메뉴 건너뛰기




Volumn 12, Issue 5, 2009, Pages 568-576

Acinetobacter baylyi ADP1 as a model for metabolic system biology

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE DIPHOSPHATE;

EID: 70349835370     PISSN: 13695274     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mib.2009.07.005     Document Type: Review
Times cited : (46)

References (83)
  • 1
    • 0141561891 scopus 로고    scopus 로고
    • Integrating 'omic' information: a bridge between genomics and systems biology
    • Ge H., Walhout A.J., and Vidal M. Integrating 'omic' information: a bridge between genomics and systems biology. Trends Genet 19 (2003) 551-560
    • (2003) Trends Genet , vol.19 , pp. 551-560
    • Ge, H.1    Walhout, A.J.2    Vidal, M.3
  • 2
    • 33644527950 scopus 로고    scopus 로고
    • The model organism as a system: integrating 'omics' data sets
    • Joyce A.R., and Palsson B.O. The model organism as a system: integrating 'omics' data sets. Nat Rev Mol Cell Biol 7 (2006) 198-210
    • (2006) Nat Rev Mol Cell Biol , vol.7 , pp. 198-210
    • Joyce, A.R.1    Palsson, B.O.2
  • 9
    • 34247612307 scopus 로고    scopus 로고
    • Multiple high-throughput analyses monitor the response of E. coli to perturbations
    • This manuscript describes the first integration of high-throughput omics data gathered on a collection of deletion mutants for the study of E. coli metabolism.
    • Ishii N., Nakahigashi K., Baba T., Robert M., Soga T., Kanai A., Hirasawa T., Naba M., Hirai K., Hoque A., et al. Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science 316 (2007) 593-597. This manuscript describes the first integration of high-throughput omics data gathered on a collection of deletion mutants for the study of E. coli metabolism.
    • (2007) Science , vol.316 , pp. 593-597
    • Ishii, N.1    Nakahigashi, K.2    Baba, T.3    Robert, M.4    Soga, T.5    Kanai, A.6    Hirasawa, T.7    Naba, M.8    Hirai, K.9    Hoque, A.10
  • 10
    • 45149111660 scopus 로고    scopus 로고
    • The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli
    • This article provides a thorough review of the main applications of genome-scale metabolic models.
    • Feist A.M., and Palsson B.O. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli. Nat Biotechnol 26 (2008) 659-667. This article provides a thorough review of the main applications of genome-scale metabolic models.
    • (2008) Nat Biotechnol , vol.26 , pp. 659-667
    • Feist, A.M.1    Palsson, B.O.2
  • 13
    • 14544268137 scopus 로고    scopus 로고
    • Uncovering transcriptional regulation of metabolism by using metabolic network topology
    • Patil K.R., and Nielsen J. Uncovering transcriptional regulation of metabolism by using metabolic network topology. Proc Natl Acad Sci U S A 102 (2005) 2685-2689
    • (2005) Proc Natl Acad Sci U S A , vol.102 , pp. 2685-2689
    • Patil, K.R.1    Nielsen, J.2
  • 14
    • 27144480292 scopus 로고    scopus 로고
    • Opportunities for genetic investigation afforded by Acinetobacter baylyi, a nutritionally versatile bacterial species that is highly competent for natural transformation
    • Young D.M., Parke D., and Ornston L.N. Opportunities for genetic investigation afforded by Acinetobacter baylyi, a nutritionally versatile bacterial species that is highly competent for natural transformation. Annu Rev Microbiol 59 (2005) 519-551
    • (2005) Annu Rev Microbiol , vol.59 , pp. 519-551
    • Young, D.M.1    Parke, D.2    Ornston, L.N.3
  • 16
    • 67650364565 scopus 로고    scopus 로고
    • Caister Academic Press, Norfolk, UK. This book offers an up-to-date overview of the physiological and metabolic current knowledge on Acinetobacter species.
