Activation of decapping involves binding of the mRNA and facilitation of the post-binding steps by the Lsm1-7–Pat1 complex

Abstract

Decapping is a critical step in the conserved 59-to-39 mRNA decay pathway of eukaryotes. The hetero-octameric Lsm1-7-Pat1 complex is required for normal rates of decapping in this pathway. This complex also protects the mRNA 39-ends from trimming in vivo. To elucidate the mechanism of decapping, we analyzed multiple lsm1 mutants, lsm1-6, lsm1-8, lsm1-9, and lsm1-14, all of which are defective in decapping and 39-end protection but unaffected in Lsm1-7-Pat1 complex integrity. The RNA binding ability of the mutant complex was found to be almost completely lost in the lsm1-8 mutant but only partially impaired in the other mutants. Importantly, overproduction of the Lsm1-9p-or Lsm1-14p-containing (but not Lsm1-8p-containing) mutant complexes in wild-type cells led to a dominant inhibition of mRNA decay. Further, the mRNA 39-end protection defect of lsm1-9 and lsm1-14 cells, but not the lsm1-8 cells, could be partly suppressed by overproduction of the corresponding mutant complexes in those cells. These results suggest the following: (1) Decapping requires both binding of the Lsm1-7-Pat1 complex to the mRNA and facilitation of the post-binding events, while binding per se is sufficient for 39-end protection. (2) A major block exists at the post-binding steps in the lsm1-9 and lsm1-14 mutants and at the binding step in the lsm1-8 mutant. Consistent with these ideas, the lsm1-9, 14 allele generated by combining the mutations of lsm1-9 and lsm1-14 alleles had almost fully lost the RNA binding activity of the complex and behaved like the lsm1-8 mutant.

Pat1 contributes to the RNA binding activity of the Lsm1-7–Pat1 complex

“…First, as expected and as we had observed previously with the wild-type complex (Chowdhury et al 2007;Chowdhury and Tharun 2009), a ∼23-kD band radiolabeled in a UV irradiation-dependent manner was clearly visible in crosslinking reactions carried out using both the complexes. This band has the expected mobility of Flag-Lsm1, and we have shown earlier via immunoprecipitation analyses that it does contain FlagLsm1 (Chowdhury et al 2007;Chowdhury and Tharun 2009). Second, in crosslinking reactions carried out using the wildtype complex, at least two more bands of lower mobility (∼65 kD and ∼97 kD) were also detectable in longer exposures, although one of them (∼97 kD) was weak.…”

“…This may partly be to do with the smaller size of the Lsm1-7 complex compared with the wild-type Lsm1-7-Pat1 complex (∼97 kD vs. ∼185 kD). Second, while the Lsm1-7-Pat1 complex clearly exhibited a higher affinity for the PGK1-A 5 RNA than the PGK1 RNA as expected and as observed earlier (Chowdhury and Tharun 2009;Chowdhury et al 2012), such binding preference could not be observed with the Lsm1-7 complex. Very similar results were also observed when the experiments were carried out using the MFA2 and MFA2-A 5 RNAs (42-mer RNA derived from the 3 ′ UTR of MFA2 and the 3 ′ -penta-adenylated version of such RNA) as substrates for gel shift assays (Fig.…”

“…Importantly, the ability of this complex to recognize the oligoadenylated status of RNAs is essential for its function in mRNA decay in vivo and is dependent on the RNA binding residues in the Sm domain of the Lsm1 subunit (Chowdhury and Tharun 2008). Nevertheless, after binding the mRNA, to activate decapping, this complex needs to facilitate additional post-binding events that are not yet fully understood (Chowdhury and Tharun 2009). This complex shares six of its subunits (Lsm2 through Lsm7) with the Lsm2-8 complex, which is localized in the nucleus and is not involved in cytoplasmic mRNA decay (Bouveret et al 2000;Tharun et al 2000;Ingelfinger et al 2002;Tharun 2009b).…”

Genetic Analysis of Resistance and Sensitivity to 2-Deoxyglucose in Saccharomyces cerevisiae

“…complex (Chowdhury and Tharun 2009). An important role for Snf1 in the regulation of mRNA turnover has recently been uncovered in studies using conditional Snf1 kinase alleles (Young et al 2012;Braun et al 2014).…”

Dcp1 links coactivators of mRNA decapping to Dcp2 by proline recognition

“…For example, in budding yeast, all mRNA decapping and 59-39 decay requires the general activator Dcp1, whereas bulk decay requires Dhh1 and the Pat1/Lsm1-7 complex, and nonsense mediated decay requires the Upf proteins (Beelman et al 1996;He et al 1997;Tharun et al 2000;Coller et al 2001;He and Jacobson 2001;Chowdhury and Tharun 2009). In Saccharomyces cerevisiae, the enhancer of decapping protein family (Edc1-3) activates decapping as part of an adaptive response to carbon source shifts or by promoting decay of specific transcripts (DeRisi et al 1997;Dunckley et al 2001;Schwartz et al 2003;Kshirsagar and Parker 2004;Badis et al 2004;Dong et al 2007).…”