RNA polymerase II CTD Evolutionary Diversity and Associated Protein Identification in Green and Red Algae
In model eukaryotes, the C-terminal domain (CTD) of the largest subunit (RPB1) of DNA-dependent RNA polymerase II is composed of tandemly repeated heptads with the consensus sequence YSPTSPS. Both the core motif and tandem structure generally are highly conserved across many model taxa, including animals, yeasts and higher plants. Broader investigations quickly revealed that the CTDs of many organisms deviate substantially from this canonical structure; however, limited sampling made it difficult to determine whether disordered sequences represent the CTD's ancestral state, or reflect degeneration from an originally repetitive structure. Therefore, I undertook the broadest investigation to date of the evolution of the RNAP II CTD across eukaryotic diversity. The results indicate that a tandem heptad CTD-structure existed in the ancestors of each major taxon, and that degeneration and reinvention of this ordered structure are common features of CTD evolution. Lineage specific modifications of heptads that were amplified initially appear to be associated with greater developmental complexity in multicellular taxa. The pattern has been taken to an extreme in both fungi and red algae. Overall, loss and reinvention of varied repeats have punctuated CTD evolution, occurring independently and sometimes repeatedly in various groups. Although present in simple, ancestral red algae, CTD tandem repeats have undergone extensive modifications and degeneration during the evolutionary transition to developmentally complex rhodophytes. In contrast, CTD repeats are conserved in both green algae and their more complex land plant relatives. Understanding the mechanistic differences that underlie these variant patterns of CTD evolution requires knowledge of CTD-associated proteins in these two lineages. To provide an initial baseline comparison, potential phospho-CTD associated proteins (PCAPs) were bound to artificially synthesized and phosphorylated CTD repeats from the unicellular green alga Chlamydomonas reinhardtii and red alga Cyanidioschyzon merolae. My results indicate that red and green algae share a number of PCAPs, including kinases and proteins involved in mRNA export. There also are important taxon-specific differences, including mRNA splicing-related PCAPs recovered from Chlamydomonas but not Cyanidioschyzon, consistent with the relative intron densities in green and red algae. This work also offers the first experimental indication that different proteins bind the two types of repeats in Cyanidioschyzon, suggesting a division of function between the proximal and distal CTD, similar to patterns identified in more developmentally complex model organisms.
Yang, Chunlin. (January 2014). RNA polymerase II CTD Evolutionary Diversity and Associated Protein Identification in Green and Red Algae (Doctoral Dissertation, East Carolina University). Retrieved from the Scholarship. (http://hdl.handle.net/10342/4715.)
Yang, Chunlin. RNA polymerase II CTD Evolutionary Diversity and Associated Protein Identification in Green and Red Algae. Doctoral Dissertation. East Carolina University, January 2014. The Scholarship. http://hdl.handle.net/10342/4715. August 14, 2018.
Yang, Chunlin, “RNA polymerase II CTD Evolutionary Diversity and Associated Protein Identification in Green and Red Algae” (Doctoral Dissertation., East Carolina University, January 2014).
Yang, Chunlin. RNA polymerase II CTD Evolutionary Diversity and Associated Protein Identification in Green and Red Algae [Doctoral Dissertation]. Greenville, NC: East Carolina University; January 2014.
East Carolina University