    • Gerischer U.C. Acinetobacter Molecular Biology (2008), Caister Academic Press, Norfolk, UK. This book offers an up-to-date overview of the physiological and metabolic current knowledge on Acinetobacter species.
    • (2008) Acinetobacter Molecular Biology
    • Gerischer, U.C.1
  • 17
    • 0015425823 scopus 로고
    • Interspecies transformation of Acinetobacter: genetic evidence for a ubiquitous genus
    • Juni E. Interspecies transformation of Acinetobacter: genetic evidence for a ubiquitous genus. J Bacteriol 112 (1972) 917-931
    • (1972) J Bacteriol , vol.112 , pp. 917-931
    • Juni, E.1
  • 18
    • 0030957269 scopus 로고    scopus 로고
    • Uptake and processing of DNA by Acinetobacter calcoaceticus-a review
    • Palmen R., and Hellingwerf K.J. Uptake and processing of DNA by Acinetobacter calcoaceticus-a review. Gene 192 (1997) 179-190
    • (1997) Gene , vol.192 , pp. 179-190
    • Palmen, R.1    Hellingwerf, K.J.2
  • 19
    • 0037133327 scopus 로고    scopus 로고
    • Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination
    • de Vries J., and Wackernagel W. Integration of foreign DNA during natural transformation of Acinetobacter sp. by homology-facilitated illegitimate recombination. Proc Natl Acad Sci U S A 99 (2002) 2094-2099
    • (2002) Proc Natl Acad Sci U S A , vol.99 , pp. 2094-2099
    • de Vries, J.1    Wackernagel, W.2
  • 24
    • 0001694417 scopus 로고
    • Occurrence of shikimic and quinic acids in angiosperms
    • Yoshida S., Tazaki K., and Minamikawa T. Occurrence of shikimic and quinic acids in angiosperms. Phytochemistry 14 (1975) 195-197
    • (1975) Phytochemistry , vol.14 , pp. 195-197
    • Yoshida, S.1    Tazaki, K.2    Minamikawa, T.3
  • 25
    • 0023218134 scopus 로고
    • Cloning and genetic organization of the pca gene cluster from Acinetobacter calcoaceticus
    • Doten R.C., Ngai K.L., Mitchell D.J., and Ornston L.N. Cloning and genetic organization of the pca gene cluster from Acinetobacter calcoaceticus. J Bacteriol 169 (1987) 3168-3174
    • (1987) J Bacteriol , vol.169 , pp. 3168-3174
    • Doten, R.C.1    Ngai, K.L.2    Mitchell, D.J.3    Ornston, L.N.4
  • 26
    • 0014083959 scopus 로고
    • Regulation of the enzymes of the beta-ketoadipate pathway in Moraxella calcoacetica. 1. General aspects
    • Canovas J.L., and Stanier R.Y. Regulation of the enzymes of the beta-ketoadipate pathway in Moraxella calcoacetica. 1. General aspects. Eur J Biochem 1 (1967) 289-300
    • (1967) Eur J Biochem , vol.1 , pp. 289-300
    • Canovas, J.L.1    Stanier, R.Y.2
  • 27
    • 0014027888 scopus 로고
    • The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida
    • Ornston L.N., and Stanier R.Y. The conversion of catechol and protocatechuate to beta-ketoadipate by Pseudomonas putida. J Biol Chem 241 (1966) 3776-3786
    • (1966) J Biol Chem , vol.241 , pp. 3776-3786
    • Ornston, L.N.1    Stanier, R.Y.2
  • 28
    • 65249143794 scopus 로고    scopus 로고
    • Role of Acinetobacter baylyi Crc in catabolite repression of enzymes for aromatic compound catabolism
    • Zimmermann T., Sorg T., Siehler S.Y., and Gerischer U. Role of Acinetobacter baylyi Crc in catabolite repression of enzymes for aromatic compound catabolism. J Bacteriol 191 (2009) 2834-2842
    • (2009) J Bacteriol , vol.191 , pp. 2834-2842
    • Zimmermann, T.1    Sorg, T.2    Siehler, S.Y.3    Gerischer, U.4
  • 29
    • 55549094460 scopus 로고    scopus 로고
    • Aromatic degradative pathways in Acinetobacter baylyi underlie carbon catabolite repression
    • An interesting study of carbon catabolism regulation of the β-ketoadipate pathway that shows that the patterns of repression for the studied cosubstrates are similar to those observed for acetate/pyruvate.
