메뉴 건너뛰기




Volumn 5, Issue 6, 2013, Pages 883-891

Transcriptomic fingerprinting of Pseudomonas putida under alternative physiological regimes

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL PROTEIN; CARRIER PROTEIN; CRC PROTEIN, PSEUDOMONAS; FRUCTOSE; GLUCOSE; GLYCEROL; HUPA PROTEIN, BACTERIA; OUTER MEMBRANE PROTEIN; REPRESSOR PROTEIN; SIGMA FACTOR; SIGMA FACTOR KATF PROTEIN, BACTERIA; SMALL INTERFERING RNA; SUCCINIC ACID; TRANSCRIPTOME;

EID: 84887648944     PISSN: None     EISSN: 17582229     Source Type: Journal    
DOI: 10.1111/1758-2229.12090     Document Type: Article
Times cited : (49)

References (48)
  • 1
    • 77957938539 scopus 로고    scopus 로고
    • Lack of CbrB in Pseudomonas putida affects not only amino acids metabolism but also different stress responses and biofilm development
    • Amador, C.I., Canosa, I., Govantes, F., and Santero, E. (2010) Lack of CbrB in Pseudomonas putida affects not only amino acids metabolism but also different stress responses and biofilm development. Environ Microbiol 12: 1748-1761.
    • (2010) Environ Microbiol , vol.12 , pp. 1748-1761
    • Amador, C.I.1    Canosa, I.2    Govantes, F.3    Santero, E.4
  • 2
    • 0030681260 scopus 로고    scopus 로고
    • The significance of digital gene expression profiles
    • Audic, S., and Claverie, J.M. (1997) The significance of digital gene expression profiles. Genome Res 7: 986-995.
    • (1997) Genome Res , vol.7 , pp. 986-995
    • Audic, S.1    Claverie, J.M.2
  • 3
    • 0034608861 scopus 로고    scopus 로고
    • Escherichia coli CspA-family RNA chaperones are transscription antiterminators
    • Bae, W., Xia, B., Inouye, M., and Severinov, K. (2000) Escherichia coli CspA-family RNA chaperones are transscription antiterminators. Proc Natl Acad Sci USA 97: 7784-7789.
    • (2000) Proc Natl Acad Sci USA , vol.97 , pp. 7784-7789
    • Bae, W.1    Xia, B.2    Inouye, M.3    Severinov, K.4
  • 4
    • 0019805971 scopus 로고
    • Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas
    • Bagdasarian, M., Lurz, R., Ruckert, B., Franklin, F.C., Bagdasarian, M.M., Frey, J., and Timmis, K.N. (1981) Specific-purpose plasmid cloning vectors. II. Broad host range, high copy number, RSF1010-derived vectors, and a host-vector system for gene cloning in Pseudomonas. Gene 16: 237-247.
    • (1981) Gene , vol.16 , pp. 237-247
    • Bagdasarian, M.1    Lurz, R.2    Ruckert, B.3    Franklin, F.C.4    Bagdasarian, M.M.5    Frey, J.6    Timmis, K.N.7
  • 5
    • 55049135859 scopus 로고    scopus 로고
    • MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries
    • Bar, M., Wyman, S.K., Fritz, B.R., Qi, J., Garg, K.S., Parkin, R.K., etal. (2008) MicroRNA discovery and profiling in human embryonic stem cells by deep sequencing of small RNA libraries. Stem Cells 26: 2496-2505.
    • (2008) Stem Cells , vol.26 , pp. 2496-2505
    • Bar, M.1    Wyman, S.K.2    Fritz, B.R.3    Qi, J.4    Garg, K.S.5    Parkin, R.K.6
  • 6
    • 0035907280 scopus 로고    scopus 로고
    • The essential HupB and HupN proteins of Pseudomonas putida provide redundant and nonspecific DNA-bending functions
    • Bartels, F., Fernandez, S., Holtel, A., Timmis, K.N., and de Lorenzo, V. (2001) The essential HupB and HupN proteins of Pseudomonas putida provide redundant and nonspecific DNA-bending functions. J Biol Chem 276: 16641-16648.
