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http://dx.doi.org/10.7845/kjm.2018.7089

Investigation of biodegradation pathway of dibenzofuran by Novosphingobium pentaromativorans US6-1 via transcriptomic and mass-spectrometric analysis  

Na, Hyeyun (Marine Biotechnology Center, KIOST)
Kwon, KaeKyoung (Marine Biotechnology Center, KIOST)
Publication Information
Korean Journal of Microbiology / v.54, no.1, 2018 , pp. 46-52 More about this Journal
Abstract
Biodegradation pathway of dibenzofuran (DBF) of Novosphingobium pentaromativorans US6-1, a high-molecular-weight polycyclic aromatic hydrocarbons degrading strain, was investigated via analysis of metabolic intermediates and transcriptome. As a result, 3(2H)-benzofuranone, a basic skeleton of the metabolic intermediates produced by lateral dioxygenation process, was detected as an intermediate. RNA-Seq analysis confirmed that most of the expressed genes upon exposure to DBF were related to the lateral degradation pathway. Based on these results, the biodegradation pathway of DBF by N. pentaromativorans US6-1 was proposed.
Keywords
Novosphingobium pentaromativorans US6-1; degradation pathway; dibenzofuran (DBF); metabolite; transcriptome;
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1 Hong, H.B., Nam, I.H., Murugesan, K., Kim, Y.M., and Chang, Y.S. 2004. Biodegradation of dibenzo-p-dioxin, dibenzofuran, and chlorodibenzo-p-dioxins by Pseudomonas veronii PH-03. Biodegradation 15, 303-313.   DOI
2 Jensen, A.M., Finster, K.W., and Karlson, U. 2003. Degradation of carbazole, dibenzothiophene, and dibenzofuran at low temperature by Pseudomonas sp. strain C3211. Environ. Toxicol. Chem. 22, 730-735.   DOI
3 Jin, S., Zhu, T., Xu, X., and Xu, Y. 2006. Biodegradation of dibenzofuran by Janibacter terrae strain XJ-1. Curr. Microbiol. 53, 30-36.   DOI
4 Le, T.T., Murugesan, K., Nam, I.H, Jeon, J.R., and Chang, Y.S. 2013. Degradation of dibenzofuran via multiple dioxygenation by a newly isolated Agrobacterium sp. PH-08. J. Appl. Microbiol. 116, 542-553.
5 Li, Q., Wang, X., Yin, G., Gai, Z., Tang, H., Ma, C., Deng, Z., and Xu, P. 2009. New metabolites in dibenzofuran cometabolic degradation by a biphenyl-cultivated Pseudomonas putida strain B6-2. Environ. Sci. Technol. 43, 8635-8642.   DOI
6 Lyu, Y., Zheng, W., Zheng, T., and Tian, Y. 2014. Biodegradation of polycyclic aromatic hydrocarbons by Novosphingobium pentaromativorans US6-1. PLoS One 9, e101438.   DOI
7 Mandal, P. 2005. Dioxin: a review of its environmental effects and its aryl hydrocarbon receptor biology. J. Comp. Physiol. B. 175, 221-230.   DOI
8 Mohammadi, M. and Sylvestre, M. 2005. Resolving the profile of metabolites generated during oxidation of dibenzofuran and chlorodibenzofurans by the biphenyl catabolic pathway enzymes. Chem. Biol. 7, 835-846.
9 Monna, L., Omori, T., and Kodama, T. 1993. Microbial degradation of dibenzofuran, fluorene, and dibenzo-p-dioxin by Staphylococcus auriculans DBF63. Appl. Environ. Microbiol. 59, 285-289.
10 Pollitt, F. 1999. Polychlorinated dibenzo-p-dioxins and polychlorinated dibenzofurans. Regul. Toxicol. Pharm. 30, S63-S68.   DOI
11 Schecter, A., Birnbaum, L., Ryan, J., and Constable, J. 2006. Dioxins: An overview. Environ. Res. 101, 419-428.   DOI
12 Schmid, A., Rothe, B., Altenbuchner, J., Ludwig, W., and Engesser, K. 1997. Characterization of three distinct extradiol dioxygenases involved in mineralization of dibenzofuran by Terrabacter sp. strain DPO360. J. Bacteriol. 179, 53-62.   DOI
13 Sohn, J.H., Kwon, K.K., Kang, J.H., Jung, H.B., and Kim, S.J. 2004. Novosphingobium pentaromativorans sp. nov., a high-molecular-mass polycyclic aromatic hydrocarbon-degrading bacterium isolated from estuarine sediment. Int. J. Syst. Evol. Microbiol. 54, 1483-1487.
