Numerous plants host inside their cells fungi and bacteria. Some of these microbes suppress plant pathogens (biocontrol), deliver nitrogen and phosphorus to their host, modulate plant growth, and act on the metabolism and stress response of the plant.
The goal of this project is to isolate endosymbiotic microbes from plants and screen the former for biocontrol and plant growth stimulation, with a particular emphasis on complementarity and synergy between fungal and bacterial endosymbionts. We will sequence the microbes' genomes, assemble them, and perform functional annotation to identify genes with the potential of anti-microbial action and mediating interspecfic molecular crosstalk. Transcriptomics will help to unravel the molecular basis of microbe-microbe and microbe-plant interactions. The system of choice is the Ericacean plant Vaccinium macrocarpon, the North American cranberry, and its natural endosymbionts.
MycAtok is a collaborative project, in which participate academics, agronomists and farmers, and which involves also metabolomics and microbiology approaches, as well as greenhouse and field trials.
The focus of our current work is on a eukaryotic group displaying most unusual gene expression: the diplonemids. In Diplonema papillatum, we discovered that its mitochondrial genome consists of ~80 different circular chromosomes, each of which carries a small piece of a gene (see list of publications). Gene modules are transcribed separately and the resulting transcripts are then joined together to contiguous mRNAs and rRNAs by a process we refer to as 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). Other diplonemid species (e.g. D. ambulator, D. sp. 2, Rhynchopus euleides) have also a multipartite mitochondrial genome, gene fragmentation und RNA editing - though 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 yet undescribed diplonemids and euglenids, in order to trace back the evolution of multipartite mitochondrial genomes, gene fragmentation, and RNA editing 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, in addition to Burger's group, BF. Lang (UdeM), M. Elias (Ostrava University, CZ), MW. Gray and A. Roger (both Dalhousie University, Halifax, CA).
This project aims at elucidating the steps that had been involved in the 'domestication' of the endosymbiotic bacterial ancestor, and at 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.