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Volumn 10, Issue 8, 2015, Pages

Genome sequence analysis of the naphthenic acid degrading and metal resistant bacterium cupriavidus gilardii CR3

Author keywords

[No Author keywords available]

Indexed keywords

CARBOXYLIC ACID; CYCLOHEXANECARBOXYLIC ACID; HEAVY METAL; NAPHTHENIC ACID; TRANSFER RNA; UNCLASSIFIED DRUG;

EID: 84942922929     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0132881     Document Type: Article
Times cited : (49)

References (65)
  • 1
    • 78649308645 scopus 로고    scopus 로고
    • Cupriavidus pampae sp. Nov., a novel herbicide-degrading bacterium isolated from agricultural soil
    • Epub 2009/12/22. PMID: 20023053
    • Cuadrado V, Gomila M, Merini L, Giulietti AM, Moore ER. Cupriavidus pampae sp. nov., a novel herbicide-degrading bacterium isolated from agricultural soil. Int J Syst Evol Microbiol. 2010; 60(Pt 11):2606-12. Epub 2009/12/22. doi: 10.1099/ijs.0.018341-0 PMID: 20023053.
    • (2010) Int J Syst Evol Microbiol , vol.60 , pp. 2606-2612
    • Cuadrado, V.1    Gomila, M.2    Merini, L.3    Giulietti, A.M.4    Moore, E.R.5
  • 2
    • 9744280392 scopus 로고    scopus 로고
    • Taxonomy of the genus Cupriavidus: A tale of lost and found
    • Epub 2004/11/17. PMID: 15545472
    • Vandamme P, Coenye T. Taxonomy of the genus Cupriavidus: a tale of lost and found. Int J Syst Evol Microbiol. 2004; 54(Pt 6):2285-9. Epub 2004/11/17. doi: 10.1099/ijs.0.63247-0 PMID: 15545472.
    • (2004) Int J Syst Evol Microbiol , vol.54 , pp. 2285-2289
    • Vandamme, P.1    Coenye, T.2
  • 3
    • 0041810321 scopus 로고    scopus 로고
    • Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. Nov
    • Epub 2003/08/02. PMID: 12892129
    • Coenye T, Goris J, De Vos P, Vandamme P, LiPuma JJ. Classification of Ralstonia pickettii-like isolates from the environment and clinical samples as Ralstonia insidiosa sp. nov. Int J Syst Evol Microbiol. 2003; 53(Pt 4):1075-80. Epub 2003/08/02. PMID: 12892129.
    • (2003) Int J Syst Evol Microbiol , vol.53 , pp. 1075-1080
    • Coenye, T.1    Goris, J.2    De Vos, P.3    Vandamme, P.4    LiPuma, J.J.5
  • 4
    • 77956398098 scopus 로고    scopus 로고
    • The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments
    • Epub 2010/05/14 PMID: 20463976; PubMed Central PMCID: PMC2864759
    • Janssen PJ, Van Houdt R, Moors H, Monsieurs P, Morin N, Michaux A, et al. The complete genome sequence of Cupriavidus metallidurans strain CH34, a master survivalist in harsh and anthropogenic environments. PLoS One. 2010; 5(5):e10433. Epub 2010/05/14. doi: 10.1371/journal.pone.0010433 PMID: 20463976; PubMed Central PMCID: PMC2864759.
    • (2010) PLoS One , vol.5 , Issue.5 , pp. e10433
    • Janssen, P.J.1    Van Houdt, R.2    Moors, H.3    Monsieurs, P.4    Morin, N.5    Michaux, A.6
  • 5
    • 80052550319 scopus 로고    scopus 로고
    • Complete genome sequence of the type strain Cupriavidus necator N-1
    • Epub 2011/07/12 PMID: 21742890; PubMed Central PMCID: PMC3165677
    • Poehlein A, Kusian B, Friedrich B, Daniel R, Bowien B. Complete genome sequence of the type strain Cupriavidus necator N-1. J Bacteriol. 2011; 193(18):5017. Epub 2011/07/12. doi: 10.1128/JB.05660-11 PMID: 21742890; PubMed Central PMCID: PMC3165677.
    • (2011) J Bacteriol , vol.193 , Issue.18 , pp. 5017
    • Poehlein, A.1    Kusian, B.2    Friedrich, B.3    Daniel, R.4    Bowien, B.5
  • 6
    • 77957826921 scopus 로고    scopus 로고
    • The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader
    • Epub 2010/03/27 PMID: 20339589; PubMed Central PMCID: PMC2842291
    • Lykidis A, Perez-Pantoja D, Ledger T, Mavromatis K, Anderson IJ, Ivanova NN, et al. The complete multipartite genome sequence of Cupriavidus necator JMP134, a versatile pollutant degrader. PLoS One. 2010; 5(3):e9729. Epub 2010/03/27. doi: 10.1371/journal.pone.0009729 PMID: 20339589; PubMed Central PMCID: PMC2842291.
    • (2010) PLoS One , vol.5 , Issue.3 , pp. e9729
    • Lykidis, A.1    Perez-Pantoja, D.2    Ledger, T.3    Mavromatis, K.4    Anderson, I.J.5    Ivanova, N.N.6
  • 7
    • 50649112392 scopus 로고    scopus 로고
    • Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
    • Epub 2008/05/21 PMID: 18490699; PubMed Central PMCID: PMC2527706
    • Amadou C, Pascal G, Mangenot S, Glew M, Bontemps C, Capela D, et al. Genome sequence of the beta-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia. Genome Res. 2008; 18(9):1472-83. Epub 2008/05/21. doi: 10.1101/gr.076448.108 PMID: 18490699; PubMed Central PMCID: PMC2527706.
