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Fukuoka H, Homma M, Ichihara S. Flagellum-independent trail formation of escherichia coli on semi-solid agar. Biosci Biotechnol Biochem 2003; 67:1802-5. [PMID: 12951517 DOI: 10.1271/bbb.67.1802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Escherichia coli can form linear trails and move in a flagellum-independent manner on semisolid agar containing carbon sources. Trail formation seemed to correlate with the growth speed and/or carbon metabolism. Cell morphology in linear trails changed into larger cell sizes. We speculate that the flagellum-independent trail formation is a new mechanism for migration of E. coli cells.
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Affiliation(s)
- Hajime Fukuoka
- The Agricultural High-Tech Research Center, Meijo University, Nagoya 468-8502, Japan.
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2
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Seoh HK, Tai PC. Catabolic repression of secB expression is positively controlled by cyclic AMP (cAMP) receptor protein-cAMP complexes at the transcriptional level. J Bacteriol 1999; 181:1892-9. [PMID: 10074084 PMCID: PMC93590 DOI: 10.1128/jb.181.6.1892-1899.1999] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
SecB, a protein export-specific chaperone, enhances the export of a subset of proteins across cytoplasmic membranes of Escherichia coli. Previous studies showed that the synthesis of SecB is repressed by the presence of glucose in the medium. The derepression of SecB requires the products of both the cya and crp genes, indicating that secB expression is under the control of catabolic repression. In this study, two secB-specific promoters were identified. In addition, 5' transcription initiation sites from these two promoters were determined by means of secB-lacZ fusions and primer extension. The distal P1 promoter appeared to be independent of carbon sources, whereas the proximal P2 promoter was shown to be subject to control by the cyclic AMP (cAMP) receptor protein (CRP)-cAMP complexes. Gel-mobility shift studies showed that this regulation results from direct interaction between the secB P2 promoter region and the CRP-cAMP complex. Moreover, the CRP binding site on the secB gene was determined by DNase I footprinting and further substantiated by mutational analysis. The identified secB CRP binding region is centered at the -61.5 region of the secB gene and differed from the putative binding sites predicted by computer analysis.
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Affiliation(s)
- H K Seoh
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
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3
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Kimata K, Inada T, Tagami H, Aiba H. A global repressor (Mlc) is involved in glucose induction of the ptsG gene encoding major glucose transporter in Escherichia coli. Mol Microbiol 1998; 29:1509-19. [PMID: 9781886 DOI: 10.1046/j.1365-2958.1998.01035.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Glucose stimulates the expression of ptsG encoding the major glucose transporter in Escherichia coli. We isolated Tn 10 insertion mutations that confer constitutive expression of ptsG. The mutated gene was identified as mlc, encoding a protein that is known to be a repressor for transcription of several genes involved in carbohydrate utilization. Expression of ptsG was eliminated in a mlc crp double-negative mutant. The Mlc protein was overproduced and purified. In vitro transcription studies demonstrated that transcription of ptsG is stimulated by CRP-cAMP and repressed by Mlc. The action of Mlc is dominant over that of CRP-cAMP. DNase I footprinting experiments revealed that CRP-cAMP binds at two sites centred at -40.5 and -95.5 and that Mlc binds at two regions centred around -8 and -175. The binding of CRP-cAMP stimulated the binding of RNA polymerase to the promoter while Mlc inhibited the binding of RNA polymerase but not the binding of CRP-cAMP. Gel-mobility shift assay indicated that glucose does not affect the Mlc binding to the ptsG promoter. Our results suggest that Mlc is responsible for the repression of ptsG transcription and that glucose modulates the Mlc activity by unknown mechanism.
