The scavenger decapping enzyme is a critical component in the eukaryotic mRNA decay machinery

Regulation of eukaryotic gene expression occurs at both the transcriptional and post-transcriptional levels. Modulation of mRNA decay is a crucial post-transcriptional step which determines the half-life of individual transcript. A major mRNA decay pathway in mammals proceeding from the 3' to 5' end is initiated with shortening of 3' poly (A) tail, followed by the degradation of RNA body by the exosome complex. The resulting cap dinucleotide is resistant to exoribonucleolytic digestion. Here, we biochemically purified the protein responsible for clearing the cap generated by 3' decay, termed scavenger decapping enzyme (DcpS). Consistent with the observed activity in extract, recombinant DcpS specifically cleaves methylated cap dinucleotides to yield methylated guanosine monophosphate and nucleotide diphosphate. Unlike the mRNA decapping enzyme Dcp2, DcpS does not function on long intact RNA, but hydrolyzes short capped RNA no longer than 10 nucleotides. Intriguingly, DcpS contains highly conserved Histidine Triad (HIT) motif which is essential for the catalytic activity. Co-crystalization of DcpS with cap substrate revealed DcpS to be an asymmetric dimer containing distinct N-terminal and C-terminal domains capable of simultaneously forming an open decapping nonproductive and closed decapping productive conformation. Conserved in eukaryotes, two putative homologs in S. cerevisiae were detected, and we demonstrated that only one of these proteins, termed Dcs1p, possesses intrinsic cap hydrolysis activity.;We next determined the regulatory role of the scavenger decapping enzyme on mRNA stability by utilizing a DCS1 disrupted strain. A three fold greater stability was detected for several mRNAs tested in cells lacking Dcs1p relative to cells expressing the protein. Further mechanistic analysis revealed 5' to 3' decay is negatively regulated in dcsl Delta, and we demonstrated 5' exoribonuclease activity is impeded in the absence of Dcs1p. Notably, the repression of mRNA turnover is a consequence of the cap hydrolysis activity rather than the Dcs1p protein itself since only expression of wild type Dcs1p but not catalytic inactive Dcs1p mutant complemented the increased stability. We postulate a model whereby the regulation of mRNA stability is mediated by either the substrates or products of Dcs1p functioning as methylated cap signaling nucleotides that subsequently inhibit 5' exoribonuclease activity.