课题组致力于细胞代谢网络运转及调控机制的定量研究，实现其人工设计与系统优化。主要研究兴趣包括：

1. 开发代谢流量分析与代谢组学分析技术；

2. 定量研究细胞代谢网络运转机制，揭示各种分子机制对代谢流量的调节与控制；

3. 开展光能自养微生物以及菌群的合成生物学研究。

围绕研究目标，利用我们在微生物学、生物工程、生物化学、计算生物学上的学科交叉优势，建立了代谢流量分析、代谢组学分析、比较基因组学、代谢网络建模等关键技术。其中，代谢流量（Metabolic flux）分析，即解析活体状态下的代谢反应速率，以表征基因、蛋白质、代谢物之间各种相互作用导致的代谢网络的动态行为和最终功能；它对于全面理解与认识生物体的物质与能量代谢过程，从而操纵生物体的生命活动，具有重要的意义。

   

071005-微生物学
081703-生物化工

微生物代谢工程和比较基因组学

1997-09--2001-09   日本九州工业大学   获得博士学位
1994-09--1997-08   浙江大学   获得硕士学位
1990-09--1994-08   浙江大学   获得学士学位

   

2008-07~现在, 中国科学院上海生命科学研究院植物生理生态研究所, 研究员
2004-05~2008-07,美国Burnham医学研究所, 博士后
2001-10~2004-04,日本庆应大学，先端生命科学研究所, 博士后

2010.09.032015.11.2514ZL201310128943.8利用蓝藻生产异戊二烯    杨琛，高翔，刘邓，高方

International Channel Shanghai (ICS) SH scientists make blue algae discovery 中国科学家发现新型蓝藻代谢途径 助力合成生物学研究

杨琛研究组发现蓝藻代谢与环境适应的新途径

我所取得生物丁醇制造技术研究新进展

学生	毕业时间	去向	现职
郑庆祥	2013博	福建漳州农业局	福建漳州农业局
刘邓	2013博	美国华盛顿大学 博后	美国华盛顿大学
张蕾	2014博	美国阿尔伯特爱因斯坦医学院 博后	美国明尼苏达大学
高翔	2016博	美国芝加哥大学 博后
夏静	2017博
聂小群	2018博	中科院上海植物生理生态研究所 博后	中科院分子植物卓越中心 博后
张昊	2019博	宾夕法尼亚大学 博后	宾夕法尼亚大学 博后
杨彬	2020博
博后	出站时间	去向	现职
陶用珍	2012年	Burnham医学研究所	中科院上海营养与健康研究所
申铁	2011年	贵州师范大学	贵州师范大学

• Xiaoqun Nie, Hua Qiang, Xu Ping, Chen Yang* (2020) Biological insights into non-model microbial hosts through stable-isotope metabolic flux analysis. Current Opinion in Biotechnology 64:32. 

• Ningning Zhuang#, Hao Zhang#, Lingting Li, Xiaoxian Wu, Chen Yang*, Yu Zhang* (2020) Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. Journal of Biological Chemistry 295: 2113-2124. 

• Bin Yang, Xiaoqun Nie, Yang Gu, Weihong Jiang, Chen Yang* (2020) Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii. Applied Environmental Microbiology 86:e02782-19. 

• Bin Yang, Xiaoqun Nie, Yang Gu, Weihong Jiang, Chen Yang* (2020) Control of solvent production by sigma-54 factor and the transcriptional activator AdhR in Clostridium beijerinckii. Microbial biotechnology 13: 328-338. 

• Xuejing Liu, Li Xie, Kuo Du, Chang Liu, Ningping Zhang, Chenjian Gu, Ying Wang, Manal F. Abdelmalek, Wenyue Dong, Xiuping Liu, Chen Niu*, Chen Yang, Anna Mae Diehl*, Jian Wu* (2020) Succinate-GPR-91 receptor signaling is responsible for nonalcoholic steatohepatitis-associated fibrosis: effects of DHA supplementation. Liver International 40: 830-843. 

• Xiaoqun Nie, Wenyue Dong, Chen Yang* (2019) Genomic reconstruction of sigma(54) regulons in Clostridiales. BMC Genomics 20:565. 

• Hao Zhang, Chen Yang* (2019) Arginine and nitrogen mobilization in cyanobacteria. Molecular Microbiology 111:863-867. 

• Hao Zhang, Yujie Liu, Xiaoqun Nie, Lixia Liu, Qiang Hua, Guo-Ping Zhao, Chen Yang* (2018) The cyanobacterial ornithine-ammonia cycle involves an arginine dihydrolase. Nature Chemical Biology 14: 575-581. 

• Yunpeng Yang#, Xiaoqun Nie#, Yuqian Jiang, Chen Yang*, Yang Gu*, Weihong Jiang* (2018) Metabolic regulation in solventogenic clostridia: regulators, mechanisms and engineering. Biotechnology Advances 36: 905-914. 