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Affiliation(s)
- K Kimata
- Department of Molecular Biology, Graduate School of Science, Nagoya University, Chikusa, Japan
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4
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Tagami H, Aiba H. A common role of CRP in transcription activation: CRP acts transiently to stimulate events leading to open complex formation at a diverse set of promoters. EMBO J 1998; 17:1759-67. [PMID: 9501097 PMCID: PMC1170523 DOI: 10.1093/emboj/17.6.1759] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
We have shown previously that the cyclic AMP receptor protein (CRP) is not required after the formation of the open complex at the lac promoter (Tagami and Aiba, 1995, Nucleic Acids Res., 19, 6705-6712). In this paper, we investigate the role of CRP in transcription activation at the malT and gal promoters. At the malT promoter, RNA polymerase (RNAP) forms a nonproductive RNAP-promoter binary complex in the absence of CRP and a productive CRP-RNAP-promoter ternary complex in the presence of CRP. CRP can be removed from the malT ternary complex by a moderate concentration of heparin. The resulting binary complex is functionally identical to the ternary complex. At the gal promoter, RNAP predominantly forms a binary complex at the P2 promoter in the absence of CRP and a ternary complex at the P1 promoter in the presence of CRP. A very high concentration of heparin is able to dissociate CRP from the galP1 ternary complex without changing the properties of the complex. These data indicate that CRP is not required for the maintenance of the ternary complex and plays no role in the subsequent steps, irrespective of the promoter. We conclude that the common role of CRP in the activation of transcription is to stimulate events leading to the formation of a productive open complex at a diverse set of CRP-dependent promoters. We suggest that the interaction between CRP and RNAP is needed only transiently for the activation of transcription.
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Affiliation(s)
- H Tagami
- Department of Molecular Biology, School of Science, Nagoya University, Chikusa, Nagoya 464-01, Japan
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5
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Tagami H, Aiba H. Role of CRP in transcription activation at Escherichia coli lac promoter: CRP is dispensable after the formation of open complex. Nucleic Acids Res 1995; 23:599-605. [PMID: 7899079 PMCID: PMC306726 DOI: 10.1093/nar/23.4.599] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
The role of cAMP receptor protein (CRP) in transcription activation at the Escherichia coli lac promoter was investigated focusing on the steps after the formation of open complex. Although CRP binding to the lac DNA is stabilized in the ternary open complex, a high concentration of heparin dissociates CRP from the open complex without affecting the interaction between RNA polymerase and promoter, resulting in a binary complex. The release of CRP is directly shown by Western blotting and DNase I footprinting. The binary complex exhibits a slightly increased gel mobility compared to the ternary complex. The binary complex retains the characteristics of the open complex in footprinting pattern which is essentially identical with that of the open complex of the lac UV5 promoter. The binary complex is competent for transcription. These results indicate that CRP is not necessary for the maintenance of active open complex. In addition, the removal of CRP does not increase the production of abortive RNAs. We conclude that the contact between CRP and RNA polymerase is not essential for transcription activation after the formation of the open complex at the lac promoter. In other words, the role of CRP in the lac promoter is restricted to the steps up to the formation of open complex.
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Affiliation(s)
- H Tagami
- Department of Molecular Biology, School of Science, Nagoya University, Japan
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6
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Lobocka M, Hennig J, Wild J, Kłopotowski T. Organization and expression of the Escherichia coli K-12 dad operon encoding the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase. J Bacteriol 1994; 176:1500-10. [PMID: 7906689 PMCID: PMC205218 DOI: 10.1128/jb.176.5.1500-1510.1994] [Citation(s) in RCA: 70] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A fragment of the Escherichia coli K-12 chromosome complementing the D-amino acid dehydrogenase and catabolic alanine racemase deficiency of a dad operon deletion mutant was cloned in a mini-Mu plasmid. The dadA and dadX genes were localized to a 3.5-kb part of the plasmid insert. The nucleotide sequence of this fragment revealed two open reading frames encoding 432- and 356-amino-acid-long proteins. We show here that they correspond to the dadA and dadX genes. The dadA gene can encode only the smaller of the two subunits of D-amino acid dehydrogenase. A computer search revealed the presence of a flavin adenine dinucleotide-binding motif in the N-terminal domain of the deduced DadA protein sequence. This is in agreement with biochemical data showing that the D-amino acid dehydrogenase contains flavin adenine dinucleotide in its active center. The predicted dadX gene product appeared to be 85% identical to a dadB-encoded catabolic alanine racemase of Salmonella typhimurium. The organization of the dadA and dadX genes confirmed our previous conclusion based on the genetic data (J. Wild, J. Hennig, M. Lobocka, W. Walczak, and T. Kłopotowski, Mol. Gen. Genet. 198:315-322, 1985) that these genes form an operon. The main transcription start points of the dad operon were determined by primer extension. They are preceded by a putative sigma 70 promoter sequence and two cyclic AMP-cyclic AMP receptor protein (cAMP-CRP) binding sites, one of higher and one of lower affinity to CRP. We propose that the high-affinity site, centered 59.5 bp upstream of the main transcription start point, plays a role in cAMP-CRP-mediated activation of dad operon expression in the absence of glucose.
