The carboxyl terminus of RAP30 is similar in sequence to region 4 of bacterial sigma factors and is required for function

Transcription factor βγ(RAP30/74) from rat liver was previously shown in biochemical studies to control the binding of RNA polymerase II to promoters by a mechanism analogous to that utilized by bacterial σ factors, by decreasing the affinity of polymerase for nonpromoter sites on DNA and by increasing the affinity of the enzyme for the preinitiation complex (Conaway, R. C., Garrett, K. P., Hanley, J. P., and Conaway, J. W. (1991) Proc. Natl. Acad. Sci. U. S. A. 88, 6205-6209). By constructing and analyzing mutants of βγ, we have identified a novel functional domain located in the carboxyl terminus of the γ(RAP30) subunit. This domain shares sequence similarity with region 4 of bacterial σ factors; in particular, it exhibits striking similarity to the carboxyl-terminal regions 4.1 and 4.2 of SpoIIIC (Bacillus subtilis σ^k). Evidence from biochemical studies argues that a mutant γ(RAPSO), lacking amino acid sequences similar to σ homology region 4.2, is able to assemble with the β(RAP74) subunit to form a mutant βγ(RAP30/74) with impaired ability to interact with RNA polymerase II.