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朱新广,研究员、博士生导师

植物系统生物学

Website: http://www.picb.ac.cn/PSB
Email: zhuxg@sippe.ac.cn

工作人员:宋青峰、曲明南、吕明菊,助理研究员;刘欣雨,实验师
博士后:Essemine Jemaa;Shahnaz Perveen、欧阳翔
研究生:王书月;常天根;赵洪龙;王燕杰;赵永耀;陈法铭;Naveed Khan、周智伟;史载
毕业研究生:信长朋、王玉、余贤斌、宋青峰、徐佳佳、陶一敏、吕明菊、肖怡、田野、曹晨思

研究工作:
主要开展光合作用系统生物学相关研究,主要包括利用系统生物学方法,建立多尺度光合作用系统模型,挖掘并实现提高光能利用效率的新途径;利用合成生物学手段提高作物光能利用效率,为高光效育种、高光效栽培提供全新技术途径;建立作物系统生物学研究平台,支持国际植物系统生物学研究;C4光合作用进化、发育及改造研究。

主要成果:
粮食事关国计民生,粮食安全举世关注。解决粮食安全的重要途径是提高作物单产。近十多年来,我国主要作物单产徘徊不前,粮食增产受到了瓶颈制约。大量理论及大田试验表明,提高作物的光能转化效率是提高作物单产的一条有效的途径。朱新广研究员一直以水稻等作物为主要研究对象,利用系统生物学研究方法,在光能利用效率领域取得一下主要成果:

1)系统研究控制作物光能利用效率的关键靶点:首次定量分析了控制作物光能利用效率的关键因素,系统探明了制约C3及C4光合效率的关键限速酶;在细胞、叶片及冠层三个尺度上,发现了控制光合原材料CO2及光能供应的关键结构及生化因子,为改良光能利用效率提供了新靶点;建立作物冠层光合作用研究的理论及测量手段—建立冠层光合作用系统模型,并研发了测量冠层光合作用、呼吸作用及蒸腾作用的设施,为大规模开展群体光合作用研究奠定基础;

2)建成ePlant系统模型,促成Crop in silico 国际协作:为了促进系统生物学在作物科学中发挥更大作用,率先提出ePlant 概念,建立了ePlant的关键模块模型,并推动了Plant in silico平台的发展。朱新广研究员的研究极大地促进了对光合作用的定量研究;由此获邀作为主编和美国密植根州立大学Tom Sharkey教授一起,为光合作用研究经典系列丛书《Advances in Photosynthesis and Respiration》编撰《Models of Plant Photosynthesis and Growth – A Multiscale Approach》一书,标志着光合作用系统生物学研究已成为国际光合研究重要领域之一。

3)系统阐明C4进化涉及的关键分子事件:在C4光合作用研究领域,研究组集中于C4进化中涉及的关键分子事件及C4工程改造所需的重要结构及生化特征。研究组通过构建C4光合系统模型,发现控制C4光能利用效率的关键酶活及细胞结构特征。进一步研究发现,PEPCK酶催化的四碳酸脱羧途径不能在自然界单独存在,而只能与NAD-ME 或者 NADP-ME催化的四碳酸脱羧途径共同存在;这样可以有利于维持C4植物在外界环境光线剧烈变化时仍有较高的光能利用效率。在C4进化方面,利用具有C4不同进化阶段的黄顶菊属的不同物种为材料,在生理、叶片结构、 转录组等不同层次系统开展比较研究,发现环式电子传递在C4途径进化的不同阶段中都起到重要作用;发现转座子介导的C3基因中的原有顺式调控原件的招募在C4进化中起到重要作用;同时,研究组利用人工进化的方法,发现低CO2 长期培养C3植物,可以有效诱导C4相关基因的表达,这为鉴定C4进化的分子机制及开展C4改造提供了新途径。

主要论文:

1.Mingnan Qu, Guangyong Zheng, Jemaa Essmine, Saber Hamdani, Qingfeng Song, Hongru Wang, Chengcai Chu, Xavier Sirault and Xin-Guang Zhu (2017)Leaf photosynthetic parameters related to biomass accumulation in a global rice diversity panel. Plant Physiology (doi: 10.1104/pp.17.00332).

2.Yi Xiao and Xin-Guang Zhu (2017) Component of mesophyll conductance and their environmental responses. Plant Cell and Environment (doi: 10.1111/pce.13040).

3.Qingfeng Song, Yu Wang, Mingnan Qu, Donald R Ort, Xin-Guang Zhu (2017)The impact of modifying antenna size of photosystem II on canopy photosynthetic efficiency – Development of a new canopy photosynthesis model scaling from metabolism to canopy level processes. Plant Cell and Environment (doi: 10.1111/pce.13041).

