Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: An initial draft to the two-dimensional annotation

BMC Microbiology

Volumn 5, Issue , 2005, Pages

  Becker, Scott A ^a   Palsson, Bernhard Ø ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL METABOLISM; BACTERIAL STRAIN; CARBON SOURCE; CATALYSIS; DRUG TARGETING; INFORMATION PROCESSING; NONHUMAN; OPEN READING FRAME; PHENOTYPE; STAPHYLOCOCCUS AUREUS;

BACTERIAL PROTEINS; COMPUTER SIMULATION; GENE DELETION; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, BACTERIAL; GENOME, BACTERIAL; STAPHYLOCOCCUS AUREUS;

BACTERIA (MICROORGANISMS); STAPHYLOCOCCUS AUREUS;

EID: 17844405878     PISSN: 14712180     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-5-8     Document Type: Article

References (78)

1. Enright MC: The evolution of a resistant pathogen-the case of MRSA. Curr Opin Pharmacol 2003, 3:474-479.
2. Somerville GA, Said-Salim B, Wickman JM, Raffel SJ, Kreiswirth BN, Musser JM: Correlation of acetate catabolism and growth yield in Staphylococcus aureus: implications for host-pathogen interactions. Infect Immun 2003, 71:4724-4732.
3. Kuroda M, Ohta T, Uchiyama I, Baba T, Yuzawa H, Kobayashi I, Cui L, Oguchi A, Aoki K, Nagai Y, Lian J, Ito T, Kanamori M, Matsumaru H, Maruyama A, Murakami H, Hosoyama A, Mizutani-Ui Y, Takahashi NK, Sawano T, Inoue R, Kaito C, Sekimizu K, Hirakawa H, Kuhara S, Goto S, Yabuzaki J, Kanehisa M, Yamashita A, Oshima K, Furuya K, Yoshino C, Shiba T, Hattori M, Ogasawara N, Hayashi H, Hiramatsu K: Whole genome sequencing of meticillin-resistant Staphylococcus aureus. Lancet 2001, 357:1225-1240.
4. Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BO: Metabolic modeling of microbial strains in silico. Trends Biochem Sci 2001, 26:179-186.
5. Price ND, Papin JA, Schilling CH, Palsson BO: Genome-scale microbial in silico models: the constraints-based approach. Trends Biotechnol 2003, 21:162-169.
6. Palsson B: Two-dimensional annotation of genomes. Nat Biotech 2004, 22:1218-1219.
7. Price ND, Reed JL, Palsson BO: Genome-scale models of microbial cells: evaluating the consequences of constraints. Nat Rev Microbiol 2004, 2:886-897.
8. Ibarra RU, Edwards JS, Palsson BO: Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 2002, 420:186-189.
9. Varma A, Palsson BO: Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110. Appl Environ Microbiol 1994, 60:3724-3731.
10. Edwards JS, Ibarra RU, Palsson BO: In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data. Nat Biotechnol 2001, 19:125-130.
11. Duarte NC, Palsson BO, Fu P: Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae. BMC Genomics 2004, 5:63.
12. Reed JL, Palsson BO: Thirteen years of building constraint-based in silico models of Escherichia coli. J Bacteriol 2003, 185:2692-2699.
13. Forster J, Famili I, Fu P, Palsson BO, Nielsen J: Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network. Genome Res 2003, 13:244-253.
14. Duarte NC, Herrgard MJ, Palsson BO: Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res 2004, 14:1298-1309.
15. Van Dien SJ, Lidstrom ME: Stoichiometric model for evaluating the metabolic capabilities of the facultative methylotroph Methylobacterium extorquens AM1, with application to reconstruction of C(3) and C(4) metabolism. Biotechnol Bioeng 2002, 78:296-312.
16. Hong SH, Kim JS, Lee SY, In YH, Choi SS, Rih JK, Kim CH, Jeong H, Hur CG, Kim JJ: The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens. Nat Biotechnol 2004, 22:1275-1281.
17. Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BO: Genome-scale metabolic model of Helicobacter pylori 26695. J Bacteriol 2002, 184:4582-4593.
18. Schilling CH, Palsson BO: Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis. J Theor Biol 2000, 203:249-283.
19. Vo TD, Greenberg HJ, Palsson BO: Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J Biol Chem 2004, 279:39532-39540.
20. Papp B, Pal C, Hurst LD: Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 2004, 429:661-664.
