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Chapter 5.1.1 : Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders

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Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, Page 1 of 2

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Abstract:

A large number of microorganisms capable of degrading xenobiotic aromatic compounds has been isolated, and applications of them for bioremediation to remove the contamination by these compounds have been studied. Recently, genome sequences of dioxin-like compound-degrading bacteria have been determined, including degraders of biphenyl, dibenzofuran, dibenzo-p-dioxin, and their chlorinated derivatives such as Burkholderia xenovorans LB400, Rhodococcus jostii RHA1, and Sphingomonas wittichii RW1. Their key enzymes and pathways to metabolize these compounds have been elucidated, and molecular mechanisms to regulate their expression have been analyzed in detail. Some of their degradative genes are located on mobile genetic elements, such as a large plasmid and an integrative and conjugative element, which could have an important role for distribution of their degradative genes. Comparisons of crystal structures of the degrading enzymes showed their putative evolutional relationships. Genome-wide analyses including transcriptome, proteome, and mutagenesis have revealed how the degraders expressed their degradative genes, how they survived in different environments, and what the key environmental factors to express their degrading ability. Combination of phytoremediation and bioaugmentation treatments was shown to be efficient for decontamination. These aspects could be essential to improve decontamination by bioremediation.

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1
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FIGURE 1

Proposed metabolic pathways for dioxin-like compounds, biphenyl, dibenzofuran, and dibenzo--dioxin. The intermediate product in brackets is unstable and spontaneously converted to the lower compound. CAT and HPD indicates catechol and 2-hydroxypenta-2,4-dienoic acid, respectively. doi: 10.1128/9781555818821.ch5.1.1.f1

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1
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References

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1. Ahmed M, Focht DD. 1973. Degradation of polychlorinated biphenyls by two species of Achromobacter. Can J Microbiol 19 : 47 52.[PubMed][CrossRef]
2. Pieper DH. 2005. Aerobic degradation of polychlorinated biphenyls. Appl Microbiol Biotechnol 67 : 170 191.[PubMed][CrossRef]
3. Chain PS, Denef VJ, Konstantinidis KT, Vergez LM, Agulló L, Reyes VL, Hauser L, Córdova M, Gómez L, González M, Land M, Lao V, Larimer F, LiPuma JJ, Mahenthiralingam E, Malfatti SA, Marx CJ, Parnell JJ, Ramette A, Richardson P, Seeger M, Smith D, Spilker T, Sul WJ, Tsoi TV, Ulrich LE, Zhulin IB, Tiedje JM. 2006. Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome shaped for versatility. Proc Natl Acad Sci USA 103 : 15280 15287.[PubMed][CrossRef]
4. McLeod MP, Warren RL, Hsiao WW, Araki N, Myhre M, Fernandes C, Miyazawa D, Wong W, Lillquist AL, Wang D, Dosanjh M, Hara H, Petrescu A, Morin RD, Yang G, Stott JM, Schein JE, Shin H, Smailus D, Siddiqui AS, Marra MA, Jones SJ, Holt R, Brinkman FS, Miyauchi K, Fukuda M, Davies JE, Mohn WW, Eltis LD. 2006. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci USA 103 : 15582 15587.[PubMed][CrossRef]
5. Yang X, Xue R, Shen C, Li S, Gao C, Wang Q, Zhao X. 2011. Genome sequence of Rhodococcus sp. strain R04, a polychlorinated-biphenyl biodegrader. J Bacteriol 193 : 5032 5033.[PubMed][CrossRef]
