메뉴 건너뛰기




Volumn 18, Issue 10, 2016, Pages 3327-3341

High-resolution analysis of the m-xylene/toluene biodegradation subtranscriptome of Pseudomonas putida mt-2

Author keywords

[No Author keywords available]

Indexed keywords

3-XYLENE; BACTERIAL PROTEIN; BENZOIC ACID DERIVATIVE; DNA BINDING PROTEIN; MESSENGER RNA; TOLUENE; TRANSCRIPTION FACTOR; XYLENE; XYLR PROTEIN, PSEUDOMONAS;

EID: 84991457495     PISSN: 14622912     EISSN: 14622920     Source Type: Journal    
DOI: 10.1111/1462-2920.13054     Document Type: Article
Times cited : (11)

References (80)
  • 1
    • 0024357889 scopus 로고
    • Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway
    • Abril, M.A., Michan, C., Timmis, K.N., and Ramos, J.L. (1989) Regulator and enzyme specificities of the TOL plasmid-encoded upper pathway for degradation of aromatic hydrocarbons and expansion of the substrate range of the pathway. J Bacteriol 171: 6782–6790.
    • (1989) J Bacteriol , vol.171 , pp. 6782-6790
    • Abril, M.A.1    Michan, C.2    Timmis, K.N.3    Ramos, J.L.4
  • 2
    • 23744431554 scopus 로고    scopus 로고
    • Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0
    • Aranda-Olmedo, I., Ramos, J.L., and Marques, S. (2005) Integration of signals through Crc and PtsN in catabolite repression of Pseudomonas putida TOL plasmid pWW0. Appl Environ Microbiol 71: 4191–4198.
    • (2005) Appl Environ Microbiol , vol.71 , pp. 4191-4198
    • Aranda-Olmedo, I.1    Ramos, J.L.2    Marques, S.3
  • 3
    • 0025005226 scopus 로고
    • The TOL plasmids: determinants of the catabolism of toluene and the xylenes
    • Assinder, S.J., and Williams, P.A. (1990) The TOL plasmids: determinants of the catabolism of toluene and the xylenes. Adv Microb Physiol 31: 1–69.
    • (1990) Adv Microb Physiol , vol.31 , pp. 1-69
    • Assinder, S.J.1    Williams, P.A.2
  • 4
    • 0031973699 scopus 로고    scopus 로고
    • Activation of the toluene-responsive regulator XylR causes a transcriptional switch between sigma 54 and sigma70 promoters at the divergent Pr/Ps region of the TOL plasmid
    • Bertoni, G., Marques, S., and de Lorenzo, V. (1998) Activation of the toluene-responsive regulator XylR causes a transcriptional switch between sigma 54 and sigma70 promoters at the divergent Pr/Ps region of the TOL plasmid. Mol Microbiol 27: 651–659.
    • (1998) Mol Microbiol , vol.27 , pp. 651-659
    • Bertoni, G.1    Marques, S.2    de Lorenzo, V.3
  • 5
    • 0037316303 scopus 로고    scopus 로고
    • A comparison of normalization methods for high density oligonucleotide array data based on variance and bias
    • Bolstad, B.M., Irizarry, R.A., Astrand, M., and Speed, T.P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 19: 185–193.
    • (2003) Bioinformatics , vol.19 , pp. 185-193
    • Bolstad, B.M.1    Irizarry, R.A.2    Astrand, M.3    Speed, T.P.4
  • 6
    • 0032589264 scopus 로고    scopus 로고
    • Ntr (PtsN) Protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid
    • Ntr (PtsN) Protein of Pseudomonas putida mediates the C source inhibition of the sigma 54-dependent Pu promoter of the TOL plasmid. J Biol Chem 274: 15562–15568.
    • (1999) J Biol Chem , vol.274 , pp. 15562-15568
    • Cases, I.1    Pérez-Martin, J.2    de Lorenzo, V.3
  • 7
    • 84917699113 scopus 로고    scopus 로고
    • Enzyme clustering accelerates processing of intermediates through metabolic channeling
    • Castellana, M., Wilson, M.Z., Xu, Y., Joshi, P., Cristea, I.M., Rabinowitz, J.D., et al. (2014) Enzyme clustering accelerates processing of intermediates through metabolic channeling. Nat Biotechnol 32: 1011–1018.
    • (2014) Nat Biotechnol , vol.32 , pp. 1011-1018
    • Castellana, M.1    Wilson, M.Z.2    Xu, Y.3    Joshi, P.4    Cristea, I.M.5    Rabinowitz, J.D.6
  • 8
    • 0026516892 scopus 로고
    • One-hour downward alkaline capillary transfer for blotting of DNA and RNA
    • Chomczynski, P. (1992) One-hour downward alkaline capillary transfer for blotting of DNA and RNA. Anal Biochem 201: 134–139.
