Ling Yuan

Ling Yuan

Professional Profile

Our research interests are centered in two main areas: 

  1. mechanistic study of transcription factors (TFs) for plant metabolic pathway regulation, and 
  2. improvement of bioenergy production through engineering tobacco plants to produce high-density biofuels and engineering enzymes for novel functions in biomass conversion. 

A new research focus in our lab is the modification of leaf characteristics and surface chemistry. The research in our lab addresses some of the key issues in molecular biology and protein biochemistry and contributes to the development of new-crop opportunities and bioenergy, two important areas in the agricultural economies of Kentucky and the nation.


  • 1989, Postdoctoral fellow, Univeristy of California, San Francisco, Pharmaceutical Chemistry
  • 1989, Ph.D., University of Texas at Austin, Biochemistry and molecular biology
  • 1983, B.S. Jinan University, Guangzhou, China, Biology

Additional Information


Singh SK, Patra B, Paul P, Liu YL, Pattanaik S. Yuan L (2021) BHLH IRIDOID SYNTHESIS 3 is a member of a bHLH gene cluster regulating terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Direct. 2021;00:e00305

Li Z, Li X, Zhang Q, Yuan L, Zhou X. (2020) Reference gene selection for transcriptional profiling in Cryptocercus punctulatus, an evolutionary link between Isoptera and Blattodea. Scientific Reports. 10(1):22169.

Liu X, Singh SK, Patra B, Liu Y, Wang B, Wang J, Pattanaik S, Yuan L. (2020) Protein-phosphatase NtPP2C2b and MAP-kinase NtMPK4 act in concert to modulate nicotine biosynthesis. Journal of Experimental Botany. (in press)

Li Y, Liang X, Zhou X, Wu Z, Yuan L, Wang Y, Li Y. (2020) Selection of Reference Genes for qRT-PCR Analysis in Medicinal Plant Glycyrrhiza under Abiotic Stresses and Hormonal Treatments. Plant (Basel) 9(11):E1441.

Singh SK, Richmond MD, Pearce RC, Bailey WA, Hou X, Pattanaik S, Yuan L. (2020) Maleic hydrazide elicits global transcriptomic changes in chemically topped tobacco to influence shoot bud development. Planta. 252(4):64

Shoji, T and Yuan, L (2020) ERF clusters: working together to regulate metabolism. Trends in Plant Science. S1360-1385(20)30245-4

Que Kong , Yuzhou Yang , Pui Man Low , Liang Guo , Ling Yuan , Wei Ma (2020) The function of the WRI1-TCP4 regulatory module in lipid biosynthesis. Plant Signal and Behavior. 15(11):1812878

Yuan, L and Grotewold, E (2020) Plant specialized metabolism. Plant Science. 298:110579

Kong Q, Singh SK, Mantyla JJ, Pattanaik S, Guo L, Yuan L, Benning C, Ma W. (2020) TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR 4 interacts with WRINKLED1 to mediate seed oil biosynthesis. Plant Physiology. (in press)

Shin JM, Yuan L, Ohme-Takagi M, Kawashima T. (2020) Cellular dynamics of double fertilization and early embryogenesis in flowering plants. Exp Zool B Mol Dev Evol. (in press)

Yuan, L. (2020) Clustered ERF Transcription Factors: Not All Created Equal. Plant Cell Physiology. 61(6):1025-1027

Wang J, Singh SK, Geng S, Zhang S, Yuan L. (2020) Genome-wide analysis of glycerol-3-phosphate O-acyltransferase gene family and functional characterization of two cutin group GPATs in Brassica napus. Planta. 251(4):93

Kong Q, Yang Y, Guo L, Yuan L, Ma W. (2020) Molecular Basis of Plant Oil Biosynthesis: Insights Gained From Studying the WRINKLED1 Transcription Factor. Front Plant Sci. 11:24.

Paul P, Singh SK, Patra B, Liu X, Pattanaik S, Yuan L. (2020) Mutually Regulated AP2/ERF Gene Clusters Modulate Biosynthesis of Specialized Metabolites in Plants. Plant Physiology. 182(2):840-856

Hongxia Wang, Yinliang Wu, Yandi Zhang, Jun Yang, Weijuan Fan, Hui Zhang, Shanshan Zhao, Ling Yuan and Peng Zhang (2019) CRISPR/Cas9-Based Mutagenesis of Starch Biosynthetic Genes in Sweet Potato (Ipomoea Batatas) for the Improvement of Starch Quality. International Journal of Molecular Sciences. 20: 4702.

