5′ Nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters

Carpousis, Agamemnon J.; Stefano, James E.; Gralla, Jay D.

doi:10.1016/0022-2836(82)90502-2

Cited by 76 publications

(44 citation statements)

References 18 publications

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“…37). Mutations within Region 4 or H5 that are predicted to reduce its interaction with the Ϫ35 DNA element and/or the ␤-flap facilitate promoter clearance, decreasing the level of abortive products relative to full-length RNA (32,(37)(38)(39). This result supports a model wherein the interaction of 70 H5 with the ␤-flap impedes the progression from initiation to elongation.…”

Section: Gross Misfolding Ofsupporting

confidence: 58%

Bacteriophage T4 MotA Activator and the β-Flap Tip of RNA Polymerase Target the Same Set of σ70 Carboxyl-terminal Residues

Bonocora

Decker

Glass

et al. 2011

Journal of Biological Chemistry

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Background: Transcriptional activators interact with RNA polymerase to redefine gene expression. Results: A phage activator engages a region of the specificity factor of E. coli RNA polymerase, which is normally bound by another portion of RNA polymerase. Conclusion: Using an activator/co-activator system, the phage hijacks the host RNA polymerase. Significance: Small transcriptional factors acting on defined local regions of RNA polymerase can fundamentally change gene expression.

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Section: Gross Misfolding Ofsupporting

confidence: 58%

Bacteriophage T4 MotA Activator and the β-Flap Tip of RNA Polymerase Target the Same Set of σ70 Carboxyl-terminal Residues

Bonocora

Decker

Glass

et al. 2011

Journal of Biological Chemistry

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“…Similarly, several other strong promoters become slightly less active in vivo when changed to make both hexamers identical with consensus, even though the final change toward consensus is different for each promoter (19,21,28). Such consensus promoters are defective in a late step of transcription initiation (21,24), suggesting that the same strong contacts with (6,21,36).…”

Section: Methodsmentioning

confidence: 99%

Hierarchies of base pair preferences in the P22 ant promoter

1991

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Oligonucleotide-directed mutagenesis was used to complete a collection of mutations in the -35 and -10 hexamers of the ant promoter of Salmonella phage P22. The effects of all 36 single-base-pair substitutions on promoter strength in vivo were measured in strains carrying the mutant promoters fused to an ant-lacZ gene on a single-copy prophage. The results of these assays show that certain consensus base pairs are more important than others; in general, the least-critical positions are among the most poorly conserved. Some mutations within the hexamers have smaller effects on promoter strength than certain mutations outside the hexamers in this and other promoters. Several different patterns of base pair preferences are observed. These hierarchies of base pair preferences correlate well (but not perfectly) with the hierarchies defined by the frequency distribution of base pairs at each position among wild-type promoters. The hierarchies observed in the ant promoter also agree well with most of the available information on base pair preferences in other promoters.The first step of transcription initiation is the association of RNA polymerase with a promoter sequence on the DNA. In eubacteria, promoter specificity is determined by a family of protein subunits called sigma (a) factors, which associate with the core enzyme (%2WB') to form the holoenzyme. The major sigma factor of Escherichia coli and Salmonella typhimurium is 70, a 70-kDa protein required for recognition of most promoters. Other classes of promoters are recognized by holoenzymes containing minor sigma factors (16).Comparisons of numerous a70-dependent promoters controlling chromosomal, plasmid, transposon, and phage genes in E. coli and S. typhimurium revealed two regions of conserved DNA sequence located approximately 10 and 35 bp upstream of the start site of transcription. Each region has a 6-bp consensus sequence, the -10 and -35 hexamers 5'-TATAAT-3' and 5'-TTGACA-3', respectively. Weakly conserved positions outside the hexamers have varied considerably in different compilations ( Fig. 1) (14,15,32). The hexamers are separated by a spacer region with a preferred length of 17 bp. Recent genetic studies strongly suggest that both regions of the promoter are directly contacted by sigma factors (8,11,23,34,41,47).Evidence that the hexamers are important determinants of promoter strength has been obtained by the analysis of promoter mutations, most of which affect base pairs within the hexamers (15). In most cases, mutations that decrease promoter activity are changes away from consensus, while mutations that increase promoter activity are changes toward consensus. Various exceptions to this rule are discussed below. Kinetic studies of several promoters show that mutations in the hexamers affect the rate parameters for early steps in the interaction between the promoter and RNA polymerase, the formation of an initial, "closed" complex and/or isomerization to a transcriptionally active, "open" complex (18, 39; for a review see reference 29). of at le...

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“…The downstream DNA is pulled progressively into the enzyme with each nucleotide addition cycle, producing a "scrunched" form within the enzyme footprint ( Figure 5). Abortive RNA transcripts lead to the release of the scrunched DNA, which is then extruded out the downstream face of RNAP (1,(56)(57)(58), only to be reeled in again upon further RNA synthesis.…”

Section: Abortive Initiationmentioning

confidence: 99%

Single-Molecule Studies of RNA Polymerase: Motoring Along

Herbert

Greenleaf

Block

2008

Annu. Rev. Biochem.

187

141

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Single-molecule techniques have advanced our understanding of transcription by RNA polymerase. A new arsenal of approaches, including single-molecule fluorescence, atomic-force microscopy, magnetic tweezers, and optical traps have been employed to probe the many facets of the transcription cycle. These approaches supply fresh insights into the means by which RNA polymerase identifies a promoter; initiates transcription, translocates and pauses along the DNA template, proofreads errors, and ultimately terminates transcription. Results from single-molecule experiments complement knowledge gained from biochemical and genetic assays by facilitating the observation of states that are otherwise obscured by ensemble averaging, such as those resulting from heterogeneity in molecular structure, elongation rate, or pause propensity. Most studies to date have been performed with bacterial RNA polymerase, but work is also being carried out with eukaryotic polymerase (Pol II) and single-subunit polymerases from bacteriophages. We discuss recent progress achieved by single-molecule studies, highlighting some of the unresolved questions and ongoing debates.

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5′ Nucleotide heterogeneity and altered initiation of transcription at mutant lac promoters

Cited by 76 publications

References 18 publications

Bacteriophage T4 MotA Activator and the β-Flap Tip of RNA Polymerase Target the Same Set of σ70 Carboxyl-terminal Residues

Bacteriophage T4 MotA Activator and the β-Flap Tip of RNA Polymerase Target the Same Set of σ70 Carboxyl-terminal Residues

Hierarchies of base pair preferences in the P22 ant promoter

Single-Molecule Studies of RNA Polymerase: Motoring Along

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