6. Tang H, Yu H, Li Q, Wang X, Gai Z, Yin G, Su F, Tao F, Ma C, Xu P. 2011. Genome sequence of Pseudomonas putida strain B6-2, a superdegrader of polycyclic aromatic hydrocarbons and dioxin-like compounds. J Bacteriol 193 : 6789 6790.[PubMed][CrossRef]
7. Triscari-Barberi T, Simone D, Calabrese FM, Attimonelli M, Hahn KR, Amoako KK, Turner RJ, Fedi S, Zannoni D. 2012. Genome sequence of the polychlorinated-biphenyl degrader Pseudomonas pseudoalcaligenes KF707. J Bacteriol 194 : 4426 4427.[PubMed][CrossRef]
8. Ohtsubo Y, Maruyama F, Mitsui H, Nagata Y, Tsuda M. 2012. Complete genome sequence of Acidovorax sp. strain KKS102, a polychlorinated-biphenyl degrader. J Bacteriol 194 : 6970 6971.[PubMed][CrossRef]
9. Miller TR, Delcher AL, Salzberg SL, Saunders E, Detter JC, Halden RU. 2010. Genome sequence of the dioxin-mineralizing bacterium Sphingomonas wittichii RW1. J Bacteriol 192 : 6101 6102.[PubMed][CrossRef]
10. Bopp LH. 1986. Degradation of highly chlorinated PCBs by Pseudomonas strain LB400. J Ind Microbiol 1 : 23 29.[CrossRef]
11. Harwood CS, Parales RE. 1996. The beta-ketoadipate pathway and the biology of self-identity. Ann Rev Microbiol 50 : 553 590.[CrossRef]
12. Gescher J, Zaar A, Mohamed M, Schägger H, Fuchs G. 2002. Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. J Bacteriol 184 : 6301 6315.[PubMed][CrossRef]
13. Denef VJ, Klappenbach JA, Patrauchan MA, Florizone C, Rodrigues JL, Tsoi TV, Verstraete W, Eltis LD, Tiedje JM. 2006. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl Environ Microbiol 72 : 585 595.[PubMed][CrossRef]
14. Denef VJ, Park J, Tsoi TV, Rouillard JM, Zhang H, Wibbenmeyer JA, Verstraete W, Gulari E, Hashsham SA, Tiedje JM. 2004. Biphenyl and benzoate metabolism in a genomic context: outlining genome-wide metabolic networks in Burkholderia xenovorans LB400. Appl Environ Microbiol 70 : 4961 4970.[PubMed][CrossRef]
15. Denef VJ, Patrauchan MA, Florizone C, Park J, Tsoi TV, Verstraete W, Tiedje JM, Eltis LD. 2005. Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400. J Bacteriol 187 : 7996 8005.[PubMed][CrossRef]
16. Pérez-Martín J, De Lorenzo V. 1997. Coactivation in vitro of the sigma54-dependent promoter Pu of the TOL plasmid of Pseudomonas putida by HU and the mammalian HMG-1 protein. J Bacteriol 179 : 2757 2760.[PubMed]
17. Patrauchan MA, Parnell JJ, McLeod MP, Florizone C, Tiedje JM, Eltis LD. 2011. Genomic analysis of the phenylacetyl-CoA pathway in Burkholderia xenovorans LB400. Arch Microbiol 193 : 641 650.[PubMed][CrossRef]
18. Méndez V, Agulló L, González M, Seeger M. 2011. The homogentisate and homoprotocatechuate central pathways are involved in 3- and 4-hydroxyphenylacetate degradation by Burkholderia xenovorans LB400. PLoS One 6 : e17583.[PubMed][CrossRef]
19. Seto M, Kimbara K, Shimura M, Hatta T, Fukuda M, Yano K. 1995. A novel transformation of polychlorinated biphenyls by Rhodococcus sp. strain RHA1. Appl Environ Microbiol 61 : 3353 3358.[PubMed]
20. Shimizu S, Kobayashi H, Masai E, Fukuda M. 2001. Characterization of the 450-kb linear plasmid in a polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl Environ Microbiol 67 : 2021 2028.[PubMed][CrossRef]
21. Okamoto S, Eltis LD. 2007. Purification and characterization of a novel nitrile hydratase from Rhodococcus sp. RHA1. Mol Microbiol 65 : 828 838.[PubMed][CrossRef]
22. Van der Geize R, Yam K, Heuser T, Wilbrink MH, Hara H, Anderton MC, Sim E, Dijkhuizen L, Davies JE, Mohn WW, Eltis LD. 2007. A gene cluster encoding cholesterol catabolism in a soil actinomycete provides insight into Mycobacterium tuberculosis survival in macrophages. Proc Natl Acad Sci USA 104 : 1947 1952.[PubMed][CrossRef]
23. Patrauchan MA, Florizone C, Eapen S, Gómez-Gil L, Sethuraman B, Fukuda M, Davies J, Mohn WW, Eltis LD. 2008. Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1. J Bacteriol 190 : 37 47.[PubMed][CrossRef]
