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Chapter 7 : Evolution of Catabolic Enzymes and Pathways

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Abstract:

This chapter focuses on prokaryotic evolution in the context of biodegradation and microbial biocatalysis. It discusses the major evolutionary families of microbial catabolic enzymes, current ideas as to how genes are recruited and acquire new functions, and how new metabolic pathways arise and are disseminated among different prokaryotes. The discussion starts with a brief history of molecular-evolution studies. Then, it will be developed using primarily one example: how soil bacteria have evolved to use the herbicide atrazine as their sole source of nitrogen. Some microbial protein superfamilies important in biodegradation and biocatalysis are provided in a tabular form in which the major headings generally follow the major Enzyme Commission (EC) headings: (i) oxidoreductases, (ii) transferases, (iii) hydrolases, (iv) lyases, (v) isomerases, and (vi) ligases; except that lyases and isomerases are clustered together. The scientific literature suggests that in some cases, industrial chemicals initially evade microbial catabolism, as evidenced by their persistence in the environment, but are later found to be readily biodegraded. Evolution is especially instructive to study microbial catabolic enzymes to learn how new enzymes evolve and are transferred globally. In this context, the study of evolution is expanding from its historical role of providing fundamental explanations to become a biological tool that offers great promise for using microbes in our efforts to develop a sustainable human society.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7

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Figures

Image of Figure 7.1
Figure 7.1

Rate of change of amino acid sequence as a function of time differs with different proteins. Adapted from reference 16.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.2
Figure 7.2

Comparison of enzymes in the bacterial mandelate pathway (left) with other evolutionarily related enzymes which catalyze reactions with structurally distinct substrates.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.3
Figure 7.3

Oxygenative route of microbial atrazine catabolism, which generally results in the accumulation of aminotriazine metabolites.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.4
Figure 7.4

Pathway of atrazine catabolism catalyzed by sp. strain ADP and other atrazine-catabolizing bacteria. (A) First three steps in atrazine catabolism. (B) Sequence identity in a short stretch of AtzABC. (C) Hypothetical divalent metal coordination by AtzABC.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.5
Figure 7.5

Global distribution of bacteria isolated for their abilities to catabolize atrazine and known to process atrazine via an initial dechlorination reaction.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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Image of Figure 7.6
Figure 7.6

In-well lysis gel showing plasmids from atrazine-degrading bacteria containing atrazine catabolism genes (shown in green). From left to right, the DNAs in the wells are derived from the following bacterial strains: sp. strain ADP; sp. strain M91-3, sp. strain PATR 2, and sp. strain SGI.

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
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References

