1887

Chapter 5.1.2 : Biodegradation of Organochlorine Pesticides

Authors: Yuji Nagata1, Michiro Tabata2, Yoshiyuki Ohtsubo3, Masataka Tsuda4
VIEW AFFILIATIONS HIDE AFFILIATIONS
Affiliations: 1: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan; 2: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan; 3: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan; 4: Department of Environmental Life Sciences, Graduate School of Life Sciences, Tohoku University, Sendai 980-8577, Japan
Content Type: Reference
Publication Year: 2016

Category: Environmental Microbiology

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.

Preview this chapter:
Preview Magnify
Zoom in
Zoomout

Biodegradation of Organochlorine Pesticides, Page 1 of 2

| /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch5.1.2-1.gif /docserver/preview/fulltext/10.1128/9781555818821/9781555818821.ch5.1.2-2.gif

Abstract:

The widespread use of organochlorine pesticides (OCPs), mainly in the past, has caused serious environmental problems. Many OCPs were recently categorized as persistent organic pollutants (POPs) that should be controlled as toxic environmental contaminants. On the other hand, many bacterial strains and consortia have been identified that can degrade OCPs, including man-made ones, and various pathways for the biodegradation of OCPs have been clarified. Especially, aerobic OCP-degrading bacteria have been analyzed in detail as an excellent model for studying the bacterial adaptation and evolution in the environment. In fact, most such degradation pathways are thought to be established by the assembly of preexisting and newly evolved pathways, involving enzymes whose functions are thought to have evolved during relatively short period. Furthermore, a large amount of bacterial genomic information is now available, and the appearance and evolution of bacteria capable of degrading man-made OCPs can be discussed on the basis of such genomic information and mobile genetic elements. These accumulating knowledge on the biodegradation of OCPs will also be useful for practical bioremediation.

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Highlighted Text: Show | Hide
Loading full text...

Full text loading...

Figures

Biodegradation of Organochlorine Pesticides
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch5.1.2-1,webId=/content/author/10.1128/9781555818821.ch5.1.2-1,properties={foaf_givenname=Yuji, foaf_name=Yuji Nagata, foaf_surname=Nagata, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch5.1.2-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch5.1.2-2,webId=/content/author/10.1128/9781555818821.ch5.1.2-2,properties={foaf_givenname=Michiro, foaf_name=Michiro Tabata, foaf_surname=Tabata, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch5.1.2-aff2]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch5.1.2-3,webId=/content/author/10.1128/9781555818821.ch5.1.2-3,properties={foaf_givenname=Yoshiyuki, foaf_name=Yoshiyuki Ohtsubo, foaf_surname=Ohtsubo, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch5.1.2-aff3]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/10.1128/9781555818821.ch5.1.2-4,webId=/content/author/10.1128/9781555818821.ch5.1.2-4,properties={foaf_givenname=Masataka, foaf_name=Masataka Tsuda, foaf_surname=Tsuda, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/10.1128/9781555818821.ch5.1.2-aff4]]}]]
Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig01
FIGURE 1

Degradation pathway of OCPs (2,4-D, 2,4,5-T, PCP, γ-HCH, and linuron) in aerobic bacteria. Reactions catalyzed by dehalogenases ( Table 2 ) are shown in bold. See text for detail. doi:10.1128/9781555818821.ch5.1.2.f1

10.1128/9781555818821/2934ch26f01_thmb.gif
10.1128/9781555818821/2934ch26f01.gif
Image of FIGURE 1
FIGURE 1

Degradation pathway of OCPs (2,4-D, 2,4,5-T, PCP, γ-HCH, and linuron) in aerobic bacteria. Reactions catalyzed by dehalogenases ( Table 2 ) are shown in bold. See text for detail. doi:10.1128/9781555818821.ch5.1.2.f1

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig02
FIGURE 2

Degradation pathway of atrazine by aerobic bacteria. See text for details. doi:10.1128/9781555818821.ch5.1.2.f2

10.1128/9781555818821/2934ch26f02_thmb.gif
10.1128/9781555818821/2934ch26f02.gif
Image of FIGURE 2
FIGURE 2

Degradation pathway of atrazine by aerobic bacteria. See text for details. doi:10.1128/9781555818821.ch5.1.2.f2

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig03
FIGURE 3

Degradation pathway of DDT in the environmant. DDT is converted to DDE and DDD by microbial activities, chemical reactions, or phytochemical reactions. Aerobic DDT-degrading bacteria hydroxylate one of the aromatic rings in DDT, and furthre convert into 4-chlorobenzoate. See text for details. doi:10.1128/9781555818821.ch5.1.2.f3

10.1128/9781555818821/2934ch26f03_thmb.gif
10.1128/9781555818821/2934ch26f03.gif
Image of FIGURE 3
FIGURE 3

Degradation pathway of DDT in the environmant. DDT is converted to DDE and DDD by microbial activities, chemical reactions, or phytochemical reactions. Aerobic DDT-degrading bacteria hydroxylate one of the aromatic rings in DDT, and furthre convert into 4-chlorobenzoate. See text for details. doi:10.1128/9781555818821.ch5.1.2.f3

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig04
FIGURE 4

Structures of other OCPs described in this chapter. doi:10.1128/9781555818821.ch5.1.2.f4

10.1128/9781555818821/2934ch26f04_thmb.gif
10.1128/9781555818821/2934ch26f04.gif
Image of FIGURE 4
FIGURE 4

Structures of other OCPs described in this chapter. doi:10.1128/9781555818821.ch5.1.2.f4

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig05
FIGURE 5

Three main replicons of UT26. Replicons are drawn in circular. Note that the size scale depends on the replicons. The top positions of the three replicons have been defined as putative replication origins (position 1). Positions of the genes, IS, and bacterial essential genes proposed by Gil et al. are marked with red, blue, and back bars, respectively. Results of GC skew and GC content are shown inside of the black scale circles: GC skew (inside), the parts higher and lower than zero were colored with cyan and magenta, respectively; GC content (outside), the parts higher and lower than average of each replicon were colored with green and red, respectively. Result of a BLASTN search of each region of the UT26 genome toward genome sequences of seven other non-γ-HCH-degrading sphingomonad strains, L-1, sp. SKA58, sp. SYK-6, RW1, RB2256, DSM 12444, and sp. PP1Y were shown outside of the black scale circles in this order. The region whose homologous sequence was found in the other strains (L-1, SKA58, SYK-6, RW1, RB2256, DSM 12444, and PP1Y from inside to outside) was colored in the gradient depending on the level of similarity as shown in explanatory note. Result of the BLASTN search of each region of the UT26 genome toward draft genome sequences of γ-HCH-degrading sphingomonad strains, B90A, sp. TKS, sp. MI1205, and sp. MM-1 were shown outside of the circle for the positions of IS in this order. See text for details. This figure was drawn by ArcWithColor (http://www.ige.tohoku.ac.jp/joho/gmProject/gmdownload.html). doi:10.1128/9781555818821.ch5.1.2.f5

10.1128/9781555818821/2934ch26f05_thmb.gif
10.1128/9781555818821/2934ch26f05.gif
Image of FIGURE 5
FIGURE 5