24. Chen HP, Chow M, Liu CC, Lau A, Liu J, Eltis LD. 2012. Vanillin catabolism in Rhodococcus jostii RHA1. Appl Environ Microbiol 78 : 586 588.[PubMed][CrossRef]
25. Mathieu J, Schloendorn J, Rittmann BE, Alvarez PJ. 2008. Microbial degradation of 7-ketocholesterol. Biodegradation 19 : 807 813.[PubMed][CrossRef]
26. Mohn WW, Wilbrink MH, Casabon I, Stewart GR, Liu J, van der Geize R, Eltis LD. 2012. Gene cluster encoding cholate catabolism in Rhodococcus spp. J Bacteriol 194 : 6712 6719.[PubMed][CrossRef]
27. Ahmad M, Roberts JN, Hardiman EM, Singh R, Eltis LD, Bugg TD. 2011. Identification of DypB from Rhodococcus jostii RHA1 as a lignin peroxidase. Biochemistry 50 : 5096 5107.[PubMed][CrossRef]
28. Wittich RM, Wilkes H, Sinnwell V, Francke W, Fortnagel P. 1992. Metabolism of dibenzo- p-dioxin by Sphingomonas sp. strain RW1. Appl Environ Microbiol 58 : 1005 1010.[PubMed]
29. Wilkes H, Wittich R, Timmis KN, Fortnagel P, Francke W. 1996. Degradation of chlorinated dibenzofurans and dibenzo- p-dioxins by Sphingomonas sp. strain RW1. Appl Environ Microbiol 62 : 367 371.[PubMed]
30. Hong HB, Chang YS, Nam IH, Fortnagel P, Schmidt S. 2002. Biotransformation of 2,7-dichloro- and 1,2,3,4-tetrachlorodibenzo- p-dioxin by Sphingomonas wittichii RW1. Appl Environ Microbiol 68 : 2584 2588.[PubMed][CrossRef]
31. Halden RU, Colquhoun DR, Wisniewski ES. 2005. Identification and phenotypic characterization of Sphingomonas wittichii strain RW1 by peptide mass fingerprinting using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Appl Environ Microbiol 71 : 2442 2451.[PubMed][CrossRef]
32. Nam IH, Kim YM, Schmidt S, Chang YS. 2006. Biotransformation of 1,2,3-tri- and 1,2,3,4,7,8-hexachlorodibenzo- p- dioxin by Sphingomonas wittichii strain RW1. Appl Environ Microbiol 72 : 112 116.[PubMed][CrossRef]
33. Armengaud J, Happe B, Timmis KN. 1998. Genetic analysis of dioxin dioxygenase of Sphingomonas sp. strain RW1: catabolic genes dispersed on the genome. J Bacteriol 180 : 3954 3966.[PubMed]
34. Kimbara K, Hashimoto T, Fukuda M, Koana T, Takagi M, Oishi M, Yano K. 1988. Isolation and characterization of a mixed culture that degrades polychlorinated biphenyls. Agric Biol Chem 52 : 2885 2891.[CrossRef]
35. Kimbara K, Hashimoto T, Fukuda M, Koana T, Takagi M, Oishi M, Yano K. 1989. Cloning and sequencing of two tandem genes involved in degradation of 2,3-dihydroxybiphenyl to benzoic acid in the polychlorinated biphenyl-degrading soil bacterium Pseudomonas sp. strain KKS102. J Bacteriol 171 : 2740 2747.[PubMed]
36. Fukuda M, Yasukochi Y, Kikuchi Y, Nagata Y, Kimbara K, Horiuchi H, Takagi M, Yano K. 1994. Identification of the bphA and bphB genes of Pseudomonas sp. strains KKS102 involved in degradation of biphenyl and polychlorinated biphenyls. Biochem Biophys Res Commun 202 : 850 856.[PubMed][CrossRef]
37. Kikuchi Y, Yasukochi Y, Nagata Y, Fukuda M, Takagi M. 1994. Nucleotide sequence and functional analysis of the meta-cleavage pathway involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102. J Bacteriol 176 : 4269 4276.[PubMed]
38. Kikuchi Y, Nagata Y, Hinata M, Kimbara K, Fukuda M, Yano K, Takagi M. 1994. Identification of the bphA4 gene encoding ferredoxin reductase involved in biphenyl and polychlorinated biphenyl degradation in Pseudomonas sp. strain KKS102. J Bacteriol 176 : 1689 1694.[PubMed]
39. Ohtsubo Y, Nagata Y, Kimbara K, Takagi M, Ohta A. 2000. Expression of the bph genes involved in biphenyl/PCB degradation in Pseudomonas sp. KKS102 induced by the biphenyl degradation intermediate, 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid. Gene 256 : 223 228.[PubMed][CrossRef]
