Transcription factor binding site detection and comparative modeling as discovery approaches in Pyrococcus

Abstract

The molecular machinery of basal archaeal transcription is similar but simpler than that of eukaryotes, while many elements of archaeal transcriptional regulation resemble those of bacteria. Together, these factors make archaeal transcription as a useful model for studying transcription. This work describes two different computational methods to study different aspects of archaeal transcription, in particular within Pyrococcus. First, the UORdb database was developed that enables transcription factor binding site searches in promoter regions on a genome-wide scale through the enrichment of the search space with prospective binding sites. The UORdb database has been expanded as a web portal for quick and flexible TFBS searching (http://scottgroup.rcc.uga.edu/scottgrp/uor_search/py/home), using both a global internal search method and external motif finders such as BioProspector, CUBIC, and MEME. This database application was crucial in identifying the Pyrococcus furiosus transcriptional regulator protein, dubbed SurR for Sulfur-response regulator, and in validating some of its regulatory binding sites throughout the P. furiosus genome. Second, a comparative model was constructed for the P. furiosus RNAP complex composed of seven protein subunits and based on the 2.8Å resolution X-ray crystallographic structure of the eukaryal open-clamp Saccharomyces cerevisiae RNAPII complex. Despite limitations in the comparative model, comparison with archaeal RNAP structures, including the 3.4Å resolution Sulfolobus solfataricus RNAP structure confirm its accuracy in modeling an archaeal RNAP, particularly with the RNAP active site region and the dock domain, an interaction site for TFIIB crucial in the process of transcription initiation.