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Bacterial Genes of Non-Heme Iron Oxygenases, Which Have a Rieske-Type Cluster, Catalyzing Initial Stages of Degradation of Chlorophenoxyacetic Acids

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Abstract

Hydroxylation of the benzoic ring by non-heme iron oxygenases having a Rieske-type cluster is the key step in the aerobic degradation of chloroaromatic compounds by bacteria. Rieske oxygenases (RO) catalyze the oxidative decarboxylation reaction unique to the enzymes of this family with the formation of corresponding phenolic compounds. This review discusses the general structure, function, and classification of ROs that catalyze the oxidation of chlorophenoxyacetic acids; genes encoding the ROs with their phylogenetic classes are also reviewed.

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References

  1. Burkatskaya, E.I., Ivanova, Z.V., and Lysina, G.G., Meditsinskoe obsledovanie lits, rabotayushchikh s pestitsidami (Medical Examination of Individuals Working with Pesticides), Kiev: Zdorov’e, 1995.

    Google Scholar 

  2. Sokolov, V.E., Klyuev, N.A., Brodskii, E.S., et al., The primary and secondary dioxin pollutions of South Vietnam, Dokl. Biol. Sci., 1996, vol. 351, nos. 1–6, pp. 616–617.

    Google Scholar 

  3. Boronin, A.M. and Tsoi, T.V., Genetic systems of biodegradation: organization and regulation of expression, Genetica (Moscow), 1989, vol. 25, no. 4, pp. 581–594.

    CAS  Google Scholar 

  4. Gibson, D.T. and Parales, R.E., Aromatic hydrocarbon dioxygenases in environmental biotechnology, Curr. Opin. Biotechnol., 2000, vol. 11, pp. 236–243. doi 10.1016/S0958-1669(00)00090-2

    Article  CAS  PubMed  Google Scholar 

  5. Barry, S.M. and Challis, G.L., Mechanism and catalytic diversity of Rieske non-heme iron-dependent oxygenases, ACS Catal., 2013, vol. 3, no. 10, pp. 2362–2370. doi 10.1021/cs400087p

    Article  CAS  Google Scholar 

  6. Shteinman, A.A., Iron-containing oxygenases: structure, mechanism of action and modeling, Usp. Khim., 2008, vol. 77, no. 11, pp. 1013–1035.

    Article  Google Scholar 

  7. Ferraro, D.J., Gakhar, L., and Ramaswamy, S., Rieske business: structure–function of Rieske non-heme oxygenases, Biochem. Biophys. Res. Commun., 2005, vol. 338, no. 1, pp. 175–190. doi 10.1016/j.bbrc.2005. 08.222

    Article  CAS  PubMed  Google Scholar 

  8. Shumkova, E.S. and Plotnikova, E.G., Oligonucleotide primers for the detection of genes encoding large biphenyl 2,3-dioxygenase subunit of bacteria of the order Actinomycetales, Vestn. Permsk. Univ., 2012, no. 1. pp. 34–40.

    Google Scholar 

  9. Danganan, C.E., Ye, R.W., Daubaras, D.L., et al., Nucleotide sequence and functional analysis of the genes encoding 2,4,5-trichlorophenoxyacetic acid oxygenase in Pseudomonas cepacia AC1100, Appl. Environ. Microbiol., 1994, vol. 60, pp. 4100–4106.

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Rice, J.F., Menn, F.-M., Hay, A.G., et al., Natural selection for 2,4,5-trichlorophenoxyacetic acid mineralizing bacteria in agent orange contaminated soil, Biodegradation, 2005, vol. 16, pp. 501–512.

    Article  CAS  PubMed  Google Scholar 

  11. Huong, N.L., Itoh, K., and Suyama, K., Diversity of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading bacteria in Vietnamese soils, Microbes Environ., 2007, vol. 22, pp. 243–256.

    Article  Google Scholar 

  12. Don, R.H. and Weightman, A.J., Transposon mutagenesis and cloning analysis of the pathways for degradation of 2,4-dichlorophenoxyacetic acid and 3-chlorobenzoate in Alcaligenes eutrophus JMP 134 (pJP4), J. Bacteriol., 1985, vol. 161, pp. 85–90.

