Chemistry at Illinois University of Illinois at Urbana-Champaign

Huimin Zhao

Centennial Endowed Chair of Chemical and
Biomolecular Engineering,
Affiliate, Department of Chemistry,
Member of the Center for Biophysics and
Computational Biology and
Institute for Genomic Biology

Professor Zhao received his B.S. in Biology from the University of Science and Technology of China in 1992. He earned a Ph.D. in Chemistry from the California Institute of Technology in 1998. After working at the Dow Chemical company for two years, he joined the faculty at the University of Illinois in 2000.

Research

Protein Engineering and Metabolic Engineering

Research in the Zhao group is focused on protein engineering and metabolic engineering. The overall research theme is to use directed evolution in combination with rational design to create proteins, receptors, biosynthetic pathways, and whole cells with improved or novel functions, followed by detailed biochemical and biophysical characterizations. There are dozens of ongoing projects in the lab, which can be generally grouped into four different areas as described below. It should be noted that although the following projects are all application-driven, we are also very interested in addressing fundamental questions related to protein structure-function relationship, enzyme catalysis, molecular recognition, gene regulation, and immunology.

Industrial Biotechnology and Bioenergy

We successfully used directed evolution and rational design approaches to develop a novel phosphite dehydrogenase based NAD(P)H regeneration system by (1) improving the enzyme activity toward NADP by 1000-fold, (2) increasing the overall activity by 6-fold, and (3) increasing the thermostability by more than 22,000-fold. The resulting technology was patented and licensed to BASF and Biocatalytics. Based on this new cofactor regeneration method, we are developing new in vitro and in vivo methods for cost-effective production of xylitol, one of the twelve platform chemicals that the Department of Energy has identified for the emerging biorefinery industry. In addition, we are interested in converting renewable feedstock such as corn stovers into biofuels including ethanol, butanol, and other long-chain alcohols. Using a combination of protein engineering, metabolic engineering, bioinformatics, and functional genomics, we attempt to address key roadblocks in fermentative production of chemicals and biofuels from renewable feedstock, including limited range and poor efficiency of sugar utilization, relatively low product yield, productivity and titer, and low tolerance level to products and/or substrates.

Drug Discovery and Development

We are using protein and metabolic engineering tools to overproduce phloroglucinol, an important pharmaceutical intermediate in E. coli. Several biosynthetic pathways and enzymes such as type I polyketide synthases and type III polyketide synthases have been characterized and engineered. In addition, novel enzymes involved in arylamine oxygenation have been discovered and characterized using various biochemical and biophysical methods such as HPLC, EPR, LC-MS, and protein crystallography. In addition, in collaboration with the Metcalf, van der Donk, Kelleher, and Satish groups at University of Illinois, we are characterizing and engineering a new class of natural products, so-called phosphonic acids, many of which show antimicrobial, anticancer, and fungal and herbicidal activities. We recently cloned the gene cluster involved in the synthesis of fosfomycin, an FDA-approved antibiotic, and are now attempting to overproduce it in both E. coli and yeast. We are also interested in another phosphonic acid compound, FR-900098, an anti-malarial agent, among many others. In addition to overproducing these antibiotics, we are also using combinatorial biosynthesis and directed evolution approaches to generate novel derivatives of phosphonic acids with the hope of discovering new antibiotics with improved biological function.

Synthetic Biology and Gene Therapy

We are using directed evolution and rational design approaches to create a variety of transcription factor based gene switches and gene circuits to precisely control the gene expression levels in mammalian cells and animals. Such gene switches and circuits are invaluable tools for gene therapy, tissue engineering, functional genomics, therapeutic protein production, and stem cell engineering. In collaboration with world-leading scientists including Drs. John Katzenellenbogen, William Helfrich, Pierre Chambon, and Daniel Metzger, we are evaluating these tools in both mammalian cells and transgenic animals and applying them to address many different biomedical challenges. In addition, we are creating homing endonuclease based gene scissors that can introduce specific double strand breaks in a target gene. Such tools represent a new therapeutic regime for gene therapy. Two genetic diseases of particular interest are cystic fibrosis and sickle cell anemia.

MHC Engineering and Immunotherapy

We are applying protein engineering and yeast cell surface display to create yeast based artificial antigen presenting cells for analysis and engineering of human class II major histocompatibility complex (MHC) molecules for diagnostic and therapeutic applications. Based on this new system, we recently developed a new method for identifying CD4+ T-cell epitopes, which is a critical but often difficult limiting step for pathogenesis studies and a wide range of immunological and clinical applications. We are now further optimizing this system and extending it to other biomedical applications such as vaccine development, tumor antigen identification, T-cell staining, and treatment of autoimmune diseases.

Publications

Z. Shao, H. Zhao, and H. Zhao. "DNA Assembler, an in vivo Genetic Method for Rapid Construction of Biochemical Pathways." Nucleic Acids Research, accepted.