    • Fischer R., Bleichrodt F.S., and Gerischer U.C. Aromatic degradative pathways in Acinetobacter baylyi underlie carbon catabolite repression. Microbiology 154 (2008) 3095-3103. An interesting study of carbon catabolism regulation of the β-ketoadipate pathway that shows that the patterns of repression for the studied cosubstrates are similar to those observed for acetate/pyruvate.
    • (2008) Microbiology , vol.154 , pp. 3095-3103
    • Fischer, R.1    Bleichrodt, F.S.2    Gerischer, U.C.3
  • 30
    • 0345451054 scopus 로고    scopus 로고
    • Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases
    • Ratajczak A., Geissdorfer W., and Hillen W. Alkane hydroxylase from Acinetobacter sp. strain ADP1 is encoded by alkM and belongs to a new family of bacterial integral-membrane hydrocarbon hydroxylases. Appl Environ Microbiol 64 (1998) 1175-1179
    • (1998) Appl Environ Microbiol , vol.64 , pp. 1175-1179
    • Ratajczak, A.1    Geissdorfer, W.2    Hillen, W.3
  • 31
    • 0344731372 scopus 로고    scopus 로고
    • The genes rubA and rubB for alkane degradation in Acinetobacter sp. strain ADP1 are in an operon with estB, encoding an esterase, and oxyR
    • Geissdorfer W., Kok R.G., Ratajczak A., Hellingwerf K.J., and Hillen W. The genes rubA and rubB for alkane degradation in Acinetobacter sp. strain ADP1 are in an operon with estB, encoding an esterase, and oxyR. J Bacteriol 181 (1999) 4292-4298
    • (1999) J Bacteriol , vol.181 , pp. 4292-4298
    • Geissdorfer, W.1    Kok, R.G.2    Ratajczak, A.3    Hellingwerf, K.J.4    Hillen, W.5
  • 32
    • 0038534422 scopus 로고    scopus 로고
    • Isolation and characterization of a novel oxygenase that catalyzes the first step of n-alkane oxidation in Acinetobacter sp. strain M-1
    • Maeng J.H., Sakai Y., Tani Y., and Kato N. Isolation and characterization of a novel oxygenase that catalyzes the first step of n-alkane oxidation in Acinetobacter sp. strain M-1. J Bacteriol 178 (1996) 3695-3700
    • (1996) J Bacteriol , vol.178 , pp. 3695-3700
    • Maeng, J.H.1    Sakai, Y.2    Tani, Y.3    Kato, N.4
  • 33
    • 0035490405 scopus 로고    scopus 로고
    • Cloning and genetic characterization of dca genes required for beta-oxidation of straight-chain dicarboxylic acids in Acinetobacter sp. strain ADP1
    • Parke D., Garcia M.A., and Ornston L.N. Cloning and genetic characterization of dca genes required for beta-oxidation of straight-chain dicarboxylic acids in Acinetobacter sp. strain ADP1. Appl Environ Microbiol 67 (2001) 4817-4827
    • (2001) Appl Environ Microbiol , vol.67 , pp. 4817-4827
    • Parke, D.1    Garcia, M.A.2    Ornston, L.N.3
  • 34
    • 33144470936 scopus 로고    scopus 로고
    • Engineering the genotype of Acinetobacter sp. strain ADP1 to enhance biosynthesis of cyanophycin
    • Elbahloul Y., and Steinbuchel A. Engineering the genotype of Acinetobacter sp. strain ADP1 to enhance biosynthesis of cyanophycin. Appl Environ Microbiol 72 (2006) 1410-1419
    • (2006) Appl Environ Microbiol , vol.72 , pp. 1410-1419
    • Elbahloul, Y.1    Steinbuchel, A.2
  • 35
    • 14544268951 scopus 로고    scopus 로고
    • The wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase from Acinetobacter sp. strain ADP1: characterization of a novel type of acyltransferase
    • Stoveken T., Kalscheuer R., Malkus U., Reichelt R., and Steinbuchel A. The wax ester synthase/acyl coenzyme A:diacylglycerol acyltransferase from Acinetobacter sp. strain ADP1: characterization of a novel type of acyltransferase. J Bacteriol 187 (2005) 1369-1376
    • (2005) J Bacteriol , vol.187 , pp. 1369-1376
    • Stoveken, T.1    Kalscheuer, R.2    Malkus, U.3    Reichelt, R.4    Steinbuchel, A.5
  • 36
    • 45549087079 scopus 로고    scopus 로고
    • Bacterial acyltransferases as an alternative for lipase-catalyzed acylation for the production of oleochemicals and fuels
    • Minireview that focuses on the biotechnological utilization of acyltransferases for the production of modified lipids from renewable resources.
