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Catalytic Promiscuity of Aromatic Ring-Hydroxylating Dioxygenases and Their Role in the Plasticity of Xenobiotic Compound Degradation

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Microbial Metabolism of Xenobiotic Compounds

Part of the book series: Microorganisms for Sustainability ((MICRO,volume 10))

Abstract

Persistent organic pollutants pose one of the most critical challenges to the humankind due to their well-established hazardous effects to the ecosystem and various life forms including the human being. Many of these pollutants are anthropogenic in nature and exhibit the tendency of recalcitrance toward natural biodegradation. Most of these pollutants belong to chemical scaffolds that were never present in the environment in the past. Consequently, the evolution of the enzymes and metabolic pathways for their metabolism and degradation over the short geological time span that these compounds have been present in the environment is considered to be rather challenging. Interestingly, microorganisms belonging to diverse taxonomic groups have been identified and characterized with the metabolic potential to degrade the anthropogenic compounds and utilize them as a source of carbon/energy. Evolution of such degradative potential is widely accepted to have occurred with one of the following mechanisms: (i) horizontal gene transfer and (ii) genome reorganization and domain shuffling. An alternative and recent theory in this regard suggests that the evolution of degradative enzymes for anthropogenic compounds may have exploited the “catalytic promiscuity” of metabolic enzymes evolved for degradation of structurally related yet distinct compounds. Noticeably, such catalytic promiscuity of metabolic enzymes has been reported for a number of enzymes involved in degradation of anthropogenic compounds. “Aromatic ring-hydroxylating dioxygenase” is one prominent group of enzymes which exhibit catalytic promiscuity, a potential that has been exploited for technological application in the field of biocatalysis as well as for enhancing the plasticity of anthropogenic xenobiotic compound degradation. The present book chapter aims to present a comprehensive account of aromatic ring-hydroxylating dioxygenases with respect to their basic introduction, classification, the molecular mechanism of action, structure-function relationship, catalytic promiscuity, and applications with respect to expansion of biocatalysis and biodegradation.

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References

  • Beil, S., Happe, B., Timmis, K. N., & Pieper, D. H. (1997). Genetic and biochemical characterization of the broad spectrum chlorobenzene dioxygenase from Burkholderia sp. strain PS12--dechlorination of 1,2,4,5-tetrachlorobenzene. European Journal of Biochemistry, 247, 190–199.

    Article  CAS  Google Scholar 

  • Beil, S., Timmis, K. N., & Pieper, D. H. (1999). Genetic and biochemical analyses of the tec operon suggest a route for evolution of chlorobenzene degradation genes. Journal of Bacteriology, 181, 341–346.

    CAS  Google Scholar 

  • Benigni, R., & Passerini, L. (2002). Carcinogenicity of the aromatic amines: From structure-activity relationships to mechanisms of action and risk assessment. Mutation Research, 511, 191–206.

    Article  CAS  Google Scholar 

  • Boyd, D. R., Sharma, N. D., & Allen, C. C. (2001). Aromatic dioxygenases: Molecular biocatalysis and applications. Current Opinion in Biotechnology, 12, 564–573.

    Article  CAS  Google Scholar 

  • Butler, C. S., & Mason, J. R. (1997). Structure-function analysis of the bacterial aromatic ring-hydroxylating dioxygenases. Advances in Microbial Physiology, 38, 47–84.

    Article  CAS  Google Scholar 

  • Carredano, E., Karlsson, A., Kauppi, B., Choudhury, D., Parales, R. E., Parales, J. V., Lee, K., Gibson, D. T., Eklund, H., & Ramaswamy, S. (2000). Substrate binding site of naphthalene 1,2-dioxygenase: Functional implications of indole binding. Journal of Molecular Biology, 296, 701–712.

    Article  CAS  Google Scholar 

  • Chakraborty, J., & Dutta, T. K. (2011). From lipid transport to oxygenation of aromatic compounds: Evolution within the Bet v1-like superfamily. Journal of Biomolecular Structure & Dynamics, 29, 67–78.