    • (1992) Anal Biochem , vol.201 , pp. 134-139
    • Chomczynski, P.1
  • 9
    • 0031969092 scopus 로고    scopus 로고
    • Transcriptional repression mediated by LysR-type regulator CatR bound at multiple binding sites
    • Chugani, S.A., Parsek, M.R., and Chakrabarty, A.M. (1998) Transcriptional repression mediated by LysR-type regulator CatR bound at multiple binding sites. J Bacteriol 180: 2367–2372.
    • (1998) J Bacteriol , vol.180 , pp. 2367-2372
    • Chugani, S.A.1    Parsek, M.R.2    Chakrabarty, A.M.3
  • 10
    • 70349329931 scopus 로고    scopus 로고
    • Cells need safety valves
    • Danchin, A. (2009) Cells need safety valves. Bioessays 31: 769–773.
    • (2009) Bioessays , vol.31 , pp. 769-773
    • Danchin, A.1
  • 11
    • 84921609773 scopus 로고    scopus 로고
    • Modularity, context-dependence, and insulation in engineered biological circuits
    • Del Vecchio, D. (2015) Modularity, context-dependence, and insulation in engineered biological circuits. Trends Biotechnol 33: 111–119.
    • (2015) Trends Biotechnol , vol.33 , pp. 111-119
    • Del Vecchio, D.1
  • 12
    • 33744951971 scopus 로고    scopus 로고
    • Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene
    • Dominguez-Cuevas, P., Gonzalez-Pastor, J.E., Marques, S., Ramos, J.L., and de Lorenzo, V. (2006) Transcriptional tradeoff between metabolic and stress-response programs in Pseudomonas putida KT2440 cells exposed to toluene. J Biol Chem 281: 11981–11991.
    • (2006) J Biol Chem , vol.281 , pp. 11981-11991
    • Dominguez-Cuevas, P.1    Gonzalez-Pastor, J.E.2    Marques, S.3    Ramos, J.L.4    de Lorenzo, V.5
  • 13
    • 36349009319 scopus 로고    scopus 로고
    • XylS-Pm promoter interactions through two helix-turn-helix motifs: identifying XylS residues important for DNA binding and activation
    • Dominguez-Cuevas, P., Marin, P., Marques, S., and Ramos, J.L. (2008) XylS-Pm promoter interactions through two helix-turn-helix motifs: identifying XylS residues important for DNA binding and activation. J Mol Biol 375: 59–69.
    • (2008) J Mol Biol , vol.375 , pp. 59-69
    • Dominguez-Cuevas, P.1    Marin, P.2    Marques, S.3    Ramos, J.L.4
  • 14
    • 77952557013 scopus 로고    scopus 로고
    • Sequential XylS-CTD binding to the Pm promoter induces DNA bending prior to activation
    • Dominguez-Cuevas, P., Ramos, J.L., and Marques, S. (2010) Sequential XylS-CTD binding to the Pm promoter induces DNA bending prior to activation. J Bacteriol 192: 2682–2690.
    • (2010) J Bacteriol , vol.192 , pp. 2682-2690
    • Dominguez-Cuevas, P.1    Ramos, J.L.2    Marques, S.3
  • 15
    • 0029920970 scopus 로고    scopus 로고
    • Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a alpha 70-dependent promoter or from alpha 70- and alpha 54-dependent tandem promoters according to the compound used for growth
    • Gallegos, M.T., Marques, S., and Ramos, J.L. (1996) Expression of the TOL plasmid xylS gene in Pseudomonas putida occurs from a alpha 70-dependent promoter or from alpha 70- and alpha 54-dependent tandem promoters according to the compound used for growth. J Bacteriol 178: 2356–2361.
    • (1996) J Bacteriol , vol.178 , pp. 2356-2361
    • Gallegos, M.T.1    Marques, S.2    Ramos, J.L.3
  • 16
    • 1542286907 scopus 로고    scopus 로고
    • Cellular XylS levels are a function of transcription of xylS from two independent promoters and the differential efficiency of translation of the two mRNAs
    • Gonzalez-Perez, M.M., Ramos, J.L., and Marques, S. (2004) Cellular XylS levels are a function of transcription of xylS from two independent promoters and the differential efficiency of translation of the two mRNAs. J Bacteriol 186: 1898–1901.
    • (2004) J Bacteriol , vol.186 , pp. 1898-1901
    • Gonzalez-Perez, M.M.1    Ramos, J.L.2    Marques, S.3
  • 17
    • 0036933239 scopus 로고    scopus 로고
    • Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida
    • Greated, A., Lambertsen, L., Williams, P.A., and Thomas, C.M. (2002) Complete sequence of the IncP-9 TOL plasmid pWW0 from Pseudomonas putida. Environ Microbiol 4: 856–871.
