Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i>
The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inver...
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MDPI AG
2021-08-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/10/9/2217 |
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| author | Robert C. Moseley Francis Motta Gerald A. Tuskan Steven B. Haase Xiaohan Yang |
| author_facet | Robert C. Moseley Francis Motta Gerald A. Tuskan Steven B. Haase Xiaohan Yang |
| author_sort | Robert C. Moseley |
| collection | DOAJ |
| description | The circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in <i>Kalanch</i><i>oë fedtschenkoi</i>. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in <i>K. fedtschenkoi</i>, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments. |
| first_indexed | 2024-03-10T07:49:21Z |
| format | Article |
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| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-10T07:49:21Z |
| publishDate | 2021-08-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-725d512ccd8343678bf95bc8d19791f82023-11-22T12:22:38ZengMDPI AGCells2073-44092021-08-01109221710.3390/cells10092217Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i>Robert C. Moseley0Francis Motta1Gerald A. Tuskan2Steven B. Haase3Xiaohan Yang4Department of Biology, Duke University, Durham, NC 27708, USADepartment of Mathematical Sciences, Florida Atlantic University, Boca Raton, FL 33431, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USADepartment of Biology, Duke University, Durham, NC 27708, USABiosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USAThe circadian clock drives time-specific gene expression, enabling biological processes to be temporally controlled. Plants that conduct crassulacean acid metabolism (CAM) photosynthesis represent an interesting case of circadian regulation of gene expression as stomatal movement is temporally inverted relative to stomatal movement in C3 plants. The mechanisms behind how the circadian clock enabled physiological differences at the molecular level is not well understood. Recently, the rescheduling of gene expression was reported as a mechanism to explain how CAM evolved from C3. Therefore, we investigated whether core circadian clock genes in CAM plants were re-phased during evolution, or whether networks of phase-specific genes were simply re-wired to different core clock genes. We identified candidate core clock genes based on gene expression features and then applied the Local Edge Machine (LEM) algorithm to infer regulatory relationships between this new set of core candidates and known core clock genes in <i>Kalanch</i><i>oë fedtschenkoi</i>. We further inferred stomata-related gene targets for known and candidate core clock genes and constructed a gene regulatory network for core clock and stomata-related genes. Our results provide new insight into the mechanism of circadian control of CAM-related genes in <i>K. fedtschenkoi</i>, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.https://www.mdpi.com/2073-4409/10/9/2217circadian clockdroughtcrassulacean acid metabolismLocal Edge Machinestomatagene expression |
| spellingShingle | Robert C. Moseley Francis Motta Gerald A. Tuskan Steven B. Haase Xiaohan Yang Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i> Cells circadian clock drought crassulacean acid metabolism Local Edge Machine stomata gene expression |
| title | Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i> |
| title_full | Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i> |
| title_fullStr | Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i> |
| title_full_unstemmed | Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i> |
| title_short | Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in <i>Kalanch</i><i>oë fedtschenkoi</i> |
| title_sort | inference of gene regulatory network uncovers the linkage between circadian clock and crassulacean acid metabolism in i kalanch i i oe fedtschenkoi i |
| topic | circadian clock drought crassulacean acid metabolism Local Edge Machine stomata gene expression |
| url | https://www.mdpi.com/2073-4409/10/9/2217 |
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