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

   

[1] Nie, Xiaoqun, Xia, Liliang, Gao, Fang, Liu, Lixia, Yang, Yi, Chen, Yingying, Duan, Huangqi, Yao, Yaxian, Chen, Zhiwei, Lu, Shun, Wang, Ying, Yang, Chen. Serum Metabolite Biomarkers Predictive of Response to PD-1 Blockade Therapy in Non-Small Cell Lung Cancer. FRONTIERS IN MOLECULAR BIOSCIENCES[J]. 2021, 8: https://doaj.org/article/307b214561e1409d8efdb7a4edbc27ad.

[2] Wenyue Dong, Xiaoqun Nie, Hong Zhu, Qingyun Liu, Kunxiong Shi, Linlin You, Yu Zhang, Hongyan Fan, Bo Yan, Chen Niu, LiangDong Lyu, GuoPing Zhao, Chen Yang. Mycobacterial fatty acid catabolism is repressed by FdmR to sustain lipogenesis and virulence. Proceedings of the National Academy of Sciences of the United States of America[J]. 2021, 118(16): 
[3] Nie, Xiaoqun, Hua, Qiang, Xu, Ping, Yang, Chen. Biological insights into non-model microbial hosts through stable-isotope metabolic flux analysis. CURRENT OPINION IN BIOTECHNOLOGYnull. 2020, 64: 32-38, http://dx.doi.org/10.1016/j.copbio.2019.09.010.

[4] Yang, Bin, Nie, Xiaoqun, Xiao, Youli, Gu, Yang, Jiang, Weihong, Yang, Chen. Ferrous-Iron-Activated Transcriptional Factor AdhR Regulates Redox Homeostasis in Clostridium beijerinckii. APPLIED AND ENVIRONMENTAL MICROBIOLOGY[J]. 2020, 86(7): https://www.webofscience.com/wos/woscc/full-record/WOS:000522978900018.

[5] Bin Yang, Xiaoqun Nie, Yang Gu, Weihong Jiang, Chen Yang. Control of solvent production by sigma‐54 factor and the transcriptional activator AdhR in Clostridium beijerinckii. Microbial Biotechnology[J]. 2020, 13(2): 328-338, https://doaj.org/article/50ac545e749848e3914ea49c8457571b.

[6] Yang Chen. Succinate-GPR-91 receptor signaling is responsible for nonalcoholic steatohepatitis-associated fibrosis: effects of DHA supplementation.. Liver International. 2020, 
[7] Wang, Weishan, Li, Shanshan, Li, Zilong, Zhang, Jingyu, Fan, Keqiang, Tan, Gaoyi, Ai, Guomin, Lam, Sin Man, Shui, Guanghou, Yang, Zhiheng, Lu, Hongzhong, Jin, Pinjiao, Li, Yihong, Chen, Xiangyin, Xia, Xuekui, Liu, Xueting, Dannelly, H Kathleen, Yang, Chen, Yang, Yi, Zhang, Siliang, Alterovitz, Gil, Xiang, Wensheng, Zhang, Lixin. Harnessing the intracellular triacylglycerols for titer improvement of polyketides in Streptomyces. NATURE BIOTECHNOLOGY[J]. 2020, 38(1): 76-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000510337700016.

[8] Chen, Chen, He, Bingshu, Liu, Xingxun, Ma, Xiaoding, Liu, Yujie, Yao, HongYan, Zhang, Peng, Yin, Junliang, Wei, Xin, Koh, HeeJong, Yang, Chen, Xue, HongWei, Fang, Zhengwu, Qiao, Yongli. Pyrophosphate-fructose 6-phosphate 1-phosphotransferase (PFP1) regulates starch biosynthesis and seed development via heterotetramer formation in rice (Oryza sativa L.). PLANT BIOTECHNOLOGY JOURNAL[J]. 2020, 18(1): 83-95, https://www.webofscience.com/wos/woscc/full-record/WOS:000530370800012.

[9] Nie, Xiaoqun, Dong, Wenyue, Yang, Chen. Genomic reconstruction of sigma(54) regulons in Clostridiales. BMC GENOMICS[J]. 2019, 20: http://dx.doi.org/10.1186/s12864-019-5918-4.

[10] , , , , , . Crystal structures and biochemical analyses of the bacterial arginine dihydrolase ArgZ suggests a "bond rotation" catalytic mechanism. The Journal of Biological Chemistry. 2019, 295(7): 2113-2124, http://dx.doi.org/10.1074/jbc.RA119.011752.

[11] Zhang, Hao, Yang, Chen. Arginine and nitrogen mobilization in cyanobacteria. MOLECULAR MICROBIOLOGYnull. 2019, 111(4): 863-867, 
[12] Zhang, Hao, Liu, Yujie, Nie, Xiaoqun, Liu, Lixia, Hua, Qiang, Zhao, GuoPing, Yang, Chen. The cyanobacterial ornithine-ammonia cycle involves an arginine dihydrolase. NATURE CHEMICAL BIOLOGY[J]. 2018, 14(6): 575-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000435445100014.

[13] Shao, Yangyang, Lu, Ning, Wu, Zhenfang, Cai, Chen, Wang, Shanshan, Zhang, LingLi, Zhou, Fan, Xiao, Shijun, Liu, Lin, Zeng, Xiaofei, Zheng, Huajun, Yang, Chen, Zhao, Zhihu, Zhao, Guoping, Zhou, JinQiu, Xue, Xiaoli, Qin, Zhongjun. Creating a functional single-chromosome yeast. NATURE[J]. 2018, 560(7718): 331-+, http://202.127.25.143/handle/331003/3385.

