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Chapter 5 : Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity

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Abstract:

The compounds to be considered in the context of biodegradation and biocatalysis are the known organic molecules, an ever-expanding set of over 10 million compounds. This chapter presents evidence from the natural-product literature to support the idea that many functional groups typically referred to as xenobiotic are in fact found in the natural biological world, exclusive of organic synthesis. A common practice in correlating the types of organic molecule with their ease of biodegradation is to define them as (i) natural products or (ii) industrial chemicals. Many organic functional groups are acted upon by the individual enzymes of biodegradation. A given enzyme typically transforms one organic functional group in isolation, for example, oxidizing an alcohol to an aldehyde or hydrolyzing an amide to a carboxylic acid and an amine. The chapter highlights the impressive diversity of biologically relevant chemical structures and provides a framework for categorizing their microbial metabolism. The diversity of organic compounds is effectively infinite, and over 10 million compounds are currently described in the chemical literature. Understanding the microbial metabolism of such a broad range of compounds necessitates an efficient categorization of microbial reactions.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5

Key Concept Ranking

Organic Chemicals
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Polycyclic Aromatic Hydrocarbons
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Figures

Image of Figure 5.1
Figure 5.1

Schematic depiction of the carbon cycle, in which CO is incorporated into organic compounds by plants and microbial autotrophs and complex organic compounds are oxidized back to CO, largely by prokaryotes.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.2
Figure 5.2

Major biological cycling of the elements of carbon, hydrogen, nitrogen, oxygen, and sulfur is catalyzed largely by microorganisms. Some representative microorganisms catalyzing certain transformations are shown.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.3
Figure 5.3

Thousands of aromatic hydrocarbons are made naturally; several representative structures are shown.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.4
Figure 5.4

Cliloromethane is made principally by microorganisms; 0.5% of the world output is made industrially.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.5
Figure 5.5

Some representative nitrogen heterocycles found in natural products.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.6
Figure 5.6

Some representative oxygen heterocycles found in natural products.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Figure 5.7

Sulfur and mixed heterocycles found in natural products.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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Image of Figure 5.8
Figure 5.8

Organic functional groups known to undergo transformation by microbes and represented in the UM-BBD.

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
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References

