Skip to main content

Probing the Molecular Physiology of the Microbial Organism, Escherichia coli Using Proteomics

  • Chapter
  • First Online:

Part of the book series: Advances in Biochemical Engineering/Biotechnology ((ABE,volume 83))

Abstract

Genomics and proteomics technologies have yielded volumes of data for more than 20 years, and they continues to produce data at an astounding rate. Has all of this data helped us understand more about life, or it is just bogging us down in details that cannot be assembled into meaningful ideas? This review of the proteomics efforts over the last couple of decades is meant to emphasize that a new scientific discipline has emerged, Molecular Physiology, and that, indeed, this discipline is contributing to our understanding of life. Molecular physiology offers the reductionisms details of individual cellular molecules and offers the systems biology multivariant and high-dimensional datasets of cellular molecules.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   169.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. VanBogelen RA, Greis KD, Blumenthal RM, Tani TH, Matthews RG (2000) Trends Microbiol 7:320

    Article  Google Scholar 

  2. VanBogelen RA, Neidhardt FC ( 1999) Preparation of Escherchia coli samples for 2-D gel analysis, 2-D proteome analysis protocols. In: Link A (ed) Methods in molecular biology, vol 112. Humana Press, chap 3

    Google Scholar 

  3. VanBogelen RA, Abshire KZ, Pertsemlidis A, Clark RL, Neidhardt FC (1996) Gene-protein database of Escherichia coli. In: Escherichia coli and Salmonella typhimurium: cellular and molecular biology, 6th edn. American Society for Microbiology, Washington, DC

    Google Scholar 

  4. VanBogelen RA, Schiller E, Thomas JD, Neidhardt FC (1999) Electrophoresis 20:2149

    Article  CAS  Google Scholar 

  5. O’Farrell PH (1975) J Biol Chem 250:4007

    CAS  Google Scholar 

  6. Anderson NL, Anderson NG (1998) Electrophoresis 19:1853

    Article  CAS  Google Scholar 

  7. Wasinger VC, Cordwell SJ, Cerpa-Poljak A, Yan JX, Gooley AA, Wilkins MR, Duncan MW, Harris R, Williams KL, Humphery-Smith I (1995) Electrophoresis 16:1090

    Article  CAS  Google Scholar 

  8. Anderson L, Sellhamer J (1997) Electrophoresis 18:533

    Article  CAS  Google Scholar 

  9. Gygi SP, Rochon PY, Franza BR, Aebersold R(1999) Mol Cell Biol 19:1720

    CAS  Google Scholar 

  10. VanBogelen RA, Olson ER (1995) Biotechnol Ann Rev 1:69

    Article  CAS  Google Scholar 

  11. Hunkapiller MW, Hood LE (1983) Science 219:650

    Article  CAS  Google Scholar 

  12. Shevchenko AJ, Podtelejnikov ON, Sagliocco AV, Eilm F, Vorm M (1996) Proc Natl Acad Sci USA 93:440

    Article  Google Scholar 

  13. Haynes PA, Gygi SP, Figeys D, Aebersold R (1998) Electrophoresis 19:1862

    Article  CAS  Google Scholar 

  14. Traini M, Gooley AA, Ou K, Wilkins MR, Tonella L, Canchez JC, Hochstrasser DF, Williams KL (1998) Electrophoresis 19:1941

    Article  CAS  Google Scholar 

  15. Herendeen SL, VanBogelen RA, Neidhardt FC(1979) J Bacteriol 139:185

    CAS  Google Scholar 

  16. Walsh BJ, Molloy MP, Williams KL (1998) Electrophoresis 19:1883

    Article  CAS  Google Scholar 

  17. Chevallet M, Santoni V, Poinas A, Rouquie D, Fuchs A, Kieffer S, Rossignol M, Lunardi J, Garin J, Rabilloud T (1998) Electrophoresis 19:1901

