Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon

Lavigne, Marc; Herbert, Michel; Kolb, Annie; Buc, Henri

doi:10.1016/0022-2836(92)90995-v

Cited by 61 publications

(53 citation statements)

References 57 publications

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“…DNA structural distortions are known to influence promoter activity (4,5). Certain oligo (A/T) tracts exhibit unusual curvature (6) and play an important role in the regulation of transcription initiation (7)(8)(9)(10)(11). A different role is attributed to the A tract when it is positioned upstream and in phase with the promoter elements.…”

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confidence: 99%

Intrinsic DNA Distortion of the Bacteriophage MumomP1 Promoter Is a Negative Regulator of Its Transcription

Basak

Olsen

Hattman

et al. 2001

Journal of Biological Chemistry

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The momP1 promoter of the bacteriophage Mu mom operon is an example of a weak promoter. It contains a 19-base pair suboptimal spacer between the ؊35 (ACCACA) and ؊10 (TAGAAT) hexamers. Escherichia coli RNA polymerase is unable to bind to momP1 on its own. DNA distortion caused by the presence of a run of six T nucleotides overlapping the 5 end of the ؊10 element might prevent RNA polymerase from binding to momP1. To investigate the influence of the T 6 run on momP1 expression, defined substitution mutations were introduced by site-directed mutagenesis. In vitro probing experiments with copper phenanthroline ((OP) 2 Cu) and DNase I revealed distinct differences in cleavage patterns among the various mutants; in addition, compared with the wild type, the mutants showed an increase (variable) in momP1 promoter activity in vivo. Promoter strength analyses were in agreement with the ability of these mutants to form open complexes as well as to produce momP1-specific transcripts. No significant role is attributed to the overlapping and divergently organized promoter, momP2, in the expression of momP1 activity, as determined by promoter disruption analysis. These data support the view that an intrinsic DNA distortion in the spacer region of momP1 acts in cis as a negative element in mom operon transcription. This is a novel mechanism of regulation of toxic gene expression.

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Intrinsic DNA Distortion of the Bacteriophage MumomP1 Promoter Is a Negative Regulator of Its Transcription

Basak

Olsen

Hattman

et al. 2001

Journal of Biological Chemistry

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“…Such a loop enhances the affinity of the complex to DNA and brings together components of the transcriptional complex that are otherwise more distant in the DNA sequence (Matthews 1992;Rippe et al 1995). Curved DNA upstream to the promoter (upstream curved sequence, or UCS) has been shown to play a functionally regulatory role in Escherichia coli (Plaskon and Wartell 1987;Bracco et al 1989;Lavigne et al 1992;Carmona and Magasanik 1996;Dethiollaz et al 1996).In many of these and other investigations, presence of the curved DNA was established experimentally by a gel-electrophoretic anomaly technique. In many publications, existing computational models were shown to predict magnitude of DNA curvature with high reliability (Boffelli et al 1992;Shpigelman et al 1993;Goodsell and Dickerson 1994).…”

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Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters

Bolshoy¹,

Nevo²

2000

Genome Res.

