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Fan J, Ning K, Zeng X, Luo Y, Wang D, Hu J, Li J, Xu H, Huang J, Wan M, Wang W, Zhang D, Shen G, Run C, Liao J, Fang L, Huang S, Jing X, Su X, Wang A, Bai L, Hu Z, Xu J, Li Y. Genomic Foundation of Starch-to-Lipid Switch in Oleaginous Chlorella spp. PLANT PHYSIOLOGY 2015; 169:2444-61. [PMID: 26486592 PMCID: PMC4677908 DOI: 10.1104/pp.15.01174] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 10/20/2015] [Indexed: 05/17/2023]
Abstract
The ability to rapidly switch the intracellular energy storage form from starch to lipids is an advantageous trait for microalgae feedstock. To probe this mechanism, we sequenced the 56.8-Mbp genome of Chlorella pyrenoidosa FACHB-9, an industrial production strain for protein, starch, and lipids. The genome exhibits positive selection and gene family expansion in lipid and carbohydrate metabolism and genes related to cell cycle and stress response. Moreover, 10 lipid metabolism genes might be originated from bacteria via horizontal gene transfer. Transcriptomic dynamics tracked via messenger RNA sequencing over six time points during metabolic switch from starch-rich heterotrophy to lipid-rich photoautotrophy revealed that under heterotrophy, genes most strongly expressed were from the tricarboxylic acid cycle, respiratory chain, oxidative phosphorylation, gluconeogenesis, glyoxylate cycle, and amino acid metabolisms, whereas those most down-regulated were from fatty acid and oxidative pentose phosphate metabolism. The shift from heterotrophy into photoautotrophy highlights up-regulation of genes from carbon fixation, photosynthesis, fatty acid biosynthesis, the oxidative pentose phosphate pathway, and starch catabolism, which resulted in a marked redirection of metabolism, where the primary carbon source of glycine is no longer supplied to cell building blocks by the tricarboxylic acid cycle and gluconeogenesis, whereas carbon skeletons from photosynthesis and starch degradation may be directly channeled into fatty acid and protein biosynthesis. By establishing the first genetic transformation in industrial oleaginous C. pyrenoidosa, we further showed that overexpression of an NAD(H) kinase from Arabidopsis (Arabidopsis thaliana) increased cellular lipid content by 110.4%, yet without reducing growth rate. These findings provide a foundation for exploiting the metabolic switch in microalgae for improved photosynthetic production of food and fuels.
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Affiliation(s)
- Jianhua Fan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Kang Ning
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Xiaowei Zeng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Yuanchan Luo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Dongmei Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Jianqiang Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Jing Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Hui Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Jianke Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Minxi Wan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Weiliang Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Daojing Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Guomin Shen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Conglin Run
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Junjie Liao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Lei Fang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Shi Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Xiaoyan Jing
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Xiaoquan Su
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Anhui Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Lili Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Zanmin Hu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Jian Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
| | - Yuanguang Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237, China (J.F., Y.Lu., H.X., J.Hua., M.W., W.W., D.Z., G.S., C.R., J.Lia., L.F., Y.Li.);Single-Cell Center, Chinese Academy of Sciences Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong 266101, China (K.N., X.Z., D.W., J.Hu., J.Li., S.H., X.J., X.S., A.W., J.X.); andInstitute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China (L.B., Z.H.)
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