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Affiliation(s)
- M Lobocka
- Department of Microbial Biochemistry, Polish Academy of Sciences, Warsaw
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7
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Okada N, Geist RT, Caparon MG. Positive transcriptional control of mry regulates virulence in the group A streptococcus. Mol Microbiol 1993; 7:893-903. [PMID: 8483419 DOI: 10.1111/j.1365-2958.1993.tb01180.x] [Citation(s) in RCA: 103] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Transcription of the antiphagocytic M protein in the group A streptococcus (Streptococcus pyogenes) is environmentally regulated in response to CO2 and requires Mry, a trans-acting positive regulatory protein. We have examined the role of Mry in environmental regulation by analysing the factors that regulate expression of the gene that encodes Mry (mry). By employing a strategy that utilizes integrational plasmids, it was found that expression of mry requires the participation of DNA sequences that extend 473 base pairs upstream of the Mry coding region. Transcription of mry, as analysed in S1 nuclease protection assays, is initiated from two separate promoters located within this extended regulatory region. Construction and analysis of transcriptional fusions between the mry promoters and a promoterless chloramphenicol acetyltransferase gene demonstrated that mry is autoregulated and environmentally regulated in response to the level of CO2. These data suggest a model for the regulation of virulence in S. pyogenes where positive transcriptional control of mry in response to environmental stimuli regulates the expression of the M protein.
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Affiliation(s)
- N Okada
- Department of Molecular Microbiology, Washington University School of Medicine, St Louis, Missouri 63110-1093
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Hanamura A, Aiba H. A new aspect of transcriptional control of the Escherichia coli crp gene: positive autoregulation. Mol Microbiol 1992; 6:2489-97. [PMID: 1328816 DOI: 10.1111/j.1365-2958.1992.tb01425.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Transcription of the Escherichia coli crp gene is negatively regulated by CRP-cAMP that binds to a specific site located downstream of the crp promoter. A second binding site for CRP-cAMP (CRP site II) exists upstream of the crp promoter. Using an in vitro transcription assay, we have demonstrated that CRP-cAMP activates transcription of crp in certain conditions. A promoter which carries an altered CRP-binding site II is no longer activated by CRP-cAMP, indicating that CRP site II mediates the activation of crp transcription. The concentrations of cAMP that are required for positive autoregulation are higher than those for negative autoregulation. Evidence for positive and negative autoregulation in vivo is presented by a quantitative S1 nuclease analysis.
