Integration of metabolic reactions and gene regulation

Molecular Biotechnology

Volumn 47, Issue 1, 2011, Pages 70-82

  Yeang, Chen Hsiang ^a  

^a INSTITUTE OF STATISTICAL SCIENCE   (Taiwan)

Author keywords

Gene regulation; High throughput assays; Metabolic reactions

Indexed keywords

GENE EXPRESSION; GENES;

CELLULAR SYSTEM; ENERGY PRODUCTIONS; ENVIRONMENTAL CHANGE; HIGH-THROUGHPUT ASSAYS; METABOLIC REACTIONS; METABOLIC STATE; REGULATORY PROGRAM;

METABOLISM;

C REACTIVE PROTEIN;

AMINO ACID SYNTHESIS; BACTERIAL METABOLISM; CARBON METABOLISM; CELL FUNCTION; ENERGY YIELD; ENVIRONMENTAL CHANGE; ENZYME ACTIVITY; ENZYME METABOLISM; ENZYME SYNTHESIS; ESCHERICHIA COLI; FEEDBACK SYSTEM; FUNGAL METABOLISM; GENE CONTROL; GENE SEQUENCE; GENETIC DATABASE; GENOMICS; GLUCOSE METABOLISM; HIGH THROUGHPUT SCREENING; METABOLISM; METABOLOMICS; MOLECULAR INTERACTION; NONHUMAN; OPERON; PROTEOMICS; REVIEW; SACCHAROMYCES CEREVISIAE; TRANSCRIPTOMICS;

EID: 79551564832     PISSN: 10736085     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12033-010-9325-y     Document Type: Review

References (125)