    • (2008) Genome Res , vol.18 , Issue.9 , pp. 1472-1483
    • Amadou, C.1    Pascal, G.2    Mangenot, S.3    Glew, M.4    Bontemps, C.5    Capela, D.6
  • 8
    • 0038240634 scopus 로고    scopus 로고
    • Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: Towards a catalogue of metal-responsive genes
    • Epub 2003/06/28
    • Mergeay M, Monchy S, Vallaeys T, Auquier V, Benotmane A, Bertin P, et al. Ralstonia metallidurans, a bacterium specifically adapted to toxic metals: towards a catalogue of metal-responsive genes. FEMS Microbiol Rev. 2003; 27(2-3):385-410. Epub 2003/06/28. doi: 10.1016/S0168-6445(03)00045-7 PMID: 12829276.
    • (2003) FEMS Microbiol Rev , vol.27 , Issue.2-3 , pp. 385-410
    • Mergeay, M.1    Monchy, S.2    Vallaeys, T.3    Auquier, V.4    Benotmane, A.5    Bertin, P.6
  • 9
    • 35048813675 scopus 로고    scopus 로고
    • Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals
    • Epub 2007/08/07 PMID: 17675385; PubMed Central PMCID: PMC2168447
    • Monchy S, Benotmane MA, Janssen P, Vallaeys T, Taghavi S, van der Lelie D, et al. Plasmids pMOL28 and pMOL30 of Cupriavidus metallidurans are specialized in the maximal viable response to heavy metals. J Bacteriol. 2007; 189(20):7417-25. Epub 2007/08/07. doi: 10.1128/JB.00375-07 PMID: 17675385; PubMed Central PMCID: PMC2168447.
    • (2007) J Bacteriol , vol.189 , Issue.20 , pp. 7417-7425
    • Monchy, S.1    Benotmane, M.A.2    Janssen, P.3    Vallaeys, T.4    Taghavi, S.5    Van Der Lelie, D.6
  • 10
    • 0029053492 scopus 로고
    • The czc operon of Alcaligenes eutrophus CH34: From resistance mechanism to the removal of heavy metals
    • Epub 1995/02/01. PMID: 7766206
    • Diels L, Dong Q, van der Lelie D, BaeyensW, Mergeay M. The czc operon of Alcaligenes eutrophus CH34: from resistance mechanism to the removal of heavy metals. J Ind Microbiol. 1995; 14(2):142-53. Epub 1995/02/01. PMID: 7766206.
    • (1995) J Ind Microbiol , vol.14 , Issue.2 , pp. 142-153
    • Diels, L.1    Dong, Q.2    Van Der Lelie, D.3    Baeyensw Mergeay, M.4
  • 11
    • 84861216358 scopus 로고    scopus 로고
    • De novo genome project of Cupriavidus basilensis OR16
    • Epub 2012/03/31. PMID:22461549; PubMed Central PMCID: PMC3318459
    • Cserhati M, Kriszt B, Szoboszlay S, Toth A, Szabo I, Tancsics A, et al. De novo genome project of Cupriavidus basilensis OR16. J Bacteriol. 2012; 194(8):2109-10. Epub 2012/03/31. doi: 10.1128/JB. 06752-11 PMID: 22461549; PubMed Central PMCID: PMC3318459.
    • (2012) J Bacteriol , vol.194 , Issue.8 , pp. 2109-2110
    • Cserhati, M.1    Kriszt, B.2    Szoboszlay, S.3    Toth, A.4    Szabo, I.5    Tancsics, A.6
  • 12
    • 84869144666 scopus 로고    scopus 로고
    • Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium
    • Epub 2012/11/02 PMID: 23115161; PubMed Central PMCID: PMC3486403
    • Hong KW, Thinagaran DA, Gan HM, Yin WF, Chan KG. Whole-Genome Sequence of Cupriavidus sp. Strain BIS7, a Heavy-Metal-Resistant Bacterium. J Bacteriol. 2012; 194(22):6324. Epub 2012/11/02. doi: 10.1128/JB.01608-12 PMID: 23115161; PubMed Central PMCID: PMC3486403.
    • (2012) J Bacteriol , vol.194 , Issue.22 , pp. 6324
    • Hong, K.W.1    Thinagaran, D.A.2    Gan, H.M.3    Yin, W.F.4    Chan, K.G.5
  • 13
    • 0034811821 scopus 로고    scopus 로고
    • Cloning and functional analysis of the pbr lead resistance determinant of Ralstonia metallidurans CH34
    • Epub 2001/09/07 PMID: 11544228; PubMed Central PMCID: PMC95457
    • Borremans B, Hobman JL, Provoost A, Brown NL, van Der Lelie D. Cloning and functional analysis of the pbr lead resistance determinant of Ralstonia metallidurans CH34. J Bacteriol. 2001; 183(19):5651-8. Epub 2001/09/07. doi: 10.1128/JB.183.19.5651-5658.2001 PMID: 11544228; PubMed Central PMCID: PMC95457.
