Interaction of the spliced Oskar localization element of Oskar mRNA with the protein PYM

Abstract

mRNAs and the process of mRNA localization are the fundamental and pivotal parts of cellular functions. mRNA localization encompasses an important role in cellular differentiation and site-specific cellular functions, from the basic cellular biochemical mechanism to advanced abdomen formation. The study of mRNA, its localization mechanism along its binding partners have always been the main focus of study for several years. As they define life, in terms of cellular and sub-cellular mechanisms. Our study also involves one of the binding partners of the localization complex, which is Pym protein. Pym protein and exon junction complex are the common localization binding partners to many mRNA localization and Oskar mRNA is one of them. Pym being one of the recycling factors of the Exon Junction Complex shows binding interactions with many components, such as RNAs, Exon junction Complex, and Ribosomes. Our results show interesting structural and binding features of the protein Pym. NMR studies reveal that Pym160, the shorter construct of Pym is structurally unfolded, with the general characteristic of an intrinsically disordered protein. It has the long helical structural element in the middle part of the protein, while both N-terminal and C-terminal ends remain highly flexible with the structurally unfolded regions. The C-terminal part of the protein is not showing any direct involvement in the interaction with the SOLE RNA. However, it is structurally a very important part of the protein, as it stabilizes the ionic and hydrophobic interactions of the protein, so that protein could able to be a stable soluble protein. We have studied the binding motifs of the protein Pym160 with SOLE RNA and its isomers. Pym160 has binding motifs in the N-terminal region and in the middle helical region. Studies have confirmed that the N-terminal part of the protein binds to the Y14-Mago heterodimer, which is an essential part of the exon junction complex. In the absence of an Exon Junction Complex, the N-terminal part of the protein binds to the RNA. So, the study of the protein Pym160 is very much interesting and essential as it is a common protein for the wide range of mRNA localization mechanisms. Our studies explain the widespread binding nature of the Pym160, which might be due to its functional significance of being a structurally unfolded protein.