TRIM proteins represent a large family of proteins involved in a broad range of biological processes from innate immunity to stem cell development. A sub-set of this family, TRIM-NHL proteins, have been shown to regulate stem cell proliferation and development. These proteins are grouped together based on the presence of C-terminal NHL repeats which were originally thought to facilitate protein-protein interactions. However, more recently some NHL repeats have been shown to bind RNA.
We identified NHL-2, a TRIM-NHL protein from C. elegans and known co-factor of let-7 and lsy-6 miRNA pathways as an RNA binding protein. NHL-2 has previously been shown to control stem cell development in somatic cells, along with modulating chromatin and meiotic chromosome organisation in the germline. Based on homologous structures we predicted residues responsible for RNA binding. We then tested alanine mutations and were able to identify which of these residues were critical to RNA binding. We subsequently solved the structure of apo NHL-2 to 1.8 angstrom resolution, revealing a 6-bladed beta propeller fold similar to other NHL repeats, with the position of the identified residues sitting close to the predicted RNA binding groove. NHL-2 has been shown to act as an essential member of gene regulatory activity in both germline and somatic cells. These results show that NHL-2 is a bona fide RNA binding protein suggesting that its role in the control of these pathways is via RNA interactions.