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Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting

Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting,10.1016/j.jmb.2009.01.052,Journal of Molecular Biology,Patricia C. Bur

Coupling σ Factor Conformation to RNA Polymerase Reorganisation for DNA Melting   (Citations: 9)
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ATP-driven remodelling of initial RNA polymerase (RNAP) promoter complexes occurs as a major post recruitment strategy used to control gene expression. Using a model-enhancer-dependent bacterial system (σ54–RNAP, Eσ54) and a slowly hydrolysed ATP analogue (ATPγS), we provide evidence for a nucleotide-dependent temporal pathway leading to DNA melting involving a small set of σ54–DNA conformational states. We demonstrate that the ATP hydrolysis-dependent remodelling of Eσ54 occurs in at least two distinct temporal steps. The first detected remodelling phase results in changes in the interactions between the promoter specificity σ54 factor and the promoter DNA. The second detected remodelling phase causes changes in the relationship between the promoter DNA and the core RNAP catalytic β/β′ subunits, correlating with the loading of template DNA into the catalytic cleft of RNAP. It would appear that, for Eσ54 promoters, loading of template DNA within the catalytic cleft of RNAP is dependent on fast ATP hydrolysis steps that trigger changes in the β′ jaw domain, thereby allowing acquisition of the open complex status.
Journal: Journal of Molecular Biology - J MOL BIOL , vol. 387, no. 2, pp. 306-319, 2009
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    • ...proximity of both of these proteins (DNA� PspF1–275 and DNA� s54) in the DNA trapped complex (9,32)...

    Nan Zhanget al. The role of the conserved phenylalanine in the p54-interacting GAFTGA ...

    • ...The Sinorhizobium meliloti nifH phosphorothioated (Operon) DNA probes were derivatized with p-azidophenacyl bromide at the � 12/� 11, � 8/� 7 and � 1/+1 position as described (33,34)...
    • ...Photo-cross-linking reactions were conducted at 378 Ci n STA buffer in a total reaction volume of 10ml as previously described (33,38)...
    • ...Previously we demonstrated that upon increased UV exposure, PspF1–275 can be efficiently cross-linked at the � 1/+1 site in the presence of ADP–AlF (30,33,35)...
    • ...Control reactions demonstrated that only in the presence of all the reaction components, which include a form of PspF1–275 capable of interacting with s54, is the cross-linked PspF1– 275–DNA species detected [data not shown; (33)]...
    • ...Interestingly, when we examined the trapped complexes formed on the duplex promoter probe (probe 1) in the presence of core RNAP, we note that the amount of cross-linked PspF1–275 DNA species was identical [data not shown; (33)] irrespective of the trapped complex formed...
    • ...within the open complex) does [data not shown; (33)]...

    Patricia C. Burrowset al. Comparative analysis of activator-Ep54 complexes formed with nucleotid...

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