Reconstruction of central carbon metabolism in Sulfolobus solfataricus using a two-dimensional gel electrophoresis map, stable isotope labelling and DNA microarray analysis

Proteomics

Volumn 6, Issue 5, 2006, Pages 1518-1529

  Snijders, Ambrosius P L ^a   Walther, Jasper ^b   Peter, Stefan ^a   Kinnman, Iris ^a   De Vos, Marjon G J ^a,b   Van De Werken, Harmen J G ^b   Brouns, Stan J J ^b   Van Der Oost, John ^b   Wright, Phillip C ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

^b WAGENINGEN UNIVERSITY   (Netherlands)

Author keywords

Archaea; DNA microarray; Glycolysis; Mass spectrometry; Metabolic labelling

Indexed keywords

NITROGEN 15; TRANSCRIPTOME;

ARTICLE; CARBON METABOLISM; CHEMICAL ANALYSIS; CITRIC ACID CYCLE; DNA DETERMINATION; DNA MICROARRAY; GENE SEQUENCE; GENETIC ANALYSIS; GENOMICS; GLUCONEOGENESIS; GLYCOLYSIS; ISOTOPE LABELING; NONHUMAN; PRIORITY JOURNAL; PROTEOMICS; SULFOLOBUS SOLFATARICUS; TWO DIMENSIONAL GEL ELECTROPHORESIS; YEAST;

ARCHAEAL PROTEINS; CARBON; ELECTROPHORESIS, GEL, TWO-DIMENSIONAL; GENE EXPRESSION PROFILING; ISOTOPES; MASS SPECTROMETRY; MOLECULAR SEQUENCE DATA; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SULFOLOBUS SOLFATARICUS;

ARCHAEA; SULFOLOBUS SOLFATARICUS;

EID: 33645062395     PISSN: 16159853     EISSN: 16159861     Source Type: Journal    
DOI: 10.1002/pmic.200402070     Document Type: Article

References (74)

