Thermodynamic analysis of biodegradation pathways

Biotechnology and Bioengineering

Volumn 103, Issue 3, 2009, Pages 532-541

  Finley, Stacey D ^a   Broadbelt, Linda J ^a   Hatzimanikatis, Vassily ^b  

^a Northwestern University   (United States)

^b EPFL   (Switzerland)

Author keywords

Complex systems; Metabolic engineering; Network analysis; Synthetic biology; Systems biology

Indexed keywords

COMPLEX SYSTEMS; METABOLIC ENGINEERING; NETWORK ANALYSIS; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY;

BIOCHEMISTRY; DEGRADATION; ELECTRIC NETWORK ANALYSIS; FREE ENERGY; GIBBS FREE ENERGY; LARGE SCALE SYSTEMS; METABOLISM; MICROBIOLOGY; THERMOANALYSIS; THERMODYNAMICS; UNCERTAINTY ANALYSIS;

BIODEGRADATION;

XENOBIOTIC AGENT;

ARTICLE; BIODEGRADATION; BIOTRANSFORMATION; METABOLIC ENGINEERING; SYSTEMS BIOLOGY; THERMODYNAMICS; BIOLOGY; FACTUAL DATABASE; METABOLISM;

BIOTRANSFORMATION; COMPUTATIONAL BIOLOGY; DATABASES, FACTUAL; METABOLISM; SYSTEMS BIOLOGY; THERMODYNAMICS; XENOBIOTICS;

EID: 65549153067     PISSN: 00063592     EISSN: 10970290     Source Type: Journal    
DOI: 10.1002/bit.22285     Document Type: Article

References (52)

