메뉴 건너뛰기




Volumn 78, Issue 8, 2012, Pages 2706-2715

Characterization of biphenyl dioxygenase sequences and activities encoded by the metagenomes of highly polychlorobiphenyl-contaminated soils

Author keywords

[No Author keywords available]

Indexed keywords

ACTIVE SITE; AMPLICONS; AROMATIC RINGS; BIPHENYL DIOXYGENASE; CELL EXTRACTS; CHLOROBIPHENYL; CLUSTER-II; CONTAMINATED SOILS; DIFFERENT SUBSTRATES; DIOXYGENASES; DNA SEGMENTS; METAGENOMES; PCR AMPLIFICATION; PRODUCT RANGES; RECOMBINANT HOSTS; RHODOCOCCUS; SEQUENCE IDENTITY; SEQUENCE SIMILARITY;

EID: 84861117179     PISSN: 00992240     EISSN: 10985336     Source Type: Journal    
DOI: 10.1128/AEM.07381-11     Document Type: Article
Times cited : (13)

References (44)
  • 1
    • 35148839449 scopus 로고    scopus 로고
    • Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation
    • Aguirre de Cárcer D, Martín M, Karlson U, Rivilla R. 2007. Changes in bacterial populations and in biphenyl dioxygenase gene diversity in a polychlorinated biphenyl-polluted soil after introduction of willow trees for rhizoremediation. Appl. Environ. Microbiol. 73:6224-6232.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 6224-6232
    • Aguirre de Cárcer, D.1    Martín, M.2    Karlson, U.3    Rivilla, R.4
  • 3
    • 0028946084 scopus 로고
    • Phylogenetic identification and in situ detection of individual microbial cells without cultivation
    • Amann RI, Ludwig W, Schleifer K-H. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59:143-169.
    • (1995) Microbiol. Rev. , vol.59 , pp. 143-169
    • Amann, R.I.1    Ludwig, W.2    Schleifer, K.-H.3
  • 4
    • 0032849333 scopus 로고    scopus 로고
    • Occurrence and expression of glutathione S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria
    • Bartels F, Backhaus S, Moore ERB, Timmis KN, Hofer B. 1999. Occurrence and expression of glutathione S-transferase-encoding bphK genes in Burkholderia sp. strain LB400 and other biphenyl-utilizing bacteria. Microbiology 145:2821-2834.
    • (1999) Microbiology , vol.145 , pp. 2821-2834
    • Bartels, F.1    Backhaus, S.2    Moore, E.R.B.3    Timmis, K.N.4    Hofer, B.5
  • 5
    • 0033572464 scopus 로고    scopus 로고
    • A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports
    • Berggren K, et al. 1999. A luminescent ruthenium complex for ultrasensitive detection of proteins immobilized on membrane supports. Anal. Biochem. 276:129 -143.
    • (1999) Anal. Biochem. , vol.276 , pp. 129-143
    • Berggren, K.1
  • 6
    • 0040684812 scopus 로고    scopus 로고
    • Tuning biphenyl dioxygenase for extended substrate specificity
    • Brühlmann F, Chen W. 1999. Tuning biphenyl dioxygenase for extended substrate specificity. Biotechnol. Bioeng. 63:544 -551.
    • (1999) Biotechnol. Bioeng. , vol.63 , pp. 544-551
    • Brühlmann, F.1    Chen, W.2
  • 7
    • 0031060718 scopus 로고    scopus 로고
    • Structure-function analysis of the bacterial aromatic ring-hydroxylating dioxygenases
    • Butler CS, Mason JR. 1997. Structure-function analysis of the bacterial aromatic ring-hydroxylating dioxygenases. Adv. Microb. Physiol. 38:47- 84.
    • (1997) Adv. Microb. Physiol. , vol.38 , pp. 47-84
    • Butler, C.S.1    Mason, J.R.2
  • 8
    • 3543137239 scopus 로고    scopus 로고
    • From PCBs to highly toxic metabolites by the biphenyl pathway
    • Cámara B, et al. 2004. From PCBs to highly toxic metabolites by the biphenyl pathway. Environ. Microbiol. 6:842- 850.
    • (2004) Environ. Microbiol. , vol.6 , pp. 842-850
    • Cámara, B.1
  • 9
    • 34247578205 scopus 로고    scopus 로고
    • Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls
    • Cámara B, et al. 2007. Generation by a widely applicable approach of a hybrid dioxygenase showing improved oxidation of polychlorobiphenyls. Appl. Environ. Microbiol. 73:2682-2689.
    • (2007) Appl. Environ. Microbiol. , vol.73 , pp. 2682-2689
    • Cámara, B.1
  • 10
    • 70849099064 scopus 로고    scopus 로고
    • Terminal-restriction fragment length polymorphism analysis of biphenyl dioxygenase genes from a polychlorinated biphenyl-polluted soil
