Transcription activation by catabolite activator protein (CAP)

Attey, 1994, Interactions between the cyclic AMP receptor protein and the alpha subunit of RNA polymerase at the E. coli galP1 promoter, Nucl. Acids Res., 22, 4375, 10.1093/nar/22.21.4375 Beckwith, 1972, Evidence for two sites in the lac promoter region, J. Mol. Biol., 69, 155, 10.1016/0022-2836(72)90031-9 Bell, 1990, Mutations that affect the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription, Nucl. Acids Res., 17, 3865, 10.1093/nar/17.10.3865 Belyaeva, 1996, Location of the C-terminal domain of the RNA polymerase alpha subunit in different open complexes at the E. coli galactose operon regulatory region, Nucl. Acids Res., 24, 2243, 10.1093/nar/24.12.2243 Belyaeva, 1998, Transcription activation at promoters carrying tandem DNA sites for the Escherichia coli cyclic AMP receptor protein, J. Mol. Biol., 277, 789, 10.1006/jmbi.1998.1666 Blatter, 1994, Domain organization of RNA polymerase alpha subunit, Cell, 78, 889, 10.1016/S0092-8674(94)90682-3 Brennan, 1991, Interactions of the helix-turn-helix binding domain, Curr. Opin. Struct. Biol., 1, 80, 10.1016/0959-440X(91)90015-L Brennan, 1992, DNA recognition by the helix-turn-helix motif, Curr. Opin. Struct. Biol., 2, 100, 10.1016/0959-440X(92)90184-9 Burgess, 1976, Purification and physical properties of E. coli RNA polymerase, 69 Busby, 1994, Promoter structure, promoter recognition, and transcription activation in prokaryotes, Cell, 79, 743, 10.1016/0092-8674(94)90063-9 Busby, 1997, Transcription activation at class II CAP-dependent promoters, Mol. Microbiol., 23, 853, 10.1046/j.1365-2958.1997.2771641.x Busby, 1994, Transcription activation by the E. coli cyclic AMP receptor protein, J. Mol. Biol., 241, 341, 10.1006/jmbi.1994.1511 Bushman, 1989, A single glutamic acid residue plays a key role in the transcriptional activation function of lambda repressor, Cell, 58, 1163, 10.1016/0092-8674(89)90514-X Chamberlin, 1976, RNA polymerase - an overview, 17 Chen, 1994, Identification of the target of a transcription activator protein by protein-protein photocrosslinking, Science, 265, 90, 10.1126/science.8016656 Czarniecki, 1997, The −45 region of the Escherichia coli lac promoter, J. Bacteriol., 179, 423, 10.1128/jb.179.2.423-429.1997 Darst, 1998, Insights into Escherichia coli RNA polymerase structure from a combination of X-ray and electron crystallography, J. Struct. Biol., 124, 115, 10.1006/jsbi.1998.4057 Ebright, 1993, Transcription activation at class I CAP-dependent promoters, Mol. Microbiol., 8, 797, 10.1111/j.1365-2958.1993.tb01626.x Ebright, 1995, Escherichia coli RNA polymerase alpha subunit, Curr. Opin. Genet. Dev., 5, 197, 10.1016/0959-437X(95)80008-5 Eichenberger, 1996, Influence of the location of the cAMP receptor protein binding site on the geometry of a transcriptional activation complex in Escherichia coli, Biochemistry, 35, 15302, 10.1021/bi961377d Emmer, 1970, Cyclic AMP receptor protein of E. coli, Proc. Natl Acad. Sci. USA, 66, 480, 10.1073/pnas.66.2.480 Eschenlauer, 1991, Escherichia coli catabolite gene activator protein mutants defective in positive control of lac operon transcription, J. Bacteriol., 173, 5024, 10.1128/jb.173.16.5024-5029.1991 Estrem, 1999, Bacterial promoter architecture, Genes Dev., 13, 2134, 10.1101/gad.13.16.2134 