    • Stoveken T., and Steinbuchel A. Bacterial acyltransferases as an alternative for lipase-catalyzed acylation for the production of oleochemicals and fuels. Angew Chem Int Ed Engl 47 (2008) 3688-3694. Minireview that focuses on the biotechnological utilization of acyltransferases for the production of modified lipids from renewable resources.
    • (2008) Angew Chem Int Ed Engl , vol.47 , pp. 3688-3694
    • Stoveken, T.1    Steinbuchel, A.2
  • 37
    • 0034603783 scopus 로고    scopus 로고
    • PCR-mediated gene replacement in Escherichia coli
    • Murphy K.C., Campellone K.G., and Poteete A.R. PCR-mediated gene replacement in Escherichia coli. Gene 246 (2000) 321-330
    • (2000) Gene , vol.246 , pp. 321-330
    • Murphy, K.C.1    Campellone, K.G.2    Poteete, A.R.3
  • 38
    • 42949142245 scopus 로고    scopus 로고
    • A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1
    • The authors report on the construction of one of the two publically available complete collections of prokaryotic mutants by gene replacement including the KEIO collection of E. coli. The article shows how the systematic analysis of these collections is used for metabolism exploration.
    • de Berardinis V., Vallenet D., Castelli V., Besnard M., Pinet A., Cruaud C., Samair S., Lechaplais C., Gyapay G., Richez C., et al. A complete collection of single-gene deletion mutants of Acinetobacter baylyi ADP1. Mol Syst Biol 4 (2008) 174. The authors report on the construction of one of the two publically available complete collections of prokaryotic mutants by gene replacement including the KEIO collection of E. coli. The article shows how the systematic analysis of these collections is used for metabolism exploration.
    • (2008) Mol Syst Biol , vol.4 , pp. 174
    • de Berardinis, V.1    Vallenet, D.2    Castelli, V.3    Besnard, M.4    Pinet, A.5    Cruaud, C.6    Samair, S.7    Lechaplais, C.8    Gyapay, G.9    Richez, C.10
  • 39
    • 33750580687 scopus 로고    scopus 로고
    • Genes involved in intrinsic antibiotic resistance of Acinetobacter baylyi
    • Gomez M.J., and Neyfakh A.A. Genes involved in intrinsic antibiotic resistance of Acinetobacter baylyi. Antimicrob Agents Chemother 50 (2006) 3562-3567
    • (2006) Antimicrob Agents Chemother , vol.50 , pp. 3562-3567
    • Gomez, M.J.1    Neyfakh, A.A.2
  • 40
    • 1342325436 scopus 로고    scopus 로고
    • Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine
    • Reader J.S., Metzgar D., Schimmel P., and de Crecy-Lagard V. Identification of four genes necessary for biosynthesis of the modified nucleoside queuosine. J Biol Chem 279 (2004) 6280-6285
    • (2004) J Biol Chem , vol.279 , pp. 6280-6285
    • Reader, J.S.1    Metzgar, D.2    Schimmel, P.3    de Crecy-Lagard, V.4
  • 41
    • 33846167103 scopus 로고    scopus 로고
    • Multiple-level regulation of genes for protocatechuate degradation in Acinetobacter baylyi includes cross-regulation
    • Siehler S.Y., Dal S., Fischer R., Patz P., and Gerischer U. Multiple-level regulation of genes for protocatechuate degradation in Acinetobacter baylyi includes cross-regulation. Appl Environ Microbiol 73 (2007) 232-242
    • (2007) Appl Environ Microbiol , vol.73 , pp. 232-242
    • Siehler, S.Y.1    Dal, S.2    Fischer, R.3    Patz, P.4    Gerischer, U.5
  • 42
