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2010

A diverse family of type III polyketide synthases in Eucalyptus species

Rubin-Pitel, S. B., Luo, Y., Lee, J. K. & Zhao, H., Aug 1 2010, In : Molecular BioSystems. 6, 8, p. 1444-1446 3 p.

Research output: Contribution to journalArticle

Eucalyptus
Polyketides
Enzymes
Biological Products
Genes

Cloning, characterization, and engineering of fungal L-arabinitol dehydrogenases

Kim, B., Sullivan, R. P. & Zhao, H., Jul 1 2010, In : Applied Microbiology and Biotechnology. 87, 4, p. 1407-1414 8 p.

Research output: Contribution to journalArticle

L-arabinitol 4-dehydrogenase
Organism Cloning
Oxidoreductases
Arabinose
Penicillium chrysogenum

Cloning and heterologous expression of the spectinabilin biosynthetic gene cluster from Streptomyces spectabilis

Choi, Y. S., Johannes, T. W., Simurdiak, M., Shao, Z., Lu, H. & Zhao, H., Feb 8 2010, In : Molecular BioSystems. 6, 2, p. 336-338 3 p.

Research output: Contribution to journalArticle

Streptomyces
Multigene Family
Organism Cloning
Polyketides
spectinabilin

Crystal structure and computational analyses provide insights into the catalytic mechanism of 2,4-diacetylphloroglucinol hydrolase PhlG from Pseudomonas fluorescens

He, Y. X., Huang, L., Xue, Y., Fei, X., Teng, Y. B., Rubin-Pitel, S. B., Zhao, H. & Zhou, C. Z., Feb 12 2010, In : Journal of Biological Chemistry. 285, 7, p. 4603-4611 9 p.

Research output: Contribution to journalArticle

Pseudomonas fluorescens
Hydrolases
Carbon
Crystal structure
Substrates

Deciphering the Late Biosynthetic Steps of Antimalarial Compound FR-900098

Johannes, T. W., DeSieno, M. A., Griffin, B. M., Thomas, P. M., Kelleher, N. L., Metcalf, W. W. & Zhao, H., Jan 29 2010, In : Chemistry and Biology. 17, 1, p. 57-64 8 p.

Research output: Contribution to journalArticle

Antimalarials
Biosynthetic Pathways
Escherichia coli
Assays
Anti-Bacterial Agents

Discovery and characterization of novel d-xylose-specific transporters from Neurospora crassa and Pichia stipitis

Du, J., Li, S. & Zhao, H., Nov 1 2010, In : Molecular BioSystems. 6, 11, p. 2150-2156 7 p.

Research output: Contribution to journalArticle

Neurospora crassa
Pichia
Xylose
Pentoses
Saccharomyces cerevisiae

Engineering of enzymes for selective catalysis

Nair, N. U., Denard, C. A. & Zhao, H., Oct 22 2010, In : Current Organic Chemistry. 14, 17, p. 1870-1882 13 p.

Research output: Contribution to journalArticle

Catalysis
Carbon
Enzymes
Substrates
Polyketide Synthases

Inverting the enantioselectivity of P450pyr monooxygenase by directed evolution

Tang, W. L., Li, Z. & Zhao, H., Aug 14 2010, In : Chemical Communications. 46, 30, p. 5461-5463 3 p.

Research output: Contribution to journalArticle

Enantioselectivity
Mixed Function Oxygenases

Overcoming glucose repression in mixed sugar fermentation by co-expressing a cellobiose transporter and a β-glucosidase in Saccharomyces cerevisiae

Li, S., Du, J., Sun, J., Galazka, J. M., Glass, N. L., Cate, J. H. D., Yang, X. & Zhao, H., Nov 1 2010, In : Molecular BioSystems. 6, 11, p. 2129-2132 4 p.

