Recent advances in the bioremediation of persistent organic pollutants via biomolecular engineering

Enzyme and Microbial Technology

Volumn 37, Issue 5, 2005, Pages 487-496

  Ee, Lui Ang ^a,b   Zhao, Huimin ^a   Obbard, Jeffrey P ^b  

^a UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^b NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Biomolecular engineering; Bioremediation; Directed evolution; Persistent organic pollutants

Indexed keywords

AROMATIC HYDROCARBONS; ENZYMES; MICROORGANISMS; PESTICIDES; POLLUTION; POLYCHLORINATED BIPHENYLS; POLYCYCLIC AROMATIC HYDROCARBONS; SUBSTRATES;

BIOMOLECULAR ENGINEERING; DIRECTED EVOLUTION; PERSISTANT ORGANIC POLLUTANTS; RATIONAL DESIGN;

BIOREMEDIATION;

ATRAZINE; BACTERIAL ENZYME; CYTOCHROME P450 ISOENZYME; FUNGAL ENZYME; LACCASE; ORGANOPHOSPHATE PESTICIDE; OXIDOREDUCTASE; PESTICIDE; POLYCHLORINATED BIPHENYL; POLYCYCLIC AROMATIC HYDROCARBON; UNSPECIFIC MONOOXYGENASE;

ARTICLE; BIOINFORMATICS; BIOREMEDIATION; CATALYSIS; DNA RECOMBINATION; ENZYME ACTIVITY; ENZYME ENGINEERING; ENZYME SPECIFICITY; GENE MUTATION; GENE TARGETING; GENETIC ENGINEERING AND GENE TECHNOLOGY; MICROBIAL DEGRADATION; ORGANIC POLLUTION; OXIDATION KINETICS; PROTEIN EXPRESSION; PROTEIN STRUCTURE; RECOMBINANT DNA TECHNOLOGY; X RAY CRYSTALLOGRAPHY;

EID: 23744475412     PISSN: 01410229     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.enzmictec.2004.07.024     Document Type: Article

References (50)

