Predicting synthetic rescues in metabolic networks

Molecular Systems Biology

Volumn 4, Issue , 2008, Pages

  Motter, Adilson E ^a   Gulbahce, Natali ^b,c,d   Almaas, Eivind ^e   Barabási, Albert László ^c,f  

^a NORTHWESTERN UNIVERSITY   (United States)

^b LOS ALAMOS NATIONAL LABORATORY   (United States)

^c NORTHEASTERN UNIVERSITY   (United States)

^d DANA FARBER CANCER INSTITUTE   (United States)

^e LAWRENCE LIVERMORE NATIONAL LABORATORY   (United States)

^f UNIVERSITY OF NOTRE DAME   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOMASS; CELL METABOLISM; GENE DELETION; GENE FUNCTION; GENE INTERACTION; GROWTH RATE; METABOLISM; NONHUMAN; PRIORITY JOURNAL; SYNTHESIS; SYSTEMS BIOLOGY; BACTERIAL GENE; BIOLOGICAL MODEL; BIOLOGY; CITRIC ACID CYCLE; ESCHERICHIA COLI; ESSENTIAL GENE; GENE EXPRESSION REGULATION; GENE REGULATORY NETWORK; GENETICS; GROWTH, DEVELOPMENT AND AGING; METHODOLOGY; PHYSIOLOGY; PREDICTION AND FORECASTING;

BIOMASS; CITRIC ACID CYCLE; COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; GENE REGULATORY NETWORKS; GENES, BACTERIAL; GENES, ESSENTIAL; METABOLIC NETWORKS AND PATHWAYS; MODELS, BIOLOGICAL; MODELS, GENETIC; PREDICTIVE VALUE OF TESTS; SYSTEMS BIOLOGY;

EID: 39149119221     PISSN: 17444292     EISSN: 17444292     Source Type: Journal    
DOI: 10.1038/msb.2008.1     Document Type: Article

References (54)

1. Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118: 4947-4957
2. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 8
3. Barabási A-L (2007) Network medicine - from obesity to the 'diseasome'. N Engl J Med 357: 404-407
4. Barabási A-L, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nat Rev Genet 5: 101-113
5. BiGG (2007) Database of Biochemically, Genetically and Genomically (BiGG) Structured Genome-Scale Metabolic Network Reconstruction. Available online at: http://bigg.ucsd.edu/
6. Bonhoeffer S, Chappey C, Parkin NT, Whitcomb JM, Petropoulos CJ (2004) Evidence for positive epistasis in HIV-1. Science 306: 1547-1550
7. Boone C, Bussey H, Andrews BJ (2007) Exploring genetic interactions and networks with yeast. Nat Rev Genet 8: 437-449
8. Burgard AP, Pharkya P, Maranas CD (2003) OptKnock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotech Bioeng 84: 647-657
9. Causey TB, Zhou S, Shanmugam KT, Ingram LO (2003) Engineering the metabolism of Escherichia coli W3110 for the conversion of sugar to redox-neutral and oxidized products: homoacetate production. Proc Natl Acad Sci USA 100: 825-832
10. Chait R, Craney A, Kishony R (2007) Antibiotic interactions that select against resistance. Nature 446: 668-671
11. Chatterjee R, Millard CS, Champion K, Clark DP, Donnelly MI (2001) Mutation of the ptsG gene results in increased production of succinate in fermentation of glucose by Escherichia coli. Appl Environ Microbiol 67: 148-154
12. Deutscher D, Meilijson I, Kupiec M, Ruppin E (2006) Multiple knockout analysis of genetic robustness in the yeast metabolic network. Nat Genet 38: 993-998
13. Duarte NC, Herrgard MJ, Palsson BO (2004) Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 14: 1298-1309
14. Edwards JS, Ibarra RU, Palsson BO (2001) In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotech 19: 125-130
15. Edwards JS, Palsson BO (2000) The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97: 5528-5533
16. Elena SF, Lenski RE (1997) Test of synergistic interactions among deleterious mutations in bacteria. Nature 390: 395-398
17. Fischer E, Sauer U (2005) Large-scale in vivo flux analysis shows rigidity and suboptimal performance of Bacillus subtilis metabolism. Nat Genet 37: 636-640
18. Fong SS, Nanchen A, Palsson BO, Sauer U (2006) Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes. J Biol Chem 281: 8024-8033
19. Fong SS, Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36: 1056-1058
20. Fraenkel DG (1987) Glycolysis, penthose phosphate pathway, and Entner-Doudoroff pathway. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology, Neidhardt FC (ed), Vol. 1, pp 142-150. Washington: Am Soc Microbiol
21. Gerdes SY, Gerdes SY, Scholle MD, Campbell JW, Balázsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabási A-L et al (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185: 5673-5684
22. Gertz EM, Wright SJ (2001) Object-Oriented Software for Quadratic Programming (OOQP). Available online at: www.cs.wisc.edu/~swright/ooqp/
23. Giaever G, Chu AM, Ni L, Connelly C, Riles L, Véronneau S, Dow S, Lucau-Danila A, Anderson K, André B, Arkin AP, Astromoff A, El-Bakkoury M, Bangham R, Benito R, Brachat S, Campanaro S, Curtiss M, Davis K, Deutschbauer A et al (2002) Functional profiling of the Saccharomyces cerevisiae genome. Nature 418: 387-391
24. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison III CA, Smith HO, Venter JC (2006) Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103: 425-430
25. Goh K-I, Cusick JE, Valle D, Childs E, Vidal M, Barabási A-L (2007) The human disease network. Proc Natl Acad Sci USA 104: 86850-86890
26. Gupta S, Clark PD (1989) Escherichia coli derivatives lacking both alcohol dehydrogenase and phosphotransacetylase grow anaerobically by lactate fermentation. J Bacteriol 171: 3650-3655
27. Hahnfeldt P, Hlatky L (2005) in preparation
28. Hartwell LH, Hopfield JJ, Leibler S, Murray AW (1999) From molecular to modular cell biology. Nature 402: C47-C52
29. Hashimoto M, Ichimura T, Mizoguchi H, Tanaka K, Fujimitsu K, Keyamura K, Ote T, Yamakawa T, Yamazaki Y, Mori H, Katayama T, Kato J (2005) Cell size and nucleoid organization of engineered Escherichia coli cells with a reduced genome. Mol Microbiol 55: 137-149
30. Herring CD, Raghunathan A, Honisch C, Patel T, Applebee MK, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR, Palsson BO (2006) Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale. Nat Genet 38: 1406-1412
31. Ho M-W, Commins J (2001) Common gene therapy vector causes cancer as well as toxic shock. ISIS Report, 20 September (The Institute of Science in Society, London)
32. Ibarra RU, Edwards JS, Palsson BO (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189
33. Kaiser J (2005) Gene therapy: putting the fingers on gene repair. Science 310: 1894-1896
34. Kimmelman J (2005) Recent developments in gene transfer: risk and ethics. BMJ 330: 79-82
35. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, Boland F, Brignell SC, Bron S, Bunai K, Chapuis J, Christiansen LC, Danchin A, Débarbouille M, Dervyn E, Deuerling E et al (2003) Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100: 4678-4683
36. Kushner JA, Haj FG, Klaman LD, Dow MA, Kahn BB, Neel BG, White MF (2004) Islet-sparing effects of protein tyrosine phosphatase-1b deficiency delays onset of diabetes in IRS2 knockout mice. Diabetes 53: 61-66
37. Makhorin A (2001) GNU Linear Programming Kit (GLPK). Available online at: www.gnu.org/software/glpk/glpk.html
38. Motter AE (2004) Cascade control and defense in complex networks. Phys Rev Lett 93: 098701
39. Ooi SL, Shoemaker DD, Boeke JD (2003) DNA helicase gene interaction network defined using synthetic lethality analyzed by microarray. Nat Genet 35: 277-286
40. Pál C, Papp B, Lercher MJ, Csermely P, Oliver SG, Hurst LD (2006) Chance and necessity in the evolution of minimal metabolic networks. Nature 440: 667-670
41. PEC (2007) Profiling of Escherichia coli chromosome (PEC) database. Available online at: http://www.shigen.nig.ac.jp/ecoli/pec/
42. Pharkya P, Maranas CD (2006) An optimization framework for identifying reaction activation/inhibition or elimination candidates for overproduction in microbial systems. Metab Eng 8: 1-13
43. Sansom OJ, Meniel VS, Muncan V, Phesse TJ, Wilkins JA, Reed KR, Vass JK, Athineos D, Clevers H, Clarke AR (2007) Myc deletion rescues Apc deficiency in the small intestine. Nature 446: 676-679
44. Sauer U (2004) High-throughput phenomics: experimental methods for mapping fluxomes. Curr Opin Biotechnol 15: 58-63
45. SDG (2007) Saccharomyces Genome Database (SGD). Available online at: http://www.yeastgenome.org/
46. Segrè D, DeLuna A, Church GM, Kishony R (2005) Modular epistasis in yeast metabolism. Nat Genet 37: 77-83
47. Segrè D, Vitkup D, Church GM (2002) Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci USA 99: 15112-15117
48. Shlomi T, Berkman O, Ruppin E (2005) Regulatory on/off minimization of metabolic flux changes after genetic perturbations. Proc Natl Acad Sci USA 102: 7695-7700
49. Steinmetz LM, Scharfe C, Deutschbauer AM, Mokranjac D, Herman ZS, Jones T, Chu AM, Giaever G, Prokisch H, Oefner PJ, Davis RW (2002) Systematic screen for human disease genes in yeast. Nat Genet 31: 400-404
50. Tong AHY, Evangelista M, Parsons AB, Xu H, Bader GD, Pagè N, Robinson M, Raghibizadeh S, Hogue CWV, Bussey H, Andrews B, Tyers M, Boone C (2001) Systematic genetic analysis with ordered arrays of yeast deletion mutants. Science 294: 2364-2368
51. Trinh CT, Carlson R, Wlaschin A, Srienc F (2006) Design, construction and performance of the most efficient biomass producing E. coli bacterium. Metabol Eng 8: 628-638
52. Vogelstein B, Lane D, Levine AJ (2000) Surfing the p53 network. Nature 408: 307-310
53. Wang XJ, Greenhalgh DA, Donehower LA, Roop DR (2000) Cooperation between Ha-ras and fos or transforming growth factor alpha overcomes a paradoxic tumor-inhibitory effect of p53 loss in transgenic mouse epidermis. Mol Carcinog 29: 67-75
54. Wong SL, Zhang LV, Tong AHY, Li Z, Goldberg DS, King OD, Lesage G, Vidal M, Andrews B, Bussey H, Boone C, Roth PF (2004) Combining biological networks to predict genetic interactions. Proc Natl Acad Sci USA 101: 15682-15687