    • (2001) J Biol Chem , vol.276 , pp. 16641-16648
    • Bartels, F.1    Fernandez, S.2    Holtel, A.3    Timmis, K.N.4    de Lorenzo, V.5
  • 7
    • 0035829361 scopus 로고    scopus 로고
    • Controlling the false discovery rate in behavior genetics research
    • Benjamini, Y., Drai, D., Elmer, G., Kafkafi, N., and Golani, I. (2001) Controlling the false discovery rate in behavior genetics research. Behav Brain Res 125: 279-284.
    • (2001) Behav Brain Res , vol.125 , pp. 279-284
    • Benjamini, Y.1    Drai, D.2    Elmer, G.3    Kafkafi, N.4    Golani, I.5
  • 8
    • 0023041804 scopus 로고
    • Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch
    • Broyles, S.S., and Pettijohn, D.E. (1986) Interaction of the Escherichia coli HU protein with DNA. Evidence for formation of nucleosome-like structures with altered DNA helical pitch. J Mol Biol 187: 47-60.
    • (1986) J Mol Biol , vol.187 , pp. 47-60
    • Broyles, S.S.1    Pettijohn, D.E.2
  • 9
    • 0036267257 scopus 로고    scopus 로고
    • The genomes of Pseudomonas encode a third HU protein
    • Cases, I., and de Lorenzo, V. (2002) The genomes of Pseudomonas encode a third HU protein. Microbiology 148: 1243-1245.
    • (2002) Microbiology , vol.148 , pp. 1243-1245
    • Cases, I.1    de Lorenzo, V.2
  • 10
    • 84860532358 scopus 로고    scopus 로고
    • Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism
    • Chavarria, M., Kleijn, R.J., Sauer, U., Pfluger-Grau, K., and de Lorenzo, V. (2012) Regulatory tasks of the phosphoenolpyruvate-phosphotransferase system of Pseudomonas putida in central carbon metabolism. mBio 3: e00028-12.
    • (2012) mBio , vol.3
    • Chavarria, M.1    Kleijn, R.J.2    Sauer, U.3    Pfluger-Grau, K.4    de Lorenzo, V.5
  • 11
    • 84871936294 scopus 로고    scopus 로고
    • Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate: phosphotransferase system of Pseudomonas putida
    • Chavarria, M., Fuhrer, T., Sauer, U., Pfluger-Grau, K., and de Lorenzo, V. (2013) Cra regulates the cross-talk between the two branches of the phosphoenolpyruvate: phosphotransferase system of Pseudomonas putida. Environ Microbiol 15: 121-132.
    • (2013) Environ Microbiol , vol.15 , pp. 121-132
    • Chavarria, M.1    Fuhrer, T.2    Sauer, U.3    Pfluger-Grau, K.4    de Lorenzo, V.5
  • 12
    • 0031576352 scopus 로고    scopus 로고
    • Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival
    • Claret, L., and Rouviere-Yaniv, J. (1997) Variation in HU composition during growth of Escherichia coli: the heterodimer is required for long term survival. J Mol Biol 273: 93-104.
    • (1997) J Mol Biol , vol.273 , pp. 93-104
    • Claret, L.1    Rouviere-Yaniv, J.2
  • 13
    • 79955017837 scopus 로고    scopus 로고
    • Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics
    • Frank, S., Klockgether, J., Hagendorf, P., Geffers, R., Schock, U., Pohl, T., etal. (2011) Pseudomonas putida KT2440 genome update by cDNA sequencing and microarray transcriptomics. Environ Microbiol 13: 1309-1326.
    • (2011) Environ Microbiol , vol.13 , pp. 1309-1326
    • Frank, S.1    Klockgether, J.2    Hagendorf, P.3    Geffers, R.4    Schock, U.5    Pohl, T.6
  • 16
    • 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
  • 17
    • 0031015217 scopus 로고    scopus 로고
    • CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone
    • Jiang, W., Hou, Y., and Inouye, M. (1997) CspA, the major cold-shock protein of Escherichia coli, is an RNA chaperone. J Biol Chem 272: 196-202.