• Yangyang Shao, Ning Lu, Zhenfang Wu, Chen Cai, Shanshan Wang, Lingli Zhang, Fan Zhou, Shijun Xiao, Lin Liu, Xiaofei Zeng, Huajun Zheng, Chen Yang, Zhihu Zhao, Guo-Ping Zhao*, Jin-Qiu Zhou*, Xiaoli Xue*, Zhongjun Qin* (2018) Creating a functional single-chromosome yeast. Nature 560: 331-335. 

• Manman Zhang, Chao Gao*, Xiaoting Guo, Shiting Guo, Zhaoqi Kang, Dan Xiao, Jinxin Yan, Fei Tao, Wen Zhang, Wenyue Dong, Pan Liu, Chen Yang, Cuiqing Ma, Ping Xu* (2018) Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. Nature Communications 9: 2114 

• 5. Elizabeth Brunk, Roger L. Chang, Jing Xia, Hooman Hefzi, James T. Yurkovich, Donghyuk Kim, Evan Buckmiller, Harris H. Wang, Byung-Kwan Cho, Chen Yang, Bernhard O. Palsson, George M. Church, Nathan E. Lewis (2018) Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences of the United States of America 115(43): 11096-11101. 

• Xiang Gao, Fang Gao, Deng Liu, Hao Zhang, Xiaoqun Nie, Chen Yang* (2016) Engineering the methylerythritol phosphate pathway in cyanobacteria for photosynthetic isoprene production from CO₂. Energy and Environmental Science 9: 1400-1411. 

• Chen Yang#, Xiang Gao#, Yu Jiang#, Bingbing Sun, Fang Gao, Sheng Yang* (2016) Synergy between methylerythritol phosphate pathway and mevalonate pathway for isoprene production in Escherichia coli. 

• Xiaoqun Nie#, Bin Yang#, Lei Zhang, Yang Gu, Sheng Yang, Weihong Jiang, Chen Yang* (2016) PTS regulation domain-containing transcriptional activator CelR and sigma factor σ⁵⁴ control cellobiose utilization in Clostridium acetobutylicum. Molecular Microbiology 100: 289-302. 

• Jingfeng Tong#, Lu Meng#, Xinwei Wang#, Lixia Liu#, Liangdong Lyu, Chuan Wang, Yang Li, Qian Gao, Chen Yang*, Chen Niu* (2016) The FBPase encoding gene glpX is required for gluconeogenesis, bacterial proliferation and division in vivo of Mycobacterium marinum. PLoS ONE 11(5): e0156663. 

• Aiyou Huang, Lixia Liu, Peipei Zhao,Chen Yang *, Guangce Wang* (2016) Metabolic flux ratio analysis and cell staining suggest the existence of C₄ photosynthesis in Phaeodactylum tricornutum. Journal of Applied Microbiology 120(3): 705-713. 

• Deng Liu and Chen Yang* (2014) The nitrogen-regulated response regulator NrrA controls cyanophycin synthesis and glycogen catabolism in the cyanobacterium Synechocystis sp. PCC 6803. Journal of Biological Chemistry 289: 2055-2071. 

• Lei Zhang, Xiaoqun Nie, Dmitry Ravcheev, Dmitry Rodionov, Jia Sheng, Yang Gu, Sheng Yang, Weihong Jiang, Chen Yang* (2014) Redox-responsive repressor Rex modulates alcohol production and oxidative stress tolerance in Clostridium acetobutylicum. Journal of Bacteriology 196(22): 3949-3963. 

• Dongfeng Liu, Guomin Ai, Qingxiang Zheng, Chang Liu, Chengying Jiang, Lixia Liu, Bo Zhang, Yiming Liu, Chen Yang*, Shuangjiang Liu* (2014) Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains. Microbial Cell Factory 13(1): 40. 

• Yongzhen Tao#, Deng Liu#, Xing Yan, Zhihua Zhou, Jeong K. Lee, Chen Yang* (2012) Network identification and flux quantification of glucose metabolism in under photoheterotrophic H₂-producing conditions. Journal of Bacteriology 194(2): 274-283. 

• Lixia Liu#, Lei Zhang#, Wei Tang, Yang Gu, Qiang Hua, Sheng Yang, Weihong Jiang, Chen Yang* (2012) Phosphoketolase pathway for xylose catabolism in Clostridium acetobutylicum revealed by ¹³C metabolic flux analysis. Journal of Bacteriology 194(19): 5413-5422. 

• Semen A. Leyn#, Fang Gao#, Chen Yang*, Dmitry A. Rodionov* (2012) N-Acetylgalactosamine utilization pathway and regulon in proteobacteria. Genomic reconstruction and experimental characterization in Shewanella. Journal of Biological Chemistry 287(33): 28047-56. 

• Yang Gu#, Yi Ding#, Cong Ren, Zhe Sun, Dmitry A. Rodionov, Weiwen Zhang, Sheng Yang, Chen Yang*, Weihong Jiang* (2010) Reconstruction of xylose utilization pathway and regulons in Firmicutes. BMC Genomics 11: 255.