Isomerization of a binary sigma–promoter DNA complex by transcription activators

Abstract

Multisubunit RNA polymerases are targets of sophisticated signal transduction pathways that link environmental or temporal cues to changes in gene expression. Here we show that the sigma 54 protein (σ54), responsible for promoter specific binding by bacterial RNA polymerase, undergoes a nucleotide hydrolysis dependent isomerization on DNA. Changes in protein structure are evident. The isomerization has all the known requirements of σ54-dependent transcription, including a dependence on enhancer binding activator proteins and occurs independently of the core RNA polymerase. We suggest that activator driven changes in σ54 conformation trigger the conversion of a transcriptionally silent RNA polymerase conformation to one able to interact productively with template DNA. Our results illustrate the types of changes that must occur for multisubunit complexes to manipulate DNA, and show that transcription activators can remodel key nucleoprotein structures to achieve direct activation of transcription.

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Figure 1: Binding of σ54 to heteroduplex DNA.
Figure 2: DNase I footprints of σ54 and supershifted DNA complexes.
Figure 3: Protease footprints of 32P end-labeled σ54.
Figure 4: Region I complements ΔIσ54 for supershifted complex formation.

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Acknowledgements

Work was supported by a Wellcome trust project grant to M.B. M.T.G. was supported by a CEC Marie Curie fellowship. We thank S. Kustu, L.J. Reitzer, R. Wassem and S.R. Wigneshweraraj for purified activator proteins, E. Morett for the pspF mutants, D. Studholme for valuable comments on the manuscript and P. Geiduschek for his constructive comments on the early work.

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Correspondence to Martin Buck.

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Cannon, W., Gallegos, M. & Buck, M. Isomerization of a binary sigma–promoter DNA complex by transcription activators. Nat Struct Mol Biol 7, 594–601 (2000). https://doi.org/10.1038/76830

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