Table1s Literature Comparison of Microarray Data in Anaerobic Growth

Table1S Literature comparison of microarray data in anaerobic growth. In order column 1 stands for E coli. identifier. Column 2 describes the gene name. The third column gives the discrete state ON or OFF. Column 4 describes the result of the compared data, if correct as literature and if incorrect different from literature. The last column shows the respective reference.

Comparison

Bongaerts, J., Zoske, S., Weidner, U. and Unden, G. 1995. Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators. Mol Microbiol16, 521-34.

Compan, I. and Touati, D. 1994. Anaerobic activation of arcA transcription in Escherichia coli: roles of Fnr and ArcA. Mol Microbiol11, 955-64.

Cronan, J.E.a.L., D. 1996. Tricarboxyl Acid Cycle and Glyoxylate Bypass. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2ed edit. (Neidhardt, F., Curtis, R., Ingraham, J.L., Lin, E.C.C., Brooks-Low, K., Magasanik, B., Reznikoff, S., Riley, M., Schaechter, M. and Umbarger, H.E., ed.), Vol. 1st, pp. 206. 2 vols. ASM Press, Washington D.C.

Darwin, A.J. and Stewart, V. 1995. Expression of the narX, narL, narP, and narQ genes of Escherichia coli K-12: regulation of the regulators. J Bacteriol177, 3865-9.

Darwin, A.J., Ziegelhoffer, E.C., Kiley, P.J. and Stewart, V. 1998. Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J Bacteriol180, 4192-8.

Garriga, X., Eliasson, R., Torrents, E., Jordan, A., Barbe, J., Gibert, I. and Reichard, P. 1996. nrdD and nrdG genes are essential for strict anaerobic growth of Escherichia coli. Biochem Biophys Res Commun229, 189-92.

Gupta, S. and Clark, D.P. 1989. Escherichia coli derivatives lacking both alcohol dehydrogenase and phosphotransacetylase grow anaerobically by lactate fermentation. J Bacteriol171, 3650-5.

Iuchi, S., Aristarkhov, A., Dong, J.M., Taylor, J.S. and Lin, E.C. 1994. Effects of nitrate respiration on expression of the Arc-controlled operons encoding succinate dehydrogenase and flavin-linked L-lactate dehydrogenase. J Bacteriol176, 1695-701.

Kessler, D.a.K., J. 1996. Anaerobic Dissimilation of Pyruvate. In Escherichia coli and Salmonella: Celullar and Molecular Biology 2nd edit. (Neidhardt, F., Curtis, R., Ingraham, J.L., Lin, E.C.C., Brooks-Low, K., Magasanil, B., Reznikoff,S., Riley, M., Schaechter, M. and Umbarger, H.E., ed.), Vol. 1st, pp. 199. 2 vols. ASM press, Washington, D.C.

Patschkowski T., B.D.M., Kiely J.K.,. 2000. Mechanisms for sensing and Responding to Oxygen Deprivation. In Bacterial Stress Responses (Storz G., H.-A. R., ed.), Vol. 1, pp. 61-68. 1 vols. ASM Press, Washington D.C.

Quail, M.A., Haydon, D.J. and Guest, J.R. 1994. The pdhR-aceEF-lpd operon of Escherichia coli expresses the pyruvate dehydrogenase complex. Mol Microbiol12, 95-104.

Spiro, S. and Guest, J.R. 1987. Regulation and over-expression of the fnr gene of Escherichia coli. J Gen Microbiol133, 3279-88.

Tyson, K.L., Bell, A.I., Cole, J.A. and Busby, S.J. 1993. Definition of nitrite and nitrate response elements at the anaerobically inducible Escherichia coli nirB promoter: interactions between FNR and NarL. Mol Microbiol7, 151-7.

Zientz, E., Janausch, I.G., Six, S. and Unden, G. 1999. Functioning of DcuC as the C4-dicarboxylate carrier during glucose fermentation by Escherichia coli. J Bacteriol181, 3716-20.

