Cooperative Institute for Research in Environmental Sciences

Shelley D. Copley

Shelley D. Copley

Research Interests

My lab studies evolution of bacteria in novel environments, and in particular the evolutionary potential lurking in the proteome due to inefficient side activities of enzymes that normally serve other functions. Current work focuses on determining how such “promiscuous” activities have been patched together into a pathway for degradation of pentachlorophenol, a toxic anthropogenic pollutant, and how the bacterium manages to survive the toxicity caused by pentachlorophenol and its degradation products. Other projects address how bacteria can adapt to deletion of an essential gene and the process by which new enzymes arise from promiscuous enzymes by a process of gene duplication and divergence.


Current Research

Enzymes are superb catalysts, capable of accelerating reactions by up to 26 orders of magnitude. The conditions required to produce and to use enzymes are “green” – they do not require toxic organic solvents and/or high temperatures and pressures that are costly in terms of energy usage.

Most microbes contain an impressive 1000-2000 enzymes. However, a change in the environment may require new enzymes. A frequent source of new enzymes is a pre-existing enzyme with a promiscuous activity; promiscuous activities are accidental side activities that arise from the highly reactive environments at enzyme active sites. When a promiscuous enzyme is recruited to do a new job, it is often inefficient. Further, there may be an “adaptive conflict” between the original and newly important activities; mutations that improve the new function often damage the old function. This conundrum is typically resolved by a process of gene duplication followed by divergence of one copy to encode an efficient new enzyme while the other copy continues to encode the original enzyme (see Figure 1).

A current project in the lab addresses evolution of a new enzyme using a model system in which a gene encoding an essential enzyme (ArgC) has been deleted. Another enzyme (ProA) present in the bacterium has a promiscuous secondary activity that corresponds to that of ArgC, but it is too inefficient to rescue growth. However, a single mutation allows the enzyme to serve both functions, albeit poorly. This “weak-link” enzyme limits growth of the bacterium; thus, the cells are under strong selective pressure for emergence of clones in which the levels of one or both enzyme activities are improved.

Using this model system in the bacterium Escherichia coli, we have found that some clones accumulate 50 copies of a genomic region containing the gene encoding the weak-link enzyme. We are currently developing a method that will allow us to follow the appearance of mutations in individual gene copies and thereby to follow the detailed dynamics of the process depicted in Fig. 1.

When we investigated this model system in a different bacterium, Salmonella enterica, we found – to our surprise - that gene amplification did not occur.  Rather, we found clones with a number of point mutations, most of which simply increased the concentration of the weak-link enzyme in the cells. This finding suggests that S. enterica lacks the capacity to undergo the process shown in Fig. 1.  

The insights emerging from this work suggest that only some microbes in a community will be able to meet the challenge of a changing environment by evolving new enzymes. We are beginning to understand the roles of important factors such as the repertoire of enzymes encoded by the genome, the nature of available promiscuous activities, and the location of genes encoding promiscuous activities in the genome. These findings have important implications for understanding how microbial communities respond to novel environmental conditions such as the presence of pesticides and industrial pollutants.

The Innovation-Amplification-Divergence model for evolution of a new enzyme (neo-B) starting from a gene encoding an enzyme with a primary activity A and a weak secondary activity b that becomes useful after a change in environment. Image: Shelley Copley

