Engineering Enzymes and Microorganisms for the Transformation of Synthetic Compounds
Abstract
The biotransformation of synthetic chemicals that enter the environment is dependent on the capacity of microbial enzymes to recognize xenobiotic substrates and catalyze reactions with stable structural elements, such as carbon-halogen bonds. The range of compounds that can be enzymatically degraded strongly influences the environmental fate of many potentially harmful compounds. Environmental recalcitrance thus is, in part, a problem of enzyme activity and specificity. This can be well illustrated with the halogenated aliphatics, which are frequently encountered as environmental pollutants due to losses and emissions during their use in industry and agriculture. Halogenated aliphatic compounds are used as blowing agents (methylchloride), cooling liquids (ethylchloride), soil fumigants (1,3-dichloropropylene, methylbromide), insecticides (hexachlorocyclohexane), intermediates in chemical synthesis (1,2-dichloroethane, vinyl chloride, chloroacetates) and as solvents (trichloroethanes, tri- and tetrachloroethene). Several related structures (e.g., chlorinated alkanes, ethers and alcohols) occur as wastes or contaminants of products.
Keywords
Methane Mono Oxygenase Active Site Cavity Soil Fumigant Hydrolase Fold Engineer EnzymePreview
Unable to display preview. Download preview PDF.
References
- Curragh, H., Flynn, O., Larkin, M. J., Stafford, T. M., Hamilton, J. T. G., and Harper, D. B., 1994. Haloalkane degradation and assimilation by Rhodococcus rhodochrous NCIMB 13064, Microbiology 140/ 1433–1442.CrossRefGoogle Scholar
- Derewenda, Z. S., and Sharpe, A. M., 1993. News from the interface: The molecular structure of triacylglyceride lipases, Trends Biochem. Sci. 18:20–25.CrossRefGoogle Scholar
- Fox, B. G., Borneman, J. G., Wackett, L. P., and Lipscomb, J. D., 1990. Haloalkane oxidation by the soluble methane monooxygenase from Methylosinus trichosporium OB3b: mechanistic and environmental implications, Biochemistry 29:6419–6427.CrossRefGoogle Scholar
- Janssen, D. B., Pries, F., and van der Ploeg, J. R., 1994. Genetics and biochemistry of dehalogenating enzymes, Ann. Rev. Microbiol. 48:163–191.CrossRefGoogle Scholar
- Kasai, N., Tsujimura, K., Unoura, K., and Suzuki, T., 1990. Degradation of 2,3-dichloro-l-propanol by a Pseudomonas sp., Agric. Biol. Chem. 54:3185–3190.CrossRefGoogle Scholar
- Kawasaki, H., Tsuda, K., Matsushita, I., and Tonomura K., 1992. Lack of homology between two haloacetate de-halogenase genes encoded on a plasmid from Moraxella sp. strain B., J. Gen. Microbiol. 138:1317–1323.CrossRefGoogle Scholar
- Keuning, S., Janssen, D. B., and Witholt, B., 1985. Purification and characterization of hydrolytic haloalkane dehalogenase from Xanthobacter autotrophicus GJ10, J. Bacteriol. 163: 635–6Google Scholar
- Kennes, C., Pries, F., Krooshof, G. H., Bokma, E., Kingma, J., and Janssen, D. B., 1995. Replacement of tryptophan residues in haloalkane dehalogenase reduces halide binding and catalytic activity, Eur. J. Biochem. 228:403–07.CrossRefGoogle Scholar
- Nagata, Y, Nariya, T., Ohtomo, R., Fukuda, M., Yano, K., and Takagi, M., 1993. Cloning and sequencing of a dehalogenase gene encoding an enzyme with hydrolase activity involved in the degradation of γ-hexachloro-cyclohexane in Pseudomonas paucimobilis, J. Bacteriol. 175: 6403–64Google Scholar
- Nakamura, T., Nagasawa, T., Yu, F., Watanabe, I., and Yamada, H., 1992. Resolution and some properties of enzymes involved in enantioselective transformation of l,3-dichloro-2-propanol to (R)-3-chloro-l,2-propanediol by Corynebacterium sp. strain N-1074, J. Bacteriol. 174:7613–7619.Google Scholar
- Ollis, D. L., Cheah, E., Cygler, M, Dijkstra, B. W., Frolow, F., Franken, S. M., Haral, M., Remington, S. J., Silman, I., Schrag, J., Sussman, J. L., Verschueren, K. H. G., and Goldman, A., 1992. The a/β-hydrolase fold, Protein Eng. 5:197–211.CrossRefGoogle Scholar