    • (2001) J Bacteriol , vol.183 , Issue.19 , pp. 5651-5658
    • Borremans, B.1    Hobman, J.L.2    Provoost, A.3    Brown, N.L.4    Van Der Lelie, D.5
  • 14
    • 3042826882 scopus 로고    scopus 로고
    • 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
    • Epub 2004/06/10 PMID: 15186344
    • Trefault N, De la Iglesia R, Molina AM, Manzano M, Ledger T, Perez-Pantoja D, et al. 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. 2004; 6(7):655-68. Epub 2004/06/10. doi: 10.1111/j.1462-2920.2004.00596.x PMID: 15186344.
    • (2004) Environ Microbiol , vol.6 , Issue.7 , pp. 655-668
    • Trefault, N.1    De La Iglesia, R.2    Molina, A.M.3    Manzano, M.4    Ledger, T.5    Perez-Pantoja, D.6
  • 15
    • 49649090880 scopus 로고    scopus 로고
    • Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134
    • Epub 2008/08/12 PMID: 18691224
    • Perez-Pantoja D, De la Iglesia R, Pieper DH, Gonzalez B. Metabolic reconstruction of aromatic compounds degradation from the genome of the amazing pollutant-degrading bacterium Cupriavidus necator JMP134. FEMS Microbiol Rev. 2008; 32(5):736-94. Epub 2008/08/12. doi: 10.1111/j.1574-6976.2008.00122.x PMID: 18691224.
    • (2008) FEMS Microbiol Rev , vol.32 , Issue.5 , pp. 736-794
    • Perez-Pantoja, D.1    De La Iglesia, R.2    Pieper, D.H.3    Gonzalez, B.4
  • 16
    • 79251643057 scopus 로고    scopus 로고
    • Screening and Evaluation of Polyhydroxybutyrate-Producing Strains from Indigenous Isolate Cupriavidus taiwanensis Strains
    • Epub 2011/02/23 PMID: 21339985; PubMed Central PMCID: PMC3039951
    • Wei YH, Chen WC, Huang CK, Wu HS, Sun YM, Lo CW, et al. Screening and Evaluation of Polyhydroxybutyrate-Producing Strains from Indigenous Isolate Cupriavidus taiwanensis Strains. Int J Mol Sci. 2011; 12(1):252-65. Epub 2011/02/23. doi: 10.3390/ijms12010252 PMID: 21339985; PubMed Central PMCID: PMC3039951.
    • (2011) Int J Mol Sci , vol.12 , Issue.1 , pp. 252-265
    • Wei, Y.H.1    Chen, W.C.2    Huang, C.K.3    Wu, H.S.4    Sun, Y.M.5    Lo, C.W.6
  • 17
    • 33749863920 scopus 로고    scopus 로고
    • Genome sequence of the bioplastic-producing "knallgas" bacterium Ralstonia eutropha H16
    • Epub 2006/09/12 PMID: 16964242
    • Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, et al. Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16. Nat Biotechnol. 2006; 24 (10):1257-62. Epub 2006/09/12. doi: 10.1038/nbt1244 PMID: 16964242.
    • (2006) Nat Biotechnol , vol.24 , Issue.10 , pp. 1257-1262
    • Pohlmann, A.1    Fricke, W.F.2    Reinecke, F.3    Kusian, B.4    Liesegang, H.5    Cramm, R.6
  • 18
    • 46749128179 scopus 로고    scopus 로고
    • Isolation and characterization of new cyclohexylacetic acid-degrading bacteria
    • Epub 2008/04/09 PMID: 18392890
    • Iwaki H, Nakai E, Nakamura S, Hasegawa Y. Isolation and characterization of new cyclohexylacetic acid-degrading bacteria. Curr Microbiol. 2008; 57(2):107-10. Epub 2008/04/09. doi: 10.1007/s00284-008-9158-0 PMID: 18392890.
    • (2008) Curr Microbiol , vol.57 , Issue.2 , pp. 107-110
    • Iwaki, H.1    Nakai, E.2    Nakamura, S.3    Hasegawa, Y.4
  • 20
    • 3442898273 scopus 로고    scopus 로고
    • A review of the occurrence and fate of naphthenic acids in aquatic environments
    • Epub 2004/08/ PMID: 15332664
    • Headley JV, McMartin DW. A review of the occurrence and fate of naphthenic acids in aquatic environments. J Environ Sci Health A Tox Hazard Subst Environ Eng. 2004; 39(8):1989-2010. Epub 2004/08/PMID: 15332664.
    • (2004) J Environ Sci Health A Tox Hazard Subst Environ Eng , vol.39 , Issue.8 , pp. 1989-2010
    • Headley, J.V.1    McMartin, D.W.2
  • 21
    • 0000820375 scopus 로고
    • Effect of sodium naphthenate on survival and some physiological-biochemical parameters of some fishes
    • Dokholyan B, Magomedov A. Effect of sodium naphthenate on survival and some physiological-biochemical parameters of some fishes. Journal of Ichthyology. 1983; 23(6):125-32.
    • (1983) Journal of Ichthyology , vol.23 , Issue.6 , pp. 125-132
    • Dokholyan, B.1    Magomedov, A.2
  • 22
    • 84863393199 scopus 로고    scopus 로고
    • Predicted toxicity of naphthenic acids present in oil sands process-affected waters to a range of environmental and human endpoints
    • Epub 2012/04/03 PMID: 22464029
    • Scarlett AG, West CE, Jones D, Galloway TS, Rowland SJ. Predicted toxicity of naphthenic acids present in oil sands process-affected waters to a range of environmental and human endpoints. Sci Total Environ. 2012; 425:119-27. Epub 2012/04/03. doi: 10.1016/j.scitotenv.2012.02.064 PMID: 22464029.
