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Shelley Copley

TitleProfessor
InstitutionUniversity of Colorado Boulder
DepartmentBiology-MCD Instruction

    Collapse Research 
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    R01GM135364     (COPLEY, SHELLEY D.)May 1, 2020 - Feb 28, 2025
    NIH
    Promiscuity, serendipity, and metabolic innovation
    Role: Principal Investigator
    R01GM134044     (COPLEY, SHELLEY D.)Aug 12, 2019 - Jul 31, 2023
    NIH
    Gene duplication and divergence: the bigger picture
    Role: Principal Investigator
    R01GM124365     (COPLEY, SHELLEY D.)Sep 1, 2017 - May 31, 2021
    NIH
    The Cellular and Molecular Effects of Synonymous Mutations
    Role: Principal Investigator
    R01GM083285     (COPLEY, SHELLEY D.)Jul 1, 2008 - Apr 30, 2018
    NIH
    Elucidation and Evolutionary Potential of a Latent Pathway for PLP Synthesis
    Role: Principal Investigator
    R01GM078554     (COPLEY, SHELLEY D.)Jul 1, 2008 - Apr 30, 2013
    NIH
    The Evolutionary Origin and Potential of Newly Recruited Enzymes
    Role: Principal Investigator
    R56GM067749     (COPLEY, SHELLEY D.)May 1, 2003 - Jul 31, 2009
    NIH
    Mechanisms and Evolutionary Potential of Promiscuous Enzyme Activities
    Role: Principal Investigator
    R01GM067749     (COPLEY, SHELLEY D.)May 1, 2003 - Aug 2, 2007
    NIH
    Recruitment of Enzymes to Serve New Functions
    Role: Principal Investigator

    Collapse Bibliographic 
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    1. Yang DD, Rusch LM, Widney KA, Morgenthaler AB, Copley SD. Synonymous edits in the Escherichia coli genome have substantial and condition-dependent effects on fitness. Proc Natl Acad Sci U S A. 2024 Jan 30; 121(5):e2316834121. PMID: 38252823.
      View in: PubMed
    2. Copley SD, Newton MS, Widney KA. How to Recruit a Promiscuous Enzyme to Serve a New Function. Biochemistry. 2023 01 17; 62(2):300-308. PMID: 35729117.
      View in: PubMed
    3. Morgenthaler AB, Fritts RK, Copley SD. Amplicon Remodeling and Genomic Mutations Drive Population Dynamics after Segmental Amplification. Mol Biol Evol. 2022 01 07; 39(1). PMID: 34581806.
      View in: PubMed
    4. Copley SD. Setting the stage for evolution of a new enzyme. Curr Opin Struct Biol. 2021 08; 69:41-49. PMID: 33865035.
      View in: PubMed
    5. Choudhury A, Fankhauser RG, Freed EF, Oh EJ, Morgenthaler AB, Bassalo MC, Copley SD, Kaar JL, Gill RT. Determinants for Efficient Editing with Cas9-Mediated Recombineering in Escherichia coli. ACS Synth Biol. 2020 May 15; 9(5):1083-1099. PMID: 32298586.
      View in: PubMed
    6. Copley SD. The physical basis and practical consequences of biological promiscuity. Phys Biol. 2020 Apr 03. PMID: 32244231.
      View in: PubMed
    7. Copley SD. Evolution of new enzymes by gene duplication and divergence. FEBS J. 2020 04; 287(7):1262-1283. PMID: 32250558.
      View in: PubMed
    8. Morgenthaler AB, Kinney WR, Ebmeier CC, Walsh CM, Snyder DJ, Cooper VS, Old WM, Copley SD. Mutations that improve efficiency of a weak-link enzyme are rare compared to adaptive mutations elsewhere in the genome. Elife. 2019 12 09; 8. PMID: 31815667.
      View in: PubMed
    9. Kim J, Flood JJ, Kristofich MR, Gidfar C, Morgenthaler AB, Fuhrer T, Sauer U, Snyder D, Cooper VS, Ebmeier CC, Old WM, Copley SD. Hidden resources in the Escherichia coli genome restore PLP synthesis and robust growth after deletion of the essential gene pdxB. Proc Natl Acad Sci U S A. 2019 11 26; 116(48):24164-24173. PMID: 31712440.
