Multimodular polyketide synthases (PKSs) are enzymatic assembly lines that synthesize many antibiotics. We seek to understand and engineer such systems, using the 6-deoxyerythronolide B synthase (DEBS) as a prototype. This revised application addresses the reviewers'major concerns by focusing primarily on two aspects of DEBS that are arguably of greatest interest to biosynthetic engineers: programmed unidirectional channeling of intermediates along the assembly line, and extender unit specificity.
Our Specific Aims are:
Aim 1 : Reconstitution and analysis of DEBS: Although DEBS has been studied for two decades, in vitro reconstitution and analysis of the entire system has not been reported. Kinetic analysis of 6-deoxyerythronolide B synthesis will not only lay the quantitative foundation for Aims 2 and 3, but will also answer basic questions of broad relevance to all of nature's PKS assembly lines.
Aim 2 : Understanding and engineering protein-protein interactions in assembly line PKSs: Our studies have suggested that three types of non-covalent protein-protein interactions can collectively explain how PKS assembly lines have been evolutionarily programmed for unidirectional chain growth. We will perform two sets of experiments to test this hypothesis. First, we will construct and analyze mutants in which the directionality of polyketide chain growth is altered. Second, by directed manipulation of protein-protein interactions, we will improve the efficiency of representative chimeric PKSs that show measurable but sub-optimal turnover.
Aim 3 : Understanding and engineering extender unit specificity of assembly line PKSs: Acyl transferase (AT) domains catalyze extender unit incorporation in each module of an assembly line PKS. Although a few cases of engineering AT specificity via homology-based approaches have been reported, the resulting PKSs are kinetically impaired and the underlying causes are unclear. We propose a fundamentally different strategy to engineer AT specificity. First, we will investigate the mechanistic basis for acyl-CoA and ACP specificity via kinetic analysis of three AT domains whose structures we have solved. The resulting methods and insights will enable quantitative interrogation of AT mutants whose design is guided by either structure-based or statistics-based principles. Finally, by re-introducing the most promising AT mutants into the DEBS assembly line, we will evaluate the consequences of AT domain engineering on the turnover rate of the full system.
Aim 4 : Preparation and evaluation of 15-propargyl-erythromycin A analogues: While not directly related to our primary future directions, during the past funding cycle we discovered 15-propargyl erythromycin A, a unique orthogonally functionalized antibiotic with similar activity to erythromycin A. With modest effort, we propose t prepare a few derivatives for ongoing studies on macrolide-ribosome interactions in our collaborator's lab. Our studies will not only open new doors for biosynthetic engineers who seek to manipulate antibiotic structure by genetic engineering, but will also highlight the broader relevance of polyketide biosynthetic research.

Public Health Relevance

Polyketide synthases are enzyme systems that synthesize complex antibiotics in an assembly line manner. By studying and engineering the erythromycin polyketide synthase, we seek to understand the operating principles of nature's assembly lines, and how they can be redesigned to make new antibiotics.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
2R01GM087934-19A1
Application #
8600581
Study Section
Special Emphasis Panel (ZRG1-BCMB-K (02))
Program Officer
Gerratana, Barbara
Project Start
1995-07-05
Project End
2017-05-31
Budget Start
2013-08-15
Budget End
2014-05-31
Support Year
19
Fiscal Year
2013
Total Cost
$385,174
Indirect Cost
$137,962
Name
Stanford University
Department
Chemistry
Type
Schools of Arts and Sciences
DUNS #
009214214
City
Stanford
State
CA
Country
United States
Zip Code
94305
Khosla, Chaitan; Herschlag, Daniel; Cane, David E et al. (2014) Assembly line polyketide synthases: mechanistic insights and unsolved problems. Biochemistry 53:2875-83
Edwards, Andrea L; Matsui, Tsutomu; Weiss, Thomas M et al. (2014) Architectures of whole-module and bimodular proteins from the 6-deoxyerythronolide B synthase. J Mol Biol 426:2229-45
O'Brien, Robert V; Davis, Ronald W; Khosla, Chaitan et al. (2014) Computational identification and analysis of orphan assembly-line polyketide synthases. J Antibiot (Tokyo) 67:89-97
Dunn, Briana J; Watts, Katharine R; Robbins, Thomas et al. (2014) Comparative analysis of the substrate specificity of trans- versus cis-acyltransferases of assembly line polyketide synthases. Biochemistry 53:3796-806
Garg, Ashish; Xie, Xinqiang; Keatinge-Clay, Adrian et al. (2014) Elucidation of the cryptic epimerase activity of redox-inactive ketoreductase domains from modular polyketide synthases by tandem equilibrium isotope exchange. J Am Chem Soc 136:10190-3
Kuo, James; Khosla, Chaitan (2014) The initiation ketosynthase (FabH) is the sole rate-limiting enzyme of the fatty acid synthase of Synechococcus sp. PCC 7002. Metab Eng 22:53-9
Walker, Mark C; Thuronyi, Benjamin W; Charkoudian, Louise K et al. (2013) Expanding the fluorine chemistry of living systems using engineered polyketide synthase pathways. Science 341:1089-94
Dunn, Briana J; Khosla, Chaitan (2013) Engineering the acyltransferase substrate specificity of assembly line polyketide synthases. J R Soc Interface 10:20130297
You, Young-Ok; Khosla, Chaitan; Cane, David E (2013) Stereochemistry of reductions catalyzed by methyl-epimerizing ketoreductase domains of polyketide synthases. J Am Chem Soc 135:7406-9
Xiao, Xirui; Yu, Xingye; Khosla, Chaitan (2013) Metabolic flux between unsaturated and saturated fatty acids is controlled by the FabA:FabB ratio in the fully reconstituted fatty acid biosynthetic pathway of Escherichia coli. Biochemistry 52:8304-12

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