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
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsPreview
Unable to display preview. Download preview PDF.
References
VanBogelen RA, Greis KD, Blumenthal RM, Tani TH, Matthews RG (2000) Trends Microbiol 7:320
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
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
VanBogelen RA, Schiller E, Thomas JD, Neidhardt FC (1999) Electrophoresis 20:2149
O’Farrell PH (1975) J Biol Chem 250:4007
Anderson NL, Anderson NG (1998) Electrophoresis 19:1853
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
Anderson L, Sellhamer J (1997) Electrophoresis 18:533
Gygi SP, Rochon PY, Franza BR, Aebersold R(1999) Mol Cell Biol 19:1720
VanBogelen RA, Olson ER (1995) Biotechnol Ann Rev 1:69
Hunkapiller MW, Hood LE (1983) Science 219:650
Shevchenko AJ, Podtelejnikov ON, Sagliocco AV, Eilm F, Vorm M (1996) Proc Natl Acad Sci USA 93:440
Haynes PA, Gygi SP, Figeys D, Aebersold R (1998) Electrophoresis 19:1862
Traini M, Gooley AA, Ou K, Wilkins MR, Tonella L, Canchez JC, Hochstrasser DF, Williams KL (1998) Electrophoresis 19:1941
Herendeen SL, VanBogelen RA, Neidhardt FC(1979) J Bacteriol 139:185
Walsh BJ, Molloy MP, Williams KL (1998) Electrophoresis 19:1883
Chevallet M, Santoni V, Poinas A, Rouquie D, Fuchs A, Kieffer S, Rossignol M, Lunardi J, Garin J, Rabilloud T (1998) Electrophoresis 19:1901
Gorg A, Obermaier C, Boguth G, Weiss W (1999) Electrophoresis 20:712
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R (1999) Nat. Biotechnol 17:994
Monardo PJ, Boutell T, Garrels JI, Latte GI (1994) Comput Appl Biosci 10:137
Smilansky Z (2110) Electrophoresis 22:1616
Steinberg TH, Lauber WM, Berggren K, Kemper C, Yue S, Patton WF (2000) Electrophoresis 21:497
Unlu M, Morgan ME, Minden JS (1997) Electrophoresis 18:2071
Antelmann H, Bernhardt J, Schmid R, Mach H, Volker U, Hecker M (1997) Electrophoresis 18:1451
Vohradsky J, Li XM, Thompson CJ (1997) Electrophoresis 18:1418
Puglia AM, Vohradsky MJ, Thompson CJ (1995) Mol Microbiol 17:737
Schmid H, Schmitter RD, Blum P, Miller M, Vonderschmitt D (1995) Electrophoresis 16:1961
Cooper S (2000) ASM News 66:71
Neidhardt FC (1999) J Bacteriol 181:7405
Neidhardt FC, Bloch PL, Smith DF (1974) J Bacteriol 119:736
Wanner BL, Kodaira R, Neidhardt FC (1977) J Bacteriol 130:212
Ron EZ, Davis BD (1971) J Bacteriol 107:391
Neidhardt FCJ, Ingraham L, Schaechter M (eds) (1990) Physiology of the bacterial cell: a molecular approach. Sinauer Associates, Sunderland MA
Abshire KZ, Neidhardt FC (1993) J Bacteriol 175:3734
Nystrom T, Albertson NH, Flardh K, Kjelleberg S (1990) FEMS Microbiol Ecol 74:120
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
Blackstock W, Weir MP (1999) Trends Biotechnol 17:121
Kamath-Loeb AS, Gross CA (1991) J Bacteriol 173:3904
Wilkins MR, Sanchez JC, Gooley AA, Humphrey-Smith I, Hochstrasser DF, Williams KL (1996) Genet Eng Rev 13:19
Link AJ, Robison K, Church GM(1991) Electrophoresis 18:1259
Pasquali C, Frutiger S, Wilkins MR, Hughes GJ, Appel RD, Bairoch A, Schaller D, Sanchez JC, Hochstrasser DF (1996) Electrophoresis 17:547
Bernhardt J, Buttner K, Scharf C, Hecker M ( 1999) Electrophoresis 20:2225
Langen H, Takacs B, Evers S, Berndt P, Lahm HW, Wipf B, Gray C, Fountoulakis M (2000) Electrophoresis 21:411