    Article  CAS  Google Scholar 

  • Chakraborty, J., Ghosal, D., Dutta, A., & Dutta, T. K. (2012). An insight into the origin and functional evolution of bacterial aromatic ring-hydroxylating oxygenases. Journal of Biomolecular Structure & Dynamics, 30, 419–436.

    Article  CAS  Google Scholar 

  • Chemerys, A., Pelletier, E., Cruaud, C., Martin, F., Violet, F., & Jouanneau, Y. (2014). Characterization of novel polycyclic aromatic hydrocarbon dioxygenases from the bacterial metagenomic DNA of a contaminated soil. Applied and Environmental Microbiology, 80, 6591–6600.

    Article  CAS  Google Scholar 

  • Copley, S. D. (2009). Evolution of efficient pathways for degradation of anthropogenic chemicals. Nature Chemical Biology, 5, 559–566.

    Article  CAS  Google Scholar 

  • Dai, M., Rogers, J. B., Warner, J. R., & Copley, S. D. (2003). A previously unrecognized step in pentachlorophenol degradation in Sphingobium chlorophenolicum is catalyzed by tetrachlorobenzoquinone reductase (PcpD). Journal of Bacteriology, 185, 302–310.

    Article  CAS  Google Scholar 

  • Diaz, E. (2004). Bacterial degradation of aromatic pollutants: A paradigm of metabolic versatility. International Microbiology, 7, 173–180.

    CAS  Google Scholar 

  • Eby, D. M., Beharry, Z. M., Coulter, E. D., Kurtz, D. M., Jr., & Neidle, E. L. (2001). Characterization and evolution of anthranilate 1,2-dioxygenase from Acinetobacter sp. strain ADP1. Journal of Bacteriology, 183, 109–118.

    Article  CAS  Google Scholar 

  • Friemann, R., Ivkovic-Jensen, M. M., Lessner, D. J., Yu, C. L., Gibson, D. T., Parales, R. E., Eklund, H., & Ramaswamy, S. (2005). Structural insight into the dioxygenation of nitroarene compounds: The crystal structure of nitrobenzene dioxygenase. Journal of Molecular Biology, 348, 1139–1151.

    Article  CAS  Google Scholar 

  • Gao, J., & Ellis, L. B. (2008). Improving infrastructure for pathway prediction (Vol. 951). In American Medical Informatics Association Annual Symposium Proceedings, Washington DC, USA

    Google Scholar 

  • Gao, J., Ellis, L. B., & Wackett, L. P. (2010). The University of Minnesota biocatalysis/biodegradation database: Improving public access. Nucleic Acids Research, 38, D488–D491.

    Article  CAS  Google Scholar 

  • Gibson, D. T., & Parales, R. E. (2000). Aromatic hydrocarbon dioxygenases in environmental biotechnology. Current Opinion in Biotechnology, 11, 236–243.

    Article  CAS  Google Scholar 

  • Hinteregger, C., Leitner, R., Loidl, M., Ferschl, A., & Streichsbier, F. (1992). Degradation of phenol and phenolic compounds by Pseudomonas putida EKII. Applied Microbiology and Biotechnology, 37, 252–259.

    Article  CAS  Google Scholar 

  • Inczefi-Gonda, A. (1999). The environmental pollutant aromatic hydrocarbon, benzpyrene has deleterious effect on hormone receptor development. Acta Biologica Hungarica, 50, 355–361.

    CAS  Google Scholar 

  • Jakoncic, J., Jouanneau, Y., Meyer, C., & Stojanoff, V. (2007). The crystal structure of the ring-hydroxylating dioxygenase from Sphingomonas CHY-1. The FEBS Journal, 274, 2470–2481.

    Article  CAS  Google Scholar 

  • Janssen, D. B., Dinkla, I. J., Poelarends, G. J., & Terpstra, P. (2005). Bacterial degradation of xenobiotic compounds: Evolution and distribution of novel enzyme activities. Environmental Microbiology, 7, 1868–1882.