21. Segre D, Vitkup D, Church GM: Analysis of optimality in natural and perturbed metabolic networks. Proc Natl Acad Sci U S A 2002, 99:15112-15117.
22. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL: Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 2004, 427:839-843.
23. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO: Integrating high-throughput and computational data elucidates bacterial networks. Nature 2004, 429:92-96.
24. Burgard AP, Pharkya P, Maranas CD: Optknock: a bilevel programming framework for identifying gene knockout strategies for microbial strain optimization. Biotechnol Bioeng 2003, 84:647-657.
25. Reed JL, Vo TD, Schilling CH, Palsson BO: An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol 2003, 4:R54.
26. Fong SS, Marciniak JY, Palsson BO: Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model. J Bacteriol 2003, 185:6400-6408.
27. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L: Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 2001, 292:929-934.
28. Edwards JS, Palsson BO: The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. Proc Natl Acad Sci U S A 2000, 97:5528-5533.
29. Dauner M, Sauer U: Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol Bioeng 2001, 76:132-143.
30. Varma A, Palsson BO: Parametric Sensitivity of Stoichiometric Flux Balance Models Applied to Wild-Type Escherichia-Coli Metabolism. Biotechnology and Bioengineering 1995, 45:69-79.
31. Edwards JS, Covert M, Palsson B: Metabolic modelling of microbes: the flux-balance approach. Environ Microbiol 2002, 4:133-140.
32. Bonarius HPJ, Schmid G, Tramper J: Flux analysis of underdetermined metabolic networks: The quest for the missing constraints. Trends in Biotechnology 1997, 15:308-314.
33. Varma A, Palsson BO: Metabolic Flux Balancing - Basic Concepts, Scientific and Practical Use. Bio-Technology 1994, 12:994-998.
34. Onoue Y, Mori M: Amino acid requirements for the growth and enterotoxin production by Staphylococcus aureus in chemically defined media. Int J Food Microbiol 1997, 36:77-82.
35. Rudin L, Sjostrom JE, Lindberg M, Philipson L: Factors affecting competence for transformation in Staphylococcus aureus. J Bacteriol 1974, 118:155-164.
36. Covert MW, Palsson BO: Transcriptional regulation in constraints-based metabolic models of Escherichia coli. J Biol Chem 2002, 277:28058-28064.
37. Crossley KB, Archer G: The staphylococci in human disease. New York, Churchill Livingstone; 1997:xvi, 682 p., [2] p. plates.
38. Ji Y, Zhang B, Van SF, Horn, Warren P, Woodnutt G, Burnham MK, Rosenberg M: Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 2001, 293:2266-2269.
39. Forsyth RA, Haselbeck RJ, Ohlsen KL, Yamamoto RT, Xu H, Trawick JD, Wall D, Wang L, Brown-Driver V, Froelich JM, C KG, King P, McCarthy M, Malone C, Misiner B, Robbins D, Tan Z, Zhu Zy ZY, Carr G, Mosca DA, Zamudio C, Foulkes JG, Zyskind JW: A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 2002, 43:1387-1400.
40. 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, Debarbouille M, Dervyn E, Deuerling E, Devine K, Devine SK, Dreesen O, Errington J, Fillinger S, Foster SJ, Fujita Y, Galizzi A, Gardan R, Eschevins C, Fukushima T, Haga K, Harwood CR, Hecker M, Hosoya D, Hullo MF, Kakeshita H, Karamata D, Kasahara Y, Kawamura F, Koga K, Koski P, Kuwana R, Imamura D, Ishimaru M, Ishikawa S, Ishio I, Le Coq D, Masson A, Mauel C, Meima R, Mellado RP, Moir A, Moriya S, Nagakawa E, Nanamiya H, Nakai S, Nygaard P, Ogura M, Ohanan T, O'Reilly M, O'Rourke M, Pragai Z, Pooley HM, Rapoport G, Rawlins JP, Rivas LA, Rivolta C, Sadaie A, Sadaie Y, Sarvas M, Sato T, Saxild HH, Scanlan E, Schumann W, Seegers JF, Sekiguchi J, Sekowska A, Seror SJ, Simon M, Stragier P, Studer R, Takamatsu H, Tanaka T, Takeuchi M, Thomaides HB, Vagner V, van Dijl JM, Watabe K, Wipat A, Yamamoto H, Yamamoto M, Yamamoto Y, Yamane K, Yata K, Yoshida K, Yoshikawa H, Zuber U, Ogasawara N: Essential Bacillus subtilis genes. Proc Natl Acad Sci U S A 2003, 100:4678-4683.
