Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA
<i>Paraburkholderia phymatum</i> STM815 is a nitrogen-fixing endosymbiont that nodulate the agriculturally important <i>Phaseolus vulgaris</i> and several other host plants. We previously showed that the nodules induced by a STM815 mutant of the gene encoding the master regul...
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MDPI AG
2021-07-01
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| Series: | Metabolites |
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| Online Access: | https://www.mdpi.com/2218-1989/11/7/455 |
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| author | Paula Bellés-Sancho Martina Lardi Yilei Liu Leo Eberl Nicola Zamboni Aurélien Bailly Gabriella Pessi |
| author_facet | Paula Bellés-Sancho Martina Lardi Yilei Liu Leo Eberl Nicola Zamboni Aurélien Bailly Gabriella Pessi |
| author_sort | Paula Bellés-Sancho |
| collection | DOAJ |
| description | <i>Paraburkholderia phymatum</i> STM815 is a nitrogen-fixing endosymbiont that nodulate the agriculturally important <i>Phaseolus vulgaris</i> and several other host plants. We previously showed that the nodules induced by a STM815 mutant of the gene encoding the master regulator of nitrogen fixation NifA showed no nitrogenase activity (Fix<sup>−</sup>) and increased in number compared to <i>P. vulgaris</i> plants infected with the wild-type strain. To further investigate the role of NifA during symbiosis, nodules from <i>P. phymatum</i> wild-type and <i>nifA</i> mutants were collected and analyzed by metabolomics and dual RNA-Sequencing, allowing us to investigate both host and symbiont transcriptome. Using this approach, several metabolites’ changes could be assigned to bacterial or plant responses. While the amount of the C<sub>4</sub>-dicarboxylic acid succinate and of several amino acids was lower in Fix<sup>−</sup> nodules, the level of indole-acetamide (IAM) and brassinosteroids increased. Transcriptome analysis identified <i>P. phymatum</i> genes involved in transport of C<sub>4</sub>-dicarboxylic acids, carbon metabolism, auxin metabolism and stress response to be differentially expressed in absence of NifA. Furthermore, <i>P. vulgaris</i> genes involved in autoregulation of nodulation (AON) are repressed in nodules in absence of NifA potentially explaining the hypernodulation phenotype of the <i>nifA</i> mutant. These results and additional validation experiments suggest that <i>P. phymatum</i> STM815 NifA is not only important to control expression of nitrogenase and related enzymes but is also involved in regulating its own auxin production and stress response. Finally, our data indicate that <i>P. vulgaris</i> does sanction the <i>nifA</i> nodules by depleting the local carbon allocation rather than by mounting a strong systemic immune response to the Fix<sup>−</sup> rhizobia. |
| first_indexed | 2024-03-10T09:32:33Z |
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| id | doaj.art-916977ad78eb4e8baf062151bc3078fa |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-03-10T09:32:33Z |
| publishDate | 2021-07-01 |
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| spelling | doaj.art-916977ad78eb4e8baf062151bc3078fa2023-11-22T04:23:00ZengMDPI AGMetabolites2218-19892021-07-0111745510.3390/metabo11070455Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifAPaula Bellés-Sancho0Martina Lardi1Yilei Liu2Leo Eberl3Nicola Zamboni4Aurélien Bailly5Gabriella Pessi6Department of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, SwitzerlandDepartment of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, SwitzerlandDepartment of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, SwitzerlandDepartment of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, SwitzerlandETH Zürich, Institute of Molecular Systems Biology, CH-8093 Zürich, SwitzerlandDepartment of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, SwitzerlandDepartment of Plant and Microbial Biology, University of Zürich, CH-8057 Zürich, Switzerland<i>Paraburkholderia phymatum</i> STM815 is a nitrogen-fixing endosymbiont that nodulate the agriculturally important <i>Phaseolus vulgaris</i> and several other host plants. We previously showed that the nodules induced by a STM815 mutant of the gene encoding the master regulator of nitrogen fixation NifA showed no nitrogenase activity (Fix<sup>−</sup>) and increased in number compared to <i>P. vulgaris</i> plants infected with the wild-type strain. To further investigate the role of NifA during symbiosis, nodules from <i>P. phymatum</i> wild-type and <i>nifA</i> mutants were collected and analyzed by metabolomics and dual RNA-Sequencing, allowing us to investigate both host and symbiont transcriptome. Using this approach, several metabolites’ changes could be assigned to bacterial or plant responses. While the amount of the C<sub>4</sub>-dicarboxylic acid succinate and of several amino acids was lower in Fix<sup>−</sup> nodules, the level of indole-acetamide (IAM) and brassinosteroids increased. Transcriptome analysis identified <i>P. phymatum</i> genes involved in transport of C<sub>4</sub>-dicarboxylic acids, carbon metabolism, auxin metabolism and stress response to be differentially expressed in absence of NifA. Furthermore, <i>P. vulgaris</i> genes involved in autoregulation of nodulation (AON) are repressed in nodules in absence of NifA potentially explaining the hypernodulation phenotype of the <i>nifA</i> mutant. These results and additional validation experiments suggest that <i>P. phymatum</i> STM815 NifA is not only important to control expression of nitrogenase and related enzymes but is also involved in regulating its own auxin production and stress response. Finally, our data indicate that <i>P. vulgaris</i> does sanction the <i>nifA</i> nodules by depleting the local carbon allocation rather than by mounting a strong systemic immune response to the Fix<sup>−</sup> rhizobia.https://www.mdpi.com/2218-1989/11/7/455symbiosisnitrogenaseC<sub>4</sub>-dicarboxylatesauxinbrassinosteroidflavonoid |
| spellingShingle | Paula Bellés-Sancho Martina Lardi Yilei Liu Leo Eberl Nicola Zamboni Aurélien Bailly Gabriella Pessi Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA Metabolites symbiosis nitrogenase C<sub>4</sub>-dicarboxylates auxin brassinosteroid flavonoid |
| title | Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA |
| title_full | Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA |
| title_fullStr | Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA |
| title_full_unstemmed | Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA |
| title_short | Metabolomics and Dual RNA-Sequencing on Root Nodules Revealed New Cellular Functions Controlled by <i>Paraburkholderia phymatum</i> NifA |
| title_sort | metabolomics and dual rna sequencing on root nodules revealed new cellular functions controlled by i paraburkholderia phymatum i nifa |
| topic | symbiosis nitrogenase C<sub>4</sub>-dicarboxylates auxin brassinosteroid flavonoid |
| url | https://www.mdpi.com/2218-1989/11/7/455 |
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