1. United Nation Environmental Program (UNEP). Stockholm convention on persisitent organic pollutants. Stockholm, Sweden; 2001.
2. M. Romantschuk, I. Sarand, T. Petanen, R. Peltola, M. Jonsson-Vihanne, and T. Koivula Means to improve the effect of in situ bioremediation of contaminated soil: an overview of novel approaches Environ Pollut 107 2000 179 185
3. N. Duran, and E. Esposito Potential applications of oxidative enzymes and phenoloxidase-like compounds in wastewater and soil treatment: a review Appl Catal B Environ 28 2000 83 99
4. K.N. Timmis, and D.H. Pieper Bacteria designed for bioremediation Trends Biotechnol 17 1999 201 204
5. Ryu, DDY, and D.H. Nam Recent progress in biomolecular engineering Biotechnol Prog 16 2000 2 16
6. F.H. Arnold Design by directed evolution Acc Chem Res 31 1998 125 131
7. C. Schmidt-Dannert Directed evolution of single proteins, metabolic pathways, and viruses Biochemistry 40 2001 13125 13136
8. H.M. Zhao, L. Giver, Z.X. Shao, J.A. Affholter, and F.H. Arnold Molecular evolution by staggered extension process (StEP) in vitro recombination Nat Biotechnol 16 1998 258 261
9. WP.C. Stemmer Rapid evolution of a protein in-vitro by DNA shuffling Nature 370 1994 389 391
10. K.E. Hammel, B. Kalyanaraman, and T.K. Kirk Oxidation of polycyclic aromatic-hydrocarbons and dibenzo P-dioxins by phanerochaete-chrysosporium ligninase J Biol Chem 261 1986 6948 6952
11. T. Bulter, M. Alcalde, V. Sieber, P. Meinhold, C. Schlachtbauer, and F.H. Arnold Functional expression of a fungal laccase in Saccharomyces cerevisiae by directed evolution Appl Environ Microbiol 69 2003 987 995
12. C.F. Harford-Cross, A.B. Carmichael, F.K. Allan, P.A. England, D.A. Rouch, and L.L. Wong Protein engineering of cytochrome P450(cam) (CYP101) for the oxidation of polycyclic aromatic hydrocarbons Prot Eng 13 2000 121 128
13. A.B. Carmichael, and L.L. Wong Protein engineering of Bacillus megaterium CYP102 - the oxidation of polycyclic aromatic hydrocarbons Eur J Biochem 268 2001 3117 3125
14. Q.S. Li, J. Ogawa, R.D. Schmid, and S. Shimizu Engineering cytochrome P450BM-3 for oxidation of polycyclic aromatic hydrocarbons Appl Environ Microbiol 67 2001 5735 5739
15. H. Joo, Z.L. Lin, and F.H. Arnold Laboratory evolution of peroxide-mediated cytochrome P450 hydroxylation Nature 399 1999 670 673
16. O. Salazar, P.C. Cirino, and F.H. Arnold Thermostabilization of a cytochrome p450 peroxygenase Chembiochem 4 2003 891 893
17. R.E. Alcock, P.A. Behnisch, K.C. Jones, and H. Hagenmaier Dioxin-like PCBs in the environment-human exposure and the significance of sources Chemosphere 37 1998 1457 1472
18. F. Bruhlmann, and W. Chen Tuning biphenyl dioxygenase for extended substrate specificity Biotechnol. Bioeng. 63 1999 544 551
19. B.D. Erickson, and F.J. Mondello Nucleotide sequencing transcriptional mapping of the genes encoding biphenyl dioxygenase, a multicomponent polychlorinated-biphenyl-degrading enzyme in Pseudomonas strain-LB400 J Bacteriol 174 1992 2903 2912
20. B.D. Erickson, and F.J. Mondello Enhanced biodegradation of polychlorinated-biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene Appl Environ Microbiol 59 1993 3858 3862
21. D.T. Gibson, D.L. Cruden, J.D. Haddock, G.J. Zylstra, and J.M. Brand Oxidation of polychlorinated-biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707 J Bacteriol 175 1993 4561 4564
22. K. Furukawa Engineering dioxygenases for efficient degradation of environmental pollutants Curr Opin Biotechnol 11 2000 244 249
23. D. Barriault, M.M. Plante, and M. Sylvestre Family shuffling of a targeted bphA region to engineer biphenyl dioxygenase J Bacteriol 184 2002 3794 3800
24. H. Suenaga, T. Watanabe, M. Sato, Ngadiman, and K. Furukawa Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering J Bacteriol 184 2002 3682 3688
25. Y. Hrywna, T.V. Tsoi, O.V. Maltseva, J.F. Quensen, and J.M. Tiedje Construction and characterization of two recombinant bacteria that grow on ortho- and para-substituted chlorobiphenyls Appl Environ Microbiol 65 1999 2163 2169
26. V. Brenner, J.J. Arensdorf, and D.D. Focht Genetic construction of PCB degraders Biodegradation 5 1994 359 377
