Evolution of the eukaryotic RNA polymerases

All eukaryotes contain at least three homologous RNA polymerases (RNAPI, RNAPII, and RNAPIII), which are directed towards their target genes by interactions with RNAP-specific general transcription factors (GTFs). Although the RNAPs transcribe a subset of nuclear genes, it is unknown if they have evolved altered functionality. An in silico approach to identify putative differences in the three RNAPs was used to identify whether any functional differences likely exist by identifying amino acids that have experienced shifts in evolutionary rates and by identifying length differences between the cleft loops of the RNAPs. The difference in the levels of concerted evolution experienced by the genes transcribed by RNAPs was then exploited to test the molecular coevolution hypothesis of Dover and Flavell (1984. Cell . 38:622-623.). According to the molecular coevolution hypothesis, concertedly evolving DNA increases the evolutionary rate of any interacting proteins. We thus compared the evolutionary rates of the three RNAPs and their GTFs, since their target genes undergo different levels of concerted evolution. Finally, the origins of the 5 subunits that are specific to RNAPIII were examined, since no homologous relationships have been identified thus far for any of these subunits. Several sites that have experienced shifts in substitution rates in the ancestral RNAPs were found in all three enzymes and these sites were clustered near the active sites in all cases. Several cleft loops with different lengths (in amino acids) between the three RNAPs were also identified. The validity of the molecular coevolution hypothesis was largely confirmed via the demonstration that most subunits of RNAPI evolve faster than those of RNAPIII and most subunits of RNAPIII evolve faster than RNAPII. This is consistent with the molecular coevolution hypothesis because RNAPI experiences higher levels of concerted evolution than the target genes of RNAPIII. The evolutionary rates of the GTFs of RNAPI and RNAPIII were also higher than those of RNAPII. Finally, four of the five RNAPIII-specific subunits were identified as homologs of RNAPII GTFs, indicating that several of the GTF paralogs existed in ancestral RNAPIII and were subsequently recruited to the enzyme before the diversification of eukaryotes