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Cerniglia C.E. Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3 (1992) 351-368
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Cerniglia, C.E.1
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A proteomics strategy for the analysis of bacterial biodegradation pathways
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An up-to-date review summarizing proteomics studies in the research of aromatic hydrocarbon degradation.
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Kim S.I., Choi J.S., and Kahng H.Y. A proteomics strategy for the analysis of bacterial biodegradation pathways. Omics 11 (2007) 280-294. An up-to-date review summarizing proteomics studies in the research of aromatic hydrocarbon degradation.
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Omics
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Kim, S.I.1
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Paradigm in biodegradation using Pseudomonas putida - a review of proteomics studies
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A highly interesting review article on proteomics methodologies and applications in P. putida studies.
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Loh K.C., and Cao B. Paradigm in biodegradation using Pseudomonas putida - a review of proteomics studies. Enzyme Microb Technol 43 (2008) 1-12. A highly interesting review article on proteomics methodologies and applications in P. putida studies.
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Loh, K.C.1
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A review on the underlying principles of aromatic hydrocarbon degradation.
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van der Meer J.R., de Vos W.M., Harayama S., and Zehnder A.J. Molecular mechanisms of genetic adaptation to xenobiotic compounds. Microbiol Rev 56 (1992) 677-694. A review on the underlying principles of aromatic hydrocarbon degradation.
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van der Meer, J.R.1
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Microbial biodegradation of polyaromatic hydrocarbons
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A recent comprehensive review on the microbial degradation of PAHs.
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Peng R.H., Xiong A.S., Xue Y., Fu X.Y., Gao F., Zhao W., Tian Y.S., and Yao Q.H. Microbial biodegradation of polyaromatic hydrocarbons. FEMS Microbiol Rev 32 (2008) 927-955. A recent comprehensive review on the microbial degradation of PAHs.
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Peng, R.H.1
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Zhao, W.6
Tian, Y.S.7
Yao, Q.H.8
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6
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43149093388
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A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases
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Kweon O., Kim S.J., Baek S., Chae J.C., Adjei M.D., Baek D.H., Kim Y.C., and Cerniglia C.E. A new classification system for bacterial Rieske non-heme iron aromatic ring-hydroxylating oxygenases. BMC Biochem 9 (2008) 11
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Kweon, O.1
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Limitations of current proteomics technologies
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Garbis S., Lubec G., and Fountoulakis M. Limitations of current proteomics technologies. J Chromatogr A 1077 (2005) 1-18
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Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodococcus sp. strain TFB
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This paper reports that Rhodococcus sp. TFB is refractory to genetic manipulation and mutational analysis. These investigators initially adopt a proteomics approach to determine how this bacterium metabolizes aromatic hydrocarbons, such as phthalate, tetraline, and naphthalene.
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Tomás-Gallardo L., Canosa I., Santero E., Camafeita E., Calvo E., López J.A., and Floriano B. Proteomic and transcriptional characterization of aromatic degradation pathways in Rhodococcus sp. strain TFB. Proteomics 6 Suppl 1 (2006) S119-S132. This paper reports that Rhodococcus sp. TFB is refractory to genetic manipulation and mutational analysis. These investigators initially adopt a proteomics approach to determine how this bacterium metabolizes aromatic hydrocarbons, such as phthalate, tetraline, and naphthalene.
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Tomás-Gallardo, L.1
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Floriano, B.7
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9
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33846251226
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Complete and integrated pyrene degradation pathway in Mycobacterium vanbaalenii PYR-1 based on systems biology
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••], describes for the first time the degradation pathways of HMW PAHs, pyrene, and fluoranthene, using advanced proteomics approaches. Metabolite and genome information were integrated to elucidate the pyrene degradation pathways.
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••], describes for the first time the degradation pathways of HMW PAHs, pyrene, and fluoranthene, using advanced proteomics approaches. Metabolite and genome information were integrated to elucidate the pyrene degradation pathways.
