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Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays

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Abstract

DNA microarray technology has become an important research tool for biotechnology and microbiology. It is now possible to characterize genetic diversity and gene expression in a genomewide manner. DNA microarrays have been applied extensively to study the biology of many bacteria including Escherichia coli, but only recently have they been developed for the Grampositive Corynebacterium glutamicum. Both bacteria are widely used for biotechnological amino acid production. In this article, in addition to the design and generation of microarrays as well as their use in hybridization experiments and subsequent data analysis, we describe recent applications of DNA microarray technology regarding amino acid production in C. glutamicum and E. coli. We also discuss the impact of functional genomics studies on fundamental as well as applied aspects of amino acid production with C. glutamicum and E. coli.

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References

  1. Eggeling, L., Pfefferle, W., and Sahm, H. (2001), in Basic Biotechnology, Ratledge, C., ed., Cambridge University Press, Cambridge, UK, pp. 281–302.

    Google Scholar 

  2. Swartz, J. R. (2001), Curr. Opin. Biotechnol. 12(2), 195–201.

    Article  PubMed  CAS  Google Scholar 

  3. Nakamura, C. E., Gatenby, A. A., Hsu, A. K.-H., et al. (2000), US patent 6,013,494.

  4. Altaras, N. E. and Cameron, D. C. (1999), Appl. Environ. Microbiol. 65(3), 1180–1185.

    PubMed  CAS  Google Scholar 

  5. Donnelly, M. I., Millard, C. S., Clark, D. P., Chen, M. J., and Rathke, J. W. (1998), Appl. Biochem. Biotechnol. 70–72, 187–198.

    PubMed  Google Scholar 

  6. Vemuri, G. N., Eiteman, M. A., and Altman, E. (2002), J. Industrial Microbiol. Biotechnol. 28(6), 325–332.

    Article  CAS  Google Scholar 

  7. Chang, D. E., Jung, H. C., Rhee, J. S., and Pan, J. G. (1999), Appl. Environ. Microbiol. 65(4), 1384–1389.

    PubMed  CAS  Google Scholar 

  8. Zhou, S., Causey, T. B., Hasona, A., Shanmugam, K. T., and Ingram, L. O. (2003), Appl. Environ. Microbiol. 69(1), 399–407.

    Article  PubMed  CAS  Google Scholar 

  9. Underwood, S. A., Zhou, S., Causey, T. B., Yomano, L. P., Shanmugam, K. T., and Ingram, L. O. (2002), Appl. Environ. Microbiol. 68(12), 6263–6272.

    Article  PubMed  CAS  Google Scholar 

  10. Niu, W., Draths, K. M., and Frost, J. W. (2002), Biotechnol. Prog. 18(2), 201–211.

    Article  PubMed  CAS  Google Scholar 

  11. Sahm, H., Eggeling, L., Eikmanns, B., and Kramer, R. (1996), Ann. NY Acad. Sci. 782, 25–39.

    Article  PubMed  CAS  Google Scholar 

  12. Sahm, H., Eggeling, L., and de Graaf, A. A. (2000), Biol. Chem. 381(9–10), 899–910.

    Article  PubMed  CAS  Google Scholar 

  13. Tauch, A., Homann, I., Mormann, S., et al. (2002), J. Biotechnol. 95(1), 25–38.

    Article  PubMed  CAS  Google Scholar 

  14. Kalinowski, J., Bathe, B., Bartels, D., et al. (2003), J. Biotechnol. 104, 5–25.

    Article  PubMed  CAS  Google Scholar 

  15. Schena, M., Shalon, D., Davis, R. W., and Brown, P. O. (1995), Science 270(5235), 467–470.

    Article  PubMed  CAS  ADS  Google Scholar 

  16. Lockhart, D. J., Dong, H., Byrne, M. C., et al. (1996), Nat. Biotechnol. 14(13), 1675–1680.

    Article  PubMed  CAS  Google Scholar 

  17. Bernstein, J. A., Khodursky, A. B., Lin, P. H., Lin-Chao, S., and Cohen, S. N. (2002), Proc. Natl. Acad. Sci. USA 99(15), 9697–9702.

    Article  PubMed  CAS  ADS  Google Scholar 

  18. Pedersen, S., Bloch, P. L., Reeh, S., and Neidhardt, F. C. (1978), Cell 14(1), 179–190.

    Article  PubMed  CAS  Google Scholar 

  19. Ficarro, S. B., McCleland, M. L., Stukenberg, P. T., Burke, D. J., Ross, M. M., Shabanowitz, J., Hunt, D. F., and White, F. M. (2002), Nat. Biotechnol. 20(3), 301–305.