Three main replicons of UT26. Replicons are drawn in circular. Note that the size scale depends on the replicons. The top positions of the three replicons have been defined as putative replication origins (position 1). Positions of the genes, IS, and bacterial essential genes proposed by Gil et al. are marked with red, blue, and back bars, respectively. Results of GC skew and GC content are shown inside of the black scale circles: GC skew (inside), the parts higher and lower than zero were colored with cyan and magenta, respectively; GC content (outside), the parts higher and lower than average of each replicon were colored with green and red, respectively. Result of a BLASTN search of each region of the UT26 genome toward genome sequences of seven other non-γ-HCH-degrading sphingomonad strains, L-1, sp. SKA58, sp. SYK-6, RW1, RB2256, DSM 12444, and sp. PP1Y were shown outside of the black scale circles in this order. The region whose homologous sequence was found in the other strains (L-1, SKA58, SYK-6, RW1, RB2256, DSM 12444, and PP1Y from inside to outside) was colored in the gradient depending on the level of similarity as shown in explanatory note. Result of the BLASTN search of each region of the UT26 genome toward draft genome sequences of γ-HCH-degrading sphingomonad strains, B90A, sp. TKS, sp. MI1205, and sp. MM-1 were shown outside of the circle for the positions of IS in this order. See text for details. This figure was drawn by ArcWithColor (http://www.ige.tohoku.ac.jp/joho/gmProject/gmdownload.html). doi:10.1128/9781555818821.ch5.1.2.f5

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig06
FIGURE 6

Neighbor-joining phylogenetic tree of 16S rRNA genes of sphingomonad strains. Neighbor-joining phylogenetic tree of the conserved sites (1,385 nucleotides) in 16S rRNA genes of 13 sphingomonad strains, UT26S (UT26_1, SJA_C1-r0010; UT26_2, SJA_C2-r0010; UT26_3, SJA_C2-r0040), B90A (B90A, NR_042943), Sp+ (Sp+, NR_042944), sp. TKS (TKS_1, TKS_2, and TKS_3: unpublished data), L-1 (L-1_1, Sphch_R0043; L-2_2, Sphch_R0058; L-1_3, Sphch_R0067), sp. SKA58 (SKA58_1, SKA58_r00366; SKA58_2, SKA58_r18278), sp. MI1205 (MI1205_1 and MI1205_2: unpublished data), sp. SYK-6 (SYK6_1, SLG_r0030; SYK6_2, SLG_r0060), RW1 (RW1_1, Swit_R0031; RW1_2, Swit_R0040), sp. MM-1 (MM-1_1, G432_r19183; MM-1_2, G432_r19185), RB2256 (RB2256, Sala_R0048), DSM 12444 (DSM_1, Saro_R0065; DSM_2, Saro_R0059; DSM_3, Saro_R0053), and sp. PP1Y (PPY_1, PP1Y_AR03; PPY_2, PP1Y_AR23; PPY_3, PP1Y_AR65) was constructed using MAFFT program (http://mafft.cbrc.jp/alignment/software/) and visualized by Njplot software. 16S rRNA gene (: gene ID 7437018) of strain K-12 substr. W3110 () was used as an out-of-group sequence. Bootstrap values calculated from 1,000 resampling using neighbor joining are shown at the respective nodes. Length of lines reflects relative evolutionary distances among the sequences. sp. SKA58 should be sp. SKA58 on the basis of comprehensive 16S rDNA analysis. However, we used for the strain according to the database to avoid confusion. γ-HCH degraders are boldface. Strains having IS are marked with black circles, and copy number of IS in each strain is shown in parentheses after the circle. doi:10.1128/9781555818821.ch5.1.2.f6

10.1128/9781555818821/2934ch26f06_thmb.gif
10.1128/9781555818821/2934ch26f06.gif
Image of FIGURE 6
FIGURE 6

Neighbor-joining phylogenetic tree of 16S rRNA genes of sphingomonad strains. Neighbor-joining phylogenetic tree of the conserved sites (1,385 nucleotides) in 16S rRNA genes of 13 sphingomonad strains, UT26S (UT26_1, SJA_C1-r0010; UT26_2, SJA_C2-r0010; UT26_3, SJA_C2-r0040), B90A (B90A, NR_042943), Sp+ (Sp+, NR_042944), sp. TKS (TKS_1, TKS_2, and TKS_3: unpublished data), L-1 (L-1_1, Sphch_R0043; L-2_2, Sphch_R0058; L-1_3, Sphch_R0067), sp. SKA58 (SKA58_1, SKA58_r00366; SKA58_2, SKA58_r18278), sp. MI1205 (MI1205_1 and MI1205_2: unpublished data), sp. SYK-6 (SYK6_1, SLG_r0030; SYK6_2, SLG_r0060), RW1 (RW1_1, Swit_R0031; RW1_2, Swit_R0040), sp. MM-1 (MM-1_1, G432_r19183; MM-1_2, G432_r19185), RB2256 (RB2256, Sala_R0048), DSM 12444 (DSM_1, Saro_R0065; DSM_2, Saro_R0059; DSM_3, Saro_R0053), and sp. PP1Y (PPY_1, PP1Y_AR03; PPY_2, PP1Y_AR23; PPY_3, PP1Y_AR65) was constructed using MAFFT program (http://mafft.cbrc.jp/alignment/software/) and visualized by Njplot software. 16S rRNA gene (: gene ID 7437018) of strain K-12 substr. W3110 () was used as an out-of-group sequence. Bootstrap values calculated from 1,000 resampling using neighbor joining are shown at the respective nodes. Length of lines reflects relative evolutionary distances among the sequences. sp. SKA58 should be sp. SKA58 on the basis of comprehensive 16S rDNA analysis. However, we used for the strain according to the database to avoid confusion. γ-HCH degraders are boldface. Strains having IS are marked with black circles, and copy number of IS in each strain is shown in parentheses after the circle. doi:10.1128/9781555818821.ch5.1.2.f6

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint
/content/10.1128/9781555818821.ch5.1.2.ch5.1.2fig07
FIGURE 7

Proposed model for the appearance and evolution of γ-HCH degraders. See text for details. doi:10.1128/9781555818821.ch5.1.2.f7

10.1128/9781555818821/2934ch26f07_thmb.gif
10.1128/9781555818821/2934ch26f07.gif
Image of FIGURE 7
FIGURE 7

Proposed model for the appearance and evolution of γ-HCH degraders. See text for details. doi:10.1128/9781555818821.ch5.1.2.f7

Citation: Nagata Y, Tabata M, Ohtsubo Y, Tsuda M. 2016. Biodegradation of Organochlorine Pesticides, p 5.1.2-1-5.1.2-30. In Yates M, Nakatsu C, Miller R, Pillai S (ed), Manual of Environmental Microbiology, Fourth Edition. ASM Press, Washington, DC. doi: 10.1128/9781555818821.ch5.1.2
Permissions and Reprints Request Permissions
Download as Powerpoint