1. Dyson, R. (1999). Origins of life. New York: Cambridge University Press.
2. Maynard Smith, J., & Szathmary, E. (1999). The origins of life: From the birth of life to the origin of language. New York: Oxford University Press.
3. A Varma BO Palsson 1994 Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild type Escherichia coli W3110 Applied and Environmental Microbiology 60 10 3724 3731 1:CAS:528:DyaK2cXmt1Kis7Y%3D
4. HPJ Bonarius G Schmid J Tramper 1997 Flux analysis of underdetermined metabolic networks: The quest for the missing constraints Trends in Biotechnology 15 308 314 1:CAS:528:DyaK2sXlt1Cns7Y%3D 10.1016/S0167-7799(97) 01067-6 (Pubitemid 27330626)
5. JS Edwards BO Palsson 1998 How will bioinformatics influence metabolic engineering? Biotechnology and Bioengineering 58 162 169 1:CAS:528: DyaK1cXht12ksrY%3D 10.1002/(SICI)1097-0290(19980420)58:2/3<162::AID- BIT8>3.0.CO;2-J (Pubitemid 28136373)
6. A Varma BO Palsson 1993 Metabolic capabilities of Escherichia coli. II. Optimal growth patterns Journal of Theoretical Biology 165 503 522 1:CAS:528:DyaK2cXivFektr8%3D 10.1006/jtbi.1993.1203 (Pubitemid 24044951)
7. Danzig, G. B., Orden, A., & Wolfe, P. (2003). The generalized simplex method for minimizing a linear form under linear inequality restraints. In R. W. Cottle (Ed.), The basic George B. Danzig. Stanford: Stanford University Press.
8. N Karmarkar 1984 A new polynomial-time algorithm for linear programming Combinatorica 4 4 373 395 10.1007/BF02579150
9. JS Edwards RU Ibarra BO Palsson 2001 In silico prediction of Escherichia coli metabolic capabilities are consistent with experimental data Nature Biotechnology 19 125 130 1:CAS:528:DC%2BD3MXhtVaisb0%3D 10.1038/84379 (Pubitemid 32144439)
10. S Schuster T Dandekar DA Fell 1999 Detection of elementary flux modes in biochemical networks: A promising tool for pathway analysis and metabolic engineering Trends in Biotechnology 17 53 60 1:CAS:528:DyaK1MXlt1Kjt7o%3D 10.1016/S0167-7799(98)01290-6 (Pubitemid 29332898)
11. S Schuster DA Fell TA Dandekar 2000 A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks Nature Biotechnology 18 326 332 1:CAS:528:DC%2BD3cXhvVyqsr4%3D 10.1038/73786 (Pubitemid 30159487)
12. J Stelling S Klamt K Bettenbrock S Schuster ED Gilles 2002 Metabolic network structure determines key aspects of functionality and regulation Nature 420 190 193 1:CAS:528:DC%2BD38Xos1GnsLw%3D 10.1038/nature01166 (Pubitemid 35340124)
13. 13 metabolic flux analysis Metabolic Engineering 3 195 206 1:CAS:528:DC%2BD3MXlt1Cls78%3D 10.1006/mben.2001.0187 (Pubitemid 32748163)
14. M Emmerling M Dauner A Ponti J Fiaux M Hochuli T Szyperski K Wuthrich JE Bailey U Sauer 2002 Metabolic flux responses to pyruvate kinase knockout in Escherichia coli Journal of Bacteriology 184 1 152 164 1:CAS:528: DC%2BD3MXpt1CmtL0%3D 10.1128/JB.184.1.152-164.2002 (Pubitemid 34007360)
15. Q Hua C Yang T Baba H Mori K Shimizu 2003 Response of the central metabolism in Escherichia coli to phosphoglucose isomerase and glucose-6-phosphate dehydrogenase knockouts Journal of Bacteriology 185 24 7053 7067 1:CAS:528:DC%2BD3sXpvVaqsL4%3D 10.1128/JB.185.24.7053-7067.2003 (Pubitemid 37509820)
16. 13 constraints Analy. Biochem. 325 308 316 1:CAS:528:DC%2BD2cXmvFKqtw%3D%3D 10.1016/j.ab.2003.10.036 (Pubitemid 38134368)
17. VR Velagapudi C Wittmann K Schneider E Heinzle 2007 Metabolic flux screening of Saccharomyces cerevisiae single knockout strains on glucose and galactose supports elucidation of gene function Journal of Bacteriology 132 4 395 404 1:CAS:528:DC%2BD2sXht12gtbrF
18. 13C-Labeled metabolic flux analysis of a fed-batch culture of elutriated Saccharomyces cerevisiae FEMS Yeast Research 7 4 511 526 1:CAS:528:DC%2BD2sXmt1ertbo%3D 10.1111/j.1567-1364.2006.00199.x (Pubitemid 46788672)
19. RJ Kleijn JM Geertman BK Nfor C Ras D Schipper JT Pronk JJ Heijnen AJ van Maris WA van Winden 2007 Metabolic flux analysis of a glycerol-overproducing Saccharomyces cerevisiae strain based on GC-MS, LC-MS and NMR-derived C-labelling data FEMS Yeast Research 7 2 216 231 1:CAS:528:DC%2BD2sXjsVyqtrc%3D 10.1111/j.1567-1364.2006.00180.x