    Article  PubMed  CAS  Google Scholar 

  20. Gavin, A. C., Bosche, M., Krause, R., et al. (2002), Nature 415(6868), 141–147.

    Article  PubMed  CAS  ADS  Google Scholar 

  21. Takizawa, P. A., DeRisi, J. L., Wilhelm, J. E., and Vale, R. D. (2000), Science 290(5490), 341–344.

    Article  PubMed  CAS  ADS  Google Scholar 

  22. Iyer, V. R., Horak, C. E., Scafe, C. S., Botstein, D., Snyder, M., and Brown, P. O. (2001), Nature, 409(6819), 533–538.

    Article  PubMed  CAS  ADS  Google Scholar 

  23. Zhu, H., Bilgin, M., Bangham, R., et al. (2001), Science 293(5537), 2101–2105.

    Article  PubMed  CAS  ADS  Google Scholar 

  24. Raamsdonk, L. M., Teusink, B., Broadhurst, D., et al. (2001), Nat. Biotechnol. 19(1), 45–50.

    Article  PubMed  CAS  Google Scholar 

  25. Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., and Gilles, E. D. (2002), Nature 420(6912), 190–193.

    Article  PubMed  CAS  ADS  Google Scholar 

  26. Lange, C., Rittmann, D., Wendisch, V. F., Bott, M., and Sahm, H. (2003), Appl. Environ. Microbiol. 69(5), 2521–2532.

    Article  PubMed  CAS  Google Scholar 

  27. Gygi, S. P., Rochon, Y., Franza, B. R., and Aebersold, R. (1999), Mol. Cell. Biol. 19(3), 1720–1730.

    PubMed  CAS  Google Scholar 

  28. Yoshida, K., Kobayashi, K., Miwa, Y., et al. (2001), Nucleic Acids Res. 29(3), 683–692.

    Article  PubMed  CAS  Google Scholar 

  29. Jurgen, B., Hanschke, R., Sarvas, M., Hecker, M., and Schweder, T. (2001), Appl. Microbiol. Biotechnol. 55(3), 326–332.

    Article  PubMed  CAS  Google Scholar 

  30. Yoon, S. H., Han, M. J., Lee, S. Y., Jeong, K. J., and Yoo, J. S. (2003), Biotechnol. Bioeng. 81(7), 753–767.

    Article  PubMed  CAS  Google Scholar 

  31. Peng, L. and Shimizu, K. (2003), Appl. Microbiol. Biotechnol. 61(2), 163–178.

    PubMed  CAS  Google Scholar 

  32. Rhodius, V., Van Dyk, T. K., Gross, C., and LaRossa, R. A. (2002), Annu. Rev. Microbiol. 56, 599–624.

    Article  PubMed  CAS  Google Scholar 

  33. Khodursky, A. B., and Bernstein, J. A. (2003), Trends Genet. 19(3), 113–115.

    Article  PubMed  CAS  Google Scholar 

  34. Conway, T. and Schoolnik, G. K. (2003), Mol. Microbiol. 47(4), 879–889.

    Article  PubMed  CAS  Google Scholar 

  35. Schoolnik, G. K. (2002), Adv. Microb. Physiol. 46, 1–45.

    PubMed  CAS  Google Scholar 

  36. Picataggio, S. K., Templeton, L. J., Smulski, D. R., and LaRossa, R. A. (2002), Methods Enzymol. 358, 177–188.

    Article  PubMed  CAS  Google Scholar 

  37. Ye, R. W., Wang, T., Bedzyk, L., and Croker, K. M. (2001), J. Microbiol. Methods 47(3), 257–272.

    Article  PubMed  CAS  Google Scholar 

  38. Hermann, T., Pfefferle, W., Baumann, C., et al. (2001), Electrophoresis 22(9), 1712–1723.

    Article  PubMed  CAS  Google Scholar 

  39. Schaffer, S., Weil, B., Nguyen, V. D., Dongmann, G., Gunther, K., Nickolaus, M., Hermann, T., and Bott, M. (2001), Electrophoresis 22(20), 4404–4422.

    Article  PubMed  CAS  Google Scholar 

  40. Liang, P. and Pardee, A. B. (1992), Science 257(5072), 967–971.

    Article  PubMed  CAS  ADS  Google Scholar 

  41. Velculescu, V. E., Zhang, L., Vogelstein, B., and Kinzler, K. W. (1995), Science 270(5235), 484–487.

    Article  PubMed  CAS  ADS  Google Scholar 

  42. Brenner, S., Johnson, M., Bridgham, J., et al. (2000), Nat. Biotechnol. 18(6), 630–634.

    Article  PubMed  CAS  ADS  Google Scholar 

  43. van Hal, N. L., Vorst, O., van Houwelingen, A. M., Kok, E. J., Peijnenburg, A., Aharoni, A., van Tunen, A. J., and Keijer, J. (2000), J. Biotechnol. 78(3), 271–280.

