in Bacteria

Year 2009, Volume: 22 Issue: 2, 77 - 82, 22.03.2010

İsmail Akyol , Uğur Çömlekçıoğlu

Abstract

Gene Regulation and Transcriptional Regulation in Bacteria

Abstract

The catabolite gene activator protein (CAP) and the fumurate nitrate reductase (FNR) are two founder members of the growing CRP-FNR protein superfamily. The consensus FNR binding site (TTGAT-N₄-ATCAA) closely resembles that of CRP to the extent that both contain a common core motif (NTGAN-N₄-NTCAN). The transcription factor FNR plays a role in altering gene expression between aerobic and anaerobic conditions but CRP regulators control the response to glucose starvation. Protein DNA interactions occur between the regulatory protein and DNA at the corresponding promoter using the consensus either CRP or FNR binding sites. Successful transcriptional activation generally requires contact between a DNA-bound activator and RNA polymerase in order to generate on effective complex. CRP promoters are grouped into two classes depending on the location of DNA binding site. Class I promoters contains transcription activator binding sites centered near position -61.5, -71, -82 or -92. Class II promoters the regulator proteins bind to a site centered at or near -41.5 so three possible contacts, α_CTD-AR1, α_NTD-AR2 and δ⁷⁰-AR3, occur between regulator and RNA polymerase. FNR and FLP act as a class II activator.

 Key Words: Transcription regulation, FNR, CAP, FLP.

 