- Omori, T., Kimura, T., Kodama, T., 1991. Cloning of haloalkane dehalogenase genes of Rhodococcus sp. m 15-3 and expression and sequencing of the genes. pp498–503. In: On-Site Bioreclamation. Processes for Xenobiotic and Hydrocarbon Treatment. R.E. Hinchee & R.F. Olfenbuffel, Eds. Butterworth-Heinemann, Boston.Google Scholar
- Pries, F., Kingma, J., Pentenga, M., van Pouderoyen, G., Jeronimus-Stratingh, C. M., Bruins, A. P., and Janssen, D. B., 1994a. Site-directed mutagenesis and oxygen isotope incorporation studies of the nucleophilic aspartate of haloalkane dehalogenase, Biochemistry 33:1242–1247.CrossRefGoogle Scholar
- Pries, F., van den Wijngaard, A. J., Bos, R., Pentenga, M., and Janssen, D. B., 1994b. The role of spontaneous cap domain mutations in haloalkane dehalogenase specificity and evolution, J. Biol. Chem. 269:17490–17494.Google Scholar
- Pries, F., Kingma, J., Krooshof, G. H., Jeronimus-Stratingh, C. M., Bruins, A. P., and Janssen, D. B., 1995. Histidine 289 is essential for hydrolysis of the alkyl-enzyme intermediate of haloalkane dehalogenase, J. Biol Chem. 270:10405–10411.CrossRefGoogle Scholar
- Poulos, T. L., Finzel, B. C., and Howard, A., 1987, High resolution crystal structure of P450cam, J. Mol Biol 195:687–700.CrossRefGoogle Scholar
- Rosenzweig, A. C., Frederick, C. A., Lippard, S. J., and Nordlund, P., 1993. Crystal structure of a bacterial non-haem iron hydroxylase that catalyses the biological oxidation of methane, 366:537–543.Google Scholar
- Sallis, P. J., Armfield, S. J., Bull, A. T., and Hardman, D. J., 1990. Isolation and characterization of a haloalkane halidohydrolase from Rhodococcus erythropolis Y2, J. Gen. Microbiol. 136:115–120.CrossRefGoogle Scholar
- Scholtz, R., Leisinger, T., Suter, F., and Cook, A. M., 1987. Characterization of 1-chlorohexane halidehydrolase, a dehalogenase of wide substrate range from an Arthrobacter sp., J. Bacteriol. 169: 5016–502Google Scholar
- Stucki, G., and Thüer, M., 1995. Experiences of a large-scale application of 1,2-dichloroethane degrading microorganisms for groundwater treatment, Environ. Sci. Technol. 29:2339–2345.CrossRefGoogle Scholar
- Tardiff,C, Greer, C. W., Labbe, D., and Lau, P. C. K., 1991, Involvement of a large plasmid in the degradation of 1,2-dichloroethane by Xanthobacter autotrophicus GJ10, Appl Environ. Microbiol. 57:1853–1857.Google Scholar
- van den Wijngaard, A. J., van der Kamp, K., van der Ploeg, J., Kazemier, B., Pries, F., and Janssen, D. B. 1992. Degradation of 1,2-dichloroethane by facultative methylotrophic bacteria, Appl Env. Microbiol. 58:976–983.Google Scholar
- Verhagen, C., Smit, E., Janssen, D. B., and van Elsas, J. D., 1995. Bacterial dichloropropene degradation in soil, screening of soils and involvement of plasmids carrying the dhlA gene, Soil Biol Biochem. 27: 1547–155CrossRefGoogle Scholar
- Verschueren, K. H. G., Franken, S. M., Rozeboom, H. J., Kalk, K. H., and Dijkstra, B. W., 1993a. Refined X-ray structure of haloalkane dehalogenase at pH6.2 and pH8.2 and implications for the reaction mechanism, J. Mol. Biol. 232:856–872.CrossRefGoogle Scholar
- Verschueren, K. H. G., Seljée, F., Rozeboom, H. J., Kalk, K. H., and Dijkstra, B. W., 1993b. Crystallographic analysis of the catalytic mechanism of haloalkane dehalogenase, Nature 363:693–698.CrossRefGoogle Scholar
- Verschueren, K. H. G., Kingma, J., Rozeboom, H. J., Kalk, K. H., Janssen, D. B., and Dijkstra, B. W., 1993c. Crystallographic and fluorescence studies of the interaction of haloalkane dehalogenase with halide ions. Studies with halide compounds reveal a halide binding site in the active site, Biochemistry 32:9031–9037.CrossRefGoogle Scholar
- Wackett, L. P., Sadowsky, M. J., Newman, L. M., Hur, H-G., and Li, S., 1994. Metabolism of polyhalogenated compounds by a genetically engineered bacterium, Nature 368:627–629.CrossRefGoogle Scholar
- Yokota, T., Fuse, H., Omori, T., and Minoda, Y, 1986. Microbial dehalogenation of haloalkanes mediated by oxygenase or halidohydrolase, Agric. Biol Chem. 50:453–460.CrossRefGoogle Scholar