/content/book/10.1128/9781555818036.chap5
1. Alexander, M. 1994. Biodegradation and Bioremediation, p. 159 176. Academic Press, San Diego, Calif.
2. Anderson, P. M.,, Y. C. Sung,, and J. A. Fuchs. 1990. The cyanase operon and cyanate metabolism. FEMS Microbiol. Rev. 7: 247 252.
3.. Blumer, M. 1976. Polycyclic aromatic compounds in nature. Sci. Am. 234: 35 45.
4. Claiborne, A.,, J. I. Yeh,, T. C. Mallett,, J. Luba,, E. J . I. Crane,, V. Charrier,, and D. Parsonage. 1999. Protein-sulfenic acids: diverse roles for an unlikely player in enzyme catalysis and redox regulation. Biochemistry 38: 15407 15416.
5. Dill, K.,, and E. L. McGowen. 1994. The biochemistry of arsenic, bismuth and antimony, p. 695 713. In S. Patai (ed.), The Chemistry of Organic Arsenic, Antimony and Bismuth, John Wiley and Sons, Chichester, United Kingdom.
6. Dobbek, H.,, L. Gremer,, O. Meyer,, and R. Huber. 1999. Crystal structure and mechanism of CO dehydrogenase, a molybdo iron-sulfur flavoprotein containing S-selanylcysteine. Proc. Natl. Acad. Sci. USA 96: 8884 8889.
7. Fehr, T ,, J. Kallen,, L. Oberer,, J. J. Sanglier,, and W. Schilling. 1999. Sanglifehrins A, B, C and D, novel cyclophilin-binding compounds isolated from Streptomyces sp. A92-308110. II. Structure, elucidation, stereochemistry and physicochemical properties. J. Antibiot. (Tokyo) 52: 474 479.
8. Ferris, J. P. 1983. Biological formation and metabolic transformations of compounds containing the cyano group, p. 325 340. In S. Patai and Z. Rappaport (ed.), The Chemistry of Triple-Bonded Functional Groups. John Wiley and Sons, Chichester, United Kingdom.
9. Fleming, R. W.,, and M. Alexander. 1972. Dimethylselenide and dimethyltelluride formation by a strain of Penicillium. Appl. Microbiol. 24: 424 429.
10. Formica, J. V.,, and M. A. Apple. 1976. Production, isolation, and properties of azetomycins. Antimicrob. Agents Chemother. 9: 214 221.
11. Franklin, T. J.,, and G. A. Snow. 1975. Biochemistry of Antimicrobial Action. Halsted Press, London, United Kingdom.
12. Gribble, G. W. 1992. Naturally occurring organohalogen compounds—a survey. J. Natl. Prod. 55: 1353 1395.
13. Gschwend, P. M.,, J. K. MacFarlane,, and K. A. Newman. 1985. Volatile halogenated organic compounds related to seawater from temperate marine microalgae. Science 227: 1033 1035.
*14.. Harbourne, J. 1988. Ecological Biochemistry, 3rd ed. Academic Press, New York, N.Y.
15. Harper, D. B. 1994. Biosynthesis of halogenated methanes. Biochem. Soc. Trans. 22: 1007 1011.
16. Hori, T.,, M. Horiguchi,, and A. Hayashi. 1984. Biochemistry of Natural C-P Compounds. Maruzen Ltd., Kyoto, Japan.
17. Horton, P. A.,, R. E. Longley,, M. Kelly-Borges,, O. J. McConnell,, and L. M. Ballas. 1994. New cytotoxic peroxylactones from the marine sponge, Plakinastrella onkodes. J. Nat. Prod. 57: 1374 1381.
18. Kameyama, T.,, A. Takahashi,, H. Matsumoto,, S. Kurasawa,, M. Hamada,, Y. Okami,, M. Ishizuka,, and T. Takeuchi. 1988. Thrazarine, a new antitumor antibiotic. I. Taxonomy, fermentation, isolation and biological properties. J. Antibiot. (Tokyo) 41: 1561 1567.
19. Kato, Y.,, K. Nakamura,, H. Sakiyama,, S. G. Mayhem,, and Y. Asano. 2000. Novel heme-containing lyase, phenylacetaldoximine dehydratase from Bacillus sp. strain OxB-1: purification, characterization, and molecular cloning of the gene. Biochemistry 39: 800 809.
20.Khalil-Rizvi, S., S. I. Toth, D. van der Helm, H. Vidavsky and M. L. Gross. 1997. Structures and characteristics of novel siderophores from plant deleterious Pseudomonas fluorescens A225 and Pseudomonas putida ATCC 39167. Biochemistry 36: 41634171.
21. Kurobane, I.,, L. Dale,, and L. C. Vining. 1987. Characterization of new viridomycins and requirements for production in cultures of Streptomyces griseus. J. Antibiot. (Tokyo) 40: 1131 1139.
22. Kyung, K. H.,, and H. P. Fleming. 1997. Antimicrobial activity of sulfur compounds derived from cabbage. J. Food Prot. 60: 67 71.
23. Lander, S. P. 1982. Naturally occurring allenes, p. 681 703. In S. R. Lander (ed.), The Chemistry of Allenes. Academic Press, New York, N.Y.
*24.. Laskin, A. I., and H. A. Lechevalier. 1977. Handbook of Microbiology, vol. 9, part A. Antibiotics. CRC Press, Boca Raton, Fla.
25. Lee, T. M.,, M. M. Siegel,, G. O. Morton,, J. J. Goodman,, R. T. Testa,, and D. B. Borders. 1995. Sufinemycin, a new antihelmintic antibiotic: fermentation, isolation and structure determination. J. Antibiot. (Tokyo) 48: 282 285.
26. Lewis, B. L.,, and H. P. Meyer. 1993. Biogeochemistry of methylgermanium species in natural waters, p. 79 99. In H. Sigel and A. Sigel (ed.), Metal Ions in Biological Systems, vol. 29. Marcel Dekker, New York, N.Y.
