Abstract
Escherichia coli and all other prokaryotes have developed elaborate mechanisms to adapt their metabolism to a rapidly changing environment. Some of these mechanisms allow the bacteria to approach or to flee particular chemicals (Adler, 1975; Boyd and Simon, 1982). We will not discuss such mechanisms here. Other mechanisms adapt the transcription rates of genes whose products are needed or not needed in a particular environment. Genes which deal with the catabolism of chemicals which suddenly appear in the environment have to be rapidly turned on. We have to recall that the inner bacterial membrane does not allow the entry of most organic chemicals. There has to be a permease, a specific pump, present which transports the chemical into the cell.
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References
Adhya S (1989): Multipartite genetic control elements: communication by DNA loop. Ann Rev Gent 23: 227–250
Adler J (1975): Chemotaxis in bacteria. Ann Rev Biochem 44: 341–356
Adler K, Beyreuther K, Fanning E, Geisler N, Gronenborn B, Klemm A, Müller-Hill B, Pfahl M, Schmitz A (1972): How Lac repressor binds to DNA. Nature 237: 322–327
Aiba H, Fujimoto S, Ozak N (1982): Molecular cloning and nucleotide sequencing of the gene for E. coli cAMP receptor protein. Nucl Acids Res 10: 1363–1378
Alberti S, Oehler S, v Wilcken-Bergmann B (1993): Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle. EMBO J 12: 3227–3236
Beckwith J, Davies J, Gallant JA, eds. (1983): Gene Function in Procaryotes. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Bell A, Gaston K, Williams R, Chapman K, Kolb A, Buc H, Minchin S, Williams J, Busby S (1990): Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription. Nucl Acids Res 18: 7243–7250
Berg JN, von Opheusden JHJ, Burgering MJM, Boelens R, Kaptein R (1990): Structure of Arc repressor in solution: Evidence for a family of β-sheet DNA-binding proteins. Nature 346: 586–589
Berg OG, Winter RB, von Hippel PH (1981): Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory. Biochemistry 20: 6929–6948
Blackwood EM, Eisenman RN (1991): Max: A helix-loop-helix zipper protein that forms a sequence-specific DNA-binding complex with myc. Science 251:1211–1217
Boyd A, Simon M (1982): Bacterial Chemotaxis. Ann Rev Physiol 44: 501–517
Bracco L, Kotlarz D, Kolb A, Dieckmann S, Buc H (1989): Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli. EMBO J 8: 4289–4296
Brennan RG (1992): DNA recognition by the helix-turn-helix motif. Curr Op Str Biol 2: 100–108
Brown M, Figge J, Hansen U, Wright C, Jeang K-T, Khoury G, Livingston DM, Roberts TM (1987): Lac repressor can regulate expression from a hybrid SV40 early promoter containing a lac operator in animal cells. Cell 49: 603–612
Chamness GC, Willson CD (1970): An unusual lac repressor mutant, J Mol Biol 53: 561–565
Cossart P, Gicquel-Sanzey B (1982): Cloning of the crp gene of Escherichia coli K 12. Nucl Acids Res 10: 1363–1378
Cowell IG (1994): Repression versus activation in the control of gene transcription. TIBS 19: 38–42
Croston GE, Kerrigan LA, Lira LM, Marshak DR, Kadonaga JT (1991): Sequence-specific antirepression of histone H1-mediated inhibition of basal RNA polymerase II transcription. Science 251: 644–649
Derman AI, Prinz WA, Belin D, Beckwith J (1993): Mutations that allow disulfide bond formation in the cytoplasm of Escherichia coli. Science 262: 1744–1747
Deuschle U, Gentz R, Bujard H (1986): Lac repressor blocks transcribing RNA polymerase and terminates transcription. Proc Natl Acad Sci USA 83: 4134–4137
de Crombrugghe B, Busby S, Buc H (1984): Cyclic AMP receptor protein: Role in transcription activation. Science 224: 831–838
Drlica K, Rouviere-Yaniv J (1987): Histonelike proteins of bacteria. Microb Rev 51: 301–319
Ebright R. (1993): Transcription activation at Class I CAP-dependent promoters. Molecular Microbiology 8 (5): 797–802
