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A A Travers

Publications and source records attributed to A A Travers.

At least 73 records · Page 4Linked to original sources
PubMed1985

Negative supercoiling induces spontaneous unwinding of a bacterial promoter.

We have examined the influence of negative supercoiling on the DNA structure of a bacterial promoter (tyrT from Escherichia coli), the transcriptional activity of which is strongly enhanced by torsional stress in vitro. Certain regions of this promoter become sensitive to digestion by single-strand-specific S1 nuclease as a consequence of negative superhelicity. These regions occur with high frequency (1 per 30-50 bp) and are normally centered on a TpA doublet. The major positions of cleavage are located in and around the -10 sequence TATGATG, the unwinding of which is a prerequisite for gene expression. An apparently trivial change in the -10 sequence from TATGATG to TATGAAG reduces both transcriptional activity and S1 nuclease sensitivity at least 10-fold. Thus the nuclease sensitivity of the promoter correlates strongly with its biological function; and both of these phenomena correlate with certain sequence-dependent structural properties of the DNA.

DNA Restriction Enzymes↗
PubMed1985

Genetically separable functional elements mediate the optimal expression and stringent regulation of a bacterial tRNA gene.

The sequences required for stringent regulation of the E. coli tyrT gene have been analyzed in vivo. Stringent control was analyzed by nuclease-mapping RNA pulse-labeled with 32PO4. A 96 bp DNA fragment carrying the tyrT promoter was sufficient to confer regulation on a plasmid-encoded tyrT-galK fusion transcript. Deletion mutations that remove sequences upstream of the primary promoter elements greatly reduce promoter activity but do not remove the regulatory response. However, a 4 bp substitution mutation, adjacent to the transcription initiation site, disrupts stringent control. Thus the optimal expression and stringent regulation of the tyrT gene appears to result from the action of genetically separable promoter elements.

Escherichia coli↗
PubMed1984

Conserved features of coordinately regulated E. coli promoters.

E. coli promoters which are coordinately regulated in response to amino acid limitation contain conserved nucleotide sequences immediately 3' to -10 region. These sequences contain predominantly either GC or AT residues depending on whether the response is respectively negative or positive. Certain classes of promoters also contain conserved sequences upstream of the primary promoter. In tRNA genes these sequences could act as a secondary polymerase binding site.

Amino Acids↗
PubMed1984

DNA structural variations in the E. coli tyrT promoter.

X-ray studies have established that the structure of a right-handed, Watson-Crick double helix can change from place to place along its length as a function of base sequence. The base pairs transmit deformations out to the phosphate backbone, where they can then be recognized by proteins and other DNA-binding reagents. Here we have examined at single-bond resolution the interactions of three commonly used nucleases (DNAase I, DNAase II, and copper-phenanthroline) with a DNA of natural origin, the 160 bp tyrT promoter. All three of these reagents seem sensitive to DNA backbone geometry rather than base sequence per se. Their sequence-dependent patterns of cleavage provide evidence for structural polymorphism of several sorts: global variation in helix groove width, global variation in radial asymmetry, and local variation in phosphate accessibility. These findings explain how sequence zones of a certain base composition, or purine-pyrimidine asymmetry, can influence the recognition of DNA by protein molecules.

Base Sequence↗
PubMed1984

Upstream elements necessary for optimal function of the hsp 70 promoter in transformed flies.

Deletion mutants of the Drosophila hsp 70 promoter region have been fused to a truncated Drosophila Adh gene lacking its own promoter. These fusion genes were introduced into the Drosophila genome using the P-element transformation system. S1 mapping of fusion transcripts in transformed flies shows that their expression is completely dependent on the function of the hsp 70 promoter, and that 97 bp of hsp 70 5'-flanking DNA is sufficient to induce transcription upon heat shock to a level similar to that of the wild-type hsp 70 gene. By contrast, a deletion containing 68 bp of 5'-flanking DNA is only inducible to a low level even though this deletion retains the consensus sequence, which is sufficient for induction and maximal expression of this gene in COS cells and Xenopus oocytes. A sequence centered at -125 with the potential for forming an S1 nuclease-sensitive structure does not affect inducibility or efficiency of expression.

