Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase‐induced strand separation of double helical DNA

  title={Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase‐induced strand separation of double helical DNA},
  author={Pieter L Dehaseth and John D. Helmann},
  journal={Molecular Microbiology},
Escherichia coli RNA polymerase is able to site‐specifically melt 12 bp of promoter DNA at temperatures far below those normally associated with DNA melting. Here we consider several models to explain how RNA polymerase destabilizes duplex DNA. One popular model proposes that upon binding to the promoter, RNA polymerase untwists the spacer DNA between the –10 and –35 regions, which results in a destabilization of the –10 region at a TA base step where melting initiates. Promoter untwisting may… 
Evidence for DNA bending at the T7 RNA polymerase promoter.
These results, viewed in the light of a recent crystal structure for the T7 RNA polymerase complex, suggest a mechanism by which binding leads directly to bending that would facilitate the melting necessary to initiate transcription.
Minus-strand origin of filamentous phage versus transcriptional promoters in recognition of RNA polymerase.
Observations suggest that sigma70 subunit directly interacts with the single-stranded nontemplate strand containing adenine residue(s) at the -10 region of promoter.
Organization of open complexes at Escherichia coli promoters. Location of promoter DNA sites close to region 2.5 of the sigma70 subunit of RNA polymerase.
A cysteine-tethered DNA cleavage agent has been used to locate the position of region 2.5 of sigma70 in transcriptionally competent complexes between Escherichia coli RNA polymerase and promoters and it is shown that region 1.5 is in close proximity to promoter DNA just upstream of the -10 hexamer.
Interactions of Escherichia coli sigma(70) within the transcription elongation complex.
It is shown that the addition of holopolymerase to the bubble-duplex construct triggers the dissociation of the sigma factor from some complexes, whereas in others the RNA oligomer is released into solution instead and suggested that both cannot be bound to the core polymerase simultaneously.
Complex Formation of E. coli RNA Polymerase with Bacteriophage T2 DNA: Long-Range Effects in DNA
It was shown that the binding of RNA polymerase under the conditions favoring the formation of open promoter complexes induces specific conformational changes in the spin-labeled DNA.
Initiation mechanisms in replication of filamentous phage DNA
  • K. Horiuchi
  • Biology, Chemistry
    Genes to cells : devoted to molecular & cellular mechanisms
  • 1997
The DNA replication origin has a much higher affinity for the holoenzyme than the transcriptional promoters, and the non‐template strand of the single‐stranded −10 region of the origin appears to be responsible for this high affinity.
Promoter recognition as measured by binding of polymerase to nontemplate strand oligonucleotide.
In transcription initiation, the DNA strands must be separated to expose the template to RNA polymerase, and specific protein-DNA interactions involving bases of the nontemplate strand form and stabilize the promoter complex in the region of unwinding.
Events during Initiation of Archaeal Transcription: Open Complex Formation and DNA-Protein Interactions
It is shown here that the RNA polymerase of the archaeon Methanococcus, in contrast to polymerase II, does not require hydrolysis of the beta-gamma bond of ATP for initiation of transcription and open complex formation on linearized DNA.
Mechanistic Differences in Promoter DNA Melting by Thermus aquaticus and Escherichia coli RNA Polymerases*
It was concluded that the different effects of the mutations on the two polymerases are exerted at a step preceding nucleation of DNA melting, and a model is presented for how this mechanistic difference between the two RNA polymerase could explain the observations.


Mutations in sigma factor that affect the temperature dependence of transcription from a promoter, but not from a mismatch bubble in double-stranded DNA.
Results support the involvement of region 2.3 in the strand separation process that accompanies open complex formation at promoters, and show that the DNA-melting defect imposed by these mutant sigma factors can be suppressed by the use of such bubble templates.
Studies on transcription of 3'-extended templates by mammalian RNA polymerase II. Parameters that affect the initiation and elongation reactions.
Variation of reaction conditions, or of the divalent metal ion, does not restore the renaturability of the DNA template, however, variation of the duplex 3'-terminal sequence of the template led to significant alterations.
Structural, Thermodynamic and Kinetic Studies of the Interaction of Eσ70 RNA Polymerase with Promoter DNA
Transcription initiation involves location and recognition of the promoter and association of Eσ70 with helical DNA and is followed by conformational changes in the protein and DNA including local DNA strand separation in the vicinity of the transcription start site to form the open complex.
Structure of DNA polymerase I Klenow fragment bound to duplex DNA
Although this cocrystal structure appears to be an editing complex, it suggests that the primer strand approaches the catalytic site of the polymerase from the direction of the 3' to 5' exonuclease domain and that the duplex DNA product may bend to enter the cleft that contains the polypeptide catalyst site.
Allosteric underwinding of DNA is a critical step in positive control of transcription by Hg-MerR
The magnitude and the direction of the Hg–MerR-induced change in twist angle are consistent with a positive control mechanism involving reorientation of conserved, but suboptimally phased, promoter elements and are inconsistent with a role for torsional stress in formation of an open complex.