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

  • Copley, SD (2017), Shining a light on enzyme promiscuity. Curr. Opin. Struct. Biol. Version: 1 47 167-175, issn: 0959-440X, ids: FR9SP, doi: 10.1016/, PubMed ID: 29169066
  • Kershner, JP; McLoughlin, SY; Kim, J; Morgenthaler, A; Ebmeier, CC; Old, WM; Copley, SD (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; Flood, J; Yurgel, S; Prunetti, L; Elbadawi-Sidhu, M; Hutinet, G; Forouhar, F; Zhang, XS; Ganesan, V; Reddy, P; Fiehn, O; Gerlt, JA; Hunt, JF; Copley, SD; de Crecy-Lagard, V (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; McLoughlin, SY; Kershner, JP; Copley, SD (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 biochemists 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; Webb, AM; Kershner, JP; Blaskowski, S; Copley, SD (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
  • Rudolph, J; Erbse, AH; Behlen, LS; Copley, SD (2014), A Radical Intermediate in the Conversion of Pentachlorophenol to Tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry Version: 1 53 (41) 6539-6549, issn: 0006-2960, ids: AR5RC, doi: 10.1021/bi5010427, PubMed ID: 25238136
  • Rokicki, J; Knox, D; Dowell, RD; Copley, SD (2014), CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics Version: 1 15 , Art. No. 65, issn: 1471-2164, ids: AA5DG, doi: 10.1186/1471-2164-15-65, PubMed ID: 24460813
  • Kim, J; Copley, SD (2013), The Orphan Protein Bis-gamma-glutamylcystine Reductase Joins the Pyridine Nucleotide Disulfide Reductase Family. Biochemistry Version: 1 52 (17) 2905-2913, issn: 0006-2960, ids: 136AZ, doi: 10.1021/bi4003343, PubMed ID: 23560638
  • Novikov, Y; Copley, SD (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; Rudolph, J; Hlouchova, K; Copley, SD (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
  • Copley, SD; Rokicki, J; Turner, P; Daligault, H; Nolan, M; Land, M (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; Rudolph, J; Pietari, JMH; Behlen, LS; Copley, SD (2012), Pentachlorophenol Hydroxylase, a Poorly Functioning Enzyme Required for Degradation of Pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry Version: 1 51 (18) 3848-3860, issn: 0006-2960, ids: 936ZG, doi: 10.1021/bi300261p, PubMed ID: 22482720
  • Kim, J; Copley, SD (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 (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
  • Chumachenko, N; Novikov, Y; Shoemaker, RK; Copley, SD (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
  • Novikov, Y; Copley, SD; Eaton, BE (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, PubMed ID: 22200980
  • Kim, JH; Kershner, JP; Novikov, Y; Shoemaker, RK; Copley, SD (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
  • Rudolph, J; Kim, J; Copley, SD (2010), Multiple Turnovers of the Nicotino-Enzyme PdxB Require alpha-Keto Acids as Cosubstrates. Biochemistry Version: 1 49 (43) 9249-9255, issn: 0006-2960, ids: 670GL, doi: 10.1021/bi101291d, PubMed ID: 20831184
  • Copley, SD (2010), Evolution and the Enzyme. Version: 1 COMPREHENSIVE NATURAL PRODUCTS II: CHEMISTRY AND BIOLOGY, VOL 8: ENZYMES AND ENZYME MECHANISMS 9-46, Ed. Mander, L; Liu, HW, ids: BA5BC, isbn: 978-0-08-045382-8
  • 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
  • Hamady, M; Widmann, J; Copley, SD; Knight, R (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; Behlen, LS; Copley, SD (2008), A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase. Biochemistry Version: 1 47 (10) 3258-3265, issn: 0006-2960, ids: 270NG, doi: 10.1021/bi702431n, PubMed ID: 18275157
  • McLoughlin, SY; Copley, SD (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
  • Kim, J; Copley, SD (2007), Why metabolic enzymes are essential or nonessential for growth of Escherichia coli k12 on glucose. Biochemistry Version: 1 46 (44) 12501-12511, issn: 0006-2960, ids: 226FA, doi: 10.1021/bi7014629, PubMed ID: 17935357