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After our analysis of the distribution of predicted intrinsic curvature along all available complete prokaryotic genomes, the genomes were divided into two groups. Curvature distribution in all prokaryotes of the first group indicated a substantial fraction of promoters characterized by intrinsic DNA curvature located within or upstream of the promoter region. We did not find this peculiar DNA curvature distribution in prokaryotes in the second group. Remarkably, all bacteria of the first group were mesophilic, whereas many prokaryotes of the second group were hyperthermophilic. We hypothesize that DNA curvature plays a biologic role in gene regulation in mesophilic as opposed to hyperthermophilic prokaryotes, i.e., DNA curvature presumably has a functional adaptive significance determined by temperature selection.The determination of complete genome sequences led to evolutionary analysis at the comprehensive level of genomes. Computer analysis of complete prokaryotic genomes has resulted in characterization of families of orthologs across a wide phylogenetic range Huynen and Bork 1998;Koonin et al. 1998), focusing primarily on gene evolution. Some recent research has studied the evolution of transcription regulation (Aravind and Koonin 1999;Gelfand et al., 2000). Our objective was to scrutinize, compare, and contrast gene regulation in Archaea and Bacteria. One such pattern of gene regulation is the presence of curved DNA upstream of a promoter, which has been described as "a common theme in prokaryotic gene expression" (Perez-Martin et al. 1994). The widely accepted hypothesis explaining the possible functional role of curvature in gene expression is that curved DNA assists in the formation of a large loop around RNA polymerase. Such a loop enhances the affinity of the complex to DNA and brings together components of the transcriptional complex that are otherwise more distant in the DNA sequence (Matthews 1992;Rippe et al. 1995). Curved DNA upstream to the promoter (upstream curved sequence, or UCS) has been shown to play a functionally regulatory role in Escherichia coli (Plaskon and Wartell 1987;Bracco et al. 1989;Lavigne et al. 1992;Carmona and Magasanik 1996;Dethiollaz et al. 1996).In many of these and other investigations, presence of the curved DNA was established experimentally by a gel-electrophoretic anomaly technique. In many publications, existing computational models were shown to predict magnitude of DNA curvature with high reliability (Boffelli et al. 1992;Shpigelman et al. 1993;Goodsell and Dickerson 1994). In a previous study ), we applied the three most popular prediction models (De Santis et al. 1990;Bolshoy et al. 1991;Goodsell and Dickerson 1994) to compare distribution of average curvature values in different sets of sequences. One of the most important results of our study was that, qualitatively, all models demonstrated identical results. All three models indicated that UCS were found in E. coli substantially more frequently than it could be expected either from random distribution of DN...

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“…In this context, bending of DNA by Crp interaction, as described for other systems such as the gal promoter (Lavigne et al, 1992), may influence the mechanism of transcription initiation. Furthermore, curved sequences could also account for uncharacterized regulatory effects (decrease in induction) caused by the presence of sequences upstream of position -193 (Fig.…”

Section: Djscussj Onmentioning

confidence: 99%

The aldA gene of Escherichia coli is under the control of at least three transcriptional regulators

1997

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Expression studies on the aldA gene encoding aldehyde dehydrogenase in Escherichia coli showed induction by two types of molecule (hydroxyaldehydes and 2-oxoglutarate), carbon catabolite repression and respiration dependence. Promoter deletion analysis showed that the proximal operator, which includes inducer-regulator complex and catabolite repression protein (Crp) recognition sites, was necessary for induction by either type of inducer, and that full induction by aldehydes required the cooperation of distal operator sequences beyond position -1 19. Interactions of the regulator protein with the -59 to -6 fragment were shown by DNA mobility shift assays. Fusions of different deletions of the aldA promoter to lac2 indicated that a Crp site proximal to the transcriptional start point (top) was functional in the CAMP-dependent catabolite repression of this system, whereas a distal control site was likely to operate in a CAMP-independent catabolite repression. DNA mobility shift and footprint analyses showed that only the tsp proximal site was bound by pure Crp with a Kd of 5.4 x 10'' M. As shown by an Arc-defective strain, the aldA gene seems to be repressed by the Arc system under anaerobiosis, displaying its physiological full induction and activity in the presence of oxygen.

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Upstream curved sequences influence the initiation of transcription at the Escherichia coli galactose operon

Cited by 61 publications

References 57 publications

Intrinsic DNA Distortion of the Bacteriophage MumomP1 Promoter Is a Negative Regulator of Its Transcription

Intrinsic DNA Distortion of the Bacteriophage MumomP1 Promoter Is a Negative Regulator of Its Transcription

Ecologic Genomics of DNA: Upstream Bending in Prokaryotic Promoters

The aldA gene of Escherichia coli is under the control of at least three transcriptional regulators

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