40. Ohtsubo Y, Delawary M, Kimbara K, Takagi M, Ohta A, Nagata Y. 2001. BphS, a key transcriptional regulator of bph genes involved in polychlorinated biphenyl/biphenyl degradation in Pseudomonas sp. KKS102. J Biol Chem 276 : 36146 36154.[PubMed][CrossRef]
41. Ohtsubo Y, Goto H, Nagata Y, Kudo T, Tsuda M. 2006. Identification of a response regulator gene for catabolite control from a PCB-degrading beta-proteobacteria, Acidovorax sp. KKS102. Mol Microbiol 60 : 1563 1575.[PubMed][CrossRef]
42. Ohtsubo Y, Ishibashi Y, Naganawa H, Hirokawa S, Atobe S, Nagata Y, Tsuda M. 2012. Conjugal transfer of polychlorinated biphenyl/biphenyl degradation genes in Acidovorax sp. strain KKS102, which are located on an integrative and conjugative element. J Bacteriol 194 : 4237 4248.[PubMed][CrossRef]
43. Toussaint A, Merlin C, Monchy S, Benotmane MA, Leplae R, Mergeay M, Springael D. 2003. The biphenyl- and 4-chlorobiphenyl-catabolic transposon Tn 4371, a member of a new family of genomic islands related to IncP and Ti plasmids. Appl Environ Microbiol 69 : 4837 4845.[PubMed][CrossRef]
44. Shintani M, Nojiri H,. 2013. Mobile genetic elements (MGEs) carrying catabolic genes, p 167 214. In Malik A,, Grohmann E,, Alves M (eds), Management of Microbial Resources in the Environment. Springer, Dordrecht.
45. Furukawa K, Miyazaki T. 1986. Cloning of a gene cluster encoding biphenyl and chlorobiphenyl degradation in Pseudomonas pseudoalcaligenes. J Bacteriol 166 : 392 398.[PubMed]
46. Taira K, Hirose J, Hayashida S, Furukawa K. 1992. Analysis of bph operon from the polychlorinated biphenyl-degrading strain of Pseudomonas pseudoalcaligenes KF707. J Biol Chem 267 : 4844 4853.[PubMed]
47. Fujihara H, Yoshida H, Matsunaga T, Goto M, Furukawa K. 2006. Cross-regulation of biphenyl- and salicylate-catabolic genes by two regulatory systems in Pseudomonas pseudoalcaligenes KF707. J Bacteriol 188 : 4690 4697.[PubMed][CrossRef]
48. Seo J, Kang SI, Kim M, Han J, Hur HG. 2011. Flavonoids biotransformation by bacterial non-heme dioxygenases, biphenyl and naphthalene dioxygenase. Appl Microbiol Biotechnol 91 : 219 228.[PubMed][CrossRef]
49. Tremaroli V, Vacchi Suzzi C, Fedi S, Ceri H, Zannoni D, Turner RJ. 2010. Tolerance of Pseudomonas pseudoalcaligenes KF707 to metals, polychlorobiphenyls and chlorobenzoates: effects on chemotaxis-, biofilm- and planktonic-grown cells. FEMS Microbiol Ecol 74 : 291 301.[PubMed][CrossRef]
50. Simura M, Koana T, Fukuda M, Kimbara K. 1996. Complete degradation of polychlorinated biphenyls by a combination of ultraviolet and biological treatments. J Ferment Bioeng 81 : 573 576.[CrossRef]
51. Hiraoka Y, Yamada T, Tone K, Futaesaku Y, Kimbara K. 2002. Flow cytometry analysis of changes in the DNA content of the polychlorinated biphenyl degrader Comamonas testosteroni TK102: effect of metabolites on cell-cell separation. Appl Environ Microbiol 68 : 5104 5112.[PubMed][CrossRef]
52. Fukuda K, Hosoyama A, Tsuchikane K, Ohji S, Yamazoe A, Fujita N, Shintani M, Kimbara K. Genome Announc. 2014 Sep 11;2(5). pii: e00865-14. doi: 10.1128/genomeA.00865-14.
53. Shimura M, Mukerjee-Dhar G, Kimbara K, Nagato H, Kiyohara H, Hatta T. 1999. Isolation and characterization of a thermophilic Bacillus sp. JF8 capable of degrading polychlorinated biphenyls and naphthalene. FEMS Microbiol Lett 178 : 87 93.[PubMed][CrossRef]
54. Mukerjee-Dhar G, Shimura M, Miyazawa D, Kimbara K, Hatta T. 2005. bph genes of the thermophilic PCB degrader, Bacillus sp. JF8: characterization of the divergent ring-hydroxylating dioxygenase and hydrolase genes upstream of the Mn-dependent BphC. Microbiology 151 : 4139 4151.[PubMed][CrossRef]
55. Shintani M, Ohtsubo Y, Fukuda K, Hosoyama A, Ohji S, Yamazoe A, Fujita N, Nagata Y, Tsuda M, Hatta T, Kimbara K. Genome Announc. 2014 Jan 23;2(1). pii: e01213-13. doi: 10.1128/genomeA.01213-13.