20. M Covert C Schilling BO Palsson 2001 Regulation of gene expression in flux balance models of metabolism Journal of Theoretical Biology 213 73 78 1:CAS:528:DC%2BD3MXot12gt7o%3D 10.1006/jtbi.2001.2405 (Pubitemid 33052300)
21. M Covert BO Palsson 2003 Constraints-based models: Regulation of gene expression reduces the steady-state solution space Journal of Theoretical Biology 221 309 325 1:CAS:528:DC%2BD3sXitVKntr8%3D 10.1006/jtbi.2003.3071 (Pubitemid 36299258)
22. N Ishii K Nakahigashi T Baba M Robert T Soga, et al. 2007 Multiple high-throughput analyses monitor the response of E. coli to perturbations Science 316 593 597 1:CAS:528:DC%2BD2sXksFeksbw%3D 10.1126/science.1132067 (Pubitemid 46683144)
23. H Kacser JA Burns 1973 The control of flux Symposia of the Society for Experimental Biology 27 65 104 1:STN:280:DyaE2c%2Fms12hug%3D%3D
24. Lehninger, A. L. (1982). Principles of biochemistry. New York: Worth Publishers.
25. D Segre D Vitkup G Church 2002 Analysis of optimality in natural and perturbed metabolic networks Proceedings of the National Academy of Sciences of the United States of America 99 23 15112 15117 1:CAS:528:DC%2BD38Xpt1yru7Y%3D 10.1073/pnas.232349399 (Pubitemid 35334618)
26. D Segre J Zucker J Katz X Lin P D'haeseleer, et al. 2003 From annotated genomes to metabolic flux models and kinetic parameter fitting OMICS 7 3 301 316 1:CAS:528:DC%2BD3sXotVClsrY%3D 10.1089/153623103322452413
27. Bertsekas, D. (1995). Nonlinear programming. Belmont, MA: Athena Scientific.
28. RU Ibarra JS Edwards BO Palsson 2002 Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth Nature 420 186 189 1:CAS:528:DC%2BD38Xos1Gns7Y%3D 10.1038/nature01149 (Pubitemid 35340123)
29. L Uyeda 1979 Phosphofructokinase Advances in Enzymology and Related Ares of Molecular Biology 48 193 244 1:CAS:528:DyaE1MXhtFKrsbY%3D
30. EB Waygood JS Mort BD Sanwal 1976 The control of pyruvate kinase of Escherichia coli. Binding of substrate and allosteric effectors to the enzyme activated by fructose 1,6-bisphosphate Biochemistry 15 2 277 282 1:CAS:528:DyaE28XntV2isg%3D%3D 10.1021/bi00647a006
31. E Stolovicki T Dror N Brenner E Braun 2006 Synthetic gene recruitment reveals adaptive reprogramming of gene regulation in yeast Genetics 173 1 75 85 1:CAS:528:DC%2BD28XlvF2isr8%3D 10.1534/genetics.106.055442 (Pubitemid 43800185)
32. H Jeong B Tombor R Albert ZN Oltvai AL Barabasi 2000 The large-scale organization of metabolic networks Nature 407 6804 651 654 1:CAS:528: DC%2BD3cXnsVOrsLs%3D 10.1038/35036627
33. JM Carlson J Doyle 2002 Complexity and robustness Proceedings of the National Academy of Science 99 Suppl 1 2538 2545 10.1073/pnas.012582499 (Pubitemid 34165063)
34. S Iuchi 1993 Phosphorylation/dephosphorylation of the receiver module at the conserved aspartate residue controls transphosphorylation activity of histidine kinase in sensor protein ArcB of Escherichia coli Journal of Biological Chemistry 268 32 23972 23980 1:CAS:528:DyaK3sXlvFOrt7o%3D
35. S Iuchi EC Lin 1988 ArcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways Proceedings of the National Academy of Science 85 6 1888 1892 1:CAS:528:DyaL1MXhs1KqsLY%3D 10.1073/pnas.85.6.1888 (Pubitemid 24315789)
36. AS Lynch EC Lin 1996 Transcriptional control mediated by the ArcA two-component response regulator protein of Escherichia coli: Characterization of DNA binding at target promoters Journal of Bacteriology 178 21 6238 6249 1:CAS:528:DyaK28Xms1Wiur4%3D
37. SJ Park J McCabe J Turna RP Gunsalus 1994 Regulation of the citrate synthase (gltA) gene of Escherichia coli in response to anaerobiosis and carbon supply: Role of the arcA gene product Journal of Bacteriology 176 16 5086 5092 1:CAS:528:DyaK2cXlsFSnt7o%3D
38. SJ Park PA Cotter RP Gunsalus 1995 Regulation of malate dehydrogenase (mdh) gene expression in Escherichia coli in response to oxygen, carbon, and heme availability Journal of Bacteriology 177 22 6652 6656 1:CAS:528: DyaK2MXptlKrtL8%3D
39. SJ Park CP Tseng RP Gunsalus 1995 Regulation of succinate dehydrogenase (sdhCDAB) operon expression in Escherichia coli in response to carbon supply and anaerobiosis: Role of ArcA and Fnr Molecular Microbiology 15 3 473 482 1:CAS:528:DyaK2MXjvFejtrc%3D 10.1111/j.1365-2958.1995.tb02261.x