Kong Q, Yuan L, Ma W. (2019) WRINKLED1, a "Master Regulator" in Transcriptional Control of Plant Oil Biosynthesis. Plants (Basel). doi: 10.3390/plants8070238.

Liu, YL, Patra, B., Pattanaik, S., Wang, Y., Yuan, L. (2019) GATA and PIF transcription factors regulate light-induced biosynthesis of vindoline in Catharanthus. Plant Physiology. 180(3):1336-1350.

Zhang Y, Deng G, Fan W, Yuan L, Wang H, Zhang P. (2019) NHX1 and eIF4A1-stacked transgenic sweet potato shows enhanced tolerance to drought stress. Plant Cell Rep. (in press) doi: 10.1007/s00299-019-02454-6.

Schluttenhofer, C. and Yuan, L. (2019) Hemp hemp hooray for cannabis research. Science. 363(6428):701-702 (Letter)

Jinzhu Jiang, Huifen Xi, Zhanwu Dai, Fatma Lecourieux, Ling Yuan, Xianju Liu, Barunava Patra, Yongzhan Wei, Shaohua Li, and Lijun Wang (2018) VvWRKY8 negatively regulates VvSTS through direct interaction with VvMYB14 to balance resveratrol biosynthesis in grapevine. Journal of Experimental Botany. 70(2):715-729

Sui X, Kumar Singh S, Patra B, Schluttenhofer C, Guo W, Pattanaik S, Yuan L. (2018) Cross-family Transcription Factor Interaction between MYC2 and GBFs Modulates Terpenoid indole Alkaloid Biosynthesis. Journal of Experimental Botany. 69(18):4267-4281

Wang J, Wang X, Geng S, Singh SK, Wang Y, Pattanaik S, Yuan L. (2018) Genome-wide identification of hexokinase gene family in Brassica napus: structure, phylogenetic analysis, expression, and functional characterization. Planta. 248(1):171-182

Xiaowei Yang, Huipeng Pan, Ling Yuan, and Xuguo Zhou (2018) Reference gene selection for RT-qPCR analysis in Harmonia axyridis, a global invasive lady beetle. Scientific Reports. 8(1):2689

Patra B, Pattanaik S, Schluttenhofer C, Yuan L. (2018) Jasmonate signaling regulates a network of bHLH factors to balance biosynthesis of monoterpenoid indole alkaloids in Catharanthus roseus. New Phytologist. 217(4):1566-1581 

Feller A, Yuan L, Grotewold E (2017) The BIF Domain in Plant bHLH Proteins is an ACT-Like Domain. Plant Cell. 29(8):1800-1802.

Schluttenhofer CM and Yuan L (2017) Challenges Towards Revitalizing Hemp - a Multifaceted Crop. Trends in Plant Science. 22(11):917-929

Shen EM, Singh, S, Ghosh JS, Patra B, Paul P, Yuan L, Pattanaik S (2017) The miRNAome of Catharanthus roseus: identification, expression analysis, and potential roles of microRNAs in regulation of terpenoid indole alkaloid biosynthesis.  Scientific Reports. 7:43027

Paul P, Singh S, Patra B, Sui X, Pattanaik S, Yuan L. (2017) A differentially regulated AP2/ERF transcription factor gene cluster acts downstream of a MAP kinase cascade to modulate terpenoid indole alkaloid biosynthesis in Catharanthus roseus. New Phytologist. 213(3):1107-1123

Wang JX, Singh S, Du C, Li C, Fan J, Pattanaik S, Yuan L (2016) Comparative transcriptomic analysis of two Brassica napus near-isogenic lines reveals a network of genes that influences seed oil accumulation. Frontiers in Plant Science. 7:1498

Huang W, Khaldun AB, Chen J, Zhang C, Lv H, Yuan L, Wang Y. (2016) A R2R3-MYB Transcription Factor Regulates the Flavonol Biosynthetic Pathway in a Traditional Chinese Medicinal Plant, Epimedium sagittatum. Frontiers in Plant Science. 7:1089.

