IP6K Gene Discovery in Plant mtDNA

IP6 Kinases (IP6Ks) are important mammalian enzymes involved in inositol phosphates metabolism. Although IP6K has not yet been identified in plant chromosomes, there are many clues suggesting its presence in vegetal cells. In particular, there are observations suggesting that the corresponding gene might be found in plant mtDNA, encrypted and hidden by virtue of editing and/or trans splicing processes. In this paper, we propose a new approach to search for the gene IP6K and applied it on mitocondrial DNA (mtDNA) of plants. To search for the gene IP6K, we applied a technique based on motif discovery by considering the nucleotide sequence corresponding to a specific tag of the IP6K family. Such a tag has been found in all IP6K genes identified up to now, as well as in all genes belonging to the Inositol Polyphosphates Kinases (IPK) superfamily, IPK tag sequence corresponds to the catalytic site of the enzyme and it can be considered as an identifier of IPK genes. In order to individuate the IPK tag sequence, that cannot be completely specified a priori, we exploited DLSME. DLSME is a software for motif extraction recently proposed, which allows for the motif structure to be only partially specified by the user. The analysis we conducted provided the relevant negative answer that IP6K does not actually occur in vegetable mtDNA.