DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions
Abstract Phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc) causes black rot and other plant diseases. Xcc senses diffusible signal factor (DSF) as a quorum-sensing (QS) signal that mediates mainly iron uptake and virulence. RpfB deactivates DSF in this DSF–QS circuit. We examined...
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Nature Portfolio
2023-05-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-35487-9 |
| _version_ | 1797811581096034304 |
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| author | Kunal Dutta Sergey Shityakov Fumito Maruyama |
| author_facet | Kunal Dutta Sergey Shityakov Fumito Maruyama |
| author_sort | Kunal Dutta |
| collection | DOAJ |
| description | Abstract Phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc) causes black rot and other plant diseases. Xcc senses diffusible signal factor (DSF) as a quorum-sensing (QS) signal that mediates mainly iron uptake and virulence. RpfB deactivates DSF in this DSF–QS circuit. We examined differential gene expression profiles of Bradyrhizobium japonicum under low versus high iron conditions and found that fadD and irr were upregulated under low iron (log2 fold change 0.825 and 1.716, respectively). In addition to having similar protein folding patterns and functional domain similarities, FadD shared 58% sequence similarity with RpfB of Xcc. The RpfB–DSF and FadD–DSF complexes had SWISSDock molecular docking scores of − 8.88 kcal/mol and − 9.85 kcal/mol, respectively, and the 100 ns molecular dynamics simulation results were in accord with the docking results. However, significant differences were found between the binding energies of FadD–DSF and RpfB–DSF, indicating possible FadD-dependent DSF turnover. The protein–protein interaction network showed that FadD connected indirectly with ABC transporter permease (ABCtp), which was also upregulated (log2 fold change 5.485). We speculate that the low iron condition may be a mimetic environmental stimulus for fadD upregulation in B. japonicum to deactivate DSF, inhibit iron uptake and virulence of DSF-producing neighbors. This finding provides a new option of using B. japonicum or a genetically improved B. japonicum as a potential biocontrol agent against Xcc, with the added benefit of plant growth-promoting properties. |
| first_indexed | 2024-03-13T07:24:50Z |
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| id | doaj.art-efe4122ee8404e92a5afd7bbc55f76cd |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-13T07:24:50Z |
| publishDate | 2023-05-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-efe4122ee8404e92a5afd7bbc55f76cd2023-06-04T11:27:00ZengNature PortfolioScientific Reports2045-23222023-05-0113111410.1038/s41598-023-35487-9DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditionsKunal Dutta0Sergey Shityakov1Fumito Maruyama2Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO UniversityLaboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO UniversityMicrobial Genomics and Ecology, The IDEC Institute, Hiroshima UniversityAbstract Phytopathogenic bacteria Xanthomonas campestris pv. campestris (Xcc) causes black rot and other plant diseases. Xcc senses diffusible signal factor (DSF) as a quorum-sensing (QS) signal that mediates mainly iron uptake and virulence. RpfB deactivates DSF in this DSF–QS circuit. We examined differential gene expression profiles of Bradyrhizobium japonicum under low versus high iron conditions and found that fadD and irr were upregulated under low iron (log2 fold change 0.825 and 1.716, respectively). In addition to having similar protein folding patterns and functional domain similarities, FadD shared 58% sequence similarity with RpfB of Xcc. The RpfB–DSF and FadD–DSF complexes had SWISSDock molecular docking scores of − 8.88 kcal/mol and − 9.85 kcal/mol, respectively, and the 100 ns molecular dynamics simulation results were in accord with the docking results. However, significant differences were found between the binding energies of FadD–DSF and RpfB–DSF, indicating possible FadD-dependent DSF turnover. The protein–protein interaction network showed that FadD connected indirectly with ABC transporter permease (ABCtp), which was also upregulated (log2 fold change 5.485). We speculate that the low iron condition may be a mimetic environmental stimulus for fadD upregulation in B. japonicum to deactivate DSF, inhibit iron uptake and virulence of DSF-producing neighbors. This finding provides a new option of using B. japonicum or a genetically improved B. japonicum as a potential biocontrol agent against Xcc, with the added benefit of plant growth-promoting properties.https://doi.org/10.1038/s41598-023-35487-9 |
| spellingShingle | Kunal Dutta Sergey Shityakov Fumito Maruyama DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions Scientific Reports |
| title | DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions |
| title_full | DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions |
| title_fullStr | DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions |
| title_full_unstemmed | DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions |
| title_short | DSF inactivator RpfB homologous FadD upregulated in Bradyrhizobium japonicum under iron limiting conditions |
| title_sort | dsf inactivator rpfb homologous fadd upregulated in bradyrhizobium japonicum under iron limiting conditions |
| url | https://doi.org/10.1038/s41598-023-35487-9 |
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