View Publications

  • Kershner, JP, SY McLoughlin, J Kim, A Morgenthaler, CC Ebmeier, WM Old and SD Copley (2016), A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate. J. Bacteriol. Version: 1 198 (20) 2853-2863, issn: 0021-9193, ids: DX4JQ, doi: 10.1128/JB.00262-16, PubMed ID: 27501982
  • Thiaville, JJ, J Flood, S Yurgel, L Prunetti, M Elbadawi-Sidhu, G Hutinet, F Forouhar, XS Zhang, V Ganesan, P Reddy, O Fiehn, JA Gerlt, JF Hunt, SD Copley and V de Crecy-Lagard (2016), Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. ACS Chem. Biol. Version: 1 11 (8) 2304-2311, issn: 1554-8929, ids: DT9UL, doi: 10.1021/acschembio.6b00279, PubMed ID: 27294475
  • Khanal, A, SY McLoughlin, JP Kershner and SD Copley (2015), Differential Effects of a Mutation on the Normal and Promiscuous Activities of Orthologs: Implications for Natural and Directed Evolution. Mol. Biol. Evol. Version: 1 32 (1) 100-108, issn: 0737-4038, ids: CC0TR, doi: 10.1093/molbev/msu271, PubMed ID: 25246702
  • Copley, SD (2015), An evolutionary biochemist's perspective on promiscuity. Trends Biochem. Sci. Version: 1 40 (2) 72-78, issn: 0968-0004, ids: CB4GR, doi: 10.1016/j.tibs.2014.12.004, PubMed ID: 25573004
  • Copley, SD (2014), An evolutionary perspective on protein moonlighting. Biochem. Soc. Trans. Version: 1 42 1684-1691, issn: 0300-5127, ids: AU2DT, doi: 10.1042/BST20140245, PubMed ID: 25399590
  • Kim, J, AM Webb, JP Kershner, S Blaskowski and SD Copley (2014), A versatile and highly efficient method for scarless genome editing in Escherichia coli and Salmonella enterica. BMC Biotechnol. Version: 1 14 , Art. No. 84, issn: 1472-6750, ids: AR6FF, doi: 10.1186/1472-6750-14-84, PubMed ID: 25255806
  • Rokicki, J, D Knox, RD Dowell and SD Copley (2014), CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics Version: 1 15 (65) , issn: 1471-2164, ids: AA5DG, doi: 10.1186/1471-2164-15-65
  • Rudolph, J, AH Erbse, LS Behlen and SD Copley (2014), A Radical Intermediate in the Conversion of Pentachlorophenol to Tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry Version: 1 53 (41) 6539-6549, issn: Jun-60, ids: AR5RC, doi: 10.1021/bi5010427, PubMed ID: 25238136
  • Novikov, Y and SD Copley (2013), Reactivity landscape of pyruvate under simulated hydrothermal vent conditions. Proc. Natl. Acad. Sci. U. S. A. Version: 1 110 (33) 13283-13288, issn: 0027-8424, ids: 200LA, doi: 10.1073/pnas.1304923110, PubMed ID: 23872841
  • Yadid, I, J Rudolph, K Hlouchova and SD Copley (2013), Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. Proc. Natl. Acad. Sci. U. S. A. Version: 1 110 (24) E2182-E2190, issn: 0027-8424, ids: 171LM, doi: 10.1073/pnas.1214052110, PubMed ID: 23676275
  • Kim, J and SD Copley (2013), The Orphan Protein Bis-gamma-glutamylcystine Reductase Joins the Pyridine Nucleotide Disulfide Reductase Family. Biochemistry Version: 1 52 (17) 2905-2913, issn: Jun-60, ids: 136AZ, doi: 10.1021/bi4003343, PubMed ID: 23560638
  • Kim, J and SD Copley (2012), Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proc. Natl. Acad. Sci. U. S. A. Version: 1 109 (42) E2856-E2864, issn: 0027-8424, ids: 029SK, doi: 10.1073/pnas.1208509109, PubMed ID: 22984162
  • Copley, SD, J Rokicki, P Turner, H Daligault, M Nolan and M Land (2012), The Whole Genome Sequence of Sphingobium chlorophenolicum L-1: Insights into the Evolution of the Pentachlorophenol Degradation Pathway. Genome Biol. Evol. Version: 1 4 (2) 184-198, issn: 1759-6653, ids: 914VJ, doi: 10.1093/gbe/evr137, PubMed ID: 22179583