    • 0030816017 scopus 로고    scopus 로고
    • Combining localized PCR mutagenesis and natural transformation in direct genetic analysis of a transcriptional regulator gene, pobR
    • Kok R.G., D'Argenio D.A., and Ornston L.N. Combining localized PCR mutagenesis and natural transformation in direct genetic analysis of a transcriptional regulator gene, pobR. J Bacteriol 179 (1997) 4270-4276
    • (1997) J Bacteriol , vol.179 , pp. 4270-4276
    • Kok, R.G.1    D'Argenio, D.A.2    Ornston, L.N.3
  • 43
    • 0031683974 scopus 로고    scopus 로고
    • Mutation analysis of PobR and PcaU, closely related transcriptional activators in acinetobacter
    • Kok R.G., D'Argenio D.A., and Ornston L.N. Mutation analysis of PobR and PcaU, closely related transcriptional activators in acinetobacter. J Bacteriol 180 (1998) 5058-5069
    • (1998) J Bacteriol , vol.180 , pp. 5058-5069
    • Kok, R.G.1    D'Argenio, D.A.2    Ornston, L.N.3
  • 44
    • 0033557326 scopus 로고    scopus 로고
    • Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus
    • Melnikov A., and Youngman P.J. Random mutagenesis by recombinational capture of PCR products in Bacillus subtilis and Acinetobacter calcoaceticus. Nucleic Acids Res 27 (1999) 1056-1062
    • (1999) Nucleic Acids Res , vol.27 , pp. 1056-1062
    • Melnikov, A.1    Youngman, P.J.2
  • 45
    • 0032916065 scopus 로고    scopus 로고
    • Phenotypic expression of PCR-generated random mutations in a Pseudomonas putida gene after its introduction into an Acinetobacter chromosome by natural transformation
    • Kok R.G., Young D.M., and Ornston L.N. Phenotypic expression of PCR-generated random mutations in a Pseudomonas putida gene after its introduction into an Acinetobacter chromosome by natural transformation. Appl Environ Microbiol 65 (1999) 1675-1680
    • (1999) Appl Environ Microbiol , vol.65 , pp. 1675-1680
    • Kok, R.G.1    Young, D.M.2    Ornston, L.N.3
  • 47
    • 0031921638 scopus 로고    scopus 로고
    • Detection of nptII (kanamycin resistance) genes in genomes of transgenic plants by marker-rescue transformation
    • de Vries J., and Wackernagel W. Detection of nptII (kanamycin resistance) genes in genomes of transgenic plants by marker-rescue transformation. Mol Gen Genet 257 (1998) 606-613
    • (1998) Mol Gen Genet , vol.257 , pp. 606-613
    • de Vries, J.1    Wackernagel, W.2
  • 48
    • 0345269196 scopus 로고    scopus 로고
    • Natural genetic transformation in monoculture Acinetobacter sp. strain BD413 biofilms
    • Hendrickx L., Hausner M., and Wuertz S. Natural genetic transformation in monoculture Acinetobacter sp. strain BD413 biofilms. Appl Environ Microbiol 69 (2003) 1721-1727
    • (2003) Appl Environ Microbiol , vol.69 , pp. 1721-1727
    • Hendrickx, L.1    Hausner, M.2    Wuertz, S.3
  • 49
    • 62349135110 scopus 로고    scopus 로고
    • A rapid biosensor-based method for quantification of free and glucose-conjugated salicylic acid
    • Defraia C.T., Schmelz E.A., and Mou Z. A rapid biosensor-based method for quantification of free and glucose-conjugated salicylic acid. Plant Methods 4 (2008) 28
    • (2008) Plant Methods , vol.4 , pp. 28
    • Defraia, C.T.1    Schmelz, E.A.2    Mou, Z.3
  • 50
    • 0031977979 scopus 로고    scopus 로고
    • Transformation of Acinetobacter sp. strain BD413 by transgenic sugar beet DNA