    • (2002) Environ Microbiol , vol.4 , pp. 856-871
    • Greated, A.1    Lambertsen, L.2    Williams, P.A.3    Thomas, C.M.4
  • 19
    • 0032923396 scopus 로고    scopus 로고
    • PcaR-mediated activation and repression of pca genes from Pseudomonas putida are propagated by its binding to both the -35 and the -10 promoter elements
    • Guo, Z., and Houghton, J.E. (1999) PcaR-mediated activation and repression of pca genes from Pseudomonas putida are propagated by its binding to both the -35 and the -10 promoter elements. Mol Microbiol 32: 253–263.
    • (1999) Mol Microbiol , vol.32 , pp. 253-263
    • Guo, Z.1    Houghton, J.E.2
  • 20
    • 0025318026 scopus 로고
    • The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes
    • Harayama, S., and Rekik, M. (1990) The meta cleavage operon of TOL degradative plasmid pWW0 comprises 13 genes. Mol Gen Genet 221: 113–120.
    • (1990) Mol Gen Genet , vol.221 , pp. 113-120
    • Harayama, S.1    Rekik, M.2
  • 21
    • 0027232202 scopus 로고
    • Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution
    • Harayama, S., and Rekik, M. (1993) Comparison of the nucleotide sequences of the meta-cleavage pathway genes of TOL plasmid pWW0 from Pseudomonas putida with other meta-cleavage genes suggests that both single and multiple nucleotide substitutions contribute to enzyme evolution. Mol Gen Genet 239: 81–89.
    • (1993) Mol Gen Genet , vol.239 , pp. 81-89
    • Harayama, S.1    Rekik, M.2
  • 22
    • 0021124798 scopus 로고
    • Transposon mutagenesis analysis of meta-cleavage pathway operon genes of the TOL plasmid of Pseudomonas putida mt-2
    • Harayama, S., Lehrbach, P.R., and Timmis, K.N. (1984) Transposon mutagenesis analysis of meta-cleavage pathway operon genes of the TOL plasmid of Pseudomonas putida mt-2. J Bacteriol 160: 251–255.
    • (1984) J Bacteriol , vol.160 , pp. 251-255
    • Harayama, S.1    Lehrbach, P.R.2    Timmis, K.N.3
  • 23
    • 0024328134 scopus 로고
    • Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products
    • Harayama, S., Rekik, M., Wubbolts, M., Rose, K., Leppik, R.A., and Timmis, K.N. (1989) Characterization of five genes in the upper-pathway operon of TOL plasmid pWW0 from Pseudomonas putida and identification of the gene products. J Bacteriol 171: 5048–5055.
    • (1989) J Bacteriol , vol.171 , pp. 5048-5055
    • Harayama, S.1    Rekik, M.2    Wubbolts, M.3    Rose, K.4    Leppik, R.A.5    Timmis, K.N.6
  • 24
    • 0029795374 scopus 로고    scopus 로고
    • The beta-ketoadipate pathway and the biology of self-identity
    • Harwood, C.S., and Parales, R.E. (1996) The beta-ketoadipate pathway and the biology of self-identity. Annu Rev Microbiol 50: 553–590.
    • (1996) Annu Rev Microbiol , vol.50 , pp. 553-590
    • Harwood, C.S.1    Parales, R.E.2
  • 25
    • 0028204795 scopus 로고
    • Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid
    • Holtel, A., Marques, S., Mohler, I., Jakubzik, U., and Timmis, K.N. (1994) Carbon source-dependent inhibition of xyl operon expression of the Pseudomonas putida TOL plasmid. J Bacteriol 176: 1773–1776.
    • (1994) J Bacteriol , vol.176 , pp. 1773-1776
    • Holtel, A.1    Marques, S.2    Mohler, I.3    Jakubzik, U.4    Timmis, K.N.5
  • 26
    • 84862935255 scopus 로고    scopus 로고
    • Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83
    • Hovik, H., Yu, W.H., Olsen, I., and Chen, T. (2012) Comprehensive transcriptome analysis of the periodontopathogenic bacterium Porphyromonas gingivalis W83. J Bacteriol 194: 100–114.
    • (2012) J Bacteriol , vol.194 , pp. 100-114
    • Hovik, H.1    Yu, W.H.2    Olsen, I.3    Chen, T.4
  • 27
    • 33747856481 scopus 로고    scopus 로고
    • Transcript mapping with high-density oligonucleotide tiling arrays
    • Huber, W., Toedling, J., and Steinmetz, L.M. (2006) Transcript mapping with high-density oligonucleotide tiling arrays. Bioinformatics 22: 1963–1970.
    • (2006) Bioinformatics , vol.22 , pp. 1963-1970
    • Huber, W.1    Toedling, J.2    Steinmetz, L.M.3
  • 28
    • 0024109569 scopus 로고
    • Cloning and expression of pca genes from Pseudomonas putida in Escherichia coli
    • Hughes, E.J., Shapiro, M.K., Houghton, J.E., and Ornston, L.N. (1988) Cloning and expression of pca genes from Pseudomonas putida in Escherichia coli. J Gen Microbiol 134: 2877–2887.