56. Shintani M, Takahashi Y, Yamane H, Nojiri H. 2010. The behavior and significance of degradative plasmids belonging to Inc groups in Pseudomonas within natural environments and microcosms. Microb Environ 25 : 253 265.[CrossRef]
57. Romine MF, Stillwell LC, Wong KK, Thurston SJ, Sisk EC, Sensen C, Gaasterland T, Fredrickson JK, Saffer JD. 1999. Complete sequence of a 184-kilobase catabolic plasmid from Sphingomonas aromaticivorans F199. J Bacteriol 181 : 1585 1602.[PubMed]
58. Stillwell LC, Thurston SJ, Schneider RP, Romine MF, Fredrickson JK, Saffer JD. 1995. Physical mapping and characterization of a catabolic plasmid from the deep-subsurface bacterium Sphingomonas sp. strain F199. J Bacteriol 177 : 4537 4539.[PubMed]
59. Lloyd-Jones G, de Jong C, Ogden R, Duetz W, Williams P. 1994. Recombination of the bph (biphenyl) catabolic genes from plasmid pWW100 and their deletion during growth on benzoate. Appl Environ Microbiol 60 : 691 696.[PubMed]
60. Kosono S, Maeda M, Fuji F, Arai H, Kudo T. 1997. Three of the seven bphC genes of Rhodococcus erythropolis TA421, isolated from a termite ecosystem, are located on an indigenous plasmid associated with biphenyl degradation. Appl Environ Microbiol 63 : 3282 3285.[PubMed]
61. Masai E, Sugiyama K, Iwashita N, Shimizu S, Hauschild JE, Hatta T, Kimbara K, Yano K, Fukuda M. 1997. The bphDEF meta-cleavage pathway genes involved in biphenyl/polychlorinated biphenyl degradation are located on a linear plasmid and separated from the initial bphACB genes in Rhodococcus sp. strain RHA1. Gene 187 : 141 149.[PubMed][CrossRef]
62. Taguchi K, Motoyama M, Kudo T. 2004. Multiplicity of 2,3-dihydroxybiphenyl dioxygenase genes in the Gram-positive polychlorinated biphenyl degrading bacterium Rhodococcus rhodochrous K37. Biosci Biotechnol Biochem 68 : 787 795.[PubMed][CrossRef]
63. Basta T, Keck A, Klein J, Stolz A. 2004. Detection and characterization of conjugative degradative plasmids in xenobiotic-degrading Sphingomonas strains. J Bacteriol 186 : 3862 3872.[PubMed][CrossRef]
64. Miyauchi K, Sukda P, Nishida T, Ito E, Matsumoto Y, Masai E, Fukuda M. 2008. Isolation of dibenzofuran-degrading bacterium, Nocardioides sp. DF412, and characterization of its dibenzofuran degradation genes. J Biosci Bioeng 105 : 628 635.[PubMed][CrossRef]
65. Peng P, Yang H, Jia R, Li L. 2013. Biodegradation of dioxin by a newly isolated Rhodococcus sp. with the involvement of self-transmissible plasmids. Appl Microbiol Biotechnol 97 : 5585 5595.[PubMed][CrossRef]
66. Nojiri H, Kamakura M, Urata M, Tanaka T, Chung JS, Takemura T, Yoshida T, Habe H, Omori T. 2002. Dioxin catabolic genes are dispersed on the Terrabacter sp. DBF63 genome. Biochem Biophys Res Commun 296 : 233 240.[PubMed][CrossRef]
67. Habe H, Chung JS, Ishida A, Kasuga K, Ide K, Takemura T, Nojiri H, Yamane H, Omori T. 2005. The fluorene catabolic linear plasmid in Terrabacter sp. strain DBF63 carries the beta-ketoadipate pathway genes, pcaRHGBDCFIJ, also found in proteobacteria. Microbiology 151 : 3713 3722.[PubMed][CrossRef]
68. Park D, Chae J, Kim Y, Iida T, Kudo T, Kim C. 2002. Chloroplast-type ferredoxin involved in reactivation of catechol 2,3-dioxygenase from Pseudomonas sp. S 47. J Biochem Mol Biol 35 : 432 436.[PubMed][CrossRef]
69. Springael D, Kreps S, Mergeay M. 1993. Identification of a catabolic transposon, Tn 4371, carrying biphenyl and 4-chlorobiphenyl degradation genes in Alcaligenes eutrophus A5. J Bacteriol 175 : 1674 1681.[PubMed]