Research output: Contribution to journalArticle

Glucosidases
Cellobiose
Xylose
Fermentation
Saccharomyces cerevisiae

Selective reduction of xylose to xylitol from a mixture of hemicellulosic sugars

Nair, N. U. & Zhao, H., Sep 1 2010, In : Metabolic Engineering. 12, 5, p. 462-468 7 p.

Research output: Contribution to journalArticle

Xylitol
Arabinose
Xylose
Sugars
Aldehyde Reductase

Structure and Engineering of l-Arabinitol 4-Dehydrogenase from Neurospora crassa

Bae, B., Sullivan, R. P., Zhao, H. & Nair, S. K., Sep 1 2010, In : Journal of Molecular Biology. 402, 1, p. 230-240 11 p.

Research output: Contribution to journalArticle

Neurospora crassa
Oxidoreductases
Arabinose
Xylulose
Coenzymes
saccharification
Cellulose
Fermentation
fermentation
yeast
2011

Altering Enzyme Substrate and Cofactor Specificity via Protein Engineering

Desieno, M., Du, J. & Zhao, H., Mar 9 2011, Protein Engineering Handbook, Volume 1 & Volume 2. Wiley-VCH, Vol. 2. p. 777-796 20 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Protein Engineering
Gene therapy
Biosynthesis
Coenzymes
Substrate Specificity

A new fluorescence complementation biosensor for detection of estrogenic compounds

Mclachlan, M. J., Katzenellenbogen, J. A. & Zhao, H., Dec 1 2011, In : Biotechnology and bioengineering. 108, 12, p. 2794-2803 10 p.

Research output: Contribution to journalArticle

Biosensing Techniques
Biosensors
Estrogens
Fluorescence
Ligands

Cell surface display of functional human MHC class II proteins: Yeast display versus insect cell display

Wen, F., Sethi, D. K., Wucherpfennig, K. W. & Zhao, H., Sep 1 2011, In : Protein Engineering, Design and Selection. 24, 9, p. 701-709 9 p.

Research output: Contribution to journalArticle

Fungal Proteins
Peptides
Insects
Display devices
Major Histocompatibility Complex

Characterization and application of the Fe(ii) and α-ketoglutarate dependent hydroxylase FrbJ

Desieno, M. A., van der Donk, W. A. & Zhao, H., Sep 28 2011, In : Chemical Communications. 47, 36, p. 10025-10027 3 p.

Research output: Contribution to journalArticle

Bioassay
Antimalarials
Mixed Function Oxygenases
Organophosphonates
Substrates

Cloning and characterization of a type III polyketide synthase from Aspergillus niger

Li, J., Luo, Y., Lee, J. K. & Zhao, H., Oct 15 2011, In : Bioorganic and Medicinal Chemistry Letters. 21, 20, p. 6085-6089 5 p.

Research output: Contribution to journalArticle

Aspergillus niger
Cloning
Aspergillus
Starters
Organism Cloning

Combinatorial optimization of a highly efficient xylose utilization pathway in saccharomyces cerevisiae

Du, J., Kim, B. & Zhao, H., Dec 1 2011, 11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings. (11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Xylose
Combinatorial optimization
Yeast
Pentoses
Enzymes

Directed evolution of the nonribosomal peptide synthetase AdmK generates new andrimid derivatives in vivo

Evans, B. S., Chen, Y., Metcalf, W. W., Zhao, H. & Kelleher, N. L., May 27 2011, In : Chemistry and Biology. 18, 5, p. 601-607 7 p.

Research output: Contribution to journalArticle

Peptide Synthases
Reengineering
Derivatives
Enzymes
Pantoea

Drug Discovery and Development by Combinatorial Biosynthesis

Desieno, M. A., Denard, C. A. & Zhao, H., May 25 2011, Enzyme Technologies: Metagenomics, Evolution, Biocatalysis, and Biosynthesis. John Wiley and Sons, p. 251-283 33 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Biosynthesis
Drug Discovery

Engineering microbial factories for synthesis of value-added products

Du, J., Shao, Z. & Zhao, H., Aug 1 2011, In : Journal of Industrial Microbiology and Biotechnology. 38, 8, p. 873-890 18 p.