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1. Armstrong, D. E.,, and G. Chesters. 1968. Adsorption catalyzed chemical hydrolysis of atrazine. Environ. Sci. Technol. 2: 683 689.
*2. Babbitt, R. C.,, and J. A. Gerlt. 1997. Understanding enzyme superfamilies: chemistry as the fundamental determinant in the evolution of new catalytic activities. J. Biol. Chem. 272: 30591 30594.
3. Boundy-Mills, K. L.,, M. L. de Souza,, R. T. Mandelbaum,, L. R Wackett,, and M. J. Sadowsky. 1997. The atzB gene of Pseudomonas sp. strain ADP encodes the second enzyme of a novel atrazine degradation pathway. Appl. Environ. Microbiol. 63: 916 923.
4. Bouquard, C., , J. Ouazzani,, J.-C. Prome,, Y. Michel-Briand,, and P. Plesiat. 1997. Dechlorination of atrazine by a Rhizobium sp. isolate. Appl. Environ. Microbiol. 63: 862 866.
5. Brown, J. E.,, D. L. Bedard,, M. J. Brennan,, J. C. Carnahan,, H. Feng,, and R. E. Wagner. 1987. Polychlorinated biphenyl dechlorination in aquatic sediments. Science 236: 709 712.
6. Chakrabarty, A. M.,, G. Chou,, and I. C. Gunsalus. 1973. Genetic regulation of octane dissimilation plasmid in Pseudomonas. Proc. Natl. Acad. Sci. USA 70: 1137 1140.
7. Cook, A. M. 1987. Biodegradation of s-triazine xenobiotics. FEMS Microbiol. Rev. 46: 93 116.
8. Cook, A. M.,, P. Beilstein,, H. Grossenbacher,, and R. Huetter. 1985. Ring cleavage and degradative pathway of cyanuric acid in bacteria. Biochem. J . 231: 25 30.
9. Darwin, C. 1859. On the Origin of Species by Means of Natural Selection, or The Preservation of Favoured Races in the Struggle for Life. John Murray, London, England.
10. Dean, A. M.,, D. E. Dykhuizen,, and D. L. Hartl. 1986. Fitness as a function of B-galactosidase activity in E. coli. Genet. Res. 48: 1 8.
11. Dehmel, U.,, K. H. Engesser,, K. N. Timmis,, and D. F. Dwyer. 1995. Cloning, nucleotide sequence, and expression of the gene encoding a novel dioxygenase involved in metabolism of carboxydiphenyl ethers in Pseudomonas pseudoalcaligenes POB310. Arch. Microbiol. 163: 35 41.
12. de Souza, M. L.,, D. Newcombe,, S. Alvey,, D. E. Crowley,, A. Hay,, M. J. Sadowsky,, and L. P. Wackett. 1998. Molecular basis of a bacterial consortium: interspecies catabolism of atrazine. Appl. Environ. Microbiol. 64: 178 184.
13. de Souza, M. L.,, M. J. Sadowsky,, and L. P. Wackett. 1996. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J. Bacteriol. 178: 4894 4900.
14. de Souza, M. L.,, L. P. Wackett,, K. L. Boundy-Mills,, R. T. Mandelbaum,, and M. J. Sadowsky. 1995. Cloning, characterization, and expression of a gene region from Pseudomonas sp. strain ADP involved in the dechlorination of atrazine. Appl. Environ. Microbiol. 61: 3373 3378.
15. de Souza, M. L.,, L. P. Wackett,, and M. J. Sadowsky. 1998. The genes encoding atrazine catabolism are located on a self-transmissible plasmid in Pseudomonas sp. strain ADP. Appl. Environ. Microbiol. 64: 2323 2326.
16. Dickerson, R. E. 1971. The structures of cytochrome c and the rates of molecular evolution. J. Mol. Evol. 1: 26 45.
17. Di Giola, D.,, M. Peel,, F. Fava,, and R. C. Wyndham. 1998. Structures of homologous composite transposons carrying cbaABC genes from Europe and North America. Appl. Environ. Microbiol. 64: 1940 1946.
*18. Doolittle, R. F. 1987. Of URFs and ORFs: a Primer on How to Analyze Derived Amino Acid Sequences. University Science Books, Mill Valley, Calif. Evolution of Catabolic Enzymes and Pathways 133.
19. Dykhuizen, D. E.,, and D. L. Hartl. 1983. Functional effects of PGI allozymes in Escherichia coli. Genetics 105: 1 18.
20. Eaton, R. W.,, and J. S. Karns. 1991. Cloning and comparison of the DNA encoding ammelide aminohydrolase and cyanuric acid amidohydrolase from three s-triazine-degrading bacterial strains. J. Bacteriol. 173: 1363 1366.
21. Erickson, L. E.,, and K. H. Lee. 1989. Degradation of atrazine and related striazines. Crit. Rev. Environ. Control 19: 1 14.
