ca homeostasis, were triggered by all stressors, while specific defense genes were also induced by individual stressors. Similar studies in different plant species could help to clarify the resistance mechanisms at the molecular level to provide information that can be utilized for marker-assisted selection.</p> |
| first_indexed | 2024-12-20T12:01:37Z |
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| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-20T12:01:37Z |
| publishDate | 2009-03-01 |
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| spelling | doaj.art-97026eee4f974420bc5caf09675d0f3f2022-12-21T19:41:31ZengBMCBMC Plant Biology1471-22292009-03-01913210.1186/1471-2229-9-32Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it>Sakurai NozomuSato ShigeruHibino TakashiSuzuki YujiKobayashi YurikoSawaki YoshiharuIkka TakashiZhao Cheng-RiShibata DaisukeKoyama Hiroyuki<p>Abstract</p> <p>Background</p> <p>Rhizotoxic ions in problem soils inhibit nutrient and water acquisition by roots, which in turn leads to reduced crop yields. Previous studies on the effects of rhizotoxic ions on root growth and physiological functions suggested that some mechanisms were common to all rhizotoxins, while others were more specific. To understand this complex system, we performed comparative transcriptomic analysis with various rhizotoxic ions, followed by bioinformatics analysis, in the model plant <it>Arabidopsis thaliana</it>.</p> <p>Results</p> <p>Roots of <it>Arabidopsis </it>were treated with the major rhizotoxic stressors, aluminum (Al) ions, cadmium (Cd) ions, copper (Cu) ions and sodium (NaCl) chloride, and the gene expression responses were analyzed by DNA array technology. The top 2.5% of genes whose expression was most increased by each stressor were compared with identify common and specific gene expression responses induced by these stressors. A number of genes encoding glutathione-S-transferases, peroxidases, Ca-binding proteins and a trehalose-synthesizing enzyme were induced by all stressors. In contrast, gene ontological categorization identified sets of genes uniquely induced by each stressor, with distinct patterns of biological processes and molecular function. These contained known resistance genes for each stressor, such as <it>AtALMT1 </it>(encoding Al-activated malate transporter) in the Al-specific group and <it>DREB </it>(encoding dehydration responsive element binding protein) in the NaCl-specific group. These gene groups are likely to reflect the common and differential cellular responses and the induction of defense systems in response to each ion. We also identified co-expressed gene groups specific to rhizotoxic ions, which might aid further detailed investigation of the response mechanisms.</p> <p>Conclusion</p> <p>In order to understand the complex responses of roots to rhizotoxic ions, we performed comparative transcriptomic analysis followed by bioinformatics characterization. Our analyses revealed that both general and specific genes were induced in <it>Arabidopsis </it>roots exposed to various rhizotoxic ions. Several defense systems, such as the production of reactive oxygen species and disturbance of Ca homeostasis, were triggered by all stressors, while specific defense genes were also induced by individual stressors. Similar studies in different plant species could help to clarify the resistance mechanisms at the molecular level to provide information that can be utilized for marker-assisted selection.</p>http://www.biomedcentral.com/1471-2229/9/32 |
| spellingShingle | Sakurai Nozomu Sato Shigeru Hibino Takashi Suzuki Yuji Kobayashi Yuriko Sawaki Yoshiharu Ikka Takashi Zhao Cheng-Ri Shibata Daisuke Koyama Hiroyuki Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it> BMC Plant Biology |
| title | Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it> |
| title_full | Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it> |
| title_fullStr | Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it> |
| title_full_unstemmed | Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it> |
| title_short | Comparative transcriptomic characterization of aluminum, sodium chloride, cadmium and copper rhizotoxicities in <it>Arabidopsis thaliana</it> |
| title_sort | comparative transcriptomic characterization of aluminum sodium chloride cadmium and copper rhizotoxicities in it arabidopsis thaliana it |
| url | http://www.biomedcentral.com/1471-2229/9/32 |
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