TRIM proteins represent a large family of proteins involved in a broad range of biological processes from innate immunity to neuronal and stem cell development. A sub-set of this family are the NHL domain containing TRIM-NHL proteins, which have been shown to regulate stem cell self-renewal, proliferation and development. This domain was originally thought to facilitate protein-protein interactions, however more recently NHL domains have been shown to directly bind RNA.
We have 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 and modulate chromatin and meiotic chromosome organisation in the germline through small RNA pathways, but the mechanism behind this remained unknown. Residues responsible for RNA binding were predicted using homologues structures and subsequently tested by mutation and binding studies to identify residues critical to RNA binding. We then solved the structure of apo NHL-2 to 1.4 angstrom resolution, revealing the mutated residues in the binding cleft of a 6-bladed beta propeller fold similar to that of other NHL domains, helping to rationalise their role in RNA binding. NHL-2 has been shown to act as an essential member of gene regulatory activity in both germline and somatic cells, with RNA binding through the NHL domain providing a potential mechanism for its function.