Ellenberger TE, Brandi CJ, Struhl K, Harrison SC (1992): The GCN4 basic region leucine zipper binds DNA as a dimer of uninterrupted α-helices: crystal structure of the protein-DNA complex. Cell 71: 1223–1237
Emmer M, de Chrombrugghe B, Ractan I, Perlman R (1970): Cyclic AMP receptor protein of E. coli: Its role in the synthesis of inducible enzymes. Proc Natl Acad Sci USA 66: 480–487
Englesberg E, Irr J, Power N, Lee J (1965): Positive control of enzyme synthesis by gene C in the L-arabinose system. J Bact 90: 946–957
Faryar K, Gatz C (1992): Construction of a tetracycline-inducible promoter in Schizosaccharomyces pombe. Curr Genet 21: 345–349
Ferré-d’Amaré A-R, Prendergast GC, Ziff EB, Burley SK (1993): Recognition by Max of its cognate DNA through a dimeric b/HLH/Z domain. Nature 363: 38–45
Fickert R, Müller-Hill B (1992): How Lac repressor finds lac operator in vitro. J Mol Biol 226: 59–68
Figge J, Wright C, Collins CJ, Roberts TM, Livingston DM (1988): Stringent regulation of stably integrated chloramphenicol acetyl transferase genes by E. coli Lac repressor in monkey cells. Cell 52: 713–722
Flashner Y, Gralla JD (1988): DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU. Cell 54: 713–721
Fritz H-J, Bicknäse H, Gleumes B, Heibach C, Rosahl S, Ehring R (1988): Characterization of two mutations in the Escherichia coli galE gene inactivating the second galactose operator and comparative studies of repressor binding. EMBO J 2: 2129–2135
Fuerst TR, Fernandez MP, Moss B (1989): Transfer of the inducible lac repressor/operator system from Escherichia coli to a vaccinia virus expression vector. Proc Natl Acad Sci USA 86: 2549–2553
Gaston K, Bell A, Kolb A, Buc H (1990): Stringent spacing requirements for transcription activation by CAP. Cell 62: 733–743
Gatz C, Frohberg C, Wendenburg R (1992): Stringent repression and homogeneous de-repression by tetracycline of a modified CaMV 35S promoter in intact transgenic tobacco plants. Plant J 3: 397–404
Gehring WJ, Müller M, Affolter M, Percival-Smith A, Billeter M, Qian YQ, Otting G, Wüthrich K (1990): The structure of the homeodomain and its functional implications. TIG 6: 323–329
Gilbert W, Müller-Hill B (1966): Isolation of the Lac repressor. Proc Natl Acad Sci USA 56: 1891–1898
Gilbert W, Müller-Hill B (1970): The lactose repressor. In: The Lactose Operon, Beckwith JR, Zipser D, eds. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Gilbert W, Majors J, Maxam A (1976): How proteins recognize DNA sequences. In: Organization and Expression of Chromosomes, Dahlem Konferenzen, Allfrey VG, Bautz EKF, McCarthy BJ, Schimke RT, Tissières A, eds. Berlin: Abakon Verlagsgesellschaft
Grunstein M (1990): Nucleosomes: regulators of transcription. TIG 6: 395–400
Guarente L, Birmingham-McDonogh O (1992): Conservation and evolution of transcriptional mechanisms in eucaryotes. TIG 6: 395–400
Guarente L, Nye JS, Hochschild A, Ptashne M (1982): Mutant phage repressor with a specific defect in its positive control function. Proc Natl Acad Sci USA 79:2236–2239
Hammer-Jespersen K, Munch-Petersen A (1975): Multiple regulation of nucleoside catabolizing enzymes: Regulation of the deo operon by the cytR and deoR gene products. Mol Gen Genet 137: 327–335
Hanes SD, Brent R (1989): DNA specificity of the Bicoid Activator Protein is determined by Homeodomain recognition helix residue 9. Cell 57: 1275–1283
Harrison SC, Aggarwal AK (1990): DNA recognition by proteins with the helix-turnhelix motif. Ann Rev Biochem 59: 933–969
Hershberger PA, deHaseth PL (1991): RNA polymerase bound to the PR promoter of bacteriophage X inhibits open complex formation at the divergently transcribed PRM promoter. J Mol Biol 222: 479–494
Hershberger P, Mita BC, Tripatara A, deHaseth PL (1992): Interference by PR-bound RNA polymerase with PRM function in vitro. J Biol Chem 268: 8943–8948
