ZNK1 is a zinc-sensor that degrades zinc transporter mRNA in trypanosomes

Zinc is essential for many biological processes but becomes deleterious when in excess. Like other cells, parasitic and other trypanosomatids sense and regulate Zn2+ uptake, but the mechanisms involved remained unknown. Here we identify a trypanosome RNA-binding protein which specifically eliminates ZIP3 Zn2+-transporter mRNA in Zn2+-replete conditions. We first demonstrated that Trypanosoma brucei ZIP3 mRNA abundance is subject to 3'-untranslated region (3'-UTR) and Zn2+-dependent negative control. We then ran a genome-wide RNA interference library screen, using a reporter associated with the ZIP3-derived 3'-UTR. The screen identified Tb927.11.9510 as a candidate Zn2+-sensor which we validated as a ZIP3 3'-UTR dependent negative regulator. We name this protein Zinc Nuclear Knuckles 1 (ZNK1) since it localises to the nucleus and contains several Zn2+-knuckle motifs. ZNK1 is conserved among trypanosomatids, and a PIN-domain suggests a ribonuclease-based mechanism. We used Cas9-editing to knockout ZNK1, and RNA-seq to assess the consequences in Zn2+-replete conditions. This revealed highly specific accumulation of ZIP3 transcripts in cells lacking ZNK1. We conclude that ZNK1 senses Zn2+-abundance and eliminates Zn2+-transporter mRNA in a Zn2+-dependent manner. Our results suggest that trypanosomatid ZNK1 binds ZIP3 3'-UTR sequences and degrades ZIP3 mRNA only when the tandem Zn2+-knuckle sensor modules are coordinated with Zn2+.