    • Gebhard F., and Smalla K. Transformation of Acinetobacter sp. strain BD413 by transgenic sugar beet DNA. Appl Environ Microbiol 64 (1998) 1550-1554
    • (1998) Appl Environ Microbiol , vol.64 , pp. 1550-1554
    • Gebhard, F.1    Smalla, K.2
  • 51
    • 23944514315 scopus 로고    scopus 로고
    • Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate
    • Huang W.E., Wang H., Zheng H., Huang L., Singer A.C., Thompson I., and Whiteley A.S. Chromosomally located gene fusions constructed in Acinetobacter sp. ADP1 for the detection of salicylate. Environ Microbiol 7 (2005) 1339-1348
    • (2005) Environ Microbiol , vol.7 , pp. 1339-1348
    • Huang, W.E.1    Wang, H.2    Zheng, H.3    Huang, L.4    Singer, A.C.5    Thompson, I.6    Whiteley, A.S.7
  • 52
    • 33947216186 scopus 로고    scopus 로고
    • A double kill gene cassette for the positive selection of transforming non-selective DNA segments in Acinetobacter baylyi BD413
    • The authors report the development of a transformation assay system in which recombinational removal of a cassette with two conditional kill genes (hok and sacB) from the recipient genome provides positive selection for non-selective DNA.
    • Harms K., de Vries J., and Wackernagel W. A double kill gene cassette for the positive selection of transforming non-selective DNA segments in Acinetobacter baylyi BD413. J Microbiol Methods 69 (2007) 107-115. The authors report the development of a transformation assay system in which recombinational removal of a cassette with two conditional kill genes (hok and sacB) from the recipient genome provides positive selection for non-selective DNA.
    • (2007) J Microbiol Methods , vol.69 , pp. 107-115
    • Harms, K.1    de Vries, J.2    Wackernagel, W.3
  • 53
    • 0026579902 scopus 로고
    • Genetic analysis of supraoperonic clustering by use of natural transformation in Acinetobacter calcoaceticus
    • Averhoff B., Gregg-Jolly L., Elsemore D., and Ornston L.N. Genetic analysis of supraoperonic clustering by use of natural transformation in Acinetobacter calcoaceticus. J Bacteriol 174 (1992) 200-204
    • (1992) J Bacteriol , vol.174 , pp. 200-204
    • Averhoff, B.1    Gregg-Jolly, L.2    Elsemore, D.3    Ornston, L.N.4
  • 54
    • 0024992448 scopus 로고
    • Recovery of DNA from the Acinetobacter calcoaceticus chromosome by gap repair
    • Gregg-Jolly L.A., and Ornston L.N. Recovery of DNA from the Acinetobacter calcoaceticus chromosome by gap repair. J Bacteriol 172 (1990) 6169-6172
    • (1990) J Bacteriol , vol.172 , pp. 6169-6172
    • Gregg-Jolly, L.A.1    Ornston, L.N.2
  • 55
    • 58149197597 scopus 로고    scopus 로고
    • DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes
    • Zhang R., and Lin Y. DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes. Nucleic Acids Res 37 (2009) D455-458
    • (2009) Nucleic Acids Res , vol.37
    • Zhang, R.1    Lin, Y.2
  • 57
    • 57549094614 scopus 로고    scopus 로고
    • Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data
    • This study presents the first genome-scale reconstruction of the A. baylyi metabolic network and mathematical model. Systematic comparisons of model predictions with experimental mutant growth phenotypes were performed to improve the model and refine the genome annotation.