    • (2012) Sci Total Environ , vol.425 , pp. 119-127
    • Scarlett, A.G.1    West, C.E.2    Jones, D.3    Galloway, T.S.4    Rowland, S.J.5
  • 23
    • 77951643495 scopus 로고    scopus 로고
    • Microbial naphthenic Acid degradation
    • Epub 2010/04/
    • Whitby C. Microbial naphthenic Acid degradation. Adv Appl Microbiol. 2010; 70:93-125. Epub 2010/04/. doi: 10.1016/S0065-2164(10)70003-4 PMID: 20359455.
    • (2010) Adv Appl Microbiol , vol.70 , pp. 93-125
    • Whitby, C.1
  • 24
    • 58149196507 scopus 로고    scopus 로고
    • Biodegradation kinetics of trans-4-methyl-1-cyclohexane carboxylic acid
    • Epub 2008/07/18 PMID: 18633718
    • Paslawski JC, Headley JV, Hill GA, Nemati M. Biodegradation kinetics of trans-4-methyl-1-cyclohexane carboxylic acid. Biodegradation. 2009; 20(1):125-33. Epub 2008/07/18. doi: 10.1007/s10532-008-9206-2 PMID: 18633718.
    • (2009) Biodegradation , vol.20 , Issue.1 , pp. 125-133
    • Paslawski, J.C.1    Headley, J.V.2    Hill, G.A.3    Nemati, M.4
  • 25
    • 84855339705 scopus 로고    scopus 로고
    • Batch and continuous biodegradation of three model naphthenic acids in a circulating packed-bed bioreactor
    • Epub 2011/12/ PMID: 22154122
    • Huang J, Nemati M, Hill G, Headley J. Batch and continuous biodegradation of three model naphthenic acids in a circulating packed-bed bioreactor. J Hazard Mater. 2012; 201-202:132-40. Epub 2011/12/. doi: 10.1016/j.jhazmat.2011.11.052 PMID: 22154122.
    • (2012) J Hazard Mater , vol.201-202 , pp. 132-140
    • Huang, J.1    Nemati, M.2    Hill, G.3    Headley, J.4
  • 26
    • 0015889153 scopus 로고
    • Corynebacterium cyclohexanicum n. Sp.: A cyclohexanecarboxylic acid utilizing bacterium
    • Epub 1973/08/01. PMID: 4584719
    • Tokuyama T, Kaneda T. Corynebacterium cyclohexanicum n. sp.: a cyclohexanecarboxylic acid utilizing bacterium. Can J Microbiol. 1973; 19(8):937-42. Epub 1973/08/01. PMID: 4584719.
    • (1973) Can J Microbiol , vol.19 , Issue.8 , pp. 937-942
    • Tokuyama, T.1    Kaneda, T.2
  • 27
    • 0016311338 scopus 로고
    • The microbial degradation of cyclohexanecarboxylic acid: A pathway involving aromatization to form p-hydroxybenzoic acid
    • Blakley E. The microbial degradation of cyclohexanecarboxylic acid: a pathway involving aromatization to form p-hydroxybenzoic acid. Canadian Journal of Microbiology. 1974; 20(10):1297-306.
    • (1974) Canadian Journal of Microbiology , vol.20 , Issue.10 , pp. 1297-1306
    • Blakley, E.1
  • 28
    • 0016836149 scopus 로고
    • The aerobic metabolism of cyclohexanecarboxylic acid by Acinetobacter anitratum
    • Epub 1975/04/01. PMID: 1156390; PubMed Central PMCID: PMC1165500
    • Rho EM, Evans WC. The aerobic metabolism of cyclohexanecarboxylic acid by Acinetobacter anitratum. Biochem J. 1975; 148(1):11-5. Epub 1975/04/01. PMID: 1156390; PubMed Central PMCID: PMC1165500.
    • (1975) Biochem J , vol.148 , Issue.1 , pp. 11-15
    • Rho, E.M.1    Evans, W.C.2
  • 29
    • 0017859433 scopus 로고
    • The microbial degradation of cyclohexanecarboxylic acid by a beta-oxidation pathway with simultaneous induction to the utilization of benzoate
    • Epub 1978/ 07/01. PMID: 679070
    • Blakley ER. The microbial degradation of cyclohexanecarboxylic acid by a beta-oxidation pathway with simultaneous induction to the utilization of benzoate. Can J Microbiol. 1978; 24(7):847-55. Epub 1978/ 07/01. PMID: 679070.
    • (1978) Can J Microbiol , vol.24 , Issue.7 , pp. 847-855
    • Blakley, E.R.1
  • 30
    • 0020264059 scopus 로고
    • The metabolism of cyclohexanecarboxylic acid and 3-cyclohexenecarboxylic acid by Pseudomonas putida
    • Epub 1982/12/01. PMID: 7168830
    • Blakley ER, Papish B. The metabolism of cyclohexanecarboxylic acid and 3-cyclohexenecarboxylic acid by Pseudomonas putida. Can J Microbiol. 1982; 28(12):1324-9. Epub 1982/12/01. PMID: 7168830.