22. Fong, P. Y.,, C. Goh,, G. Tan,, and H. M. Tan. 1997. Identification and genetic analysis of Tn5542, a transposable element carrying the bedD and bedClClBA genes in Pseudomonas putida ML2, p. 53. In Abstracts of the Sixth International Congress on Pseudomonas: Molecular Biology and Biotechnology, Madrid, Spain.
23. Fukumori, E., , and C. R. Saint. 1997. Nucleotide sequence and regulational analysis of genes involved in conversion of aniline to catechol in Pseudomonas putida UCC22 (pTDNl). J. Bacteriol. 179: 399 408.
24. Gerlt, J. A.,, and R. C. Babbitt. 1998. Mechanistically diverse enzyme superfamilies: the importance of chemistry in the evolution of catalysis. Curr. Opin. Chem. Biol. 2: 607 612.
25. Holm, L.,, and C. Sander. 1997. An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. Proteins Struct. Fund. Genet. 28: 72 82.
26. Horak, R.,, and M. Kivisaar. 1998. Expression of the transposase gene tnpA of Tn4652 is positively affected by integration host factor. J. Bacteriol. 180: 2822 2829.
27. Horowitz, N. H. 1945. On the evolution of biochemical synthesis. Proc. Natl. Acad. Sci. USA 31: 153 157.
28. Hudlicky, T.,, D. Gonzalez,, and D. T. Gibson. 1999. Enzymatic dihydroxylation of aromatics in enantioselective synthesis: expanding asymmetric methodology. Aldrichim. Acta 32: 35 62.
29. Junker, F.,, and A. M. Cook. 1997. Conjugative plasmids and the degradation of arylsulfonates in Comamonas testosteroni. Appl. Environ. Microbiol. 63: 2403 2410.
30. Kato, K.,, K. Ohtsuki,, H. Mitsuda,, T. Yomo,, S. Negoro,, and I. Urabe. 1994. Insertion sequence IS6100 on plasmid pOAD2, which degrades nylon oligomers. J. Bacteriol. 176: 1197 1200.
31. Kawasaki, H.,, K. Tsuda,, I. Matsushita,, and K. Tunomura. 1992. Lack of homology between two haloacetate dehalogenase genes encoded on a plasmid from Moraxella sp. strain B. J. Gen. Microbiol. 138: 1317 1323.
32. Kreitman, M. 1983. Nucleotide polymorphism at the alcohol dehydrogenase locus of Drosophila melanogaster. Nature 304: 412 117.
33. Lange, S. J.,, and L. J . Que. 1998. Oxygen activating nonheme iron enzymes. Curr. Opin. Chem. Biol. 2: 159 172.
34. Mandelbaum, R. T.,, D. L. Allan,, and L. R Wackett. 1995. Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl. Environ. Microbiol. 61: 1451 1457.
35. Maymo-Gatell, X.,, Y. Chien,, J. M. Gossett,, and S. H. Zinder. 1997. Isolation of a bacterium that reductively dechlorinates tetrachloroethene to ethene. Science 276: 1568 1571.
36. Mulbry, W. W.,, P. C. Kearney,, J. O. Nelson,, and J. S. Karns. 1987. Physical comparison of parathion hydrolase plasmids from Pseudomonas diminuta and Flavobacterium sp. Plasmid 18: 173 177.
37. Nagy, I.,, F. Compernolle,, K. Ghys,, J. Vanderleyden,, and R. de Mot. 1995. A single cytochrome P-450 system is involved in degradation of the herbicides EPTC (ethyl dipropylthiocarbamate) and atrazine by Rhodococcus sp. strain NI86/21. Appl. Environ. Microbiol. 61: 2056 2060.
38. Nakatsu, C., , J. Ng,, R. Singh,, N. Straug,, and C. Wyndham. 1991. Chlorobenzoate catabolic transposon Tn5271 is a composite class I element with flanking class II insertion sequences. Proc. Natl. Acad. Sci. USA 88: 8312 8316.
39. Nishi, A.,, K. Tominaga,, and K. Furukuwa. 1998. Horizontal transfer of the chromosomal gene clusters coding for biphenyl and salicylate metabolism in Pseudomonas putida KF715, p. 92. In Abstracts of the First International Conference of the Federation of Asia-Pacific Microbiology Societies, Singapore.
*40. Petsko, G. A.,, G. L. Kenyon,, J. A. Gerlt,, D. Ringe,, and J. W. Kozarich. 1993. On the origin of enzymatic species. Trends Biochem. Sci. 18: 372 376.
41. Radosevich, M.,, S. J. Traina,, Y. Hao,, and O. H. Tuovinen. 1995. Degradation and mineralization of atrazine by a soil bacterial isolate. Appl. Environ. Microbiol. 61: 297 302.
