Pat1 activates late steps in mRNA decay by multiple mechanisms

Abstract

Pat1 is a hub for mRNA metabolism, acting in pre-mRNA splicing, translation repression, and mRNA decay. A critical step in all 5′-3′ mRNA decay pathways is removal of the 5′ cap structure, which precedes and permits digestion of the RNA body by conserved exonucleases. During bulk 5′-3′ decay, the Pat1/Lsm1-7 complex engages mRNA at the 3′ end and promotes hydrolysis of the cap structure by Dcp1/Dcp2 at the 5′ end through an unknown mechanism. We reconstitute Pat1 with 5′ and 3′ decay factors and show how it activates multiple steps in late mRNA decay. First, we find that Pat1 stabilizes binding of the Lsm1-7 complex to RNA using two conserved short-linear interaction motifs. Second, Pat1 directly activates decapping by binding elements in the disordered C-terminal extension of Dcp2, alleviating autoinhibition and promoting substrate binding. Our results uncover the molecular mechanism of how separate domains of Pat1 coordinate the assembly and activation of a decapping messenger ribonucleoprotein (mRNP) that promotes 5′-3′ mRNA degradation.

Molecular basis for the distinct cellular functions of the Lsm1-7 and Lsm2-8 complexes

“…Taken together, our data suggest an allosteric model for Pat1-mediated stimulation of Lsm1-7 binding (12,24). In this model, Pat1 binding displaces the Lsm1 C-terminal domain to stimulate RNA binding affinity and relax specificity ( Figure 6).…”

“…The Lsm1-7 complex is cytoplasmic and mediates messenger-RNA (mRNA) decay, a major post-transcriptional mechanism for regulating gene expression (6)(7)(8)(9). Binding of the Lsm1-7 complex to mRNA is a key event in the decay pathway as it also binds the protein Pat1 (10)(11)(12). Pat1 then recruits a complex consisting of the decapping enzyme Dcp2 and its activators Dcp1, Edc1 and Edc2 (13).…”

“…In addition to activating mRNA decapping, Lsm1-7 has many other functions including formation of phase-separated processing bodies (P-bodies) (16,17), protecting 3′ ends of mRNA from 3′-5′ degradation by the exosome (18,19), stabilizing specific RNAs during starvation and autophagy (20), suppressing translation of stress-activated RNAs during osmotic shock (21), and promoting translation of viral RNAs (22). Human and S. pombe Lsm1-7 complexes bind tightly to oligouridylate (hereafter, oligoU) RNAs (12,23). In contrast, the Lsm1-7-Pat1 complex binds tightly to oligoadenylate (hereafter, oligoA) RNAs (10,12,24).…”

“…Human and S. pombe Lsm1-7 complexes bind tightly to oligouridylate (hereafter, oligoU) RNAs (12,23). In contrast, the Lsm1-7-Pat1 complex binds tightly to oligoadenylate (hereafter, oligoA) RNAs (10,12,24). The molecular basis for these interactions is unknown.…”

Pat1 increases the range of decay factors and RNA bound by the Lsm1-7 complex

“…1). Because PatMC does not bind RNA with 265 appreciable affinity on its own, we suggest that Pat1 may allow the Lsm1-7 complex to 266 bind sequences which it has inherently weaker affinity for and therefore expand the 267 complex's target repertoire (Lobel et al 2019) (Fig. S1G).…”