    • (1988) J Gen Microbiol , vol.134 , pp. 2877-2887
    • Hughes, E.J.1    Shapiro, M.K.2    Houghton, J.E.3    Ornston, L.N.4
  • 29
    • 0025604499 scopus 로고
    • Growth-phase-dependent expression of the Pseudomonas putida TOL plasmid pWW0 catabolic genes
    • Hugouvieux-Cotte-Pattat, N., Kohler, T., Rekik, M., and Harayama, S. (1990) Growth-phase-dependent expression of the Pseudomonas putida TOL plasmid pWW0 catabolic genes. J Bacteriol 172: 6651–6660.
    • (1990) J Bacteriol , vol.172 , pp. 6651-6660
    • Hugouvieux-Cotte-Pattat, N.1    Kohler, T.2    Rekik, M.3    Harayama, S.4
  • 30
    • 0036933805 scopus 로고    scopus 로고
    • Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440
    • Jimenez, J.I., Minambres, B., Garcia, J.L., and Diaz, E. (2002) Genomic analysis of the aromatic catabolic pathways from Pseudomonas putida KT2440. Environ Microbiol 4: 824–841.
    • (2002) Environ Microbiol , vol.4 , pp. 824-841
    • Jimenez, J.I.1    Minambres, B.2    Garcia, J.L.3    Diaz, E.4
  • 31
    • 84892653758 scopus 로고    scopus 로고
    • A second chromosomal copy of the catA gene endows Pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol
    • Jimenez, J.I., Perez-Pantoja, D., Chavarria, M., Diaz, E., and de Lorenzo, V. (2014) A second chromosomal copy of the catA gene endows Pseudomonas putida mt-2 with an enzymatic safety valve for excess of catechol. Environ Microbiol 16: 1767–1778.
    • (2014) Environ Microbiol , vol.16 , pp. 1767-1778
    • Jimenez, J.I.1    Perez-Pantoja, D.2    Chavarria, M.3    Diaz, E.4    de Lorenzo, V.5
  • 32
    • 84887648944 scopus 로고    scopus 로고
    • Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes
    • Kim, J., Oliveros, J.C., Nikel, P.I., de Lorenzo, V., and Silva-Rocha, R. (2013) Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes. Environ Microbiol Rep 5: 883–891.
    • (2013) Environ Microbiol Rep , vol.5 , pp. 883-891
    • Kim, J.1    Oliveros, J.C.2    Nikel, P.I.3    de Lorenzo, V.4    Silva-Rocha, R.5
  • 33
    • 77957967615 scopus 로고    scopus 로고
    • The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid
    • Koutinas, M., Lam, M.C., Kiparissides, A., Silva-Rocha, R., Godinho, M., Livingston, A.G., et al. (2010) The regulatory logic of m-xylene biodegradation by Pseudomonas putida mt-2 exposed by dynamic modelling of the principal node Ps/Pr of the TOL plasmid. Environ Microbiol 12: 1705–1718.
    • (2010) Environ Microbiol , vol.12 , pp. 1705-1718
    • Koutinas, M.1    Lam, M.C.2    Kiparissides, A.3    Silva-Rocha, R.4    Godinho, M.5    Livingston, A.G.6
  • 34
    • 84869465095 scopus 로고    scopus 로고
    • From fields to fuels: recent advances in the microbial production of biofuels
    • Kung, Y., Runguphan, W., and Keasling, J.D. (2012) From fields to fuels: recent advances in the microbial production of biofuels. ACS Synth Biol 1: 498–513.
    • (2012) ACS Synth Biol , vol.1 , pp. 498-513
    • Kung, Y.1    Runguphan, W.2    Keasling, J.D.3
  • 35
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li, H., and Durbin, R. (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754–1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 36
    • 84934300609 scopus 로고    scopus 로고
    • Chemical reactivity drives spatiotemporal organisation of bacterial metabolism
    • de Lorenzo, V., Sekowska, A., and Danchin, A. (2014) Chemical reactivity drives spatiotemporal organisation of bacterial metabolism. FEMS Microbiol Rev 39: 96–119.
    • (2014) FEMS Microbiol Rev , vol.39 , pp. 96-119
    • de Lorenzo, V.1    Sekowska, A.2    Danchin, A.3
  • 37
    • 79551524281 scopus 로고    scopus 로고
    • Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods
    • Mader, U., Nicolas, P., Richard, H., Bessieres, P., and Aymerich, S. (2011) Comprehensive identification and quantification of microbial transcriptomes by genome-wide unbiased methods. Curr Opin Biotechnol 22: 32–41.