41. Peterson JD, Umayam LA, Dickinson T, Hickey EK, White O: The Comprehensive Microbial Resource. Nucleic Acids Res 2001, 29:123-125.
42. Kanehisa M, Goto S, Kawashima S, Nakaya A: The KEGG databases at GenomeNet. Nucleic Acids Res 2002, 30:42-46.
43. Sonenshein AL, Hoch JA, Losick R: Bacillus subtilis and its closest relatives : from genes to cells. Washington, D.C., ASM Press; 2002:xvi, 629 p..
44. Theodore TS, Panos C: Protein and fatty acid composition of mesosomal vesicles and plasma membranes of Staphylococcus aureus. J Bacteriol 1973, 116:571-576.
45. Freiberg C, Brunner NA, Schiffer G, Lampe T, Pohlmann J, Brands M, Raabe M, Habich D, Ziegelbauer K: Identification and characterization of the first class of potent bacterial acetyl-CoA carboxylase inhibitors with antibacterial activity. J Biol Chem 2004, 279:26066-26073.
46. Bulloch EM, Jones MA, Parker EJ, Osborne AP, Stephens E, Davies GM, Coggins JR, Abell C: Identification of 4-amino-4-deoxychorismate synthase as the molecular target for the antimicrobial action of (6s)-6-fluoroshikimate. J Am Chem Soc 2004, 126:9912-9913.
47. Mukhopadhyay R, Kapoor P, Madhubala R: Antileishmanial effect of a potent S-adenosylmethionine decarboxylase inhibitor: CGP 40215A. Pharmacol Res 1996, 33:67-70.
48. Guo J, Wu YQ, Rattendi D, Bacchi CJ, Woster PM: S-(5′-deoxy- 5′-adenosyl)-1-aminoxy-4-(methylsulfonio)-2-cyclopentene (AdoMao): an irreversible inhibitor of S-adenosylmethionine decarboxylase with potent in vitro antitrypanosomal activity. J Med Chem 1995, 38:1770-1777.
49. Cooney DA, Milman HA, Jayaram HN, Homan ER: Inhibition of L-asparagine synthetase by mucochloric and mucobromic acids. Enzyme 1976, 21:524-539.
50. Boehlein SK, Nakatsu T, Hiratake J, Thirumoorthy R, Stewart JD, Richards NG, Schuster SM: Characterization of inhibitors acting at the synthetase site of Escherichia coli asparagine synthetase B. Biochemistry 2001, 40:11168-11175.
51. Rosowsky A, Fu H, Chan DC, Queener SF: Synthesis of 2,4-diamino-6- [2′-O-(omega-carboxyalkyl)oxydibenz[ b,f]azepin-5-yl]methylpt eridines as potent and selective inhibitors of Pneumocystis carinii, Toxoplasma gondii, and Mycobacterium avium dihydrofolate reductase. J Med Chem 2004, 47:2475-2485.
52. Johnson T, Khan IA, Avery MA, Grant J, Meshnick SR: Quantitative structure-activity relationship studies of a series of sulfa drugs as inhibitors of Pneumocystis carinii dihydropteroate synthetase. Antimicrob Agents Chemother 1998, 42:1454-1458.
53. Grape M, Sundstrom L, Kronvall G: Sulphonamide resistance gene sul3 found in Escherichia coli isolates from human sources. J Antimicrob Chemother 2003, 52:1022-1024.
54. Tian F, Montchamp JL, Frost JW: Inhibitor Ionization as a Determinant of Binding to 3-Dehydroquinate Synthase. J Org Chem 1996, 61:7373-7381.
55. Hartman HA, Edmondson DE, McCormick DB: Riboflavin 5′- pyrophosphate: a contaminant of commercial FAD, a coenzyme for FAD-dependent oxidases, and an inhibitor of FAD synthetase. Anal Biochem 1992, 202:348-355.
56. Rejman J, Kozubek A: Inhibitory effect of natural phenolic lipids upon NAD-dependent dehydrogenases and on triglyceride accumulation in 3T3-L1 cells in culture. J Agric Food Chem 2004, 52:246-250.
57. Winkler BS, Kapousta-Bruneau N, Arnold MJ, Green DG: Effects of inhibiting glutamine synthetase and blocking glutamate uptake on b-wave generation in the isolated rat retina. Vis Neurosci 1999, 16:345-353.
58. Obojska A, Berlicki L, Kafarski P, Lejczak B, Chicca M, Forlani G: Herbicidal pyridyl derivatives of aminomethylene-bisphosphonic acid inhibit plant glutamine synthetase. J Agric Food Chem 2004, 52:3337-3344.
59. Loida PJ, Thompson RL, Walker DM, CaJacob CA: Novel inhibitors of glutamyl-tRNA(Glu) reductase identified through cellbased screening of the heme/chlorophyll biosynthetic pathway. Arch Biochem Biophys 1999, 372:230-237.