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Trefault, N., De la Iglesia, R., Molina, A.M., et al., Genetic organization of the catabolic plasmid pJP4 from Ralstonia eutropha JMP134 (pJP4) reveals mechanisms of adaptation to chloroaromatic pollutants and evolution of specialized chloroaromatic degradation pathways, Environ. Microbiol., 2004, vol. 6, no. 7, pp. 655–668.

    Article  CAS  PubMed  Google Scholar 

  14. Kamagata, Y., Fulthorpe, R.R., and Tamura, K., Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria, Appl. Environ. Microbiol., 1997, vol. 63, no. 6, pp. 2266–2272.

    CAS  PubMed  PubMed Central  Google Scholar 

  15. Fulthorpe, R.R., McGowan, C., Maltseva, O.V., et al., 2,4-Dichlorophenoxyacetic acid-degrading bacteria are mosaics of catabolic genes, Appl. Environ. Microbiol., 1995, vol. 61, no. 9, pp. 3274–3281.

    CAS  PubMed  PubMed Central  Google Scholar 

  16. McGowan, C., Fulthorpe, R., Wright, A., and Tiedje, J.M., Evidence for interspecies gene transfer in the evolution of 2,4-dichlorophenoxyacetic acid degraders, Appl. Environ. Microbiol., 1998, vol. 64, no. 10, pp. 4089–4092.

    CAS  PubMed  PubMed Central  Google Scholar 

  17. Ka, J.O., Holben, W.E., and Tiedje, J.M., Genetic and phenotypic diversity of 2,4-dichlorophenoxyacetic acid (2,4-D)-degrading bacteria isolated from 2,4-Dtreated field soils, Appl. Environ. Microbiol., 1994, vol. 60, no. 4, pp. 1106–1115.

    CAS  PubMed  PubMed Central  Google Scholar 

  18. Itoh, K., Tashiro, Y., Uobe, K., et al., Root nodule Bradyrhizobium spp. harbor tfdAα and cadA, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins, Appl. Environ. Microbiol., 2004, vol. 70, no. 4, pp. 2110–2118. doi 10.1128/AEM.70.4.2110-2118.2004

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kilbane, J.J., Chatterjee, D.K., Karns, J.S., et al., Biodegradation of 2,4,5-trichlorophenoxyacetic acid by a pure culture of Pseudomonas cepacia, Appl. Environ. Microbiol., 1982, vol. 44, no. 1, pp. 72–78.

    CAS  PubMed  PubMed Central  Google Scholar 

  20. Xun, L. and Wagnon, K.B., Purification and properties of component B of 2,4,5-trichlorophenoxyacetate oxygenase from Pseudomonas cepacia AC1100, Appl. Environ. Microbiol., 1995, vol. 61, no. 9, pp. 3499–3502.

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Hayashi, S., Sano, T., Suyama, K., and Itoh, K., 2,4-Dichlorophenoxyacetic acid (2,4-D)- and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading gene cluster in the soybean root-nodulating bacterium Bradyrhizobium elkanii USDA94, Microbiol. Res., 2016, vol. 188, pp. 62–71. doi 10.1016/j.micres.2016.04.014

    Article  PubMed  Google Scholar 

  22. Altschul, S.F., Gish, W., Miller, W., et al., Basic local alignment search tool, J. Mol. Biol., 1990, vol. 215, no. 3, pp. 403–410.

    Article  CAS  PubMed  Google Scholar 

  23. Thompson, J.D., Higgins, D.G., and Gibson, T.J., CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice, Nucleic Acids Res., 1994, vol. 22, pp. 4673–4680.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Hall, T.A., BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT, Nucleic Acids Symp. Ser., 1999, vol. 41, pp. 95–98.

    CAS  Google Scholar 

  25. Dumitru, R., Jiang, W.Z., Weeks, D.P., and Wilson, M.A., Crystal structure of dicamba monooxygenase: a Rieske nonheme oxygenase that catalyzes oxidative demethylation, J. Mol. Biol., 2009, vol. 392, no. 2, pp. 498–510. doi 10.1016/j.jmb.2009.07.021

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zharikova, N.V., Markusheva, T.V., Galkin, E.G., et al., Raoutella planticola—a new strain degrader of 2,4,5-trichlorophenoxyacetic acid, Prikl. Biokhim. Mikrobiol., 2006, vol. 42, no. 3, pp. 292–297.

