title: Unraveling the Light-Specific Metabolic and Regulatory Signatures of Rice through Combined in Silico Modeling and Multiomics Analysis.
abstract: Light quality is an important signaling component upon which plants orchestrate various morphological processes, including seed germination and seedling photomorphogenesis. However, it is still unclear how plants, especially food crops, sense various light qualities and modulate their cellular growth and other developmental processes. Therefore, in this work, we initially profiled the transcripts of a model crop, rice (Oryza sativa), under four different light treatments (blue, green, red, and white) as well as in the dark. Concurrently, we reconstructed a fully compartmentalized genome-scale metabolic model of rice cells, iOS2164, containing 2,164 unique genes, 2,283 reactions, and 1,999 metabolites. We then combined the model with transcriptome profiles to elucidate the light-specific transcriptional signatures of rice metabolism. Clearly, light signals mediated rice gene expressions, differentially regulating numerous metabolic pathways: photosynthesis and secondary metabolism were up-regulated in blue light, whereas reserve carbohydrates degradation was pronounced in the dark. The topological analysis of gene expression data with the rice genome-scale metabolic model further uncovered that phytohormones, such as abscisate, ethylene, gibberellin, and jasmonate, are the key biomarkers of light-mediated regulation, and subsequent analysis of the associated genes' promoter regions identified several light-specific transcription factors. Finally, the transcriptional control of rice metabolism by red and blue light signals was assessed by integrating the transcriptome and metabolome data with constraint-based modeling. The biological insights gained from this integrative systems biology approach offer several potential applications, such as improving the agronomic traits of food crops and designing light-specific synthetic gene circuits in microbial and mammalian systems.
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576 (M.L., B.M., D.-Y.L.);Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668 (M.L., D.-Y.L.);Metabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea (S.-H.L.);Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea (J.K.K.); andDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea (S.-H.H.).
authors.forename: Meiyappan
authors.identifier: http://orcid.org/0000-0003-2356-3458
authors.initials: M
authors.lastname: Lakshmanan
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576 (M.L., B.M., D.-Y.L.);Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668 (M.L., D.-Y.L.);Metabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea (S.-H.L.);Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea (J.K.K.); andDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea (S.-H.H.).
authors.forename: Sun-Hyung
authors.initials: SH
authors.lastname: Lim
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576 (M.L., B.M., D.-Y.L.);Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668 (M.L., D.-Y.L.);Metabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea (S.-H.L.);Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea (J.K.K.); andDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea (S.-H.H.).
authors.forename: Bijayalaxmi
authors.identifier: http://orcid.org/0000-0002-8226-2367
authors.initials: B
authors.lastname: Mohanty
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576 (M.L., B.M., D.-Y.L.);Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668 (M.L., D.-Y.L.);Metabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea (S.-H.L.);Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea (J.K.K.); andDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea (S.-H.H.).
authors.forename: Jae Kwang
authors.initials: JK
authors.lastname: Kim
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576 (M.L., B.M., D.-Y.L.);Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668 (M.L., D.-Y.L.);Metabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea (S.-H.L.);Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea (J.K.K.); andDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea (S.-H.H.) sunhwa@khu.ac.kr cheld@nus.edu.sg.
authors.forename: Sun-Hwa
authors.initials: SH
authors.lastname: Ha
authors.affiliation: Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117576 (M.L., B.M., D.-Y.L.);Bioprocessing Technology Institute, Agency for Science, Technology and Research, Singapore 138668 (M.L., D.-Y.L.);Metabolic Engineering Division, National Academy of Agricultural Science, Rural Development Administration, Jeonju 560-500, Republic of Korea (S.-H.L.);Division of Life Sciences, College of Life Sciences and Bioengineering, Incheon National University, Incheon 406-772, Republic of Korea (J.K.K.); andDepartment of Genetic Engineering and Graduate School of Biotechnology, College of Life Sciences, Kyung Hee University, Yongin 446-701, Republic of Korea (S.-H.H.) sunhwa@khu.ac.kr cheld@nus.edu.sg.
authors.forename: Dong-Yup
authors.identifier: http://orcid.org/0000-0003-0901-708X
authors.initials: DY
authors.lastname: Lee
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D020869:Gene Expression Profiling / Q000379:methods*; D018506:Gene Expression Regulation, Plant / Q000528:radiation effects; D053263:Gene Regulatory Networks / Q000235:genetics / Q000528:radiation effects; D017343:Genes, Plant / Q000235:genetics; D008027:Light; D055442:Metabolome / Q000235:genetics / Q000528:radiation effects*; D055432:Metabolomics / Q000379:methods*; D008954:Models, Biological; D008957:Models, Genetic; D012275:Oryza / Q000235:genetics / Q000378:metabolism / Q000528:radiation effects*; D015398:Signal Transduction / Q000235:genetics / Q000528:radiation effects; D059467:Transcriptome / Q000528:radiation effects*