Heterogeneous nuclear ribonucleoprotein K protein associates with multiple mitochondrial transcripts within the organelle

Heterogeneous nuclear ribonucleoprotein K (hnRNP K) protein interacts with a subset of cellular RNAs. We used K protein as a bait in the yeast three-hybrid screen to identify RNAs that bind K protein in vivo. A large number of K protein-binding RNA clones were identified from a human hybrid RNA library. These sequences consisted of C-rich patches and were G-poor. Unexpectedly, several of the RNA clones were encoded by the mitochondrial genome. In a subsequent three-hybrid screen of a hybrid RNA library generated from a mouse liver mitochondrial genome, K protein bound RNA sequences encoded by different loci spanning nearly the entire mitochondrial genome. Western blot analysis of extracts from mitochondria and mitochondrial fractions showed that K protein is localized within mitoplasts. Reverse transcriptase PCR of RNA co-immunoprecipitated with K protein from lysates of isolated mitochondria showed that K protein is associated with several processed mitochondrial transcripts. In contrast, in the same assay, the polycistronic nascent mtRNA bound K protein weakly or not at all. Results of this study suggest that K protein acts within functional modules that are responsible for expression of genes in mitochondria.