      View in: PubMed
    10. Flood JJ, Copley SD. Genome-Wide Analysis of Transcriptional Changes and Genes That Contribute to Fitness during Degradation of the Anthropogenic Pollutant Pentachlorophenol by Sphingobium chlorophenolicum. mSystems. 2018 Nov-Dec; 3(6). PMID: 30505947.
      View in: PubMed
    11. Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD. Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme. PLoS Genet. 2018 08; 14(8):e1007615. PMID: 30148850.
      View in: PubMed
    12. Mikkonen A, Yl?ranta K, Tiirola M, Dutra LAL, Salmi P, Romantschuk M, Copley S, Ik?heimo J, Sinkkonen A. Successful aerobic bioremediation of groundwater contaminated with higher chlorinated phenols by indigenous degrader bacteria. Water Res. 2018 07 01; 138:118-128. PMID: 29574199.
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    13. Copley SD. Shining a light on enzyme promiscuity. Curr Opin Struct Biol. 2017 12; 47:167-175. PMID: 29169066.
      View in: PubMed
    14. Kershner JP, Yu McLoughlin S, Kim J, Morgenthaler A, Ebmeier CC, Old WM, Copley SD. A Synonymous Mutation Upstream of the Gene Encoding a Weak-Link Enzyme Causes an Ultrasensitive Response in Growth Rate. J Bacteriol. 2016 10 15; 198(20):2853-63. PMID: 27501982.
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    15. Thiaville JJ, Flood J, Yurgel S, Prunetti L, Elbadawi-Sidhu M, Hutinet G, Forouhar F, Zhang X, Ganesan V, Reddy P, Fiehn O, Gerlt JA, Hunt JF, Copley SD, de Cr?cy-Lagard V. Members of a Novel Kinase Family (DUF1537) Can Recycle Toxic Intermediates into an Essential Metabolite. ACS Chem Biol. 2016 08 19; 11(8):2304-11. PMID: 27294475.
      View in: PubMed
    16. Copley SD. An evolutionary biochemist's perspective on promiscuity. Trends Biochem Sci. 2015 Feb; 40(2):72-8. PMID: 25573004.
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    17. Copley SD. An evolutionary perspective on protein moonlighting. Biochem Soc Trans. 2014 Dec; 42(6):1684-91. PMID: 25399590.
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    18. Rudolph J, Erbse AH, Behlen LS, Copley SD. A radical intermediate in the conversion of pentachlorophenol to tetrachlorohydroquinone by Sphingobium chlorophenolicum. Biochemistry. 2014 Oct 21; 53(41):6539-49. PMID: 25238136.
      View in: PubMed
    19. Kim J, Webb AM, Kershner JP, Blaskowski S, Copley SD. A versatile and highly efficient method for scarless genome editing in Escherichia coli and Salmonella enterica. BMC Biotechnol. 2014 Sep 25; 14:84. PMID: 25255806.
      View in: PubMed
    20. Khanal A, Yu McLoughlin S, Kershner JP, Copley SD. Differential effects of a mutation on the normal and promiscuous activities of orthologs: implications for natural and directed evolution. Mol Biol Evol. 2015 Jan; 32(1):100-8. PMID: 25246702.
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    21. Rokicki J, Knox D, Dowell RD, Copley SD. CodaChrome: a tool for the visualization of proteome conservation across all fully sequenced bacterial genomes. BMC Genomics. 2014 Jan 24; 15:65. PMID: 24460813.
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    22. Novikov Y, Copley SD. Reactivity landscape of pyruvate under simulated hydrothermal vent conditions. Proc Natl Acad Sci U S A. 2013 Aug 13; 110(33):13283-8. PMID: 23872841.
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    23. Yadid I, Rudolph J, Hlouchova K, Copley SD. Sequestration of a highly reactive intermediate in an evolving pathway for degradation of pentachlorophenol. Proc Natl Acad Sci U S A. 2013 Jun 11; 110(24):E2182-90. PMID: 23676275.
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    24. Kim J, Copley SD. The orphan protein bis-?-glutamylcystine reductase joins the pyridine nucleotide disulfide reductase family. Biochemistry. 2013 Apr 30; 52(17):2905-13. PMID: 23560638.