References

/content/book/10.1128/9781555818821.ch5.1.2
1. Ogata Y, Takada H, Mizukawa K, Hirai H, Iwasa S, Endo S, Mato Y, Saha M, Okuda K, Nakashima A, Murakami M, Zurcher N, Booyatumanondo R, Zakaria MP, Dung le Q, Gordon M, Miguez C, Suzuki S, Moore C, Karapanagioti HK, Weerts S, McClurg T, Burres E, Smith W, Van Velkenburg M, Lang JS, Lang RC, Laursen D, Danner B, Stewardson N, Thompson RC. 2009. International Pellet Watch: global monitoring of persistent organic pollutants (POPs) in coastal waters. 1. Initial phase data on PCBs, DDTs, and HCHs. Mar Pollut Bull 58 : 1437– 1446.[PubMed][CrossRef]
2. El-Shahawi MS, Hamza A, Bashammakh AS, Al-Saggaf WT. 2010. An overview on the accumulation, distribution, transformations, toxicity and analytical methods for the monitoring of persistent organic pollutants. Talanta 80 : 1587– 1597.[PubMed][CrossRef]
3. Vijgen J, Abhilash PC, Li YF, Lal R, Forter M, Torres J, Singh N, Yunus M, Tian C, Schaffer A, Weber R. 2011. Hexachlorocyclohexane (HCH) as new Stockholm Convention POPs—a global perspective on the management of lindane and its waste isomers. Environ Sci Pollut Res Int 18 : 152– 162.[PubMed][CrossRef]
4. Tarcau D, Cucu-Man S, Boruvkova J, Klanova J, Covaci A. 2013. Organochlorine pesticides in soil, moss and tree-bark from North-Eastern Romania. Sci Total Environ 456–457 : 317– 324.[PubMed][CrossRef]
5. Kumar KS, Watanabe K, Takemori H, Iseki N, Masunaga S, Takasuga T. 2005. Analysis of UNEP priority POPs using HRGC-HRMS and their contamination profiles in livers and eggs of great cormorants ( Phalacrocorax carbo) from Japan. Archives of Environ Contam Toxicol 48 : 538– 551.[CrossRef]
6. Kengara FO, Schramm KW, Doerfler U, Munch JC, Henkelmann B, Welzl G, Bernhoeft S, Hense B, Schroll R. 2010. Degradation capacity of a 1,2,4-trichlorobenzene mineralizing microbial community for traces of organochlorine pesticides. Sci Total Environ 408 : 3359– 3366.[PubMed][CrossRef]
7. Menzies R, Soares Quinete N, Gardinali P, Seba D. 2013. Baseline occurrence of organochlorine pesticides and other xenobiotics in the marine environment: Caribbean and Pacific collections. Mar Pollut Bullet 70 : 289– 295.[CrossRef]
8. Dennie D, Gladu II, Lepine F, Villemur R, Bisaillon J, Beaudet R. 1998. Spectrum of the reductive dehalogenation activity of desulfitobacterium frappieri PCP-1. Appl Environ Microbiol 64 : 4603– 4606.[PubMed]
9. Futagami T, Goto M, Furukawa K. 2008. Biochemical and genetic bases of dehalorespiration. Chemical Record 8 : 1– 12.[PubMed][CrossRef]
10. Bisaillon A, Beaudet R, Lepine F, Deziel E, Villemur R. 2010. Identification and characterization of a novel CprA reductive dehalogenase specific to highly chlorinated phenols from Desulfitobacterium hafniense strain PCP-1. Appl Environ Microbiol 76 : 7536– 7540.[PubMed][CrossRef]
11. Ning D, Wang H. 2012. Involvement of cytochrome P450 in pentachlorophenol transformation in a white rot fungus Phanerochaete chrysosporium. PLoS One 7 : e45887.[PubMed][CrossRef]
12. Itoh K, Kinoshita M, Morishita S, Chida M, Suyama K. 2013. Characterization of 2,4-dichlorophenoxyacetic acid and 2,4,5-trichlorophenoxyacetic acid-degrading fungi in Vietnamese soils. FEMS Microbiol Ecol 84 : 124– 132.[PubMed][CrossRef]
13. Perez-Pantoja D, De la Iglesia R, Pieper DH, Gonzalez B. 2008. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134. FEMS Microbiol Rev 32 : 736– 794.[PubMed][CrossRef]
14. Zaborina O, Daubaras DL, Zago A, Xun L, Saido K, Klem T, Nikolic D, Chakrabarty AM. 1998. Novel pathway for conversion of chlorohydroxyquinol to maleylacetate in Burkholderia cepacia AC1100. J Bacteriol 180 : 4667– 4675.[PubMed]
15. Copley SD, Rokicki J, Turner P, Daligault H, Nolan M, Land M. 2011. The whole genome sequence of Sphingobium chlorophenolicum L-1: insights into the evolution of the pentachlorophenol degradation pathway. Genome Biol Evol 4 : 184– 198.[PubMed][CrossRef]
16. Nagata Y, Natsui S, Endo R, Ohtsubo Y, Ichikawa N, Ankai A, Oguchi A, Fukui S, Fujita N, Tsuda M. 2011. Genomic organization and genomic structural rearrangements of Sphingobium japonicum UT26, an archetypal γ-hexachlorocyclohexane-degrading bacterium. Enz Microb Technol 49 : 499– 508.[CrossRef]
17. Anand S, Sangwan N, Lata P, Kaur J, Dua A, Singh AK, Verma M, Kaur J, Khurana JP, Khurana P, Mathur S, Lal R. 2012. Genome sequence of Sphingobium indicum B90A, a hexachlorocyclohexane-degrading bacterium. J Bacteriol 194 : 4471– 4472.[PubMed][CrossRef]
18. Ceremonie H, Boubakri H, Mavingui P, Simonet P, Vogel TM. 2006. Plasmid-encoded γ-hexachlorocyclohexane degradation genes and insertion sequences in Sphingobium francense ( ex-Sphingomonas paucimobilis Sp+). FEMS Microbiol Lett 257 : 243– 252.[PubMed][CrossRef]
19. Wu J, Hong Q, Sun Y, Hong Y, Yan Q, Li S. 2007. Analysis of the role of LinA and LinB in biodegradation of 6-hexachlorocyclohexane. Environ Microbiol 9 : 2331– 2340.[PubMed][CrossRef]
20. Ito M, Prokop Z, Klvana M, Otsubo Y, Tsuda M, Damborsky J, Nagata Y. 2007. Degradation of p-hexachlorocyclohexane by haloalkane dehalogenase LinB from γ-hexachlorocyclohexane-utilizing bacterium Sphingobium sp. MI1205. Arch Microbiol 188 : 313– 325.[PubMed][CrossRef]
21. Tabata M, Ohtsubo Y, Ohhata S, Tsuda M, Nagata Y. 2013. Complete genome sequence of the γ-hexachlorocyclohexane-degrading bacterium Sphingomonas sp. strain MM-1. Genome Announce 1 : 300247-13 .[CrossRef]
22. Nadeau LJ, Menn FM, Breen A, Sayler GS. 1994. Aerobic degradation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by Alcaligenes eutrophus A5. Appl Environ Microbiol 60 : 51– 55.[PubMed]
23. Fang H, Dong B, Yan H, Tang F, Yu Y. 2010. Characterization of a bacterial strain capable of degrading DDT congeners and its use in bioremediation of contaminated soil. J Haz Mat 184 : 281– 289.[CrossRef]
24. Gao B, Liu WB, Jia LY, Xu L, Xie J. 2011. Isolation and characterization of an Alcaligenes sp. strain DG-5 capable of degrading DDTs under aerobic conditions. J Environ Sci Health Part B 46 : 257– 263.[CrossRef]
25. Matsumoto E, Kawanaka Y, Yun SJ, Oyaizu H. 2008. Isolation of dieldrin- and endrin-degrading bacteria using 1,2-epoxycyclohexane as a structural analog of both compounds. Appl Microbiol Biotechnol 80 : 1095– 1103.[PubMed][CrossRef]