  • Warner, JR; Copley, SD (2007), Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates. Biochemistry Version: 1 46 (14) 4438-4447, issn: 0006-2960, ids: 152OD, doi: 10.1021/bi0620104, PubMed ID: 17355122
  • Warner, JR; Copley, SD (2007), Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry Version: 1 46 (45) 13211-13222, issn: 0006-2960, ids: 228XT, doi: 10.1021/bi701069n, PubMed ID: 17956123
  • Copley, SD; Smith, E; Morowitz, HJ (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
  • Warner, JR; Lawson, SL; Copley, SD (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: 0006-2960, ids: 950TG, doi: 10.1021/bi050666b, PubMed ID: 16042413
  • Cleland, CE; Copley, SD (2005), The possibility of alternative microbial life on Earth. Int. J. Astrobiol. Version: 1 4 (4-Mar) 165-173, issn: 1473-5504, ids: V28BK, doi: 10.1017/S147355040500279X
  • Dai, MH; Ziesman, S; Ratcliffe, T; Gill, RT; Copley, SD (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
  • Copley, SD; Smith, E; Morowitz, HJ (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; Novak, WRP; Babbitt, PC (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, PubMed ID: 15518547
  • Dai, MH; Copley, SD (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; Rogers, JB; Warner, JR; Copley, SD (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; McCarthy, DL; Copley, SD (2002), The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution. Biochemistry Version: 1 41 (4) 1308-1314, issn: 0006-2960, ids: 517LM, doi: 10.1021/bi0117495, PubMed ID: 11802731
  • Kiefer, PM; Copley, SD (2002), Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry Version: 1 41 (4) 1315-1322, issn: 0006-2960, ids: 517LM, doi: 10.1021/bi0117504, PubMed ID: 11802732
  • Copley, SD; Anandarajah, K; Kiefer, PJ (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: 0009-2797, ids: 424QY
  • Anandarajah, K; Kiefer, PM; Donohoe, BS; Copley, SD (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: 0006-2960, 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; Copley, SD (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; Resing, K; Lawson, SL; Babbitt, PC; Copley, SD (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: 0006-2960, ids: 208XB, doi: 10.1021/bi990103y, PubMed ID: 10387005
  • Copley, SD (1998), Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates. Curr. Opin. Chem. Biol. Version: 1 2 (5) 613-617, issn: 1367-5931, ids: 135YT, doi: 10.1016/S1367-5931(98)80092-6, PubMed ID: 9818187
  • McCarthy, DL; Louie, DF; Copley, SD (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: 0002-7863, ids: YG901, doi: 10.1021/ja9726365
  • McCarthy, DL; Claude, AA; Copley, SD (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
  • 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, PubMed ID: 9115409
  • Willett, WS; Copley, SD (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; Navarrete, S; Willett, WS; Babbitt, PC; Copley, SD (1996), Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry Version: 1 35 (46) 14634-14642, issn: 0006-2960, ids: VU224, doi: 10.1021/bi961730f, PubMed ID: 8931562
  • CROOKS, GP; XU, L; BARKLEY, RM; COPLEY, SD (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: 0002-7863, ids: TD410, doi: 10.1021/ja00149a001
  • CROOKS, GP; COPLEY, SD (1994), PURIFICATION AND CHARACTERIZATION OF 4-CHLOROBENZOYL COA DEHALOGENASE FROM ARTHROBACTER SP STRAIN 4-CB1. Biochemistry Version: 1 33 (38) 11645-11649, issn: 0006-2960, ids: PJ293, doi: 10.1021/bi00204a028, PubMed ID: 7918379
  • COPLEY, SD; FRANK, E; KIRSCH, WM; KOCH, TH (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, PubMed ID: 1621954
  • COPLEY, SD; CROOKS, GP (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
  • 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
  • KOVACHY, RJ; COPLEY, SD; ALLEN, RH (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, PubMed ID: 6885824