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J Bacteriol
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Kim, S.J.1
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11
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33644540488
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Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis
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Kim Y.H., Cho K., Yun S.H., Kim J.Y., Kwon K.H., Yoo J.S., and Kim S.I. Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis. Proteomics 6 (2006) 1301-1318
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Kim, Y.H.1
Cho, K.2
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Kim, J.Y.4
Kwon, K.H.5
Yoo, J.S.6
Kim, S.I.7
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12
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33846298496
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Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress
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Agulló L., Cámara B., Martínez P., Latorre V., and Seeger M. Response to (chloro)biphenyls of the polychlorobiphenyl-degrader Burkholderia xenovorans LB400 involves stress proteins also induced by heat shock and oxidative stress. FEMS Microbiol Lett 267 (2007) 167-175
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FEMS Microbiol Lett
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Agulló, L.1
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Latorre, V.4
Seeger, M.5
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13
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34547754608
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Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400
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Martínez P., Agulló L., Hernández M., and Seeger M. Chlorobenzoate inhibits growth and induces stress proteins in the PCB-degrading bacterium Burkholderia xenovorans LB400. Arch Microbiol 188 (2007) 289-297
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Martínez, P.1
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14
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28044450599
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Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400
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This study reveals, using a proteomics approach, that the expression of genes involved in the pathways of aromatic hydrocarbon degradation is strongly dependent on growth substrate and growth phase.
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Denef V.J., Patrauchan M.A., Florizone C., Park J., Tsoi T.V., Verstraete W., Tiedje J.M., and Eltis L.D. Growth substrate- and phase-specific expression of biphenyl, benzoate, and C1 metabolic pathways in Burkholderia xenovorans LB400. J Bacteriol 187 (2005) 7996-8005. This study reveals, using a proteomics approach, that the expression of genes involved in the pathways of aromatic hydrocarbon degradation is strongly dependent on growth substrate and growth phase.
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J Bacteriol
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Denef, V.J.1
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15
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Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400
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Denef V.J., Klappenbach J.A., Patrauchan M.A., Florizone C., Rodrigues J.L., Tsoi T.V., Verstraete W., Eltis L.D., and Tiedje J.M. Genetic and genomic insights into the role of benzoate-catabolic pathway redundancy in Burkholderia xenovorans LB400. Appl Environ Microbiol 72 (2006) 585-595
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Denef, V.J.1
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Tsoi, T.V.6
Verstraete, W.7
Eltis, L.D.8
Tiedje, J.M.9
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16
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21144442133
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Phenylacetate catabolism in Rhodococcus sp. strain RHA1: a central pathway for degradation of aromatic compounds
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Navarro-Llorens J.M., Patrauchan M.A., Stewart G.R., Davies J.E., Eltis L.D., and Mohn W.W. Phenylacetate catabolism in Rhodococcus sp. strain RHA1: a central pathway for degradation of aromatic compounds. J Bacteriol 187 (2005) 4497-4504
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J Bacteriol
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Navarro-Llorens, J.M.1
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Eltis, L.D.5
Mohn, W.W.6
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17
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20444506446
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Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence
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This proteomic study confirms the upregulation of some products of the ben and cat genes involved in catechol degradation and pca genes in protocatechuate degradation.
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Patrauchan M.A., Florizone C., Dosanjh M., Mohn W.W., Davies J., and Eltis L.D. Catabolism of benzoate and phthalate in Rhodococcus sp. strain RHA1: redundancies and convergence. J Bacteriol 187 (2005) 4050-4063. This proteomic study confirms the upregulation of some products of the ben and cat genes involved in catechol degradation and pca genes in protocatechuate degradation.
