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Mining Metabolic Diversity in Plants
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Evolutionary mechanism underlying metabolic diversity
School of Agriculture and Biotechnology
Shanghai Jiaotong University
@Zhenhua_Hunan
PUBLICATIONS
# first author * corresponding author
People from SJTU (current lab) in Bold
2021
Wenbing Su#, Yi Jing#, Shoukai Lin#, Zhen Yue#, Xianghui Yang#, Jiabao Xu, Jincheng Wu, Zhike Zhang, Rui Xia, Jiaojiao Zhu, Ning An, Haixin Chen, Yanping Hong, Yuan Yuan, Ting Long, Ling Zhang, Yuanyuan Jiang, Zongli Liu, Hailan Zhang, Yongshun Gao, Yuexue Liu, Hailan Lin, Huicong Wang, Levi Yant, Shunquan Lin* and Zhenhua Liu*. Polyploidy underlies co-option and diversification of biosynthetic triterpene pathways in the apple tribe. PNAS. 118.20 (2021): e2101767118.
Yan Li#, Aymeric Leveau#, Qiang Zhao#, Qi Feng, Hengyun Lu, Jiashun Miao, Zheyong Xue, Azahara C. Martin, Eva Wegel, Jing Wang, Anastasia Orme, Maria-Dolores Rey, Miroslava Karafiátová, Jan Vrána, Burkhard Steuernagel, Ryan Joynson, Charlotte Owen, James Reed, Thomas Louveau, Michael J Stephenson, Lei Zhang, Xuehui Huang, Tao Huang, Danling Fan, Congcong Zhou, Qilin Tian, Wenjun Li, Yiqi Lu, Jiaying Chen, Yan Zhao, Ying Lu, Chuanrang Zhu, Zhenhua Liu, Guy Polturak, Rebecca Casson, Lionel Hill, Graham Moore, Rachel Melton, Neil Hall, Brande B H Wulff, Jaroslav Doležel, Tim Langdon, Bin Han* and Anne Osbourn*. Subtelomeric assembly of a multi-gene pathway for antimicrobial defense compounds in cereals. Nat Commun 12, 2563 (2021). https://doi.org/10.1038/s41467-021-22920-8
2020
Zhenhua Liu#, Jitender Cheema, Marielle Vigouroux, Lionel Hill, James Reed, Pirita Paajanen, Levi Yant and Anne Osbourn*. Formation and diversification of a paradigm biosynthetic gene cluster in plants. Nature Communications 11, 5354 (2020). https://www.nature.com/articles/s41467-020-19153-6
Comprehensive analysis of a paradigm biosynthetic gene cluster (BGC) at within and between species level reveals dynamics governing conservation and diversification of BGCs in plants.
Media report:
https://www.jic.ac.uk/news/new-research-sheds-light-on-complex-genetic-and-metabolic-traits-in-plants/
Shicheng Zou#, Jincheng Wu#, Muhammad Qasim Shahid, Yehua He, Shunquan Lin, Zhenhua Liu* & Xianghui Yang*. Identification of key taste components in loquat using widely targeted metabolomics. Food Chemistry https://doi.org/10.1016/j.foodchem.2020.126822 (2020)
Whole-genome duplication (WGD) plays important roles in plant evolution and function, yet little is known about how WGD underlies metabolic diversification of natural products that bear significant medicinal properties, especially in nonmodel trees. Here, we reveal how WGD laid the foundation for co-option and differentiation of medicinally important ursane triterpene pathway duplicates, generating distinct chemotypes between species and between developmental stages in the apple tribe. After generating chromosome-level assemblies of a widely cultivated loquat variety and Gillenia trifoliata, we define differentially evolved, duplicated gene pathways and date the WGD in the apple tribe at 13.5 to 27.1 Mya, much more recent than previously thought. We then functionally characterize contrasting metabolic pathways responsible for major triterpene biosynthesis in G. trifoliata and loquat, which pre- and postdate the Maleae WGD, respectively. Our work mechanistically details the metabolic diversity that arose post-WGD and provides insights into the genomic basis of medicinal properties of loquat, which has been used in both traditional and modern medicines.