    • (1982) Can J Microbiol , vol.28 , Issue.12 , pp. 1324-1329
    • Blakley, E.R.1    Papish, B.2
  • 31
    • 79951809386 scopus 로고    scopus 로고
    • Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching
    • PMID: 20962873
    • Johnson RJ, Smith BE, Sutton PA, McGenity TJ, Rowland SJ, Whitby C. Microbial biodegradation of aromatic alkanoic naphthenic acids is affected by the degree of alkyl side chain branching. The ISME journal. 2011; 5(3):486-96. doi: 10.1038/ismej.2010.146 PMID: 20962873
    • (2011) The ISME Journal , vol.5 , Issue.3 , pp. 486-496
    • Johnson, R.J.1    Smith, B.E.2    Sutton, P.A.3    McGenity, T.J.4    Rowland, S.J.5    Whitby, C.6
  • 32
    • 34547166952 scopus 로고    scopus 로고
    • Microbial diversity in natural asphalts of the Rancho la Brea Tar Pits
    • Epub 2007/04/10 PMID: 17416692; PubMed Central PMCID: PMC1932828
    • Kim JS, Crowley DE. Microbial diversity in natural asphalts of the Rancho La Brea Tar Pits. Appl Environ Microbiol. 2007; 73(14):4579-91. Epub 2007/04/10. doi: 10.1128/AEM.01372-06 PMID: 17416692; PubMed Central PMCID: PMC1932828.
    • (2007) Appl Environ Microbiol , vol.73 , Issue.14 , pp. 4579-4591
    • Kim, J.S.1    Crowley, D.E.2
  • 33
    • 84863230041 scopus 로고    scopus 로고
    • Introducing EzTaxon-e: A prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species
    • Epub 2011/12/06 PMID: 22140171
    • Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol. 2012; 62(Pt 3):716-21. Epub 2011/12/06. doi: 10.1099/ijs.0.038075-0 PMID: 22140171.
    • (2012) Int J Syst Evol Microbiol , vol.62 , pp. 716-721
    • Kim, O.S.1    Cho, Y.J.2    Lee, K.3    Yoon, S.H.4    Kim, M.5    Na, H.6
  • 34
    • 0030801002 scopus 로고    scopus 로고
    • Gapped BLAST and PSIBLAST: A new generation of protein database search programs
    • Epub 1997/09/01. PMID: 9254694; PubMed Central PMCID: PMC146917
    • Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSIBLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997; 25 (17):3389-402. Epub 1997/09/01. PMID: 9254694; PubMed Central PMCID: PMC146917.
    • (1997) Nucleic Acids Res , vol.25 , Issue.17 , pp. 3389-3402
    • Altschul, S.F.1    Madden, T.L.2    Schaffer, A.A.3    Zhang, J.4    Zhang, Z.5    Miller, W.6
  • 35
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memory-efficient short-read de novo assembler
    • Epub 2012/01/01 PMID: 23587118; PubMed Central PMCID: PMC3626529
    • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. Gigascience. 2012; 1(1):18. Epub 2012/01/01. doi: 10.1186/2047-217X-1-18 PMID: 23587118; PubMed Central PMCID: PMC3626529.
    • (2012) Gigascience , vol.1 , Issue.1 , pp. 18
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6
  • 36
    • 75649124547 scopus 로고    scopus 로고
    • De novo assembly of human genomes with massively parallel short read sequencing
    • Epub 2009/12/19
    • Li R, Zhu H, Ruan J, Qian W, Fang X, Shi Z, et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res. 2010; 20(2):265-72. Epub 2009/12/19. doi: 10.1101/gr. 097261.109 PMID: 20019144; PubMed Central PMCID: PMC2813482.
    • (2010) Genome Res , vol.20 , Issue.2 , pp. 265-272
    • Li, R.1    Zhu, H.2    Ruan, J.3    Qian, W.4    Fang, X.5    Shi, Z.6
  • 37
    • 84880798154 scopus 로고    scopus 로고
    • Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
    • Epub 2013/05/07 PMID: 23644548
    • Chin CS, Alexander DH, Marks P, Klammer AA, Drake J, Heiner C, et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods. 2013; 10(6):563-9. Epub 2013/05/07. doi: 10.1038/nmeth.2474 PMID: 23644548.
    • (2013) Nat Methods , vol.10 , Issue.6 , pp. 563-569
    • Chin, C.S.1    Alexander, D.H.2    Marks, P.3    Klammer, A.A.4    Drake, J.5    Heiner, C.6
  • 38
    • 84869814079 scopus 로고    scopus 로고
    • Mind the gap: Upgrading genomes with Pacific Biosciences RS long-read sequencing technology
    • Epub 2012/ 11/28 PMID: 23185243; PubMed Central PMCID: PMC3504050
    • English AC, Richards S, Han Y, Wang M, Vee V, Qu J, et al. Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology. PLoS One. 2012; 7(11):e47768. Epub 2012/ 11/28. doi: 10.1371/journal.pone.0047768 PMID: 23185243; PubMed Central PMCID: PMC3504050.
    • (2012) PLoS One , vol.7 , Issue.11 , pp. e47768
    • English, A.C.1    Richards, S.2    Han, Y.3    Wang, M.4    Vee, V.5    Qu, J.6
  • 39
    • 0035875343 scopus 로고    scopus 로고
    • GeneMarkS: A self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
    • Epub 2001/06/19. PMID: 11410670; PubMed Central PMCID: PMC55746
    • Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001; 29(12):2607-18. Epub 2001/06/19. PMID: 11410670; PubMed Central PMCID: PMC55746.
