Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer

Abstract

Protein oligomerization is one mechanism by which homogenous solutions can separate into distinct liquid phases, enabling assembly of membraneless organelles. Survival Motor Neuron (SMN) is the eponymous component of a large macromolecular complex that chaperones biogenesis of eukaryotic ribonucleoproteins, and localizes to distinct membraneless organelles in both the nucleus and cytoplasm. SMN forms the oligomeric core of this complex, and missense mutations within its YG box domain are known to cause Spinal Muscular Atrophy (SMA). The SMN YG box utilizes a variation of the glycine zipper motif to form dimers, but the mechanism of higher-order oligomerization remains unknown. Here, we use a combination of molecular genetic, bioinformatic, biophysical, and computational approaches to show that formation of higher-order SMN oligomers depends on a set of YG box residues that are not involved in dimerization. Mutation of key residues within this new structural motif restricts assembly of SMN to dimers and causes locomotor dysfunction and viability defects in animal models.

Assembly of higher-order SMN oligomers is essential for metazoan viability and requires an exposed structural motif present in the YG zipper dimer

“…While this manuscript was under consideration ( 57 ), the crystal structure of a non-native fusion between the Gem2 domain and YG box of spSMN was reported ( 58 ). In that structure (PDB ID 7BB3), the YG box dimers interact to form a polymer of antiparallel stacked dimers in the crystal lattice, with the Gem2 domain helices forming an independent array of hydrophobic interactions.…”

A homozygous missense variant in the YG box domain in an individual with severe spinal muscular atrophy: a case report and variant characterization

“…The pathogenic variant, c.796T>C (p.Ser266Pro), is located in the highly conserved YG-box domain important for SMN selfoligomerization (Lorson et al, 1998;Gupta et al, 2021). Genetic manipulations of amino acids in this domain have established a direct correlation between oligomerization and SMA clinical type (Lorson et al, 1998).…”

“…Phylogenetically speaking, the YG box is the most highly conserved subdomain of SMN and performs an essential function in self-oligomerization (Lorson et al, 1998;Gupta et al, 2021). The human YG box dimer adopts an alpha-helical structure (Martin et al, 2012) that does not directly involve Ser266.…”

“…The human YG box dimer adopts an alpha-helical structure (Martin et al, 2012) that does not directly involve Ser266. Instead, this residue forms part of a motif that is required for higher-order multimerization (Gupta et al, 2021). The so-called small-or s-motif includes Ser266 and Ser270 and, in vivo, these residues do not tolerate large, bulky substitution mutations such as Ser266Gln or Ser270Phe [Gupta et al (2021) and references therein].…”

“…Instead, this residue forms part of a motif that is required for higher-order multimerization (Gupta et al, 2021). The so-called small-or s-motif includes Ser266 and Ser270 and, in vivo, these residues do not tolerate large, bulky substitution mutations such as Ser266Gln or Ser270Phe [Gupta et al (2021) and references therein]. To probe the effect of the variant on YG-box tetramerization, we carried out extensive molecular dynamics simulations (Supplementary material) on both the wild-type and mutant YG-box peptides.…”