Table2S Literature comparison of microarray data in heat shock. In order column 1 stands for E coli. identifier. Column 2 describes the gene name. The third column gives the discrete state ON or OFF. Column 4 describes the result of the compared data, if correct as literature and if incorrect different from literature. The last column shows the respective reference.

Gene name

Reference

Dartigalongue, C., Missiakas, D. and Raina, S. 2001. Characterization of the Escherichia coli sigma E regulon. J Biol Chem276, 20866-75.

Gross, C.A. 1996. Funtion and Regulation of Heat Shock Proteins. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger H.E., ed.), Vol. 1, pp. 1382. 2 vols. ASM Press, Washington D.C.

Kim, K.I., Park, S.C., Kang, S.H., Cheong, G.W. and Chung, C.H. 1999. Selective degradation of unfolded proteins by the self- compartmentalizing HtrA protease, a periplasmic heat shock protein in Escherichia coli. J Mol Biol294, 1363-74.

Qi, H., Menzel, R. and Tse-Dinh, Y.C. 1997. Regulation of Escherichia coli topA gene transcription: involvement of a sigmaS-dependent promoter. J Mol Biol267, 481-9.

Salgado, H., Gama-Castro, S., Martínez, A., Díaz-Peredo, E., Sánchez-Solano, F., Santos-Zavaleta, E., Gutiérrez-Rios, R. and Collado-Vides, J. 2002. RegulonDB (version 4.0): Transcriptional Regulation and Operon Organization in Escherichia coli K-12. Nucleic Acids ResSubmitted.

Seol, J.H., Yoo, S.J., Shin, D.H., Shim, Y.K., Kang, M.S., Goldberg, A.L. and Chung, C.H. 1997. The heat-shock protein HslVU from Escherichia coli is a protein- activated ATPase as well as an ATP-dependent proteinase. Eur J Biochem247, 1143-50.

Tan, J., Jakob, U. and Bardwell, J.C. 2002. Overexpression of two different GTPases rescues a null mutation in a heat-induced rRNA methyltransferase. J Bacteriol184, 2692-8.

Thomas, J.G. and Baneyx, F. 1998. Roles of the Escherichia coli small heat shock proteins IbpA and IbpB in thermal stress management: comparison with ClpA, ClpB, and HtpG In vivo. J Bacteriol180, 5165-72.

Tsui, H.C., Feng, G. and Winkler, M.E. 1996. Transcription of the mutL repair, miaA tRNA modification, hfq pleiotropic regulator, and hflA region protease genes of Escherichia coli K-12 from clustered Esigma32-specific promoters during heat shock. J Bacteriol178, 5719-31.

Table3S Literature comparison of microarray data in stationary phase. In order column 1 stands for E coli. identifier. Column 2 describes the gene name. The third column gives the discrete state ON or OFF. Column 4 describes the result of the compared data, if correct as literature and if incorrect different from literature. The last column shows the respective reference.

Gene name

Reference

Bohringer, J., Fischer, D., Mosler, G. and Hengge-Aronis, R. 1995. UDP-glucose is a potential intracellular signal molecule in the control of expression of sigma S and sigma S-dependent genes in Escherichia coli. J Bacteriol177, 413-22.

Cunningham, L., Gruer, M.J. and Guest, J.R. 1997. Transcriptional regulation of the aconitase genes (acnA and acnB) of Escherichia coli. Microbiology143, 3795-805.

Death, A. and Ferenci, T. 1994. Between feast and famine: endogenous inducer synthesis in the adaptation of Escherichia coli to growth with limiting carbohydrates. J Bacteriol176, 5101-7.

Hengge-Aronis, R. 1996. Regulation of Gene Expression during Entry to into Stationary Phase. In Escherichia coli and Salmonella: cellular and molecular biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger H.E., ed.), Vol. 1, pp. 1497. 2 vols. ASM Press, Washington D.C.