      View in: PubMed
    25. Kim J, Copley SD. Inhibitory cross-talk upon introduction of a new metabolic pathway into an existing metabolic network. Proc Natl Acad Sci U S A. 2012 Oct 16; 109(42):E2856-64. PMID: 22984162.
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    26. Copley SD. Moonlighting is mainstream: paradigm adjustment required. Bioessays. 2012 Jul; 34(7):578-88. PMID: 22696112.
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    27. Hlouchova K, Rudolph J, Pietari JM, Behlen LS, Copley SD. Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry. 2012 May 08; 51(18):3848-60. PMID: 22482720.
      View in: PubMed
    28. Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M. The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol. 2012; 4(2):184-98. PMID: 22179583.
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    29. Copley SD. Toward a systems biology perspective on enzyme evolution. J Biol Chem. 2012 Jan 02; 287(1):3-10. PMID: 22069330.
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    30. Chumachenko N, Novikov Y, Shoemaker RK, Copley SD. A dimethyl ketal-protected benzoin-based linker suitable for photolytic release of unprotected peptides. J Org Chem. 2011 Nov 18; 76(22):9409-16. PMID: 21950361.
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    31. Novikov Y, Copley SD, Eaton BE. A Simple Route for Synthesis of 4-Phospho-D-Erythronate. Tetrahedron Lett. 2011 Apr 20; 52(16):1913-1915. PMID: 22200980.
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    32. Kim J, Kershner JP, Novikov Y, Shoemaker RK, Copley SD. Three serendipitous pathways in E. coli can bypass a block in pyridoxal-5'-phosphate synthesis. Mol Syst Biol. 2010 Nov 30; 6:436. PMID: 21119630.
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    33. Rudolph J, Kim J, Copley SD. Multiple turnovers of the nicotino-enzyme PdxB require a-keto acids as cosubstrates. Biochemistry. 2010 Nov 02; 49(43):9249-55. PMID: 20831184.
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    34. Copley SD. Prediction of function in protein superfamilies. F1000 Biol Rep. 2009 Dec 09; 1:91. PMID: 20948600.
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    35. Copley SD. Evolution of efficient pathways for degradation of anthropogenic chemicals. Nat Chem Biol. 2009 Aug; 5(8):559-66. PMID: 19620997.
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    36. Copley S, Rappuoli R. Genomics of ecology and industrial microbiology. Curr Opin Microbiol. 2009 Jun; 12(3):221-2. PMID: 19481500.
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    37. McLoughlin SY, Copley SD. A compromise required by gene sharing enables survival: Implications for evolution of new enzyme activities. Proc Natl Acad Sci U S A. 2008 Sep 09; 105(36):13497-502. PMID: 18757760.
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    38. Hamady M, Widmann J, Copley SD, Knight R. MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs. Genome Biol. 2008; 9(8):R128. PMID: 18706079.
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    39. Warner JR, Behlen LS, Copley SD. A trade-off between catalytic power and substrate inhibition in TCHQ dehalogenase. Biochemistry. 2008 Mar 11; 47(10):3258-65. PMID: 18275157.
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    40. Warner JR, Copley SD. Pre-steady-state kinetic studies of the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry. 2007 Nov 13; 46(45):13211-22. PMID: 17956123.
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    41. Kim J, Copley SD. Why metabolic enzymes are essential or nonessential for growth of Escherichia coli K12 on glucose. Biochemistry. 2007 Nov 06; 46(44):12501-11. PMID: 17935357.
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    42. Copley SD, Smith E, Morowitz HJ. The origin of the RNA world: co-evolution of genes and metabolism. Bioorg Chem. 2007 Dec; 35(6):430-43. PMID: 17897696.
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    43. Warner JR, Copley SD. Mechanism of the severe inhibition of tetrachlorohydroquinone dehalogenase by its aromatic substrates. Biochemistry. 2007 Apr 10; 46(14):4438-47. PMID: 17355122.
      View in: PubMed
    44. Warner JR, Lawson SL, Copley SD. A mechanistic investigation of the thiol-disulfide exchange step in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry. 2005 Aug 02; 44(30):10360-8. PMID: 16042413.
      View in: PubMed
    45. Copley SD, Smith E, Morowitz HJ. 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. 2005 Mar 22; 102(12):4442-7. PMID: 15764708.