    • (2011) Curr Opin Biotechnol , vol.22 , pp. 32-41
    • Mader, U.1    Nicolas, P.2    Richard, H.3    Bessieres, P.4    Aymerich, S.5
  • 38
    • 0027367102 scopus 로고
    • Analysis of the mRNA structure of the Pseudomonas putida TOL meta fission pathway operon around the transcription initiation point, the xylTE and the xylFJ regions
    • Marques, S., Ramos, J.L., and Timmis, K.N. (1993) Analysis of the mRNA structure of the Pseudomonas putida TOL meta fission pathway operon around the transcription initiation point, the xylTE and the xylFJ regions. Biochim Biophys Acta 1216: 227–236.
    • (1993) Biochim Biophys Acta , vol.1216 , pp. 227-236
    • Marques, S.1    Ramos, J.L.2    Timmis, K.N.3
  • 39
    • 0028274784 scopus 로고
    • Transcriptional induction kinetics from the promoters of the catabolic pathways of TOL plasmid pWW0 of Pseudomonas putida for metabolism of aromatics
    • Marques, S., Holtel, A., Timmis, K.N., and Ramos, J.L. (1994) Transcriptional induction kinetics from the promoters of the catabolic pathways of TOL plasmid pWW0 of Pseudomonas putida for metabolism of aromatics. J Bacteriol 176: 2517–2524.
    • (1994) J Bacteriol , vol.176 , pp. 2517-2524
    • Marques, S.1    Holtel, A.2    Timmis, K.N.3    Ramos, J.L.4
  • 40
    • 0032586644 scopus 로고    scopus 로고
    • The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma 32 or sigma 38 depending on the growth phase
    • Marques, S., Manzanera, M., Gonzalez-Perez, M.M., Gallegos, M.T., and Ramos, J.L. (1999) The XylS-dependent Pm promoter is transcribed in vivo by RNA polymerase with sigma 32 or sigma 38 depending on the growth phase. Mol Microbiol 31: 1105–1113.
    • (1999) Mol Microbiol , vol.31 , pp. 1105-1113
    • Marques, S.1    Manzanera, M.2    Gonzalez-Perez, M.M.3    Gallegos, M.T.4    Ramos, J.L.5
  • 41
    • 82355181976 scopus 로고    scopus 로고
    • Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria
    • Martinez-Garcia, E., and de Lorenzo, V. (2012) Transposon-based and plasmid-based genetic tools for editing genomes of gram-negative bacteria. Methods Mol Biol 813: 267–283.
    • (2012) Methods Mol Biol , vol.813 , pp. 267-283
    • Martinez-Garcia, E.1    de Lorenzo, V.2
  • 42
    • 60549092956 scopus 로고    scopus 로고
    • High-resolution mapping of plasmid transcriptomes in different host bacteria
    • Miyakoshi, M., Nishida, H., Shintani, M., Yamane, H., and Nojiri, H. (2009) High-resolution mapping of plasmid transcriptomes in different host bacteria. BMC Genomics 10: 12.
    • (2009) BMC Genomics , vol.10 , pp. 12
    • Miyakoshi, M.1    Nishida, H.2    Shintani, M.3    Yamane, H.4    Nojiri, H.5
  • 43
    • 77955289214 scopus 로고    scopus 로고
    • The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes
    • Moreno, R., Fonseca, P., and Rojo, F. (2010) The Crc global regulator inhibits the Pseudomonas putida pWW0 toluene/xylene assimilation pathway by repressing the translation of regulatory and structural genes. J Biol Chem 285: 24412–24419.
    • (2010) J Biol Chem , vol.285 , pp. 24412-24419
    • Moreno, R.1    Fonseca, P.2    Rojo, F.3
  • 44
    • 70349739736 scopus 로고    scopus 로고
    • The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets
    • Nicol, J.W., Helt, G.A., Blanchard, S.G., Jr, Raja, A., and Loraine, A.E. (2009) The Integrated Genome Browser: free software for distribution and exploration of genome-scale datasets. Bioinformatics 25: 2730–2731.
    • (2009) Bioinformatics , vol.25 , pp. 2730-2731
    • Nicol, J.W.1    Helt, G.A.2    Blanchard, S.G.3    Raja, A.4    Loraine, A.E.5
  • 45
    • 84871436225 scopus 로고    scopus 로고
    • Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene
    • Nikel, P.I., and de Lorenzo, V. (2013) Engineering an anaerobic metabolic regime in Pseudomonas putida KT2440 for the anoxic biodegradation of 1,3-dichloroprop-1-ene. Metab Eng 15: 98–112.
    • (2013) Metab Eng , vol.15 , pp. 98-112
    • Nikel, P.I.1    de Lorenzo, V.2
  • 46
    • 84910027662 scopus 로고    scopus 로고
    • Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis
    • Nikel, P.I., and de Lorenzo, V. (2014) Robustness of Pseudomonas putida KT2440 as a host for ethanol biosynthesis. N Biotechnol 31: 562–571.