Ishihama, A. 2000. Functional modulation of Escherichia coli RNA polymerase. Annu Rev Microbiol54, 499-518.

Nystrom, T. 1999. Starvation, cessation of growth and bacterial aging. Curr Opin Microbiol2, 214-9.

Rabinowitch, H.D., Sklan, D., Chace, D.H., Stevens, R.D. and Fridovich, I. 1993. Escherichia coli produces linoleic acid during late stationary phase. J Bacteriol175, 5324-8.

Wackwitz, B., Bongaerts, J., Goodman, S.D. and Unden, G. 1999. Growth phase-dependent regulation of nuoA-N expression in Escherichia coli K-12 by the Fis protein: upstream binding sites and bioenergetic significance. Mol Gen Genet262, 876-83.

Weichart, D., Lange, R., Henneberg, N. and Hengge-Aronis, R. 1993. Identification and characterization of stationary phase-inducible genes in Escherichia coli. Mol Microbiol10, 407-20.

Table4S Comparison between literature and microarray data in minimal media. In order column 1 stands for E coli. identifier. Column 2 describes the gene name. The third column gives the discrete state ON or OFF. Column 4 describes the result of the compared data, if correct as literature and if incorrect different from literature. The last column shows the respective reference.

Reference

Ahmad, D. and Newman, E.B. 1988. A deficiency in cyclic AMP results in pH-sensitive growth of Escherichia coli K-12. J Bacteriol170, 3443-7.

Cronan, J.E.a.L., D. 1996. Tricarboxyl Acid Cycle and Glyoxylate Bypass. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2ed edit. (Neidhardt, F., Curtis, R., Ingraham, J.L., Lin, E.C.C., Brooks-Low, K., Magasanik, B., Reznikoff, S., Riley, M., Schaechter, M. and Umbarger, H.E., ed.), Vol. 1st, pp. 206. 2 vols. ASM Press, Washington D.C.

Fraenkel, D.G. 1996. Glycolysis. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger, H.E., ed.), Vol. 1, pp. 189. 2 vols. ASM Press, Washington D.C.

Glansdorff, N. 1996. Biosynthesis of Arginine and Polyamines. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger, H.E., ed.), Vol. 1, pp. 408. 2 vols. ASM Press, Wasington D.C.

Greene, R.C. 1996. Biosynthesis of Methionine. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger, H.E., ed.), Vol. 1, pp. 542. 2 vols. ASM Press, Washington D.C.

Kredich, N.M. 1996. Biosyntheis of Cysteine. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger, H.E., ed.), Vol. 1, pp. 514. 2 vols. ASM Press, Washington D.C.

Patte, J.C. 1996. Biosyntheis of Threonine and Lysine. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger, H.E., ed.), Vol. 1, pp. 528. 2 vols. ASM Press, Washington D.C.

Pittard, A.J. 1996. Biosynthesis of Aromatic Amino Acids. In Escherichia coli and Salmonella: Cellular and Molecular Biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger, H.E., ed.), Vol. 1, pp. 458. 2 vols. ASM Press, Washington D.C.

Reitzer, L.J. 1996. Ammonia Assimilation and the Biosynhtesis of Glutamine, Glutamate, Aspartate, Asparaginre, L-alanine and D-alanine. In Escherichia coli and Salmonella: cellular and molecular biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger H.E., ed.), Vol. 1, pp. 391. 2 vols. ASM Press, Washington D.C.

Stauffer, G.V. 1996. Biosynthesis of Serine, Glysine and One-carbon Units. In Escherichia coli and Salmonella: cellular and molecular biology 2nd edit. (Neidhardt, F. C., Curtiss III, R., Ingraham, J.L., Lin, E.C.C., Brooks Low, K., Magasanik, B., Reziikoff W.S., Riley, M., Schaechter, M., and Umbarger H.E., ed.), Vol. 1, pp. 506. 2 vols. ASM Press, Washington D.C.