Flatow, 1996, Analysis of the spacer DNA between the cyclic AMP receptor protein site and the lac promoter, J. Bacteriol., 178, 2436, 10.1128/jb.178.8.2436-2439.1996 Forsman, 1992, Antirepression function in Escherichia coli for the cAMP-cAMP receptor protein transcriptional activator, Proc. Natl Acad. Sci. USA, 89, 9880, 10.1073/pnas.89.20.9880 Gaal, 1996, DNA-binding determinants of the alpha subunit of RNA polymerase, Genes Dev., 10, 16, 10.1101/gad.10.1.16 Gaston, 1990, Stringent spacing requirements for transcription activation by CRP, Cell, 62, 733, 10.1016/0092-8674(90)90118-X Goff, 1984, Coliphage-induced ADP-ribosylation of Escherichia coli RNA polymerase, Methods Enzymol., 106, 418, 10.1016/0076-6879(84)06045-6 Gralla, 1996, Organization and function of transcription regulatory elements, 1232 Gross, 1998, The functional and regulatory roles of sigma factors in transcription, Cold Spring Harbor Symp. Quant. Biol., 63, 141, 10.1101/sqb.1998.63.141 Guest, 1996, The FNR modulon and FNR-regulated gene expression, 317 Hawley, 1982, Mechanism of activation of transcription initiation from the lambda PRM promoter, J. Mol. Biol., 157, 493, 10.1016/0022-2836(82)90473-9 Heyduk, 1993, CAP-RNA polymerase interaction in solution in the absence of promoter DNA, Nature, 364, 548, 10.1038/364548a0 Hochschild, 1998, Protein-protein contacts that activate and repress prokaryotic transcription, Cell, 92, 597, 10.1016/S0092-8674(00)81126-5 Igarashi, 1991, Bipartite functional map of the E. coli RNA polymerase α subunit, Cell, 65, 1015, 10.1016/0092-8674(91)90553-B Igarashi, 1991, Functional map of the alpha subunit of Escherichia coli RNA polymerase, Proc. Natl Acad. Sci. USA, 88, 8958, 10.1073/pnas.88.20.8958 Jeon, 1995, Solution structure of the activator contact domain of the RNA polymerase α subunit, Science, 270, 1495, 10.1126/science.270.5241.1495 Jeon, 1997, Flexible linker in the RNA polymerase alpha subunit facilitates the independent motion of the C-terminal activator contact domain, J. Mol. Biol., 267, 953, 10.1006/jmbi.1997.0902 Jin, 1995, Evidence for contact between the cyclic AMP receptor protein and the σ70 subunit of Escherichia coli RNA polymerase, J. Biol. Chem., 270, 19213, 10.1074/jbc.270.33.19213 Joung, 1993, Synergistic activation of transcription by Escherichia coli cAMP receptor protein, Proc. Natl Acad. Sci. USA, 90, 3083, 10.1073/pnas.90.7.3083 Joung, 1994, Synergistic activation of transcription by bacteriophage λ cI protein and E. coli cAMP receptor protein, Science, 265, 1863, 10.1126/science.8091212 Kainz, 1998, The C-terminal domain of the alpha subunit of Escherichia coli RNA polymerase is required for Rho-dependent transcription termination, J. Mol. Biol., 284, 1379, 10.1006/jmbi.1998.2272 Kallipolitis, 1997, Protein-protein communication, Cell, 89, 1101, 10.1016/S0092-8674(00)80297-4 Kolb, 1993, Transcriptional regulation by cyclic AMP and its receptor protein, Annu. Rev. Biochem., 62, 749, 10.1146/annurev.bi.62.070193.003533 Kolb, 1993, E. coli RNA polymerase, deleted in the C-terminal part of its α-subunit, interacts differently with the cAMP-CRP complex at the lacP1 and at the galP1 promoter, Nucl. Acids Res., 21, 319, 10.1093/nar/21.2.319 Langdon, 1999, A novel genetic method for dissecting the mechanism of transcriptional activator synergy by