Crystal structures and RNA-binding properties of Lsm proteins from archaea Sulfolobus acidocaldarius and Methanococcus vannielii: Similarity and difference of the U-binding mode

Biochimie. 2020 Aug;175:1-12. doi: 10.1016/j.biochi.2020.05.001. Epub 2020 May 15.

Abstract

Sm and Sm-like (Lsm) proteins are considered as an evolutionary conserved family involved in RNA metabolism in organisms from bacteria and archaea to human. Currently, the function of Sm-like archaeal proteins (SmAP) is not well understood. Here, we report the crystal structures of SmAP proteins from Sulfolobus acidocaldarius and Methanococcus vannielii and a comparative analysis of their RNA-binding sites. Our data show that these SmAPs have only a uridine-specific RNA-binding site, unlike their bacterial homolog Hfq, which has three different RNA-binding sites. Moreover, variations in the amino acid composition of the U-binding sites of the two SmAPs lead to a difference in protein affinity for oligo(U) RNA. Surface plasmon resonance data and nucleotide-binding analysis confirm the high affinity of SmAPs for uridine nucleotides and oligo(U) RNA and the reduced affinity for adenines, guanines, cytidines and corresponding oligo-RNAs. In addition, we demonstrate that MvaSmAP1 and SacSmAP2 are capable of melting an RNA hairpin and, apparently, promote its interaction with complementary RNA.

Keywords: Hfq; Methanococcus vannielii; RNA-Protein interaction; Sm-like proteins; SmAP; Sulfolobus acidocaldarius.

MeSH terms

  • Archaeal Proteins / chemistry*
  • Binding Sites
  • Crystallography, X-Ray
  • Methanococcus / chemistry*
  • Poly U / chemistry*
  • RNA-Binding Proteins / chemistry*
  • Sulfolobus acidocaldarius / chemistry*

Substances

  • Archaeal Proteins
  • RNA-Binding Proteins
  • Poly U