Cooperative Institute for Research in Environmental Sciences

Shelley D. Copley

Shelley D. Copley

Biodegradation of recalcitrant pollutants; mechanistic studies of enzymes involved in biodegradation.


Current Research

Adaptation of E. coli to use a novel pathway for vitamin B6 synthesis

We are currently investigating the mechanisms by which the six mutations enhance growth rate. This effort requires consideration of the effects of mutations on specific proteins, as well as effects that are propagated through the complex metabolic and regulatory networks. One mutation increases the concentration of an enzyme required in the novel and relatively inefficient pathway for PLP synthesis, presumably resulting in increased production of PLP. Two other mutations appear to act by redirecting fluxes through the metabolic network. These mutations may increase the concentrations of the alpha-keto acid precursors of amino acids and compensating, to some degree, for the decreased level of PLP-containing transaminases. Pyridoxal 5’-phosphate (PLP, aka vitamin B6) is a cofactor required for 40 different enzymes in Escherichia coli, including the transaminase enzymes that generate amino acids needed for protein synthesis. Deletion of a gene required for PLP synthesis prevents growth of E. coli on glucose as a sole carbon source because the cells cannot make amino acids. We have adapted a strain of E. coli (lacking an enzyme in the PLP biosynthesis pathway) to grow on glucose as a sole carbon source nearly as well as wild type E. coli. This strain, which we call the “champion,” has reconstituted a pathway for synthesis of PLP via a novel route as a consequence of only six mutations. By reconstructing strains containing various combinations of these mutations, we found that the order in which the mutations occur is critical; some of the mutations are beneficial in some genetic backgrounds, but detrimental in others.

This project is providing new insights into the ways in which mutations can reprogram the metabolic networks of bacteria and allow cells to adapt to new challenges.


The structure of pyridoxal 5'-phosphate (PLP). b) The "champion" grows nearly as fast as wild type (wt) E. coli. c)


View Publications

  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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, 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
  • 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
  • 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, 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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