26. Sakakibara F, Takagi K, Kataoka R, Kiyota H, Sato Y, Okada S. 2011. Isolation and identification of dieldrin-degrading Pseudonocardia sp. strain KSF27 using a soil-charcoal perfusion method with aldrin trans-diol as a structural analog of dieldrin. Biochem Biophys Res Commun 411 : 76– 81.[PubMed][CrossRef]
27. Martinez B, Tomkins J, Wackett LP, Wing R, Sadowsky MJ. 2001. Complete nucleotide sequence and organization of the atrazine catabolic plasmid pADP-1 from Pseudomonas sp. strain ADP. J Bacteriol 183 : 5684– 5697.[PubMed][CrossRef]
28. Mongodin EF, Shapir N, Daugherty SC, DeBoy RT, Emerson JB, Shvartzbeyn A, Radune D, Vamathevan J, Riggs F, Grinberg V, Khouri H, Wackett LP, Nelson KE, Sadowsky MJ. 2006. Secrets of soil survival revealed by the genome sequence of Arthrobacter aurescens TC1. PLoS Genet 2 : e214.[PubMed][CrossRef]
29. Mulbry WW, Zhu H, Nour SM, Topp E. 2002. The triazine hydrolase gene trzN from Nocardioides sp. strain C190: cloning and construction of gene-specific primers. FEMS Microbiol Lett 206 : 75– 79.[PubMed][CrossRef]
30. Dejonghe W, Berteloot E, Goris J, Boon N, Crul K, Maertens S, Hofte M, De Vos P, Verstraete W, Top EM. 2003. Synergistic degradation of linuron by a bacterial consortium and isolation of a single linuron-degrading Variovorax strain. Appl Environ Microbiol 69 : 1532– 1541.[PubMed][CrossRef]
31. Bers K, Leroy B, Breugelmans P, Albers P, Lavigne R, Sorensen SR, Aamand J, De Mot R, Wattiez R, Springael D. 2011. A novel hydrolase identified by genomic-proteomic analysis of phenylurea herbicide mineralization by Variovorax sp. strain SRS16. Appl Environ Microbiol 77 : 8754– 8764.[PubMed][CrossRef]
32. Satsuma K. 2010. Mineralisation of the herbicide linuron by Variovorax sp. strain RA8 isolated from Japanese river sediment using an ecosystem model (microcosm). Pest Manag Sci 66 : 847– 852.[PubMed]
33. Turnbull GA, Ousley M, Walker A, Shaw E, Morgan JA. 2001. Degradation of substituted phenylurea herbicides by Arthrobacter globiformis strain D47 and characterization of a plasmid-associated hydrolase gene, puhA. Appl Environ Microbiol 67 : 2270– 2275.[PubMed][CrossRef]
34. Khurana JL, Jackson CJ, Scott C, Pandey G, Horne I, Russell RJ, Herlt A, Easton CJ, Oakeshott JG. 2009. Characterization of the phenylurea hydrolases A and B: founding members of a novel amidohydrolase subgroup. Biochem J 418 : 431– 441.[PubMed][CrossRef]
35. Satsuma K, Masuda M, Sato K. 2012. O-Demethylation and successive oxidative dechlorination of methoxychlor by Bradyrhizobium sp. strain 17–4, isolated from river sediment. Appl Environ Microbiol 78 : 5313– 5319.[PubMed][CrossRef]
36. Megharaj M, Ramakrishnan B, Venkateswarlu K, Sethunathan N, Naidu R. 2011. Bioremediation approaches for organic pollutants: a critical perspective. Environ Int 37 : 1362– 1375.[PubMed][CrossRef]
37. Top EM, Springael D. 2003. The role of mobile genetic elements in bacterial adaptation to xenobiotic organic compounds. Curr Opin Biotechnol 14 : 262– 269.[PubMed][CrossRef]
38. Lykidis A, Perez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, Hooper SD, Lapidus A, Lucas S, Gonzalez B, Kyrpides NC. 2010. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS One 5 : e9729.[PubMed][CrossRef]
39. Harwood CS, Parales RE. 1996. The beta-ketoadipate pathway and the biology of self-identity. Ann Rev Microbiol 50 : 553– 590.[CrossRef]
40. Hausinger RP, Fukumori F. 1995. Characterization of the first enzyme in 2,4-dichlorophenoxyacetic acid metabolism. Environ Health Perspect 103( Suppl 5) : 37– 39.[PubMed][CrossRef]
41. Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Perez-Pantoja D, Sanchez MA, Stuardo M, Gonzalez B. 2004. 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 6 : 655– 668.[PubMed][CrossRef]
42. Top EM, Maltseva OV, Forney LJ. 1996. Capture of a catabolic plasmid that encodes only 2,4-dichlorophenoxyacetic acid:alpha-ketoglutaric acid dioxygenase (TfdA) by genetic complementation. Appl Environ Microbiol 62 : 2470– 2476.[PubMed]
43. Itoh K, Tashiro Y, Uobe K, Kamagata Y, Suyama K, Yamamoto H. 2004. Root nodule Bradyrhizobium spp. harbor tfdAα and cadA, homologous with genes encoding 2,4-dichlorophenoxyacetic acid-degrading proteins. Appl Environ Microbiol 70 : 2110– 2118.[PubMed][CrossRef]
44. Kamagata Y, Fulthorpe RR, Tamura K, Takami H, Forney LJ, Tiedje JM. 1997. Pristine environments harbor a new group of oligotrophic 2,4-dichlorophenoxyacetic acid-degrading bacteria. Appl Environ Microbiol 63 : 2266– 2272.[PubMed]
45. Kitagawa W, Takami S, Miyauchi K, Masai E, Kamagata Y, Tiedje JM, Fukuda M. 2002. Novel 2,4-dichlorophenoxyacetic acid degradation genes from oligotrophic Bradyrhizobium sp. strain HW13 isolated from a pristine environment. J Bacteriol 184 : 509– 518.[PubMed][CrossRef]
46. Kellogg ST, Chatterjee DK, Chakrabarty AM. 1981. Plasmid-assisted molecular breeding: new technique for enhanced biodegradation of persistent toxic chemicals. Science 214 : 1133– 1135.[PubMed][CrossRef]
47. Hubner A, Danganan CE, Xun L, Chakrabarty AM, Hendrickson W. 1998. Genes for 2,4,5-trichlorophenoxyacetic acid metabolism in Burkholderia cepacia AC1100: characterization of the tftC and tftD genes and locations of the tft operons on multiple replicons. Appl Environ Microbiol 64 : 2086– 2093.[PubMed]
48. Gisi MR, Xun L. 2003. Characterization of chlorophenol 4-monooxygenase (TftD) and NADH:flavin adenine dinucleotide oxidoreductase (TftC) of Burkholderia cepacia AC1100. J Bacteriol 185 : 2786– 2792.[PubMed][CrossRef]
49. Golovleva LA, Pertsova RN, Evtushenko LI, Baskunov BP. 1990. Degradation of 2,4,5-trichlorophenoxyacetic acid by a Nocardioides simplex culture. Biodegradation 1 : 263– 271.[PubMed][CrossRef]
50. Rice JF, Menn FM, Hay AG, Sanseverino J, Sayler GS. 2005. Natural selection for 2,4,5-trichlorophenoxyacetic acid mineralizing bacteria in agent orange contaminated soil. Biodegradation 16 : 501– 512.[PubMed][CrossRef]
51. Huong N, Itoh K, Suyama K. 2007. Diversity of 2,4-dichlorophenoxyacetic acid (2,4-D) and 2,4,5-trichlorophenoxyacetic acid (2,4,5-T)-degrading bacteria in Vietnamese soils. Microb Environ 22 : 243– 256.[CrossRef]
52. Daubaras DL, Danganan CE, Hubner A, Ye RW, Hendrickson W, Chakrabarty AM. 1996. Biodegradation of 2,4,5-trichlorophenoxyacetic acid by Burkholderia cepacia strain AC1100: evolutionary insight. Gene 179 : 1– 8.[PubMed][CrossRef]
