The Lsm1-7/Pat1 complex binds to stress-activated mRNAs and modulates the response to hyperosmotic shock

PLoS Genet. 2018 Jul 30;14(7):e1007563. doi: 10.1371/journal.pgen.1007563. eCollection 2018 Jul.

Abstract

RNA-binding proteins (RBPs) establish the cellular fate of a transcript, but an understanding of these processes has been limited by a lack of identified specific interactions between RNA and protein molecules. Using MS2 RNA tagging, we have purified proteins associated with individual mRNA species induced by osmotic stress, STL1 and GPD1. We found members of the Lsm1-7/Pat1 RBP complex to preferentially bind these mRNAs, relative to the non-stress induced mRNAs, HYP2 and ASH1. To assess the functional importance, we mutated components of the Lsm1-7/Pat1 RBP complex and analyzed the impact on expression of osmostress gene products. We observed a defect in global translation inhibition under osmotic stress in pat1 and lsm1 mutants, which correlated with an abnormally high association of both non-stress and stress-induced mRNAs to translationally active polysomes. Additionally, for stress-induced proteins normally triggered only by moderate or high osmostress, in the mutants the protein levels rose high already at weak hyperosmosis. Analysis of ribosome passage on mRNAs through co-translational decay from the 5' end (5P-Seq) showed increased ribosome accumulation in lsm1 and pat1 mutants upstream of the start codon. This effect was particularly strong for mRNAs induced under osmostress. Thus, our results indicate that, in addition to its role in degradation, the Lsm1-7/Pat1 complex acts as a selective translational repressor, having stronger effect over the translation initiation of heavily expressed mRNAs. Binding of the Lsm1-7/Pat1p complex to osmostress-induced mRNAs mitigates their translation, suppressing it in conditions of weak or no stress, and avoiding a hyperresponse when triggered.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Glycerol-3-Phosphate Dehydrogenase (NAD+) / genetics
  • Glycerol-3-Phosphate Dehydrogenase (NAD+) / metabolism
  • Membrane Transport Proteins / genetics
  • Membrane Transport Proteins / metabolism
  • Osmotic Pressure / physiology*
  • Protein Binding / physiology
  • Protein Biosynthesis / physiology
  • RNA Cap-Binding Proteins / genetics
  • RNA Cap-Binding Proteins / metabolism*
  • RNA, Messenger / metabolism*
  • RNA-Binding Proteins / genetics
  • RNA-Binding Proteins / metabolism*
  • Repressor Proteins / genetics
  • Saccharomyces cerevisiae / physiology*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae Proteins / metabolism*

Substances

  • ASH1 protein, S cerevisiae
  • LSM1 protein, S cerevisiae
  • Membrane Transport Proteins
  • PAT1 protein, S cerevisiae
  • RNA Cap-Binding Proteins
  • RNA, Messenger
  • RNA-Binding Proteins
  • Repressor Proteins
  • STL1 protein, S cerevisiae
  • Saccharomyces cerevisiae Proteins
  • GPD1 protein, S cerevisiae
  • Glycerol-3-Phosphate Dehydrogenase (NAD+)

Grants and funding

This work was supported by grants from the Swedish Research Council (www.vr.se), grant no. 2010 4645 (PS) and 2016-01842 (VP), the Swedish Cancer Fund (www.cancerfonden.se/), grant no. 2013-512 and 2016-378 (PS), Knut and Alice Wallenberg Foundation (www.wallenberg.com/kaw), grant no. 2016.0123 (VP), Carl Tryggers Foundation (www.carltryggersstiftelse.se/) grant no. KF13:8 and CTS 14:466 (PS), Ragnar Söderberg Foundation (ragnarsoderbergsstiftelse.se/) (VP), the regional Valencian government (www.gva.es/), grant no. PROMETEO II 2015/006 (PA), the Spanish ministry of economy and competitiveness (http://www.mineco.gob.es/), grant no. BFU2013-48643-C3-3-P and BFU2016-77728-C3-3-P (PA), Instituto de Salud Carlos III (www.isciii.es/) and the European Regional Development Fund (http://ec.europa.eu/regional_policy/en/funding/erdf/), grant PT13/0001/0035 (MS). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.