    • Durot M., Le Fevre F., de Berardinis V., Kreimeyer A., Vallenet D., Combe C., Smidtas S., Salanoubat M., Weissenbach J., and Schachter V. Iterative reconstruction of a global metabolic model of Acinetobacter baylyi ADP1 using high-throughput growth phenotype and gene essentiality data. BMC Syst Biol 2 (2008) 85. This study presents the first genome-scale reconstruction of the A. baylyi metabolic network and mathematical model. Systematic comparisons of model predictions with experimental mutant growth phenotypes were performed to improve the model and refine the genome annotation.
    • (2008) BMC Syst Biol , vol.2 , pp. 85
    • Durot, M.1    Le Fevre, F.2    de Berardinis, V.3    Kreimeyer, A.4    Vallenet, D.5    Combe, C.6    Smidtas, S.7    Salanoubat, M.8    Weissenbach, J.9    Schachter, V.10
  • 59
    • 1642565398 scopus 로고    scopus 로고
    • Large-scale identification of essential Salmonella genes by trapping lethal insertions
    • Knuth K., Niesalla H., Hueck C.J., and Fuchs T.M. Large-scale identification of essential Salmonella genes by trapping lethal insertions. Mol Microbiol 51 (2004) 1729-1744
    • (2004) Mol Microbiol , vol.51 , pp. 1729-1744
    • Knuth, K.1    Niesalla, H.2    Hueck, C.J.3    Fuchs, T.M.4
  • 60
    • 0037154255 scopus 로고    scopus 로고
    • A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae
    • Akerley B.J., Rubin E.J., Novick V.L., Amaya K., Judson N., and Mekalanos J.J. A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc Natl Acad Sci USA 99 (2002) 966-971
    • (2002) Proc Natl Acad Sci USA , vol.99 , pp. 966-971
    • Akerley, B.J.1    Rubin, E.J.2    Novick, V.L.3    Amaya, K.4    Judson, N.5    Mekalanos, J.J.6
  • 62
    • 9244239747 scopus 로고    scopus 로고
    • Global transposon mutagenesis and essential gene analysis of Helicobacter pylori
    • Salama N.R., Shepherd B., and Falkow S. Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J Bacteriol 186 (2004) 7926-7935
    • (2004) J Bacteriol , vol.186 , pp. 7926-7935
    • Salama, N.R.1    Shepherd, B.2    Falkow, S.3
  • 64
    • 33646594074 scopus 로고    scopus 로고
    • High-throughput transposon mutagenesis of Corynebacterium glutamicum and construction of a single-gene disruptant mutant library
    • Suzuki N., Okai N., Nonaka H., Tsuge Y., Inui M., and Yukawa H. High-throughput transposon mutagenesis of Corynebacterium glutamicum and construction of a single-gene disruptant mutant library. Appl Environ Microbiol 72 (2006) 3750-3755
    • (2006) Appl Environ Microbiol , vol.72 , pp. 3750-3755
    • Suzuki, N.1    Okai, N.2    Nonaka, H.3    Tsuge, Y.4    Inui, M.5    Yukawa, H.6
  • 65
    • 0345701347 scopus 로고    scopus 로고
    • Genes required for mycobacterial growth defined by high density mutagenesis
    • Sassetti C.M., Boyd D.H., and Rubin E.J. Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48 (2003) 77-84
    • (2003) Mol Microbiol , vol.48 , pp. 77-84
    • Sassetti, C.M.1    Boyd, D.H.2    Rubin, E.J.3
  • 71
    • 47049103143 scopus 로고    scopus 로고
    • New insights into the alternative D-glucarate degradation pathway
    • A report of the first phenomics study of ADP1 mutant collection to discover missing genes of a catabolic pathway. Identified genes were biochemically validated.