53. Huang Y, Xun R, Chen G, Xun L. 2008. Maintenance role of a glutathionyl-hydroquinone lyase (PcpF) in pentachlorophenol degradation by Sphingobium chlorophenolicum ATCC 39723. J Bacteriol 190 : 7595– 7600.[PubMed][CrossRef]
54. Orser CS, Lange CC, Xun L, Zahrt TC, Schneider BJ. 1993. Cloning, sequence analysis, and expression of the Flavobacterium pentachlorophenol-4-monooxygenase gene in Escherichia coli. J Bacteriol 175 : 411– 416.[PubMed]
55. Orser CS, Dutton J, Lange C, Jablonski P, Xun L, Hargis M. 1993. Characterization of a Flavobacterium glutathione S-transferase gene involved reductive dechlorination. J Bacteriol 175 : 2640– 2644.[PubMed]
56. Hlouchova K, Rudolph J, Pietari JM, Behlen LS, Copley SD. 2012. Pentachlorophenol hydroxylase, a poorly functioning enzyme required for degradation of pentachlorophenol by Sphingobium chlorophenolicum. Biochemistry 51 : 3848– 3860.[PubMed][CrossRef]
57. Cai M, Xun L. 2002. Organization and regulation of pentachlorophenol-degrading genes in Sphingobium chlorophenolicum ATCC 39723. J Bacteriol 184 : 4672– 4680.[PubMed][CrossRef]
58. Ohtsubo Y, Miyauchi K, Kanda K, Hatta T, Kiyohara H, Senda T, Nagata Y, Mitsui Y, Takagi M. 1999. PcpA, which is involved in the degradation of pentachlorophenol in Sphingomonas chlorophenolica ATCC39723, is a novel type of ring-cleavage dioxygenase. FEBS Lett 459 : 395– 398.[PubMed][CrossRef]
59. Xu L, Resing K, Lawson SL, Babbitt PC, Copley SD. 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.[PubMed][CrossRef]
60. Xun L, Bohuslavek J, Cai M. 1999. Characterization of 2,6-dichloro-p-hydroquinone 1,2-dioxygenase (PcpA) of Sphingomonas chlorophenolica ATCC 39723. Biochem Biophys Res Commun 266 : 322– 325.[PubMed][CrossRef]
61. Machonkin TE, Holland PL, Smith KN, Liberman JS, Dinescu A, Cundari TR, Rocks SS. 2010. Determination of the active site of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone dioxygenase (PcpA). J Biol Inorg Chem 15 : 291– 301.[PubMed][CrossRef]
62. Machonkin TE, Doerner AE. 2011. Substrate specificity of Sphingobium chlorophenolicum 2,6-dichlorohydroquinone 1,2-dioxygenase. Biochemistry 50 : 8899– 8913.[PubMed][CrossRef]
63. Sun W, Sammynaiken R, Chen L, Maley J, Schatte G, Zhou Y, Yang J. 2011. Sphingobium chlorophenolicum dichlorohydroquinone dioxygenase (PcpA) is alkaline resistant and thermally stable. Int J Biol Sci 7 : 1171– 1179.[PubMed][CrossRef]
64. Karn SK, Chakrabarti SK, Reddy MS. 2011. Degradation of pentachlorophenol by Kocuria sp. CL2 isolated from secondary sludge of pulp and paper mill. Biodegradation 22 : 63– 69.[PubMed][CrossRef]
65. Phillips TM, Seech AG, Lee H, Trevors JT. 2005. Biodegradation of hexachlorocyclohexane (HCH) by microorganisms. Biodegradation 16 : 363– 392.[PubMed][CrossRef]
66. Lal R, Pandey G, Sharma P, Kumari K, Malhotra S, Pandey R, Raina V, Kohler HP, Holliger C, Jackson C, Oakeshott JG. 2010. Biochemistry of microbial degradation of hexachlorocyclohexane and prospects for bioremediation. Microbiol Mol Biol Rev 74 : 58– 80.[PubMed][CrossRef]
67. Willett KL, Ulrich EM, Hites RA. 1998. Differential toxicity and environmental fates of hexachlorocyclohexane isomers. Environ Sci Technol 32 : 2197– 2207.[CrossRef]
68. Nagata Y, Endo R, Ito M, Ohtsubo Y, Tsuda M. 2007. Aerobic degradation of lindane (γ-hexachlorocyclohexane) in bacteria and its biochemical and molecular basis. Appl Microbiol Biotechnol 76 : 741– 752.[PubMed][CrossRef]
69. Miyauchi K, Lee HS, Fukuda M, Takagi M, Nagata Y. 2002. Cloning and characterization of linR, involved in regulation of the downstream pathway for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. Appl Environ Microbiol 68 : 1803– 1807.[PubMed][CrossRef]
70. Sharma P, Pandey R, Kumari K, Pandey G, Jackson CJ, Russell RJ, Oakeshott JG, Lal R. 2011. Kinetic and sequence-structure-function analysis of known LinA variants with different hexachlorocyclohexane isomers. PLoS One 6 : e25128.[PubMed][CrossRef]
71. Bala K, Geueke B, Miska ME, Rentsch D, Poiger T, Dadhwal M, Lal R, Holliger C, Kohler HP. 2012. Enzymatic conversion of ε-hexachlorocyclohexane and a heptachlorocyclohexane isomer, two neglected components of technical hexachlorocyclohexane. Environ Sci Technol 46 : 4051– 4058.[PubMed][CrossRef]
72. Geueke B, Garg N, Ghosh S, Fleischmann T, Holliger C, Lal R, Kohler HP. 2012. Metabolomics of hexachlorocyclohexane (HCH) transformation: ratio of LinA to LinB determines metabolic fate of HCH isomers. Environ Microbiol 15 : 1040– 1049.[PubMed][CrossRef]
73. Benimeli CS, Amoroso MJ, Chaile AP, Castro GR. 2003. Isolation of four aquatic streptomycetes strains capable of growth on organochlorine pesticides. Biores Technol 89 : 133– 138.[CrossRef]
74. Benimeli CS, Castro GR, Chaile AP, Amoroso MJ. 2006. Lindane removal induction by Streptomyces sp. M7. J Basic Microbiol 46 : 348– 357.[PubMed][CrossRef]
75. Saez JM, Benimeli CS, Amoroso MJ. 2012. Lindane removal by pure and mixed cultures of immobilized actinobacteria. Chemosphere 89 : 982– 987.[PubMed][CrossRef]
76. Camacho-Perez B, Rios-Leal E, Rinderknecht-Seijas N, Poggi-Varaldo HM. 2011. Enzymes involved in the biodegradation of hexachlorocyclohexane: a mini review. J Environ Manage 95 ( Suppl) : S306– S318.[PubMed][CrossRef]
77. Udikovic-Kolic N, Scott C, Martin-Laurent F. 2012. Evolution of atrazine-degrading capabilities in the environment. Appl Microbiol Biotechnol 96 : 1175– 1189.[PubMed][CrossRef]
78. Shapir N, Mongodin EF, Sadowsky MJ, Daugherty SC, Nelson KE, Wackett LP. 2007. Evolution of catabolic pathways: genomic insights into microbial s-triazine metabolism. J Bacteriol 189 : 674– 682.[PubMed][CrossRef]
79. Seffernick JL, Reynolds E, Fedorov AA, Fedorov E, Almo SC, Sadowsky MJ, Wackett LP. 2010. X-ray structure and mutational analysis of the atrazine chlorohydrolase TrzN. J Biol Chem 285 : 30606– 30614.[PubMed][CrossRef]
80. Scott C, Jackson CJ, Coppin CW, Mourant RG, Hilton ME, Sutherland TD, Russell RJ, Oakeshott JG. 2009. Catalytic improvement and evolution of atrazine chlorohydrolase. Appl Environ Microbiol 75 : 2184– 2191.[PubMed][CrossRef]
81. Shapir N, Pedersen C, Gil O, Strong L, Seffernick J, Sadowsky MJ, Wackett LP. 2006. TrzN from Arthrobacter aurescens TC1 is a zinc amidohydrolase. J Bacteriol 188 : 5859– 5864.[PubMed][CrossRef]
82. Topp E, Mulbry WM, Zhu H, Nour SM, Cuppels D. 2000. Characterization of s-triazine herbicide metabolism by a Nocardioides sp. isolated from agricultural soils. Appl Environ Microbiol 66 : 3134– 3141.[PubMed][CrossRef]
