Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): An in silico genome-scale characterization of single- and double-deletion mutants

Journal of Bacteriology

Volumn 187, Issue 16, 2005, Pages 5818-5830

  Thiele, Ines ^a   Vo, Thuy D ^a   Price, Nathan D ^a   Palsson, Bernhard Ø ^a  

^a UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ISOPRENOID; LIPOPOLYSACCHARIDE;

ARTICLE; BACTERIAL METABOLISM; BACTERIAL STRAIN; GENE DELETION; GENE MUTATION; GENOME; HELICOBACTER PYLORI; KNOCKOUT GENE; NONHUMAN; PHENOTYPE; PRIORITY JOURNAL;

BIOTIN; ENERGY METABOLISM; GENE DELETION; GENES, LETHAL; GENOME, BACTERIAL; HELICOBACTER PYLORI; MODELS, GENETIC; MUTAGENESIS; PHENOTYPE; REPRODUCIBILITY OF RESULTS;

HELICOBACTER PYLORI;

EID: 23644452487     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.187.16.5818-5830.2005     Document Type: Article

References (50)

1. Boneca, I. G., H. de Reuse, J. C. Epinat, M. Pupin, A. Labigne, and I. Moszer. 2003. A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res. 31:1704-1714.
2. Burns, B. P., S. L. Hazell, G. L. Mendz, T. Kolesnikow, D. Tillet, and B. A. Neilan. 2000. The Helicobacter pylori pyrB gene encoding aspartate carbamoyltransferase is essential for bacterial survival. Arch. Biochem. Biophys. 380:78-84.
3. Chalker, A. F., H. W. Minehart, N. J. Hughes, K. K. Koretke, M. A. Lonetto, K. K. Brinkman, P. V. Warren, A. Lupas, M. J. Stanhope, J. R. Brown, and P. S. Hoffman. 2001. Systematic identification of selective essential genes in Helicobacter pylori by genome prioritization and allelic replacement mutagenesis. J. Bacteriol. 183:1259-1268.
4. Chevalier, C., J. M. Thiberge, R. L. Ferrero, and A. Labigne. 1999. Essential role of Helicobacter pylori gamma-glutamyltranspeptidase for the colonization of the gastric mucosa of mice. Mol. Microbiol. 31:1359-1372.
5. Chirica, L. C., C. Petersson, M. Hurtig, B. H. Jonsson, T. Boren, and S. Lindskog. 2002. Expression and localization of alpha- and beta-carbonic anhydrase in Helicobacter pylori. Biochim. Biophys. Acta 1601:192-199.
6. Copeland, R. A., J. Marcinkeviciene, T. S. Haque, L. M. Kopcho, W. Jiang, K. Wang, L. D. Ecret, C. Sizemore, K. A. Amsler, L. Foster, S. Tadesse, A. P. Combs, A. M. Stern, G. L. Trainor, A. Slee, M. J. Rogers, and F. Hobbs. 2000. Helicobacter pylori-selective antibacterials based on inhibition of pyrimidine biosynthesis. J. Biol. Chem. 275:33373-33378.
7. De Reuse, H., A. Labigne, and D. Mengin-Lecreulx. 1997. The Helicobacter pylori ureC gene codes for a phosphoglucosamine mutase. J. Bacteriol. 179:3488-3493.
8. Duarte, N. C., M. J. Herrgard, and B. Palsson. 2004. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. Genome Res. 14:1298-1309.
9. Edwards, J. S., R. Ramakrishna, C. H. Schilling, and B. O. Palsson. 1999. Metabolic flux balance analysis, p. 13-57. In S. Y. Lee and E. T. Papoutsakis (ed.), Metabolic engineering. Marcel Dekker, Inc., New York, N.Y.
10. Fassbinder, F., M. Kist, and S. Bereswill. 2000. Structural and functional analysis of the riboflavin synthesis genes encoding GTP cyclohydrolase II (ribA), DHBP synthase (ribBA), riboflavin synthase (ribC), and riboflavin deaminase/reductase (ribD) from Helicobacter pylori strain P1. FEMS Microbiol. Lett. 191:191-197.
11. Garner, R. M., J. Fulkerson, Jr., and H. L. T. Mobley. 1998. Helicobacter pylori glutamine synthetase lacks features associated with transcriptional and posttranslational regulation. Infect. Immun. 66:1839-1847.
12. Ge, Z., Q. Jiang, M. S. Kalisiak, and D. E. Taylor. 1997. Cloning and functional characterization of Helicobacter pylori fumarate reductase operon comprising three structural genes coding for subunits C, A and B. Gene 204:227-234.