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Affiliation(s)
- A Hanamura
- Department of Molecular Biology, School of Science, Nagoya University, Japan
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9
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Gunasekera A, Ebright Y, Ebright R. DNA sequence determinants for binding of the Escherichia coli catabolite gene activator protein. J Biol Chem 1992. [DOI: 10.1016/s0021-9258(18)42099-6] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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10
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Hussey C. Recombinant plasmids. SAFETY IN INDUSTRIAL MICROBIOLOGY AND BIOTECHNOLOGY 1992. [PMCID: PMC7155667 DOI: 10.1016/b978-0-7506-1105-3.50010-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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11
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Igarashi K, Hanamura A, Makino K, Aiba H, Aiba H, Mizuno T, Nakata A, Ishihama A. Functional map of the alpha subunit of Escherichia coli RNA polymerase: two modes of transcription activation by positive factors. Proc Natl Acad Sci U S A 1991; 88:8958-62. [PMID: 1833768 PMCID: PMC52630 DOI: 10.1073/pnas.88.20.8958] [Citation(s) in RCA: 100] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The role of the alpha subunit of Escherichia coli RNA polymerase in transcription activation by positive factors was investigated using two reconstituted mutant RNA polymerases (containing C-terminally truncated alpha subunits) and three positive factors [the cAMP receptor protein (CRP), OmpR, and PhoB]. The mutant RNA polymerases did not respond to transcription activation by activator proteins that bind upstream of the respective promoters. Transcription by these mutant enzymes was, however, activated in the cases where activators bind to target sites that overlap the promoter -35 region. Two different mechanisms are proposed for the positive control of transcription by activator proteins, one requiring the C-terminal domain of the alpha subunit, and the other not requiring it.
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Affiliation(s)
- K Igarashi
- National Institute of Genetics, Department of Molecular Genetics, Shizuoka, Japan
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12
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Tobe T, Nagai S, Okada N, Adler B, Yoshikawa M, Sasakawa C. Temperature-regulated expression of invasion genes in Shigella flexneri is controlled through the transcriptional activation of the virB gene on the large plasmid. Mol Microbiol 1991; 5:887-93. [PMID: 1857209 DOI: 10.1111/j.1365-2958.1991.tb00762.x] [Citation(s) in RCA: 118] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The invasion phenotype of shigellae is subject to thermoregulation that is known to be expressed through activation of some invasion (inv) genes such as ipaB, ipaC, and ipaD encoded by the large virulence plasmid of Shigella flexneri. The expression of ipa genes is regulated positively by virF through the activation of virB on the plasmid. To identify the mediator for the thermoregulation of the large plasmid, we have studied the effect of temperature on the transcription of virF and virB genes and ipa and the other two inv operons. The results showed that transcription of virB was affected by temperature more strictly than that of virF. Analysis of the mRNA level of virB at different levels of virF transcription indicated that virB transcription depended upon both temperature and virF. On the other hand, transcriptions of ipa and the other two inv operons depended on the activation of virB transcription but not on temperature. By inducing virB transcription from a tac promoter fused with the virB region, invasion ability was restored to a virF-deletion mutant at 30 degrees C as well as at 37 degrees C. By using conditions in which the temperature-dependent expression of the invasion phenotype was circumvented by the induction of virB transcription, intercellular spreading ability in a virF+, virB::Tn5 strain was shown to be expressed even at 30 degrees C. These results suggest that the virB transcription stage is the main target for the thermoregulation.
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Affiliation(s)
- T Tobe
- Department of Bacteriology, University of Tokyo, Japan
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13
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Valentin-Hansen P, Holst B, Søgaard-Andersen L, Martinussen J, Nesvera J, Douthwaite SR. Design of cAMP-CRP-activated promoters in Escherichia coli. Mol Microbiol 1991; 5:433-7. [PMID: 1645842 DOI: 10.1111/j.1365-2958.1991.tb02126.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We have studied the deoP2 promoter of Escherichia coli to define features that are required for optimal activation by the complex of adenosine 3',5' monophosphate (cAMP) and the cAMP receptor protein (CRP). Systematic mutagenesis of deoP2 shows that the distance between the CRP site and the -10 hexamer is the crucial factor in determining whether the promoter is activated by cAMP-CRP. Based on these observations, we propose that cAMP-CRP-activated promoters can be created by correctly aligning a CRP target and a -10 hexamer. This idea has been successfully tested by converting both a CRP-independent promoter and a sequence resembling the consensus -10 hexamer to strongly cAMP-CRP-activated promoters.
