Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i>
In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in <i>Arabidopsis</i> but remains largely unknown in legumes. The orthologs of the <i>FLC</i> gene, a major regul...
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MDPI AG
2023-12-01
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| author | Maria A. Duk Vitaly V. Gursky Maria G. Samsonova Svetlana Yu. Surkova |
| author_facet | Maria A. Duk Vitaly V. Gursky Maria G. Samsonova Svetlana Yu. Surkova |
| author_sort | Maria A. Duk |
| collection | DOAJ |
| description | In many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in <i>Arabidopsis</i> but remains largely unknown in legumes. The orthologs of the <i>FLC</i> gene, a major regulator of vernalization response in <i>Arabidopsis</i>, are absent or non-functional in the vernalization-sensitive legume species. Nevertheless, the legume integrator genes <i>FT</i> and <i>SOC1</i> are involved in the transition of the vernalization signal to meristem identity genes, including <i>PIM</i> (<i>AP1</i> ortholog). However, the regulatory contribution of these genes to <i>PIM</i> activation in legumes remains elusive. Here, we presented the theoretical and data-driven analyses of a feed-forward regulatory motif that includes a vernalization-responsive <i>FT</i> gene and several <i>SOC1</i> genes, which independently activate <i>PIM</i> and thereby mediate floral transition. Our theoretical model showed that the multiple regulatory branches in this regulatory motif facilitated the elimination of no-sense signals and amplified useful signals from the upstream regulator. We further developed and analyzed four data-driven models of <i>PIM</i> activation in <i>Medicago trancatula</i> in vernalized and non-vernalized conditions in wild-type and <i>fta1-1</i> mutants. The model with <i>FTa1</i> providing both direct activation and indirect activation via three intermediate activators, <i>SOC1a</i>, <i>SOC1b</i>, and <i>SOC1c</i>, resulted in the most relevant <i>PIM</i> dynamics. In this model, the difference between regulatory inputs of <i>SOC1</i> genes was nonessential. As a result, in the <i>M. trancatula</i> model, the cumulative action of <i>SOC1a</i>, <i>SOC1b</i>, and <i>SOC1c</i> was favored. Overall, in this study, we first presented the in silico analysis of vernalization-induced flowering in legumes. The considered vernalization network motif can be supplemented with additional regulatory branches as new experimental data become available. |
| first_indexed | 2024-03-08T10:44:06Z |
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| id | doaj.art-29f0baf6de5a4636b9ac24c97f5b5226 |
| institution | Directory Open Access Journal |
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| last_indexed | 2024-03-08T10:44:06Z |
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| spelling | doaj.art-29f0baf6de5a4636b9ac24c97f5b52262024-01-26T17:20:27ZengMDPI AGLife2075-17292023-12-011412610.3390/life14010026Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i>Maria A. Duk0Vitaly V. Gursky1Maria G. Samsonova2Svetlana Yu. Surkova3Mathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, RussiaTheoretical Department, Ioffe Institute, 194021 St. Petersburg, RussiaMathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, RussiaMathematical Biology and Bioinformatics Laboratory, Peter the Great Saint Petersburg Polytechnic University, 195251 St. Petersburg, RussiaIn many plant species, flowering is promoted by the cold treatment or vernalization. The mechanism of vernalization-induced flowering has been extensively studied in <i>Arabidopsis</i> but remains largely unknown in legumes. The orthologs of the <i>FLC</i> gene, a major regulator of vernalization response in <i>Arabidopsis</i>, are absent or non-functional in the vernalization-sensitive legume species. Nevertheless, the legume integrator genes <i>FT</i> and <i>SOC1</i> are involved in the transition of the vernalization signal to meristem identity genes, including <i>PIM</i> (<i>AP1</i> ortholog). However, the regulatory contribution of these genes to <i>PIM</i> activation in legumes remains elusive. Here, we presented the theoretical and data-driven analyses of a feed-forward regulatory motif that includes a vernalization-responsive <i>FT</i> gene and several <i>SOC1</i> genes, which independently activate <i>PIM</i> and thereby mediate floral transition. Our theoretical model showed that the multiple regulatory branches in this regulatory motif facilitated the elimination of no-sense signals and amplified useful signals from the upstream regulator. We further developed and analyzed four data-driven models of <i>PIM</i> activation in <i>Medicago trancatula</i> in vernalized and non-vernalized conditions in wild-type and <i>fta1-1</i> mutants. The model with <i>FTa1</i> providing both direct activation and indirect activation via three intermediate activators, <i>SOC1a</i>, <i>SOC1b</i>, and <i>SOC1c</i>, resulted in the most relevant <i>PIM</i> dynamics. In this model, the difference between regulatory inputs of <i>SOC1</i> genes was nonessential. As a result, in the <i>M. trancatula</i> model, the cumulative action of <i>SOC1a</i>, <i>SOC1b</i>, and <i>SOC1c</i> was favored. Overall, in this study, we first presented the in silico analysis of vernalization-induced flowering in legumes. The considered vernalization network motif can be supplemented with additional regulatory branches as new experimental data become available.https://www.mdpi.com/2075-1729/14/1/26vernalizationlegumesgene networksdynamical modelfeed-forward loop<i>Medicago trancatula</i> |
| spellingShingle | Maria A. Duk Vitaly V. Gursky Maria G. Samsonova Svetlana Yu. Surkova Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i> Life vernalization legumes gene networks dynamical model feed-forward loop <i>Medicago trancatula</i> |
| title | Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i> |
| title_full | Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i> |
| title_fullStr | Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i> |
| title_full_unstemmed | Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i> |
| title_short | Modeling the Flowering Activation Motif during Vernalization in Legumes: A Case Study of <i>M. trancatula</i> |
| title_sort | modeling the flowering activation motif during vernalization in legumes a case study of i m trancatula i |
| topic | vernalization legumes gene networks dynamical model feed-forward loop <i>Medicago trancatula</i> |
| url | https://www.mdpi.com/2075-1729/14/1/26 |
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