Analysis of the occurrence of promoter-sites in DNA

Mulligan, Martin E.; McClure, William R.

doi:10.1093/nar/14.1.109

Cited by 80 publications

(41 citation statements)

References 34 publications

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“…Two cryptic promoters activated in del18 and ins1 and in del224 and del364 each contain T at position Ϫ15 (Table 4). Other studies (10,12,18,23) indicate that T at position Ϫ15 and G at position Ϫ14 are needed for efficient transcription in promoters that lack clear Ϫ35 regions, or for the strengthening of already functional promoters (10), and suggest that T at position Ϫ15 is a key element in the activation of these two cryptic udpPs. We further propose that the several cryptic promoter-like se-quences in the udpP region may also contribute to regulation at WT udpP, perhaps by sequestering RNA polymerase or by facilitating DNA bending or melting.…”

Section: Discussionmentioning

confidence: 96%

Analysis of CRP-CytR interactions at the Escherichia coli udp promoter

et al. 1996

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Multiprotein complexes regulate the transcription of certain bacterial genes in a sensitive, physiologically responsive manner. In particular, the transcription of genes needed for utilization of nucleosides in Escherichia coli is regulated by a repressor protein, CytR, in concert with the cyclic AMP (cAMP)-activated form of cAMP receptor protein (CRP). We studied this regulation by selecting and characterizing spontaneous constitutive mutations in the promoter of the udp (uridine phosphorylase) gene, one of the genes most strongly regulated by CytR. We found deletions, duplications, and point mutations that affect key regulatory sites in the udp promoter, insertion sequence element insertions that activated cryptic internal promoters or provided new promoters, and large duplications that may have increased expression by udp gene amplification. Unusual duplications and deletions that resulted in constitutive udp expression that depended on the presence of CytR were also found. Our results support the model in which repression normally involves the binding of CytR to cAMP-CRP to form a complex which binds to specific sites in the udp promoter, without direct interaction between CytR protein and a specific operator DNA sequence, and in which induction by specific inducer cytidine involves dissociation of CytR from cAMP-CRP and then RNA polymerase interaction with cAMP-CRP bound to a site upstream of the transcription start point. The stimulation of udp expression by CytR in certain mutants may reflect its stabilization of cAMP-CRP binding to target DNA and illustrates that only modest evolutionary changes could allow particular multiprotein complexes to serve as either repressors or transcriptional activators.Multiprotein complexes, long recognized as regulators of expression of many eukaryotic genes, can also be important in the regulation of prokaryotic gene expression (1). This is exemplified by the genes encoding the array of membrane proteins and intracellular enzymes that take up and catabolize deoxy-and ribonucleosides in Escherichia coli (19). Much of the expression of nucleoside utilization genes is coordinated by a repressor protein, CytR, acting in concert with the cyclic AMP (cAMP)-activated form of the cAMP receptor protein (CRP) (2, 9, 27). The three promoters that have been analyzed most extensively (deoP2, cddP, and tsxP) each contain two binding sites for CRP (CRP1 and CRP2) but are otherwise dissimilar in sequence (Fig. 1). The current view is that transcription from these promoters involves CRP binding to CRP1 and that repression involves the binding of CytR protein to CRPs that are, in turn, bound to both CRP1 and CRP2 in the promoter region. It had been speculated that CytR binding to specific DNA sequences would also be important in repression, since CytR exhibits considerable homology to other repressors (21, 32). An imperfect inverted-repeat motif (5Ј-TGCAAN 2-3 TTGCA) is present in each of these promoters and is considered a candidate CytR recognition sequence (24). In this model, inductio...

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Section: Discussionmentioning

confidence: 96%

Analysis of CRP-CytR interactions at the Escherichia coli udp promoter

et al. 1996

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“…1). The putative soxR and soxS promoters have similarity scores (28,29) them only at the 99% confidence level for u70 promoters among random segments of a sequence with this base composition. Low scores are typical of weakly expressed or positively activated genes (see Discussion).…”

Section: Methodsmentioning

confidence: 99%

Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli

1991

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soxR governs a superoxide response regulon that contains the genes for endonuclease IV, Mn2+-superoxide dismutase, and glucose 6-phosphate dehydrogenase. The soxR gene encodes a 17-kDa protein; some mutations of this gene cause constitutive overexpression of the regulon. Induction by paraquat (methyl viologen) requires both soxR and a new gene, soxS. soxS is adjacent to soxR, it encodes a 13-kDa protein, and it is required for paraquat resistance. These functions were revealed by studies in which the sequence of the 1.1-kb soxR-soxS region was determined, the 5' ends of the mRNAs were mapped, and complementation tests were performed with soxRS plasmids containing deletions of known sequence. The two genes are divergently transcribed, and the transcripts overlap. The soxS promoter is within the 85-nucleotide intergenic region, whereas the soxR promoter is within soxS. soxS mRNA increases after induction. Both protein products have possible DNA-binding (helix-turn-helix) domains. SoxR contains four cysteines (CX2CXCX5C) that might be part of a sensor region. SoxS shows 17 to 31 % homology to the C-terminal portions of members of the AraC family of positive regulators.

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“…There were a sequence similar to the TATTTA consensus promoter sequence (-10 region) and two sequences, TTAGGT and TTAATA, similar to the consensus RNA polymerase-binding site (23) proximal to appB (Fig. 4).…”

Section: Attatttctattgatagaaaaactttatccggcaaagacggcaaagaaattgaacttggamentioning

confidence: 96%

The Actinobacillus pleuropneumoniae hemolysin determinant: unlinked appCA and appBD loci flanked by pseudogenes

1991

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The appBD genes encoding the secretion functions for the 110-kDa RTX hemolysin of Actinobacillus pleuropneumoniae have been cloned and sequenced. Unlike analogous genes from other RTX determinants, the appBD genes do not lie immediately downstream from the hemolysin structural gene, appA. Although isolated from a diverse group of gram-negative organisms, the appBD genes and the characterized RTX BD genes from other organisms all exhibit a high degree of homology at both the DNA and predicted amino acid sequence levels. Analysis of the DNA sequences 3' to appA and 5' to appB suggests that these regions harbor remnant RTX B and A pseudogenes, respectively. Although the appA gene is most similar to the lktA gene from Pasteurella haemolytica (Y. F. Chang, R. Young, and D. K. Struck, DNA 8:635-647, 1989), the RTX A pseudogene upstream from appB most closely resembles the hlyB gene from Escherichia coli, suggesting that the appCA and appBD operons were derived from different ancestral RTX determinants.

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Analysis of the occurrence of promoter-sites in DNA

Cited by 80 publications

References 34 publications

Analysis of CRP-CytR interactions at the Escherichia coli udp promoter

Analysis of CRP-CytR interactions at the Escherichia coli udp promoter

Two divergently transcribed genes, soxR and soxS, control a superoxide response regulon of Escherichia coli

The Actinobacillus pleuropneumoniae hemolysin determinant: unlinked appCA and appBD loci flanked by pseudogenes

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