    • Capodicasa S, et al. 2009. Terminal-restriction fragment length polymorphism analysis of biphenyl dioxygenase genes from a polychlorinated biphenyl-polluted soil. Res. Microbiol. 160:742-750.
    • (2009) Res. Microbiol. , vol.160 , pp. 742-750
    • Capodicasa, S.1
  • 11
    • 0036896381 scopus 로고    scopus 로고
    • Identification and analysis of a bottleneck in PCB biodegradation
    • Dai S, et al. 2002. Identification and analysis of a bottleneck in PCB biodegradation. Nat. Struct. Biol. 9:934 -939.
    • (2002) Nat. Struct. Biol. , vol.9 , pp. 934-939
    • Dai, S.1
  • 13
    • 0029875264 scopus 로고    scopus 로고
    • Aroclor 1221 aerobic dechlorination by a bacterial coculture: role of chlorobenzoic acid degrading bacteria in the process
    • Fava F. 1996. Aroclor 1221 aerobic dechlorination by a bacterial coculture: role of chlorobenzoic acid degrading bacteria in the process. Chemosphere 32:1477-1483.
    • (1996) Chemosphere , vol.32 , pp. 1477-1483
    • Fava, F.1
  • 14
    • 0027223958 scopus 로고
    • Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon)
    • Furukawa K, Hirose J, Suyama A, Zaiki T, Hayashida SJ. 1993. Gene components responsible for discrete substrate specificity in the metabolism of biphenyl (bph operon) and toluene (tod operon). J. Bacteriol. 175: 5224-5232.
    • (1993) J. Bacteriol. , vol.175 , pp. 5224-5232
    • Furukawa, K.1    Hirose, J.2    Suyama, A.3    Zaiki, T.4    Hayashida, S.J.5
  • 15
    • 3843075198 scopus 로고    scopus 로고
    • Biphenyl dioxygenases: functional versatilities and directed evolution
    • Furukawa K, Suenaga H, Goto M. 2004. Biphenyl dioxygenases: functional versatilities and directed evolution. J. Bacteriol. 186:5189 -5196.
    • (2004) J. Bacteriol. , vol.186 , pp. 5189-5196
    • Furukawa, K.1    Suenaga, H.2    Goto, M.3
  • 16
    • 77954296666 scopus 로고    scopus 로고
    • A new bioinformatics analysis tools framework at EMBL-EBI
    • Goujon M, et al. 2010. A new bioinformatics analysis tools framework at EMBL-EBI. Nucleic Acids Res. 38(Suppl. 2):W695-W699.
    • (2010) Nucleic Acids Res , vol.38 , Issue.SUPPL. 2
    • Goujon, M.1
  • 17
    • 0026464545 scopus 로고
    • Degradation of Aroclor 1221 and survival of strains in soil microcosms
    • Havel J, Reineke W. 1992. Degradation of Aroclor 1221 and survival of strains in soil microcosms. Appl. Microbiol. Biotechnol. 38:129 -134.
    • (1992) Appl. Microbiol. Biotechnol. , vol.38 , pp. 129-134
    • Havel, J.1    Reineke, W.2
  • 18
    • 76349086053 scopus 로고    scopus 로고
    • Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment
    • Iwai S, et al. 2010. Gene-targeted-metagenomics reveals extensive diversity of aromatic dioxygenase genes in the environment. ISME J. 4:279-285.
    • (2010) ISME J , vol.4 , pp. 279-285
    • Iwai, S.1
  • 19
    • 0037804252 scopus 로고    scopus 로고
    • A genetic system for the rapid isolation of aromaticring-hydroxylating dioxygenase activities
    • Kahl S, Hofer B. 2003. A genetic system for the rapid isolation of aromaticring-hydroxylating dioxygenase activities. Microbiology 149:1475-1481.
    • (2003) Microbiology , vol.149 , pp. 1475-1481
    • Kahl, S.1    Hofer, B.2
  • 20
    • 0031874757 scopus 로고    scopus 로고
    • Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase
    • Kumamaru T, Suenaga H, Mitsuoka M, Watanabe T, Furukawa K. 1998. Enhanced degradation of polychlorinated biphenyls by directed evolution of biphenyl dioxygenase. Nat. Biotechnol. 16:663- 666.
    • (1998) Nat. Biotechnol. , vol.16 , pp. 663-666
    • Kumamaru, T.1    Suenaga, H.2    Mitsuoka, M.3    Watanabe, T.4    Furukawa, K.5
  • 21
    • 78650864361 scopus 로고    scopus 로고
    • Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution
    • Kumar P, et al. 2011. Structural insight into the expanded PCB-degrading abilities of a biphenyl dioxygenase obtained by directed evolution. J. Mol. Biol. 405:531-547.
    • (2011) J. Mol. Biol. , vol.405 , pp. 531-547
    • Kumar, P.1
  • 22
    • 36448991500 scopus 로고    scopus 로고
    • ClustalW and ClustalX version 2
    • Larkin MA, et al. 2007. ClustalW and ClustalX version 2. Bioinformatics 23:2947-2948.