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    46. Dai M, Ziesman S, Ratcliffe T, Gill RT, Copley SD. Visualization of protoplast fusion and quantitation of recombination in fused protoplasts of auxotrophic strains of Escherichia coli. Metab Eng. 2005 Jan; 7(1):45-52. PMID: 15974564.
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    47. Copley SD, Novak WR, Babbitt PC. Divergence of function in the thioredoxin fold suprafamily: evidence for evolution of peroxiredoxins from a thioredoxin-like ancestor. Biochemistry. 2004 Nov 09; 43(44):13981-95. PMID: 15518547.
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    48. Dai M, Copley SD. Genome shuffling improves degradation of the anthropogenic pesticide pentachlorophenol by Sphingobium chlorophenolicum ATCC 39723. Appl Environ Microbiol. 2004 Apr; 70(4):2391-7. PMID: 15066836.
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    49. Copley SD. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol. 2003 Apr; 7(2):265-72. PMID: 12714060.
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    50. Dai M, Rogers JB, Warner JR, Copley SD. A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD). J Bacteriol. 2003 Jan; 185(1):302-10. PMID: 12486067.
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    51. Kiefer PM, McCarthy DL, Copley SD. The reaction catalyzed by tetrachlorohydroquinone dehalogenase does not involve nucleophilic aromatic substitution. Biochemistry. 2002 Jan 29; 41(4):1308-14. PMID: 11802731.
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    52. Kiefer PM, Copley SD. Characterization of the initial steps in the reductive dehalogenation catalyzed by tetrachlorohydroquinone dehalogenase. Biochemistry. 2002 Jan 29; 41(4):1315-22. PMID: 11802732.
      View in: PubMed
    53. Copley SD. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Trends Biochem Sci. 2000 Jun; 25(6):261-5. PMID: 10838562.
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    54. Anandarajah K, Kiefer PM, Donohoe BS, Copley SD. Recruitment of a double bond isomerase to serve as a reductive dehalogenase during biodegradation of pentachlorophenol. Biochemistry. 2000 May 09; 39(18):5303-11. PMID: 10820000.
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    55. Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD. Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry. 1999 Jun 15; 38(24):7659-69. PMID: 10387005.
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    56. Copley SD. Microbial dehalogenases: enzymes recruited to convert xenobiotic substrates. Curr Opin Chem Biol. 1998 Oct; 2(5):613-7. PMID: 9818187.
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    57. McCarthy DL, Claude AA, Copley SD. In vivo levels of chlorinated hydroquinones in a pentachlorophenol-degrading bacterium. Appl Environ Microbiol. 1997 May; 63(5):1883-8. PMID: 9143119.
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    58. Copley SD. Diverse mechanistic approaches to difficult chemical transformations: microbial dehalogenation of chlorinated aromatic compounds. Chem Biol. 1997 Mar; 4(3):169-74. PMID: 9115409.
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    59. McCarthy DL, Navarrete S, Willett WS, Babbitt PC, Copley SD. Exploration of the relationship between tetrachlorohydroquinone dehalogenase and the glutathione S-transferase superfamily. Biochemistry. 1996 Nov 19; 35(46):14634-42. PMID: 8931562.
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    60. Willett WS, Copley SD. Identification and localization of a stable sulfenic acid in peroxide-treated tetrachlorohydroquinone dehalogenase using electrospray mass spectrometry. Chem Biol. 1996 Oct; 3(10):851-7. PMID: 8939704.
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    61. Crooks GP, Copley SD. Purification and characterization of 4-chlorobenzoyl CoA dehalogenase from Arthrobacter sp. strain 4-CB1. Biochemistry. 1994 Sep 27; 33(38):11645-9. PMID: 7918379.
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    62. Copley SD, Crooks GP. Enzymic Dehalogenation of 4-Chlorobenzoyl Coenzyme A in Acinetobacter sp. Strain 4-CB1. Appl Environ Microbiol. 1992 Apr; 58(4):1385-7. PMID: 16348702.
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    63. Copley SD, Frank E, Kirsch WM, Koch TH. Detection and possible origins of aminomalonic acid in protein hydrolysates. Anal Biochem. 1992 Feb 14; 201(1):152-7. PMID: 1621954.
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