    Article  PubMed  Google Scholar 

  44. Hayward, R. E., Derisi, J. L., Alfadhli, S., Kaslow, D. C., Brown, P. O., and Rathod, P. K. (2000), Mol. Microbiol. 35(1), 6–14.

    Article  PubMed  CAS  Google Scholar 

  45. Rhodius, V. A. and LaRossa, R. A. (2003), Curr Opin Microbiol. 6(2), 114–119.

    Article  PubMed  CAS  Google Scholar 

  46. Khodursky, A. B., Bernstein, J. A., Peter, B. J., Rhodius, V., Wendisch, V. F., and Zimmer, D. P. (2003), Methods Mol. Biol. 224, 61–78.

    PubMed  CAS  Google Scholar 

  47. Muffler, A., Bettermann, S., Haushalter, M., Horlein, A., Neveling, U., Schramm, M., and Sorgenfrei, O. (2002), J. Biotechnol. 98(2–3), 255–268.

    Article  PubMed  CAS  Google Scholar 

  48. Ishige, T., Krause, M., Bott, M., Wendisch, V. F., and Sahm, H. (2003), J. Bacteriol. 185(15), 4519–4529.

    Article  PubMed  CAS  Google Scholar 

  49. Gerstmair, R., Wendisch, V. F., Schnicke, S., Ruan, H., Farwick, M., Reinscheid, D., and Eikmanns, B. J. (2003), J. Biotechnol. 104(1–3), 99–122.

    Article  CAS  Google Scholar 

  50. Tjaden, B., Haynor, D. R., Stolyar, S., Rosenow, C., and Kolker, E. (2002), Bioinformatics 18(Suppl. 1), S337-S344.

    PubMed  Google Scholar 

  51. Storz, G. (2002), Science 296(5571), 1260–1263.

    Article  PubMed  CAS  ADS  Google Scholar 

  52. DeRisi, J. L., Iyer, V. R., and Brown, P. O. (1997), Science 278(5338), 680–686.

    Article  PubMed  CAS  ADS  Google Scholar 

  53. Richmond, C. S., Glasner, J. D., Mau, R., Jin, H., and Blattner, F. R. (1999), Nucleic Acids Res. 27(19), 3821–3835.

    Article  PubMed  CAS  Google Scholar 

  54. Khodursky, A. B., Peter, B. J., Cozzarelli, N. R., Botstein, D., Brown, P. O., and Yanofsky, C. (2000), Proc. Natl. Acad. Sci. USA 97(22), 12,170–12,175.

    Article  CAS  Google Scholar 

  55. Zimmer, D. P., Soupene, E., Lee, H. L., Wendisch, V. F., Khodursky, A. B., Peter, B. J., Bender, R. A., and Kustu, S. (2000), Proc. Natl. Acad. Sci. USA 97(26), 14,674–14,679.

    Article  CAS  Google Scholar 

  56. Wei, Y., Lee, J. M., Richmond, C., Blattner, F. R., Rafalski, J. A., and LaRossa, R. A. (2001), J. Bacteriol. 183(2), 545–556.

    Article  PubMed  CAS  Google Scholar 

  57. Polen, T., Rittmann, D., Wendisch, V. F., and Sahm, H. (2003), Appl. Environ. Microbiol. 69(3), 1759–1774.

    Article  PubMed  CAS  Google Scholar 

  58. Wilson, M., DeRisi, J., Kristensen, H. H., Imboden, P., Rane, S., Brown, P. O., and Schoolnik, G. K. (1999), Proc. Natl. Acad. Sci. USA 96(22), 12,833–12,838.

    Article  CAS  Google Scholar 

  59. Oshima, T., Aiba, H., Masuda, Y., Kanaya, S., Sugiura, M., Wanner, B. L., Mori, H., and Mizuno, T. (2002), Mol. Microbiol. 46(1), 281–291.

    Article  PubMed  CAS  Google Scholar 

  60. de Saizieu, A., Certa, U., Warrington, J., Gray, C., Keck, W., and Mous, J. (1998), Nat. Biotechnol. 16(1), 45–48.

    Article  PubMed  Google Scholar 

  61. Loos, A., Glanemann, C., Willis, L. B., O’Brien, X. M., Lessard, P. A., Gerstmeir, R., Guillouet, S., and Sinskey, A. J. (2001), Appl. Environ. Microbiol. 67(5), 2310–2318.

