Professor, MCDB



Ph.D.: Harvard University, 1987

Evolution in Action: Examination of a Evolving Metabolic Pathway

A major focus is the evolution of a new metabolic pathway in Sphingobium chlorophenolicum, a soil bacterium that can mineralize pentachlorophenol (PCP). PCP is an anthropogenic compound first introduced as a pesticide in 1936. S. chlorophenolicum has assembled a new metabolic pathway by patching together enzymes recruited from pre-existing pathways. Our studies address the origin of enzymes that are serving new functions and how well these enzymes are performing their new roles. We are also using in vitro evolution techniques to improve the bacterium’s ability to degrade PCP.

Searching for Catalytic Promiscuity

Although most enzymes have evolved to be very effective catalysts for specific reactions, many also catalyze other reactions due to the presence of highly reactive groups in the active site.  These “promiscuous” reactions are generally rather inefficient and of no use to the organism.  However, promiscuous enzymes provide a repertoire of capabilities that can be drawn upon when conditions change and a new catalytic activity is important for fitness.  We are examining catalytic promiscuity in E. coli by identifying genes for which overexpression or mutation restores viability in mutant strains lacking critical metabolic enzymes by encoding proteins that can be recruited to serve the function of the missing enzyme.  We are determining the level of promiscuous activities in recruited proteins, as well as their original functions and structural folds.  For selected cases, in vitro evolution will be used to attempt to improve the level of the targeted enzyme activity in the recruited protein. 

Convergent Evolution of Enzymatic Activities in Different Structural Contexts

There is generally more than one way to do anything, and this is true at the molecular level as well.  A new project in the lab addresses convergent evolution of catalytic function in proteins that have different structures. The goal of this project is to employ both experimental and bioinformatics methods to improve our understanding of the number of reactions for which catalysis can be provided by multiple protein scaffolds.  We plan to find new examples of convergently evolved enzymes by identifying genes encoding “missing enzymes” in thermophilic microbes and using bioinformatics techniques to mine public databases  to identify enzymatic reactions  catalyzed by non-homologous proteins. 

Catalysis in Pre-Biotic Chemical Reaction Networks

Our interest in the evolution of catalysts also includes the era before the emergence of macromolecules.   We are examining the ability of dinucleotides to catalyze chemical reactions.  In particular, we are testing the hypothesis that dinucleotides enhanced the rates of synthetic reactions leading to amino acids in a small-molecule reaction network that preceded the RNA translation apparatus, but created an association between amino acids and the first two bases of their codons that was retained when translation emerged later in evolution.

Warner, J. P., Lawson, S. L., and Copley, S. D.. "A Mechanistic Investigation of the Thiol-Disulfide Exchange Step in the Reductive Dehalogenation Catalyzed by Tetrachlorohydroquinone Dehalogenase", Biochemistry, 2005, 44, 10360-10368.

Copley, S. D., Smith, D. E., and Morowitz, H. G.  “A Mechanism for the Association of Amino Acids with their Codons and the Origin of the Genetic Code”, Proceedings of the National Academy of Sciences, 2005, 102, 4442-4447.

Copley, S. D., Novak, W., and Babbitt, P. C.  “Divergence of Function in the Thioredoxin-Fold Suprafamily:  Evidence for Evolution of Peroxiredoxins from Thioredoxins”, Biochemistry 43, 13981-13995, 2004.

Dai, M.-H. and Copley, S. D.  “Genome Shuffling Improves Degradation of the Anthropogenic Pesticide Pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723”, Appl. Env. Microbiol. 70, 2391-2397, 2004.

Dai, M.H., Rogers, J. B., Warner, J. P., and Copley, S. D. “A Previously Unrecognized Step in Pentachlorophenol Degradation in Sphingobium chlorophenolicum is Catalyzed by Tetrachlorobenzoquinone Reductase (PcpD)”, Journal of Bacteriology185, 302-310, 2003.

Copley, S. D.  “Enzymes with extra talents:  moonlighting functions and catalytic promiscuity”, Curr. Opin. Chem. Biol. 7, 2003.

Copley, S. D.  “Evolution of a Metabolic Pathway for Degradation of a Toxic Xenobiotic:  The Patchwork Approach”, Trends in Biochemical Sciences26, 261-265, 2000.

Anandarajah, K.; Kiefer, P. M.; Donohoe, B. S. and Copley, S. D.  “Recruitment of a Double Bond Isomerase to Serve as a Reductive Dehalogenase During Biodegradation of Pentachlorophenol”, Biochemistry, 39, 5303-5311, 2000.