Identification of the gene coding for the largest subunit of RNA polymerase I (A) of Drosophila melanogaster

The gene coding for the largest subunit (RPA1) of RNA polymerase I (A) of Drosophila melanogaster (DmRPA1) was cloned and sequenced. The gene is interrupted by seven small introns and the cDNA reveals an open reading frame of 4932 nucleotides. The deduced polypeptide consists of 1644 amino acids with a calculated molecular weight of 185 kDa. Although the protein sequence exhibits the specific pattern of conserved regions found in all RNA polymerase largest subunits characterized so far! the overall sequence similarity among the RPA I subunits of different species is much lower than seen with the corresponding subunits of RNA polymerases II and III. Two highly divergent hydrophilic domains characteristic for RPA1 separate the conserved blocks a and b in the N-terminal region and blocks g and h in the C-terminal section, respectively. In both cases the distance between the homologous blocks is enlarged by about 70 amino acids relative to the largest subunits of RNA polymerases II and III, and the corresponding subunit of the archaebacterial enzyme. Compared with RPA1 sequences of lower eukaryotes, the C-terminal hydrophilic domain in DmRPA1 is similar in length and acidity whereas the N-terminal domain is slightly shorter but retains the same basicity. The sequence insertions do not feature common motifs, suggesting a role for them in the interaction of RNA polymerase I with proteins required for the species-specific transcription of rDNA. The RPA1 subunits of Drosophila melanogaster and lower eukaryotes share an additional Zn-binding motif at the N-terminus with archaebacterial and RPC1 subunits, testifying to the complex evolutionary relationships among the RNA polymerases.