    Article  PubMed  CAS  Google Scholar 

  62. Hayashi, M., Mizoguchi, H., Shiraishi, N., Obayashi, M., Nakagawa, S., Imai, J., Watanabe, S., Ota, T., and Ikeda, M. (2002), Biosci. Biotechnol. Biochem. 66(6), 1337–1344.

    Article  PubMed  CAS  Google Scholar 

  63. Wendisch, V. F., Zimmer, D. P., Khodursky, A., Peter, B., Cozzarelli, N., and Kustu, S. (2001), Anal Biochem. 290(2), 205–213.

    Article  PubMed  CAS  Google Scholar 

  64. Brazma, A., Parkinson, H., Sarkans, U., et al. (2003), Nucleic Acids Res. 31(1), 68–71.

    Article  PubMed  CAS  Google Scholar 

  65. Diehn, M., Sherlock, G., Binkley, G., et al. (2003), Nucleic Acids Res. 31(1), 219–223.

    Article  PubMed  CAS  Google Scholar 

  66. Gollub, J., Ball, C. A., Binkley, G., et al. (2003), Nucleic Acids Res. 31(1), 94–96.

    Article  PubMed  CAS  Google Scholar 

  67. Conway, T., Kraus, B., Tucker, D. L., Smalley, D. J., Dorman, A. F., and McKibben, L. (2002), Biotechniques 32(1), 110, 112–114, 116, 118, 119.

    PubMed  CAS  Google Scholar 

  68. Pan, W. (2002), Bioinformatics 18(4), 546–554.

    Article  PubMed  CAS  Google Scholar 

  69. Arfin, S. M., Long, A. D., Ito, E. T., Tolleri, L., Riehle, M. M., Paegle, E. S., and Hatfield, G. W. (2000), J. Biol. Chem. 275(38), 29,672–29,684.

    Article  CAS  Google Scholar 

  70. Eisen, M. B., Spellman, P. T., Brown, P. O., and Botstein, D. (1998), Proc. Natl. Acad. Sci. USA 95(25), 14,863–14,868.

    Article  CAS  Google Scholar 

  71. Tamames, J., Clark, D., Herrero, J., Dopazo, J., Blaschke, C., Fernandez, J. M., Oliveros, J. C., and Valencia, A. (2002), J. Biotechnol. 98(2–3), 269–283.

    Article  PubMed  CAS  Google Scholar 

  72. Sabatti, C., Rohlin, L., Oh, M. K., and Liao, J. C. (2002), Nucleic Acids Res. 30(13), 2886–2893.

    Article  PubMed  CAS  Google Scholar 

  73. Niehrs, C. and Pollet, N. (1999), Nature 402(6761), 483–487.

    Article  PubMed  CAS  ADS  Google Scholar 

  74. Niebisch, A. and Bott, M. (2001), Arch. Microbiol. 175(4), 282–294.

    Article  PubMed  CAS  Google Scholar 

  75. Hacia, J. G., Brody, L. C., Chee, M. S., Fodor, S. P., and Collins, F. S. (1996), Nat. Genet. 14(4), 441–447.

    Article  PubMed  CAS  Google Scholar 

  76. Behr, M. A., Wilson, M. A., Gill, W. P., Salamon, H., Schoolnik, G. K., Rane, S., and Small, P. M. (1999), Science 284(5419), 1520–1523.

    Article  PubMed  CAS  ADS  Google Scholar 

  77. Jishage, M. and Ishihama, A. (1997), J. Bacteriol. 179(3), 959–963.

    PubMed  CAS  Google Scholar 

  78. Ochman, H. and Jones, I. B. (2000), EMBO J. 19(24), 6637–6643.

    Article  PubMed  CAS  Google Scholar 

  79. Perkins, J. D., Health, J. D., Sharma, B. R., and Weinstock, G. M. (1993), J. Mol. Biol. 232(2), 419–445.

    Article  PubMed  CAS  Google Scholar 

  80. Blattner, F. R., Plunkett, G. 3rd, Bloch, C. A., et al. (1997), Science 277(5331), 1453–1474.

    Article  PubMed  CAS  Google Scholar 

  81. Zeppenfeld, T., Larisch, C., Lengeler, J. W., and Jahreis, K. (2000), J. Bacteriol. 182(16), 4443–4452.

    Article  PubMed  CAS  Google Scholar 

  82. Bailey, J. E., Sburlati, A., Hatzimanikatis, V., Lee, K., Renner, W. A., and Tsai, P. S. (1996), Biotechnol. Bioeng. 52, 109–121.

    Article  CAS  Google Scholar 

  83. Ohnishi, J., Mitsuhashi, S., Hayashi, M., Ando, S., Yokoi, H., Ochiai, K., and Ikeda, M. (2002), Appl. Microbiol. Biotechnol. 58(2), 217–223.

    Article  PubMed  CAS  Google Scholar 

  84. Cho, R. J., Fromont-Racine, M., Wodicka, L., Feierbach, B., Stearns, T., Legrain, P., Lockhart, D. J., and Davis, R. W. (1998), Proc. Natl. Acad. Sci. USA 95(7), 3752–3757.

    Article  PubMed  CAS  ADS  Google Scholar 

  85. Sassetti, C. M., Boyd, D. H., and Rubin, E. J. (2001), Proc. Natl. Acad. Sci. USA 98(22), 12,712–12,717.

    Article  CAS  Google Scholar 

  86. Gill, R. T., Wildt, S., Yang, Y. T., Ziesman, S., and Stephanopoulos, G. (2002), Proc. Natl. Acad. Sci. USA 99(10), 7033–7038.

    Article  PubMed  CAS  ADS  Google Scholar 

  87. Reitzer, L. (2003), Annu. Rev. Microbiol. 57, 155–176.

    Article  PubMed  CAS  Google Scholar 

  88. Ikeda, T. P., Shauger, A. E., and Kustu, S. (1996), J Mol Biol. 259(4), 589–607.

    Article  PubMed  CAS  Google Scholar 

  89. Burkovski, A. (2003), Arch. Microbiol. 179(2), 83–88.

    PubMed  CAS  Google Scholar 

  90. Jakoby, M., Nolden, L., Meier-Wagner, J., Kramer, R., and Burkovski, A. (2000), Mol. Microbiol. 37(4), 964–977.

    Article  PubMed  CAS  Google Scholar 

  91. Calvo, J. M. and Matthews, R. G. (1994), Microbiol. Rev. 58, 466–490.

    PubMed  CAS  Google Scholar 

  92. Hung, S. P., Baldi, P., and Hatfield, G. W. (2002), J. Biol. Chem. 277(43), 40,309–40,323.

    Article  CAS  Google Scholar 

  93. Tani, T. H., Khodursky, A., Blumenthal, R. M., Brown, P. O., and Matthews, R. G. (2002), Proc. Natl. Acad. Sci. USA 99(21), 13,471–13,476.

    Article  CAS  Google Scholar 

  94. Radmacher, E., Vaitsikova, A., Burger, U., Krumbach, K., Sahm, H., and Eggeling, L. (2002), Appl. Environ. Microbiol. 68(5), 2246–2250.

    Article  PubMed  CAS  Google Scholar 

  95. Eggeling, L., Morbach, S., and Sahm, H. (1997), J. Biotechnol. 56(Pt. 7), 167–182.

    Article  CAS  Google Scholar 

  96. Tauch, A., Hermann, T., Burkovski, A., Kramer, R., Puhler, A., and Kalinowski, J. (1998), Arch. Microbiol. 169(4), 303–312.

    Article  PubMed  CAS  Google Scholar 

  97. Yang, J., Wang, P., and Pittard, A. J. (1999), J. Bacteriol. 181(20), 6411–6418.

    PubMed  CAS  Google Scholar 

  98. Pittard, A. J. (1996), in Escherichia coli and Salmonella: Cellular and Molecular Biology, Neidhardt, F. C., ed., ASM Press, Washington, DC, pp. 458–484.

    Google Scholar 

  99. LaRossa, R. A., Van Dyk, T. K., and Smulski, D. R. (1987), J. Bacteriol. 169(4), 1372–1378.

    PubMed  CAS  Google Scholar 

  100. Whipp, M. J., Camakaris, H., and Pittard, A. J. (1998), Gene 209(1–2), 185–192.

    Article  PubMed  CAS  Google Scholar 

  101. Kirkpatrick, C., Maurer, L. M., Oyelakin, N. E., Yoncheva, Y. N., Maurer, R., and Slonczewski, J. L. (2001), J. Bacteriol. 183(21), 6466–6477.

    Article  PubMed  CAS  Google Scholar 

  102. Lee, S. Y. (1996), Trends Biotechnol. 14(3), 98–105.

    Article  PubMed  CAS  Google Scholar 

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    Tino Polen & Volker F. Wendisch

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Polen, T., Wendisch, V.F. Genomewide expression analysis in amino acid-producing bacteria using DNA microarrays. Appl Biochem Biotechnol 118, 215–232 (2004). https://doi.org/10.1385/ABAB:118:1-3:215

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