60. He A, Rosazza JP: GTP cyclohydrolase I: purification, characterization, and effects of inhibition on nitric oxide synthase in nocardia species. Appl Environ Microbiol 2003, 69:7507-7513.
61. Shen RS, Alam A, Zhang YX: Inhibition of GTP cyclohydrolase I by pterins. Biochim Biophys Acta 1988, 965:9-15.
62. Mason RP, Walter MF, Jacob RF: Effects of HMG-CoA reductase inhibitors on endothelial function: role of microdomains and oxidative stress. Circulation 2004, 109:II34-41.
63. Miller TL, Wolin MJ: Inhibition of growth of methane-producing bacteria of the ruminant forestomach by hydroxymethylglutaryl-SCoA reductase inhibitors. J Dairy Sci 2001, 84:1445-1448.
64. Tomoda H, Ohbayashi N, Kumagai H, Hashizume H, Sunazuka T, Omura S: Differential inhibition of HMG-CoA synthase and pancreatic lipase by the specific chiral isomers of beta-lactone DU-6622. Biochem Biophys Res Commun 1999, 265:536-540.
65. Wrensford LV, Rodwell VW, Anderson VE: 3-Hydroxy-3-methylglutaryldithio- coenzyme A: a potent inhibitor of Pseudomonas mevalonii HMG-CoA reductase. Biochem Med Metab Biol 1991, 45:204-208.
66. Thompson K, Dunford JE, Ebetino FH, Rogers MJ: Identification of a bisphosphonate that inhibits isopentenyl diphosphate isomerase and farnesyl diphosphate synthase. Biochem Biophys Res Commun 2002, 290:869-873.
67. Kappler F, Vrudhula VM, Hampton A: Toward the synthesis of isozyme-specific enzyme inhibitors. Potent inhibitors of rat methionine adenosyltransferases. Effect of one-atom elongation of the ribose-P alpha bridge in two covalent adducts of L-methionine and beta,gamma-imido-ATP. J Med Chem 1988, 31:384-389.
68. Sozzani S, Agwu DE, McCall CE, O'Flaherty JT, Schmitt JD, Kent JD, McPhail LC: Propranolol, a phosphatidate phosphohydrolase inhibitor, also inhibits protein kinase C. J Biol Chem 1992, 267:20481-20488.
69. Nord LD, Willis RC, Breen TS, Avery TL, Finch RA, Sanghvi YS, Revankar GR, Robins RK: Inhibition of phosphoribosylpyrophosphate synthetase by 4-methoxy-(MRPP) and 4-amino-8-(D-ribofuranosylamino) pyrimido[5,4-d]pyrimidine (ARPP). Biochem Pharmacol 1989, 38:3543-3549.
70. Cushman M, Sambaiah T, Jin G, Illarionov B, Fischer M, Bacher A: Design, synthesis, and evaluation of 9-D-ribitylamino-1,3,7,9-tetrahydro-2,6,8- purinetriones bearing alkyl phosphate and alpha,alpha-difluorophosphonate substituents as inhibitors of tiboflavin synthase and lumazine synthase. J Org Chem 2004, 69:601-612.
71. Lakanen JR, Pegg AE, Coward JK: Synthesis and biochemical evaluation of adenosylspermidine, a nucleoside-polyamine adduct inhibitor of spermidine synthase. J Med Chem 1995, 38:2714-2727.
72. Mattila T, Honkanen-Buzalski T, Poso H: Reversible inhibition of bacterial growth after specific inhibition of spermidine synthase by dicyclohexylamine. Biochem J 1984, 223:823-830.
73. Sempuku K: Photoinactivation of the thiamin transport system in Saccharomyces cerevisiae with azidobenzoyl derivatives of thiamin. Biochim Biophys Acta 1988, 944:177-184.
74. Iwashima A, Nishimura H, Nishino H: Inhibition of thiamine transport in baker's yeast by methylene blue. Experientia 1980, 36:1153-1154.
75. Lin S, Del Razo LM, Styblo M, Wang C, Cullen WR, Thomas DJ: Arsenicals inhibit thioredoxin reductase in cultured rat hepatocytes. Chem Res Toxicol 2001, 14:305-311.
76. Smith AD, Guidry CA, Morris VC, Levander OA: Aurothioglucose inhibits murine thioredoxin reductase activity in vivo. J Nutr 1999, 129:194-198.
77. Winans KA, Bertozzi CR: An inhibitor of the human UDP-Glc-NAc 4-epimerase identified from a uridine-based library: a strategy to inhibit O-linked glycosylation. Chem Biol 2002, 9:113-129.
78. Andres CJ, Bronson JJ, D'Andrea SV, Deshpande MS, Falk PJ, Grant-Young KA, Harte WE, Ho HT, Misco PF, Robertson JG, Stock D, Sun Y, Walsh AW: 4-Thiazolidinones: novel inhibitors of the bacterial enzyme MurB. Bioorg Med Chem Lett 2000, 10:715-717.