    Article  CAS  Google Scholar 

  • Jindrova, E., Chocova, M., Demnerova, K., & Brenner, V. (2002). Bacterial aerobic degradation of benzene, toluene, ethylbenzene and xylene. Folia Microbiologia (Praha), 47, 83–93.

    Article  CAS  Google Scholar 

  • Jones, K. C., & de Voogt, P. (1999). Persistent organic pollutants (POPs): State of the science. Environmental Pollution, 100, 209–221.

    Article  CAS  Google Scholar 

  • Kabumoto, H., Miyazaki, K., & Arisawa, A. (2009). Directed evolution of the actinomycete cytochrome P450moxA (CYP105) for enhanced activity. Bioscience, Biotechnology, and Biochemistry, 73, 1922–1927.

    Article  CAS  Google Scholar 

  • Kadiyala, V., & Spain, J. C. (1998). A two-component monooxygenase catalyzes both the hydroxylation of p-nitrophenol and the oxidative release of nitrite from 4-nitrocatechol in Bacillus sphaericus JS905. Applied and Environmental Microbiology, 64, 2479–2484.

    CAS  Google Scholar 

  • Kallubai, M., Amineni, U., Mallavarapu, M., & Kadiyala, V. (2015). In silico approach to support that p-nitrophenol monooxygenase from Arthrobacter sp. strain JS443 catalyzes the initial two sequential monooxygenations. Interdisciplinary Sciences, 7, 157–167.

    CAS  Google Scholar 

  • Karandikar, R., Badri, A., & Phale, P. S. (2015). Biochemical characterization of inducible ‘Reductase’ component of benzoate dioxygenase and phthalate isomer dioxygenases from Pseudomonas aeruginosa strain PP4. Applied Biochemistry and Biotechnology, 177, 318–333.

    Article  CAS  Google Scholar 

  • Kauppi, B., Lee, K., Carredano, E., Parales, R. E., Gibson, D. T., Eklund, H., & Ramaswamy, S. (1998). Structure of an aromatic-ring-hydroxylating dioxygenase-naphthalene 1,2-dioxygenase. Structure, 6, 571–586.

    Article  CAS  Google Scholar 

  • Keane, A., Phoenix, P., Ghoshal, S., & Lau, P. C. (2002). Exposing culprit organic pollutants: A review. Journal of Microbiological Methods, 49, 103–119.

    Article  CAS  Google Scholar 

  • Khan, A. A., Kim, S. J., Paine, D. D., & Cerniglia, C. E. (2002). Classification of a polycyclic aromatic hydrocarbon-metabolizing bacterium, Mycobacterium sp. strain PYR-1, as Mycobacterium vanbaalenii sp. nov. International Journal of Systematic and Evolutionary Microbiology, 52, 1997–2002.

    CAS  Google Scholar 

  • Khersonsky, O., & Tawfik, D. S. (2010). Enzyme promiscuity: A mechanistic and evolutionary perspective. Annual Review of Biochemistry, 79, 471–505.

    Article  CAS  Google Scholar 

  • Kim, S. J., Song, J., Kweon, O., Holland, R. D., Kim, D. W., Kim, J., Yu, L. R., & Cerniglia, C. E. (2012). Functional robustness of a polycyclic aromatic hydrocarbon metabolic network examined in a nidA aromatic ring-hydroxylating oxygenase mutant of Mycobacterium vanbaalenii PYR-1. Applied and Environmental Microbiology, 78, 3715–3723.

    Article  CAS  Google Scholar 

  • Kimura, N., Kitagawa, W., Mori, T., Nakashima, N., Tamura, T., & Kamagata, Y. (2006). Genetic and biochemical characterization of the dioxygenase involved in lateral dioxygenation of dibenzofuran from Rhodococcus opacus strain SAO101. Applied Microbiology and Biotechnology, 73, 474–484.