83. Shapir N, Rosendahl C, Johnson G, Andreina M, Sadowsky MJ, Wackett LP. 2005. Substrate specificity and colorimetric assay for recombinant TrzN derived from Arthrobacter aurescens TC1. Appl Environ Microbiol 71 : 2214– 2220.[PubMed][CrossRef]
84. Shapir N, Osborne JP, Johnson G, Sadowsky MJ, Wackett LP. 2002. Purification, substrate range, and metal center of AtzC: the N-isopropylammelide aminohydrolase involved in bacterial atrazine metabolism. J Bacteriol 184 : 5376– 5384.[PubMed][CrossRef]
85. Seffernick JL, Shapir N, Schoeb M, Johnson G, Sadowsky MJ, Wackett LP. 2002. Enzymatic degradation of chlorodiamino-s-triazine. Appl Environ Microbiol 68 : 4672– 4675.[PubMed][CrossRef]
86. Karns JS. 1999. Gene sequence and properties of an s-triazine ring-cleavage enzyme from Pseudomonas sp. strain NRRLB-12227. Appl Environ Microbiol 65 : 3512– 3517.[PubMed]
87. Fruchey I, Shapir N, Sadowsky MJ, Wackett LP. 2003. On the origins of cyanuric acid hydrolase: purification, substrates, and prevalence of AtzD from Pseudomonas sp. strain ADP. Appl Environ Microbiol 69 : 3653– 3657.[PubMed][CrossRef]
88. Mandelbaum RT, Allan DL, Wackett LP. 1995. Isolation and characterization of a Pseudomonas sp. that mineralizes the s-triazine herbicide atrazine. Appl Environ Microbiol 61 : 1451– 1457.[PubMed]
89. Garcia-Gonzalez V, Govantes F, Porrua O, Santero E. 2005. Regulation of the Pseudomonas sp. strain ADP cyanuric acid degradation operon. J Bacteriol 187 : 155– 167.[PubMed][CrossRef]
90. Sorensen SR, Rasmussen J, Jacobsen CS, Jacobsen OS, Juhler RK, Aamand J. 2005. Elucidating the key member of a linuron-mineralizing bacterial community by PCR and reverse transcription-PCR denaturing gradient gel electrophoresis 16S rRNA gene fingerprinting and cultivation. Appl Environ Microbiol 71 : 4144– 4148.[PubMed][CrossRef]
91. El-Fantroussi S, Verstraete W, Top EM. 2000. Enrichment and molecular characterization of a bacterial culture that degrades methoxy-methyl urea herbicides and their aniline derivatives. Appl Environ Microbiol 66 : 5110– 5115.[PubMed][CrossRef]
92. Breugelmans P, D'Huys PJ, De Mot R, Springael D. 2007. Characterization of novel linuron-mineralizing bacterial consortia enriched from long-term linuron-treated agricultural soils. FEMS Microbiol Ecol 62 : 374– 385.[PubMed][CrossRef]
93. Satola B, Wubbeler JH, Steinbuchel A. 2013. Metabolic characteristics of the species Variovorax paradoxus. Appl Microbiol Biotechnol 97 : 541– 560.[PubMed][CrossRef]
94. Bers K, Sniegowski K, De Mot R, Springael D. 2012. Dynamics of the linuron hydrolase libA gene pool size in response to linuron application and environmental perturbations in agricultural soil and on-farm biopurification systems. Appl Environ Microbiol 78 : 2783– 2789.[PubMed][CrossRef]
95. Sudharshan S, Naidu R, Mallavarapu M, Bolan N. 2012. DDT remediation in contaminated soils: a review of recent studies. Biodegradation 23 : 851– 863.[PubMed][CrossRef]
96. Bao P, Hu ZY, Wang XJ, Chen J, Ba YX, Hua J, Zhu CY, Zhong M, Wu CY. 2012. Dechlorination of p,p'-DDTs coupled with sulfate reduction by novel sulfate-reducing bacterium Clostridium sp. BXM. Environ Pollut 162 : 303– 310.[PubMed][CrossRef]
97. Li FB, Li XM, Zhou SG, Zhuang L, Cao F, Huang DY, Xu W, Liu TX, Feng CH. 2010. Enhanced reductive dechlorination of DDT in an anaerobic system of dissimilatory iron-reducing bacteria and iron oxide. Environ Pollut 158 : 1733– 1740.[PubMed][CrossRef]
98. Nadeau LJ, Sayler GS, Spain JC. 1998. Oxidation of 1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) by Alcaligenes eutrophus A5. Arch Microbiol 171 : 44– 49.[PubMed][CrossRef]
99. Hay AG, Focht DD. 2000. Transformation of 1,1-dichloro-2,2-(4-chlorophenyl)ethane (DDD) by Ralstonia eutropha strain A5. FEMS Microbiol Ecol 31 : 249– 253.[PubMed][CrossRef]
100. Hay AG, Focht DD. 1998. Cometabolism of 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene by Pseudomonas acidovorans M3GY grown on biphenyl. Appl Environ Microbiol 64 : 2141– 2146.[PubMed]
101. Kamanavalli CM, Ninnekar HZ. 2004. Biodegradation of DDT by a Pseudomonas species. Curr Microbiol 48 : 10– 13.[PubMed][CrossRef]
102. Aislabie J, Davison AD, Boul HL, Franzmann PD, Jardine DR, Karuso P. 1999. Isolation of Terrabacter sp. strain DDE-1, which metabolizes 1,1-dichloro-2,2-bis(4-chlorophenyl)ethylene when induced with biphenyl. Appl Environ Microbiol 65 : 5607– 5611.[PubMed]
103. L'Abbee 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]
104. Rangachary L, Rajagopalan RP, Singh TM, Krishnan MH. 2012. Purification and characterization of DDT-dehydrohalogenase from Pseudomonas putida T5. Prep Biochem Biotechnol 42 : 60– 76.[PubMed][CrossRef]
105. Purnomo AS, Kamei I, Kondo R. 2008. Degradation of 1,1,1-trichloro-2,2-bis (4-chlorophenyl) ethane (DDT) by brown-rot fungi. J Biosci Bioeng 105 : 614– 621.[PubMed][CrossRef]
106. Xiao P, Mori T, Kamei I, Kondo R. 2011. A novel metabolic pathway for biodegradation of DDT by the white rot fungi, Phlebia lindtneri and Phlebia brevispora. Biodegradation 22 : 859– 867.[PubMed][CrossRef]
107. Sari AA, Tachibana S, Itoh K. 2012. Determination of co-metabolism for 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT) degradation with enzymes from Trametes versicolor U97. J Biosci Bioeng 114 : 176– 181.[PubMed][CrossRef]
108. Huang Y, Wang J. 2013. Degradation and mineralization of DDT by the ectomycorrhizal fungi, Xerocomus chrysenteron. Chemosphere 92 : 760– 764. 101.[PubMed][CrossRef]
109. Suhara H, Adachi A, Kamei I, Maekawa N. 2011. Degradation of chlorinated pesticide DDT by litter-decomposing basidiomycetes. Biodegradation 22 : 1075– 1086.[PubMed][CrossRef]
110. Matsumoto E, Kawanaka Y, Yun SJ, Oyaizu H. 2009. Bioremediation of the organochlorine pesticides, dieldrin and endrin, and their occurrence in the environment. Appl Environ Microbiol 84 : 205– 216, 103.
111. Xiao P, Mori T, Kamei I, Kiyota H, Takagi K, Kondo R. 2011. Novel metabolic pathways of organochlorine pesticides dieldrin and aldrin by the white rot fungi of the genus Phlebia. Chemosphere 85 : 218– 224.[PubMed][CrossRef]
112. Kataoka R, Takagi K, Kamei I, Kiyota H, Sato Y. 2010. Biodegradation of dieldrin by a soil fungus isolated from a soil with annual endosulfan applications. Environ Sci Technol 44 : 6343– 6349.[PubMed][CrossRef]