Research output: Contribution to journalReview article

Biofuels
Industrial plants
Synthetic Biology
Metabolic engineering
Metabolic Engineering

Engineering saccharomyces cerevisiae for biofuel production from lignocellulosic biomass

Du, J. & Zhao, H., Dec 1 2011, 11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings. (11AIChE - 2011 AIChE Annual Meeting, Conference Proceedings).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Pentoses
Biofuels
Yeast
Biomass
Xylose

Further biochemical studies on aminopyrrolnitrin oxygenase (PrnD)

Tiwari, M. K., Lee, J. K., Moon, H. J. & Zhao, H., May 15 2011, In : Bioorganic and Medicinal Chemistry Letters. 21, 10, p. 2873-2876 4 p.

Research output: Contribution to journalArticle

Oxygenases
Mutagenesis
Dimerization
Operon
Site-Directed Mutagenesis

Genome-scale consequences of cofactor balancing in engineered pentose utilization pathways in Saccharomyces cerevisiae

Ghosh, A., Zhao, H. & Price, N. D., Nov 4 2011, In : PloS one. 6, 11, e27316.

Research output: Contribution to journalArticle

Pentoses
pentoses
Xylose
Arabinose
xylose

Highlights of biocatalysis and biomimetic catalysis

Zhao, H., Sep 2 2011, In : ACS Catalysis. 1, 9, p. 1119-1120 2 p.

Research output: Contribution to journalEditorial

Biomimetics
Catalysis
Biocatalysis

New N-acetyltransferase fold in the structure and mechanism of the phosphonate biosynthetic enzyme FrbF

Bae, B., Cobb, R. E., DeSieno, M. A., Zhao, H. & Nair, S. K., Oct 14 2011, In : Journal of Biological Chemistry. 286, 41, p. 36132-36141 10 p.

Research output: Contribution to journalArticle

Organophosphonates
Acetyltransferases
Enzymes
Cytidine Monophosphate
Cytidine

Rapid characterization and engineering of natural product biosynthetic pathways via DNA assembler

Shao, Z., Luo, Y. & Zhao, H., Apr 1 2011, In : Molecular BioSystems. 7, 4, p. 1056-1059 4 p.

Research output: Contribution to journalArticle

Biosynthetic Pathways
Biological Products
Synthetic Biology
Homologous Recombination
DNA

Synthetic biology: Putting synthesis into biology

Liang, J., Luo, Y. & Zhao, H., Jan 1 2011, In : Wiley Interdisciplinary Reviews: Systems Biology and Medicine. 3, 1, p. 7-20 14 p.

Research output: Contribution to journalReview article

Synthetic Biology
DNA
Machinery
Genes
Health
2012

A type III polyketide synthase from Rhizobium etli condenses malonyl CoAs to a heptaketide pyrone with unusually high catalytic efficiency

Jeya, M., Kim, T. S., Kumar Tiwari, M., Li, J., Zhao, H. & Lee, J. K., Dec 2012, In : Molecular BioSystems. 8, 12, p. 3103-3106 4 p.

Research output: Contribution to journalArticle

Rhizobium etli
Pyrones
Malonyl Coenzyme A
Acetyl Coenzyme A
Molecular Dynamics Simulation

Biocatalyst development by directed evolution

Wang, M., Si, T. & Zhao, H., Jul 1 2012, In : Bioresource Technology. 115, p. 117-125 9 p.

Research output: Contribution to journalArticle

Biocatalysts
Enzymes
chemical process
drug
Catalyst selectivity

Cloning and characterization of a panel of constitutive promoters for applications in pathway engineering in Saccharomyces cerevisiae

Sun, J., Shao, Z., Zhao, H., Nair, N., Wen, F., Xu, J. H. & Zhao, H., Aug 1 2012, In : Biotechnology and bioengineering. 109, 8, p. 2082-2092 11 p.