identical activators, Proc. Natl Acad. Sci. USA, 10.1073/pnas.96.22.12673 Law, 1999, Interactions between the Escherichia coli cAMP receptor protein and the C-terminal domain of the α subunit of RNA polymerase at class I promoters, Biochem. J., 337, 415, 10.1042/0264-6021:3370415 Li, 1998, Transcription activation by Escherichia coli FNR protein, Nucl. Acids Res., 26, 2075, 10.1093/nar/26.9.2075 Li, 1994, Target of the transcriptional activation function of phage λ cI protein, Science, 263, 75, 10.1126/science.8272867 Liu, 1995, NusA interferes with interactions between the nascent RNA and the C-terminal domain of the alpha subunit of RNA polymerase in Escherichia coli transcription complexes, Proc. Natl Acad. Sci. USA, 92, 5012, 10.1073/pnas.92.11.5012 Liu, 1996, Role of Escherichia coli RNA polymerase alpha subunit in modulation of pausing, termination and anti-termination by the transcription elongation factor NusA, EMBO J., 15, 150, 10.1002/j.1460-2075.1996.tb00343.x Lloyd, 1998, Spacing requirements for interactions between the C-terminal domain of the α subunit of Escherichia coli RNA polymerase and the cyclic AMP receptor protein, Biochem. J., 330, 413, 10.1042/bj3300413 Lobell, 1991, AraC DNA looping, J. Mol. Biol., 218, 45, 10.1016/0022-2836(91)90872-4 Lonetto, 1998, Identification of a contact site for different transcription activators in Region 4 of the Escherichia coli RNA polymerase σ70 subunit, J. Mol. Biol., 284, 1353, 10.1006/jmbi.1998.2268 Malan, 1984, Mechanism of CRP-cAMP activation of the lac operon, J. Mol. Biol., 180, 881, 10.1016/0022-2836(84)90262-6 Malhotra, 1996, Crystal structure of a σ70 subunit fragment from E. coli RNA polymerase, Cell, 87, 127, 10.1016/S0092-8674(00)81329-X McKay, 1981, Structure of catabolite gene activator protein at 2.9 Angstroms resolution suggests binding to left-handed B-DNA, Nature, 290, 744, 10.1038/290744a0 Meibom, 1999, Dissection of a surface-exposed portion of the cAMP-CRP complex that mediates transcription activation and repression, Mol. Microbiol., 32, 497, 10.1046/j.1365-2958.1999.01362.x Merkel, 1995, Transcription activation at the Escherichia coli uhpT promoter by the catabolite gene activator protein, J. Bacteriol., 177, 1712, 10.1128/jb.177.7.1712-1718.1995 Meyer-Almes, 1994, The structure of the RNA polymerase-promoter complex, J. Mol. Biol., 236, 1, 10.1006/jmbi.1994.1112 Miller, 1997, RNA polymerase beta′ subunit, Science, 275, 1655, 10.1126/science.275.5306.1655 Mollegaard, 1993, Characterization of promoter recognition complexes formed by CRP and CytR for repression and by CRP and RNA polymerase for activation of transcription on the Escherichia coli deo P2 promoter, J. Biol. Chem., 268, 17471, 10.1016/S0021-9258(19)85358-9 Murakami, 1996, Transcription factor recognition surface on the RNA polymerase α subunit is involved in contact with the DNA enhancer element, EMBO J., 15, 4358, 10.1002/j.1460-2075.1996.tb00809.x Murakami, 1997, Positioning of two alpha subunit carboxy-terminal domains of RNA polymerase along promoter DNA by two transcription factors, Proc. Natl Acad. Sci. USA, 94, 11274, 10.1073/pnas.94.21.11274 Nechaev, 1999, Inhibition of Escherichia coli RNA polymerase by bacteriophage T7 gene 2 protein, J. Mol. Biol., 289, 815, 10.1006/jmbi.1999.2782 Negishi, 1995, Structural map of the alpha