13. Harris, A. G., F. E. Hinds, A. G. Beckhouse, T. Kolesnikow, and S. L. Hazell. 2002. Resistance to hydrogen peroxide in Helicobacter pylori: role of catalase (KatA) and Fur, and functional analysis of a novel gene product designated 'KatA-associated protein', KapA (HP0874). Microbiology 148:3813-3825.
14. Hazell, S. L., and G. L. Mendz. 1997. How Helicobacter pylori works: an overview of the metabolism of Helicobacter pylori. Helicobacter 2:1-12.
15. Hirai, Y., M. Haque, T. Yoshida, K. Yokota, T. Yasuda, and K. Oguma. 1995. Unique cholesteryl glucosides in Helicobacter pylori: composition and structural analysis. J. Bacteriol. 177:5327-5333.
16. Hughes, N. J., C. L. Clayton, P. A. Chalk, and D. J. Kelly. 1998. Helicobacter pylori porCDAB and oorDABC genes encode distinct pyruvate:flavodoxin and 2-oxoglutarate:acceptor oxidoreductases which mediate electron transport to NADP. J. Bacteriol. 180:1119-1128.
17. Hughes, N. J., D. J. Kelly, A. A. Davison, P. A. Chalk, and C. L. Clayton. 1995. Characterisation of Helicobacter pylori pyruvate:flavodoxin oxidoreductase. Gut 37:A18.
18. Jenks, P. J., C. Chevalier, C. Ecobichon, and A. Labigne. 2001. Identification of nonessential Helicobacter pylori genes using random mutagenesis and loop amplification. Res. Microbiol. 152:725-734.
19. Kanehisa, M. 1997. A database for post-genome analysis. Trends Genet. 13:375-376.
20. Kanehisa, M., and S. Goto. 2000. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res. 28:27-30.
21. Karita, M., M. L. Etterbeek, M. H. Forsyth, M. K. R. Tummuru, and M. J. Blaser. 1997. Characterization of Helicobacter pylori dapE and construction of a conditionally lethal dapE mutant. Infect. Immun. 65:4158-4164.
22. Kauffman, K. J., P. Prakash, and J. S. Edwards. 2003. Advances in flux balance analysis. Curr. Opin. Biotechnol. 14:491-496.
23. Kelly, D. J. 1998. The physiology and metabolism of the human gastric pathogen Helicobacter pylori. Adv. Microb. Physiol. 40:137-189.
24. Kwon, D. H., J. S. Woo, C. L. Perng, M. F. Go, D. Y. Graham, and F. A. El-Zaatari. 1998. The effect of galE gene inactivation on lipopolysaccharide profile of Helicobacter pylori. Curr. Microbiol. 37:144-148.
25. Marais, A., G. L. Mendz, S. L. Hazell, and F. Mégraud. 1999. Metabolism and genetics of Helicobacter pylori: the genome era. Microbiol. Mol. Biol. Rev. 63:642-674.
26. McGee, D. J., F. J. Radcliff, G. L. Mendz, R. L. Ferrero, and H. L. T. Mobley. 1999. Helicobacter pylori rocF is required for arginase activity and acid protection in vitro but is not essential for colonization of mice or for urease activity. J. Bacteriol. 181:7314-7322.
27. Mendz, G. L., B. P. Burns, and S. L. Hazell. 1995. Characterisation of glucose transport in Helicobacter pylori. Biochim. Biophys. Acta 1244:269-276.
28. Mendz, G. L., and S. L. Hazell. 1995. Aminoacid utilization by Helicobacter pylori. Int. J. Biochem. Cell Biol. 27:1085-1093.
29. Mendz, G. L., and S. L. Hazell. 1991. Evidence for a pentose phosphate pathway in Helicobacter pylori. FEMS Microbiol. Lett. 84:331-336.
30. Mendz, G. L., S. L. Hazell, and B. P. Burns. 1994. The Entner-Doudoroff pathway in Helicobacter pylori. Arch. Biochem. Biophys. 312:349-356.
31. Mendz, G. L., S. L. Hazell, and B. P. Burns. 1993. Glucose utilization and lactate production by Helicobacter pylori. J. Gen. Microbiol. 139:3023-3028.
32. Mendz, G. L., S. L. Hazell, and L. van Gorkom. 1994. Pyruvate metabolism in Helicobacter pylori. Arch. Microbiol. 162:187-192.