    • (1997) J Biol Chem , vol.272 , pp. 196-202
    • Jiang, W.1    Hou, Y.2    Inouye, M.3
  • 18
    • 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
  • 20
    • 0036936782 scopus 로고    scopus 로고
    • Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01
    • Martinez-Bueno, M.A., Tobes, R., Rey, M., and Ramos, J.L. (2002) Detection of multiple extracytoplasmic function (ECF) sigma factors in the genome of Pseudomonas putida KT2440 and their counterparts in Pseudomonas aeruginosa PA01. Environ Microbiol 4: 842-855.
    • (2002) Environ Microbiol , vol.4 , pp. 842-855
    • Martinez-Bueno, M.A.1    Tobes, R.2    Rey, M.3    Ramos, J.L.4
  • 21
    • 33748313067 scopus 로고    scopus 로고
    • Inactivation of the Pseudomonas putida cytochrome o-ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases
    • Morales, G., Ugidos, A., and Rojo, F. (2006) Inactivation of the Pseudomonas putida cytochrome o-ubiquinol oxidase leads to a significant change in the transcriptome and to increased expression of the CIO and cbb3-1 terminal oxidases. Environ Microbiol 8: 1764-1774.
    • (2006) Environ Microbiol , vol.8 , pp. 1764-1774
    • Morales, G.1    Ugidos, A.2    Rojo, F.3
  • 22
    • 67649201763 scopus 로고    scopus 로고
    • The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: evidence from proteomic and genomic analyses
    • Moreno, R., Martinez-Gomariz, M., Yuste, L., Gil, C., and Rojo, F. (2009) The Pseudomonas putida Crc global regulator controls the hierarchical assimilation of amino acids in a complete medium: evidence from proteomic and genomic analyses. Proteomics 9: 2910-2928.
    • (2009) Proteomics , vol.9 , pp. 2910-2928
    • Moreno, R.1    Martinez-Gomariz, M.2    Yuste, L.3    Gil, C.4    Rojo, F.5
  • 23
    • 84155165433 scopus 로고    scopus 로고
    • Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression
    • Moreno, R., Fonseca, P., and Rojo, F. (2012) Two small RNAs, CrcY and CrcZ, act in concert to sequester the Crc global regulator in Pseudomonas putida, modulating catabolite repression. Mol Microbiol 83: 24-40.
    • (2012) Mol Microbiol , vol.83 , pp. 24-40
    • Moreno, R.1    Fonseca, P.2    Rojo, F.3
  • 24
    • 0036933705 scopus 로고    scopus 로고
    • Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440
    • Nelson, K.E., Weinel, C., Paulsen, I.T., Dodson, R.J., Hilbert, H., Martins dos Santos, V.A., etal. (2002) Complete genome sequence and comparative analysis of the metabolically versatile Pseudomonas putida KT2440. Environ Microbiol 4: 799-808.
    • (2002) Environ Microbiol , vol.4 , pp. 799-808
    • Nelson, K.E.1    Weinel, C.2    Paulsen, I.T.3    Dodson, R.J.4    Hilbert, H.5    Martins dos Santos, V.A.6
  • 25
    • 84891629337 scopus 로고    scopus 로고
    • Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440
    • Nikel, P.I., Kim, J., and de Lorenzo, V. (2013) Metabolic and regulatory rearrangements underlying glycerol metabolism in Pseudomonas putida KT2440. Environ Microbiol. (in press).
    • (2013) Environ Microbiol
    • Nikel, P.I.1    Kim, J.2    de Lorenzo, V.3
  • 26
    • 54449092307 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
    • Nogales, J., Palsson, B., and Thiele, I. (2008) A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2: 79.
