Ling Yuan

Faculty

University of Kentucky, PSS
KTRDC
1401 University Drive (Office:123)
Lexington, KY 40546-0236
Phone (859) 257-4806
Fax (859) 323-1077
Email lyuan3@uky.edu

Specialty
Gene transcriptional regulation, protein engineering, directed evolution, metabolic pathway engineering

Education

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

My research interests are focused in two areas. One is the engineering and mechanistic study of transcription factors (TF) for regulation of plant metabolic pathways. Long term goals include the creation of Master Transcription Factors (MTF) capable of controlling an entire metabolic pathway. Recent achievements in my laboratory not only demonstrate the feasibility of the MTF approach, but also shed light on synergistic effects between functional domains of TF on transactivation. We also verify the novel function of the engineered TFs using technology tools such as RNAi and transgenic plants. In addition, I am interested in protein- and metabolic-engineering for the improvement of bioenergy production. My laboratory applies directed enzyme evolution technologies to enhance the performance of hydrolases for biomass conversion and to modify the substrate specificities of these enzymes. Additional research efforts include the redirection of microbial metabolic pathways for the improvement of hydrogen production. My current research is supported by the US Department of Agriculture, the Department of Energy, The Kentucky Office of Energy Policy and Kentucky Tobacco Research and Development Center, University of Kentucky.

This person page last updated on 2012-12-05

Classes

Abt301 - Writing and Presentation in Life Sciences; Credits - 2
This class is intended to refine skills in communicating and evaluating science-based knowledge. Specific focus is given to the agricultural, biological, and bio-medical sciences. One major goal is to facilitate the writing of an Agricultural Biotechnology Independent Research Proposal. In the process, students will learn how to evaluate relevant literature, think about science and the scientific process, and communicate scientific results and implications. This course should further the students' experience with science, enhance their appreciation for the scientific process, and what it means to conduct scientific research..
Instructors: Ling Yuan

Pls609 - Plant Biochemistry; Credits - 3
The course will consider the chemical constituents of plants (with emphasis on biologically or nutritionally significant compounds unique to plants), their biosynthesis, contribution to key metabolic and defense processes and the regulation of their synthesis. Included will be discussions of photosynthesis, carbohydrates, lipids, isoprenoids and phenylpropanoids, nitrogen fixation, nitrogen and sulfur reduction and assimilation, alkaloids and additional secondary compounds, frontiers in plant biochemistry. Prereq: BCH 607 or equivalent or consent of instructor. (Same as BCH/PPA 609.) .
Instructors: Ling Yuan David Hildebrand

Research/Teaching Publications

Books and Book Chapters

Ling Yuan and Sharyn Perry (Editors) 2011. Plant Transcription Factors: Methods and Protocols. Methods in Molecular Biology. Vol. 754

Pattanaik, S., J.R. Werkman, and L. Yuan. 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.
Authors in PSS Dept.: Ling Yuan Joshua Werkman Sitakanta Pattanaik

Pattanaik, S., Werkman, JR., and Ling Yuan, 2011. Biomolecular fluorescence complementation as a tool to study interactions of regulatory proteins in plant protoplasts Plant Transcription Factors. in Methods in Molecular Biology. (Yuan and Perry, ed) 754: 185-193

Werkman, J.R., Pattanaik, S, and Ling Yuan. 2011. Directed evolution through DNA shuffling for the improvement and understanding of genes and promoters Plant Transcription Factors. in Methods in Molecular Biology. (Yuan and Perry, ed.) 754: 325-342

Werkman, J.R., S. Pattanaik, and L. Yuan. 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.
Authors in PSS Dept.: Ling Yuan Joshua Werkman Sitakanta Pattanaik

Yuan, L., and S.E. Perry 2011. eds. Plant Transcription Factors: Methods and Protocols, vol. 754. IN: Methods in Molecular Biology, Humana Press (J.M. Walker, series ed.), New York.
Authors in PSS Dept.: Ling Yuan Sharyn Perry

Pattanaik, S., J.H. Werkman, Q. Kong, and L. Yuan. 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.
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Refereed Journal Articles

Patra, Barunava, Pattanaik, Sitakanta and Ling Yuan 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. (in press)

Kong, Q., Pattanaik, S., Feller, A., Werkman, JR., Chai, C., Wang, Y., Grotewold, E., and Ling Yuan. 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
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Que, K., S. Pattaniak, A. Feller, J. Werkman, C. Chai, Y. Wang, E. Grotewold, and L. Yuan. 2012. A regulatory switch enforced by bHLH and ACT domain-mediated dimerization of the maise transcription factor R. Proceeding of National Academy of Sciences, U.S.A. 109: E2091-2097.

Bai, Y., S. Pattanaik, B. Patra, J.R. Werkman, C.H. Xie, and L. Yuan. 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.
Authors in PSS Dept.: Ling Yuan Joshua Werkman Sitakanta Pattanaik

Bai, Y.H., Pattanaik, S., Patra, B., Werkman, J.R., Xie, C.H. and Yuan, L. 2011. Flavonoid-related basic helix-loop-helix regulator, NtAn1a and NtAn1b, of tobacco have originated from two ancestors and are functionally active. Planta. 234: 363-375

Jordan, D.B., K. Wagschal, Z.M. Fan, L. Yuan, J.D. Braker, and C. Heng. 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.

