An interferon-inducible mitochondrial circuit implicated in cell death, regulated by miRNAs, and conserved in vertebrates uncovered by evolution-guided studies

Abstract

Abstract Genomes are shaped by selective pressure imposed by pathogens. For instance, over evolutionary time direct-binding of immune factors, such as pattern-recognition receptors, by pathogen-encoded inhibitors can leave a historical record of this pressure as elevated rates of amino acid replacement across closely related species - a hallmark of positive selection. We hypothesized that positive selection could be leveraged to ascribe novel immune functions to poorly characterized genes. Using signatures of positive selection similar to those observed in critical antiviral genes (e.g. APOBEC3G, PKR), we carried out an evolution-guided screen to identify novel immune factors. Our top-candidate is a small mitochondrial protein strongly induced by interferon in human and mouse cells, conserved to zebrafish, and encoded by a poxvirus. Loss-of-function analysis uncovered a defect in staurosporine-induced cell death in the presence of interferon in the absence of this factor. Unexpectedly, this defect appears due to a miRNA, which is perfectly conserved (22/22nt) in certain fish species, encoded by the ISG mRNA. This miRNA targets a highly-conserved sequence in its paralog, a factor also rapidly evolving; a constitutively expressed mitochondrial protein that interacts with the OXPHOS complexes and conserved to yeast. Strikingly, another paralog and a related miRNA (that targets the same microRNA response element in the other paralog) are upregulated in response to hypoxic stress. These data allude to a vertebrate-specific circuit implicated in cell death that is induced by distinct types of cellular stress (e.g. infection, hypoxia), regulated by related miRNAs, implemented by mitochondrial paralogs and antagonized by viruses.