H. Zhao and W. Chen. "Chemical Biotechnology: Microbial Solutions to Global Change." Current Opinion in Biotechnology, in press. 

N. Nair and H. Zhao. "Mutagenic Inverted Repeat Assisted Genome Engineering (MIRAGE)." Nucleic Acids Research, in press.

K. M. D. Islam, M. Dilcher, C. Thurow, I. Krimmelbein, C. Vock, V. Gonzalez, H. Zhao, L. Tietze, and C. Gatz. "Directed Evolution of Estrogen Receptor Proteins with Altered Ligand-binding Specificities." Protein Engineering, Design, and Selection, accepted

F. Wen, S. Rubin-Pitel, and H. Zhao. "Engineering of Therapeutic Protein." In Protein Engineering and Design, (J. Cochran and S. Park, Eds.), CRC Press, Taylor & Francis Group, Boca Raton, FL, accepted.

E. Ang, J. P. Obbard, and H. Zhao. "Directed Evolution of Aniline Dioxygenase with Improved and Novel Activity." Applied Microbiology and Biotechnology, in press.

S. Rubin-Pitel, H. Zhang, J. S. Brunzelle, T. Vu, H. Zhao, and S. Nair. "Unique Structural Elements Dictate the Specificity of the Pentaketide Resorcylic Acid Synthase from Neurospora crassa." Chemistry and Biology, 15, 1079-1090 (2008). 

A. C. Eliot, B. M. Griffin, P. M. Thomas, T. W. Johannes, N. L. Kelleher, H. Zhao and W. W. Metcalf. "Cloning, Expression, and Biochemical Characterization of Streptomyces rubellomurinus Genes Required for Biosynthesis of Antimalarial Compound FR900098." Chemistry and Biology, 765-770 (2008). 

Z. Shao, J. A. V. Blodgett, B. T. Circello, R. Woodyer, G. Li, W. A. van der Donk, W. W. Metcalf, and H. Zhao. "Biosynthesis of 2-Hydroxyethylphosphonate, an Unexpected Intermediate Common to Multiple Phosphonate Biosynthetic Pathways." Journal of Biological Chemistry, 23161-23168 (2008).

Y. Choi, H. Zhang, J. S. Brunzelle, S. Nair, and H. Zhao. "In vitro Reconstitution and Structure of an Arylamine N-Oxygenase Involved in Biosynthesis of Aureothin." Proceedings of National Academy of Sciences of the United States of America, 105, 6858-6863 (2008).

Z. Shao, J. A. V. Blodgett, B. T. Circello, R. Woodyer, G. Li, W. A. van der Donk, W. W. Metcalf, and H. Zhao. "Biosynthesis of 2-Hydroxyethylphosphonate, an Unexpected Intermediate Common to Multiple Phosphonate Biosynthetic Pathways." Journal of Biological Chemistry, 283, 23161-23168 (2008).

A. C. Eliot, B. M. Griffin, P. M. Thomas, T. W. Johannes, N. L. Kelleher, H. Zhao and W. W. Metcalf. "Cloning, Expression, and Biochemical Characterization of Streptomyces rubellomurinus Genes Required for Biosynthesis of Antimalarial Compound FR900098." Chemistry and Biology, 15, 765-770 (2008).

S. Rubin-Pitel, H. Zhang, J. S. Brunzelle, T. Vu, H. Zhao, and S. Nair. "Distinct Structural Elements Dictate the Specificity of the Pentaketide Resorcylic Acid Synthase from Neurospora crassa." Chemistry and Biology, 15, 1079-1090 (2008).

T. Johannes, R. Woodyer, and H. Zhao. "Efficient Regeneration of NADPH using an Engineered Phosphite Dehydrogenase," Biotechnology and Bioengineering, 96, 18-26 (2007).

Awards

  • Fellow of the American Institute for Medical and Biological Engineering (AIMBE), 2009
  • Engineering Council Award for Excellence in Advising, UIUC College of Engineering, 2008
  • Young Investigator Award, American Chemical Society (ACS) Division of Biochemical Technology, 2008
  • University Scholar, UIUC, 2007
  • Outstanding Overseas Young Chinese Scholars Award, 2007
  • Helen Corley Petit Scholar, 2006
  • DuPont Young Investigator Award, 2005
  • Xerox Award for Faculty Research, UIUC College of Engineering, 2005
  • Beckman Fellow, UIUC Center for Advanced Study, 2005-2006
  • Excellence in Teaching Award, UIUC School of Chemical Sciences, 2004
  • NSF CAREER Award, 2004
  • Collins Scholar, UIUC Academy for Excellence in Engineering Education, 2001
  • Special Recognition Award, Dow Chemical Company, 1999, 2000

Highlights

Patents

Photo of Huimin Zhao