4.Yi Xiao, Tiangen Chang, Qingfeng Song, Shuyue Wang, Danny Tholen, Yu Wang, Changpeng Xin, Guangyong Zheng, Honglong Zhao, Xin-Guang Zhu (2017) ePlant for quantitative and predictive plant science research in the big data era. Quantitative Biology (Accepted).

5.Amy Marshall-Colon, Stephen P. Long, Douglas K. Allen, Gabrielle Allen, Daniel A. Beard, Bedrich Benes, Susanne von Caemmerer, AJ Christensen, Donna J. Cox, John C. Hart, Peter M. Hirst, Kavya Kannan, Daniel S. Katz, Jonathan P. Lynch, Andrew J. Millar, Balaji Panneerselvam, Nathan D. Price, Przemyslaw Prusinkiewicz, David Raila, Rachel G. Shekar, Stuti Shrivastava, Diwakar Shukla, Venkatraman Srinivasan, Mark Stitt, Eberhard O. Voit, Yu Wang, Xinyou Yin, Xin-Guang Zhu (2017). Crops in silico: Generating Virtual Crops Using an Integrative and Multi-scale Modeling Platform. Frontiers in Plant Science doi: 8:786. doi: 10.3389/fpls.2017.00786.

6.Jemaa Essemine, Yi Xiao, Hualing Mi, Xin-Guang Zhu (2017) Cyclic electron flow may provide some protection against PSII photoinhibition in rice (Oryza sativa L.) leaves under heat stress. Journal of Plant Physiology 211: 138-146.

7.Yu Wang, Qingfeng Song, Deepak Jaiswal, de Souza Amanda, Stephen P Long, Xin-Guang Zhu (2017) Development of a three-dimensional ray-tracing model of sugarcane canopy photosynthesis and its application in assessing impacts of varied row spacing. BioEnery Research (doi:10.1007/s12155-017-9823-x).

8.Tian-Gen Chang and Xin-Guang Zhu (2017) Source sink interaction: a century old concept under the light of modern molecular systems biology. Journal of Experimental Botany doi: 10.1093/jxb/erx002.

9.Xin-Guang Zhu, Martin Parry, Yonglong Lu, Matthew Heard, Guangguo Ying, Simon Vaughan, Jianbo Shen, Alan Jenkins, Yunpeng Wang, Silvia Lacorte, Tingping Ouyang, Francisco Pedrero Salcedo, Jun Niu, John Quinton, Chunling Luo, Fusuo Zhang, Gan Zhang, Achim Dobermann, William Davies, Kevin Jones, and David Tyfield(2016)Building the new international science of the agri-food-water-environment nexus. Ecosystem Health and Sustainability 2016 (2).

10.Shuyue Wang, Danny Tholen, Xin-Guang Zhu (2016) C4 photosynthesis in C3 rice: a theoretical analysis of biochemical and anatomical factors. Plant Cell and Environment 40(1): 80-94.

11.Yi Xiao, Danny Tholen, Xin-Guang Zhu (2016) The influence of leaf anatomy on the internal light environment and photosynthetic electron transport rate. Journal of Experimental Botany 67(21): 6021-6035.

12.Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen, and Xin-Guang Zhu (2016) CMIP: a software package capable of reconstructing gene regulatory networks using genome-scale data with parallel computing strategy. BMC Bioinformatics 17(17): 137-144.

13.Jiajia Xu, Andrea Bräutigam, Yuanyuan Li, Andreas P. M. Weber and Xin-Guang Zhu (2016) Systems analysis of cis-regulatory motifs in C4 photosynthesis genes using maize and rice leaf transcriptomic data during a process of de-etiolation. Journal of Experimental Botany 67: 5105-5117.

14.Qing-Feng Song, Dairui Chen, Stephen P Long, Xin-Guang Zhu (2016) A user-friendly means to scale from the biochemistry of photosynthesis to whole crop canopies and production in time and space - development of Java WIMOVAC. Plant Cell and Environment 40: 51-55.

15.Mingnan Qu, Saber Hamdani, Wenzhen Li, Shimei Wang, Jiuyou Tang, Zhuo Chen, Qingfeng Song, Ming Li, Honglong Zhao, Tiangen Chang, Chengcai Chu and Xin-Guang Zhu (2016) Rapid stomatal response to fluctuating light: an under-explored mechanism to improve drought tolerance in rice. Functional Plant Biology 43: 727-738.