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J Bacteriol
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Patrauchan, M.A.1
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18
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37549066316
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Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1
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Patrauchan M.A., Florizone C., Eapen S., Gómez-Gil L., Sethuraman B., Fukuda M., Davies J., Mohn W.W., and Eltis L.D. Roles of ring-hydroxylating dioxygenases in styrene and benzene catabolism in Rhodococcus jostii RHA1. J Bacteriol 190 (2008) 37-47
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Patrauchan, M.A.1
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19
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58149177511
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Proteomic and molecular investigation on the physiological adaptation of Comamonas sp. strain CNB-1 growing on 4-chloronitrobenzene
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Zhang Y., Wu J.F., Zeyer J., Meng B., Liu L., Jiang C.Y., Liu S.Q., and Liu S.J. Proteomic and molecular investigation on the physiological adaptation of Comamonas sp. strain CNB-1 growing on 4-chloronitrobenzene. Biodegradation 20 (2009) 55-66
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Zhang, Y.1
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20
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33746191929
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The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse
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McLeod M.P., Warren R.L., Hsiao W.W., Araki N., Myhre M., Fernandes C., Miyazawa D., Wong W., Lillquist A.L., Wang D., et al. The complete genome of Rhodococcus sp. RHA1 provides insights into a catabolic powerhouse. Proc Natl Acad Sci U S A 103 (2006) 15582-15587
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McLeod, M.P.1
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Miyazawa, D.7
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Wang, D.10
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21
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8744256465
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Proteome analysis of Pseudomonas sp. K82 biodegradation pathways
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Kim S.I., Kim J.Y., Yun S.H., Kim J.H., Leem S.H., and Lee C. Proteome analysis of Pseudomonas sp. K82 biodegradation pathways. Proteomics 4 (2004) 3610-3621
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Kim, S.I.1
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22
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0036374159
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Enhanced detection and characterization of protocatechuate 3,4-dioxygenase in Acinetobacter lwoffii K24 by proteomics using a column separation
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Kahng H.Y., Cho K., Song S.Y., Kim S.J., Leem S.H., and Kim S.I. Enhanced detection and characterization of protocatechuate 3,4-dioxygenase in Acinetobacter lwoffii K24 by proteomics using a column separation. Biochem Biophys Res Commun 295 (2002) 903-909
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Kahng, H.Y.1
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Kim, S.I.6
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23
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Media containing aromatic compounds induce peculiar proteins in Acinetobacter radioresistens, as revealed by proteome analysis
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Giuffrida M.G., Pessione E., Mazzoli R., Dellavalle G., Barello C., Conti A., and Giunta C. Media containing aromatic compounds induce peculiar proteins in Acinetobacter radioresistens, as revealed by proteome analysis. Electrophoresis 22 (2001) 1705-1711
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Giuffrida, M.G.1
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24
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33846990172
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Characterization of beta-ketoadipate pathway from multi-drug resistance bacterium, Acinetobacter baumannii DU202 by proteomic approach
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Park S.H., Kim J.W., Yun S.H., Leem S.H., Kahng H.Y., and Kim S.I. Characterization of beta-ketoadipate pathway from multi-drug resistance bacterium, Acinetobacter baumannii DU202 by proteomic approach. J Microbiol 44 (2006) 632-640
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Park, S.H.1
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Kim, S.I.6
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25
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Degradation of aromatic compounds by Acinetobacter radioresistens S13: growth characteristics on single substrates and mixtures
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Mazzoli R., Pessione E., Giuffrida M.G., Fattori P., Barello C., Giunta C., and Lindley N.D. Degradation of aromatic compounds by Acinetobacter radioresistens S13: growth characteristics on single substrates and mixtures. Arch Microbiol 188 (2007) 55-68
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Mazzoli, R.1
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26
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The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds
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Morales G., Linares J.F., Beloso A., Albar J.P., Martínez J.L., and Rojo F. The Pseudomonas putida Crc global regulator controls the expression of genes from several chromosomal catabolic pathways for aromatic compounds. J Bacteriol 186 (2004) 1337-1344
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Morales, G.1
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27
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Proteome investigation of the global regulatory role of sigma 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867
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Zhao B., Yeo C.C., and Poh C.L. Proteome investigation of the global regulatory role of sigma 54 in response to gentisate induction in Pseudomonas alcaligenes NCIMB 9867. Proteomics 5 (2005) 1868-1876
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Zhao, B.1
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Induction of ortho- and meta-cleavage pathways in Pseudomonas in biodegradation of high benzoate concentration: MS identification of catabolic enzymes
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Cao B., Geng A., and Loh K.C. Induction of ortho- and meta-cleavage pathways in Pseudomonas in biodegradation of high benzoate concentration: MS identification of catabolic enzymes. Appl Microbiol Biotechnol 81 (2008) 99-107
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29
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Comparative proteomes of Corynebacterium glutamicum grown on aromatic compounds revealed novel proteins involved in aromatic degradation and a clear link between aromatic catabolism and gluconeogenesis via fructose-1,6-bisphosphatase
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Qi S.W., Chaudhry M.T., Zhang Y., Meng B., Huang Y., Zhao K.X., Poetsch A., Jiang C.Y., Liu S., and Liu S.J. Comparative proteomes of Corynebacterium glutamicum grown on aromatic compounds revealed novel proteins involved in aromatic degradation and a clear link between aromatic catabolism and gluconeogenesis via fructose-1,6-bisphosphatase. Proteomics 7 (2007) 3775-3787
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Liu, S.J.10
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0036844165
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Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii
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This paper is an excellent example of the application of proteomics for elucidating new pathways of aromatic hydrocarbon metabolism.