Xu Z, Cheng K, Li X, Yang J, Xu S, Cao X, Hu X, Xie W, Yuan L, Ambrose M, Chen G, Mi H, Luo D. (2016) Transcriptional and Post-transcriptional Modulation of SQU and KEW Activities in the Control of Dorsal-ventral Asymmetric Flower Development in Lotus japonicus. Molecular Plant. 9(5):722-736.

Wang JX, Nie J., Pattanaik S, Yuan L. (2016) Efficient Agrobacterium-mediated transformation of Artemisia annua L. using young inflorescence. In Vitro Cellular & Developmental Biology - Plant. 52 (2): 204–211.

Hongxia Wang, JunYang, Min Zhang, Weijuan Fan, Nurit Firo, Sitakanta Pattanaik, Ling Yuan,, and Peng Zhang 2015 Altered Phenylpropanoid Metabolism in the Maize Lc-Expressed Sweet Potato (Ipomoea batatas) Affects Storage Root Development. Scientific Reports. 6:18645  Abstract

Singh SK, Wu Y, Ghosh JS, Pattanaik S, Fisher C, Wang Y, Lawson D, Yuan L 2015 RNA-sequencing Reveals Global Transcriptomic Changes in Nicotiana tabacum Responding to Topping and Treatment of Axillary-shoot Control Chemicals. Scientific Reports. 5:18148. Abstract

Chen J, Xu Y, Wei G, Liao S, Zhang Y, Huang W, Yuan L and Wang Y 2015 Chemotypic and genetic diversity in Epimedium sagittatum from different geographical regions of China.Phytochemistry. 116:180-7 Abstract

Jia X, Shen J, Liu H, Li F, Ding N, Gao C, Pattanaik S, Patra B, Li R , and Yuan L. 2015 Small tandem target mimic-mediated blockage of microRNA858 induces anthocyanin accumulation in tomato. Planta.  Abstract

Schluttenhofer CM and Yuan L 2015 Regulation of Specialized Metabolism by WRKY Transcription Factors.Plant physiology. 167(2):295-306. Abstract

Yuan L and Grotewold E 2015 Metabolic engineering to enhance the value of plants as green factories.Metabolic Engineering.27:83-91. Abstract

Schluttenhofer CM, Pattanaik S, Patra B, and Yuan L 2014 Analyses of Catharanthus roseus and Arabidopsis thaliana WRKY transcription factors reveal involvement in jasmonate signaling.BMC Genomics 15:502. Abstract

Pattanaik S, Patra B, Singh SK and Yuan L 2014 An overview of the gene regulatory network controlling trichome development in the model plant, Arabidopsis.Frontier in Plant Cell Biology 5:259. Abstract

Singh SK, Heng C, Braker JD, Chan VJ, Lee CC, Jordan DB, Yuan L and Wagschal K. 2014 Directed evolution of GH43 beta-xylosidase XylBH43 thermal stability and L186 saturation mutagenesis.Journal of Industrial Microbiology and Biotechnology 41(3):489-98. Abstract

Patra B, Schluttenhofer CM, Wu Y, Pattanaik S and Yuan L 2013 Transcriptional regulation of secondary metabolism in plants. BBA-Gene Regulatory Mechanisms 1829(11):1236-4. Abstract

Yang Z , Patra B, Li R, Pattanaik S and Yuan L 2013 Promoter analysis reveals cis-regulatory motifs associated with the expression of the WRKY transcription factor CrWRKY1 in Catharanthus roseus. Planta.238 (6)1039-1049 Abstract

Huang W, Sun W, Lv H, Luo M, Zeng S, Pattanaik S, Yuan L and Wang Y 2013 A R2R3-MYB Transcription Factor from Epimedium sagittatum Regulates the Flavonoid Biosynthetic Pathway. Plos One 8(8): e70778. Abstract

Patra B, Pattanaik S and Yuan L 2013. Proteolytic degradation of the flavonoid regulators, TRANSPARENT TESTA8 and TRANSPARENT TESTA GLABRA1, in Arabidopsis is mediated by the ubiquitin/26Sproteasome system. Plant Signaling and Behavior.8:e25901 Abstract