40. SJ Park G Chao RP Gunsalus 1997 Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: Roles of ArcA, Fnr, and the upstream sdhCDAB promoter Journal of Bacteriology 179 13 4138 4142 1:CAS:528:DyaK2sXkt1Gnurg%3D
41. A Perrenoud U Sauer 2005 Impact of global transcriptional regulation by ArcA, ArcB, Cra, Crp, Cya, Fnr, and Mlc on glucose catabolism in Escherichia coli Journal of Bacteriology 187 9 3171 3179 1:CAS:528:DC%2BD2MXjvVGqtb4%3D 10.1128/JB.187.9.3171-3179.2005 (Pubitemid 40571610)
42. Saier, M. H., Ramseier, T. M., & Reizer, J. (1996). Regulation of carbon utilization. In F. C. Neidhardt, et al. (Eds.), Escherichia coli and Salmonella: Cellular and molecular biology. Washington, DC: ASM Press.
43. D Zheng C Constantinidou JL Hobman SD Minchin 2004 Identification of the CRP regulon using in vitro and in vivo transcriptional profiling Nucleic Acids Research 32 19 5874 5893 1:CAS:528:DC%2BD2cXhtVSqsrjL 10.1093/nar/gkh908 (Pubitemid 39619170)
44. DC Grainger D Hurd M Harrison J Holdstock SJ Busby 2005 Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome Proceedings of the National Academy of Sciences of the United States of America 102 49 17693 17698 1:CAS:528:DC%2BD2MXhtlegs7zE 10.1073/pnas.0506687102 (Pubitemid 41803559)
45. RS Makman EW Sutherland 1965 Adenosine 3', 5'-phosphate in Escherichia coli Journal of Biological Chemistry 240 1309 1314 1:CAS:528: DyaF2MXksFKlsQ%3D%3D
46. MH Saier TM Ramseier 1997 The catabolite repressor/activator (Cra) protein of enteric bacteria Journal of Bacteriology 178 3411 3417
47. S Henikoff GW Haughn JM Calvo JC Wallace 1988 A large family of bacterial activator proteins Proceedings of the National Academy of Sciences of the United States of America 85 18 6602 6606 1:CAS:528:DyaL1MXhvVKrtLo%3D 10.1073/pnas.85.18.6602
48. CH Su RC Greene 1971 Regulation of methionine biosynthesis in Escherichia coli: Mapping of the metJ locus and properties of a metJ plus-metJ minus diploid Proceedings of the National Academy of Sciences of the United States of America 68 2 367 371 1:CAS:528:DyaE3MXhtlKqsLs%3D 10.1073/pnas.68.2.367
49. J Pittard H Camakaris J Yang 2005 The TyrR regulon Molecular Microbiology 55 1 16 26 1:CAS:528:DC%2BD2MXotlSktw%3D%3D 10.1111/j.1365-2958.2004.04385.x (Pubitemid 40127881)
50. D Griggs M Johnston 1991 Regulated expression of Gal4 activator gene in yeast provides a sensitive genetic switch for glucose repression Proceedings of the National Academy of Sciences of the United States of America 88 19 8597 8601 1:CAS:528:DyaK3MXmslWku7g%3D 10.1073/pnas.88.19.8597
51. D Lohr P Venkov J Zlatanova 1995 Transcriptional regulation in the yeast Gal gene family: A complex genetic network The FASEB Journal 9 777 787 1:CAS:528:DyaK2MXmvFCltbY%3D
52. K Natarajan MR Meyer BM Jackson D Slade C Roberts AG Hinnebusch MJ Marton 2001 Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast Molecular and Cellular Biology 21 13 4347 4368 1:CAS:528:DC%2BD3MXksVOrtL0%3D 10.1128/MCB.21.13.4347-4368.2001 (Pubitemid 32565316)
53. T Lee N Rinaldi F Robert D Odom Z Bar-Joseph, et al. 2002 A transcriptional regulatory network map for Saccharomyces cerevisiae Science 298 799 804 1:CAS:528:DC%2BD38XotFSntL0%3D 10.1126/science.1075090 (Pubitemid 35231527)
54. V Denis H Boucherie C Monribot B Daignan-Fornier 1998 Role of the Myb-like protein Bas1p in Saccharomyces cerevisiae: A proteome analysis Molecular Microbiology 30 3 557 566 1:CAS:528:DyaK1cXnsVKisbo%3D 10.1046/j.1365-2958.1998.01087.x (Pubitemid 28497931)
55. W Xiao G Rank 1990 Branched chain amino acid regulation of the ilv2 locus in Saccharomyces cerevisiae Genome 33 4 596 603 1:CAS:528:DyaK3cXmt1Gnu7k%3D
56. K O'Connel Y Surdin-Kerjan R Baker 1995 Role of the Saccharomyces cerevisiae general regulatory factor cp1 in methionine biosynthetic gene transcription Molecular and Cellular Biology 15 1879 1888
57. SB Carroll 2005 Evolution at two levels: On genes and form PLoS Biol 3 7 e245 10.1371/journal.pbio.0030245 1:CAS:528:DC%2BD2MXmtlSlt7Y%3D (Pubitemid 41032181)