  • Copley, SD (2012), Moonlighting is mainstream: Paradigm adjustment required. Bioessays Version: 1 34 (7) 578-588, issn: 0265-9247, ids: 958KG, doi: 10.1002/bies.201100191, PubMed ID: 22696112
  • Hlouchova, K, J Rudolph, JMH Pietari, LS Behlen and SD Copley (2012), Pentachlorophenol Hydroxylase, a Poorly Functioning Enzyme Required for Degradation of Pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry Version: 1 51 (18) 3848-3860, issn: Jun-60, ids: 936ZG, doi: 10.1021/bi300261p, PubMed ID: 22482720
  • Copley, SD (2012), Toward a Systems Biology Perspective on Enzyme Evolution. J. Biol. Chem. Version: 1 287 (1) 3-10, issn: 0021-9258, ids: 870PW, doi: 10.1074/jbc.R111.254714, PubMed ID: 22069330
  • Novikov, Y, SD Copley and BE Eaton (2011), A simple route for synthesis of 4-phospho-D-erythronate. Tetrahedron Lett. Version: 1 52 (16) 1913-1915, issn: 0040-4039, ids: 765YV, doi: 10.1016/j.tetlet.2011.02.045
  • Chumachenko, N, Y Novikov, RK Shoemaker and SD Copley (2011), A Dimethyl Ketal-Protected Benzoin-Based Linker Suitable for Photolytic Release of Unprotected Peptides. J. Org. Chem. Version: 1 76 (22) 9409-9416, issn: 0022-3263, ids: 844NN, doi: 10.1021/jo2017263, PubMed ID: 21950361
  • Rudolph, J, J Kim and SD Copley (2010), Multiple Turnovers of the Nicotino-Enzyme PdxB Require alpha-Keto Acids as Cosubstrates. Biochemistry Version: 1 49 (43) 9249-9255, issn: Jun-60, ids: 670GL, doi: 10.1021/bi101291d, PubMed ID: 20831184
  • Kim, JH, JP Kershner, Y Novikov, RK Shoemaker and SD Copley (2010), Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5 '-phosphate synthesis. Mol. Syst. Biol. Version: 1 6 , Art. No. 436, issn: 1744-4292, ids: 691GI, doi: 10.1038/msb.2010.88, PubMed ID: 21119630
  • Copley, SD (2009), Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat. Chem. Biol. Version: 1 5 (8) 560-567, issn: 1552-4450, ids: 473LV, doi: 10.1038/nchembio.197, PubMed ID: 19620997
  • McLoughlin, SY and SD Copley (2008), A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities. Proc. Natl. Acad. Sci. U. S. A. Version: 1 105 (36) 13497-13502, issn: 0027-8424, ids: 349AR, doi: 10.1073/pnas.0804804105, PubMed ID: 18757760
  • Hamady, M, J Widmann, SD Copley and R Knight (2008), MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs. Genome Biol. Version: 1 9 (8) , Art. No. R128, issn: 1474-760X, ids: 355IA, doi: 10.1186/gb-2008-9-8-r128, PubMed ID: 18706079
  • Warner, JR, LS Behlen and SD Copley (2008), A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase. Biochemistry Version: 1 47 (10) 3258-3265, issn: Jun-60, ids: 270NG, doi: 10.1021/bi702431n, PubMed ID: 18275157
  • Warner, JR and SD Copley (2007), Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates. Biochemistry Version: 1 46 (14) 4438-4447, issn: Jun-60, ids: 152OD, doi: 10.1021/bi0620104, PubMed ID: 17355122
  • Kim, J and SD Copley (2007), Why metabolic enzymes are essential or nonessential for growth of Escherichia coli k12 on glucose. Biochemistry Version: 1 46 (44) 12501-12511, issn: Jun-60, ids: 226FA, doi: 10.1021/bi7014629, PubMed ID: 17935357
  • Warner, JR and SD Copley (2007), Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry Version: 1 46 (45) 13211-13222, issn: Jun-60, ids: 228XT, doi: 10.1021/bi701069n, PubMed ID: 17956123
  • Copley, SD, E Smith and HJ Morowitz (2007), The origin of the RNA world: Co-evolution of genes and metabolism. Bioorganic Chem. Version: 1 35 (6) 430-443, issn: 0045-2068, ids: 237GV, doi: 10.1016/j.bioorg.2007.08.001, PubMed ID: 17897696
