Mapping of subunit-subunit contact surfaces on the β subunit of Escherichia coli RNA polymerase

The RNA polymerase core enzyme of Escherichia coli is composed of 2 alpha, 1 beta, and 1 beta' subunits. Previously we mapped the alpha-alpha, alpha-beta, and alpha-beta' contact sites on the alpha subunit. Here we analyzed the alpha subunit contact sites on the beta subunit by using various experimental approaches: (i) comparison of the proteolytic cleavage map between the unassembled free beta subunit and the alpha(2)beta complex; (ii) analysis of the binary complex formation between His(6)-tagged intact alpha subunit and various truncated beta fragments; and (iii) analysis of the complex formation between the alpha subunit and various His(6)-tagged beta fragments. The results altogether indicate that two regions of the beta subunit are involved in the full activity of a binding, that is, the primary contact site between residues 737 and 904 and the secondary region with assembly control activity downstream from residue 1138. All of the alpha subunit-beta fragment binary complexes identified in this study were found to bind beta' subunit and form pseudo-core complexes, indicating that the regions of beta involved in alpha subunit contact also participate in interaction with the beta' subunit.