27. Lim, H.,, K. Kubota,, A. Kobayashi,, T. Seki,, and T. Ariga. 1999. Inhibitory effect of sulfur-containing compounds in Scorodocarpus borneenis Becc. on the aggregation of rabbit platelets. Biosci. Biotechnol. Biochem. 63: 298 301.
28. McCay, D. S.,, E. K. J. Gibson,, K. K. Thomas-Keprta,, H. Vali,, C. S. Romanek,, S. J. Clemett,, X. D. F. Chillier,, C. R. Maechling,, and R. N. Zare. 1996. Search for past life on Mars: possible relic biogenic activity in martian meteorite ALH84001. Science 273: 924 930.
29. Miyadera, T. 1975. Biological formation and reactions of hydrazo, azo and azoxy group, p. 495 539. In S. Patai (ed.), The Chemistry of Hydrazo, Azo and Azoxy Groups. John Wiley and Sons, Chichester, United Kingdom.
30. Nishino, S. F.,, and J. C. Spain. 1993. Degradation of nitrobenzene by a Pseudomonas pseudoalcaligenes. Appl. Environ. Microbiol. 59: 2520 2525.
31. Nojiri, M.,, H. Nakayama,, M. Odaka,, M. Yohda,, K. Takio,, and I. Endo. 2000. Cobalt-substituted Fe-type nitrile hydratase of Rhodococcus sp. N-771. FEBS Lett. 465: 173 177.
32. Noller, C. R. 1957. Chemistry of Organic Compounds. Saunders, Philadelphia, Pa.
33.Oldfield, C , O. Pogrebinsky, J. Simmonds, E. S. Olson, and C. F. Kulpa. 1997. Elucidation of the metabolic pathway for dibenzothiophene desulphurization by Rhodococcus sp. strain IGTS8 (ATCC 53968). Microbiology 143: 29612973.
34. Reid, K. A.,, J. T. Hamilton,, R. D. Bowden,, D. O'Hagan,, L. Dasaradhi,, M. R. Amin,, and D. B. Harper. 1995. Biosynthesis of fluorinated secondary metabolites by Streptomyces cattleya. Microbiology 141: 1385 1393.
35. Rocha, E. R.,, and C. J. Smith. 1999. Role of the alkyl hydroperoxide reductase (ahpCF) gene in oxidative stress defense of the obligate anaerobe Bacteroides fragilis. J. Bacteriol. 181: 5701 5710.
36. Rosner, B. M.,, F. A. Rainey,, R. M. Kroppenstedt,, and B. Schink. 1997. Acetylene degradation by new isolates of aerobic bacteria and comparison of acetylene hydratase enzymes. FEMS Microbiol. Lett. 148: 175 180.
37. Schmidt, U.,, and F. Huber. 1976. Methylation of organolead and lead(II) compounds to (CH3)4Pb by microorganisms. Nature 259: 157 158.
38. Schwartz, D.,, J. Recktenwald,, S. Pelzer,, and W. Wohlleben. 1998. Isolation and characterization of the PEP-phosphomutase and the phosphonopyruvate decarboxylase genes from the phosphinothricin tripeptide producer Streptomyces viridochromogenes Tu494. FEMS Microbiol. Lett. 163: 149 157.
39. Soda, K.,, and N. Esaki. 1987. Biochemistry of physiologically active selenium compounds, p. 349 365. In S. Patai (ed.), The Chemistry of Organic Selenium and Tellurium Compounds. John Wiley and Sons, Chicester, United Kingdom.
40. Stadtman, T. C. 1990. Selenium biochemistry. Annu. Rev. Biochem. 59: 111 127.
41. Stierle, A. 1993. Taxol and taxane production by Taxomyces andreanae, an endophytic fungus of Pacific yew. Science 260: 214 216.
42. Takai, H.,, M. Yoshida,, T. Iida,, I. Matsubara,, and K. Shirahata. 1976. Natural product hydrazide. J. Antibiot. (Tokyo) 29: 1253 1257.
43. Vahter, M.,, and E. Marafante. 1993. Metabolism of alkyl arsenic and antimony compounds, p. 161 184. In H. Sigel and A. Sigel (ed.), Metal Ions in Biological Systems, vol. 29. Marcel Dekker Inc., New York, N.Y.
44. Vannelli, T.,, M. Messmer,, A. Studer,, S. Vuilleumer,, and T. Leisinger. 1999. A corrinoid-dependent catabolic pathway for growth of a Methylobacterium strain with chloromethane. Proc. Natl. Acad. Sci. USA 96: 4615 4620.
45. Walton, K.,, M. M. Coombss,, R. Walker,, and C. Ioannides. 1997. Bioactivation of mushroom hydrazines to mutagenic products by mammalian and fungal enzymes. Mutat. Res. 381: 131 139.
46. Weber, A. A. 1993. Direct inhibition of platelet function by organic nitrates via nitric oxide formation. Eur. J. Pharmacol. 247: 29 37.
47.Xue, Y, L. Zhao, H.-W. Liu, and D. H. Sherman. 1998. A gene cluster for macrolide antibiotic biosynthesis in Streptomyces venezuelae: architecture of metabolic diversity. Proc. Natl. Acad. Sci. USA 95: 1211112116.
48. Yonezawa, Y.,, M. Fukui,, T. Yoshida,, A. Ochi,, T. Tanaka,, Y. Noguti,, T. Kowata,, Y. Sato,, A. S. Masunaga,, and Y. Urushigawa. 1994. Degradation of tri-nbutyltin in Ise Bay sediment. Chemosphere 29: 1349 1356.

Tables

Generic image for table
Table 5.1

Major classes of secondary plant compounds

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
Generic image for table
Table 5.2

Organic functional groups found in natural products

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5
Generic image for table
Table 5.3

Naturally produced cycloalkane ring compounds

Citation: Wackett L, Hershberger C. 2001. Organic Functional Group Diversity: the Unity of Biochemistry Is Dwarfed by Its Diversity, p 71-93. In Biocatalysis and Biodegration. ASM Press, Washington, DC. doi: 10.1128/9781555818036.ch5

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