    Article  CAS  Google Scholar 

  18. Gorg A, Obermaier C, Boguth G, Weiss W (1999) Electrophoresis 20:712

    Article  CAS  Google Scholar 

  19. Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Nat. Biotechnol 17:994

    Article  CAS  Google Scholar 

  20. Monardo PJ, Boutell T, Garrels JI, Latte GI (1994) Comput Appl Biosci 10:137

    CAS  Google Scholar 

  21. Smilansky Z (2110) Electrophoresis 22:1616

    Article  Google Scholar 

  22. Steinberg TH, Lauber WM, Berggren K, Kemper C, Yue S, Patton WF (2000) Electrophoresis 21:497

    Article  CAS  Google Scholar 

  23. Unlu M, Morgan ME, Minden JS (1997) Electrophoresis 18:2071

    Article  CAS  Google Scholar 

  24. Antelmann H, Bernhardt J, Schmid R, Mach H, Volker U, Hecker M (1997) Electrophoresis 18:1451

    Article  CAS  Google Scholar 

  25. Vohradsky J, Li XM, Thompson CJ (1997) Electrophoresis 18:1418

    Article  CAS  Google Scholar 

  26. Puglia AM, Vohradsky MJ, Thompson CJ (1995) Mol Microbiol 17:737

    Article  CAS  Google Scholar 

  27. Schmid H, Schmitter RD, Blum P, Miller M, Vonderschmitt D (1995) Electrophoresis 16:1961

    Article  CAS  Google Scholar 

  28. Cooper S (2000) ASM News 66:71

    Google Scholar 

  29. Neidhardt FC (1999) J Bacteriol 181:7405

    CAS  Google Scholar 

  30. Neidhardt FC, Bloch PL, Smith DF (1974) J Bacteriol 119:736

    CAS  Google Scholar 

  31. Wanner BL, Kodaira R, Neidhardt FC (1977) J Bacteriol 130:212

    CAS  Google Scholar 

  32. Ron EZ, Davis BD (1971) J Bacteriol 107:391

    CAS  Google Scholar 

  33. Neidhardt FCJ, Ingraham L, Schaechter M (eds) (1990) Physiology of the bacterial cell: a molecular approach. Sinauer Associates, Sunderland MA

    Google Scholar 

  34. Abshire KZ, Neidhardt FC (1993) J Bacteriol 175:3734

    CAS  Google Scholar 

  35. Nystrom T, Albertson NH, Flardh K, Kjelleberg S (1990) FEMS Microbiol Ecol 74:120

    Article  Google Scholar 

  36. Binz PA, Muller M, Walther M, Bienvenut WV, Gras R, Hoogland C, Bouchet G, Gasteiger E, Gabbretti R, Gay S, Palagi P, Wilkins MR, Rouge V, Tonella L, Paesano S, Rossellat G, Karmime A, Bairoch A, Sanchez JC, Appel RD, Hochstrasser DF (1999) Anal Chem 71:4981

    Article  CAS  Google Scholar 

  37. Blackstock W, Weir MP (1999) Trends Biotechnol 17:121

    Article  CAS  Google Scholar 

  38. Kamath-Loeb AS, Gross CA (1991) J Bacteriol 173:3904

    CAS  Google Scholar 

  39. Wilkins MR, Sanchez JC, Gooley AA, Humphrey-Smith I, Hochstrasser DF, Williams KL (1996) Genet Eng Rev 13:19

    CAS  Google Scholar 

  40. Link AJ, Robison K, Church GM(1991) Electrophoresis 18:1259

    Article  Google Scholar 

  41. Pasquali C, Frutiger S, Wilkins MR, Hughes GJ, Appel RD, Bairoch A, Schaller D, Sanchez JC, Hochstrasser DF (1996) Electrophoresis 17:547

    Article  CAS  Google Scholar 

  42. Bernhardt J, Buttner K, Scharf C, Hecker M ( 1999) Electrophoresis 20:2225

    Article  CAS  Google Scholar 

  43. Langen H, Takacs B, Evers S, Berndt P, Lahm HW, Wipf B, Gray C, Fountoulakis M (2000) Electrophoresis 21:411

    Article  CAS  Google Scholar 

  44. Sazuka T, Yamaguchi M, Ohara O (1999) Electrophoresis 20:2160

    Article  CAS  Google Scholar 

  45. Cordwell SJ, Humphery-Smith I (1997) Electrophoresis 18:1410

    Article  CAS  Google Scholar 

  46. Cordwell SJ, Basseal DJ, Humphery-Smith I (1997) Electrophoresis 18:1335

    Article  CAS  Google Scholar 

  47. Henzel WJ, Billeci TM, Stults J, Wong SC, Grimley C, Watanabe C (1993) Proc Natl Acad Sci USA 90:5011

    Article  CAS  Google Scholar 

  48. Mann M, Hojrup P, Roepstorff P (1993) Biol Mass Spectrom 22:338

    Article  CAS  Google Scholar 

  49. Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Proc Natl Acad Sci USA 96:4285

