Similarity between subunit 8 of yeast RNA polymerase II (RPB8) and the second-largest subunits of eukaryotic RNA polymerases.

Abstract

The three eukaryotic RNA polymerases consist of about 9-13 small subunits and two large subunits, which form the major part of the catalytic site (1, 2). The genes encoding the two large subunits have been isolated for a variety of organisms. In addition, the genes coding for the 9 small subunits of yeast RNA polymerase II as well as most of the small subunits of yeast RNA polymerase I and III have been cloned and sequenced. The two large subunits of the eukaryotic RNA polymerases are the structural and functional homologues of the E. coli RNA polymerase ,3' and (3 subunit (2-4). Five of the small subunits (ABC27 = RPB5, ABC23 = RPB6, ABC14.4 = RPB8, ABC1IOa = RPB1Oa, ABC1I0, = RPB1O(3) are common to all three nuclear RNA polymerases of yeast and two additional subunits (AC40, AC 19) are common to RNA polymerases I and Im (4-6). All of these common subunits are essential for cell viability (3-5). Using the PC/GENE FSTPSCAN program we searched for similarities to the second-largest subunit of Drosophila RNA polymerase II (DmRP140) in the SWISS-PROT database. By this approach we identified a weak similarity to subunit 8 of yeast RNA polymerase II (RPB8). In the DmRP140 sequence this similarity resides within region H, which is one of nine regions (A-I) highly conserved within the second-largest subunits of RNA polymerases (3, 4). The alignment of amino acids 62-1 13 of RPB8 (of a total of 146 amino acids (5)) and the second-largest subunits of yeast and Drosophila RNA polymerases shows between 17 and 27% identical residues and between 27 and 41 % similarity taking into account conservative exchanges (Figure 1). By high affinity labeling of the E. coli RNA polymerase two amino acid residues of the subunit were identified to be involved in interaction with the priming dinucleotide (7). These two residues, a lysine residue at position 1065 and a histidine residue at position 1237, are conserved in all known second-largest subunits of eukaryotic and bacterial RNA polymerases and are located in the homology regions H and I, respectively. A mutation of lysine 1065 to an arginine does not inactivate the catalytic function but inhibits the transition from initiation to elongation (8, 9). Interestingly, the corresponding position of this lysine residue in the RPB8 sequence is occupied by an arginine. The occurence of RPB8 in all three RNA polymerases and the necessity for cell viability underlines the functional importance of this subunit (5). The homology to a region of the second-largest subunit involved in a basic mechanism of transcription suggests a possible auxiliary role of RPB8 in the catalytic function of eukaryotic RNA polymerases.