subunit of Escherichia coli RNA polymerase, J. Mol. Biol., 248, 723, 10.1006/jmbi.1995.0254 Niu, 1994, Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). I. Saturation and alanine scanning mutagenesis, J. Mol. Biol., 243, 595, 10.1016/0022-2836(94)90034-5 Niu, 1996, Transcription activation at class II CAP-dependent promoters, Cell, 87, 1123, 10.1016/S0092-8674(00)81806-1 Noel, 1998, CAP, the −45 region, and RNA polymerase, J. Mol. Biol., 282, 495, 10.1006/jmbi.1998.2040 Orphanides, 1996, The general transcription factors of RNA polymerase II, Genes Dev., 10, 2657, 10.1101/gad.10.21.2657 Parkinson, 1996, Structure of the CAP-DNA complex at 2.5 Å resolution, J. Mol. Biol., 260, 395, 10.1006/jmbi.1996.0409 Parkinson, 1996, Aromatic hydrogen bond in sequence-specific protein-DNA interaction, Nature Struct. Biol., 3, 837, 10.1038/nsb1096-837 Passner, 1998, The structure of a CAP-DNA complex having two cAMP molecules bound to each monomer, Proc. Natl Acad. Sci. USA, 94, 2843, 10.1073/pnas.94.7.2843 Perez-Martin, 1993, Protein-induced bending as a transcriptional switch, Science, 260, 805, 10.1126/science.8387228 Polyakov, 1995, Three-dimensional structure of E. coli core RNA polymerase, Cell, 83, 365, 10.1016/0092-8674(95)90114-0 Rees, 1993, Evidence of DNA bending in transcription complexes imaged by scanning force microscopy, Science, 260, 1646, 10.1126/science.8503010 Ren, 1988, Cooperative DNA binding of heterologous proteins, Proc. Natl Acad. Sci. USA, 85, 4138, 10.1073/pnas.85.12.4138 Rhodius, 1998, Positive activation of gene expression, Curr. Opin. Microbiol., 1, 152, 10.1016/S1369-5274(98)80005-2 Rhodius, 1997, Transcription activation at class II CRP-dependent promoters, Nucl. Acids Res., 25, 326, 10.1093/nar/25.2.326 Richet, 1991, A new mechanism for coactivation of transcription initiation, Cell, 66, 1185, 10.1016/0092-8674(91)90041-V Rivetti, 1999, Wrapping of DNA around the E. coli RNA polymerase open promoter complex, EMBO J., 18, 4464, 10.1093/emboj/18.16.4464 Roeder, 1996, The role of general initiation factors in transcription by RNA polymerase II, Trends Biochem. Sci., 21, 327, 10.1016/S0968-0004(96)10050-5 Ross, 1993, A third recognition element in bacterial promoters, Science, 262, 1407, 10.1126/science.8248780 Ryu, 1994, An arcane role of DNA in transcription activation, Proc. Natl Acad. Sci. USA, 91, 8582, 10.1073/pnas.91.18.8582 Savery, 1995, Transcription activation at Escherichia coli promoters dependent on the cyclic AMP receptor protein, Biochem. J., 309, 77, 10.1042/bj3090077 Savery, 1996, Regulation of promoters by two transcription activators, Biochem. Soc. Trans., 24, 351, 10.1042/bst0240351 Savery, 1998, Transcription activation at class II CRP-dependent promoters, EMBO J., 17, 3439, 10.1093/emboj/17.12.3439 Schauer, 1996, The alpha subunit of RNA polymerase and transcription antitermination, Mol. Microbiol., 21, 839, 10.1046/j.1365-2958.1996.451409.x Schultz, 1991, Crystal structure of a CAP-DNA complex, Science, 253, 1001, 10.1126/science.1653449 Scott, 1995, Transcriptional coactivation at the ansB promoters, Mol. Microbiol., 18, 521, 10.1111/j.1365-2958.1995.mmi_18030521.x Severinov, 1994, A non-essential domain of Escherichia coli RNA polymerase required for the action of the termination factor Alc, J. Biol. Chem., 269, 14254, 