27. M. Radosevich, S.J. Traina, and O.H. Tuovinen Biodegradation of atrazine in surface soils and subsurface sediments collected from an agricultural research farm Biodegradation 7 1996 137 149
28. M.L. de Souza, L.P. Wackett, K.L. Boundymills, R.T. Mandelbaum, and M.J. Sadowsky Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain Adp involved in the dechlorination of atrazine Appl Environ Microbiol 61 1995 3373 3378
29. M.L. de Souza, M.J. Sadowsky, and L.P. Wackett Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization J Bacteriol 178 1996 4894 4900
30. M.J. Sadowsky, Z.K. Tong, M. de Souza, and L.P. Wackett AtzC is a new member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes J Bacteriol 180 1998 152 158
31. J.L. Seffernick, N. Shapir, M. Schoeb, G. Johnson, M.J. Sadowsky, and L.P. Wackett Enzymatic degradation of chlorodiamino-s-triazine Appl Environ Microbiol 68 2002 4672 4675
32. L.P. Wackett Directed evolution of new enzymes and pathways for environmental biocatalysis Ann Ny Acad Sci 864 1998 142 152
33. S. Raillard, A. Krebber, Y.C. Chen, J.E. Ness, E. Bermudez, and R. Trinidad Novel enzyme activities and functional plasticity revealed by recombining highly homologous enzymes Chem Biol 8 2001 891 898
34. L.R. Webster, G.H. McKenzie, and H.T. Moriarty Organophosphate-based pesticides and genetic damage implicated in bladder cancer Cancer Genet Cytogenet 133 2002 112 117
35. S.B. Hong, and F.M. Raushel Metal-substrate interactions facilitate the catalytic activity of the bacterial phosphotriesterase Biochemistry 35 1996 10904 10912
36. S.B. Hong, and F.M. Raushel Stereochemical preferences for chiral substrates by the bacterial phosphotriesterase Chem Biol Interact 119-120 1999 225 234
37. S.B. Hong, and F.M. Raushel Stereochemical constraints on the substrate specificity of phosphotriesterase Biochemistry 38 1999 1159 1165
38. J.L. Vanhooke, M.M. Benning, F.M. Raushel, and H.M. Holden Three-dimensional structure of the zinc-containing phosphotriesterase with the bound substrate analog diethyl 4-methylbenzylphosphonate Biochemistry 35 1996 6020 6025
39. M. Chen-Goodspeed, M.A. Sogorb, F.Y. Wu, S.B. Hong, and F.M. Raushel Structural determinants of the substrate and stereochemical specificity of phosphotriesterase Biochemistry 40 2001 1325 1331
40. M. Chen-Goodspeed, M.A. Sogorb, F.Y. Wu, and F.M. Raushel Enhancement, relaxation, and reversal of the stereoselectivity for phosphotriesterase by rational evolution of active site residues Biochemistry 40 2001 1332 1339
41. D.P. Dumas, S.R. Caldwell, J.R. Wild, and F.M. Raushel Purification, properties of the phosphotriesterase from Pseudomonas diminuta J Biol Chem 264 1989 19659 19665
42. C.M. Cho, A. Mulchandani, and W. Chen Bacterial cell surface display of organophosphorus hydrolase for selective screening of improved hydrolysis of organophosphate nerve agents Appl Environ Microbiol 68 2002 2026 2030
43. A.D. Griffiths, and D.S. Tawfik Directed evolution of an extremely fast phosphotriesterase by in vitro compartmentalization EMBO J 22 2003 24 35
44. D.S. Tawfik, and A.D. Griffiths Man-made cell-like compartments for molecular evolution Nat Biotechnol 16 1998 652 656
45. F.J. Ghadessy, J.L. Ong, and P. Holliger Directed evolution of polymerase function by compartmentalized self-replication Proc Natl Acad Sci USA 98 2001 4552 4557
46. S. Ripp, D.E. Nivens, Y. Ahn, C. Werner, J. Jarrell, and J.P. Easter Controlled field release of a bioluminescent genetically engineered microorganism for bioremediation process monitoring and control Environ Sci Technol 34 2000 846 853
47. L.C. Strong, H. McTavish, M.J. Sadowsky, and L.P. Wackett Field-scale remediation of atrazine-contaminated soil using recombinant Escherichia coli expressing atrazine chlorohydrolase Environ Microbiol 2 2000 91 98
48. G. Giddings Tansley review no. 99 - the release of genetically engineered micro-organisms and viruses into the environment New Phytol 140 1998 173 184
49. G.S. Sayler, and S. Ripp Field applications of genetically engineered microorganisms for bioremediation processes Curr Opin Biotechnol 11 2000 286 289
50. M.E. Watanabe Can bioremediation bounce back? Nat Biotechnol 19 2001 1111 1115