1. Alberty RA. 1998. Calculation of standard transformed formation properties of biochemical reactants and standard apparent reduction potentials of half reactions. Arch Biochem Biophys 358(1):25-39. (Pubitemid 28471370)
2. Alberty RA. 2003. Thermodynamics of biochemical reactions. Hoboken: John Wiley & Sons.
3. Alexander M. 1985. Biodegradation of organic chemicals. Environ Sci Technol 18(2):106-111. (Pubitemid 15169984)
4. Alexander M. 1999. Biodegradation and bioremediation. San Diego: Academic Press, Inc. p. 302.
5. Benson SW. 1976. Thermochemical kinetics: Methods for the estimation of thermochemical data and rate parameters. New York: John Wiley & Sons.
6. Boethling RS, Alexander M. 1979. Effect of concentration of organic chemicals on their biodegradation by natural microbial communities. Appl Environ Microbiol 37(6):1211-1216. (Pubitemid 9202308)
7. Boopathy R. 2000. Factors limiting bioremediation technologies. Bioresour Technol 74(1):63-67. (Pubitemid 30190278)
8. Bugg TDH, Winfield CJ. 1998. Enzymatic cleavage of aromatic rings: Mechanistic aspects of catechol dioxygenases and later enzymes of bacterial oxidative cleavage pathways. Nat Prod Rep 5:513-530. (Pubitemid 28514544)
9. Chen W, Mulchandani A, Deshusses MA. 2005. Environmental biotechnology: Challenges and opportunities for chemical engineering. AIChE J 51(3):690-695. (Pubitemid 40440743)
10. Darvas F. 1987. MetabolExpert, an expert system for predicting metabolism of substances. In: Kaiser K, editor. QSAR in environmental toxicology. Riedel: Dordrecht. p. 71-81.
11. Dolfing J. 2000. Energetics of anaerobic degradation pathways of chlorinated aliphatic compounds. Microb Ecol 40:2-7.
12. Dolfing J. 2003. Thermodynamic considerations for dehalogenation. In: Haggblom MM, editor. Dehalogenation: Microbial processes and environmental applications. Secaucus, NJ: Kluwer Academic Publishers. p. 89-114.
13. Dolfing J, Harrison BK. 1992. Gibbs free energy of formation of halogenated aromatic compounds and their potential role as electron acceptors in anaerobic environments. Environ Sci Technol 26:2213-2218.
14. Dolfing J, Janssen DB. 1994. Estimates of Gibbs free energies of formation of chlorinated aliphatic compounds. Biodegradation 5:21-28. (Pubitemid 2082795)
15. Donnelly MI, Wolfe RS. 1986. The role of formylmethanofuran: Tetrahydromethanopterin formyltransferase in methanogenesis from carbon dioxide. J Biol Chem 261(35):16653-16659.
16. Dua M, Singh A, Sethunathan N, Johri AK. 2002. Biotechnology and bioremediation: Successes and limitations. Appl Microbiol Biotechnol 59:143-152. (Pubitemid 34756953)
17. Eaton RW, Chapman PJ. 1992. Bacterial metabolism of naphthalene: Construction and use of recombinant bacteria to study ring cleavage of 1,2-dihydroxynaphthalene and subsequent reactions. J Bacteriol 174(23):7542-7554.
18. Ellis LB, Wackett LP. 2006. The University of Minnesota Biocatalysis/ Biodegradation Database: The first decade. Nucleic Acids Res 34:D517-D521.
19. Erickson BD, Mondello FJ. 1993. Enhanced biodegradation of polychlorinated biphenyls after site-directed mutagenesis of a biphenyl dioxygenase gene. Appl Environ Microbiol 59:3858-3862. (Pubitemid 23327592)
20. Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BO. 2007. A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information. Mol Syst Biol 3:1-18. (Pubitemid 47013445)
21. Fournier D, Halasz A, Spain J, Fiurasek P, Hawari J. 2002. Determination of key metabolites during biodegradation of hexahydro-1,3,5-trinitro- 1,3,5-triazine with Rhodococcus sp. strain DN22. Appl Environ Microbiol 68(1):166-172. (Pubitemid 34031176)
22. Goldberg RN, Tewari YB, Bhat TN. 2004. Thermodynamics of enzymecatalyzed reactions - A database for quantitative biochemistry. Bioinformatics 20(16):2874-2877. (Pubitemid 39530187)
23. Gomez MJ, Pazos F, Guijarro FJ, de Lorenzo V, Valencia A. 2007. The environmental fate of organic pollutants through the global microbial metabolism. Mol Syst Biol 3:1-11. (Pubitemid 46878943)
24. Greene N, P.N Judson PN, Langowski JJ, Marchant CA. 1999. Knowledge-based expert systems for toxicity and metabolism prediction: DEREK, StAR and METEOR. SAR QSAR Environ Res 10:299-314.
25. Hatzimanikatis V, Li C, Ionita JA, Henry CS, Jankowski MD, Broadbelt LJ. 2005. Exploring the diversity of complex metabolic networks. Bioinformatics 21(8):1603-1609. (Pubitemid 40542718)
26. Henry CS, Jankowski MD, Broadbelt LJ, Hatzimanikatis V. 2006. Genome-scale thermodynamic analysis of Escherichia coli metabolism. Biophys J 90:1453-1461.
