Determination of intersubunit distances and subunit shape parameters in DNA-dependent RNA polymerase by neutron small-angle scattering

Abstract

In all organisms the multi-subunit enzyme DNA-dependent RNA polymerase catalyses the first basic step in gene expression, the transcription of DNA into RNA. The neutron small-angle scattering effects were studied in the Guinier region by applying the contrast-matching technique. Isotopic labelling was realised by culturing fully deuterated E. coli cells in a heavy-water medium containing deuterated substrates. One or two completely deuterated components (subunits) of polymerase holoenzyme (composition formula α2ββ′σ, molecular weight 497000) were recombined with the remaining natural (`hydrogenated') subunits for these neutron measurements. Measurements are presented of radii of gyration R, overall shapes, and pair distances d, of three components (subunits α2β,β′) in RNA polymerase of E. coli. The subunits β′, β and α2 are obviously rather elongated in situ and exhibit (as scattering-equivalent prolate ellipsoids) axial ratios of about 7:1 up to 9:1. The intersubunit centre of gravity distances were analysed to be 7.3 ± 0.8 nm for β−β′, 8.2 ± 1.2 nm for α2−β′ and 7.0 ± 1.7 nm for α2−β.