113. Xiao P, Mori T, Kondo R. 2011. Biotransformation of the organochlorine pesticide trans-chlordane by wood-rot fungi. New Biotechnol 29 : 107– 115.[CrossRef]
114. Xiao P, Mori T, Kamei I, Kondo R. 2011. Metabolism of organochlorine pesticide heptachlor and its metabolite heptachlor epoxide by white rot fungi, belonging to genus Phlebia. FEMS Microbiol Lett 314 : 140– 146.[PubMed][CrossRef]
115. Jayachandran G, Gorisch H, Adrian L. 2003. Dehalorespiration with hexachlorobenzene and pentachlorobenzene by Dehalococcoides sp. strain CBDB1. Arch Microbiol 180 : 411– 416.[PubMed][CrossRef]
116. Fennell DE, Nijenhuis I, Wilson SF, Zinder SH, Haggblom MM. 2004. Dehalococcoides ethenogenes strain 195 reductively dechlorinates diverse chlorinated aromatic pollutants. Environ Sci Technol 38 : 2075– 2081.[PubMed][CrossRef]
117. Wu Q, Milliken CE, Meier GP, Watts JE, Sowers KR, May HD. 2002. Dechlorination of chlorobenzenes by a culture containing bacterium DF-1, a PCB dechlorinating microorganism. Environ Sci Technol 36 : 3290– 3294.[PubMed][CrossRef]
118. Adrian L, Rahnenfuhrer J, Gobom J, Holscher T. 2007. Identification of a chlorobenzene reductive dehalogenase in Dehalococcoides sp. strain CBDB1. Appl Environ Microbiol 73 : 7717– 7724.[PubMed][CrossRef]
119. Tas N, van Eekert MH, Wagner A, Schraa G, de Vos WM, Smidt H. 2011. Role of “ Dehalococcoides” spp. in the anaerobic transformation of hexachlorobenzene in European rivers. Appl Environ Microbiol 77 : 4437– 4445.[PubMed][CrossRef]
120. Duan TH, Adrian L. 2013. Enrichment of hexachlorobenzene and 1,3,5-trichlorobenzene transforming bacteria from sediments in Germany and Vietnam. Biodegradation 24 : 513– 520.[PubMed][CrossRef]
121. Takagi K, Iwasaki A, Kamei I, Satsuma K, Yoshioka Y, Harada N. 2009. Aerobic mineralization of hexachlorobenzene by newly isolated pentachloronitrobenzene-degrading Nocardioides sp. strain PD653. Appl Environ Microbiol 75 : 4452– 4458.[PubMed][CrossRef]
122. Xu F, Bell SG, Rao Z, Wong LL. 2007. Structure-activity correlations in pentachlorobenzene oxidation by engineered cytochrome P450cam. Protein Eng Des Sel 20 : 473– 480.[PubMed][CrossRef]
123. Yan DZ, Liu H, Zhou NY. 2006. Conversion of Sphingobium chlorophenolicum ATCC 39723 to a hexachlorobenzene degrader by metabolic engineering. Appl Environ Microbiol 72 : 2283– 2286.[PubMed][CrossRef]
124. Bezchlebova J, Cernohlavkova J, Lana J, Sochova I, Kobeticova K, Hofman J. 2007. Effects of toxaphene on soil organisms. Ecotoxicol Environ Safety 68 : 326– 334.[PubMed][CrossRef]
125. Lacayo-Romero M, Quillaguaman J, van Bavel B, Mattiasson B. 2005. A toxaphene-degrading bacterium related to Enterobacter cloacae, strain D1 isolated from aged contaminated soil in Nicaragua. Syst Appl Microbiol 28 : 632– 639.[PubMed][CrossRef]
126. Lacayo Romero M, Terrazas E, van Bavel B, Mattiasson B. 2006. Degradation of toxaphene by Bjerkandera sp. strain BOL13 using waste biomass as a cosubstrate. Appl Microbiol Biotechnol 71 : 549– 554.[PubMed][CrossRef]
127. Fernandez-Bayo JD, Saison C, Voltz M, Disko U, Hofmann D, Berns AE. 2013. Chlordecone fate and mineralisation in a tropical soil (andosol) microcosm under aerobic conditions. Sci Total Environ 463 : 395– 403.[PubMed][CrossRef]
128. Copley SD. 2000. Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach. Tre Biochem Sci 25 : 261– 265.[CrossRef]
129. Copley SD. 2003. Enzymes with extra talents: moonlighting functions and catalytic promiscuity. Curr Opin Chem Biol 7 : 265– 272.[PubMed][CrossRef]
130. Janssen DB, Dinkla IJ, Poelarends GJ, Terpstra P. 2005. Bacterial degradation of xenobiotic compounds: evolution and distribution of novel enzyme activities. Environ Microbiol 7 : 1868– 1882.[PubMed][CrossRef]
131. Copley SD. 2009. Evolution of efficient pathways for degradation of anthropogenic chemicals. Nature Chem Biol 5 : 559– 566.[CrossRef]
132. Fetzner S. 1998. Bacterial dehalogenation. Appl Microbiol Biotechnol 50 : 633– 657.[PubMed][CrossRef]
133. Janssen DB, Oppentocht JE, Poelarends GJ. 2001. Microbial dehalogenation. Cur Opin Biotechnol 12 : 254– 258.[CrossRef]
134. de Jong RM, Dijkstra BW. 2003. Structure and mechanism of bacterial dehalogenases: different ways to cleave a carbon-halogen bond. Curr Opin Struc Biol 13 : 722– 730.[CrossRef]
135. Nagata Y, Miyauchi K, Damborsky J, Manova K, Ansorgova A, Takagi M. 1997. Purification and characterization of a haloalkane dehalogenase of a new substrate class from a γ-hexachlorocyclohexane-degrading bacterium, Sphingomonas paucimobilis UT26. Appl Environ Microbiol 63 : 3707– 3710.[PubMed]
136. de Souza ML, Sadowsky MJ, Wackett LP. 1996. Atrazine chlorohydrolase from Pseudomonas sp. strain ADP: gene sequence, enzyme purification, and protein characterization. J Bacteriol 178 : 4894– 4900.[PubMed]
137. Miyauchi K, Suh S-K, Nagata Y, Takagi M. 1998. Cloning and sequencing of a 2,5-dichlorohydroquinone reductive dehalogenase gene whose product is involved in degradation of γ-hexachlorocyclohexane by Sphingomonas paucimobilis. J Bacteriol 180 : 1354– 1359.[PubMed]
138. Nagata Y, Hatta T, Imai R, Kimbara K, Fukuda M, Yano K, Takagi M. 1993. Purification and characterization of γ-hexachlorocyclohexane (γ-HCH) dehydrochlorinase (LinA) from Pseudomonas paucimobilis. Biosci Biotech Biochem 57 : 1582– 1583.[CrossRef]
139. Seibert V, Stadler-Fritzsche K, Schlomann M. 1993. Purification and characterization of maleylacetate reductase from Alcaligenes eutrophus JMP134(pJP4). J Bacteriol 175 : 6745– 6754.[PubMed]
140. Endo R, Kamakura M, Miyauchi K, Fukuda M, Ohtsubo Y, Tsuda M, Nagata Y. 2005. Identification and characterization of genes involved in the downstream degradation pathway of γ-hexachlorocyclohexane in Sphingomonas paucimobilis UT26. J Bacteriol 187 : 847– 853.[PubMed][CrossRef]
141. Perkins EJ, Gordon MP, Caceres O, Lurquin PF. 1990. Organization and sequence analysis of the 2,4-dichlorophenol hydroxylase and dichlorocatechol oxidative operons of plasmid pJP4. J Bacteriol 172 : 2351– 2359.[PubMed]
142. Miyauchi K, Adachi Y, Nagata Y, Takagi M. 1999. Cloning and sequencing of a novel meta-cleavage dioxygenase gene whose product is involved in degradation of γ-hexachlorocyclohexane in Sphingomonas paucimobilis. J Bacteriol 181 : 6712– 6719.[PubMed]
143. Gribble GW. 2003. The diversity of naturally produced organohalogens. Chemosphere 52 : 289– 297.[PubMed][CrossRef]