    Article  CAS  Google Scholar 

  • Kovacic, P., & Somanathan, R. (2014). Nitroaromatic compounds: Environmental toxicity, carcinogenicity, mutagenicity, therapy and mechanism. Journal of Applied Toxicology, 34, 810–824.

    Article  CAS  Google Scholar 

  • Kweon, O., Kim, S. J., Baek, S., Chae, J. C., Adjei, M. D., Baek, D. H., Kim, Y. C., & Cerniglia, C. E. (2008). A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC Biochemistry, 9, 11.

    Article  Google Scholar 

  • Kweon, O., Kim, S. J., Kim, D. W., Kim, J. M., Kim, H. L., Ahn, Y., Sutherland, J. B., & Cerniglia, C. E. (2014). Pleiotropic and epistatic behavior of a ring-hydroxylating oxygenase system in the polycyclic aromatic hydrocarbon metabolic network from Mycobacterium vanbaalenii PYR-1. Journal of Bacteriology, 196, 3503–3515.

    Article  Google Scholar 

  • Lal, R., Pandey, G., Sharma, P., Kumari, K., Malhotra, S., Pandey, R., Raina, V., Kohler, H. P., Holliger, C., Jackson, C., & Oakeshott, J. G. (2010). Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiology and Molecular Biology Reviews, 74, 58–80.

    Article  CAS  Google Scholar 

  • Lessner, D. J., Johnson, G. R., Parales, R. E., Spain, J. C., & Gibson, D. T. (2002). Molecular characterization and substrate specificity of nitrobenzene dioxygenase from Comamonas sp. strain JS765. Applied and Environmental Microbiology, 68, 634–641.

    Article  CAS  Google Scholar 

  • Liu, H., Wang, S. J., Zhang, J. J., Dai, H., Tang, H., & Zhou, N. Y. (2011). Patchwork assembly of nag-like nitroarene dioxygenase genes and the 3-chlorocatechol degradation cluster for evolution of the 2-chloronitrobenzene catabolism pathway in Pseudomonas stutzeri ZWLR2-1. Applied and Environmental Microbiology, 77, 4547–4552.

    Article  CAS  Google Scholar 

  • Maia, K. (2009). Degradation of nitroaromatic compounds: A model to study evolution of metabolic pathways. Molecular Microbiology, 74, 777–781.

    Article  Google Scholar 

  • Martin, F., Malagnoux, L., Violet, F., Jakoncic, J., & Jouanneau, Y. (2013). Diversity and catalytic potential of PAH-specific ring-hydroxylating dioxygenases from a hydrocarbon-contaminated soil. Applied Microbiology and Biotechnology, 97, 5125–5135.

    Article  CAS  Google Scholar 

  • Martinez-Nunez, M. A., Rodriguez-Escamilla, Z., Rodriguez-Vazquez, K., & Perez-Rueda, E. (2017). Tracing the repertoire of promiscuous enzymes along the metabolic pathways in archaeal organisms. Life (Basel), 7, pii: E30.

    Google Scholar 

  • Moody, J. D., Freeman, J. P., Fu, P. P., & Cerniglia, C. E. (2004). Degradation of benzo[a]pyrene by Mycobacterium vanbaalenii PYR-1. Applied and Environmental Microbiology, 70, 340–345.

    Article  CAS  Google Scholar 

  • Nam, J. W., Nojiri, H., Yoshida, T., Habe, H., Yamane, H., & Omori, T. (2001). New classification system for oxygenase components involved in ring-hydroxylating oxygenations. Bioscience, Biotechnology, and Biochemistry, 65, 254–263.

    Article  CAS  Google Scholar 

  • O’Brien, P. J. (2006). Catalytic promiscuity and the divergent evolution of DNA repair enzymes. Chemical Reviews, 106, 720–752.

    Article  Google Scholar 

  • Overwin, H., Gonzalez, M., Mendez, V., Seeger, M., Wray, V., & Hofer, B. (2016). An aryl dioxygenase shows remarkable double dioxygenation capacity for diverse bis-aryl compounds, provided they are carbocyclic. Applied Microbiology and Biotechnology, 100, 8053–8061.