70. Merlin C, Springael D, Toussaint A. 1999. Tn 4371: a modular structure encoding a phage-like integrase, a Pseudomonas-like catabolic pathway, and RP4/Ti-like transfer functions. Plasmid 41 : 40 54.[PubMed][CrossRef]
71. Nishi A, Tominaga K, Furukawa K. 2000. A 90-kilobase conjugative chromosomal element coding for biphenyl and salicylate catabolism in Pseudomonas putida KF715. J Bacteriol 182 : 1949 1955.[PubMed][CrossRef]
72. Kimura N, Kamagata Y. 2009. Impact of dibenzofuran/dibenzo- p-dioxin amendment on bacterial community from forest soil and ring-hydroxylating dioxygenase gene populations. Appl Microbiol Biotechnol 84 : 365 373.[PubMed][CrossRef]
73. Gibson DT, Cruden DL, Haddock JD, Zylstra GJ, Brand JM. 1993. Oxidation of polychlorinated biphenyls by Pseudomonas sp. strain LB400 and Pseudomonas pseudoalcaligenes KF707. J Bacteriol 175 : 4561 4564.[PubMed]
74. 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.[PubMed]
75. Mondello FJ, Turcich MP, Lobos JH, Erickson BD. 1997. Identification and modification of biphenyl dioxygenase sequences that determine the specificity of polychlorinated biphenyl degradation. Appl Environ Microbiol 63 : 3096 3103.[PubMed]
76. Kimura N, Nishi A, Goto M, Furukawa K. 1997. Functional analyses of a variety of chimeric dioxygenases constructed from two biphenyl dioxygenases that are similar structurally but different functionally. J Bacteriol 179 : 3936 3943.[PubMed]
77. Suenaga H, Watanabe T, Sato M, Furukawa K. 2002. Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J Bacteriol 184 : 3682 3688.[PubMed][CrossRef]
78. Furusawa Y, Nagarajan V, Tanokura M, Masai E, Fukuda M, Senda T. 2004. Crystal structure of the terminal oxygenase component of biphenyl dioxygenase derived from Rhodococcus sp. strain RHA1. J Mol Biol 342 : 1041 1052.[PubMed][CrossRef]
79. Kumar P, Mohammadi M, Viger JF, Barriault D, Gomez-Gil L, Eltis LD, Bolin JT, Sylvestre M. 2011. Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution. J Mol Biol 405 : 531 547.[PubMed][CrossRef]
80. Gómez-Gil L, Kumar P, Barriault D, Bolin JT, Sylvestre M, Eltis LD. 2007. Characterization of biphenyl dioxygenase of Pandoraea pnomenusa B-356 as a potent polychlorinated biphenyl-degrading enzyme. J Bacteriol 189 : 5705 5715.[PubMed][CrossRef]
81. L'Abbée JB, Tu Y, Barriault D, Sylvestre M. 2011. Insight into the metabolism of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by biphenyl dioxygenases. Arch Biochem Biophys 516 : 35 44.[PubMed][CrossRef]
82. Ahmad D, Sylvestre M, Sondossi M, Massé R. 1991. Bioconversion of 2-hydroxy-6-oxo-6-(4′-chlorophenyl)hexa-2,4-dienoic acid, the meta-cleavage product of 4-chlorobiphenyl. J Gen Microbiol 137 : 1375 1385.[PubMed][CrossRef]
83. Ahmad D, Massé R, Sylvestre M. 1990. Cloning and expression of genes involved in 4-chlorobiphenyl transformation by Pseudomonas testosteroni: homology to polychlorobiphenyl-degrading genes in other bacteria. Gene 86 : 53 61.[PubMed][CrossRef]
84. Pham TT, Tu Y, Sylvestre M. 2012. Remarkable ability of Pandoraea pnomenusa B356 biphenyl dioxygenase to metabolize simple flavonoids. Appl Environ Microbiol 78 : 3560 3570.[PubMed][CrossRef]
85. Pham TT, Sylvestre M. 2013. Has the bacterial biphenyl catabolic pathway evolved primarily to degrade biphenyl? The diphenylmethane case. J Bacteriol 195 : 3563 3574.[PubMed][CrossRef]
86. Colbert CL, Agar NY, Kumar P, Chakko MN, Sinha SC, Powlowski JB, Eltis LD, Bolin JT. 2013. Structural characterization of Pandoraea pnomenusa B-356 biphenyl dioxygenase reveals features of potent polychlorinated biphenyl-degrading enzymes. PLoS One 8 : e52550.[PubMed][CrossRef]
