Computational prediction and experimental verification of the gene encoding the NAD+/NADP+-dependent succinate semialdehyde dehydrogenase in Escherichia coli

Journal of Bacteriology

Volumn 189, Issue 22, 2007, Pages 8073-8078

  Fuhrer, Tobias ^a   Chen, Lifeng ^b   Sauer, Uwe ^a   Vitkup, Dennis ^b  

^a ETH ZURICH   (Switzerland)

^b Och Spine at New York Presbyterian Hospitals   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; NITROGEN; PUTRESCINE; SUCCINATE SEMIALDEHYDE DEHYDROGENASE [NAD(P)];

ARTICLE; BACTERIAL GENE; BACTERIAL GROWTH; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE EXPRESSION; NITROGEN METABOLISM; NONHUMAN; PREDICTIVE VALIDITY; PRIORITY JOURNAL; YNEI GENE;

COMPUTER SIMULATION; ESCHERICHIA COLI; GENE DELETION; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; SUCCINATE-SEMIALDEHYDE DEHYDROGENASE;

ESCHERICHIA COLI;

EID: 36549066706     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01027-07     Document Type: Article

References (47)

1. Andrade, M. A., N. P. Brown, C. Leroy, S. Hoersch, A. de Daruvar, C. Reich, A. Franchini, J. Tamames, A. Valencia, C. Ouzounis, and C. Sander. 1999. Automated genome sequence analysis and annotation. Bioinformatics 15: 391-412.
2. Baba, T., T. Ara, M. Hasegawa, Y. Takai, Y. Okumura, M. Baba, K. A. Datsenko, M. Tomita, B. L. Wanner, and H. Mori. 2006. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2:2006.0008.
3. Ball, C. A., J. A. Awad, J. Demeter, J. Gollub, J. M. Hebert, T. Hernandez-Boussard, H. Jin, J. C. Matese, M. Nitzberg, F. Wymore, Z. K. Zachariah, P. O. Brown, and G. Sherlock. 2005. The Stanford Microarray Database accommodates additional microarray platforms and data formats. Nucleic Acids Res. 33:D580-D582.
4. Bork, P., L. J. Jensen, C. von Mering, A. K. Ramani, I. Lee, and E. M. Marcotte. 2004. Protein interaction networks from yeast to human. Curr. Opin. Struct. Biol. 14:292-299.
5. Bowers, P. M., M. Pellegrini, M. J. Thompson, J. Fierro, T. O. Yeates, and D. Eisenberg. 2004. Prolinks: a database of protein functional linkages derived from coevolution. Genome Biol. 5:R35.
6. Cash, C. D., M. Maitre, L. Ossola, and P. Mandel. 1978. Purification and properties of two succinate semialdehyde dehydrogenases from human brain. Biochim. Biophys. Acta 524:26-36.
7. Chattopadhyay, M. K., C. W. Tabor, and H. Tabor. 2006. Polyamine deficiency leads to accumulation of reactive oxygen species in a spe2Delta mutant of Saccharomyces cerevisiae. Yeast 23:751-761.
8. Chen, L., and D. Vitkup. 2007. Distribution of orphan metabolic activities. Trends Biotechnol. 25:343-348.
9. Chen, L. F., and D. Vitkup. 2006. Predicting genes for orphan metabolic activities using phylogenetic profiles. Genome Biol. 7:R17.
10. Datsenko, K. A., and B. L. Wanner. 2000. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl. Acad. Sci. USA 97:6640-6645.
11. Davis, R. H., D. R. Morris, and P. Coffino. 1992. Sequestered end products and enzyme regulation: the case of ornithine decarboxylase. Microbiol. Rev. 56:280-290.
12. Donnelly, M. I., and R. A. Cooper. 1981. Succinic semialdehyde dehydrogenases of Escherichia coli: their role in the degradation of p-hydroxyphenylacetate and gamma-aminobutyrate. Eur. J. Biochem. 113:555-561.
13. Donnelly, M. I., and R. A. Cooper. 1981. Two succinic semialdehyde dehydrogenases are induced when Escherichia coli K-12 is grown on gamma-aminobutyrate. J. Bacteriol. 145:1425-1427.
14. Dover, S., and Y. S. Halpern. 1972. Utilization of gamma-aminobutyric acid as the sole carbon and nitrogen source by Escherichia coli K-12 mutants. J. Bacteriol. 109:835-843.
15. Eisenberg, D., E. M. Marcotte, I. Xenarios, and T. O. Yeates. 2000. Protein function in the post-genomic era. Nature 405:823-826.
16. Enright, A. J., I. Iliopoulos, N. C. Kyrpides, and C. A. Ouzounis. 1999. Protein interaction maps for complete genomes based on gene fusion events. Nature 402:86-90.
17. Faith, J. J., B. Hayete, J. T. Thaden, I. Mogno, J. Wierzbowski, G. Cottarel, S. Kasif, J. J. Collins, and T. S. Gardner. 2007. Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol. 5:e8.
18. Freund, Y., and R. E. Schapire. 1999. A short introduction to Boosting. J. Jpn. Soc. Artif. Intelligence 14:771-780.
19. Gornall, A., W. Bardawill, and M. David. 1949. Determinations of serum proteins by means of the Biuret reaction. J. Biol. Chem. 177:751-766.
20. He, Y., K. Kashiwagi, J. Fukuchi, K. Terao, A. Shirahata, and K. Igarashi. 1993. Correlation between the inhibition of cell growth by accumulated polyamines and the decrease of magnesium and ATP. Eur. J. Biochem. 217:89-96.