    CAS  PubMed  Google Scholar 

  27. Zharikova, N.V., Zhurenko, E.Yu., Korobov, V.V., et al., Biodiversity of bacteria–degraders of chlorinated phenoxy acids, Vestn. Orenb. Gos. Univ., 2009, no. 6 (112), pp. 121–123.

    Google Scholar 

  28. Zharikova, N.V., Zhurenko, E.Yu., Korobov, V.V., et al., Characterization of the bacterial consortium degrading 2,4,5-trichlorophenoxyacetic acid, Vestn. Ural. Med. Akad. Nauki, 2011, no. 4-1, p. 173.

    Google Scholar 

  29. Zharikova, N.V., Iasakov, T.R., Bumazhkin, B.K., et al., Isolation and sequence analysis of pCS36-4CPA, a small plasmid from Citrobacter sp. 36-4CPA, Saudi J. Biol. Sci., 2016. doi 10.1016/j.sjbs.2016.02.014

    Google Scholar 

  30. Kitagawa, W., Takami, S., Miyauchi, K., et al., Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment, J. Bacteriol., 2002, vol. 184, pp. 509–518.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  31. Shimojo, M., Kawakami, M., and Amada, K., Analysis of genes encoding the 2,4-dichlorophenoxyacetic aciddegrading enzyme from Sphingomonas agrestis 58-1, J. Biosci. Bioeng., 2009, vol. 108, no. 1, pp. 56–59. doi 10.1016/j.jbiosc.2009.02.018

    Article  CAS  PubMed  Google Scholar 

  32. Nielsen, T.K., Xu, Z., Gözdereliler, E., et al., Novel insight into the genetic context of the cadAB genes from a 4-chloro-2-methylphenoxyacetic acid-degrading Sphingomonas, PLoS One, 2013, vol. 8, no. 12. doi 10.1371/journal.pone.0083346

    Google Scholar 

  33. Saitou, N. and Nei, M., The neighbor-joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 1987, vol. 4, pp. 406–425.

    CAS  PubMed  Google Scholar 

  34. Kumar, S., Stecher, G., and Tamura, K., MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets, Mol. Biol. Evol., 2016, vol. 33, pp. 1870–1874.

    Article  CAS  PubMed  Google Scholar 

  35. Tamura, K., Nei, M., and Kumar, S., Prospects for inferring very large phylogenies by using the neighborjoining method, Proc. Natl. Acad. Sci. U.S.A., 2004, vol. 101, pp. 11030–11035.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Felsenstein, J., Confidence limits on phylogenies: an approach using the bootstrap, Evolution, 1985, vol. 39, pp. 783–791.

    Article  PubMed  Google Scholar 

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Authors and Affiliations

  1. Ufa Institute of Biology, Russian Academy of Sciences, Ufa, 450054, Russia

    N. V. Zharikova, T. R. Iasakov, E. I. Zhurenko, V. V. Korobov & T. V. Markusheva

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  1. N. V. Zharikova
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  2. T. R. Iasakov
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  3. E. I. Zhurenko
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  4. V. V. Korobov
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  5. T. V. Markusheva
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Correspondence to N. V. Zharikova.

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Original Russian Text © N.V. Zharikova, T.R. Iasakov, E.I. Zhurenko, V.V. Korobov, T.V. Markusheva, 2018, published in Genetika, 2018, Vol. 54, No. 3, pp. 292–305.

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Zharikova, N.V., Iasakov, T.R., Zhurenko, E.I. et al. Bacterial Genes of Non-Heme Iron Oxygenases, Which Have a Rieske-Type Cluster, Catalyzing Initial Stages of Degradation of Chlorophenoxyacetic Acids. Russ J Genet 54, 284–295 (2018). https://doi.org/10.1134/S1022795418030171

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  • DOI: https://doi.org/10.1134/S1022795418030171

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