Jordan, D.B., Wagschal, K., Fan, ZM, Yuan, L., Braker, J.D. 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. (in press)

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

Suttipanta, N., S. Pattanaik, M. Kulshrestha, B. Patra, S.K. Singh, and L. Yuan. 2011. The transcription factor CrWRKY1 positively regulates terpenoid indole alkaloid biosynthesis in Catharanthus roseus. Plant Physiology 157:2081-2093.
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

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

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

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

Pattanaik, S., Q. Kong, D. Zaitlin, J.H. Werkman, C.H. Xie, B. Patra, and L. Yuan. 2010. Isolation and functional characterization of a floral tissuespecific R2R3 MYB regulator from tobacco. Planta 231:1061-1076.
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Fan, Z.M., J.H. Werkman, and L. Yuan. 2009. Engineering a multifunctional hemicellulase. Biotechnology Letters 31:751-757.

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

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

Fan, ZM., Wagschal, K., Lee, C.C., Kong, Q., Shen, K.A., Maiti, I.B., and Ling Yuan, 2009. The Construction and Characterization of Two Xylan-degrading Chimeric Enzymes. Biotechnology and Bioengineering. 102(3): 684-692

Pattanaik, S., C.H. Xie, and L. Yuan. 2008. The interaction domains of the plant Myc-like bHLH transcription factors can regulate the transactivation strength. Planta 227:707-715.
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Pattanaik, S., C.H. Xie and L. Yuan 2008. The Interaction Domains of the Plant Myc-like bHLH Transcription Factors Can Regulate the Transcription Strength. Planta. 227(3): 707-715

Pattanaik, S., C.H. Xie, and L. Yuan. 2008. Creation of master transcription factors to regulate plant metabolic pathways. Acta Horticulturae 756:109-118.
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Zeng, Q., F. Qiu, and L. Yuan. 2008. Production of artemisinin by genetically modified microbes. Biotechnology Letters 30:581-592.

Suttipanta, N., Pattanaik, S., Gunjun, S., Xie, CH, Littleton, J. and Yuan, L. 2007. Promoter analysis of the Catharanthus roseus geraniol 10-hydroxylase gene involved in terpenoid indole alkaloid biosynthesis. Biochim Biophys Acta, 1769:139-148

Suttipanta, N., S. Pattanaik, S. Gunjan, J. Littleton, and L. Yuan. 2007. Promoter analysis of the Catharanthus roseus geranial 10-hydroxylase gene involved in terpenoid indole alkaloid biosynthesis. Biochemica et Biophysica Acta 1769:139-148.
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Chatterjee, R., and L. Yuan. 2006. Directed evolution of metabolic pathways. Trends in Biotechnology. 24(1): 28-38

Pattanaik, S., C.H. Xie, Q. Kong, K.A. Shen, and L. Yuan 2006. Directed evolution of plant helix-loop-helix transcription factors for the improvement of transactivation properties. Biochim Biophys Acta, 1759: 308-318
Authors in PSS Dept.: Ling Yuan Sitakanta Pattanaik

Yuan, L., I. Kurek, J. English and R. Keenan. 2005. Laboratory-directed protein evolution. Microbiology and Molecular Biology Reviews. 69(3): 373-392

Zheng W, Wise ML, Wyrick A, Metz JG, Yuan L, Gerwick WH. 2002. Polyenoic fatty acid isomerase from the marine alga Ptilota filicina: protein characterization and functional expression of the cloned cDNA. Arch Biochem Biophys. 401(1):11-20.

Facciotti, M., Burtain, P., and Ling Yuan 1999. Improved Stearate Phenotype in Transgenic Canola Expressing a Modified Acyl-acyl Carrier Protein Thioesterase. Nature Biotechnology. 17 (6): 593-597.

Huang YS, Chaudhary S, Thurmond JM, Bobik EG Jr, Yuan L, Chan GM, Kirchner SJ, Mukerji P, Knutzon DS. 1999. Cloning of delta12- and delta6-desaturases from Mortierella alpina and recombinant production of gamma-linolenic acid in Saccharomyces cerevisiae. Lipids 34(7):649-59.

Facciotti, M. T. andLing Yuan, 1998. Molecular Dissection of the Plant ACP-thioesterases. Fett/Lipid 100 (4-5): 167-172.

Knauf, V.C and Ling Yuan, 1997. Modification of Plant Components. Current Opinion in Biotechnology. 8: 227-233.

Ling Yuan, B. A. Nelson, and G. Caryl. 1996. The Catalytic Cysteine and Histidine in the Plant Acyl-ACP Thioesterases. Journal of Biological Chemistry 271: 3417-3419.

Ling Yuan, T. A. Voelker and D. J. Hawkins 1995. Modification of the Substrate Specificity of an Acyl-ACP Thioesterase by Protein Engineering. Proceeding of National Academy of Science U.S.A. 92: 10639-10643.