58. R Barrangou MA Azcarate-Peril T Duong S Conners RM Kelly TR Klaenhammer 2006 Global analysis of carbohydrate utilization by Lactobacillus acidophilus using cDNA microarrays Proceedings of the National Academy of Sciences of the United States of America 103 10 3816 3821 1:CAS:528:DC%2BD28XivFWisLo%3D 10.1073/pnas.0511287103 (Pubitemid 43376638)
59. Q Hua C Yang T Baba H Mori K Shimizu 2004 Analysis of gene expression in Escherichia coli in response to changes of growth-limiting nutrient in chemostat cultures Applied and Environmental Microbiology 70 4 2354 2366 1:CAS:528:DC%2BD2cXjtlOhsrk%3D 10.1128/AEM.70.4.2354-2366.2004 (Pubitemid 38500539)
60. MK Oh J Liao 2000 Gene expression profiling by DNA microarrays and metabolic fluxes in Escherichia coli Biotechnology Progress 16 278 286 1:CAS:528:DC%2BD3cXhsFWru7g%3D 10.1021/bp000002n (Pubitemid 30228657)
61. JD Monod 1947 The phenomenon of enzymatic adaptation and its bearing on problems of genetics and cellular differentiation Growth 11 223 289 1:CAS:528:DyaH1MXmsFOq
62. F Jacob J Monod 1961 Genetic regulatory mechanisms in the synthesis of proteins Journal of Molecular Biology 3 318 356 1:CAS:528:DyaF3MXhtFyrsLo%3D 10.1016/S0022-2836(61)80072-7
63. VV Smeianov P Wechter JR Broadbent JE Hughes BT Rodriguez, et al. 2007 Comparative high-density microarray analysis of gene expression during growth of Lactobacillus helveticus in milk versus rich culture medium Applied and Environmental Microbiology 73 8 2661 2672 1:CAS:528:DC%2BD2sXkvFeqsb8%3D 10.1128/AEM.00005-07 (Pubitemid 46668760)
64. T Durfee AM Hansen H Zhi FR Blattner DJ Jin 2008 Transcription profiling of the stringent response in Escherichia coli Journal of Bacteriology 190 3 1084 1096 1:CAS:528:DC%2BD1cXhsFSgsL0%3D 10.1128/JB.01092-07 (Pubitemid 351170952)
65. RA Gutierrez LV Lejay A Dean F Chiaromonte DE Shasha GM Coruzzi 2007 Qualitative network models and genome-wide expression data define carbon/nitrogen-responsive molecular machines in Arabidopsis Genome Biology 8 1 R7 10.1186/gb-2007-8-1-r7 1:CAS:528:DC%2BD2sXhsVSgsr0%3D (Pubitemid 351910995)
66. S Ma Q Gong HJ Bohnert 2006 Dissecting salt stress pathways Journal of Experimental Botany 57 5 1097 1107 1:CAS:528:DC%2BD28Xis1Glsrk%3D 10.1093/jxb/erj098
67. AP Gasch PT Spellman CM Kao O Carmel-Harel MB Eisen G Storz D Botstein PO Brown 2000 Genomic expression programs in the response of yeast cells to environmental changes Molecular Biology of the Cell 11 12 4241 4257 1:CAS:528:DC%2BD3cXovFansbw%3D
68. KA Siddiquee MJ Arauzo-Bravo K Shimizu 2004 Effect of a pyruvate kinase (pykF-gene) knockout mutation on the control of gene expression and metabolic fluxes in Escherichia coli FEMS Microbiology Letters 235 1 25 33 1:CAS:528:DC%2BD2cXktF2rsr8%3D 10.1111/j.1574-6968.2004.tb09563.x
69. T Ideker V Thorsson JA Ranish R Christmas J Buhler, et al. 2001 Integrated genomic and proteomic analyses of a systematically perturbed metabolic network Science 292 5518 929 934 1:CAS:528:DC%2BD3MXjsVSrt7c%3D 10.1126/science.292.5518.929 (Pubitemid 32422490)
70. TR Hughes MJ Marton AR Jones CJ Roberts R Stoughton, et al. 2000 Functional discovery via a compendium of expression profiles Cell 102 1 109 126 1:CAS:528:DC%2BD3cXkvFCrtrg%3D 10.1016/S0092-8674(00)00015-5
71. G Giaever AM Chu L Ni C Connelly L Riles, et al. 2002 Functional profiling of the Saccharomyces cerevisiae genome Nature 418 6896 387 391 1:CAS:528:DC%2BD38XlsFajt7k%3D 10.1038/nature00935 (Pubitemid 34826834)
72. GM Santangelo 2006 Glucose signaling in Saccharomyces cerevisiae Microbiology and Molecular Biology Reviews 70 1 253 282 1:CAS:528: DC%2BD28Xjs1Sgs70%3D 10.1128/MMBR.70.1.253-282.2006
73. TE Edwards DJ Klein AR Ferre-D'Amare 2007 Riboswitches: Small-molecule recognition by gene regulatory RNAs Current Opinion in Structural Biology 17 3 273 279 1:CAS:528:DC%2BD2sXnsFKlu7s%3D 10.1016/j.sbi.2007.05.004 (Pubitemid 47021358)
74. W Winkler A Nahvi RR Breaker 2002 Thiamine derivatives bind messenger RNAs directly to regulate bacterial gene expression Nature 419 6910 952 956 1:CAS:528:DC%2BD38Xot1Kluro%3D 10.1038/nature01145 (Pubitemid 35339632)