    • Aghaie A., Lechaplais C., Sirven P., Tricot S., Besnard-Gonnet M., Muselet D., de Berardinis V., Kreimeyer A., Gyapay G., Salanoubat M., et al. New insights into the alternative D-glucarate degradation pathway. J Biol Chem 283 (2008) 15638-15646. A report of the first phenomics study of ADP1 mutant collection to discover missing genes of a catabolic pathway. Identified genes were biochemically validated.
    • (2008) J Biol Chem , vol.283 , pp. 15638-15646
    • Aghaie, A.1    Lechaplais, C.2    Sirven, P.3    Tricot, S.4    Besnard-Gonnet, M.5    Muselet, D.6    de Berardinis, V.7    Kreimeyer, A.8    Gyapay, G.9    Salanoubat, M.10
  • 72
    • 63049098068 scopus 로고    scopus 로고
    • Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?
    • Boyer F., Fichant G., Berthod J., Vandenbrouck Y., and Attree I. Dissecting the bacterial type VI secretion system by a genome wide in silico analysis: what can be learned from available microbial genomic resources?. BMC Genomics 10 (2009) 104
    • (2009) BMC Genomics , vol.10 , pp. 104
    • Boyer, F.1    Fichant, G.2    Berthod, J.3    Vandenbrouck, Y.4    Attree, I.5
  • 76
    • 27144533653 scopus 로고    scopus 로고
    • Reconstructing the metabolic network of a bacterium from its genome
    • Francke C., Siezen R.J., and Teusink B. Reconstructing the metabolic network of a bacterium from its genome. Trends Microbiol 13 (2005) 550-558
    • (2005) Trends Microbiol , vol.13 , pp. 550-558
    • Francke, C.1    Siezen, R.J.2    Teusink, B.3
  • 77
    • 9544253891 scopus 로고    scopus 로고
    • Genome-scale models of microbial cells: evaluating the consequences of constraints
    • Price N.D., Reed J.L., and Palsson B.O. Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2 (2004) 886-897
    • (2004) Nat Rev Microbiol , vol.2 , pp. 886-897
    • Price, N.D.1    Reed, J.L.2    Palsson, B.O.3
  • 78
    • 41149163825 scopus 로고    scopus 로고
    • Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1
    • Oberhardt M.A., Puchalka J., Fryer K.E., Martins dos Santos V.A., and Papin J.A. Genome-scale metabolic network analysis of the opportunistic pathogen Pseudomonas aeruginosa PAO1. J Bacteriol 190 (2008) 2790-2803
    • (2008) J Bacteriol , vol.190 , pp. 2790-2803
    • Oberhardt, M.A.1    Puchalka, J.2    Fryer, K.E.3    Martins dos Santos, V.A.4    Papin, J.A.5
  • 79
    • 54449092307 scopus 로고    scopus 로고
    • A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory
    • Nogales J., Palsson B.O., and Thiele I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst Biol 2 (2008) 79
    • (2008) BMC Syst Biol , vol.2 , pp. 79
    • Nogales, J.1    Palsson, B.O.2    Thiele, I.3
  • 81
    • 57549102595 scopus 로고    scopus 로고
    • Genome-scale models of bacterial metabolism: reconstruction and applications
    • Durot M., Bourguignon P.Y., and Schachter V. Genome-scale models of bacterial metabolism: reconstruction and applications. FEMS Microbiol Rev 33 (2009) 164-190
    • (2009) FEMS Microbiol Rev , vol.33 , pp. 164-190
    • Durot, M.1    Bourguignon, P.Y.2    Schachter, V.3
  • 83
    • 36249028746 scopus 로고    scopus 로고
    • Finding novel metabolic genes through plant-prokaryote phylogenomics
    • de Crecy-Lagard V., and Hanson A.D. Finding novel metabolic genes through plant-prokaryote phylogenomics. Trends Microbiol 15 (2007) 563-570
    • (2007) Trends Microbiol , vol.15 , pp. 563-570
    • de Crecy-Lagard, V.1    Hanson, A.D.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.