Patra B, Pattanaik S and Yuan L 2013. Ubiquitin protein ligase 3 mediates the proteasomal degradation of GLABROUS 3 and ENHANCER OF GLABROUS 3, regulators of trichome development and flavonoid biosynthesis in Arabidopsis. The Plant Journal 74(3):435-47. Abstract

Kong Q, Pattanaik S, Feller A, Werkman JR , Chai C, Wang Y, Grotewold E and Yuan L 2012 Regulatory switch enforced by basic helix-loop-helix and ACT-domain mediated dimerizations of the maize transcription factor R. Proceeding of National Academy of Sciences U.S.A. 109: E2091-2097.  Abstract

Bai Y, Pattanaik S, Patra B, Werkman JR, Xie CH and Yuan L 2011 Flavonoid-related basic helixloop- helix regulators, NtAn1a and NtAn1b, of tobacco have originated from two ancestors and are functionally active. Planta 234:363-375.  Abstract

Jordan DB, Wagscha K, Fan ZM, Yuan L, Braker JD and Heng C 2011 Engineering lower inhibitor affinities in beta-D-xylosidase of Selenomonas ruminantium by site-directed mutagenesis of Trp145. Journal of Industrial Microbiology and Biotechnology 38:1821-1835.  Abstract

Suttipanta N, Pattanaik S, Kulshrestha M, Patra B, Singh SK and Yuan L 2011 The Transcription Factor CrWRKY1 Positively Regulates Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus. Plant Physiology. 157: 2081-2093.  Abstract

Fan ZM and Yuan L 2010 Production of Multifunctional Chimeric Enzymes in Plants: a promising Approach for Degrading Plant Cell Wall from Within. Plant Biotechnology Journal. 8:308-315.  Abstract

Fan ZM, Yuan L, Jordan DB, Wagschal K, Heng C and Braker JD 2010 Engineering Lower Inhibitor Affinities in Beta-D-xylosidase. Applied Microbiology and Biotechnology. 86(4):1099-1113. Abstract

Pattanaik S, Kong Q, Zaitlin D, Werkman JR, Xie CH, Patra, B, and Yuan L, 2010 Isolation and functional characterization of a floral tissue-specific R2R3 MYB regulator from tobacco. Planta. 231(5):1061-1076. Abstract

Fan ZM, Werkman JR, and Yuan L 2009 Engineering a multifunctional hemicellulase. Biotechnology Letters 31:751-757. Abstract

Fan ZM, Yuan L and Chatterjee R 2009 Increased Hydrogen Production by Genetic Engineering of Escherichia coli. PLoS ONE 4(2): e4432.  Abstract

Fan ZM, Wagschal K, Chen W, Montross MD, Lee CC and Yuan L 2009 Multimeric Hemicellulases Facilitate Biomass Conversion. Applied and Environmental Microbiology. 75: 1754-1757. Abstract


Yuan L and Perry S (Editors) 2011 Plant Transcription Factors: Methods and Protocols. Methods in Molecular Biology. Vol. 754. Abstract

Pattanaik S, Werkman JR and Yuan L 2011 Biomolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts. pp. 185-193. IN: L. Yuan, and S. Perry, eds. Plant Transcription Factors: Methods and Protocols. vol. 754, Methods in Molecular Biology. Humana Press, New York. Abstract

Werkman JR, Pattanaik S, and Yuan L 2011 Directed evolution through DNA shuffling for the improvement and understanding of genes and promoters. Chapter 19, pp. 325-342. IN: L. Yuan and S.E. Perry, eds. Plant Transcription Factors: Methods and Protocols, vol. 54. In Methods in Molecular Biology (J.M. Walker, series ed.), Humana Press, New York.  Abstract

Pattanaik S, Werkman JR, Kong Q and Yuan L 2010 Site-directed mutagenesis and saturation mutagenesis for the functional study of transcription factors involved in plant secondary metabolite biosynthesis. pp. 47-57. IN: Metabolic Engineering of Plant Secondary Pathways, vol. 643 in Methods in Molecular Biology, Springer, New York. Abstract