14 Van den Berg, M., De Jongh, J., Poiger, H., and Olson, J.R. 1994. The toxicokinetics and metabolism of polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs) and their relevance for toxicity. Crit. Rev. Toxicol. 24, 1-74.   DOI
15 Xu, P., Yu, B., Li, F.L., Cai, X.F., and Ma, C.Q. 2006. Microbial degradation of sulfur, mitrogen and oxygen heterocycles. Trends Microbiol. 14, 398-405.   DOI
16 WHO. 2010. Preventing disease through healthy environments. exposure to dioxins and dioxin-like substances: a major public health concern. World Health Organization. http://www.who.int/ipcs/features/dioxins.pdf..
17 Wilkes, H., Wittich, R.M., Timmis, K.N., Fortnagel, P., and Francke, W. 1996. Degradation of chlor-inated dibenzofurans and dibenzo-p-dioxins by Sphingomonas sp. strain RW1. Appl. Environ. Microbiol. 62, 367-371.
18 Wittich, R.M., Wilkes, H., Sinnwell, V., Francke, W., and Fortnagel, P. 1992. Metabolism of dibenzo-p-dioxin by Sphingomonas sp. strain RW1. Appl. Environ. Microbiol. 58, 1005-1010.
19 Zhang, Y., Zhu, Y.X., Kwon, K.K., Park, J.H., and Kim, S.J. 2004. Novel method for determining pyrene biodegradation using synchronous fluorimetry. Chemosphere 55, 389-394.   DOI
20 Yun, S.H., Choi, C.W., Lee, Y.G., Kwon, J., Leem, S.H., Chung, Y.H., Kahng, H.Y., Kim, S.J., Kwon, K.K., and Kim, S.I. 2014. Proteomic characterization of plasmid pLA1 for biodegradation of polycyclic aromatic hydrocarbons in the marine bacterium, Novosphingobium pentaromativorans US6-1. PLoS One 9, e90812.   DOI
21 Fortnagel, P., Harms, H., Wittich, R.M., Krohn, S., Meyer, H., Sinnwell, V., Wilkes, H., and Francke, W. 1990. Metabolism of dibenzofuran by Pseudomonas sp. strain HH69 and the mixed culture HH27. Appl. Environ. Microbiol. 56, 1148-1156.
22 Bordajandi, L.R., Gomez, G., Abad, E., Rivera, J., Del Mar Fernandez-Baston, M., Blasco, J., Gonzalez, M.J. 2004. Survey of persistent organochlorine contaminants (PCBs, PCDD/Fs, and PAHs), heavy metals (Cu, Cd, Zn, Pb, and Hg), and arsenic in food samples from Huelva (Spain): levels and health implications. J. Agric. Food Chem. 52, 992-1001.   DOI
23 Chai, B., Tsoi, T.V., Iwai, S., Liu, C., Fish, J.A., Gu, C., Johnson, T.A., Zylstra, G., Teppen, B.J., Li, H., et al. 2016. Sphingomonas wittichii strain RW1 genome-wide gene expression shifts in response to dioxins and clay. PLoS One 11, e0157008.   DOI
24 Chang, Y.S. 2008. Recent developments in microbial biotransformation and biodegradation of dioxins. J. Mol. Microbiol. Biotechnol. 15, 152-171.   DOI
25 Choi, D.H., Kwon, Y.M., Kwon, K.K., and Kim, S.J. 2015. Complete genome sequence of Novosphingobium pentaromativorans US6-$1^T$. Stand. Genomic Sci. 10, 107.   DOI
26 Fiedler, H., Abad, E., van Bavel, B., de Boer, J., Bogdal, C., and Malisch, R. 2013. The need for capacity building and first results for the Stockholm Convention Global Monitoring Plan. Trends Anal. Chem. 46, 72-84.
27 Fukuda, K., Nagata, S., and Taniguchi, H. 2001. Isolation and characterization of dibenzofuran-degrading bacteria. FEMS Microbiol. Lett. 208, 179-185.
28 Hiraishi, A. 2003. Biodiversity of dioxin-degrading microorganisms and potential utilization in bioremediation. Microbes Environ. 18, 105-125.
29 Gai, Z., Yu, B., Li, L., Wang, Y., Ma, C., Feng, J., Deng, Z., and Xu, P. 2007. Cometabolic degradation of dibenzofuran and dibenzothiophene by a newly isolated carbazole degrading Sphingomonas sp. strain. Appl. Environ. Microbiol. 73, 2832-2838.   DOI
30 Hay, A. 1979. Dioxin: the 10-year battle that began with agent orange. Nature 278, 108-109.