    • (2008) BMC Syst Biol , vol.2 , pp. 79
    • Nogales, J.1    Palsson, B.2    Thiele, I.3
  • 27
    • 84988735230 scopus 로고    scopus 로고
    • The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction
    • Oberto, J., Nabti, S., Jooste, V., Mignot, H., and Rouviere-Yaniv, J. (2009) The HU regulon is composed of genes responding to anaerobiosis, acid stress, high osmolarity and SOS induction. PLoS ONE 4: e4367.
    • (2009) PLoS ONE , vol.4
    • Oberto, J.1    Nabti, S.2    Jooste, V.3    Mignot, H.4    Rouviere-Yaniv, J.5
  • 28
    • 77952552068 scopus 로고    scopus 로고
    • Regulatory roles of the bacterial nitrogen-related phosphotransferase system
    • Pfluger-Grau, K., and Gorke, B. (2010) Regulatory roles of the bacterial nitrogen-related phosphotransferase system. Trends Microbiol 18: 205-214.
    • (2010) Trends Microbiol , vol.18 , pp. 205-214
    • Pfluger-Grau, K.1    Gorke, B.2
  • 29
    • 78751666283 scopus 로고    scopus 로고
    • RNA remodeling and gene regulation by cold shock proteins
    • Phadtare, S., and Severinov, K. (2010) RNA remodeling and gene regulation by cold shock proteins. RNA Biol 7: 788-795.
    • (2010) RNA Biol , vol.7 , pp. 788-795
    • Phadtare, S.1    Severinov, K.2
  • 30
    • 0033515646 scopus 로고    scopus 로고
    • Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA
    • Pinson, V., Takahashi, M., and Rouviere-Yaniv, J. (1999) Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA. J Mol Biol 287: 485-497.
    • (1999) J Mol Biol , vol.287 , pp. 485-497
    • Pinson, V.1    Takahashi, M.2    Rouviere-Yaniv, J.3
  • 33
    • 55449096123 scopus 로고    scopus 로고
    • Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
    • Puchalka, J., Oberhardt, M.A., Godinho, M., Bielecka, A., Regenhardt, D., Timmis, K.N., etal. (2008) Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology. PLoS Comput Biol 4: e1000210.
    • (2008) PLoS Comput Biol , vol.4
    • Puchalka, J.1    Oberhardt, M.A.2    Godinho, M.3    Bielecka, A.4    Regenhardt, D.5    Timmis, K.N.6
  • 34
    • 0031780471 scopus 로고    scopus 로고
    • Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440
    • Ramos-Gonzalez, M.I., and Molin, S. (1998) Cloning, sequencing, and phenotypic characterization of the rpoS gene from Pseudomonas putida KT2440. J Bacteriol 180: 3421-3431.
    • (1998) J Bacteriol , vol.180 , pp. 3421-3431
    • Ramos-Gonzalez, M.I.1    Molin, S.2
  • 35
    • 0037823447 scopus 로고    scopus 로고
    • Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure
    • Ramstein, J., Hervouet, N., Coste, F., Zelwer, C., Oberto, J., and Castaing, B. (2003) Evidence of a thermal unfolding dimeric intermediate for the Escherichia coli histone-like HU proteins: thermodynamics and structure. J Mol Biol 331: 101-121.
    • (2003) J Mol Biol , vol.331 , pp. 101-121
    • Ramstein, J.1    Hervouet, N.2    Coste, F.3    Zelwer, C.4    Oberto, J.5    Castaing, B.6
  • 37
    • 77955132055 scopus 로고    scopus 로고
    • Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment
    • Rojo, F. (2010) Carbon catabolite repression in Pseudomonas: optimizing metabolic versatility and interactions with the environment. FEMS Microbiol Rev 34: 658-684.
    • (2010) FEMS Microbiol Rev , vol.34 , pp. 658-684
    • Rojo, F.1
  • 38
    • 18944369815 scopus 로고    scopus 로고
    • Levels and activity of the Pseudomonas putida global regulatory protein Crc vary according to growth conditions
    • Ruiz-Manzano, A., Yuste, L., and Rojo, F. (2005) Levels and activity of the Pseudomonas putida global regulatory protein Crc vary according to growth conditions. J Bacteriol 187: 3678-3686.