    Article  CAS  Google Scholar 

  • Perry, L. L., & Zylstra, G. J. (2007). Cloning of a gene cluster involved in the catabolism of p-nitrophenol by Arthrobacter sp. strain JS443 and characterization of the p-nitrophenol monooxygenase. Journal of Bacteriology, 189, 7563–7572.

    Article  CAS  Google Scholar 

  • Phale, P. S., Basu, A., Majhi, P. D., Deveryshetty, J., Vamsee-Krishna, C., & Shrivastava, R. (2007). Metabolic diversity in bacterial degradation of aromatic compounds. OMICS, 11, 252–279.

    Article  CAS  Google Scholar 

  • Resnick, S. M., & Gibson, D. T. (1996). Regio- and stereospecific oxidation of fluorene, dibenzofuran, and dibenzothiophene by naphthalene dioxygenase from Pseudomonas sp. strain NCIB 9816-4. Applied and Environmental Microbiology, 62, 4073–4080.

    CAS  Google Scholar 

  • Russell, R. J., Scott, C., Jackson, C. J., Pandey, R., Pandey, G., Taylor, M. C., Coppin, C. W., Liu, J. W., & Oakeshott, J. G. (2011). The evolution of new enzyme function: Lessons from xenobiotic metabolizing bacteria versus insecticide-resistant insects. Evolutionary Applications, 4, 225–248.

    Article  CAS  Google Scholar 

  • Schuler, L., Jouanneau, Y., Chadhain, S. M., Meyer, C., Pouli, M., Zylstra, G. J., Hols, P., & Agathos, S. N. (2009). Characterization of a ring-hydroxylating dioxygenase from phenanthrene-degrading Sphingomonas sp. strain LH128 able to oxidize benz[a]anthracene. Applied Microbiology and Biotechnology, 83, 465–475.

    Article  CAS  Google Scholar 

  • Selvakumaran, S., Kapley, A., Kashyap, S. M., Daginawala, H. F., Kalia, V. C., & Purohit, H. J. (2011). Diversity of aromatic ring-hydroxylating dioxygenase gene in Citrobacter. Bioresource Technology, 102, 4600–4609.

    Article  CAS  Google Scholar 

  • Shahin, M. M. (1987). Relationships between structure and mutagenic activity of environmental chemicals. Mutation Research, 181, 243–256.

    Article  CAS  Google Scholar 

  • Singleton, D. R., Hu, J., & Aitken, M. D. (2012). Heterologous expression of polycyclic aromatic hydrocarbon ring-hydroxylating dioxygenase genes from a novel pyrene-degrading betaproteobacterium. Applied and Environmental Microbiology, 78, 3552–3559.

    Article  CAS  Google Scholar 

  • Srinivasan, B., Marks, H., Mitra, S., Smalley, D. M., & Skolnick, J. (2016). Catalytic and substrate promiscuity: Distinct multiple chemistries catalysed by the phosphatase domain of receptor protein tyrosine phosphatase. The Biochemical Journal, 473, 2165–2177.

    Article  CAS  Google Scholar 

  • Suen, W. C., Haigler, B. E., & Spain, J. C. (1996). 2,4-Dinitrotoluene dioxygenase from Burkholderia sp. strain DNT: Similarity to naphthalene dioxygenase. Journal of Bacteriology, 178, 4926–4934.

    Article  CAS  Google Scholar 

  • Unterlass, J. E., Wood, R. J., Basle, A., Tucker, J., Cano, C., Noble, M. M. E., & Curtin, N. J. (2017). Structural insights into the enzymatic activity and potential substrate promiscuity of human 3-phosphoglycerate dehydrogenase (PHGDH). Oncotarget, 8, 104478–104491.

    Article  Google Scholar 

  • van der Meer, J. R. (1997). Evolution of novel metabolic pathways for the degradation of chloroaromatic compounds. Antonie Van Leeuwenhoek, 71, 159–178.

