Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi
Abstract
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 Kalanchoë fedtschenkoi. 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 K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plantsmore »
- Authors:
-
[2];
[3];
[3]
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Duke Univ., Durham, NC (United States)
- Duke Univ., Durham, NC (United States)
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1817615
- Grant/Contract Number:
- AC05-00OR22725; SC0008834
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Cells
- Additional Journal Information:
- Journal Volume: 10; Journal Issue: 9; Journal ID: ISSN 2073-4409
- Publisher:
- MDPI
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; circadian clock; drought; crassulacean acid metabolism; Local Edge Machine; stomata; gene expression
Citation Formats
Moseley, Robert C., Motta, Francis, Tuskan, Gerald A., Haase, Steve, and Yang, Xiaohan. Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. United States: N. p., 2021.
Web. doi:10.3390/cells10092217.
Moseley, Robert C., Motta, Francis, Tuskan, Gerald A., Haase, Steve, & Yang, Xiaohan. Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi. United States. https://doi.org/10.3390/cells10092217
Moseley, Robert C., Motta, Francis, Tuskan, Gerald A., Haase, Steve, and Yang, Xiaohan. Fri .
"Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi". United States. https://doi.org/10.3390/cells10092217. https://www.osti.gov/servlets/purl/1817615.
@article{osti_1817615,
title = {Inference of Gene Regulatory Network Uncovers the Linkage between Circadian Clock and Crassulacean Acid Metabolism in Kalanchoë fedtschenkoi},
author = {Moseley, Robert C. and Motta, Francis and Tuskan, Gerald A. and Haase, Steve and Yang, Xiaohan},
abstractNote = {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 Kalanchoë fedtschenkoi. 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 K. fedtschenkoi, facilitating the engineering of CAM machinery into non-CAM plants for sustainable crop production in water-limited environments.},
doi = {10.3390/cells10092217},
journal = {Cells},
number = 9,
volume = 10,
place = {United States},
year = {Fri Aug 27 00:00:00 EDT 2021},
month = {Fri Aug 27 00:00:00 EDT 2021}
}
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