The Interactions of the Largest Subunit of RNA Polymerase II with Other Cellular Proteins: a Bioinformatic Approach

Abstract

The function of a protein is governed by its interaction with other proteins inside a cell. Therefore, it is important to identify the interacting partners of a particular protein to decipher its function. The protein interaction networks are generally determined by bioinformatic as well as experimental methodologies such as yeast two hybrid, mass spectrometry, immunoprecipitation, and fluorescence resonance energy transfer assays. Here, we have analyzed bioinformatically the interactions of Rpb1p (the largest subunit of RNA Polymerase II) with other proteins in yeast, using Cytoscape software and Biogrid/ Biomart database. We find that Rpb1p interacts with a large number of proteins involved in mRNA synthesis, processing, export, and other cellular processes. These results validate the application of such bioinformatic approach to determine the interactome for other cellular proteins.Keywords: bioinformatics, protein interactions, Rbp1, yeast, human. IntroductionAll cellular processes are carried out by the concerted actions of proteins through specific interaction networks. Therefore, protein function annotation has become an important area of research in post-genomic sequencing era. Thus, an understanding of various cellular processes demands elucidation of the protein-protein interaction networks within cell. Several experimental methodologies such as yeast two hybrid, mass spectrometry, immunoprecipitation, and fluorescence resonance energy transfer assays have been employed to decipher cellular protein-protein interactions. Based on these experimental studies, several bioinformatic tools have been developed to comprehensively analyze protein interaction networks of different cellular proteins. Here, we have used the Cytoscape software (Zhang et al., 2007) and Biogrid/ Biomart database to identify the interactions of the largest subunit of RNA Polymerase II (RNAPII), Rpb1, with other proteins in yeast. Such analysis has revealed a large number of primary interactions of Rpb1p with many proteins involved in the regulation of transcription, chromatin structure, DNA repair, and other cellular events as discussed below. Rpb1 and its interactions with other RNAPII subunitsThe protein coding genes are transcribed into mRNA by RNAPII that is highly conserved from yeast to human. RNAPII is composed of 12 different subunits. These subunits are Rpb1, Rpb2, Rpb3, Rpb4, Rpb5, Rpb6, Rpb7, Rpb8, Rpb9, Rpb10, Rpb11, and Rpb12. Rpb1 is the largest subunit, and is essential to maintain the structural integrity of RNAPII. Moreover, it has Mg 2+ -dependent polymerase activity. The Rpb1 and Rpb2 subunits are located at the core of RNAPII with smaller subunits at the surface (Cramer et al., 2001(Cramer et al., , 2008Bushnell and Kornberg, 2003;Cramer, 2004). Thus, Rpb1 interacts with several RNAPII subunits as also observed in this bioinformatic analysis (Fig. 1).An important feature of Rpb1 is its c-terminal domain (CTD) that consists of multiple heptapeptide repeats (YSPTSPS) (Buratowski, 2003;Egloff and Murphy, 2008)...