87. Patrauchan MA, Miyazawa D, LeBlanc JC, Aiga C, Florizone C, Dosanjh M, Davies J, Eltis LD, Mohn WW. 2012. Proteomic analysis of survival of Rhodococcus jostii RHA1 during carbon starvation. Appl Environ Microbiol 78 : 6714 6725.[PubMed][CrossRef]
88. LeBlanc JC, Gonçalves ER, Mohn WW. 2008. Global response to desiccation stress in the soil actinomycete Rhodococcus jostii RHA1. Appl Environ Microbiol 74 : 2627 2636.[PubMed][CrossRef]
89. Iino T, Wang Y, Miyauchi K, Kasai D, Masai E, Fujii T, Ogawa N, Fukuda M. 2012. Specific gene responses of Rhodococcus jostii RHA1 during growth in soil. Appl Environ Microbiol 78 : 6954 6962.[PubMed][CrossRef]
90. Parnell JJ, Denef VJ, Park J, Tsoi T, Tiedje JM. 2010. Environmentally relevant parameters affecting PCB degradation: carbon source- and growth phase-mitigated effects of the expression of the biphenyl pathway and associated genes in Burkholderia xenovorans LB400. Biodegradation 21 : 147 156.[PubMed][CrossRef]
91. Marx CJ, Miller JA, Chistoserdova L, Lidstrom ME. 2004. Multiple formaldehyde oxidation/detoxification pathways in Burkholderia fungorum LB400. J Bacteriol 186 : 2173 2178.[PubMed][CrossRef]
92. Parnell JJ, Park J, Denef V, Tsoi T, Hashsham S, Quensen J, Tiedje JM. 2006. Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress. Appl Environ Microbiol 72 : 6607 6614.[PubMed][CrossRef]
93. Johnson DR, Coronado E, Moreno-Forero SK, Heipieper HJ, van der Meer JR. 2011. Transcriptome and membrane fatty acid analyses reveal different strategies for responding to permeating and non-permeating solutes in the bacterium Sphingomonas wittichii. BMC Microbiol 11 : 250.[PubMed][CrossRef]
94. Coronado E, Roggo C, Johnson DR, van der Meer JR. 2012. Genome-wide analysis of salicylate and dibenzofuran metabolism in Sphingomonas wittichii RW1. Front Microbiol 3 : 300.[PubMed][CrossRef]
95. Roggo C, Coronado E, Moreno-Forero SK, Harshman K, Weber J, van der Meer JR. 2013. Genome-wide transposon insertion scanning of environmental survival functions in the polycyclic aromatic hydrocarbon degrading bacterium Sphingomonas wittichii RW1. Environ Microbiol 15 : 2681 2695.[PubMed]
96. Colquhoun DR, Hartmann EM, Halden RU. 2012. Proteomic profiling of the dioxin-degrading bacterium Sphingomonas wittichii RW1. J Biomed Biotechnol 2012 : 408690.[PubMed][CrossRef]
97. Tehrani R, Van Aken B. 2013. Hydroxylated polychlorinated biphenyls in the environment: sources, fate, and toxicities. Environ Sci Pollut Res Int 21 : 6334 6335.[PubMed][CrossRef]
98. Tehrani R, Lyv MM, Van Aken B. 2013. Transformation of hydroxylated derivatives of 2,5-dichlorobiphenyl and 2,4,6-trichlorobiphenyl by Burkholderia xenovorans LB400. Environ Sci Pollut Res Int 21 : 6346 6353.[PubMed][CrossRef]
99. Shimomura Y, Ohno R, Kawai F, Kimbara K. 2006. Method for assessment of viability and morphological changes of bacteria in the early stage of colony formation on a simulated natural environment. Appl Environ Microbiol 72 : 5037 5042.[PubMed][CrossRef]
100. Yamada T, Shimomura Y, Hiraoka Y, Kimbara K. 2006. Oxidative stress by biphenyl metabolites induces inhibition of bacterial cell separation. Appl Microbiol Biotechnol 73 : 452 457.[PubMed][CrossRef]
101. Ponce BL, Latorre VK, González M, Seeger M. 2011. Antioxidant compounds improved PCB-degradation by Burkholderia xenovorans strain LB400. Enzyme Microb Technol 49 : 509 516.[PubMed][CrossRef]
102. Uhlík O, Jecná K, Leigh MB, Macková M, Macek T. 2009. DNA-based stable isotope probing: a link between community structure and function. Sci Total Environ 407 : 3611 3619.[PubMed][CrossRef]
