The activation of RNA polymerase by alkylammonium ions

Intrasubunit nucleotide binding in ribonucleic acid polymerase

1. Periodate oxidation of the ribose ring was used to synthesize derivatives of nucleoside triphosphates. 2. These oxidized nucleoside triphosphates. 2. These oxidized nucleoside triphosphates are competitive inhibitors of RNA polymerase. 3. On incubation, together with NaBH4, these oxidized labelled nucleotides are covalently bound to Escherichia coli RNA polymerase. 4. Nucleoside triphosphate substrates decrease the extent of labelling. 5. A lysine residue in an alpha-subunit is labelled. 6. The significance of these results in relation to the location of the nucleotide-binding site is discussed.

An adenosine triphosphate-dependent deoxyribonuclease from Alcaligenes faecalis

A deoxyribonuclease was purified approx. 800-fold from crude extracts of the bacterium Alcaligenes faecalis. The enzyme requires ATP and Mn2+; ATP could be replaced by any other ribo- or deoxyribo-nucleoside triphosphate, and Mn2+ could be replaced by Mg2+ in 0.1 M-Tris/HCl, pH 8.0 at 37 degrees C. The enzyme could degrade linear duplex or denaturated DNA, but was inactive with closed-circular duplex DNA from bacteriophase PM-2. In the course of nucleolytic activity, ATP was hydrolysed. We have measured deoxyribonuclease and adenoxine triphosphatase activity in the presence of various salts, and found that the amount of ATP hydrolysis associated with a given amount of deoxyribonuclease activity was decreased in the presence of tetraethylammonium ions. Since these ions decrease the stability of the DNA helix, we conclude that one function of the ATP hydrolysis is to unwind the DNA.

Rifampicin binding as a probe for subunit interactions in Escherchia coli RNA polymerase

The binding of the inhibitor rifampicin to RNA polymerase (alpha2betabeta') and its deficient subunit mixtures was investigated. The ability of beta to bind stoichiometric amounts of rifampicin was restored by formation of the alpha2beta subassembly. beta,beta' alpha, betabeta' and alpha2beta' were unable to bind rifampicin. RNA polymerase denatured with 6 M guanidine hydrochloride and dialysed against a renaturing buffer at 0degrees C ("renatured inactive enzyme") bound stoichiometric amounts of rifampicin but had lost the ability of bind dna. compared with native RNA polymerase "renatured inactive" enzyme possessed a markedly different tertiary structure as judged by limited proteolysis.

Structural properties of Escherichia coli RNA polymerase Subunits

1. The surface of the RNA-polymerase-DNA complex possesses an exposed polypeptide loop. 2. Proteinases with differing specificities (trypsin, chymotrypsin, subtilisin and clostripain) preferentially cleave the exposed region. 3. The cleaved polypeptide is reassembled into RNA polymerase by renaturation from a solvent which promotes a random coil conformation. 4. Isolated beta subunit has a proteolytically resistant nucleus of approximately 70000 molecular weight. This resistant polypeptide may be generated by trypsin, chymotrypsin, subiilisin or clostripain. 5. Isolated alpha subunits are comparatively resistant to proteolysis. 6. Although of similar molecular weights beta and beta' appear to have unrelated primary sequences and markedly different conformations in free solution. 7. Digestion of the beta subunit may be blocked by formation of the alpha2beta subassembly. 8. Evidence is presented suggesting that beta' in the intact enzyme (alpha2beta beta') possesses the exposed polypeptide loop.