Evolution of transcription in archaea and the early-diverging eukaryote, Giardia lamblia

Comparative analyses are at the core of modern biology, providing insight into the evolution of life and specific cellular systems. This thesis analyzes transcription systems in Archaea and Eucarya in an effort to understand the evolution of this fundamental cellular process. Projects span from analyses of the archaeal RNA polymerase to a unique genome survey of transcription components in an early-diverging eukaryote. It is apparent that the evolution of transcriptional machinery can be subdivided into the evolution of a core system and the evolution of a peripheral set of factors modulating the activity and specificity of the core. We see the core in the similarity of RNA polymerases and modes of initiation between Archaea and Eucarya; through protein-protein interaction studies, we demonstrated that the RNA polymerases from each domain adopt a similar architecture. We see the periphery in an analysis of the genome of Giardia lamblia, highlighting the divergence of transcription systems during the early evolution of Eucarya. During the survey, the TATA-binding protein (TBP) from Giardia lamblia was observed to be highly degenerate relative to all known TBPs. Comparative modeling of giardial TBP with eukaryotic TBP crystal structures reveals altered binding surfaces for interactions with DNA and transcription factors. A comparative analysis of post-transcriptional modification of RNA in the three domains of life illustrates the uniqueness of each domain. It is likely that Archaea do not modify RNA by post-transcriptional polyadenylation, a process adopted for disparate functions in both the bacterial and eukaryal domains.