1. Zillig, W., Stetter, K. O., Wunderl, S., Schulz, W., Priess, H. et al., Arch. Microbiol. 1980, 125, 259-269.
2. She, Q., Singh, R. K., Confalonieri, F., Zivanovic, Y., Allard, G. et al., Proc. Natl. Acad. Sci. USA 2001, 98, 7835-7840.
3. Peterson, J. D., Umayam, L. A., Dickinson, T., Mickey, E. K., White, O., Nucleic Acids Res. 2001, 29, 123-125.
4. Cannio, R., Contursi, P., Rossi, M., Bartolucci, S., Extremophiles 2001, 5, 153-159.
5. Stedman, K. M., Schleper, C., Rumpf, E., Zillig, W., Genetics 1999, 152, 1397-1405.
6. Worthington, P., Hoang, V., Perez-Pomares, F., Blum, P., J. Bacteriol. 2003, 185, 482-488.
7. Jonuscheit, M., Martusewitsch, E., Stedman, K. M., Schleper, C., Mol. Microbiol. 2003, 48, 1241-1252.
8. Contursi, P., Cannio, R., Prato, S., Fiorentino, G., Rossi, M. et al., FEMS Microbiol. Lett. 2003, 218, 115-120.
9. Verhees, C. H., Kengen, S. W., Tuininga, J. E., Schut, G. J., Adams, M. W. et al., Biochem. J. 2003, 375, 231-246.
10. Adams, M. W. W., Holden, J. F., Menon, A. L., Schut, G. J., Grunden, A. M. et al., J. Bacteriol. 2001, 183, 716-724.
11. Schonheit, P., Schafer, T., World J. Microbiol. Biotechnol. 1995, 11, 26-57.
12. Schafer, G., Biochim. Biophys. Acta 1996, 1277, 163-200.
13. De Rosa, M., Gambacorta, A., Nicolaus, B., Giardina, P., Poerio, E. et al., Biochem. J. 1984, 224, 407-414.
14. Ahmed, H., Ettema, T. J. G., Tjaden, B., Geerling, A. C. M., van der Oost, J. et al., Biochem. J. 2005, 390, 529-540.
15. Lamble, H. J., Heyer, N. I., Bull, S. D., Hough, D. W., Danson, M. J., J. Biol. Chem. 2003, 278, 34066-34072.
16. Lamble, H. J., Heyer, N. I., Bull, S. D., Hough, D. W., Danson, M. J., J. Biol. Chem. 2003, 278, 34066-34072.
17. Schut, G. J., Brehm, S. D., Datta, S., Adams, M. W., J. Bacteriol. 2003, 185, 3935-3947.
18. Zaigler, A., Schuster, S. C., Soppa, J., Mol. Microbiol. 2003, 48, 1089-1105.
19. Snijders, A. P., de Vos, M. G., Wright, P. C., J. Proteome Res. 2005, 4, 578-585.
20. Pappin, D. J., Hojrup, P., Bleasby, A. J., Curr. Biol. 1993, 3, 327-332.
21. Brinkman, A. B., Bell, S. D., Lebbink, R. J., de Vos, W. M., van der Oost, J., J. Biol. Chem. 2002, 277, 29537-29549.
22. Lundgren, M., Andersson, A., Chen, L., Nilsson, P., Bernander, R., Proc. Natl. Acad. Sci. USA 2004, 101, 7046-7051.
23. Andersson, A., Bernander, R., Nilsson, P., Bioinformatics 2005, 21, 325-332.
24. Tusher, V. G., Tibshirani, R., Chu, G., Proc. Natl. Acad. Sci. USA 2001, 98, 5116-5121.
25. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z. et al., Nucleic Acids Res. 1997, 25, 3389-3402.
26. Schomburg, I., Chang, A., Ebeling, C., Gremse, M., Heldt, C. et al., Nucleic Acids Res. 2004, 32, D431-D433.
27. Tatusov, R. L., Fedorova, N. D., Jackson, J. D., Jacobs, A. R., Kiryutin, B. et al., BMC Bioinformatics2003, 4: 41.
28. Mulder, N. J., Apweiler, R., Attwood, T. K., Bairoch, A., Bateman, A. et al., Nucleic Acids Res. 2005, 33, D201-D205.
29. Overbeek, R., Larsen, N., Walunas, T., D'Souza, M., Pusch, G. et al., Nucleic Acids Res. 2003, 31, 164-171.
30. Huynen, M. A., Dandekar, T., Bork, P., Trends Microbiol. 1999, 7, 281-291.
31. Ronimus, R. S., Morgan, H. W., Archaea 2003, 1, 199-221.
32. Kanehisa, M., Goto, S., Kawashima, S., Okuno, Y., Hattori, M., Nucleic Acids Res. 2004, 32, D277-D280.
33. Giometti, C. S., Reich, C., Tollaksen, S., Babnigg, G., Lim, H. et al., J. Chromatogr. B Analyt. Technol. Biomed. Life Sci. 2002, 782, 227-243.
34. Snijders, A. P. L., de Vos, M. G., Koning, B., Wright, P. C., Electrophoresis 2005, 26, 3191-3199.
35. Elferink, M. G., Albers, S. V., Konings, W. N., Driessen, A. J., Mol. Microbiol. 2001, 39, 1494-1503.
36. Danson, M. J., Adv. Microb. Physiol. 1988, 29, 165-231.