    Article  CAS  Google Scholar 

  50. Shaw G (1993) Proc Natl Acad Sci USA 90:5138

    Article  CAS  Google Scholar 

  51. Yates JR III, Speicher S, Griffin PR, Hunkapiller T (1993) Anal Biochem 214:397

    Article  CAS  Google Scholar 

  52. Wasinger VC, Urquhart BL, Humphery-Smith I (1999) Electrophoresis 20:2196

    Article  CAS  Google Scholar 

  53. Fountoulakis M, Takacs MF, Berndt P, Langen H, Takacs B (1999) Electrophoresis 20:2181

    Article  CAS  Google Scholar 

  54. Cordwell SJ, Nouwens AS, Verrills NM, McPherson JC, Hains PG, Van Dyk DD, Walsh BJ (2000) Electrophorsis (in press)

    Google Scholar 

  55. Mollenkopf HJ, Jungblut PR, Raupach B, Mattow J, Lamer S, Zimny-Arndt U, Schaible UE, Kaufmann SHE (1999) Electrophoresis 20(11):2172

    Article  CAS  Google Scholar 

  56. Neidhardt FC, VanBogelen RA (2000) Proteomic analysis of bacterial stresss responses. In: Storz G, Hengge-Aronis R (eds) Bacterial stress response. American Society for Microbiology, Washington DC

    Google Scholar 

  57. Neidhardt FC, VanBogelen RA (1981) Biochem Biophy Res Comm 100:894

    Article  CAS  Google Scholar 

  58. Neidhardt FC, VanBogelen RA, Lau ET (1983) J Bacteriol 153:597

    CAS  Google Scholar 

  59. Hirshfield IN, Bloch PL, VanBogelen RA, Neidhardt FC (1983) J Bacteriol 146:345

    Google Scholar 

  60. Clark RL, Neidhardt FC (1990) J Bacteriol 172:3237

    CAS  Google Scholar 

  61. Emmerich RV, Hirshfield IN (1987) J Bacteriol 169:5311

    CAS  Google Scholar 

  62. VanBogelen RA, Vaughn V, Neidhardt FC (1983) J Bacteriol 153:1066

    CAS  Google Scholar 

  63. Neidhardt FC, Phillips TA, VanBogelen RA, Smith MW, Georgalis Y, Subramanian AR (1981) J Bacteriol 145:513

    CAS  Google Scholar 

  64. VanBogelen RA, Hutton ME, Neidhardt FC (1990) Electophoresis 11:1131

    Article  CAS  Google Scholar 

  65. Matthews RG, Neidhardt FC (1989) J Bacteriol 171:2619

    CAS  Google Scholar 

  66. Neidhardt FC, VanBogelen RA, Vaughn V (1984) Ann Rev Genet 18:295

    Article  CAS  Google Scholar 

  67. Phillips TA, VanBogelen RA, Neidhardt FC (1984) J Bacteriol 159:283

    CAS  Google Scholar 

  68. Tilly K, VanBogelen RA, Georgeopoulos C, Neidhardt FC (1983) J Bacteriol 154:1505

    CAS  Google Scholar 

  69. Christman MF, Morgan RW, Jacobson FS, Ames BN (1985) Cell 41:753

    Article  CAS  Google Scholar 

  70. Ernsting BR, Atkinson MR, Ninfa AJ, Matthews RG (1992) J Bacteriol 174:1109

    CAS  Google Scholar 

  71. Chersi A, Dzionara M, Donner D, Wittman HG(1968) Mol Gen Genet 101:82

    Article  CAS  Google Scholar 

  72. Link AJ, Hayes LG, Carmack EB, Yates JR III (1997) Electrophoresis 18:1259

    Article  CAS  Google Scholar 

  73. Teixeira-Gomes A, Cloeckaert PA, Bezard G, Bowden RA, Dubray G, Zygmunt MS (1997) Electrophoresis 18:1491

    Article  CAS  Google Scholar 

  74. VanBogelen RA, Abshire KZ, Moldover B, Olson ER, Neidhardt FC (1997) Electrophoresis 18:1243

    Article  CAS  Google Scholar 

  75. Cavalcoli JD, VanBogelen RA, Andrews PC, Moldover B (1997) Electrophoresis 18:2703

    Article  CAS  Google Scholar 

  76. Karlin S, Mrazek J, Campbell AM (1998) Mol Microbiol 29:1341

    Article  CAS  Google Scholar 

  77. Salgado H, Santos-Zavalenta A, Gama-Castro S, Millan-Zarate D, Blattner FR, Collado-Vides J (2000) Nucl Acid Res 28:65