75. A Nahvi N Sudarsan M Ebert X Zou KL Brown R Breaker 2002 Genetic control by a metabolite binding mRNA Chemistry and Biology 9 9 1043 1049 1:CAS:528:DC%2BD38Xnt1GgurY%3D 10.1016/S1074-5521(02)00224-7 (Pubitemid 35273725)
76. JN Kim RR Breaker 2008 Purine sensing by riboswitches Biology of the Cell 100 1 1 11 1:CAS:528:DC%2BD2sXhsVent73F 10.1042/BC20070088 (Pubitemid 351201429)
77. CT Harbison DB Gordon TI Lee, et al. 2004 Transcriptional regulatory code of a eukaryote genome Nature 431 7004 99 104 1:CAS:528:DC%2BD2cXntFClu7k%3D 10.1038/nature02800 (Pubitemid 39215116)
78. A Barski S Cuddapah K Cui TY Roh D Schones Z Wang G Wei I Chepelev K Zhao 2007 High-resolution profiling of histone methylation in the human genome Cell 129 823 837 1:CAS:528:DC%2BD2sXmtFKjsro%3D 10.1016/j.cell.2007.05.009 (Pubitemid 46802390)
79. JD Keene SA Tenenbaum 2002 Eukaryotic mRNPs may represent posttranscriptional operons Molecular Cell 9 6 1161 1167 1:CAS:528: DC%2BD38Xlt1Sksbw%3D 10.1016/S1097-2765(02)00559-2 (Pubitemid 34722296)
80. P Kharchenko GM Church D Vitkup 2005 Expression dynamics of a cellular metabolic network Molecular Systems Biology 1 2005.0016 10.1038/msb4100023 1:CAS:528:DC%2BD2MXoslGqtrs%3D
81. H Wei S Persson T Metha V Srinivasasainagendra L Chen GP Page C Somerville A Loraine 2006 Transcriptional coordination of the metabolic network in Aabidopsis Plant Physiology 142 762 774 1:CAS:528:DC%2BD28XhtFartr7O 10.1104/pp.106.080358 (Pubitemid 44583145)
82. H Ge Z Liu GM Church M Vidal 2001 Correlation between transcriptome and interactome mapping data from Saccharomyces cerevisiae Nature Genetics 29 4 482 486 1:CAS:528:DC%2BD3MXovFGju7c%3D 10.1038/ng776 (Pubitemid 34326702)
83. A Zaslaver AE Mayo R Rosenberg P Bashkin H Sberro M Tsalyuk MG Surette U Alon 2004 Just-in-time transcription program in metabolic pathways Nature Genetics 36 5 486 491 1:CAS:528:DC%2BD2cXjsFSnt7s%3D 10.1038/ng1348 (Pubitemid 38620033)
84. J Ihmels R Levy N Barkai 2004 Principles of transcriptional control in the metabolic network of Saccharomyces cerevisiae Nature Biotechnology 22 1 86 92 1:CAS:528:DC%2BD2cXls1ar 10.1038/nbt918 (Pubitemid 38057961)
85. Y Bilu T Shlomi N Barkai E Ruppin 2006 Conservation of expression and sequence of metabolic genes is reflected by activity across metabolic states PLoS Computational Biology 2 8 e106 10.1371/journal.pcbi.0020106 1:CAS:528:DC%2BD28XovVKrsrw%3D (Pubitemid 44298481)
86. O Martinez-Perez A Lopez-Sanchez F Reyes-Ramirez B Floriano E Santero 2007 Integrated response to inducers by communication between a catabolic pathway and its regulatory system Journal of Bacteriology 189 10 3768 3775 1:CAS:528:DC%2BD2sXlvFGjtbc%3D 10.1128/JB.00057-07 (Pubitemid 46740174)
87. PD Karp CA Ouzounis C Moore-Kochlacs L Goldovsky P Kaipa, et al. 2005 Expansion of the BioCyc collection of pathway/genome databases to 160 genomes Nucleic Acids Research 33 19 6083 6089 1:CAS:528:DC%2BD2MXht1entLvK 10.1093/nar/gki892 (Pubitemid 41742547)
88. R Caspi H Foerster CA Fulcher R Hopkinson J Ingraham, et al. 2006 MetaCyc: A multiorganism database of metabolic pathways and enzymes Nucleic Acids Research 34 D511 D516 1:CAS:528:DC%2BD28XisFynsw%3D%3D 10.1093/nar/gkj128
89. PD Karp IM Keseler A Shearer M Latendresse M Krummenacker, et al. 2007 Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Research 35 22 7577 7590 1:CAS:528:DC%2BD1cXisF2jsw%3D%3D 10.1093/nar/gkm740
90. NC Duarte SA Becker N Jamshidi I Thiele ML Mo TD Vo R Srivas BO Palsson 2007 Global reconstruction of the human metabolic network based on genomic and bibliomic data Proceedings of the National Academy of Science 104 6 1777 1782 1:CAS:528:DC%2BD2sXitVaqu7w%3D 10.1073/pnas.0610772104 (Pubitemid 46239855)
91. LA Mueller P Zhang SY Rhee 2003 AraCyc: A biochemical pathway database for Arabidopsis Plant Physiology 132 2 453 460 1:CAS:528:DC%2BD3sXkslersL0%3D 10.1104/pp.102.017236 (Pubitemid 36715048)
92. JM Cherry C Ball S Weng G Juvik R Schmidt, et al. 1997 Genetic and physical maps of Saccharomyces cerevisiae Nature 387 6632 Suppl 67 73 1:CAS:528:DyaK2sXjsFGitbs%3D
93. HW Mewes D Frishman C Gruber B Geier D Haase, et al. 2000 MIPS: A database for genomes and protein sequences Nucleic Acids Research 28 1 37 40 1:CAS:528:DC%2BD3cXhvVGqu70%3D 10.1093/nar/28.1.37
94. M Kanehisa S Goto 2000 KEGG: Kyoto Encyclopedia of Genes and Genomes Nucleic Acids Research 28 27 30 1:CAS:528:DC%2BD3cXhvVGqu74%3D 10.1093/nar/28.1.27
95. MW Covert EM Knight JL Reed MJ Herrgard BO Palsson 2004 Integrating high-throughput and computational data elucidates bacterial networks Nature 429 6987 92 96 1:CAS:528:DC%2BD2cXjs1Kiur4%3D 10.1038/nature02456 (Pubitemid 38620557)
96. MJ Herrgard SS Fong BO Palsson 2006 Identification of genome-scale metabolic network models using experimentally measured flux profiles PLoS Computational Biology 2 7 e72 10.1371/journal.pcbi.0020072 1:CAS:528: DC%2BD28Xns1ChsLo%3D (Pubitemid 44147379)
97. T Shlomi Y Eisenberg R Sharan E Ruppin 2007 A genome-scale computational study of the interplay between transcriptional regulation and metabolism Molecular Systems Biology 3 101 10.1038/msb4100141 (Pubitemid 46625181)
98. I Gat-Viks A Tanay R Shamir 2004 Modeling and analysis of heterogeneous regulation in biological networks Journal of Computational Biology 11 6 1034 1049 1:CAS:528:DC%2BD2MXhtFersb4%3D 10.1089/cmb.2004.11.1034 (Pubitemid 40171211)
99. CH Yeang M Vingron 2006 A joint model of regulatory and metabolic networks BMC Bioinformatics 7 332 10.1186/1471-2105-7-332 1:CAS:528: DC%2BD28Xns1eqt70%3D (Pubitemid 44322142)
100. A Narang 2006 Comparative analysis of some models of gene regulation in mixed-substrate microbial growth Journal of Theoretical Biology 242 2 489 501 1:CAS:528:DC%2BD28XotlCisbw%3D 10.1016/j.jtbi.2006.03.017 (Pubitemid 44232823)
101. B Kofahl E Klipp 2004 Modelling the dynamics of the yeast pheromone pathway Yeast 21 10 831 850 1:CAS:528:DC%2BD2cXntVantb0%3D 10.1002/yea.1122 (Pubitemid 39162579)
102. JD Varner 2000 Large-scale prediction of phenotype: Concept Biotechnology and Bioengineering 69 6 664 678 1:CAS:528:DC%2BD3cXmsVyiu7c%3D 10.1002/1097-0290(20000920)69:6<664::AID-BIT11>3.0.CO;2-H (Pubitemid 30663769)
103. AP Burgard P Pharkya CD Maranas 2003 Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization Biotechnology and Bioengineering 84 6 647 657 1:CAS:528: DC%2BD3sXptFWmsL0%3D 10.1002/bit.10803 (Pubitemid 37420336)
104. KR Patil I Rocha J Forster J Nielsen 2005 Evolutionary programming as a platform for in silico metabolic engineering BMC Bioinformatics 6 308 10.1186/1471-2105-6-308 1:CAS:528:DC%2BD28Xpsl2isw%3D%3D (Pubitemid 43046105)
105. HU Kim TY Kim SY Lee 2008 Metabolic flux analysis and metabolic engineering of microorganisms Molecular BioSystems 4 113 120 10.1039/b712395g 1:CAS:528:DC%2BD1cXovFKmsg%3D%3D
106. MY Hirai M Yano M Yano DB Goodenowe S Kanaya T Kimura M Awazuhara M Arita T Fujiwara K Saito 2004 Integration of transcriptomics and metabolomics for understanding of global responses to nutritional stresses in Arabidopsis thaliana Proceedings of the National Academy of Sciences of the United States of America 101 27 10205 10210 1:CAS:528:DC%2BD2cXlvFOhsbw%3D 10.1073/pnas. 0403218101 (Pubitemid 38891220)
107. E Barros S Lezar MJ Anttonen JP van Dijk RM Roehlig EJ Kok KH Engel 2010 Comparison of two GM maize varieties with a near-isogenic non-GM variety using transcriptomics, proteomics and metabolomics Plant Biotechnology Journal 8 436 451 1:CAS:528:DC%2BC3cXmslChsbs%3D 10.1111/j.1467-7652.2009.00487.x
108. A Skirycz S De Bodt T Obata I De Clercq H Claeys R De Rycke M Andriankaja O Van Aken F Van Breusegem AR Fernie D Inze 2010 Developmental stage specificity and the role of mitochondrial metabolism in the response of Arabidopsis leaves to prolonged mild osmotic stress Plant Physiology 152 226 244 1:CAS:528:DC%2BC3cXmsF2mu7o%3D 10.1104/pp.109.148965
109. S Depuydt S Trenkamp AR Fernie S Elftieh JP Renou M Vuylsteke M Holsters D Vereecke 2009 An Integrated genomics approach to define niche establishment by Rhodococcus fascians Plant Physiology 149 1366 1386 1:CAS:528: DC%2BD1MXlsFCitbk%3D 10.1104/pp.108.131805