Research output: Contribution to journalArticle

Cloning
Yeast
Saccharomyces cerevisiae
Organism Cloning
Xylans

CmlI is an N-oxygenase in the biosynthesis of chloramphenicol

Lu, H., Chanco, E. & Zhao, H., Sep 16 2012, In : Tetrahedron. 68, 37, p. 7651-7654 4 p.

Research output: Contribution to journalArticle

Oxygenases
Biosynthesis
Chloramphenicol
Enzymes
Ferrozine

Crystal structures of phosphite dehydrogenase provide insights into nicotinamide cofactor regeneration

Zou, Y., Zhang, H., Brunzelle, J. S., Johannes, T. W., Woodyer, R., Hung, J. E., Nair, N., van der Donk, W. A., Zhao, H. & Nair, S. K., May 29 2012, In : Biochemistry. 51, 21, p. 4263-4270 8 p.

Research output: Contribution to journalArticle

Niacinamide
Regeneration
Crystal structure
NAD
Phosphites

Customized optimization of metabolic pathways by combinatorial transcriptional engineering

Du, J., Yuan, Y., Si, T., Lian, J. & Zhao, H., Oct 1 2012, In : Nucleic acids research. 40, 18, p. e142

Research output: Contribution to journalArticle

Metabolic Networks and Pathways
Cellobiose
Xylose
Synthetic Biology
Metabolic Engineering

Direct cloning of large genomic sequences

Cobb, R. E. & Zhao, H., May 1 2012, In : Nature Biotechnology. 30, 5, p. 405-406 2 p.

Research output: Contribution to journalShort survey

Exodeoxyribonucleases
Cloning
Escherichia coli Proteins
Homologous Recombination
Molecular Cloning

Direct conversion of xylan to ethanol by recombinant Saccharomyces cerevisiae strains displaying an engineered minihemicellulosome

Sun, J., Wen, F., Si, T., Xu, J. H. & Zhao, H., Jun 1 2012, In : Applied and environmental microbiology. 78, 11, p. 3837-3845 9 p.

Research output: Contribution to journalArticle

Xylans
arabinoxylan
Xylose
xylan
xylose

Directed evolution: An evolving and enabling synthetic biology tool

Cobb, R. E., Si, T. & Zhao, H., Aug 1 2012, In : Current Opinion in Chemical Biology. 16, 3-4, p. 285-291 7 p.

Research output: Contribution to journalReview article

Synthetic Biology
Biological systems
Genes
Genome
Research

DNA assembler: A synthetic biology tool for characterizing and engineering natural product gene clusters

Shao, Z. & Zhao, H., 2012, Natural Product Biosynthesis by Microorganisms and Plants, Part C. Academic Press Inc., p. 203-224 22 p. (Methods in Enzymology; vol. 517).

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthetic Biology
Biosynthetic Pathways
Multigene Family
Biological Products
Genes

DNA assembler method for construction of zeaxanthin-producing strains of saccharomyces cerevisiae

Shao, Z., Luo, Y. & Zhao, H., Jul 27 2012, Microbial Carotenoids From Fungi: Methods and Protocols. Jose-Luis, B. (ed.). p. 251-262 12 p. (Methods in Molecular Biology; vol. 898).

Research output: Chapter in Book/Report/Conference proceedingChapter

Saccharomyces cerevisiae
Synthetic Biology
Metabolic Engineering
Homologous Recombination
DNA

Improving the thermostability of lipase Lip2 from Yarrowia lipolytica

Wen, S., Tan, T. & Zhao, H., Dec 5 2012, In : Journal of Biotechnology. 164, 2, p. 248-253 6 p.

Research output: Contribution to journalArticle

Yarrowia
Lipases
Lipase
Enzymes
Half-Life

Investigation of the role of Arg301 identified in the X-ray structure of phosphite dehydrogenase

Hung, J. E., Fogle, E. J., Christman, H. D., Johannes, T. W., Zhao, H., Metcalf, W. W. & Van Der Donk, W. A., May 29 2012, In : Biochemistry. 51, 21, p. 4254-4262 9 p.