Heyduk T, Lee JC, Ebright YW, Blatter EE, Zhou Y, Ebright RH (1993): CAP interacts with RNA polymerase in solution in the absence of promoter DNA. Nature 264: 548–549
Hochschild A, Irwin N, Ptashne M (1983): Repressor structure and the mechanism of positive control. Cell 32: 319–325
Hu MC-T, Davidson N (1987): The inducible lac operator-repressor system is functional in mammalian cells. Cell 48: 555–566
Igarashi K, Hanamura A, Makino K, Aiba H, Aiba H, Mizuno T, Nataka A, Ishihama A (1991): Functional map of the a subunit of Escherichia coli RNA polymerase: Two models of transcription activation by positive factors. Proc Natl Acad Sci USA 88: 8958–8962
Igarashi K, Ishihama, A (1991): Bipartite functional map of the E. coli RNA polymerase subunit: Involvement of the C-terminal region in transcription activation by cAMP-CRP. Cell 65: 1015–1022
Irani MH, Orosz L, Adhya S (1983): A control element within a structural gene: the gal operon of Escherichia coli. Cell 32: 783–788
Jacob F, Monod J (1961): Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318–356
Janson L, Pettersson U (1990): Cooperative interactions between transcription factors Spl and OFT-1. Proc Natl Acad Sci USA 87: 4732–4736
Jobe A, Bourgeois S (1972): The Lac repressor-operator interaction VII. A repressor with unique binding properties: the X86 repressor. J Mol Biol 72: 139–152
Johnson AD, Meyer BJ, Ptashne M (1979): Interactions between DNA-bound repressors govern regulation by the λ phage repressor. Proc Natl Acad Sci USA 76: 5061–5065
Johnson PF, McKnight SL (1989): Eucaryotic transcriptional regulatory proteins. Annu Rev Biochem 58: 799–839
Jordan SR, Pabo CO (1988): Structure of the Lambda complex at 2.5 Å resolution: Details of the repressor-operator interactions. Science 242: 839–899
Kao-Huang Y, Revzin A, Butler A, O’Conner P, Noble D, von Hippel P (1977): Nonspecific DNA binding of genome-regulating proteins as a biological control mechanism: Measurement of DNA-bound E. coli lac repressor in vivo. Proc Nat Acad Sci USA 74: 4228–4232
Kaptein R, Zuiderweg ERP, Scheek RM, Boelens R, van Gunsteren WF (1985): A protein structure from nuclear magnetic resonance data. Lac repressor headpiece. J Mol Biol 182: 179–182
Khoury AM, Nick HS, Lu P (1991): In vivo interaction of Escherichia coli Lac repressor N-terminal fragments with the lac operator. J Mol Biol 219: 623–634
Kleinschmidt C, Tovar K, Hillen, W, Porschke D (1987): Dynamics of repressor-operator recognition: The Tn/0-encoded tetracycline resistance control. Biochemistry 27: 1094–1104
Knight KL, Bowie JV, Vershon AK, Kelley RD, Sauer RT (1989): The Arc and Mnt repressors. A new class of sequence-specific DNA-binding protein. J Biol Chem 264: 3639–3642
Kolb A, Busby S, Garges S, Adhya S (1993): Transcriptional regulation by cAMP and its receptor protein. Ann Rev Biochem 62: 749–795
Kolkhof P (1992): Specificities of three tight-binding Lac repressors. Nucl Acids Res 20: 5035–5039
Kolkhof P, Teichmann D, Kisters-Woike B, Wilcken-Bergmann Bv, Müller-Hill B (1992): Lac repressor with the helix-turn-helix motif of cro binds to lac operator. EMBO J 11:3031–3038
Kristie TM, LeBovitz JH, Sharp PA (1989): The octamer-binding proteins form multi-protein complexes with the HSV a TIF regulatory protein. EMBO J 8:4229–4238
Lawrence, PA (1992): The making of a fly. The genetics of animal design. London: Blackwell Scientific Publications
Laybourn PJ, Kadonaga JT (1991): Role of nucleosomal cores and histone H1 in regulation of transcription by RNA polymerase II. Science 254: 238–245
Li M, Moyle H, Susskind MM (1994): Target of the transcriptional activation function of phage λcl protein. Science 263: 75–77
Lin S-Y, Riggs AD (1975): The general affinity of lac repressor for E. coli DNA: Implications for gene regulation in procaryotes and eucaryotes. Cell 4: 107–111
