The focus of our current work is on diplonemids, a eukaryotic group displaying most unusual gene expression. In Diplonema papillatum, we discovered that it's mitochondrial genome consists of ~80 different circular chromosomes, each of which carries a small gene module (see list of publications). Gene modules are transcribed individually and then joined together to contiguous mRNAs and rRNAs by trans-splicing.
Further, we detected several two types of RNA editing, affecting about 2/3 of genes. One proceeds by insertion of multiple Us at a given site, the other by nucleotide substitutions (C to U and A to I). We also observe a multipartite mitochondrial genome, gene fragmentation und RNA editing in other diplonemids(D. ambulator, D. sp. 2, Rhynchopus euleides), - with resourceful variations on the theme.
Our working hypothesis is that trans-splicing and RNA editing in diplonemids is directed by trans-factors, probably proteins. To test this hypothesis, we are employing genomics, transcriptomics, proteomics and bioinformatics approaches. Experimental data help to formulate specific search strategies and vice versa, bioinformatics hypotheses are being tested experimentally.
In addition, we have started exploring mtDNAs of other members of Euglenozoa, notably euglenids, basal kinetoplastids and yet undescribed diplonemids, in order to trace back the evolution and dispersal of RNA editing and multipartite mitochondrial genomes in this lineage.
As of now, we have draft assemblies from Andalucia godoyi and Reclinomonas americana, which are in the process of being completed and function-annotated. The 'Jakobids genome consortium' includes the research groups of G. Burger and BF. Lang (UdeM), M. Elias (Ostrava, Czech Rep.), MW. Gray and A. Roger (Dalhousie, Halifax, Canada).
This project aims at elucidating the steps that were involved in the 'domestication' of the endosymbiotic bacterial ancestor, and tracing the processes by which the predecessor of mitochondria was transformed into a eukaryotic organelle. These questions can now be tackled effectively through our discovery of mitochondrial DNAs resembling bacterial genomes in miniature: in unicellular, flagellated protozoans called jakobids.
We are investigating Andalucia godoyi to find out the degree to which mitochondrial information processing --from gene via RNA to protein-- resembles that of bacteria or rather 'modern' mitochondria as we known them from animals, fungi, and plants. Our approach combines classical biochemistry, new generation genomics methodologies and bioinformatics.