144. Wagner C, El Omari M, Konig GM. 2009. Biohalogenation: nature's way to synthesize halogenated metabolites (dagger). J Nat Prod 72 : 540– 553.[PubMed][CrossRef]
145. Kurihara T, Esaki N. 2008. Bacterial hydrolytic dehalogenases and related enzymes: occurrences, reaction mechanisms, and applications. Chem Record 8 : 67– 74.[CrossRef]
146. Nagasawa S, Kikuchi R, Nagata Y, Takagi M, Matsuo M. 1993. Stereochemical analysis of γ-HCH degradation by Pseudomonas paucimobilis UT26. Chemosphere 26 : 1187– 1201.[CrossRef]
147. Trantirek L, Hynkova K, Nagata Y, Murzin A, Ansorgova A, Sklenar V, Damborsky J. 2001. Reaction mechanism and stereochemistry of γ-hexachlorocyclohexane dehydrochlorinase LinA. J Biol Chem 276 : 7734– 7740.[PubMed][CrossRef]
148. Nagata Y, Mori K, Takagi M, Murzin AG, Damborsky J. 2001. Identification of protein fold and catalytic residues of γ-hexachlorocyclohexane dehydrochlorinase LinA. Proteins 45 : 471– 477.[PubMed][CrossRef]
149. Okai M, Kubota K, Fukuda M, Nagata Y, Nagata K, Tanokura M. 2010. Crystal structure of γ-hexachlorocyclohexane dehydrochlorinase LinA from Sphingobium japonicum UT26. J Mol Biol 403 : 260– 269.[PubMed][CrossRef]
150. Kumari R, Subudhi S, Suar M, Dhingra G, Raina V, Dogra C, Lal S, van der Meer JR, Holliger C, Lal R. 2002. Cloning and characterization of lin genes responsible for the degradation of hexachlorocyclohexane isomers by Sphingomonas paucimobilis strain B90. Appl Environ Microbiol 68 : 6021– 6028.[PubMed][CrossRef]
151. Suar M, Hauser A, Poiger T, Buser HR, Muller MD, Dogra C, Raina V, Holliger C, van der Meer JR, Lal R, Kohler HP. 2005. Enantioselective transformation of a-hexachlorocyclohexane by the dehydrochlorinases LinA1 and LinA2 from the soil bacterium Sphingomonas paucimobilis B90A. Appl Environ Microbiol 71 : 8514– 8518.[PubMed][CrossRef]
152. Macwan AS, Kukshal V, Srivastava N, Javed S, Kumar A, Ramachandran R. 2012. Crystal structure of the hexachlorocyclohexane dehydrochlorinase (LinA-type2): mutational analysis, thermostability and enantioselectivity. PLoS One 7 : e50373.[PubMed][CrossRef]
153. Macwan AS, Javed S, Kumar A. 2011. Isolation of a novel thermostable dehydrochlorinase (LinA) from a soil metagenome. 3 Biotech 1 : 193– 198.[PubMed][CrossRef]
154. Nagata Y, Miyauchi K, Takagi M. 1999. Complete analysis of genes and enzymes for γ-hexachlorocyclohexane degradation in Sphingomonas paucimobilis UT26. J Ind Microbiol Biotechnol 23 : 380– 390.[PubMed][CrossRef]
155. Boubakri H, Beuf M, Simonet P, Vogel TM. 2006. Development of metagenomic DNA shuffling for the construction of a xenobiotic gene. Gene 375 : 87– 94.[PubMed][CrossRef]
156. Peisajovich SG, Rockah L, Tawfik DS. 2006. Evolution of new protein topologies through multistep gene rearrangements. Nat Genet 38 : 168– 174.[PubMed][CrossRef]
157. Koudelakova T, Chovancova E, Brezovsky J, Monincova M, Fortova A, Jarkovsky J, Damborsky J. 2011. Substrate specificity of haloalkane dehalogenases. Biochem J 435 : 345– 354.[PubMed][CrossRef]
158. Koudelakova T, Bidmanova S, Dvorak P, Pavelka A, Chaloupkova R, Prokop Z, Damborsky J. 2013. Haloalkane dehalogenases: biotechnological applications. Biotechnol J 8 : 32– 45.[PubMed][CrossRef]
159. Marek J, Vevodova J, Smatanova IK, Nagata Y, Svensson LA, Newman J, Takagi M, Damborsky J. 2000. Crystal structure of the haloalkane dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39 : 14082– 14086.[PubMed][CrossRef]
160. Oakley AJ, Prokop Z, Bohac M, Kmunicek J, Jedlicka T, Monincova M, Kuta-Smatanova I, Nagata Y, Damborsky J, Wilce MC. 2002. Exploring the structure and activity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26: evidence for product- and water-mediated inhibition. Biochemistry 41 : 4847– 4855.[PubMed][CrossRef]
161. Oakley AJ, Klvana M, Otyepka M, Nagata Y, Wilce MC, Damborsky J. 2004. Crystal structure of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26 at 0.95 A resolution: dynamics of catalytic residues. Biochemistry 43 : 870– 878.[PubMed][CrossRef]
162. Streltsov VA, Prokop Z, Damborsky J, Nagata Y, Oakley A, Wilce MCJ. 2003. Haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray crystallographic studies of dehalogenation of brominated substrates. Biochemistry 42 : 10104– 10112.[PubMed][CrossRef]
163. Prokop Z, Monincova M, Chaloupkova R, Klvana M, Nagata Y, Janssen DB, Damborsky J. 2003. Catalytic mechanism of the haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. J Biol Chem 278 : 45094– 45100.[PubMed][CrossRef]
164. Chaloupkova R, Sykorova J, Prokop Z, Jesenska A, Monincova M, Pavlova M, Tsuda M, Nagata Y, Damborsky J. 2003. Modification of activity and specificity of haloalkane dehalogenase from Sphingomonas paucimobilis UT26 by engineering of its entrance tunnel. J Biol Chem 278 : 52622– 52628.[PubMed][CrossRef]
165. Nagata Y, Prokop Z, Marvanova S, Sykorova J, Monincova M, Tsuda M, Damborsky J. 2003. Reconstruction of mycobacterial dehalogenase Rv2579 by cumulative mutagenesis of haloalkane dehalogenase LinB. Appl Environ Microbiol 69 : 2349– 2355.[PubMed][CrossRef]
166. Damborsky J, Rorije E, Jesenska A, Nagata Y, Klopman G, Peijnenburg WJGM. 2001. Structure-specificity relationships for haloalkane dehalogenases. Environ Toxi Chem 20 : 2681– 2689.
167. Kmunicek J, Hynkova K, Jedlicka T, Nagata Y, Negri A, Gago F, Wade RC, Damborsky J. 2005. Quantitative analysis of substrate specificity of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Biochemistry 44 : 3390– 3401.[PubMed][CrossRef]
168. Okai M, Ohtsuka J, Imai LF, Mase T, Moriuchi R, Tsuda M, Nagata K, Nagata Y, Tanokura M. 2013. Crystal structure and site-directed mutagenesis analyses of haloalkane dehalogenase LinB from Sphingobium sp. strain MI1205. J Bacteriol 195 : 2642– 2651.[PubMed][CrossRef]
169. Nagata Y, Prokop Z, Sato Y, Jerabek P, Kumar A, Ohtsubo Y, Tsuda M, Damborsky J. 2005. Degradation of β-hexachlorocyclohexane by haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Appl Environ Microbiol 71 : 2183– 2185.[PubMed][CrossRef]
170. Sharma P, Raina V, Kumari R, Malhotra S, Dogra C, Kumari H, Kohler HP, Buser HR, Holliger C, Lal R. 2006. Haloalkane dehalogenase LinB is responsible for β- and δ-hexachlorocyclohexane transformation in Sphingobium indicum B90A. Appl Environ Microbiol 72 : 5720– 5727.[PubMed][CrossRef]