21. Heinemann, M., A. Kummel, R. Ruinatscha, and S. Panke. 2005. In silico genome-scale reconstruction and validation of the Staphylococcus aureus metabolic network. Biotechnol. Bioeng. 92:850-864.
22. Jakoby, W. B., and E. M. Scott. 1959. Aldehyde oxidation. III. Succinic semialdehyde dehydrogenase. J. Biol. Chem. 234:937-940.
23. Jansen, R., H. Yu, D. Greenbaum, Y. Kluger, N. J. Krogan, S. Chung, A. Emili, M. Snyder, J. F. Greenblatt, and M. Gerstein. 2003. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 302:449-453.
24. Karp, P. D. 2004. Call for an enzyme genomics initiative. Genome Biol. 5:401.
25. Kharchenko, P., L. Chen, Y. Freund, D. Vitkup, and G. M. Church. 2006. Identifying metabolic enzymes with multiple types of association evidence. BMC Bioinformatics 7:177.
26. Kharchenko, P., G. M. Church, and D. Vitkup. 2005. Expression dynamics of a cellular metabolic network. Mol. Syst. Biol. 1:2005.0016.
27. Kharchenko, P., D. Vitkup, and G. M. Church. 2004. Filling gaps in a metabolic network using expression information. Bioinformatics 20(Suppl. 1):I178-I185.
28. Kitagawa, M., T. Ara, M. Arifuzzaman, T. Ioka-Nakamichi, E. Inamoto, H. Toyonaga, and H. Mori. 2005. Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12:291-299.
29. Kuepfer, L., U. Sauer, and L. M. Blank. 2005. Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res. 15:1421-1430.
30. Kurihara, S., S. Oda, K. Kato, H. G. Kim, T. Koyanagi, H. Kumagai, and H. Suzuki. 2005. A novel putrescine utilization pathway involves gamma-glutamylated intermediates of Escherichia coli K-12. J. Biol. Chem. 280:4602-4608.
31. Lespinet, O., and B. Labedan. 2005. Orphan enzymes? Science 307:42.
32. Marek, L. E., and J. M. Henson. 1988. Cloning and expression of the Escherichia coli K-12 sad gene. J. Bacteriol. 170:991-994.
33. Markowitz, V. M., F. Korzeniewski, K. Palaniappan, E. Szeto, G. Werner, A. Padki, X. Zhao, I. Dubchak, P. Hugenholtz, I. Anderson, A. Lykidis, K. Mavromatis, N. Ivanova, and N. C. Kyrpides. 2006. The integrated microbial genomes (IMG) system. Nucleic Acids Res. 34:D344-D348.
34. Misra, R. V., R. S. Horler, W. Reindl, I. I. Goryanin, and G. H. Thomas. 2005. EchoBASE: an integrated post-genomic database for Escherichia coli. Nucleic Acids Res. 33:D329-D333.
35. Overbeek, R., M. Fonstein, M. D'Souza, G. D. Pusch, and N. Maltsev. 1999. The use of gene clusters to infer functional coupling. Proc. Natl. Acad. Sci. USA 96:2896-2901.
36. 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.
37. Rost, B. 2002. Enzyme function less conserved than anticipated. J. Mol. Biol. 318:595-608.
38. Samsonova, N. N., S. V. Smirnov, A. E. Novikova, and L. R. Ptitsyn. 2005. Identification of Escherichia coli K12 YdcW protein as a gamma-aminobutyraldehyde dehydrogenase. FEBS Lett. 579:4107-4112.
39. Schneider, B. L., A. K. Kiupakis, and L. J. Reitzer. 1998. Arginine catabolism and the arginine succinyltransferase pathway in Escherichia coli. J. Bacteriol. 180:4278-4286.
40. Schneider, B. L., S. Ruback, A. K. Kiupakis, H. Kasbarian, C. Pybus, and L. Reitzer. 2002. The Escherichia coli gabDTPC operon: specific gamma-aminobutyrate catabolism and nonspecific induction. J. Bacteriol. 184:6976-6986.
41. Skinner, M. A., and R. A. Cooper. 1982. An Escherichia coli mutant defective in the NAD-dependent succinate semialdehyde dehydrogenase. Arch. Microbiol. 132:270-275.
42. Tabor, C. W., and H. Tabor. 1985. Polyamines in microorganisms. Microbiol. Rev. 49:81-99.
43. Tian, W., and J. Skolnick. 2003. How well is enzyme function conserved as a function of pairwise sequence identity? J. Mol. Biol. 333:863-582.
44. von Mering, C., L. J. Jensen, B. Snel, S. D. Hooper, M. Krupp, M. Foglierini, N. Jouffre, M. A. Huynen, and P. Bork. 2005. STRING: known and predicted protein-protein associations, integrated and transferred across organisms. Nucleic Acids Res. 33:D433-D437.
45. Wilson, C. A., J. Kreychman, and M. Gerstein. 2000. Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores. J. Mol. Biol. 297:233-249.
46. Yanai, I., A. Derti, and C. DeLisi. 2001. Genes linked by fusion events are generally of the same functional category, a systematic analysis of 30 microbial genomes. Proc. Natl. Acad. Sci. USA 98:7940-7945.
47. Zimmer, D. P., E. Soupene, H. L. Lee, V. F. Wendisch, A. B. Khodursky, B. J. Peter, R. A. Bender, and S. Kustu. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc. Natl. Acad. Sci. USA 97:14674-14679.