Little JW (1984): Autodigestion of lex A and phage lambda repressors. Proc Natl Acad Sci USA 81: 1357–1359
Losick R, Chamberlin M (1976): RNA Polymerase. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Malan TP, McLure WR (1984): Dual promoter control of the Escherichia coli Lactose operon. Cell 39: 173–180
Maniatis T, Ptashne M, Backman K, Kleid D, Flashman S, Jeffrey A, Maurer R (1975): Recognition sequences of repressor and polymerase in the operators of bacteriophage lambda. Cell 5: 109–113
Meyer BJ, Maurer R, Ptashne M (1980): Gene regulation at the right operator (OR) of bacteriophage λ II. O R 1, O R 2, and O R 3: their roles in mediating the effects of repressor and cro. J Mol Biol 139: 163–194
McKnight SL, Yamamoto KR (1992): Transcriptional Regulation. Vol. 1 and 2. Cold Spring Harbour: Cold Spring Harbor Laboratory Press
Miller JH, Reznikoff WS, eds. (1978): The Operon. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Mitchell PJ, Tjian R (1989): Transcriptional regulation in mammalian cells by sequence-specific DNA-binding proteins. Science 245: 371–378
Mowbray SL, Cole LB (1992): 1.6 Å X-ray structure of the periplasmic ribose receptor from Escherichia coli. J Mol Biol 225: 155–175
Müller (1994): unpublished observation
Müller MM, Gerstner T, Schaffner W (1988): Enhancer sequences and regulation of gene transcription. Eur J Biochem 176: 485–495
Müller-Hill B (1971): Lac Repressor. Angew Chem Int Ed 10: 160–172
Müller-Hill B (1983): Sequence homology between Lac and Gal repressors and three sugar-binding periplasmatic proteins. Nature 302: 163–164
Nichols JC, Vyas NK, Quiocho FA, Matthews KS (1993): Models of Lactose repressor core based on alignment with sugar-binding proteins is concordant with genetic and chemical data. J Biol Chem 268: 17602–17612
Nicklin MJH, Casari G (1991): A single mutation in a truncated Fos protein allows it to interact with the TRE in vitro. Oncogene 6: 173–179
Oehler S, Amouyal M, Kolkhof P, Wilcken-Bergmann Bv, Müller-Hill B (1994); Quality and position of the three lac operators of E. coli define efficiency of repression. EMBO J 13; 3348–3355
Oehler S, Eismann ER, Krämer H, Müller-Hill B (1990): The three operators of the lac Operon cooperate in repression. EMBO J 9: 973–979
Ogata RT, Gilbert W (1978): An amino-terminal fragment of Lac repressor binds specifically to lac operator. Proc Natl Acad Sci USA 75: 5851–5854
Otwinowski Z, Schevitz RW, Zhang R-G, Lawson CL, Joachimiak A, Marmorstein RQ, Luisi BF, Sigler PB (1988): Crystal structure of trp repressor/operator complex at atomic resolution. Nature 335: 321–329
Pabo CO, Sauer RT (1984): Protein-DNA recognition. Ann Rev Biochem 53: 293–321
Pabo CO, Sauer RT, Sturtevant, JM, Ptashne M (1979): The X repressor contains two domains. Proc Natl Acad Sci USA 76: 1608–1612
Paulmier N, Yaniv M, von Wilcken-Bergmann B, Müller-Hill B (1987): gal4 transcription activator protein of yeast can function as a repressor in Escherichia coli. EMBO J 6: 3539–3542
Pettijohn DE (1988): Histone-like proteins and bacterial chromosome structure. J Biol Chem 263: 12793–12796
Pfahl M (1976): Lac repressor-operator interaction. Analysis of the X86 repressor mutant.J Mol Biol 106: 857–869
Pirrotta V (1975): Sequence of the OR operator of phage λ Nature 254: 114–117
Ptashne M (1992): A genetic Switch. Cambridge: Blackwell Scientific Publications & Cell Press
Ptashne M, Backmann K, Humayun MZ, Jeffrey A, Maurer R, Meyer B, Sauer RT (1976): Autoregulation and function of a repressor in bacteriophage lambda. Science 194: 156–161
Ransone LJ, Wamley P, Morley KL, Verma A (1990): Domain swapping reveals the modular nature of Fos, Jun, and CREB proteins. Mol Cell Biol 10: 4565–4573
Reitzer LJ, Magasanik B (1986): Transcription of gin A in E. coli is stimulated by activator bound to sites far from the promoter. Cell 45: 785–792