10.1016/S0021-9258(17)36782-0 Søgaard-Andersen, 1991, Single amino acid substitutions in the cAMP receptor protein specifically abolish regulation by the CytR repressor in Escherichia coli, Proc. Natl Acad. Sci. USA, 88, 4921, 10.1073/pnas.88.11.4921 Straney, 1989, Synergy between Escherichia coli CAP protein and RNA polymerase in the lac promoter open complex, J. Mol. Biol., 206, 41, 10.1016/0022-2836(89)90522-6 Tagami, 1995, Role of CRP in transcription activation at the Escherichia coli lac promoter, Nucl. Acids Res., 23, 599, 10.1093/nar/23.4.599 Tagami, 1998, A common role of CRP in transcription activation, EMBO J., 17, 1759, 10.1093/emboj/17.6.1759 Tagami, 1999, An inactive open complex mediated by an UP element at Escherichia coli promoters, Proc. Natl Acad. Sci. USA, 96, 7202, 10.1073/pnas.96.13.7202 Tang, 1994, Location, structure, and function of the target of a transcriptional activator protein, Genes Dev., 8, 3058, 10.1101/gad.8.24.3058 Ushida, 1990, Helical phase dependent action of CRP, Nucl. Acids Res., 18, 6325, 10.1093/nar/18.21.6325 Valentin-Hansen, 1996, A flexible partnership, Mol. Microbiol., 20, 461, 10.1046/j.1365-2958.1996.5341056.x West, 1993, Interactions between the Escherichia coli cyclic AMP receptor protein and RNA polymerase at class II promoters, Mol. Microbiol., 10, 789, 10.1111/j.1365-2958.1993.tb00949.x Williams, 1991, The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins, Nucl. Acids Res., 19, 6705, 10.1093/nar/19.24.6705 Williams, 1996, Orientation of functional activating regions in the E. coli CRP protein during transcription activation at class II promoters, Nucl. Acids Res., 24, 1112, 10.1093/nar/24.6.1112 Williams, 1997, Transcription activation at class I FNR-dependent promoters, Nucl. Acids Res., 25, 4028, 10.1093/nar/25.20.4028 Wing, 1995, Spacing requirements for transcription activation by Escherichia coli FNR protein, J. Bacteriol., 177, 6704, 10.1128/jb.177.23.6704-6710.1995 Zhang, 1998, Structure of the Escherichia coli RNA polymerase alpha subunit amino-terminal domain, Science, 281, 262, 10.1126/science.281.5374.262 Zhang, 1998, Catabolite gene activator protein mutations affecting activity of the araBAD promoter, J. Bacteriol., 180, 195, 10.1128/JB.180.2.195-200.1998 Zhou, 1993, Identification of the activating region of CAP, Proc. Natl Acad. Sci. USA, 90, 6081, 10.1073/pnas.90.13.6081 Zhou, 1993, Identification of the functional subunit of a dimeric transcription activator protein by use of “oriented heterodimers”, Cell, 73, 375, 10.1016/0092-8674(93)90236-J Zhou, 1994, Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters, J. Mol. Biol., 243, 603, 10.1016/0022-2836(94)90035-3 Zhou, 1994, The functional subunit of a dimeric transcription activator protein depends on promoter architecture, EMBO J., 13, 4549, 10.1002/j.1460-2075.1994.tb06776.x Zou, 1992, Mapping the cAMP receptor protein contact site on the alpha subunit of Escherichia coli RNA polymerase, Mol. Microbiol., 6, 2599, 10.1111/j.1365-2958.1992.tb01437.x Zou, 1993, Asymmetric arrangement of two alpha subunits within Escherichia coli RNA polymerase. Involvement of one alpha subunit in contact with cAMP receptor protein, J. Mol. Biol., 11, 1283 Zubay, 1970, Mechanism of activation of catabolite-sensitive genes, Proc. Natl Acad. Sci. USA, 66, 104, 10.1073/pnas.66.1.104