Summary The DNA-dependent RNA polymerase of the thermophilic archaeon Sulfolobus acidocaldarius (RNAP, EC 2.7.7.6) was shown to consist of thirteen components ranging in size from 122 kDa to approximately 5 kDa. They were named B, A′, A″, D, E, F, G, H, I, K, L, M and N. The staining intensities indicate that they occur in an equimolar ratio. The complexity of the enzyme resembles that of eucaryal RNA polymerases. Most RNAP components and two subassemblies containing the components D plus L and E plus I could be separated in electrophoresis on a cellulose acetate support. The D-L subunit-complex exhibited a typical yellow colour with an absorbance maximum of 400 nm. Inductive coupled plasma mass spectroscopy showed the absence of heavy metal atoms in this complex, but the presence of two zinc ions per RNAP molecule. The subunit G is phosphorylated. The component F was separated into five subspecies differing in charge density. By anion exchange chromatography an F-free RNAP and five variants, each containing a different F-component (F5 to F1 were separated. Renaturation of total dissociated RNAP led to an activity recovery of up to 30%. On this basis experiments to reconstitute a functional enzyme from the separated subunits were done. The components A″, E, H and K appeared to be required for the basic activity of the RNAP. Crystallization of the RNAP yielded needle shaped and rhomboid crystals of a size of up to 0.5 mm. Only F-containing RNAP could be crystallized, but no x-ray diffraction was obtained so far. Genes encoding small subunits of the RNAP of S. acidocaldarius were compared to genes of small components of the eucaryal polymerases A (I), B (II) and C (III). Subunit K was shown to be homologous to the eucaryal component ABC23, N to ABC10s and L to AC19. No homologies to bacterial subunits were found. The components E, F and G have so far no bacterial or eucaryal counterparts. In contrast to the genes of the subunits H, B, A′ and A″, which are transcribed jointly, the genes encoding the smaller subunits were transcribed separately. A further hint to a close relationship between archaeal and eucaryal transcription machinery was the discovery of a gene directly downstream of subunit L, which had a high similarity to the eucaryal transcription factor TFIIS. In vitro transcription of the 16S/23S rRNA-promoter of S. shibatae, the promoter of transcript 3 of the Sulfolobus virus SSV1 and of mutant derivatives with a cell-free extract or with purified RNAP of S. shibatae showed that the RNAP is able to recognize the correct start site by itself and independent of Box A, whereas with a cell-free extract the start point of transcription was determined by the position of box A. We conclude that one or more factors present in the cell-free extract are involved in box A directed transcription-initiation.
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