    • (2001) Nucleic Acids Res , vol.29 , Issue.12 , pp. 2607-2618
    • Besemer, J.1    Lomsadze, A.2    Borodovsky, M.3
  • 40
    • 34147132825 scopus 로고    scopus 로고
    • Identifying bacterial genes and endosymbiont DNA with Glimmer
    • Epub 2007/01/24 PMID: 17237039; PubMed Central PMCID: PMC2387122
    • Delcher AL, Bratke KA, Powers EC, Salzberg SL. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics. 2007; 23(6):673-9. Epub 2007/01/24. doi: 10.1093/bioinformatics/ btm009 PMID: 17237039; PubMed Central PMCID: PMC2387122.
    • (2007) Bioinformatics , vol.23 , Issue.6 , pp. 673-679
    • Delcher, A.L.1    Bratke, K.A.2    Powers, E.C.3    Salzberg, S.L.4
  • 41
    • 0034800374 scopus 로고    scopus 로고
    • InterProScan-an integration platform for the signature-recognition methods in InterPro
    • Epub 2001/10/09. PMID: 11590104
    • Zdobnov EM, Apweiler R. InterProScan-an integration platform for the signature-recognition methods in InterPro. Bioinformatics. 2001; 17(9):847-8. Epub 2001/10/09. PMID: 11590104.
    • (2001) Bioinformatics , vol.17 , Issue.9 , pp. 847-848
    • Zdobnov, E.M.1    Apweiler, R.2
  • 42
    • 34547588704 scopus 로고    scopus 로고
    • KAAS: An automatic genome annotation and pathway reconstruction server
    • Epub 2007/ 05/29 PMID: 17526522; PubMed Central PMCID: PMC1933193
    • Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M. KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res. 2007; 35(Web Server issue):W182-5. Epub 2007/ 05/29. doi: 10.1093/nar/gkm321 PMID: 17526522; PubMed Central PMCID: PMC1933193.
    • (2007) Nucleic Acids Res , vol.35 , Issue.Web Server issue , pp. W182-W185
    • Moriya, Y.1    Itoh, M.2    Okuda, S.3    Yoshizawa, A.C.4    Kanehisa, M.5
  • 43
    • 0030660581 scopus 로고    scopus 로고
    • A genomic perspective on protein families
    • Epub 1997/10/24. PMID: 9381173
    • Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997; 278 (5338):631-7. Epub 1997/10/24. PMID: 9381173.
    • (1997) Science , vol.278 , Issue.5338 , pp. 631-637
    • Tatusov, R.L.1    Koonin, E.V.2    Lipman, D.J.3
  • 44
    • 0030854739 scopus 로고    scopus 로고
    • Eddy SR. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
    • Epub 1997/03/01. PMID: 9023104; PubMed Central PMCID: PMC146525
    • Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997; 25(5):955-64. Epub 1997/03/01. PMID: 9023104; PubMed Central PMCID: PMC146525.
    • (1997) Nucleic Acids Res , vol.25 , Issue.5 , pp. 955-964
    • Lowe, T.M.1
  • 45
    • 34250665888 scopus 로고    scopus 로고
    • RNAmmer: Consistent and rapid annotation of ribosomal RNA genes
    • Epub 2007/04/25 PMID: 17452365; PubMed Central PMCID: PMC1888812
    • Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW. RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res. 2007; 35(9):3100-8. Epub 2007/04/25. doi: 10.1093/nar/gkm160 PMID: 17452365; PubMed Central PMCID: PMC1888812.
    • (2007) Nucleic Acids Res , vol.35 , Issue.9 , pp. 3100-3108
    • Lagesen, K.1    Hallin, P.2    Rodland, E.A.3    Staerfeldt, H.H.4    Rognes, T.5    Ussery, D.W.6
  • 46
    • 79957613599 scopus 로고    scopus 로고
    • MEGA5: Molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods
    • Epub 2011/05/07 PMID: 21546353; PubMed Central PMCID: PMC3203626
    • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 2011; 28(10):2731-9. Epub 2011/05/07. doi: 10.1093/molbev/msr121 PMID: 21546353; PubMed Central PMCID: PMC3203626.
    • (2011) Mol Biol Evol , vol.28 , Issue.10 , pp. 2731-2739
    • Tamura, K.1    Peterson, D.2    Peterson, N.3    Stecher, G.4    Nei, M.5    Kumar, S.6
  • 47
    • 3543051830 scopus 로고    scopus 로고
    • Mauve: Multiple alignment of conserved genomic sequence with rearrangements
    • Epub 2004/07/03
    • Darling AC, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res. 2004; 14(7):1394-403. Epub 2004/07/03. doi: 10.1101/gr. 2289704 PMID: 15231754; PubMed Central PMCID: PMC442156.
    • (2004) Genome Res , vol.14 , Issue.7 , pp. 1394-1403
    • Darling, A.C.1    Mau, B.2    Blattner, F.R.3    Perna, N.T.4
  • 48
    • 84856571322 scopus 로고    scopus 로고
    • PGAP: Pan-genomes analysis pipeline
    • Epub 2011/12/02 PMID: 22130594; PubMed Central PMCID: PMC3268234
    • Zhao Y, Wu J, Yang J, Sun S, Xiao J, Yu J. PGAP: pan-genomes analysis pipeline. Bioinformatics. 2012; 28(3):416-8. Epub 2011/12/02. doi: 10.1093/bioinformatics/btr655 PMID: 22130594; PubMed Central PMCID: PMC3268234.