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14
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Bell A, Gaston K, Williams R, Chapman K, Kolb A, Buc H, Minchin S, Williams J, Busby S. Mutations that alter the ability of the Escherichia coli cyclic AMP receptor protein to activate transcription. Nucleic Acids Res 1990; 18:7243-50. [PMID: 2259621 PMCID: PMC332859 DOI: 10.1093/nar/18.24.7243] [Citation(s) in RCA: 155] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The effects of a number of mutations in the E. coli cyclic AMP receptor protein (CRP) have been determined by monitoring the in vivo expression and in vitro open complex formation at two semi-synthetic promoters that are totally CRP-dependent. At one promoter the CRP-binding site is centered around 41.5 base pairs upstream from the transcription start whilst at the other promoter it is 61.5 base pairs upstream. The CRP mutation E171K reduces expression from both promoters whilst H159L renders CRP totally inactive: neither mutation stops CRP binding at either promoter. The mutations K52N and K52Q reverse the effect of H159L and 'reeducate' CRP to activate transcription. CRP carrying both H159L and K52N activates transcription from the promoter with the CRP site at -41.5 better than wild type CRP. In sharp contrast, this doubly changed CRP is totally inactive with respect to the activation of transcription from the promoter carrying the CRP site at -61.5. Our results suggest that CRP can use different contacts and/or conformations during transcription activation at promoters with different architectures.
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Affiliation(s)
- A Bell
- School of Biochemistry, University of Birmingham, UK
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Ushida C, Aiba H. Helical phase dependent action of CRP: effect of the distance between the CRP site and the -35 region on promoter activity. Nucleic Acids Res 1990; 18:6325-30. [PMID: 2173826 PMCID: PMC332499 DOI: 10.1093/nar/18.21.6325] [Citation(s) in RCA: 121] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
A plasmid carrying a CRP-dependent promoter fused to the lac structural genes was manipulated to construct a set of spacing mutants that have varying lengths between the CRP binding site and the -35 region. The lengths of the spacer were changed over 45 bp by inserting or deleting nucleotides. DNase I footprinting analysis revealed that the spacer length did not affect the binding of cAMP-CRP to the CRP site. The effect of the spacer length on transcription activation by cAMP-CRP was tested in vivo by beta-galactosidase and quantitative S1 assays with crp+ and delta crp cells harboring plasmids. Insertions or deletions of non-integral helical turns, which displace the CRP site onto the opposite face of DNA helix compared to the original promoter, eliminated completely the activation of transcription. In contrast, changing the spacer length by integral helical turns allowed the promoter to respond to CRP, although the degree of activation varied with the length of the spacer. We conclude that stereospecific positioning of CRP and RNA polymerase on the DNA helix is strictly required for CRP action. The data support a model that CRP stimulates transcription by directly contacting RNA polymerase.
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Affiliation(s)
- C Ushida
- Department of Chemistry, University of Tsukuba, Japan
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Abstract
The cyclic AMP receptor protein-cAMP complex (CRP-cAMP) binds at a variety of distances upstream of several E. coli promoters and activates transcription. We have constructed a model system in which a consensus CRP binding site is placed at different distances upstream of the melR promoter. CRP-cAMP activates transcription from melR when bound at a number of positions, all of which lie on the same face of the DNA helix. The two distances at which transcription is strongly activated correspond exactly to those at which CRP-cAMP binds upstream of the well-studied galP1 and lac promoters. Footprinting of the synthetic promoters reveals that RNA polymerase makes identical contacts with their -10 regions even though CRP-cAMP binds at a different distance in each case. Kinetic analysis in vitro indicates that CRP-cAMP activates transcription from these promoters in similar but distinct ways. A model is proposed to explain this two-position activation.
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Affiliation(s)
- K Gaston
- Unité de Physicochimie des Macromolécules Biologiques, URA 1149 du CNRS, Institut Pasteur, Paris, France
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