103. Uhlik O, Strejcek M, Junkova P, Sanda M, Hroudova M, Vlcek C, Mackova M, Macek T. 2011. Matrix-assisted laser desorption ionization (MALDI)-time of flight mass spectrometry- and MALDI biotyper-based identification of cultured biphenyl-metabolizing bacteria from contaminated horseradish rhizosphere soil. Appl Environ Microbiol 77 : 6858 6866.[PubMed][CrossRef]
104. Uhlik O, Jecna K, Mackova M, Vlcek C, Hroudova M, Demnerova K, Paces V, Macek T. 2009. Biphenyl-metabolizing bacteria in the rhizosphere of horseradish and bulk soil contaminated by polychlorinated biphenyls as revealed by stable isotope probing. Appl Environ Microbiol 75 : 6471 6477.[PubMed][CrossRef]
105. Federici E, Giubilei MA, Covino S, Zanaroli G, Fava F, D'Annibale A, Petruccioli M. 2012. Addition of maize stalks and soybean oil to a historically PCB-contaminated soil: effect on degradation performance and indigenous microbiota. Nat Biotechnol 30 : 69 79.[CrossRef]
106. Toussaint JP, Pham TT, Barriault D, Sylvestre M. 2012. Plant exudates promote PCB degradation by a rhodococcal rhizobacteria. Appl Microbiol Biotechnol 95 : 1589 1603.[PubMed][CrossRef]
107. Wang Y, Oyaizu H. 2011. Enhanced remediation of dioxins-spiked soil by a plant-microbe system using a dibenzofuran-degrading Comamonas sp. and Trifolium repens L. Chemosphere 85 : 1109 1114.[PubMed][CrossRef]
108. Bokare V, Murugesan K, Kim JH, Kim EJ, Chang YS. 2012. Integrated hybrid treatment for the remediation of 2,3,7,8-tetrachlorodibenzo- p-dioxin. Sci Total Environ 435–436 : 563 566.[PubMed][CrossRef]
109. Liu X, Germaine KJ, Ryan D, Dowling DN. 2010. Whole-cell fluorescent biosensors for bioavailability and biodegradation of polychlorinated biphenyls. Sensors 10 : 1377 1398.[PubMed][CrossRef]
110. Liu X, Germaine KJ, Ryan D, Dowling DN. 2010. Genetically modified Pseudomonas biosensing biodegraders to detect PCB and chlorobenzoate bioavailability and biodegradation in contaminated soils. Bioeng Bugs 1 : 198 206.[PubMed][CrossRef]
111. Turner K, Xu S, Pasini P, Deo S, Bachas L, Daunert S. 2007. Hydroxylated polychlorinated biphenyl detection based on a genetically engineered bioluminescent whole-cell sensing system. Anal Chem 79 : 5740 5745.[PubMed][CrossRef]
112. Teasley Hamorsky K, Ensor CM, Dikici E, Pasini P, Bachas L, Daunert S. 2012. Bioluminescence inhibition assay for the detection of hydroxylated polychlorinated biphenyls. Anal Chem 84 : 7648 7655.[PubMed][CrossRef]
113. Head JF, Inouye S, Teranishi K, Shimomura O. 2000. The crystal structure of the photoprotein aequorin at 2.3 A resolution. Nature 405 : 372 376.[PubMed][CrossRef]
114. Hernández-Sánchez V, Lang E, Wittich RM. 2013. The three-species consortium of genetically improved strains Cupriavidus necator RW112, Burkholderia xenovorans RW118, and Pseudomonas pseudoalcaligenes RW120 grows with technical polychlorobiphenyl, Aroclor 1242. Front Microbiol 4 : 90.[PubMed][CrossRef]

Tables

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TABLE 1

Dioxin-like compound-degraders whose genome sequences were determined

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1
Generic image for table
TABLE 2

(Putative) mobile genetic elements carrying degradative genes for dioxin-like compounds

Citation: Shintani M, Kimbara K. 2016. Genomic Features and Genome-Wide Analyses of Dioxin-Like Compound Degraders, p 5.1.1-1-5.1.1-10. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.1

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