110. S Malitsky E Blum H Less I Venger M Elbaz S Morin Y Eshed A Aharoni 2008 The transcript and metabolite networks affected by the two clades of Arabidopsis glucosinolate biosynthesis regulators Plant Physiology 148 2021 2049 1:CAS:528:DC%2BD1cXhsFemtrbK 10.1104/pp.108.124784 (Pubitemid 352847479)
111. MA Farag BE Deavours A De Fatima M Naoumkina RA Dixon LW Sumner 2009 Integrated metabolite and transcript profiling identify a biosynthetic mechanism for hispidol in Medicago truncatula cell cultures Plant Physiology 151 1096 1113 1:CAS:528:DC%2BD1MXhsVCjsbrE 10.1104/pp.109.141481
112. K Urano Y Kurihara M Seki K Shinozaki 2010 'Omics' analyses of regulatory networks in plant abiotic stress responses Current Opinion in Plant Biology 13 132 138 1:CAS:528:DC%2BC3cXlsFahsrs%3D 10.1016/j.pbi.2009.12.006
113. A Iyer-Pascuzzi J Simpson L Herrera-Estrella PN Benfey 2009 Functional genomics of root growth and development in Arabidopsis Current Opinion in Plant Biology 12 2 165 171 1:CAS:528:DC%2BD1MXjsVOgtbg%3D 10.1016/j.pbi.2008.11.002
114. SJ Lee A Trostela P Lea R Harinarayananb PC FitzGerald S Adhya 2009 Cellular stress created by intermediary metabolite imbalances Proceedings of the National Academy of Sciences of the United States of America 106 46 19515 19520 1:CAS:528:DC%2BD1MXhsFGitrrE 10.1073/pnas.0910586106
115. D Rossouw T Naes FF Bauer 2008 Linking gene regulation and the exo-metabolome: A comparative transcriptomics approach to identify genes that impact on the production of volatile aroma compounds in yeast BMC Genomics 9 530 10.1186/1471-2164-9-530 1:CAS:528:DC%2BD1MXislGi
116. KC Tan SVS Ipcho RD Trengove RP Olivier PS Solomon 2009 Assessing the impact of transcriptomics, proteomics and metabolomics on fungal phytopathology Molecular Plant Pathology 10 5 703 715 1:CAS:528:DC%2BD1MXhtFCgsbfK 10.1111/j.1364-3703.2009.00565.x
117. MR Andersen J Nielsen 2009 Current status of systems biology in Aspergilli Fungal Genetics and Biology 46 S180 S190 1:CAS:528: DC%2BD1MXisFKjtbY%3D 10.1016/j.fgb.2008.07.006
118. SJ Park SY Lee J Cho TY Kim JW Lee JH Park MJ Han 2005 Global physiological understanding and metabolic engineering of microorganisms based on omics studies Applied Microbiology and Biotechnology 68 567 579 1:CAS:528:DC%2BD2MXhtFGhtLvP 10.1007/s00253-005-0081-z (Pubitemid 41549972)
119. J Raes P Bork 2008 Molecular eco-systems biology: Towards an understanding of community function Nature Reviews Microbiology 6 693 699 1:CAS:528:DC%2BD1cXpvVWjs7c%3D 10.1038/nrmicro1935
120. X Yang B Zhang C Molony E Chudin K Hao J Zhu A Gaedigk C Suver H Zhong JS Leeder FP Guengerich SC Strom E Schuetz TH Rushmore RG Ulrich GW Slatter EE Schadt A Kasarskis PY Lum 2010 Systematic genetic and genomic analysis of cytochrome P450 enzyme activities in human liver Genome Research 20 8 1020 1036 1:CAS:528:DC%2BC3cXhtVahsrvK 10.1101/gr.103341.109
121. CL Waterman RA Currie LA Cottrell J Dow J Wright CJ Waterfield JL Griffin 2010 An integrated functional genomic study of acute phenobarbital exposure in the rat BMC Genomics 11 9 10.1186/1471-2164-11-9 1:CAS:528: DC%2BC3cXmtlensw%3D%3D
122. JG Bundy JK Sidhu F Rana DJ Spurgeon C Svendsen JF Wren SR Stürzenbaum AJ Morgan P Kille 2008 'Systems toxicology' approach identifies coordinated metabolic responses to copper in a terrestrial non-model invertebrate, the earthworm Lumbricus rubellus BMC Biology 6 25 10.1186/1741-7007-6-25 1:CAS:528:DC%2BD1cXntleqsr4%3D (Pubitemid 351850957)
123. R Kaddurah-Daouk KRR Krishnan 2009 Metabolomics: A global biochemical approach to the study of central nervous system diseases Neuropsychopharmacology Reviews 34 173 186 1:CAS:528:DC%2BD1cXhsVyru73K 10.1038/npp.2008.174
124. J Wang G Wu H Zhou F Wang 2009 Emerging technologies for amino acid nutrition research in the post-genome era Amino Acids 37 177 186 10.1007/s00726-008-0193-8 1:CAS:528:DC%2BD1MXltlemtL8%3D
125. SG Tringe EM Rubin 2005 Metagenomics: DNA sequencing of environmental samples Nature Reviews Genetics 6 11 805 814 1:CAS:528:DC%2BD2MXhtFygt77F 10.1038/nrg1709