27. Henry CS, Broadbelt LJ, Hatzimanikatis V. 2007. Thermodynamics-based metabolic flux analysis. Biophys J 92:1792-1805. (Pubitemid 46393490)
28. Holmes DA, Harrison BK, Dolfing J. 1993. Estimation of Gibbs free energies of formation for polychlorinated biphenyls. Environ Sci Technol 27:725-731. (Pubitemid 23129304)
29. Hou BK, Wackett LP, Ellis LB. 2003. Microbial pathway prediction: A functional group approach. J Chem Inf Comput Sci 43(3):1051-1057.
30. Jain RK, Kapur M, Labana S, Lal B, Sharma PM, Bhattacharya D, Thakur IS. 2005. Microbial diversity: Application of microorganisms for the biodegradation of xenobiotics. Curr Sci 89:101-112. (Pubitemid 41666053)
31. Jankowski MD, Henry CS, Broadbelt LJ, Hatzimanikatis V. 2008. Group contribution method for thermodynamic analysis of complex metabolic networks. Biophys J 95:1487-1499.
32. Jaworska J, Dimitrov S, Nikolova N, Mekenyan O. 2002. Probabilistic assessment of biodegradability based on metabolic pathways: Catabol system. SAR QSAR Environ Res 13(2):307-323.
33. Klopman G, Dimayuga M, Talafous J. 1994. META. 1. A program for the evaluation of metabolic transformation of chemicals. J Chem Inf Comput Sci 34(6):1320-1325.
34. Kovar K, Chaloupka V, Egli T. 2002. A threshold substrate concentration is required to initiate the degradation of 3-phenylpropionic acid in Escherichia coli. Acta Biotechnol 22:285-298. (Pubitemid 34830737)
35. Kummel A, Panke S, Heinemann M. 2006. Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data. Mol Syst Biol 2: 2006.0034. (Pubitemid 43948142)
36. Maskow T, von Stockar U. 2005. How reliable are thermodynamic feasibility statements of biochemical pathways? Biotechnol Bioeng 92(2):223-2230.
37. Mavrovouniotis ML. 1990. Group contributions for estimating standard Gibbs energies of formation of biochemical compounds in aqueous solution. Biotechnol Bioeng 36:1070-1082.
38. Mavrovouniotis ML. 1991. Estimation of standard Gibbs energy changes of biotransformations. J Biol Chem 266:14440-14445. (Pubitemid 21907522)
39. Minkevich IG, Eroshin VK. 1973. Productivity and heat generation of fermentation under oxygen limitation. Folia Microbiol 18:376-385.
40. Paul D, Pandey G, Pandey J, Jain RK. 2005. Accessing microbial diversity for bioremediation and environmental restoration. Trends Biotechnol 23(3):135-142. (Pubitemid 40269846)
41. Pieper DH, Reineke W. 2000. Enteineering bacteria for bioremediation. Curr Opin Biotechnol 11:262-270.
42. Rapp P, Timmis KN. 1999. Degradation of chlorobenzenes at nanomolar concentrations by Burkholderia sp. strain PS14 in liquid cultures and in soil. Appl Environ Microbiol 65(6):2547-2552. (Pubitemid 129526290)
43. Schach S, Schwarz G, Fetzner S, Lingens F. 1993. Microbial metabolism of quinoline and related compounds. XVII. Degradation of 3-methylquinoline by Comamonas testosteroni 63. Biol Chem Hoppe Seyler 374(3):175-181.
44. Shelley MD, Autenrieth RL, Wild JR, Dale BE. 1996. Thermodynamic analysis of trinitrotoluene biodegradation and mineralization pathways. Biotechnol Bioeng 50:198-205. (Pubitemid 26187027)
45. Sutherland TD, Horne I, Weir KM, Coppin CW, Williams MR, Selleck M, Russell RJ, Oakeshott JG. 2004. Enzymatic bioremediation: From enzyme discovery to applications. Clin Exp Pharmacol Physiol 31:817-821. (Pubitemid 39556860)
46. Thauer RK. 1998. Biochemistry of methanogenesis: A tribute to Marjory Stephenson. Microbiology 144:2377-2406.
47. Thauer RK, Jungermann K, Decker K. 1977. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol Rev 41:100-180. (Pubitemid 8082287)
48. van Herwijnen R, Springael D, Slot P, Govers HAJ, Parsons JR. 2003. Degradation of anthracene by Mycobacterium sp. strain LB501T proceeds via a novel pathway, through o-phthalic acid. Appl Environ Microbiol 69(1):186-190. (Pubitemid 36077474)
49. VanBriessen JM. 2001. Thermodynamic yield predictions for biodegradation through oxygenase activation reactions. Biodegradation 12:265-281. (Pubitemid 34045002)
50. Wagman DD. 1982. NBS tables of chemical thermodynamic properties: Selected values for inorganic and C1 and C2 organic substances in SI units. New York; Washington, DC: American Chemical Society and American. Institute of Physics.
51. Watanabe K. 2001. Microorganisms relevant to bioremediation. Curr Opin Biotechnol 12:237-241. (Pubitemid 32524334)
52. Yuan Z, VanBriessen JM. 2002. Yield prediction and stoichiometry of multi-step biodegradation reactions involving oxygenation. Biotechnol Bioeng 80(1):100-113.