Research output: Contribution to journalArticle

Phosphites
Hydroxy Acids
X-Rays
X rays
Oxidoreductases

Mechanistic studies on the flavin:NADH reductase (PrnF) from Pseudomonas fluorescens involved in arylamine oxygenation

Tiwari, M. K., Singh, R. K., Lee, J. K. & Zhao, H., Feb 1 2012, In : Bioorganic and Medicinal Chemistry Letters. 22, 3, p. 1344-1347 4 p.

Research output: Contribution to journalArticle

Pseudomonas fluorescens
Flavin-Adenine Dinucleotide
Oxygenation
NAD
Oxidoreductases

Mutagenic inverted repeats assisted genome engineering (MIRAGE) in saccharomyces cerevisiae: Deletion of gal7

Nair, N. U. & Zhao, H., Jan 20 2012, Microbial Metabolic Engineering: Methods and Protocols. Cheng, Q. (ed.). p. 63-73 11 p. (Methods in Molecular Biology; vol. 834).

Research output: Chapter in Book/Report/Conference proceedingChapter

Synthetic Biology
Metabolic Engineering
Systems Biology
Point Mutation
Saccharomyces cerevisiae

Optimized TAL effector nucleases (TALENs) for use in treatment of sickle cell disease

Sun, N., Liang, J., Abil, Z. & Zhao, H., Mar 1 2012, In : Molecular BioSystems. 8, 4, p. 1255-1263 9 p.

Research output: Contribution to journalArticle

Sickle Cell Anemia
Therapeutics
Targeted Gene Repair
Globins
Transcription Activator-Like Effectors

Recent advances in targeted genome engineering in mammalian systems

Sun, N., Abil, Z. & Zhao, H., Sep 1 2012, In : Biotechnology Journal. 7, 9, p. 1074-1087 14 p.

Research output: Contribution to journalReview article

Genome
Homologous Recombination
Gene Targeting
Double-Stranded DNA Breaks
Endonucleases

Role of conserved glycine in zinc-dependent medium chain dehydrogenase/reductase superfamily

Tiwari, M. K., Singh, R. K., Singh, R., Jeya, M., Zhao, H. & Lee, J. K., Jun 1 2012, In : Journal of Biological Chemistry. 287, 23, p. 19429-19439 11 p.

Research output: Contribution to journalArticle

Glycine
Zinc
Oxidoreductases
Mutagenesis
Metals

Strain Improvement via Evolutionary Engineering

Kim, B., Du, J. & Zhao, H., Oct 24 2012, Engineering Complex Phenotypes in Industrial Strains. John Wiley and Sons, p. 111-131 21 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

The Botrytis cinerea type III polyketide synthase shows unprecedented high catalytic efficiency toward long chain acyl-CoAs

Jeya, M., Kim, T. S., Tiwari, M. K., Li, J., Zhao, H. & Lee, J. K., Nov 1 2012, In : Molecular BioSystems. 8, 11, p. 2864-2867 4 p.

Research output: Contribution to journalArticle

Resorcinols
Pyrones
Palmitoyl Coenzyme A
Malonyl Coenzyme A
Botrytis
2013

Activation and characterization of a cryptic polycyclic tetramate macrolactam biosynthetic gene cluster

Luo, Y., Huang, H., Liang, J., Wang, M., Lu, L., Shao, Z., Cobb, R. E. & Zhao, H., Dec 5 2013, In : Nature communications. 4, 2894.

Research output: Contribution to journalArticle

Multigene Family
genes
Genes
Chemical activation
activation

Challenges and opportunities in synthetic biology for chemical engineers

Luo, Y., Lee, J. K. & Zhao, H., Nov 5 2013, In : Chemical Engineering Science. 103, p. 115-119 5 p.

Research output: Contribution to journalArticle

Synthetic Biology
Engineers
Modularization
Biofuels
Biological systems