16.Jemaa Essemine, Mingnan Qu, Hualing Mi and Xin-Guang Zhu (2016) Response of chloroplast NAD(P)H dehydrogenase-mediated cyclic electron flow to a shortage or lack in ferredoxin-quinone oxidoreductase-dependent pathway in rice following short-term heat stress. Frontiers in Plant Science 7: 383 doi: 10.3389/fpls.2016.00383.

17.Chensi Cao, Jiajia Xu, Guangyong Zheng, Xin-Guang Zhu (2016) Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis. BMC Genomics 17:201.

18.Qing-Feng Song, Han Xiao, Xianglin Xiao, Xin-Guang Zhu (2016) A new canopy photosynthesis and transpiration measurement system (CAPTS) for canopy gas exchange research. Agricultural and Forest Meteorology 217:101-107.

19.Qing-Feng Song, Chengcai Chu, Martin Parry, Xin-Guang Zhu (2016) Genetics based dynamic systems model of canopy photosynthesis: the key to improve light and resource use efficiencies for crops. Food and Energy Security, doi: 10.1002/fes3.74.

20.Shuoqi Chang, Tiangen Chang, Qingfeng Song, Xin-Guang Zhu*, Qiyun Deng* (2016) Photosynthetic and agronomic traits of an elite hybrid rice Y-Liang-You 900 with a record-high yield. Field Crops Research 187: 49-57.

21.Xin-Guang Zhu, Jonathan P. Lynch, David S. LeBauer, Andrew J. Millar, Mark Stitt, Stephen P. Long (2015). Plants in silico: why, why now and what?--an integrative platform for plant systems biology research. Plant Cell and Environment 39:1049-1057.

22.Donald R. Ort, Sabeeha S. Merchant, Jean Alric, Alice Barkan, Robert E. Blankenship, Ralph Bock, Roberta Croce, Maureen R. Hanson, Julian Hibberd, Derek L. Lindstrom, Stephen P. Long, Thomas A. Moore, James Moroney, Krishna K. Niyogi, Martin Parry, Pamela Peralta-Yahya, Roger Prince, Kevin Redding, Martin Spalding, Klaas van Wijk, Wim F.J. Vermaas, Susanne von Caemmerer, Andreas Weber, Todd Yeates, Joshua Yuan, Xin-Guang Zhu (2015) Redesigning photosynthesis to sustainably meet global food and bioenergy demand. PNAS 112:8529-36.

23.Saber Hamdani, Mingnan Qu, Chang-Peng Xin, Chengcai Chu, Govindjee, Xin-Guang Zhu (2015) Variations between the photosynthetic properties of elite and landrace Chinese rice cultivars revealed by simultaneous measurements of 820 nm transmission signal and chlorophyll a fluorescence induction. Journal of Plant Physiology 177: 128-138.

24.Ming-Ju Amy Lyu, Udo Gowik, Steve Kelly, Sarah Covshoff, Julia Mallmann, Peter Westhoff, Julian M. Hibberd, Matt Stata, Rowan F. Sage, Haorong Lu, Xiaofeng Wei, Gane Ka-Shu Wong, Xin-Guang Zhu (2015) RNA-Seq based phylogeny recapitulates previous phylogeny of the genus Flaveria (Asteraceae) with some modifications. BMC Evolutionary Biology 15:116.

25.Stephen P. Long, Amy Marshall-Colon, Xin-Guang Zhu (2015) Meeting the global food demand of the future by engineering crop photosynthesis and yield potential. Cell 161: 56-66.

26.Changpeng Xin, Danny Tholen, Xin-Guang Zhu (2015) The benefit of photorespiratory bypass – How can they work? Plant Physiology 167: 574-585.

27.Ming R, VanBuren R, Wai CM, Tang H, Schatz MC, Bowers JE, Lyons E, Wang M-L, Chen J, Biggers E, Zhang J, Huang L, Zhang L, Miao W, Zhang J, Ye Z, Miao C, Lin Z, Wang H, Zhou H, Yim WC, Priest HD, Zheng C, Woodhouse M, Edger PP, Guyot R, Guo H-B, Guo H, Zheng G, Singh R, Sharma A, Min X, Zheng Y, Lee H, Gurtowski J, Sedlazeck FJ, Harkess A, McKain MR, Liao Z, Fang J, Liu J, Zhang X, Zhang Q, Hu W, Qin Y, Wang K, Chen L-Y, Shirley N, Lin Y-R, Liu L-Y, Hernandez AG, Wright CL, Bulone V, Tuskan GA, Heath K, Zee F, Moore PH, Sunkar R, Leebens-Mack JH, Mockler T, Bennetzen JL, Freeling M, Sankoff D, Paterson AH, Zhu X-G, Yang X, Smith JAC, Cushman JC, Paull RE, Yu Q (2015) The pineapple genome and the evolution of CAM photosynthesis. Nat Genetetics 47: 1435-1442.