    • (2014) N Biotechnol , vol.31 , pp. 562-571
    • Nikel, P.I.1    de Lorenzo, V.2
  • 47
    • 84898874640 scopus 로고    scopus 로고
    • Biotechnological domestication of pseudomonads using synthetic biology
    • Nikel, P.I., Martinez-Garcia, E., and de Lorenzo, V. (2014) Biotechnological domestication of pseudomonads using synthetic biology. Nat Rev Microbiol 12: 368–379.
    • (2014) Nat Rev Microbiol , vol.12 , pp. 368-379
    • Nikel, P.I.1    Martinez-Garcia, E.2    de Lorenzo, V.3
  • 48
    • 0027239529 scopus 로고
    • Regulation of the pcaIJ genes for aromatic acid degradation in Pseudomonas putida
    • Parales, R.E., and Harwood, C.S. (1993) Regulation of the pcaIJ genes for aromatic acid degradation in Pseudomonas putida. J Bacteriol 175: 5829–5838.
    • (1993) J Bacteriol , vol.175 , pp. 5829-5838
    • Parales, R.E.1    Harwood, C.S.2
  • 50
    • 0028980296 scopus 로고
    • The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR
    • Perez-Martin, J., and de Lorenzo, V. (1995) The sigma 54-dependent promoter Ps of the TOL plasmid of Pseudomonas putida requires HU for transcriptional activation in vivo by XylR. J Bacteriol 177: 3758–3763.
    • (1995) J Bacteriol , vol.177 , pp. 3758-3763
    • Perez-Martin, J.1    de Lorenzo, V.2
  • 51
    • 84921884150 scopus 로고    scopus 로고
    • The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in m-xylene biodegradation
    • Perez-Pantoja, D., Kim, J., Silva-Rocha, R., and de Lorenzo, V. (2014) The differential response of the Pben promoter of Pseudomonas putida mt-2 to BenR and XylS prevents metabolic conflicts in m-xylene biodegradation. Environ Microbiol 17: 64–75.
    • (2014) Environ Microbiol , vol.17 , pp. 64-75
    • Perez-Pantoja, D.1    Kim, J.2    Silva-Rocha, R.3    de Lorenzo, V.4
  • 52
    • 36148972085 scopus 로고    scopus 로고
    • Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D
    • Perocchi, F., Xu, Z., Clauder-Munster, S., and Steinmetz, L.M. (2007) Antisense artifacts in transcriptome microarray experiments are resolved by actinomycin D. Nucl Acids Res 35: e128.
    • (2007) Nucl Acids Res , vol.35
    • Perocchi, F.1    Xu, Z.2    Clauder-Munster, S.3    Steinmetz, L.M.4
  • 53
    • 0030860391 scopus 로고    scopus 로고
    • Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators
    • Ramos, J.L., Marques, S., and Timmis, K.N. (1997) Transcriptional control of the Pseudomonas TOL plasmid catabolic operons is achieved through an interplay of host factors and plasmid-encoded regulators. Annu Rev Microbiol 51: 341–373.
    • (1997) Annu Rev Microbiol , vol.51 , pp. 341-373
    • Ramos, J.L.1    Marques, S.2    Timmis, K.N.3
  • 54
    • 1542319979 scopus 로고    scopus 로고
    • Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures
    • Rescalli, E., Saini, S., Bartocci, C., Rychlewski, L., De Lorenzo, V., and Bertoni, G. (2004) Novel physiological modulation of the Pu promoter of TOL plasmid: negative regulatory role of the TurA protein of Pseudomonas putida in the response to suboptimal growth temperatures. J Biol Chem 279: 7777–7784.
    • (2004) J Biol Chem , vol.279 , pp. 7777-7784
    • Rescalli, E.1    Saini, S.2    Bartocci, C.3    Rychlewski, L.4    De Lorenzo, V.5    Bertoni, G.6
  • 55
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson, M.D., and Oshlack, A. (2010) A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol 11: R25.
    • (2010) Genome Biol , vol.11 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 56
    • 41149085992 scopus 로고    scopus 로고
    • Small-sample estimation of negative binomial dispersion, with applications to SAGE data
    • Robinson, M.D., and Smyth, G.K. (2008) Small-sample estimation of negative binomial dispersion, with applications to SAGE data. Biostatistics 9: 321–332.
    • (2008) Biostatistics , vol.9 , pp. 321-332
    • Robinson, M.D.1    Smyth, G.K.2
  • 57
    • 0023644204 scopus 로고
    • Assemblage of ortho cleavage route for simultaneous degradation of chloro- and methylaromatics
    • Rojo, F., Pieper, D.H., Engesser, K.H., Knackmuss, H.J., and Timmis, K.N. (1987) Assemblage of ortho cleavage route for simultaneous degradation of chloro- and methylaromatics. Science 238: 1395–1398.