33. Mobley, H. L. T., G. L. Mendz, and S. L. Hazell. 2001. Helicobacter pylori: physiology and genetics. ASM Press, Washington, D.C.
34. Nedenskov, P. 1994. Nutritional requirements for growth of Helicobacter pylori. Appl. Environ. Microbiol. 60:3450-3453.
35. Neidhardt, F. C., J. L. Ingraham, and M. Schaechter. 1990. Physiology of the bacterial cell. Sinauer Associates, Inc., Sunderland, Mass.
36. Pitson, S. M., G. L. Mendz, S. Srinivasan, and S. L. Hazell. 1999. The tricarboxylic acid cycle of Helicobacter pylori. Eur. J. Biochem. 260:258-267.
37. Reed, J. L., T. D. Vo, C. H. Schilling, and B. O. Palsson. 2003. An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR). Genome Biol. 4:R54.1-R54.12.
38. Reynolds, D. J., and C. W. Penn. 1994. Characteristics of Helicobacter pylori growth in a defined medium and determination of its amino acid requirements. Microbiology 140:2649-2656.
39. Schilling, C. H., M. W. Covert, I. Famili, G. M. Church, J. S. Edwards, and B. O. Palsson. 2002. Genome-scale metabolic model of Helicobacter pylori 26695. J. Bacteriol. 184:4582-4593.
40. Seyler, R. W., Jr., J. W. Olson, and R. J. Maier. 2001. Superoxide dismutase-deficient mutants of Helicobacter pylori are hypersensitive to oxidative stress and defective in host colonization. Infect. Immun. 69:4034-4040.
41. Skouloubris, S., J.-M. Thiberge, A. Labigne, and H. De Reuse. 1998. The Helicobacter pylori UreI protein is not involved in urease activity but is essential for bacterial survival in vivo. Infect. Immun. 66:4517-4521.
42. Stingl, K., E.-M. Uhlemann, G. Deckers-Hebestreit, R. Schmid, E. P. Bakker, and K. Altendorf. 2001. Prolonged survival and cytoplasmic pH homeostasis of Helicobacter pylori at pH 1. Infect. Immun. 69:1178-1181.
43. Stoner, G. L., and M. A. Eisenberg. 1975. Purification and properties of 7, 8-diaminopelargonic acid aminotransferase. J. Biol. Chem. 250:4029-4036.
44. Tomb, J. F., O. White, A. R. Kerlavage, R. A. Clayton, G. G. Sutton, R. D. Fleischmann, K. A. Ketchum, H. P. Klenk, S. Gill, B. A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E. F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H. G. Khalak, A. Glodek, K. McKenney, L. M. Fitzegerald, N. Lee, M. D. Adams, E. K. Hickey, D. E. Berg, J. D. Gocayne, T. R. Utterback, J. D. Peterson, J. M. Kelley, M. D. Cotton, J. M. Weidman, C. Fujii, C. Bowman, L. Watthey, E. Wallin, W. S. Hayes, M. Borodovsky, P. D. Karp, H. O. Smith, C. M. Fraser, and J. C. Venter. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388:539-547.
45. Varma, A., B. W. Boesch, and B. O. Palsson. 1993. Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates. Appl. Environ. Microbiol. 59:2465-2473.
46. Varma, A., and B. O. Palsson. 1995. Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism. Biotechnol. Bioeng. 45:69-79.
47. Vo, T. D., H. J. Greenberg, and B. O. Palsson. 2004. Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data. J. Biol. Chem. 279:39532-39540.
48. Waidner, B., S. Greiner, S. Odenbreit, H. Kavermann, J. Velayudhan, F. Stähler, J. Guhl, E. Bissé, A. H. M. van Vliet, S. C. Andrews, J. G. Kusters, D. J. Kelly, R. Haas, M. Kist, and S. Bereswill. 2002. Essential role of ferritin Pfr in Helicobacter pylori iron metabolism and gastric colonization. Infect. Immun. 70:3923-3929.
49. Wanken, A. E., T. Conway, and K. A. Eaton. 2003. The Entner-Doudoroff pathway has little effect on Helicobacter pylori colonization of mice. Infect. Immun. 71:2920-2923.
50. Worst, D. J., M. M. Gerrits, C. M. J. E. Vandenbroucke-Grauls, and J. G. Kusters. 1998. Helicobacter pylori ribBA-mediated riboflavin production is involved in iron acquisition. J. Bacteriol. 180:1473-1479.