28.Yuanyuan Li, Jiajia Xu, Noor UI Haq, Hui Zhang, Xin-Guang Zhu (2014) Was low CO2 a driving force of C4 evolution? Arabidopsis responses to long-term low CO2 stress. Journal of Experimental Botany 65: 3657-67.

29.Yu Wang, Stephen P Long, Xin-Guang Zhu (2014) Elements required for an efficient NADP-Malic Enzyme type C4 photosynthesis. Plant Physiology 164: 2231-2246.

30.Yu Wang, Andrea Bräutigam, Andreas PM Weber, Xin-Guang Zhu (2014) Three distinct biochemical subtypes of C4 photosynthesis? A modeling analysis. Journal of Experimental Botany 65:3567-78.

31.Mark Stitt and Xin-Guang Zhu (2014) The large pools of metabolites involved in intercellular metabolite shuttles in C4 photosynthesis provide enormous flexibility and robustness in a fluctuating light environment. Plant Cell and Environment 37:1985-8.

32.Changpeng Xin, Jin Yang, Xin-Guang Zhu (2013) A model of chlorophyll a fluorescence induction kinetics with explicit description of structural constraints of individual photosystem II units. Photosynthesis Research 117: 339-354.

33.Qingfeng Song, Guilian Zhang, Xin-Guang Zhu (2013) Optimal crop canopy architecture to maximise canopy photosynthetic CO2 uptake under elevated CO2 – a theoretical study using a mechanistic model of canopy photosynthesis. Functional Plant Biology 40: 108-124.

34.Xin-Guang Zhu, Yu Wang, Donald R Ort and Stephen P Long (2012) e-Photosynthesis: a comprehensive dynamic mechanistic model of C3 photosynthesis: from light capture to sucrose synthesis. Plant Cell & Environment 36:1711-27.

35.Danny Tholen, Carolina Boom, Xin-Guang Zhu (2012) Opinion: prospects for improving photosynthesis by altering leaf anatomy. Plant Science 197: 92-101.

36.Danny Tholen, Gilbert Ethier, Steeve Pepin, Bernard Genty, Xin-Guang Zhu (2012). Variable mesophyll conductance revisited -- theoretical background and experimental implications. Plant Cell & Environment 35: 2087-103.

37.Xin-Guang Zhu, Qingfeng Song, Donald R Ort (2012) Elements of a dynamic systems model of canopy photosynthesis. Current Opinion in Plant Biology 15: 237-44.

38.Fu-Qiao Xu, Wei-Min Ma, Xin-Guang Zhu (2011) Introducing pyruvate oxidase into the chloroplast of Chlamydomonas reinhardtii increases oxygen consumption and promotes hydrogen production. International Journal of Hydrogen Research 36: 10648-10654.

39.Rowan Sage, Xin-Guang Zhu (2011) Exploiting the engine of C4 photosynthesis. Journal of Experimental Botany 62:2989-3000.

40.Vivek Thakur, Samart Wanchana, Mercedes Xu, Richard Bruskiewich, William Paul Quick, Axel Mosig, Xin-Guang Zhu (2011) Characterization of parameters in plant microRNA prediction. BMC Genomics 12:108.

41.Danny Tholen, Xin-Guang Zhu (2011) The mechanistic basis of internal conductance – A theoretical analysis using a 3D reaction diffusion model of mesophyll cell photosynthesis. Plant Physiology 156:90-105.

42.Xin-Guang Zhu, Guilian Zhang, Danny Tholen, Yu Wang, Changpeng Xin, Qingfeng Song (2011) The next generation models for crops and agro-ecosystems. Science China: Information Sciences 54(3) 1-9.

43.Xin-Guang Zhu, Lanlan Shan, Yu Wang, William Paul Quick (2010) C4 Rice – an arena for systems biology research. Journal of Integrative Plant Biology 52:762-70.

44.Xin-Guang Zhu, Stephen P Long, Donald R Ort (2010) Improving photosynthetic eficiency for greater yield. Annual Review of Plant Biology 61: 235-261.

45.Xin-Guang Zhu (2010) Systems-level modeling—A new approach for engineering efficient photosynthetic machinery. Journal of Biotechnology 149: 201-209.

 
 
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