42. Rheinwald, J. G.,, A. M. Chakrabarty,, and I. C. Gunsalus. 1973. A transmissible plasmid controlling camphor oxidation in Pseudomonas putida. Proc. Natl. Acad. Sci. USA 70: 885 889.
43. Romine, M. E.,, L. C. Stillwell,, K. K. Wong,, S. J. Thurston,, E. C. Sisk,, C. Sensen,, T. Gaasterland,, J. K. Fredrickson,, and J. D. Saffer. 1999. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J. Bacteriol. 181: 1585 1602.
44. Sadowsky, M. J.,, M. L. de Souza,, Z. Tong,, and L. P. Wackett. 1998. AtzC is a member of the amidohydrolase protein superfamily and is homologous to other atrazine-metabolizing enzymes. J. Bacteriol. 180: 152 158.
45. Scholten, J. D.,, K.-H. Chang,, P. C. Babbitt,, H. Charest,, M. M. Sylvestre,, and D. Dunaway-Mariano. 1991. Novel enzymic hydrolytic dehalogenation of a chlorinated aromatic. Science 253: 182 185.
46. Serdar, C. M.,, and D. T. Gibson. 1989. Studies of nucleotide sequence homology between naphthalene-utilizing strains of bacteria. Biochem. Biophys. Res. Commun. 164: 772 779.
47. Shao, Z. Q.,, and R. Behki. 1996. Characterization of the expression of the thcB gene, coding for a pesticide-degrading cytochrome P-450 in Rhodococcus strains. Appl. Environ. Microbiol. 62: 403 407.
48. Springael, D.,, S. Kreps,, and M. Mergeay. 1993. Identification of a catabolic transposon, Tn4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in Alcaligenes eutrophus A5. J. Bacteriol. 175: 1674 1681.
*49. Tan, H.-M. 1999. Bacterial catabolic transposons. Appl. Microbiol. Biotechnol. 51: 1 12.
50. Tsuda, M.,, and T. lino. 1987. Genetic analysis of a transposon carrying toluene degrading genes on a TOL-plasmid pWWO. Mol. Gen. Genet. 210: 270 276.
51. Tsuda, M.,, and T. lino. 1988. Identification and characterization of Tn4653, a transposon converting the toluene transposon Tn4651 on TOL plasmid pWWO. Mol. Gen. Genet. 213: 72 77.
52. Tsuda, M.,, and T. lino. 1990. Naphthalene degrading genes on plasmid NAH7 are on a defective transposon. Mol. Gen. Genet. 223: 33 39.
53. van der Meer, T. R.,, A. J. Zehnder,, and W. M. de Vos. 1991. Identification of a novel composite transposable element, Tn52S0, carrying chlorobenzene dioxygenase genes of Pseudomonas sp. strain P51. J. Bacteriol. 173: 7077 7083.
54. van der Ploeg, J.,, M. Willemsen,, G. van Hall,, and D. B. Janssen. 1995. Adaptation of Xanthobacter autotrophicus GI10 to bromoacetate due to activation and mobilization of the haloacetate dehalogenase gene by insertion element 1- S1247. J. Bacteriol. 177: 1348 1356.
55. Watson, J. D.,, and F. H. C. Crick. 1953. A structure of deoxyribosenucleic acid. Nature 171: 737 738.
56. Williams, P. A.,, S. J. Assinder,, P. Marco,, K. J. O'Donnell,, C. L. Poh,, L. E. Shaw,, and M. K. Winson,. 1992. Catabolic gene duplications in TOL plasmids, p. 341 352. In E. Galli,, S. Silver,, and B. Witholt (ed.), Pseudomonas: Molecular Biology and Biotechnology. American Society for Microbiology, Washington, D.C..
*57. Woese, C. R.,, and G. E. Fox. 1977. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc. Natl. Acad. Sci. USA 74: 5088 5090.
58. Xiang, H.,, L. Luo,, K. L. Taylor,, and D. Dunaway-Mariano. 1999. Interchange of catalytic activity within the 2-enoyl-coenzyme A hydratase/isomerase superfamily based on a common active site template. Biochemistry 38: 7638 7652.
*59. Zuckerkandl, E.,, and L. Pauling. 1965. Molecules as documents of evolutionary history. J. Theor. Biol. 8: 357 366.

Tables

Generic image for table
Table 7.1

Microbial biodegradative-enzyme families based on signature sequences

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7
Generic image for table
Table 7.2

Catabolic transposons in bacteria

Citation: Wackett L, Hershberger C. 2001. Evolution of Catabolic Enzymes and Pathways, p 115-134. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch7

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