    • (1987) Science , vol.238 , pp. 1395-1398
    • Rojo, F.1    Pieper, D.H.2    Engesser, K.H.3    Knackmuss, H.J.4    Timmis, K.N.5
  • 58
    • 0027937565 scopus 로고
    • Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate
    • Romero-Steiner, S., Parales, R.E., Harwood, C.S., and Houghton, J.E. (1994) Characterization of the pcaR regulatory gene from Pseudomonas putida, which is required for the complete degradation of p-hydroxybenzoate. J Bacteriol 176: 5771–5779.
    • (1994) J Bacteriol , vol.176 , pp. 5771-5779
    • Romero-Steiner, S.1    Parales, R.E.2    Harwood, C.S.3    Houghton, J.E.4
  • 59
    • 0025914926 scopus 로고
    • Functional analysis of the Pseudomonas putida regulatory protein CatR: transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting
    • Rothmel, R.K., Shinabarger, D.L., Parsek, M.R., Aldrich, T.L., and Chakrabarty, A.M. (1991) Functional analysis of the Pseudomonas putida regulatory protein CatR: transcriptional studies and determination of the CatR DNA-binding site by hydroxyl-radical footprinting. J Bacteriol 173: 4717–4724.
    • (1991) J Bacteriol , vol.173 , pp. 4717-4724
    • Rothmel, R.K.1    Shinabarger, D.L.2    Parsek, M.R.3    Aldrich, T.L.4    Chakrabarty, A.M.5
  • 60
    • 0027446708 scopus 로고
    • Molecular biology of the LysR family of transcriptional regulators
    • Schell, M.A. (1993) Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47: 597–626.
    • (1993) Annu Rev Microbiol , vol.47 , pp. 597-626
    • Schell, M.A.1
  • 62
    • 84859517094 scopus 로고    scopus 로고
    • A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria
    • Silva-Rocha, R., and de Lorenzo, V. (2012) A GFP-lacZ bicistronic reporter system for promoter analysis in environmental gram-negative bacteria. PLoS ONE 7: e34675.
    • (2012) PLoS ONE , vol.7
    • Silva-Rocha, R.1    de Lorenzo, V.2
  • 63
    • 84904820242 scopus 로고    scopus 로고
    • The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida
    • Silva-Rocha, R., and de Lorenzo, V. (2014) The pWW0 plasmid imposes a stochastic expression regime to the chromosomal ortho pathway for benzoate metabolism in Pseudomonas putida. FEMS Microbiol Lett 356: 176–183.
    • (2014) FEMS Microbiol Lett , vol.356 , pp. 176-183
    • Silva-Rocha, R.1    de Lorenzo, V.2
  • 64
    • 80052612366 scopus 로고    scopus 로고
    • The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms
    • Silva-Rocha, R., Tamames, J., dos Santos, V.M., and de Lorenzo, V. (2011a) The logicome of environmental bacteria: merging catabolic and regulatory events with Boolean formalisms. Environ Microbiol 13: 2389–2402.
    • (2011) Environ Microbiol , vol.13 , pp. 2389-2402
    • Silva-Rocha, R.1    Tamames, J.2    dos Santos, V.M.3    de Lorenzo, V.4
  • 65
    • 81055148316 scopus 로고    scopus 로고
    • The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene
    • Silva-Rocha, R., de Jong, H., Tamames, J., and de Lorenzo, V. (2011b) The logic layout of the TOL network of Pseudomonas putida pWW0 plasmid stems from a metabolic amplifier motif (MAM) that optimizes biodegradation of m-xylene. BMC Syst Biol 5: 191.
    • (2011) BMC Syst Biol , vol.5 , pp. 191
    • Silva-Rocha, R.1    de Jong, H.2    Tamames, J.3    de Lorenzo, V.4
  • 66
    • 84876567509 scopus 로고    scopus 로고
    • The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes
    • Silva-Rocha, R., Martinez-Garcia, E., Calles, B., Chavarria, M., Arce-Rodriguez, A., de Las Heras, A., et al. (2013) The Standard European Vector Architecture (SEVA): a coherent platform for the analysis and deployment of complex prokaryotic phenotypes. Nucl Acids Res 41: D666–D675.
    • (2013) Nucl Acids Res , vol.41 , pp. D666-D675
    • Silva-Rocha, R.1    Martinez-Garcia, E.2    Calles, B.3    Chavarria, M.4    Arce-Rodriguez, A.5    de Las Heras, A.6
  • 67
    • 4544341015 scopus 로고    scopus 로고
    • Linear models and empirical bayes methods for assessing differential expression in microarray experiments
    • Smyth, G.K. (2004) Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol 3: Article3.
    • (2004) Stat Appl Genet Mol Biol , vol.3 , pp. Article3
    • Smyth, G.K.1
  • 68
    • 0242333835 scopus 로고    scopus 로고
    • Normalization of cDNA microarray data
    • Smyth, G.K., and Speed, T. (2003) Normalization of cDNA microarray data. Methods 31: 265–273.