Alcohol Dehydrogenase↗
PubMed1983

RNA polymerase interactions with the upstream region of the E. coli tyrT promoter.

The rate of in vivo transcription from the E. coli tRNA and rRNA promoters depends on both cellular growth rate and aminoacid availability. To investigate the molecular mechanisms involved we determined the extent of interaction of RNA polymerase with the promoter of the tyrT stable RNA gene. We show that the enzyme can protect from DNAase I digestion a region of at least 85 bp of the wild-type tyrT promoter and only approximately 62 bp of the lacUV5 mRNA promoter, the protected region extending on the antisense strand to approximately 65 and 42 bp respectively upstream of the transcription startpoint. A mutant tyrT promoter, tyrTp27, is protected more extensively, RNA polymerase interactions extending to at least approximately -130. We propose that these upstream interactions of RNA polymerase perform two functions; activating initiation by polymerase bound at the primary binding site and increasing the concentration of polymerase in the vicinity of the tyrT promoter, thus allowing a high rate of maximal expression and enabling the promoter to be regulated over a wide range of activity.

Base Sequence↗
PubMed1982

PpGpp regulates the binding of two RNA polymerase molecules to the tyrT promoter.

Bacterial promoters differ in the number of RNA polymerase molecules that bind to form a filterable polymerase-promoter complex. We show that two holoenzyme molecules interact with the tyrT promoter, probably as a dimer. This interaction is inhibited by ppGpp. By contrast a single holoenzyme monomer suffices for complex formation at the lacUV5 promoter. We propose that In vivo promoter selection by monomeric and dimeric forms of the enzyme could coordinate the synthesis of stable RNA with that of mRNA and could also account in part for the switch in transcriptional selectivity during the stringent response.

Base Sequence↗
PubMed1980

Translation initiation factor 2 alters transcriptional selectivity of Escherichia coli ribonucleic acid polymerase.

Preparations of translation initiation factor IF-2 strongly stimulate the production of rRNA by Escherichia coli RNA polymerase but have little effect on the synthesis of other RNA species. The factor alters the sedimentation characteristics of RNA polymerase holoenzyme. We suggest a mechanism by which IF-2 alters the pattern of transcriptional selectivity of RNA polymerase.

DNA-Directed RNA Polymerases↗
PubMed1980

Functional heterogeneity of Escherichia coli ribonucleic acid polymerase holoenzyme.

On zone sedimentation Escherichia coli RNA polymerase holoenzyme exhibits functional heterogeneity with respect to template preference, regulation by ppGpp, and affinity for fMet-tRNA. The template preference of a subpopulation of RNA polymerase molecules correlates with both its sedimentation position and its ability to respond to effectors of polymerase selectivity. Incubation of such functionally distinct populations of enzyme molecules at physiological temperatures results in functional and structural equivalence. We suggest that RNA polymerase normally exists as a mixture of interconvertible forms and that promoter selection can be controlled by varying the number and proportions of forms present.

DNA-Directed RNA Polymerases↗
PubMed1980

Formylmethionyl-tRNA alters RNA polymerase specificity.

Escherichia coli fMet-tRNAfMet alters the pattern of promoter selection of E. coli RNA polymerase (RNA nucleotidyltransferase, nucleosidetriphosphate:RNA nucleotidyltransferase; EC 2.7.7.6), affecting RNA synthesis from the rRNA, suIII+tRNA, and lac promoters in different ways. The in vitro synthesis of the stable RNA species is selectively decreased, whereas that of lac RNA from both the wild-type and mutant UV5 promoters is selectively increased at high ionic strength. The functional effect of fMet-tRNAfMet resembles that of the nucleotide guanosine 3'-diphosphate 5'-diphosphate (ppGpp). This nucleotide competes with the binding of fMet-tRnafMet to RNA polymerase.

Binding, Competitive↗
PubMed1980

Promoter sequence for stringent control of bacterial ribonucleic acid synthesis.

In bacterial promoters subject to stringent control the heptanucleotide sequence spanning nucleotide positions -5 to +2 (defining the -10 region [D. Pribnow, J. Mol. Biol. 99:419-443, 1975] as positions -12 to -6) is highly conserved. This conserved region, for which the best consensus sequence is [Formula: see text] is absent from promoters which are not under stringent control.

Bacterial Proteins↗