Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110
The dynamic adaptation of bacteria to environmental changes is achieved through the coordinated expression of many genes, which constitutes a transcriptional regulatory network (TRN). <i>Bradyrhizobium diazoefficiens</i> USDA110 is an important model strain for the study of symbiotic nit...
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MDPI AG
2023-08-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/24/16/12544 |
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| author | Zhi-Peng Gao Wei-Cheng Gu Jie Li Qin-Tian Qiu Bin-Guang Ma |
| author_facet | Zhi-Peng Gao Wei-Cheng Gu Jie Li Qin-Tian Qiu Bin-Guang Ma |
| author_sort | Zhi-Peng Gao |
| collection | DOAJ |
| description | The dynamic adaptation of bacteria to environmental changes is achieved through the coordinated expression of many genes, which constitutes a transcriptional regulatory network (TRN). <i>Bradyrhizobium diazoefficiens</i> USDA110 is an important model strain for the study of symbiotic nitrogen fixation (SNF), and its SNF ability largely depends on the TRN. In this study, independent component analysis was applied to 226 high-quality gene expression profiles of <i>B. diazoefficiens</i> USDA110 microarray datasets, from which 64 iModulons were identified. Using these iModulons and their condition-specific activity levels, we (1) provided new insights into the connection between the FixLJ-FixK<sub>2</sub>-FixK<sub>1</sub> regulatory cascade and quorum sensing, (2) discovered the independence of the FixLJ-FixK<sub>2</sub>-FixK<sub>1</sub> and NifA/RpoN regulatory cascades in response to oxygen, (3) identified the FixLJ-FixK<sub>2</sub> cascade as a mediator connecting the FixK<sub>2</sub>-2 iModulon and the Phenylalanine iModulon, (4) described the differential activation of iModulons in <i>B. diazoefficiens</i> USDA110 under different environmental conditions, and (5) proposed a notion of active-TRN based on the changes in iModulon activity to better illustrate the relationship between gene regulation and environmental condition. In sum, this research offered an iModulon-based TRN for <i>B. diazoefficiens</i> USDA110, which formed a foundation for comprehensively understanding the intricate transcriptional regulation during SNF. |
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| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T23:53:02Z |
| publishDate | 2023-08-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-0d78dd8123314f96b7a16468b8cf8ff52023-11-19T01:24:37ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672023-08-0124161254410.3390/ijms241612544Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110Zhi-Peng Gao0Wei-Cheng Gu1Jie Li2Qin-Tian Qiu3Bin-Guang Ma4Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, ChinaHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, ChinaHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, ChinaHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, ChinaHubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, ChinaThe dynamic adaptation of bacteria to environmental changes is achieved through the coordinated expression of many genes, which constitutes a transcriptional regulatory network (TRN). <i>Bradyrhizobium diazoefficiens</i> USDA110 is an important model strain for the study of symbiotic nitrogen fixation (SNF), and its SNF ability largely depends on the TRN. In this study, independent component analysis was applied to 226 high-quality gene expression profiles of <i>B. diazoefficiens</i> USDA110 microarray datasets, from which 64 iModulons were identified. Using these iModulons and their condition-specific activity levels, we (1) provided new insights into the connection between the FixLJ-FixK<sub>2</sub>-FixK<sub>1</sub> regulatory cascade and quorum sensing, (2) discovered the independence of the FixLJ-FixK<sub>2</sub>-FixK<sub>1</sub> and NifA/RpoN regulatory cascades in response to oxygen, (3) identified the FixLJ-FixK<sub>2</sub> cascade as a mediator connecting the FixK<sub>2</sub>-2 iModulon and the Phenylalanine iModulon, (4) described the differential activation of iModulons in <i>B. diazoefficiens</i> USDA110 under different environmental conditions, and (5) proposed a notion of active-TRN based on the changes in iModulon activity to better illustrate the relationship between gene regulation and environmental condition. In sum, this research offered an iModulon-based TRN for <i>B. diazoefficiens</i> USDA110, which formed a foundation for comprehensively understanding the intricate transcriptional regulation during SNF.https://www.mdpi.com/1422-0067/24/16/12544independent component analysistranscriptional regulatory networkfunctional modulestranscriptomerhizobia<i>Bradyrhizobium diazoefficiens</i> |
| spellingShingle | Zhi-Peng Gao Wei-Cheng Gu Jie Li Qin-Tian Qiu Bin-Guang Ma Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110 International Journal of Molecular Sciences independent component analysis transcriptional regulatory network functional modules transcriptome rhizobia <i>Bradyrhizobium diazoefficiens</i> |
| title | Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110 |
| title_full | Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110 |
| title_fullStr | Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110 |
| title_full_unstemmed | Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110 |
| title_short | Independent Component Analysis Reveals the Transcriptional Regulatory Modules in <i>Bradyrhizobium diazoefficiens</i> USDA110 |
| title_sort | independent component analysis reveals the transcriptional regulatory modules in i bradyrhizobium diazoefficiens i usda110 |
| topic | independent component analysis transcriptional regulatory network functional modules transcriptome rhizobia <i>Bradyrhizobium diazoefficiens</i> |
| url | https://www.mdpi.com/1422-0067/24/16/12544 |
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