Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation

Abstract

Sm-like (Lsm) proteins have been identified in all organisms and are related to RNA metabolism. Here, we report that Arabidopsis nuclear AtLSM8 protein, as well as AtLSM5, which localizes to both the cytoplasm and nucleus, function in pre-mRNA splicing, while AtLSM5 and the exclusively cytoplasmic AtLSM1 contribute to 5′–3′ mRNA decay. In lsm8 and sad1/lsm5 mutants, U6 small nuclear RNA (snRNA) was reduced and unspliced mRNA precursors accumulated, whereas mRNA stability was mainly affected in plants lacking AtLSM1 and AtLSM5. Some of the mRNAs affected in lsm1a lsm1b and sad1/lsm5 plants were also substrates of the cytoplasmic 5′–3′ exonuclease AtXRN4 and of the decapping enzyme AtDCP2. Surprisingly, a subset of substrates was also stabilized in the mutant lacking AtLSM8, which supports the notion that plant mRNAs are actively degraded in the nucleus. Localization of LSM components, purification of LSM-interacting proteins as well as functional analyses strongly suggest that at least two LSM complexes with conserved activities in RNA metabolism, AtLSM1-7 and AtLSM2-8, exist also in plants.

Role for LSM genes in the regulation of circadian rhythms

“…Among the AS events affected in the lsm4 and sad1/lsm5 mutants, we found an increase in the proportion of IR events relative to their frequency in wildtype plants, which is consistent with previous findings reported for the sad1/lsm5 mutant (Fig. 4C) (29,36). Representative examples of alterations in AS observed in the mutants using the Integrative Genome Browser (IGB) (37) are shown in Fig.…”

“…The nuclear complex consists of LSM2 to LSM8 and is required for U6 snRNA stabilization and proper pre-mRNA splicing. The cytoplasmic complex consists of LSM1 to LSM7 and is required for Pbody formation, mRNA decapping, and accurate mRNA decay in the cytoplasm (36,39). LSM4 and LSM5 are part of both complexes and, therefore, although alterations in circadian period are likely to result in part from defective splicing of specific clock genes, part of the circadian phenotype may result from the role of LSM proteins in regulating the mRNA stability of a subset of clock genes.…”

Alternative Splicing at the Intersection of Biological Timing, Development, and Stress Responses

“…It encodes the homolog of LSm5 protein, a component of the U6 snRNP core (Perea-Resa et al, 2012). Recently, reduced levels of U6 snRNA and accumulation of unspliced pre-mRNAs have been observed in the sad1/lsm5 mutant, suggesting that it has a role in pre-mRNA splicing by contributing to U6 stability (Golisz et al, 2013). Similarly, the lsm4 mutant is hypersensitive to salt and ABA and shows mis-splicing .…”

Investigating splicing in two disparate organisms: a highly reduced spliceosome in Cyandioschyzon Merolae and additional functionality in Saccharomyces Cerevisiae's PRP24

“…In eukaryotes, there exist a cytoplasmic set of LSm proteins (LSm 1-7) that function to decap mRNA during degradation events and a nuclear set of LSm proteins (LSm 2-8) that bind to the 3' end of the U6 snRNA and seem to assist with the recycling of U4 and U6 into the U4/U6 di-snRNP (Golisz et al 2013;Beggs 2005). While they are functionally distinct, both sets of LSm proteins share six of seven proteins in their heptameric ring with the only difference being the presence of LSm1 in the cytoplasmic set and LSm8 in the nuclear set.…”

“…A rather simple way to investigate this question would be to express the identified LSm proteins and perform binding assays with C. merolae's U6 snRNA to determine whether the LSm complex is capable of binding U6 as is the case with the splicing LSms in other organisms (Golisz et al 2013;Beggs 2005). Similarly, expression and binding assays with C.…”