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Gescher J., Zaar A., Mohamed M., Schägger H., and Fuchs G. Genes coding for a new pathway of aerobic benzoate metabolism in Azoarcus evansii. J Bacteriol 184 (2002) 6301-6315. This paper is an excellent example of the application of proteomics for elucidating new pathways of aromatic hydrocarbon metabolism.
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J Bacteriol
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Gescher, J.1
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Widada J., Nojiri H., Kasuga K., Yoshida T., Habe H., and Omori T. Molecular detection and diversity of polycyclic aromatic hydrocarbon-degrading bacteria isolated from geographically diverse sites. Appl Microbiol Biotechnol 58 (2002) 202-209
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Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1
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A seminal paper in the cloning and functional characterization of a ring-hydroxylating oxygenase involved in the degradation of HMW PAHs.
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Khan A.A., Wang R.F., Cao W.W., Doerge D.R., Wennerstrom D., and Cerniglia C.E. Molecular cloning, nucleotide sequence, and expression of genes encoding a polycyclic aromatic ring dioxygenase from Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 67 (2001) 3577-3585. A seminal paper in the cloning and functional characterization of a ring-hydroxylating oxygenase involved in the degradation of HMW PAHs.
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Cloning, expression, and characterization of the katG gene, encoding catalase-peroxidase, from the polycyclic aromatic hydrocarbon-degrading bacterium Mycobacterium sp. strain PYR-1
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Wang R.F., Wennerstrom D., Cao W.W., Khan A.A., and Cerniglia C.E. Cloning, expression, and characterization of the katG gene, encoding catalase-peroxidase, from the polycyclic aromatic hydrocarbon-degrading bacterium Mycobacterium sp. strain PYR-1. Appl Environ Microbiol 66 (2000) 4300-4304
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Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods
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Kim S.J., Jones R.C., Cha C.J., Kweon O., Edmondson R.D., and Cerniglia C.E. Identification of proteins induced by polycyclic aromatic hydrocarbon in Mycobacterium vanbaalenii PYR-1 using two-dimensional polyacrylamide gel electrophoresis and de novo sequencing methods. Proteomics 4 (2004) 3899-3908
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This study reveals important information on substrate specificity and the induction pattern of an aromatic ring hydroxylating oxygenase involved in HMW PAH degradation by a Mycobacterium strain.
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Kim S.J., Kweon O., Freeman J.P., Jones R.C., Adjei M.D., Jhoo J.W., Edmondson R.D., and Cerniglia C.E. Molecular cloning and expression of genes encoding a novel dioxygenase involved in low- and high-molecular-weight polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Appl Environ Microbiol 72 (2006) 1045-1054. This study reveals important information on substrate specificity and the induction pattern of an aromatic ring hydroxylating oxygenase involved in HMW PAH degradation by a Mycobacterium strain.
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Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1
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This paper reports the first analysis of the M. vanbaalenii PYR-1 complete genome sequence to understand the molecular background for the degradation of HMW PAHs.
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Kim S.J., Kweon O., Jones R.C., Edmondson R.D., and Cerniglia C.E. Genomic analysis of polycyclic aromatic hydrocarbon degradation in Mycobacterium vanbaalenii PYR-1. Biodegradation 19 (2008) 859-881. This paper reports the first analysis of the M. vanbaalenii PYR-1 complete genome sequence to understand the molecular background for the degradation of HMW PAHs.
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Proteomic analysis of Acinetobacter lwoffii K24 by 2-D gel electrophoresis and electrospray ionization quadrupole-time of flight mass spectrometry
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Kim E.A., Kim J.Y., Kim S.J., Park K.R., Chung H.J., Leem S.H., and Kim S.I. Proteomic analysis of Acinetobacter lwoffii K24 by 2-D gel electrophoresis and electrospray ionization quadrupole-time of flight mass spectrometry. J Microbiol Methods 57 (2004) 337-349
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Kim S.I., Song S.Y., Kim K.W., Ho E.M., and Oh K.H. Proteomic analysis of the benzoate degradation pathway in Acinetobacter sp. KS-1. Res Microbiol 154 (2003) 697-703
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Yoon Y.H., Yun S.H., Park S.H., Seol S.Y., Leem S.H., and Kim S.I. Characterization of a new catechol branch of the β-ketoadipate pathway induced for benzoate degradation in Acinetobacter lwoffii K24. Biochem Biophys Res Commun 360 (2007) 513-519
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