Sazuka T, Yamaguchi M, Ohara O (1999) Electrophoresis 20:2160
Cordwell SJ, Humphery-Smith I (1997) Electrophoresis 18:1410
Cordwell SJ, Basseal DJ, Humphery-Smith I (1997) Electrophoresis 18:1335
Henzel WJ, Billeci TM, Stults J, Wong SC, Grimley C, Watanabe C (1993) Proc Natl Acad Sci USA 90:5011
Mann M, Hojrup P, Roepstorff P (1993) Biol Mass Spectrom 22:338
Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO (1999) Proc Natl Acad Sci USA 96:4285
Shaw G (1993) Proc Natl Acad Sci USA 90:5138
Yates JR III, Speicher S, Griffin PR, Hunkapiller T (1993) Anal Biochem 214:397
Wasinger VC, Urquhart BL, Humphery-Smith I (1999) Electrophoresis 20:2196
Fountoulakis M, Takacs MF, Berndt P, Langen H, Takacs B (1999) Electrophoresis 20:2181
Cordwell SJ, Nouwens AS, Verrills NM, McPherson JC, Hains PG, Van Dyk DD, Walsh BJ (2000) Electrophorsis (in press)
Mollenkopf HJ, Jungblut PR, Raupach B, Mattow J, Lamer S, Zimny-Arndt U, Schaible UE, Kaufmann SHE (1999) Electrophoresis 20(11):2172
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
Neidhardt FC, VanBogelen RA (1981) Biochem Biophy Res Comm 100:894
Neidhardt FC, VanBogelen RA, Lau ET (1983) J Bacteriol 153:597
Hirshfield IN, Bloch PL, VanBogelen RA, Neidhardt FC (1983) J Bacteriol 146:345
Clark RL, Neidhardt FC (1990) J Bacteriol 172:3237
Emmerich RV, Hirshfield IN (1987) J Bacteriol 169:5311
VanBogelen RA, Vaughn V, Neidhardt FC (1983) J Bacteriol 153:1066
Neidhardt FC, Phillips TA, VanBogelen RA, Smith MW, Georgalis Y, Subramanian AR (1981) J Bacteriol 145:513
VanBogelen RA, Hutton ME, Neidhardt FC (1990) Electophoresis 11:1131
Matthews RG, Neidhardt FC (1989) J Bacteriol 171:2619
Neidhardt FC, VanBogelen RA, Vaughn V (1984) Ann Rev Genet 18:295
Phillips TA, VanBogelen RA, Neidhardt FC (1984) J Bacteriol 159:283
Tilly K, VanBogelen RA, Georgeopoulos C, Neidhardt FC (1983) J Bacteriol 154:1505
Christman MF, Morgan RW, Jacobson FS, Ames BN (1985) Cell 41:753
Ernsting BR, Atkinson MR, Ninfa AJ, Matthews RG (1992) J Bacteriol 174:1109
Chersi A, Dzionara M, Donner D, Wittman HG(1968) Mol Gen Genet 101:82
Link AJ, Hayes LG, Carmack EB, Yates JR III (1997) Electrophoresis 18:1259
Teixeira-Gomes A, Cloeckaert PA, Bezard G, Bowden RA, Dubray G, Zygmunt MS (1997) Electrophoresis 18:1491
VanBogelen RA, Abshire KZ, Moldover B, Olson ER, Neidhardt FC (1997) Electrophoresis 18:1243
Cavalcoli JD, VanBogelen RA, Andrews PC, Moldover B (1997) Electrophoresis 18:2703
Karlin S, Mrazek J, Campbell AM (1998) Mol Microbiol 29:1341
Salgado H, Santos-Zavalenta A, Gama-Castro S, Millan-Zarate D, Blattner FR, Collado-Vides J (2000) Nucl Acid Res 28:65
Clarke L, Carbon J (1976) Cell 9:91
Sancar A, Hack AM, Rupp WD (1979) J Bacteriol 137:692
Reeve J (1979) Methods Enzymol 68:493
Neidhardt FC, Wirth R, Smith MW, VanBogelen RA (1980) J Bacteriol 143:535
Neidhardt FC, Vaughn V, Phillips TA, Bloch PL (1983) Microbiol Rev 47:231
Kohara I, Akiyama K, Isono K (1987) Cell 50:495
Neidhardt FC, Appleby DB, Sankar P, Hutton ME, Phillips TA (1989) Electrophoresis 10:116
Studier FW, Moffat BA (1986) J Mol Biol 189:113
Sankar P, Hutton ME, VanBogelen RA, Clark RL, Neidhardt FC (1993) J Bacteriol 175:5145
Chuang SE, Daniels DL, Blattner FR (1993) J Bacteriol 175:2026