    Article  CAS  Google Scholar 

  78. Clarke L, Carbon J (1976) Cell 9:91

    Article  CAS  Google Scholar 

  79. Sancar A, Hack AM, Rupp WD (1979) J Bacteriol 137:692

    CAS  Google Scholar 

  80. Reeve J (1979) Methods Enzymol 68:493

    Article  CAS  Google Scholar 

  81. Neidhardt FC, Wirth R, Smith MW, VanBogelen RA (1980) J Bacteriol 143:535

    CAS  Google Scholar 

  82. Neidhardt FC, Vaughn V, Phillips TA, Bloch PL (1983) Microbiol Rev 47:231

    CAS  Google Scholar 

  83. Kohara I, Akiyama K, Isono K (1987) Cell 50:495

    Article  CAS  Google Scholar 

  84. Neidhardt FC, Appleby DB, Sankar P, Hutton ME, Phillips TA (1989) Electrophoresis 10:116

    Article  CAS  Google Scholar 

  85. Studier FW, Moffat BA (1986) J Mol Biol 189:113

    Article  CAS  Google Scholar 

  86. Sankar P, Hutton ME, VanBogelen RA, Clark RL, Neidhardt FC (1993) J Bacteriol 175:5145

    CAS  Google Scholar 

  87. Chuang SE, Daniels DL, Blattner FR (1993) J Bacteriol 175:2026

    CAS  Google Scholar 

  88. Lemaux PG, Herendeen SL, Bloch PL, Neidhardt FC (1978) Cell 13:427

    Article  CAS  Google Scholar 

  89. Anderson NG, Anderson NL (1981) JAMA 246:2620

    Article  CAS  Google Scholar 

  90. VanBogelen RA, Neidhardt FC (1990) FEMS Microbiol Ecol 74:121

    Article  CAS  Google Scholar 

  91. Yamamori T, Yura T (1982) Proc Natl Acad Sci USA 79:860

    Article  CAS  Google Scholar 

  92. Ostling J, McDougald D, Marouga R, Kjelleberg S (1997) Electrophoresis 18:1441

    Article  CAS  Google Scholar 

  93. Fujita N, Ishihama A (1987) Mol Gen Genet 210:10

    Article  CAS  Google Scholar 

  94. Straus DB, Walter WA, Gross CA (1987) Nature 329:348

    Article  CAS  Google Scholar 

  95. Nagai H, Yuzawa H, Yura T (1991) Proc Natl Acad Sci USA 88:10,515

    CAS  Google Scholar 

  96. Grossman AD, Erickson JW, Gross CA (1984) Cell 38:383

    Article  CAS  Google Scholar 

  97. Landick R, Vaughn V, Lau ET, VanBogelen RA, Erickson JW, Neidhardt FC (1984) Cell 38:175

    Article  CAS  Google Scholar 

  98. Liberek K, Galitski TP, Zylicz M, Georgopoulos C (1992) Proc Natl Acad Sci USA 89:3516

    Article  CAS  Google Scholar 

  99. Pedersen S, Bloch PL, Reeh S, Neidhardt FC (1978) Cell 14:179

    Article  CAS  Google Scholar 

  100. Bravo R, Celis JE (1980) J Cell Biol 84:795

    Article  CAS  Google Scholar 

  101. Bravo R, Celis JE (1982) Clin Chem 28:766

    CAS  Google Scholar 

  102. Bloch PL, Phillips TA, Neidhardt FC (1980) J Bacteriol 141:1409

    CAS  Google Scholar 

  103. Phillips TA, Bloch PL, Neidhardt FC ( 1980) J Bacteriol 144:1024

    CAS  Google Scholar 

  104. Celis JE, Bravo R (eds) (1984) Two-dimensional gel electrophoresis of proteins: methods and applications. Academic Press, London New York

    Google Scholar 

  105. Gottesman S, Neidhardt FC (1983) Global control systems. In: Beckwith J, Davies J, Gallant JA (eds) Gene function in prokaryotes. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  106. Schlesinger MJ, Ashburner M, Tissieres A (eds) (1982) Heat shock from bacteria to man. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY

    Google Scholar 

  107. Aicher LD, Wahl A, Arce GO, Steiner S (1998) Electrophoresis 19:1998

    Article  CAS  Google Scholar 

  108. VanBogelen RA, Olson ER, Wanner BL, Neidhardt FC (1996) J Bacteriol 178:4344

    CAS  Google Scholar 

  109. Phan-Thanh L, Gormon T (1997) Electrophoresis 18:1464

    Article  CAS  Google Scholar 

  110. VanBogelen RA, Neidhardt FC (1990) Proc Natl Acad Sci USA 87:5589

    Article  CAS  Google Scholar 

  111. Bochner BR, Lee PC, Wilson SW, Cutter CW, Ames BN (1984) Cell 37:225

    Article  CAS  Google Scholar 

  112. Lee PC, Bochner BR, Ames BN (1983) Proc Natl Acad Sci USA 80:7496

    Article  CAS  Google Scholar 

  113. Courgeon AM, Maisonhaute C, Best-Belpomme M (1984) Cell Res 153:515

    Article  CAS  Google Scholar 

  114. VanBogelen RA, Kelley PM, Neidhardt FC (1987) J Bacteriol 169:26

    CAS  Google Scholar 

  115. VanBogelen RA, Acton M, Neidhardt FC (1987) Genes Develop 1:535

    Google Scholar 

  116. Abshire KZ, Neidhardt FC (1993) J Bacteriol 175:3744

    CAS  Google Scholar 

  117. Golub TR, Slonim DK, Tamayo P, Huard C, Gassenbeek M, Mesirov JP, Coller H, Loh ML, Downing JR, Caligiuri MA, Bloomfield CD, Lander ES (1999) Science 286:531

    Article  CAS  Google Scholar 

  118. Huang S (1999) J Mol Med 77:469

    Article  CAS  Google Scholar 

  119. Gulino A (1999) Forum (Genova) 9:37

    CAS  Google Scholar 

  120. Edwards JS, Palsson BO (1998) Biotechnol Bioeng 58:162–169

    Article  CAS  Google Scholar 

  121. Ehlde M, Zacchi G (1995) CABIOS 11:201

    CAS  Google Scholar 

  122. Hofmeyr JH (1986) Comput Appl Biosci 1:5

    Google Scholar 

  123. Liao JC (1993) Curr Opin Biotechnol 2:211

    Article  Google Scholar 

  124. Mendes P (1997) Trends Biochem Sci 22:361

    Article  CAS  Google Scholar 

  125. Palsson BO (1997) Nature Biotechnol 15:3

    Article  CAS  Google Scholar 

  126. Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE (1999) J Bacteriol 181:6679

    CAS  Google Scholar 

  127. Schilling CH, Edwards JS, Palsson BO (1999) Biotechnol Prog 3:288

    Article  Google Scholar 

  128. Stephanopoulos G (1994) Curr Opin Biotechnol 2:196

    Article  Google Scholar 

  129. El-Gewely MR (1995) Biotechnology domain. In: El-Gewely MR (ed) Biotechnology annual review, vol 1. Elsevier, Amsterdam Lausanne New York Oxford Shannon Tokoyo, pp 5–68

    Chapter  Google Scholar 

  130. Schaaff I, Heinisch J, Zimmermann FK (1989) Yeast 5:285

    Article  CAS  Google Scholar 

  131. Bailey JE (1999) Nat Biotechnol 17:616

    Article  CAS  Google Scholar 

  132. Arkin A, Ross J, McAdams HH (1998) Genetics 149:1633

    CAS  Google Scholar 

  133. Bray D, Bourret RB, Simon MI (1993) Mol Biol Cell 4:469

    CAS  Google Scholar 

  134. Gillespie DT (1999) J Phy Chem 81:2340

    Article  Google Scholar 

  135. McAdams HH, Arkin A (1997) Proc Natl Acad Sci USA 94:814

    Article  CAS  Google Scholar 

  136. McAdams HH, Shapiro L (1995) Science 269:650

    Article  CAS  Google Scholar 

  137. Meyers S, Friedland P (1984) Nucl Acid Res 12:1

    Article  CAS  Google Scholar 

  138. Abbott A (1999) Nature 402:219

    Article  CAS  Google Scholar 

  139. Reddy B, Yin J (1999) AIDS Res Human Retroviruses 15:273

    Article  CAS  Google Scholar 

  140. Tomita MK, Hashimoto K, Takahashi TS, Shimizu Y, Matsuzaki F, Miyoshi K, Saito S, Tanida K, Yugi K, Venter JC, Hutchison CA III (1999) Bioinformatics 15:72

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2003 Springer-Verlag Berlin Heidelberg

About this chapter

Cite this chapter

Van Bogelen, R.A. (2003). Probing the Molecular Physiology of the Microbial Organism, Escherichia coli Using Proteomics. In: Hecker, M., et al. Proteomics of Microorganisms. Advances in Biochemical Engineering/Biotechnology, vol 83. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-36459-5_2

Download citation

  • DOI: https://doi.org/10.1007/3-540-36459-5_2

  • Received:

  • Published:

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-00546-9

  • Online ISBN: 978-3-540-36459-7

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics