Structural and functional analysis of critical proteins involved in mRNA decay

Abstract

mRNA degradation is important for gene expression in eukaryotic cells. Three proteins, Ski8, Dhh1 and hUpf1 involved in mRNA decay, have been structurally and functionally studied. Ski8, a WD-repeat protein, plays an essential role in 3'-to-5' mRNA decay. Crystal structure of Ski8 shows a seven-bladed i??-propeller with the top face revealed to be involved in protein-protein interaction by structural and mutagenesis analysis. Dhh1, a DEAD-box protein, functions both to repress translation and enhance decapping. The structure of the truncated Dhh1 represents a two RecA-like architecture with a unique arrangement. A conformational change and a prominent RNA binding site have been identified by structural analysis combined with mutagenesis studies. Upf1, a SF1 RNA helicase, plays a critical role in nonsense-mediated mRNA decay. Crystal structures of the catalytic core of human Upf1 determined in three states (phosphate-, AMPPNP- and ADP-bound forms) reveal an overall structure composed of two RecA-like domains with two additional domains protruding from the N-terminal RecA-like domain. Structural analysis combined with mutagenesis studies presented a likely ssRNA binding channel, a cycle of conformational change coupled to ATP binding/hydrolysis and a mechanism of ATP-modulated RNA binding.