  • Dai, MH, S Ziesman, T Ratcliffe, RT Gill and SD Copley (2005), Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metab. Eng. Version: 1 7 (1) 45-52, issn: 1096-7176, ids: 904LI, doi: 10.1016/j.ymben.2004.09.002, PubMed ID: 15974564
  • Warner, JR, SL Lawson and SD Copley (2005), A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry Version: 1 44 (30) 10360-10368, issn: Jun-60, ids: 950TG, doi: 10.1021/bi050666b, PubMed ID: 16042413
  • Copley, SD, E Smith and HJ Morowitz (2005), A mechanism for the association of amino acids with their codons and the origin of the genetic code. Proc. Natl. Acad. Sci. U. S. A. Version: 1 102 (12) 4442-4447, issn: 0027-8424, ids: 909IY, doi: 10.1073/pnas.0501049102, PubMed ID: 15764708
  • Copley, SD, WRP Novak and PC Babbitt (2004), Divergence of function in the thioredoxin fold suprafamily: Evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry Version: 1 43 (44) 13981-13995, issn: 0006-2960, ids: 868UV, doi: 10.1021/bi048947r
  • Dai, MH and SD Copley (2004), Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl. Environ. Microbiol. Version: 1 70 (4) 2391-2397, issn: 0099-2240, ids: 811SS, doi: 10.1128/AEM.70.4.2391-2397.2004, PubMed ID: 15066836
  • Copley, SD (2003), Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr. Opin. Chem. Biol. Version: 1 7 (2) 265-272, issn: 1367-5931, ids: 676FB, doi: 10.1016/S1367-5931(03)00032-2, PubMed ID: 12714060
  • Dai, MH, JB Rogers, JR Warner and SD Copley (2003), A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD). J. Bacteriol. Version: 1 185 (1) 302-310, issn: 0021-9193, ids: 629LJ, doi: 10.1128/JB.185.1.302-310.2003, PubMed ID: 12486067
  • Kiefer, PM and SD Copley (2002), Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry Version: 1 41 (4) 1315-1322, issn: Jun-60, ids: 517LM, doi: 10.1021/bi0117504, PubMed ID: 11802732
  • Kiefer, PM, DL McCarthy and SD Copley (2002), The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution. Biochemistry Version: 1 41 (4) 1308-1314, issn: Jun-60, ids: 517LM, doi: 10.1021/bi0117495, PubMed ID: 11802731
  • Copley, SD, K Anandarajah and PJ Kiefer (2001), A tale of two enzymes: tetrachlorohydroquinone dehalogenase and maleylacetoacetate isomerase. Chem.-Biol. Interact. Version: 1 International Conference on Glutathione Transferases 133 (3-Jan) 200-203, UPPSALA, SWEDEN, MAY 19-23, 2000, issn: Sep-97, ids: 424QY
  • Anandarajah, K, PM Kiefer, BS Donohoe and SD Copley (2000), Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry Version: 1 39 (18) 5303-5311, issn: Jun-60, ids: 312PD, doi: 10.1021/bi9923813, PubMed ID: 10820000
  • Copley, SD (2000), Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem. Sci. Version: 1 25 (6) 261-265, issn: 0968-0004, ids: 322UU, doi: 10.1016/S0968-0004(00)01562-0, PubMed ID: 10838562
  • Fall, R and SD Copley (2000), Bacterial sources and sinks of isoprene, a reactive atmospheric hydrocarbon. Environ. Microbiol. Version: 1 2 (2) 123-130, issn: 1462-2912, ids: 315HE, doi: 10.1046/j.1462-2920.2000.00095.x, PubMed ID: 11220299
  • Xu, L, K Resing, SL Lawson, PC Babbitt and SD Copley (1999), Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry Version: 1 38 (24) 7659-7669, issn: Jun-60, ids: 208XB, doi: 10.1021/bi990103y, PubMed ID: 10387005
  • McCarthy, DL, DF Louie and SD Copley (1997), Identification of a covalent intermediate between glutathione and cysteine13 formed during catalysis by tetrachlorohydroquinone dehalogenase. J. Am. Chem. Soc. Version: 1 119 (46) 11337-11338, issn: Feb-63, ids: YG901, doi: 10.1021/ja9726365