Renkawitz R (1990): Transcriptional repression in eucaryotes. TIG 6: 192–196
ReznikofT WS, Abelson JN (1978): The Lac promoter. In: The Operon, Miller JH, Reznikoff WS, eds. Cold Spring Harbor: Cold Spring Harbor Laboratory Press
Reznikoff WS, Winter RB, Hurley CK (1974): The location of the repressor binding sites in the lac operon. Proc Natl Acad Sci USA 79: 2314–2318
Rickenberg HV, Cohen GN, Buttin G, Monod J (1956): La galactoside-permease d’Escherichia coli. Ann Inst Pasteur 91: 829–857
Roberts JW, Roberts CW (1975): Proteolytic cleavage of bacteriophage Lambda repressor in induction. Proc Natl Acad Sci USA 72: 147–151
Schmitz A, Galas DJ (1979): The interaction of RNA polymerase and lac repressor with the lac control region. Nucl Acids Res 6: 111–137
Schüle R, Muller M, Kaltschmidt C, Renkawitz R (1988): Many transcription factors interact synergetically with steroid receptors. Science 242: 1418–1420
Schultz SC, Shields GC, Steitz TA (1991): Crystal structure of a CAP-DNA complex: The DNA is bent by 90°. Science 253: 1001–1007
Schwartz M (1967): Sur l’existence chez Escherichia coli K12 d’une régulation commune à la biosynthèse des receptors du bacteriophage et au métabolisme du maltose. Ann Inst Pasteur 113: 685–704
Sellitti MA, Pavco PA, Steege DA (1987): Lac repressor blocks in vivo transcription of lac control region DNA. Proc Natl Acad Sci USA 84: 3199–3203
Shore D, Langowski J, Baldwin RL (1981): DNA flexibility studied by covalent closure of short fragments into circles. Proc Natl Acad Sci USA 78: 4833–4837
Simons (1984): unpublished observation
Sogaard-Anderson L, Pedersen H, Holst B, Valentin-Hansen P (1991): A novel function of the cAMP-CRP complex in Escherichia coli: cAMP-CRP repressor an adaptor for the CytR repressor in the deo operon. Mol Microbiol 5: 969–975
Somers WS, Phillips SEV (1992): Crystal structure of the met repressor-operator complex at 2.8 A resolution reveals DNA recognition by β strands. Nature 359: 387–393
Staacke D, Walter B, Kisters-Woike B, Wilcken-Bergmann Bv, Müller-Hill B (1990): How Trp repressor binds to its operator. EMBO J 9: 1963–1967
Straney SB, Crothers DM (1987): Lac repressor is a transient gene activating protein. Cell 51: 699–707
Struhl K (1989): Molecular mechanism of transcriptional regulation in yeast. Annu Rev Biochem 58: 1051–1077
Takeda Y (1979): Specific repression of in vitro transcription by the Cro repressor of bacteriophage λ. J Mol Biol 127: 177–189
Teichmann (1991): unpublished observation
Vyas NK, Vyas MN, Quiocho FA (1988): Sugar and signal-transducer binding sites of the Escherichia coli galactose chemoreceptor protein. Science 242: 1290–1295
Vyas NK, Vyas MN, Quiocho FA (1991): Comparison of the periplasmic receptors for L-arabinose, D-glucose/D-galactose, and D-ribose. J Biol Chem. 266: 5226–5237
Walker GC (1984): Mutagenesis and inducible responses to deoxyribonucleic acid damage in Escherichia coli. Microbiol Rev 48: 60–93
Williams R, Bell A, Sims G, Busby S (1991): The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins. Nucl Acids Res 19: 6705–6712
Zhou Y, Busby S, Ebright RH (1993): Identification of the functional subunit of a dimeric transcription activator protein by use of oriented heterodimers. Cell 73: 375–379
Zubay G, Schwartz D, Beckwith J (1970): Mechanism of activation of catabolite-sensitive genes: A positive control system. Proc Natl Acad Sci USA 66: 104–110
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Oehler, S., Müller-Hill, B. (1995). Prokaryotic control of transcription: How and why does it differ from eukaryotic control?. In: Baeuerle, P.A. (eds) Inducible Gene Expression, Volume 1. Progress in Gene Expression. Birkhäuser Boston. https://doi.org/10.1007/978-1-4684-6840-3_1
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