    • (2012) Bioinformatics , vol.28 , Issue.3 , pp. 416-418
    • Zhao, Y.1    Wu, J.2    Yang, J.3    Sun, S.4    Xiao, J.5    Yu, J.6
  • 50
    • 77954268488 scopus 로고    scopus 로고
    • PathPred: An enzyme-catalyzed metabolic pathway prediction server
    • Epub 2010/05/04 PMID: 20435670; PubMed Central PMCID: PMC2896155
    • Moriya Y, Shigemizu D, Hattori M, Tokimatsu T, Kotera M, Goto S, et al. PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 2010; 38(Web Server issue):W138-43. Epub 2010/05/04. doi: 10.1093/nar/gkq318 PMID: 20435670; PubMed Central PMCID: PMC2896155.
    • (2010) Nucleic Acids Res , vol.38 , Issue.Web Server issue , pp. W138-W143
    • Moriya, Y.1    Shigemizu, D.2    Hattori, M.3    Tokimatsu, T.4    Kotera, M.5    Goto, S.6
  • 51
    • 83555165173 scopus 로고    scopus 로고
    • Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network
    • Epub 2011/06/28 PMID: 21706166
    • Monsieurs P, Moors H, Van Houdt R, Janssen PJ, Janssen A, Coninx I, et al. Heavy metal resistance in Cupriavidus metallidurans CH34 is governed by an intricate transcriptional network. Biometals. 2011; 24(6):1133-51. Epub 2011/06/28. doi: 10.1007/s10534-011-9473-y PMID: 21706166.
    • (2011) Biometals , vol.24 , Issue.6 , pp. 1133-1151
    • Monsieurs, P.1    Moors, H.2    Van Houdt, R.3    Janssen, P.J.4    Janssen, A.5    Coninx, I.6
  • 52
    • 0035217838 scopus 로고    scopus 로고
    • Diversity of silver resistance genes in IncH incompatibility group plasmids
    • Epub 2001/12/12. PMID: 11739772
    • Gupta A, Phung LT, Taylor DE, Silver S. Diversity of silver resistance genes in IncH incompatibility group plasmids. Microbiology. 2001; 147(Pt 12):3393-402. Epub 2001/12/12. PMID: 11739772.
    • (2001) Microbiology , vol.147 , pp. 3393-3402
    • Gupta, A.1    Phung, L.T.2    Taylor, D.E.3    Silver, S.4
  • 55
    • 0032905563 scopus 로고    scopus 로고
    • Molecular basis for resistance to silver cations in Salmonella
    • Epub 1999/02/04 PMID: 9930866
    • Gupta A, Matsui K, Lo JF, Silver S. Molecular basis for resistance to silver cations in Salmonella. Nat Med. 1999; 5(2):183-8. Epub 1999/02/04. doi: 10.1038/5545 PMID: 9930866.
    • (1999) Nat Med , vol.5 , Issue.2 , pp. 183-188
    • Gupta, A.1    Matsui, K.2    Lo, J.F.3    Silver, S.4
  • 56
    • 0037903225 scopus 로고    scopus 로고
    • Bacterial silver resistance: Molecular biology and uses and misuses of silver compounds
    • Epub 2003/06/28
    • Silver S. Bacterial silver resistance: molecular biology and uses and misuses of silver compounds. FEMS Microbiol Rev. 2003; 27(2-3):341-53. Epub 2003/06/28. doi: 10.1016/S0168-6445(03)00047-0 PMID: 12829274.
    • (2003) FEMS Microbiol Rev , vol.27 , Issue.2-3 , pp. 341-353
    • Silver, S.1
  • 57
    • 0037701544 scopus 로고    scopus 로고
    • Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli
    • Epub 2003/06/19. PMID: 12813074; PubMed Central PMCID: PMC161567
    • Franke S, Grass G, Rensing C, Nies DH. Molecular analysis of the copper-transporting efflux system CusCFBA of Escherichia coli. J Bacteriol. 2003; 185(13):3804-12. Epub 2003/06/19. PMID: 12813074; PubMed Central PMCID: PMC161567.
    • (2003) J Bacteriol , vol.185 , Issue.13 , pp. 3804-3812
    • Franke, S.1    Grass, G.2    Rensing, C.3    Nies, D.H.4
  • 58
    • 0037212306 scopus 로고    scopus 로고
    • New genes involved in chromate resistance in Ralstonia metallidurans strain CH34
    • Epub 2002/12/10
    • Juhnke S, Peitzsch N, Hubener N, Grosse C, Nies DH. New genes involved in chromate resistance in Ralstonia metallidurans strain CH34. Arch Microbiol. 2002; 179(1):15-25. Epub 2002/12/10. doi: 10. 1007/s00203-002-0492-5 PMID: 12471500.
    • (2002) Arch Microbiol , vol.179 , Issue.1 , pp. 15-25
    • Juhnke, S.1    Peitzsch, N.2    Hubener, N.3    Grosse, C.4    Nies, D.H.5
  • 59
    • 0025220508 scopus 로고
    • Nucleotide sequence and expression of a plasmid-encoded chromate resistance determinant from Alcaligenes eutrophus
    • Epub 1990/04/ PMID: 2180932
    • Nies A, Nies DH, Silver S. Nucleotide sequence and expression of a plasmid-encoded chromate resistance determinant from Alcaligenes eutrophus. J Biol Chem. 1990; 265(10):5648-53. Epub 1990/04/ PMID: 2180932.