    • (2005) J Bacteriol , vol.187 , pp. 3678-3686
    • Ruiz-Manzano, A.1    Yuste, L.2    Rojo, F.3
  • 40
    • 10044292705 scopus 로고    scopus 로고
    • Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440
    • dos Santos, V.A., Heim, S., Moore, E.R., Stratz, M., and Timmis, K.N. (2004) Insights into the genomic basis of niche specificity of Pseudomonas putida KT2440. Environ Microbiol 6: 1264-1286.
    • (2004) Environ Microbiol , vol.6 , pp. 1264-1286
    • dos Santos, V.A.1    Heim, S.2    Moore, E.R.3    Stratz, M.4    Timmis, K.N.5
  • 41
    • 78449268845 scopus 로고    scopus 로고
    • Interdependence of cell growth and gene expression: origins and consequences
    • Scott, M., Gunderson, C.W., Mateescu, E.M., Zhang, Z., and Hwa, T. (2010) Interdependence of cell growth and gene expression: origins and consequences. Science 330: 1099-1102.
    • (2010) Science , vol.330 , pp. 1099-1102
    • Scott, M.1    Gunderson, C.W.2    Mateescu, E.M.3    Zhang, Z.4    Hwa, T.5
  • 43
    • 50849105413 scopus 로고    scopus 로고
    • Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq
    • Sittka, A., Lucchini, S., Papenfort, K., Sharma, C.M., Rolle, K., Binnewies, T.T., etal. (2008) Deep sequencing analysis of small noncoding RNA and mRNA targets of the global post-transcriptional regulator, Hfq. PLoS Genet 4: e1000163.
    • (2008) PLoS Genet , vol.4
    • Sittka, A.1    Lucchini, S.2    Papenfort, K.3    Sharma, C.M.4    Rolle, K.5    Binnewies, T.T.6
  • 44
    • 14644438364 scopus 로고    scopus 로고
    • Circular genome visualization and exploration using CGView
    • Stothard, P., and Wishart, D.S. (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21: 537-539.
    • (2005) Bioinformatics , vol.21 , pp. 537-539
    • Stothard, P.1    Wishart, D.S.2
  • 45
    • 0037709130 scopus 로고    scopus 로고
    • Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different?
    • Venturi, V. (2003) Control of rpoS transcription in Escherichia coli and Pseudomonas: why so different? Mol Microbiol 49: 1-9.
    • (2003) Mol Microbiol , vol.49 , pp. 1-9
    • Venturi, V.1
  • 46
    • 57749195712 scopus 로고    scopus 로고
    • RNA-Seq: a revolutionary tool for transcriptomics
    • Wang, Z., Gerstein, M., and Snyder, M. (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10: 57-63.
    • (2009) Nat Rev Genet , vol.10 , pp. 57-63
    • Wang, Z.1    Gerstein, M.2    Snyder, M.3
  • 47
    • 0030856635 scopus 로고    scopus 로고
    • Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli
    • Yamanaka, K., and Inouye, M. (1997) Growth-phase-dependent expression of cspD, encoding a member of the CspA family in Escherichia coli. J Bacteriol 179: 5126-5130.
    • (1997) J Bacteriol , vol.179 , pp. 5126-5130
    • Yamanaka, K.1    Inouye, M.2
  • 48
    • 0035057105 scopus 로고    scopus 로고
    • CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli
    • Yamanaka, K., Zheng, W., Crooke, E., Wang, Y.H., and Inouye, M. (2001) CspD, a novel DNA replication inhibitor induced during the stationary phase in Escherichia coli. Mol Microbiol 39: 1572-1584.
    • (2001) Mol Microbiol , vol.39 , pp. 1572-1584
    • Yamanaka, K.1    Zheng, W.2    Crooke, E.3    Wang, Y.H.4    Inouye, M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.