Lemaux PG, Herendeen SL, Bloch PL, Neidhardt FC (1978) Cell 13:427
Anderson NG, Anderson NL (1981) JAMA 246:2620
VanBogelen RA, Neidhardt FC (1990) FEMS Microbiol Ecol 74:121
Yamamori T, Yura T (1982) Proc Natl Acad Sci USA 79:860
Ostling J, McDougald D, Marouga R, Kjelleberg S (1997) Electrophoresis 18:1441
Fujita N, Ishihama A (1987) Mol Gen Genet 210:10
Straus DB, Walter WA, Gross CA (1987) Nature 329:348
Nagai H, Yuzawa H, Yura T (1991) Proc Natl Acad Sci USA 88:10,515
Grossman AD, Erickson JW, Gross CA (1984) Cell 38:383
Landick R, Vaughn V, Lau ET, VanBogelen RA, Erickson JW, Neidhardt FC (1984) Cell 38:175
Liberek K, Galitski TP, Zylicz M, Georgopoulos C (1992) Proc Natl Acad Sci USA 89:3516
Pedersen S, Bloch PL, Reeh S, Neidhardt FC (1978) Cell 14:179
Bravo R, Celis JE (1980) J Cell Biol 84:795
Bravo R, Celis JE (1982) Clin Chem 28:766
Bloch PL, Phillips TA, Neidhardt FC (1980) J Bacteriol 141:1409
Phillips TA, Bloch PL, Neidhardt FC ( 1980) J Bacteriol 144:1024
Celis JE, Bravo R (eds) (1984) Two-dimensional gel electrophoresis of proteins: methods and applications. Academic Press, London New York
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
Schlesinger MJ, Ashburner M, Tissieres A (eds) (1982) Heat shock from bacteria to man. Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
Aicher LD, Wahl A, Arce GO, Steiner S (1998) Electrophoresis 19:1998
VanBogelen RA, Olson ER, Wanner BL, Neidhardt FC (1996) J Bacteriol 178:4344
Phan-Thanh L, Gormon T (1997) Electrophoresis 18:1464
VanBogelen RA, Neidhardt FC (1990) Proc Natl Acad Sci USA 87:5589
Bochner BR, Lee PC, Wilson SW, Cutter CW, Ames BN (1984) Cell 37:225
Lee PC, Bochner BR, Ames BN (1983) Proc Natl Acad Sci USA 80:7496
Courgeon AM, Maisonhaute C, Best-Belpomme M (1984) Cell Res 153:515
VanBogelen RA, Kelley PM, Neidhardt FC (1987) J Bacteriol 169:26
VanBogelen RA, Acton M, Neidhardt FC (1987) Genes Develop 1:535
Abshire KZ, Neidhardt FC (1993) J Bacteriol 175:3744
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
Huang S (1999) J Mol Med 77:469
Gulino A (1999) Forum (Genova) 9:37
Edwards JS, Palsson BO (1998) Biotechnol Bioeng 58:162–169
Ehlde M, Zacchi G (1995) CABIOS 11:201
Hofmeyr JH (1986) Comput Appl Biosci 1:5
Liao JC (1993) Curr Opin Biotechnol 2:211
Mendes P (1997) Trends Biochem Sci 22:361
Palsson BO (1997) Nature Biotechnol 15:3
Sauer U, Lasko DR, Fiaux J, Hochuli M, Glaser R, Szyperski T, Wuthrich K, Bailey JE (1999) J Bacteriol 181:6679
Schilling CH, Edwards JS, Palsson BO (1999) Biotechnol Prog 3:288
Stephanopoulos G (1994) Curr Opin Biotechnol 2:196
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
Schaaff I, Heinisch J, Zimmermann FK (1989) Yeast 5:285
Bailey JE (1999) Nat Biotechnol 17:616
Arkin A, Ross J, McAdams HH (1998) Genetics 149:1633
Bray D, Bourret RB, Simon MI (1993) Mol Biol Cell 4:469
Gillespie DT (1999) J Phy Chem 81:2340
McAdams HH, Arkin A (1997) Proc Natl Acad Sci USA 94:814
McAdams HH, Shapiro L (1995) Science 269:650
Meyers S, Friedland P (1984) Nucl Acid Res 12:1
Abbott A (1999) Nature 402:219
Reddy B, Yin J (1999) AIDS Res Human Retroviruses 15:273
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
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights 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