    • (2007) Bioinformatics , vol.23 , pp. 2947-2948
    • Larkin, M.A.1
  • 23
    • 33845873289 scopus 로고    scopus 로고
    • Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation
    • Letunic I, Bork P. 2007. Interactive tree of life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23:127-128.
    • (2007) Bioinformatics , vol.23 , pp. 127-128
    • Letunic, I.1    Bork, P.2
  • 24
    • 79960004119 scopus 로고    scopus 로고
    • Interactive tree of life v2: online annotation and display of phylogenetic trees made easy
    • Letunic I, Bork P. 2011. Interactive tree of life v2: online annotation and display of phylogenetic trees made easy. Nucleic Acids Res. 39(Suppl. 2): W475-W478.
    • (2011) Nucleic Acids Res , vol.39 , Issue.SUPPL. 2
    • Letunic, I.1    Bork, P.2
  • 25
    • 0036900864 scopus 로고    scopus 로고
    • Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space
    • Lorenz P, Liebeton K, Niehaus F, Eck J. 2002. Screening for novel enzymes for biocatalytic processes: accessing the metagenome as a resource of novel functional sequence space. Curr. Opin. Biotechnol. 13: 572-577.
    • (2002) Curr. Opin. Biotechnol. , vol.13 , pp. 572-577
    • Lorenz, P.1    Liebeton, K.2    Niehaus, F.3    Eck, J.4
  • 26
    • 0033140436 scopus 로고    scopus 로고
    • Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil
    • Nogales B, Moore ERB, Abraham W-R, Timmis KN. 1999. Identification of the metabolically active members of a bacterial community in a polychlorinated biphenyl-polluted moorland soil. Environ. Microbiol. 1:199 -212.
    • (1999) Environ. Microbiol. , vol.1 , pp. 199-212
    • Nogales, B.1    Moore, E.R.B.2    Abraham, W.-R.3    Timmis, K.N.4
  • 27
    • 0035321749 scopus 로고    scopus 로고
    • Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenylpolluted soil
    • Nogales B, et al. 2001. Combined use of 16S ribosomal DNA and 16S rRNA to study the bacterial community of polychlorinated biphenylpolluted soil. Appl. Environ. Microbiol. 67:1874 -1884.
    • (2001) Appl. Environ. Microbiol. , vol.67 , pp. 1874-1884
    • Nogales, B.1
  • 28
    • 33750058274 scopus 로고    scopus 로고
    • Coping with polychlorinated biphenyl (PCB) toxicity: physiological and genome-wide responses of Burkholderia xenovorans LB400 to PCB-mediated stress
    • Parnell JJ, et al. 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.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 6607-6614
    • Parnell, J.J.1
  • 29
    • 0025891425 scopus 로고
    • Correlation of aqueous solubility and octanol-water partition coefficient based on molecular structure
    • Patil GS. 1991. Correlation of aqueous solubility and octanol-water partition coefficient based on molecular structure. Chemosphere 22:723-738.
    • (1991) Chemosphere , vol.22 , pp. 723-738
    • Patil, G.S.1
  • 30
    • 0037224809 scopus 로고    scopus 로고
    • 2- Hydroxypenta-2,4-dienoate metabolic pathway genes in a strong polychlorinated biphenyl degrader Rhodococcus sp. strain RHA1
    • Sakai M, Miyauchi K, Kato N, Masai E, Fukuda M. 2003. 2-Hydroxypenta-2,4-dienoate metabolic pathway genes in a strong polychlorinated biphenyl degrader, Rhodococcus sp. strain RHA1. Appl. Environ. Microbiol. 69:427- 433.
    • (2003) Appl. Environ. Microbiol. , vol.69 , pp. 427-433
    • Sakai, M.1    Miyauchi, K.2    Kato, N.3    Masai, E.4    Fukuda, M.5
  • 32
  • 33
    • 0034717267 scopus 로고    scopus 로고
    • Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls
    • Seah SY, et al. 2000. Identification of a serine hydrolase as a key determinant in the microbial degradation of polychlorinated biphenyls. J. Biol. Chem. 275:15701-15708.
    • (2000) J. Biol. Chem. , vol.275 , pp. 15701-15708
    • Seah, S.Y.1
  • 34
    • 0029032311 scopus 로고
    • Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400
    • Seeger M, Timmis KN, Hofer B. 1995. Conversion of chlorobiphenyls into phenylhexadienoates and benzoates by the enzymes of the upper pathway for polychlorobiphenyl degradation encoded by the bph locus of Pseudomonas sp. strain LB400. Appl. Environ. Microbiol. 61:761-768.
    • (1995) Appl. Environ. Microbiol. , vol.61 , pp. 761-768
    • Seeger, M.1    Timmis, K.N.2    Hofer, B.3
  • 35
    • 0032765989 scopus 로고    scopus 로고
    • Regiospecificity of dioxygenation of di-to pentachlorobiphenyls and their degradation to chlorobenzoates by the bph-encoded catabolic pathway of Burkholderia sp. strain LB400
    • Seeger M, Zielinski M, Timmis KN, Hofer B. 1999. Regiospecificity of dioxygenation of di- to pentachlorobiphenyls and their degradation to chlorobenzoates by the bph-encoded catabolic pathway of Burkholderia sp. strain LB400. Appl. Environ. Microbiol. 65:3614 -3621.
    • (1999) Appl. Environ. Microbiol. , vol.65 , pp. 3614-3621
    • Seeger, M.1    Zielinski, M.2    Timmis, K.N.3    Hofer, B.4
  • 36
    • 0035933899 scopus 로고    scopus 로고
    • Emergence of multifunctional oxygenase activities by random priming recombination
    • Suenaga H, Goto M, Furukawa K. 2001. Emergence of multifunctional oxygenase activities by random priming recombination. J. Biol. Chem. 276:22500 -22506.
    • (2001) J. Biol. Chem. , vol.276 , pp. 22500-22506
    • Suenaga, H.1    Goto, M.2    Furukawa, K.3
  • 37
    • 34547748431 scopus 로고    scopus 로고
    • Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds
    • Suenaga H, Ohnuki T, Miyazaki K. 2007. Functional screening of a metagenomic library for genes involved in microbial degradation of aromatic compounds. Environ. Microbiol. 9:2289 -2297.
    • (2007) Environ. Microbiol. , vol.9 , pp. 2289-2297
    • Suenaga, H.1    Ohnuki, T.2    Miyazaki, K.3
  • 38
    • 0036285535 scopus 로고    scopus 로고
    • Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering
    • Suenaga H, Watanabe T, Sato M, Ngadiman Furukawa K. 2002. Alteration of regiospecificity in biphenyl dioxygenase by active-site engineering. J. Bacteriol. 184:3682-3688.
    • (2002) J. Bacteriol. , vol.184 , pp. 3682-3688
    • Suenaga, H.1    Watanabe, T.2    Sato, M.3    Ngadiman Furukawa, K.4
  • 39
    • 72649090171 scopus 로고    scopus 로고
    • Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis
    • Suenaga H, et al. 2009. Novel organization of aromatic degradation pathway genes in a microbial community as revealed by metagenomic analysis. ISME J. 3:1335-1348.
    • (2009) ISME J , vol.3 , pp. 1335-1348
    • Suenaga, H.1
  • 41
    • 34247842950 scopus 로고    scopus 로고
    • Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples
    • Witzig R, et al. 2007. Molecular detection and diversity of novel diterpenoid dioxygenase DitA1 genes from proteobacterial strains and soil samples. Environ. Microbiol. 9:1202-1218.
    • (2007) Environ. Microbiol. , vol.9 , pp. 1202-1218
    • Witzig, R.1
  • 42
    • 0036667430 scopus 로고    scopus 로고
    • The principal determinants for the structure of the substrate-binding pocket are located within a central core of a biphenyl dioxygenase alpha subunit
    • Zielinski M, Backhaus S, Hofer B. 2002. The principal determinants for the structure of the substrate-binding pocket are located within a central core of a biphenyl dioxygenase alpha subunit. Microbiology 148:2439-2448.
    • (2002) Microbiology , vol.148 , pp. 2439-2448
    • Zielinski, M.1    Backhaus, S.2    Hofer, B.3
  • 43
    • 0344393452 scopus 로고    scopus 로고
    • Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction
    • Zielinski M, Kahl S, Hecht H-J, Hofer B. 2003. Pinpointing biphenyl dioxygenase residues that are crucial for substrate interaction. J. Bacteriol. 185:6976-6980.
    • (2003) J. Bacteriol. , vol.185 , pp. 6976-6980
    • Zielinski, M.1    Kahl, S.2    Hecht, H.-J.3    Hofer, B.4
  • 44
    • 33644941536 scopus 로고    scopus 로고
    • Generation of novel-substrate-accepting biphenyl dioxygenases through segmental random mutagenesis and identification of residues involved in enzyme specificity
    • Zielinski M, et al. 2006. Generation of novel-substrate-accepting biphenyl dioxygenases through segmental random mutagenesis and identification of residues involved in enzyme specificity. Appl. Environ. Microbiol. 72:2191-2199.
    • (2006) Appl. Environ. Microbiol. , vol.72 , pp. 2191-2199
    • Zielinski, M.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.