Yuan, Ling

Group: Ling Yuan, Department of Plant and Soil Sciences, College of Agriculture, Food and Environment

Detailed group research activities:

Structure/function Relationship and Regulation of Plant Transcription Factors:

TFs are regulatory proteins that modulate gene transcription. Our approach to understanding the regulatory mechanism relies on dissection of the structure/function relationships of TFs involved in regulating plant secondary pathways. We are particularly interested in two families of TFs, the basic helix-loop-helix (bHLH) and MYB TFs that are involved in several well-known plant metabolic pathways, including the flavonoid biosynthetic pathway. The combinatorial regulation of gene expression by the bHLH/MYB complex has been established as an excellent model for understanding plant metabolic pathway control.

We uncovered a mechanism by which a dimerization domain in a bHLH TF behaves as a switch that permits different configurations of TF regulatory complexes to be tethered to different promoters, helping to explain the elusive question of how genes lacking conserved cis-elements in their promoters can be coordinately regulated.

Transcriptional Regulation of Terpenoid Indole Alkaloid Biosynthesis:

The medicinal plant Madagascar periwinkle (Catharanthus roseus) produces a large array of terpenoid indole alkaloids (TIAs), an important source of natural or semisynthetic anticancer drugs. However, the transcriptional regulation of the TIA pathway is poorly understood. We utilized various genomic tools and discovered that WRKY TFs are involved in regulation of TIA biosynthesis and functionally characterized the first C. roseus WRKY TF for its role in this pathway.

Improvement of Bioenergy Production:

Currently, we are a member of FOLIUM (Tobacco as a platform for foliar biosynthesis of advanced hydrocarbon fuels), a project supported by the DOE (ARPA-E), and aims at producing high-density liquid fuels in green biomass by introducing genes from microorganisms and other plants, resulting in accumulation of hydrocarbon fuels in tobacco leaves and stems.

The other research area is the creation of multi-functional enzymes for lignocellulosic biomass conversion by directed enzyme evolution and the creation of artificial multidomain enzymes. Several of the engineered enzymes display synergistic effects that lead to higher efficiencies in xylan-degradation compared to the parental enzyme mixtures and can reduce the total number of proteins required in biomass conversion. In addition, we continue to work in collaboration with two USDA labs to apply directed evolution technologies to improve cellulosic hydrolases, particularly in properties related to product inhibition and thermostability. 
DLX cluster project: DNA-binding site recognition in the plant MIKC MADS domain transcription factors

Student:

Joshua R. Werkman, Staff 04/29/2021 (graduate RA; defended July 2013)

Sanjay Kumar Singh, KTRDC

Computational methods: molecular dynamics – all-atom and course-grain (available on DLX)

Software:

Amber/AmberTools
NAMD
GNUplot
R
Pymol (not on DLX)
VMD
Curves+/Canal (not on DLX)

Project description: Unanswered questions remain concerning DNA-binding site recognition in MADs domain TFs. While animals and yeast typically possess 4-5 MADS genes, plants typically possess over 100 genes and are vital to the regulation of morphology, reproduction, and metabolism in plants. Additionally, the sequence space within plant MADS domains is significantly greater than what is found for animals or yeast. This provides an opportunity to examine how these differences influence the binding mechanics towards distinct cis-element sequences.

The high-performance computing resources provided through the University of Kentucky’s Center for Computational Sciences is allowing us to model multiple, yet unique, DNA-protein complexes such the Arabidopsis AGL15 homodimer, which is involved in plant embryo development, and the Arabidopsis FLC-SVP heterodimer, which is involved in the repression of flowering during winter. Modeling these complexes through molecular dynamics is allowing us to better understand the dynamics of DNA-binding site-recognition in the MADS domain family of transcription factors and is providing us with a means for hypothesis advancement in conjunction with wet-laboratory techniques such as DNA-protein interaction ELISA (DPI-ELISA) and mutagenesis.

Publications:

Werkman, J. R. (2013) DNA-binding site recognition by bHLH and MADS-domain transcription factors. (Doctoral dissertation). University of Kentucky, Lexington, KY