    • (2003) Methods , vol.31 , pp. 265-273
    • Smyth, G.K.1    Speed, T.2
  • 69
    • 72849114230 scopus 로고    scopus 로고
    • Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity
    • Sorek, R., and Cossart, P. (2010) Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 11: 9–16.
    • (2010) Nat Rev Genet , vol.11 , pp. 9-16
    • Sorek, R.1    Cossart, P.2
  • 70
    • 79961135005 scopus 로고    scopus 로고
    • Vienna, Austria, R Foundation for Statistical Computing
    • The Development Core Team (2011) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
    • (2011) R: A Language and Environment for Statistical Computing
  • 71
    • 78149421813 scopus 로고    scopus 로고
    • Bacterial antisense RNAs: how many are there, and what are they doing?
    • Thomason, M.K., and Storz, G. (2010) Bacterial antisense RNAs: how many are there, and what are they doing? Annu Rev Genet 44: 167–188.
    • (2010) Annu Rev Genet , vol.44 , pp. 167-188
    • Thomason, M.K.1    Storz, G.2
  • 72
    • 84875634162 scopus 로고    scopus 로고
    • Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
    • Thorvaldsdottir, H., Robinson, J.T., and Mesirov, J.P. (2012) Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform 14: 178–192.
    • (2012) Brief Bioinform , vol.14 , pp. 178-192
    • Thorvaldsdottir, H.1    Robinson, J.T.2    Mesirov, J.P.3
  • 74
    • 10044274277 scopus 로고    scopus 로고
    • Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma 54 Pu promoter of Pseudomonas putida
    • Velazquez, F., di Bartolo, I., and de Lorenzo, V. (2004) Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma 54 Pu promoter of Pseudomonas putida. J Bacteriol 186: 8267–8275.
    • (2004) J Bacteriol , vol.186 , pp. 8267-8275
    • Velazquez, F.1    di Bartolo, I.2    de Lorenzo, V.3
  • 75
    • 25144446779 scopus 로고    scopus 로고
    • Inferring the genetic network of m-xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2
    • Velazquez, F., Parro, V., and de Lorenzo, V. (2005) Inferring the genetic network of m-xylene metabolism through expression profiling of the xyl genes of Pseudomonas putida mt-2. Mol Microbiol 57: 1557–1569.
    • (2005) Mol Microbiol , vol.57 , pp. 1557-1569
    • Velazquez, F.1    Parro, V.2    de Lorenzo, V.3
  • 76
    • 47049120518 scopus 로고    scopus 로고
    • Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma 54-promoter Pu to the response regulator PprA
    • Vitale, E., Milani, A., Renzi, F., Galli, E., Rescalli, E., de Lorenzo, V., and Bertoni, G. (2008) Transcriptional wiring of the TOL plasmid regulatory network to its host involves the submission of the sigma 54-promoter Pu to the response regulator PprA. Mol Microbiol 69: 698–713.
    • (2008) Mol Microbiol , vol.69 , pp. 698-713
    • Vitale, E.1    Milani, A.2    Renzi, F.3    Galli, E.4    Rescalli, E.5    de Lorenzo, V.6    Bertoni, G.7
  • 77
    • 0025068630 scopus 로고
    • Molecular cloning of the xylL-xylE region from the P. putida TOL plasmid, pDK1
    • Voss, J.A., Khedairy, H., Baker, R.F., and Benjamin, R.C. (1990) Molecular cloning of the xylL-xylE region from the P. putida TOL plasmid, pDK1. SAAS Bull Biochem Biotechnol 3: 54–57.
    • (1990) SAAS Bull Biochem Biotechnol , vol.3 , pp. 54-57
    • Voss, J.A.1    Khedairy, H.2    Baker, R.F.3    Benjamin, R.C.4
  • 78
    • 0031024264 scopus 로고    scopus 로고
    • xylUW, two genes at the start of the upper pathway operon of TOL plasmid pWW0, appear to play no essential part in determining its catabolic phenotype
    • Williams, P.A., Shaw, L.M., Pitt, C.W., and Vrecl, M. (1997) xylUW, two genes at the start of the upper pathway operon of TOL plasmid pWW0, appear to play no essential part in determining its catabolic phenotype. Microbiology 143: 101–107.
    • (1997) Microbiology , vol.143 , pp. 101-107
    • Williams, P.A.1    Shaw, L.M.2    Pitt, C.W.3    Vrecl, M.4
  • 79
    • 0016593935 scopus 로고
    • Metabolism of toluene and xylenes by Pseudomonas putida (arvilla) mt-2: evidence for a new function of the TOL plasmid
    • Worsey, M.J., and Williams, P.A. (1975) Metabolism of toluene and xylenes by Pseudomonas putida (arvilla) mt-2: evidence for a new function of the TOL plasmid. J Bacteriol 124: 7–13.
    • (1975) J Bacteriol , vol.124 , pp. 7-13
    • Worsey, M.J.1    Williams, P.A.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.