  • Copley, SD (1997), Diverse mechanistic approaches to difficult chemical transformations: Microbial dehalogenation of chlorinated aromatic compounds. Chem. Biol. Version: 1 4 (3) 169-174, issn: 1074-5521, ids: WV743, doi: 10.1016/S1074-5521(97)90285-4
  • McCarthy, DL, AA Claude and SD Copley (1997), In vivo levels of chlorinated hydroquinones in a pentachlorophenol-degrading bacterium. Appl. Environ. Microbiol. Version: 1 63 (5) 1883-1888, issn: 0099-2240, ids: WX361, PubMed ID: 9143119
  • Willett, WS and SD Copley (1996), Identification and localization of a stable sulfenic acid in peroxide-treated tetrachlorohydroquinone dehalogenase using electrospray mass spectrometry. Chem. Biol. Version: 1 3 (10) 851-857, issn: 1074-5521, ids: VR145, PubMed ID: 8939704
  • McCarthy, DL, S Navarrete, WS Willett, PC Babbitt and SD Copley (1996), Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry Version: 1 35 (46) 14634-14642, issn: Jun-60, ids: VU224, doi: 10.1021/bi961730f, PubMed ID: 8931562
  • CROOKS, GP, L XU, RM BARKLEY and SD COPLEY (1995), EXPLORATION OF POSSIBLE MECHANISMS FOR 4-CHLOROBENZOYL COA DEHALOGENASE - EVIDENCE FOR AN ARYL-ENZYME INTERMEDIATE. J. Am. Chem. Soc. Version: 1 117 (44) 10791-10798, issn: Feb-63, ids: TD410, doi: 10.1021/ja00149a001
  • CROOKS, GP and SD COPLEY (1994), PURIFICATION AND CHARACTERIZATION OF 4-CHLOROBENZOYL COA DEHALOGENASE FROM ARTHROBACTER SP STRAIN 4-CB1. Biochemistry Version: 1 33 (38) 11645-11649, issn: Jun-60, ids: PJ293, doi: 10.1021/bi00204a028, PubMed ID: 7918379
  • CROOKS, GP and SD COPLEY (1993), A SURPRISING EFFECT OF LEAVING GROUP ON THE NUCLEOPHILIC AROMATIC-SUBSTITUTION REACTION CATALYZED BY 4-CHLOROBENZOYL-COA DEHALOGENASE. J. Am. Chem. Soc. Version: 1 115 (14) 6422-6423, issn: Feb-63, ids: LT173, doi: 10.1021/ja00067a072
  • COPLEY, SD, E FRANK, WM KIRSCH and TH KOCH (1992), DETECTION AND POSSIBLE ORIGINS OF AMINOMALONIC ACID IN PROTEIN HYDROLYSATES. Anal. Biochem. Version: 1 201 (1) 152-157, issn: 0003-2697, ids: HE336, doi: 10.1016/0003-2697(92)90188-D
  • COPLEY, SD and GP CROOKS (1992), ENZYMATIC DEHALOGENATION OF 4-CHLOROBENZOYL COENZYME-A IN ACINETOBACTER SP STRAIN 4-CB1. Appl. Environ. Microbiol. Version: 1 58 (4) 1385-1387, issn: 0099-2240, ids: HM121, PubMed ID: 16348702
  • COPLEY, SD and JR KNOWLES (1987), THE CONFORMATIONAL EQUILIBRIUM OF CHORISMATE IN SOLUTION - IMPLICATIONS FOR THE MECHANISM OF THE NONENZYMATIC AND THE ENZYME-CATALYZED REARRANGEMENT OF CHORISMATE TO PREPHENATE. J. Am. Chem. Soc. Version: 1 109 (16) 5008-5013, issn: 0002-7863, ids: J5208, doi: 10.1021/ja00250a040
  • GUILFORD, WJ, SD COPLEY and JR KNOWLES (1987), ON THE MECHANISM OF THE CHORISMATE MUTASE REACTION. J. Am. Chem. Soc. Version: 1 109 (16) 5013-5019, issn: 0002-7863, ids: J5208, doi: 10.1021/ja00250a041
  • COPLEY, SD and JR KNOWLES (1985), THE UNCATALYZED CLAISEN REARRANGEMENT OF CHORISMATE TO PREPHENATE PREFERS A TRANSITION-STATE OF CHAIRLIKE GEOMETRY. J. Am. Chem. Soc. Version: 1 107 (18) 5306-5308, issn: 0002-7863, ids: AQE67, doi: 10.1021/ja00304a064
  • GRIMSHAW, CE, SG SOGO, SD COPLEY and JR KNOWLES (1984), SYNTHESIS OF STEREOSELECTIVELY LABELED [9-H-2,H-3] CHORISMATE AND THE STEREOCHEMICAL COURSE OF "5-ENOLPYRUVOYLSHIKIMATE-3-PHOSPHATE SYNTHETASE. J. Am. Chem. Soc. Version: 1 106 (9) 2699-2700, issn: 0002-7863, ids: SP772, doi: 10.1021/ja00321a037
  • KOVACHY, RJ, SD COPLEY and RH ALLEN (1983), RECOGNITION, ISOLATION, AND CHARACTERIZATION OF RAT-LIVER D-METHYLMALONYL COENZYME-A HYDROLASE. J. Biol. Chem. Version: 1 258 (18) 1415-1421, issn: 0021-9258, ids: RH492