    • (1990) J Biol Chem , vol.265 , Issue.10 , pp. 5648-5653
    • Nies, A.1    Nies, D.H.2    Silver, S.3
  • 60
    • 0035059229 scopus 로고    scopus 로고
    • NreB from Achromobacter xylosoxidans 31A Is a nickel-induced transporter conferring nickel resistance
    • Epub 2001/04/09 PMID: 11292799; PubMed Central PMCID: PMC99496
    • Grass G, Fan B, Rosen BP, Lemke K, Schlegel HG, Rensing C. NreB from Achromobacter xylosoxidans 31A Is a nickel-induced transporter conferring nickel resistance. J Bacteriol. 2001; 183(9):2803-7. Epub 2001/04/09. doi: 10.1128/JB.183.9.2803-2807.2001 PMID: 11292799; PubMed Central PMCID: PMC99496.
    • (2001) J Bacteriol , vol.183 , Issue.9 , pp. 2803-2807
    • Grass, G.1    Fan, B.2    Rosen, B.P.3    Lemke, K.4    Schlegel, H.G.5    Rensing, C.6
  • 61
    • 84888585567 scopus 로고    scopus 로고
    • Role of MerC, MerE, MerF, MerT, and/or MerP in resistance to mercurials and the transport of mercurials in Escherichia coli
    • Epub 2013/08/30 PMID: 23985830
    • Sone Y, Nakamura R, Pan-Hou H, Itoh T, Kiyono M. Role of MerC, MerE, MerF, MerT, and/or MerP in resistance to mercurials and the transport of mercurials in Escherichia coli. Biol Pharm Bull. 2013; 36 (11):1835-41. Epub 2013/08/30. doi: 10.1248/bpb.b13-00554 PMID: 23985830.
    • (2013) Biol Pharm Bull , vol.36 , Issue.11 , pp. 1835-1841
    • Sone, Y.1    Nakamura, R.2    Pan-Hou, H.3    Itoh, T.4    Kiyono, M.5
  • 62
    • 70349897065 scopus 로고    scopus 로고
    • An efflux transporter PbrA and a phosphatase PbrB cooperate in a lead-resistance mechanism in bacteria
    • Epub 2009/09/10 PMID: 19737357
    • Hynninen A, Touze T, Pitkanen L, Mengin-Lecreulx D, Virta M. An efflux transporter PbrA and a phosphatase PbrB cooperate in a lead-resistance mechanism in bacteria. Mol Microbiol. 2009; 74(2):384-94. Epub 2009/09/10. doi: 10.1111/j.1365-2958.2009.06868.x PMID: 19737357.
    • (2009) Mol Microbiol , vol.74 , Issue.2 , pp. 384-394
    • Hynninen, A.1    Touze, T.2    Pitkanen, L.3    Mengin-Lecreulx, D.4    Virta, M.5
  • 63
    • 55749085128 scopus 로고    scopus 로고
    • The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide
    • Epub 2008/09/09 PMID: 18776016; PubMed Central PMCID: PMC2580707
    • Branco R, Chung AP, Johnston T, Gurel V, Morais P, Zhitkovich A. The chromate-inducible chrBACF operon from the transposable element TnOtChr confers resistance to chromium(VI) and superoxide. J Bacteriol. 2008; 190(21):6996-7003. Epub 2008/09/09. doi: 10.1128/JB.00289-08 PMID: 18776016; PubMed Central PMCID: PMC2580707.
    • (2008) J Bacteriol , vol.190 , Issue.21 , pp. 6996-7003
    • Branco, R.1    Chung, A.P.2    Johnston, T.3    Gurel, V.4    Morais, P.5    Zhitkovich, A.6
  • 64
    • 79952967236 scopus 로고    scopus 로고
    • Structural and metal binding characterization of the C-terminal metallochaperone domain of membrane fusion protein SilB from Cupriavidus metallidurans CH34
    • Epub 2011/02/09 PMID: 21299248
    • Bersch B, Derfoufi KM, De Angelis F, Auquier V, Ekende EN, Mergeay M, et al. Structural and metal binding characterization of the C-terminal metallochaperone domain of membrane fusion protein SilB from Cupriavidus metallidurans CH34. Biochemistry. 2011; 50(12):2194-204. Epub 2011/02/09. doi: 10.1021/bi200005k PMID: 21299248.
    • (2011) Biochemistry , vol.50 , Issue.12 , pp. 2194-2204
    • Bersch, B.1    Derfoufi, K.M.2    De Angelis, F.3    Auquier, V.4    Ekende, E.N.5    Mergeay, M.6
  • 65
    • 0021925630 scopus 로고
    • Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals
    • Epub 1985/04/01. PMID: 3884593; PubMed Central PMCID: PMC218993
    • Mergeay M, Nies D, Schlegel HG, Gerits J, Charles P, Van Gijsegem F. Alcaligenes eutrophus CH34 is a facultative chemolithotroph with plasmid-bound resistance to heavy metals. J Bacteriol. 1985; 162 (1):328-34. Epub 1985/04/01. PMID: 3884593; PubMed Central PMCID: PMC218993
    • (1985) J Bacteriol , vol.162 , Issue.1 , pp. 328-334
    • Mergeay, M.1    Nies, D.2    Schlegel, H.G.3    Gerits, J.4    Charles, P.5    Van Gijsegem, F.6


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