Metabolic causes underlying better taste of white-fleshed loquat in comparison to yellow fleshed loquat fruit.
2019
Zhenhua Liu#, Hernando G. Suarez Duran#, Yosapol Harnvanichvech, Michael J. Stephenson, M. Eric Schranz, David Nelson, Marnix H. Medema* and Anne Osbourn*. Drivers of metabolic diversification: How dynamic genomic neighborhoods generate new biosynthetic pathways in the Brassicaceae. New Phytologist, doi: 10.1111/nph.16338 (2019)
New Phytologist invited Reuben J. Peters to comment on this work:
Doing the gene shuffle to close synteny: dynamic assembly of biosynthetic gene clusters https://doi.org/10.1111/nph.16631
Zhixue Wang#, Leiyun Yang, Zhenhua Liu, Minghui Lu, Yiheng Lan, Tieliu Shi, Dianxing Wu, and Jian Hua*. Natural variations of growth thermo-responsiveness determined by SAUR26/27/28 proteins in Arabidopsis thaliana. New Phytologist. doi: 10.1111/nph.15956 (2019)
Alber Annette#, Renault Hugues, Basilio Lopes, Alexandra Bassard, Jean-Etienne, Liu Zhenhua，Ullmann Pascaline, Lesot Agnès, Bihel Frédéric, Schmitt Martine, Werck-Reichhart Danièle*, Ehlting Juergen*. Evolution of coumaroyl conjugate 3-hydroxylases in land plants: Lignin biosynthesis and defense. The Plant Journal. doi.org/10.1111/tpj.14373 (2019)
2016
Zhenhua Liu#, Raquel Tavarez, Evan S. Forsythe, Francois André, Raphaël Lugan, Gabriella Jonasson, Stéphanie Boutet Mercey, Takayuki Tohge, Mark Beilstein, Danièle Werck-Reichhart*, Hugues Renault. Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism. Nature Communications. 7, 13026 doi: 10.1038/ncomms13026 (2016).
(a) Initial steps of the CYP98A8/9 evolution shared by lineages I, II and III. The initial CYP98A3 retroposition event in Brassicales (100-70 Ma) led to the CYP98A8/9 ancestral gene, which became a phenolamide 30-hydroxylase. The retroposition was followed by a tandem gene duplication in Brassicaceae around 45 Ma leading to the CYP98A8 and CYP98A9 sister genes. CYP98A8 then acquired an additional function, the phenolamide 50-hydrolase activity. (b) Further evolution of CYP98A8 and CYP98A9 in the lineage I of the Brassicaceae, CYP98A8 lost the phenolamide 30-hydroxylase activity in vivo, and maintained only the 50-hydroxylase activity. Meanwhile, CYP98A9 maintained the 30-hydroxylase activity, and simultaneously gained naringenin 30-hydroxylase activity. (c) Further evolution of CYP98A8 and CYP98A9 in the lineages II and III of the Brassicaceae, in lineages II and III, the CYP98A9 copy was lost, and CYP98A8 maintained both 30- and 50-hydroxylase activities.
2015
Zhenhua Liu#, Benoît Boachon, Raphaël Lugan, Raquel Tavares, Mathieu Erhardt, Jérôme Mutterer, Valérie Demais, Stéphanie Pateyron, Véronique Brunaud, Toshiyuki Ohnishi, Ales Pencik, Patrick Achard, Fan Gong, Peter Hedden, Danièle Werck-Reichhart*, Hugues Renault. A conserved cytochrome P450 evolved in seed plants regulates flower maturation. Molecular Plant. 10.1016/j.molp.2015.09.002 (2015).
2010
Zhenhua Liu#, Wenjie Bao, Wanqi Liang, Jingyuan Yin, Dabing Zhang*. Identification of gamyb-4 and analysis of the regulatory role of GAMYB in rice anther development. Journal of integrative plant biology. 52, 670-678. (2010).
GAMYB, a positive regulator in the phytohormone Gibberellin (GA) signaling pathway, is a key component controlling anther development. It also bears huge potential for generating hybrid rice lines.
Comprehensive evolutionary analysis reveal important functions of cytochrome P450 CYP715 family in seed plants.