The single subunit DNA-dependent RNA polymerase (RNAP) that is encoded by bacteriophage T7 is the prototype of a class of relatively simple RNAPs that includes the RNAPs of the related phages T3 and SP6, as well as the mitochondrial RNAPs. The T7 enzyme has been crystallized, and recent genetic and biochemical analyses have facilitated an interpretation of this structure. A growing body of evidence suggests that the phage-like RNAPs are related to other nucleotide polymerases such as DNA polymerases, RNA-dependent RNA polymerases, and reverse transcriptases. In this work, we review information concerning the structure and function of T7 RNAP, and evidence in support of its assignment to a broader class of nucleotide polymerases.
The amino acid at position 748 in T7 RNA polymerase (RNAP) functions to discriminate base pairs at positions -10 and -11 in the promoter. We have constructed a series of T7 RNAP mutants having all possible amino acid substitutions at this position. Surprisingly, most (13/19) (Fig. 1A). In the case of T3 vs. T7 promoter specificity, the base pairs at -10 and -11 are the primary determinants of specific promoter recognition, and a T7 promoter variant having the corresponding T3 base pairs substituted at these positions (designated Pr7 -10C, -liC; the letter denotes the base on the nontemplate strand) is utilized by T3 RNAP but not by T7 RNAP (12). Previous work demonstrated that recognition of these base pairs involves the amino acid residue at position 748 (Asn) and that a T7 RNAP mutant having the corresponding T3 amino acid (Asp) at this position (denoted T7-N748D) preferentially utilizes PT7 -10C, -llC over a consensus T7 promoter (PrH) (10,13,14). To account for this specificity, it has been proposed that residue N748 makes specific hydrogen bonds with the base pair at -11 (and possibly at -10) in the major groove (10,11,14). This model is supported by a preliminary 3.1-A electron density map of T7 RNAP that places N748 within a putative DNA-binding cleft (15,16).To understand further the nature of the interaction(s) between the residue at position 748 and base pairs in the -11 region of the promoter, we constructed a series of T7 RNAPs having each of the 20 amino acids at this position. The activities and promoter preferences of these RNAPs were determined through the use of a collection of T7 promoter variants having all possible-single base-pair substitutions at -10, anmino acid substitutions result in active RNAPs, and many of these exhibit altered promoter specificities. In view of prior observations that altered-specificity mutants are rare among DNA-binding proteins (17)
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