37. Kawarabayasi, Y., Hino, Y., Horikawa, H., Jin-no, K., Takahashi, M. et al., DNA Res. 2001, 8, 123-140.
38. Selig, M., Xavier, K. B., Santos, H., Schonheit, P., Arch. Microbiol. 1997, 167, 217-232.
39. Skorko, R., Osipiuk, J., Stetter, K. O., J. Bacteriol. 1989, 171, 5162-5164.
40. Satory, M., Furlinger, M., Haltrich, D., Kulbe, K. B., Pittner, F. et al., Biotechnol. Lett. 1997, 19, 1205-1208.
41. Brock, T. D., Brock, K. M., Belly, R. T., Weiss, R. L., Arch. Microbiol. 1972, 84, 54-68.
42. Danson, M. J., Black, S. C., Woodland, D. L., Wood, P. A., FEBS 1985, 179, 120-124.
43. Sako, Y., Takai, K., Uchida, A., Ishida, Y., FEBS Lett. 1996, 392, 148-152.
44. Ettema, T. J., Makarova, K. S., Jellema, G. L., Gierman, H. J., Koonin, E. V. et al., J. Bacteriol. 2004, 186, 7754-7762.
45. Uhrigshardt, H., Walden, M., John, H., Anemuller, S., Eur. J. Biochem. 2001, 268, 1760-1771.
46. Uhrigshardt, H., Walden, M., John, H., Petersen, A., Anemuller, S., FEBS Lett. 2002, 513, 223-229.
47. Bartolucci, S., Rella, R., Guagliardi, A., Raia, C. A., Gambacorta, A. et al., J. Biol. Chem. 1987, 262, 7725-7731.
48. Fukuda, W., Fukui, T., Atomi, H., Imanaka, T., J. Bacteriol. 2004, 186, 4620-4627.
49. Kerscher, L., Nowitzki, S., Oesterhelt, D., Eur. J. Biochem. 1982, 128, 223-230.
50. Zhang, Q., Iwasaki, T., Wakagi, T., Oshima, T., J. Biochem. (Tokyo) 1996, 120, 587-599.
51. Fukuda, E., Wakagi, T., Biochim. Biophys Acta 2002, 1597, 74-80.
52. Russo, A. D., Rullo, R., Masullo, M., Ianniciello, G., Arcari, P. et al., Biochem. Mol. Biol. Int. 1995, 36, 123-135.
53. Camacho, M. L., Brown, R. A., Bonete, M. J., Danson, M. J., Hough, D. W., FEMS Microbiol Lett. 1995, 134, 85-90.
54. Hartl, T., Grossebuter, W., Gorisch, H., Stezowski, J. J., Biol. Chem. Hoppe Seyler 1987, 368, 259-267.
55. Kim, S., Lee, S. B., Biochem. J. 2005, 387, 271-280.
56. Lamble, H. J., Milburn, C. C., Taylor, G. L., Hough, D. W., Danson, M. J., FEBS Lett. 2004, 576, 133-136.
57. Buchanan, C. L., Connaris, H., Danson, M. J., Reeve, C. D., Hough, D. W., Biochem. J. 1999, 343, 563-570.
58. Brunner, N. A., Brinkmann, H., Siebers, B., Hensel, R., J. Biol. Chem. 1998, 273, 6149-6156.
59. Kardinahl, S., Schmidt, C. L., Hansen, T., Anemuller, S., Petersen, A. et al., Eur. J. Biochem. 1999, 260, 540-548.
60. Schramm, A., Siebers, B., Tjaden, B., Brinkmann, H., Hensel, R., J. Bacteriol. 2000, 182, 2001-2009.
61. van der Oost, J., Huynen, M. A., Verhees, C. H., FEMS Microbiol. Lett. 2002, 212, 111-120.
62. Peak, M. J., Peak, J. G., Stevens, F. J., Blamey, J., Mai, X. et al., Arch. Biochem. Biophys. 1994, 313, 280-286.
63. Hutchins, A. M., Holden, J. F., Adams, M. W., J. Bacteriol. 2001, 183, 709-715.
64. Hess, D., Kruger, K., Knappik, A., Palm, P., Hensel, R., Eur. J. Biochem. 1995, 233, 227-237.
65. Kohlhoff, M., Dahm, A., Hensel, R., FEBS Lett. 1996, 383, 245-250.
66. Siebers, B., Brinkmann, H., Dorr, C., Tjaden, B., Lilie, H. et al., J. Biol. Chem. 2001, 276, 28710-28718.
67. Nishimasu, H., Fushinobu, S., Shoun, H., Wakagi, T., Structure (Camb) 2004, 12, 949-959.
68. Hansen, T., Wendorff, D., Schonheit, P., J. Biol. Chem. 2004, 279, 2262-2272.
69. Solow, B., Bischoff, K. M., Zylka, M. J., Kennelly, P. J., Protein Sci. 1998, 7, 105-111.
70. Smith, L. D., Stevenson, K. J., Hough, D. W., Danson, M. J., FEBS Lett. 1987, 225, 277-281.
71. Lohlein-Werhahn, G., Goepfert, P., Eggerer, H., Biol. Chem. Hoppe Seyler 1988, 369, 109-113.
72. Janssen, S., Schafer, G., Anemuller, S., Moll, R., J. Bacteriol. 1997, 179, 5560-5569.
73. Puchegger, S., Redl, B., Stoffler, G., J. Gen. Microbiol. 1990, 136, 1537-1541.
74. Colombo, S., Grisa, M., Tortora, P., Vanoni, M., FEBS Lett. 1994, 337, 93-98.