    Article  Google Scholar 

  • van der Meer, J. R., Werlen, C., Nishino, S. F., & Spain, J. C. (1998). Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Applied and Environmental Microbiology, 64, 4185–4193.

    Google Scholar 

  • Verma, M. K., & Pulicherla, K. K. (2016). Enzyme promiscuity in earthworm serine protease: Substrate versatility and therapeutic potential. Amino Acids, 48, 941–948.

    Article  CAS  Google Scholar 

  • Vikram, S., Pandey, J., Kumar, S., & Raghava, G. P. (2013). Genes involved in degradation of para-nitrophenol are differentially arranged in form of non-contiguous gene clusters in Burkholderia sp. strain SJ98. PLoS One, 8, e84766.

    Article  Google Scholar 

  • Wackett, L. P. (2009). Questioning our perceptions about evolution of biodegradative enzymes. Current Opinion in Microbiology, 12, 244–251.

    Article  CAS  Google Scholar 

  • Werlen, C., Kohler, H. P., & van der Meer, J. R. (1996). The broad substrate chlorobenzene dioxygenase and cis-chlorobenzene dihydrodiol dehydrogenase of Pseudomonas sp. strain P51 are linked evolutionarily to the enzymes for benzene and toluene degradation. The Journal of Biological Chemistry, 271, 4009–4016.

    Article  CAS  Google Scholar 

  • Xu, L., Resing, K., Lawson, S. L., Babbitt, P. C., & Copley, S. D. (1999). Evidence that pcpA encodes 2,6-dichlorohydroquinone dioxygenase, the ring cleavage enzyme required for pentachlorophenol degradation in Sphingomonas chlorophenolica strain ATCC 39723. Biochemistry, 38, 7659–7669.

    Article  CAS  Google Scholar 

  • Yavas, A., & Icgen, B. (2018). Diversity of the aromatic-ring-hydroxylating dioxygenases in the monoaromatic hydrocarbon degraders held by a Common Ancestor. The Bulletin of Environmental Contamination and Toxicology. https://doi.org/10.1007/s00128-018-2350-4

    Article  CAS  Google Scholar 

  • Zafra, G., Taylor, T. D., Absalon, A. E., & Cortes-Espinosa, D. V. (2016). Comparative metagenomic analysis of PAH degradation in soil by a mixed microbial consortium. Journal of Hazardous Materials, 318, 702–710.

    Article  CAS  Google Scholar 

  • Zeng, J., Zhu, Q., Wu, Y., Chen, H., & Lin, X. (2017). Characterization of a polycyclic aromatic ring-hydroxylation dioxygenase from Mycobacterium sp. NJS-P. Chemosphere, 185, 67–74.

    Article  CAS  Google Scholar 

  • Zhang, C., & Anderson, A. J. (2012). Multiplicity of genes for aromatic ring-hydroxylating dioxygenases in Mycobacterium isolate KMS and their regulation. Biodegradation, 23, 585–596.

    Article  CAS  Google Scholar 

  • Zhou, H. W., Guo, C. L., Wong, Y. S., & Tam, N. F. (2006). Genetic diversity of dioxygenase genes in polycyclic aromatic hydrocarbon-degrading bacteria isolated from mangrove sediments. FEMS Microbiology Letters, 262, 148–157.

    Article  CAS  Google Scholar 

  • Zylstra, G. J., & Gibson, D. T. (1991). Aromatic hydrocarbon degradation: A molecular approach. Genetic Engineering (New York), 13, 183–203.

    Article  CAS  Google Scholar 

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Verma, N. et al. (2019). Catalytic Promiscuity of Aromatic Ring-Hydroxylating Dioxygenases and Their Role in the Plasticity of Xenobiotic Compound Degradation. In: Arora, P. (eds) Microbial Metabolism of Xenobiotic Compounds. Microorganisms for Sustainability, vol 10. Springer, Singapore. https://doi.org/10.1007/978-981-13-7462-3_6

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