Keywords

Transcription regulation, FNR, CAP, FLP

References

• Korner, H., Sofia, H.J., Zumft, G.W., “Phylogeny of the bacterial superfamily of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs”, FEMS Microbiol. Rev., 27: 559-592 (2003).
• Fischer, H.M., “Genetic-regulation of nitrogen fixation in rhizobia”, Microbiol. Rev., 58: 352-386 (1994).
• Spiro, S., “The FNR family of transcriptional regulators”, Antonie van Leeuwenhoek, 66: 23-36 (1994).
• Green, J., Scott, C., Guest, J.R., “Functional versatility in the CRP-FNR superfamily of transcription factors: FNR and FLP”, Adv. Microb. Physiol., 44: 1-34 (2001).
• Kiley, P.J., Beinert, H., “Oxygen sensing by the global regulator, FNR: the role of the iron-sulfur cluster”, FEMS Microbiol. Rev., 22: 341-352 (1999).
• Guest, J.R., Green, J., Irvine, A.S., Spiro, S., “The FNR modulon and FNR regulated gene expression”, In Regulation of Gene Expression in Escherichia coli, Edited by E.C.C. Lin and A.S., Lynch: R.G., Landes Company, 317-341 (1996).
• Bell, A.I., Gaston, K.L., Cole, J.A., Busby, S., “Cloning of binding sequences for the Escherichia coli transcription activators, fnr and crp location of bases involved in discrimination between FNR and CRP”, Nucleic Acids Res., 17: 3865-3874 (1989).
• Zhang, X.P., Ebright, R.H., “Substitution of 2 base-pairs (1 base pair per dna half-site) within the Escherichia coli lac promoter dna site for catabolite gene activator protein places the lac promoter in the fnr regulon”, J. Biol. Chem., 265: 12400-12403 (1990).
• Vega-Palas, M.A., Flores, E., Herrero, A., “Ntca, a global nitrogen regulator from the cyanobacterium synechococcus that belongs to the crp family of bacterial regulators”, Mol. Microbiol., 6: 18531859 (1992).
• Herrero, A., Muro-Pastor, A.M., Flores, E., “Nitrogen control in cyanobacteria”, J. Bacteriol., 183: 411-425 (2001).
• Kolb, A., Busby, S., Buc, H., Garges, S., Adhya, S., “Transcriptional Regulation by cAMP and its receptor protein”, Annu. Rev. Biochem., 62: 749795 (1993).
• Gaston, K., Kolb, A., Busby, S., “Binding of the Escherichia coli cyclicamp receptor protein to dna fragments containing consensus nucleotidesequences”, Biochem. J., 261: 649-653 (1989).
• Spiro, S., Guest, J.R., “FNR and its role in oxygenregulated gene-expression in Escherichia coli”, FEMS Microbiol. Rev., 75: 399-428 (1990).
• Schultz, S.C., Shields, G.C., Steitz, T.A., “Crystalstructure of a CAP-DNA complex - the dna is bent by 90- degrees”, Sci., 253: 1001-1007 (1991).
• Busby, S., Ebright, R.H., “Transcription activation by catabolite activator protein (CAP)”, J. Mol. Biol., 293: 199-213 (1999).
• Ebright, R.H., “Transcription activation at class-i cap-dependent promoters”, Mol. Microbiol., 8: 797-802 (1993).
• Popescu, C.V., Bates, D.M., Beinert, H., Munck, E., Kiley, P.J., “Mossbauer spectroscopy as a tool for the study of activation/inactivation of the transcription regulator FNR in whole cells of Escherichia coli”, Proc. Natl. Acad. Sci., USA, 95: 13431-13435 (1998).
• Unden, G., Achebach, S., Holighaus, G., Tran, H.Q., Wackwitz, B., Zeuner, Y., “Control of FNR function of Escherichia coli by O-2 and reducing conditions”, J. Mol. Microbiol. Biotechnol., 4: 263-268 (2002).
• Khoroshilova, N., Popescu, C., Munck, E., Beinert, H., Kiley, P.J., “Iron-sulfur cluster disassembly in the FNR protein of Escherichia coli by O-2: [4Fe4S] to [2Fe-2S] conversion with loss of biological activity”, Proc. Natl. Acad. Sci., USA, 94: 60876092 (1997).
• Lazazzera, B.A., Beinert, H., Khoroshilova, N., Kennedy, M.C., Kiley, P.J., “DNA binding and dimerization of the Fe-S-containing FNR protein from Escherichia coli are regulated by oxygen”, J. Biol. Chem., 271: 2762-2768 (1996).
• Green, J., Trageser, M., Six, S., Unden, G., Guest, J.R., “Characterization of the Fnr protein of Escherichia coli, an iron-binding transcriptional regulator”, Proc. R. Soc. London Ser. B-Biol. Sci., 244: 137-144 (1991).
• Green, J., Sharrocks, A.D., Green, B., Geisow, M., Guest, J.R., “Properties of Fnr proteins substituted at each of the 5 cysteine residues”, Mol. Microbiol., 8: 61-68 (1993).
• Moore, L.J., Kiley, P.J., “Characterization of the dimerization domain in the FNR transcription factor”, J. Biol. Chem., 276: 45744-45750 (2001).
• Ralph, E.T., Scott, C., Jordan, P.A., Thomson, A.J., Guest, J.R., Green, J., “Anaerobic acquisition of [4Fe 4S] clusters by the inactive FNR (C20S) variant and restoration of activity by second-site amino acid substitutions”, Mol. Microbiol., 39: 1199-1211 (2001).
• Sharrocks, A.D., Green, J., Guest, J.R., “Invivo and invitro mutants of fnr the anaerobic transcriptional regulator of Escherichia coli”, FEBS Lett., 270: 119-122 (1990).
• Melville, S.B., Gunsalus, R.P., “Mutations in FNR that alter anaerobic regulation of electron transport-associated genes in Escherichia coli”, J. Biol. Chem., 265: 18733-18736 (1990).
• Scott, C., Green, J., “Miscoordination of the ironsulfur clusters of the anaerobic transcription factor, FNR, allows simple repression but not activation”, J. Biol. Chem., 277: 1749-1754 (2002).
• Bates, D.M., Lazazzera, B.A., Kiley, P.J., “Characterization of fnr asterisk mutant proteins indicates 2 distinct mechanisms for altering oxygen regulation of the Escherichia coli transcription factor FNR”, J. Bacteriol., 177: 3972-3978 (1995).
• Bates, D.M., Popescu, C.V., Khoroshilova, N., Vogt, K., Beinert, H., Munck, E., Kiley, P.J., “Substitution of leucine 28 with histidine in the Escherichia coli transcription factor FNR results in increased stability of the [4Fe-4S](2+) cluster to oxygen”, J .Biol. Chem., 275: 6234-6240 (2000).
• Busby, S., Kolb, A., “The CAP modulon, in Regulation of Gene expression in Escherichia coli”, Austin, TX: R. G. Landes Company, 255279 (1996).
• Gunasekera, A., Ebright, Y.W., Ebright, R.H., “DNA-sequence determinants for binding of the Escherichia coli catabolite gene activator protein”, J. Biol. Chem., 267: 14713-14720 (1992).
• Ziegelhoffer, E.C., Kiley, P.J., “In-vitro analysis of a constitutively active mutant form of the Escherichia coli global transcription factor FNR”, J. Mol. Biol., 245: 351-361 (1995).
• Irvine, A.S., Guest, J.R., “Lactobacillus casei contains a member of the CRP-FNR family”, Nucleic Acids Res., 21: 753 (1993).
• Gostick, D.O., Green, J., Irvine, A.S., Gasson, M.J., Guest, J.R., “A novel regulatory switch mediated by the FNR-like protein of Lactobacillus casei”, Microbiol., 144: 705-717 (1998).
• Gostick, D.O., Griffin, H.G., Shearman, C.A., Scott, C., Green, J., Gasson, M.J., Guest, J.R., “Two operons that encode FNR like proteins in Lactococcus lactis”, Mol. Microbiol., 31: 15231535 (1999).
• Scott, C., Rawsthorne, H., Upadhyay, M., Shearman, C.A., Gasson, M.J., Guest, J.R., Green, J., “Zinc uptake, oxidative stress and the FNR-like proteins of Lactococcus lactis”, Fems Microbiol. Lett., 192: 85-89 (2000).
• Akyol, I., “The role of FNR like proteins in Lactococcus lactis”, PhD thesis, University of East Anglia, U.K. (2002).