The sole LSm complex in Cyanidioschyzon merolae associates with pre-mRNA splicing and mRNA degradation factors

RNA. 2017 Jun;23(6):952-967. doi: 10.1261/rna.058487.116. Epub 2017 Mar 21.

Abstract

Proteins of the Sm and Sm-like (LSm) families, referred to collectively as (L)Sm proteins, are found in all three domains of life and are known to promote a variety of RNA processes such as base-pair formation, unwinding, RNA degradation, and RNA stabilization. In eukaryotes, (L)Sm proteins have been studied, inter alia, for their role in pre-mRNA splicing. In many organisms, the LSm proteins form two distinct complexes, one consisting of LSm1-7 that is involved in mRNA degradation in the cytoplasm, and the other consisting of LSm2-8 that binds spliceosomal U6 snRNA in the nucleus. We recently characterized the splicing proteins from the red alga Cyanidioschyzon merolae and found that it has only seven LSm proteins. The identities of CmLSm2-CmLSm7 were unambiguous, but the seventh protein was similar to LSm1 and LSm8. Here, we use in vitro binding measurements, microscopy, and affinity purification-mass spectrometry to demonstrate a canonical splicing function for the C. merolae LSm complex and experimentally validate our bioinformatic predictions of a reduced spliceosome in this organism. Copurification of Pat1 and its associated mRNA degradation proteins with the LSm proteins, along with evidence of a cytoplasmic fraction of CmLSm complexes, argues that this complex is involved in both splicing and cytoplasmic mRNA degradation. Intriguingly, the Pat1 complex also copurifies with all four snRNAs, suggesting the possibility of a spliceosome-associated pre-mRNA degradation complex in the nucleus.

Keywords: Cyanidioschyzon merolae; LSm complex; Pat1; U6 snRNA; mRNA degradation; pre-mRNA splicing.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Base Sequence
  • Computational Biology / methods
  • Immunoprecipitation
  • Models, Molecular
  • Nucleic Acid Conformation
  • Phylogeny
  • Protein Binding
  • Protein Conformation
  • Protein Transport
  • RNA Precursors / chemistry
  • RNA Precursors / genetics*
  • RNA Splicing*
  • RNA Stability
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics*
  • RNA, Small Nuclear / chemistry
  • RNA, Small Nuclear / genetics
  • RNA-Binding Proteins / chemistry
  • RNA-Binding Proteins / metabolism*
  • Rhodophyta / genetics*
  • Rhodophyta / metabolism*
  • Tandem Mass Spectrometry

Substances

  • RNA Precursors
  • RNA, Messenger
  • RNA, Small Nuclear
  • RNA-Binding Proteins
  • U6 small nuclear RNA