[14] Brunk, Elizabeth, Chang, Roger L, Xia, Jing, Hefzi, Hooman, Yurkovich, James T, Kim, Donghyuk, Buckmiller, Evan, Wang, Harris H, Cho, ByungKwan, Yang, Chen, Palsson, Bernhard O, Church, George M, Lewis, Nathan E. Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA[J]. 2018, 115(43): 11096-11101, https://www.webofscience.com/wos/woscc/full-record/WOS:000448040500079.

[15] 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. Increased glutarate production by blocking the glutaryl-CoA dehydrogenation pathway and a catabolic pathway involving L-2-hydroxyglutarate. NATURE COMMUNICATIONS[J]. 2018, 9(1): https://doaj.org/article/410d386a718d45bba309100ab02c7216.

[16] Yang, Yunpeng, Nie, Xiaoqun, Jiang, Yuqian, Yang, Chen, Gu, Yang, Jiang, Weihong. Metabolic regulation in solventogenic clostridia: regulators, mechanisms and engineering. BIOTECHNOLOGY ADVANCESnull. 2018, 36(4): 905-914, http://dx.doi.org/10.1016/j.biotechadv.2018.02.012.

[17] Lu-Men Chao, Yao-Qian Liu, Dian-Yang Chen, Xue-Yi Xue, Ying-Bo Mao, Xiao-Ya Chen. Arabidopsis Transcription Factors SPL1 and SPL12 Confer Plant Thermotolerance at Reproductive Stage. 分子植物：英文版[J]. 2017, 10(5): 735-748, http://lib.cqvip.com/Qikan/Article/Detail?id=672324842.

[18] Nie, Xiaoqun, Yang, Bin, Zhang, Lei, Gu, Yang, Yang, Sheng, Jiang, Weihong, Yang, Chen. PTS regulation domain-containing transcriptional activator CelR and sigma factor sigma(54) control cellobiose utilization in Clostridium acetobutylicum. MOLECULAR MICROBIOLOGY[J]. 2016, 100(2): 289-302, http://dx.doi.org/10.1111/mmi.13316.

[19] Tong, Jingfeng, Meng, Lu, Wang, Xinwei, Liu, Lixia, Lyu, Liangdong, Wang, Chuan, Li, Yang, Gao, Qian, Yang, Chen, Niu, Chen. The FBPase Encoding Gene glpX Is Required for Gluconeogenesis, Bacterial Proliferation and Division In Vivo of Mycobacterium marinum. PLOS ONE[J]. 2016, 11(5): https://doaj.org/article/5718e5e69cab46e4bc3f51229c38ce49.

[20] Yang Chen, Gao Xiang, Jiang Yu, Sun Bingbing, Gao Fang, Yang Sheng. Synergy between methylerythritol phosphate pathway and mevalonate pathway for isoprene production in Escherichia coli. Metabolic Engineering[J]. 2016, 
[21] Gao, Xiang, Gao, Fang, Liu, Deng, Zhang, Hao, Nie, Xiaoqun, Yang, Chen. Engineering the methylerythritol phosphate pathway in cyanobacteria for photosynthetic isoprene production from CO2. ENERGY & ENVIRONMENTAL SCIENCE[J]. 2016, 9(4): 1400-1411, http://dx.doi.org/10.1039/c5ee03102h.

[22] Yang Chen. Metabolic flux ratio analysis and cell staining suggest the existence of C4 photosynthesis in Phaeodactylum tricornutum. Journal of Applied Microbiology. 2015, 
[23] Zhang, Lei, Nie, Xiaoqun, Ravcheev, Dmitry A, Rodionov, Dmitry A, Sheng, Jia, Gu, Yang, Yang, Sheng, Jiang, Weihong, Yang, Chen. Redox-Responsive Repressor Rex Modulates Alcohol Production and Oxidative Stress Tolerance in Clostridium acetobutylicum. JOURNAL OF BACTERIOLOGY[J]. 2014, 196(22): 3949-3963, https://www.webofscience.com/wos/woscc/full-record/WOS:000343930600014.

[24] Liu, DongFeng, Ai, GuoMin, Zheng, QingXiang, Liu, Chang, Jiang, ChengYing, Liu, LiXia, Zhang, Bo, Liu, YiMing, Yang, Chen, Liu, ShuangJiang. Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains. MICROBIAL CELL FACTORIES[J]. 2014, 13(1): 40-40, https://www.webofscience.com/wos/woscc/full-record/WOS:000334713200001.

[25] Deng Liu, Chen Yang. The Nitrogen-regulated Response Regulator NrrA Controls Cyanophycin Synthesis and Glycogen Catabolism in the Cyanobacterium Synechocystis sp. PCC 6803 *. The Journal of Biological Chemistry. 2013, 289(4): 2055-2071, 
[26] Tao, Yongzhen, Liu, Deng, Yan, Xing, Zhou, Zhihua, Lee, Jeong K, Yang, Chen. Network Identification and Flux Quantification of Glucose Metabolism in Rhodobacter sphaeroides under Photoheterotrophic H-2-Producing Conditions. JOURNAL OF BACTERIOLOGY[J]. 2012, 194(2): 274-283, http://dx.doi.org/10.1128/JB.05624-11.

[27] Leyn, Semen A, Gao, Fang, Yang, Chen, Rodionov, Dmitry A. N-Acetylgalactosamine Utilization Pathway and Regulon in Proteobacteria GENOMIC RECONSTRUCTION AND EXPERIMENTAL CHARACTERIZATION IN SHEWANELLA. JOURNAL OF BIOLOGICAL CHEMISTRY[J]. 2012, 287(33): 28047-28056, http://dx.doi.org/10.1074/jbc.M112.382333.

杨琛研究组发现致病分枝杆菌脂肪酸代谢的调控机制

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	中国科学院深圳先进技术研究院 副研究员
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