Gertraud Burger | research and collaborations

General Research Interests

  1. Evolution of organelles and the eukaryotic cell as a whole.

  2. The make-up of the nuclear genome from primitive eukaryotes.

  3. Experimental and in silico comparative genomics.

  4. Post-transcriptional processes in mitochondria: machineries, mechanisms and evolution.

  5. Integrated biological databases.

  6. Development of bioinformatics approaches and software for comparative genomics research.

Current Projects

  1. Unconventional genome architecture, eccentric gene structures and inventive gene expression mechanisms in mitochondria of unicellular marine eukaryotes
  2. We are studying the extraordinary biological diversity outside the 'main-stream' eukaryotic phyla.

    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 a contiguous mRNA by trans-splicing.

    Further, we detected several two types of RNA editing, affection 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).

    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.

  3. Genomes and transcriptomes of diplonemids - the portal to unraveling novelty
  4. To get insight into the trans-splicing and RNA editing machinery in diplonemid mitochondria (see project described above), and also to infer the metabolic capacity of these protists, we are sequencing the mitochondrial genomes of three other diplonemids (D. ambulator, D. sp. 2, Rhynchopus euleides), their transcriptomes and also the nuclear genome of Diplonema papillatum.

    This project is a collaboration with Julius Lukes (University of South Bohemia). The first draft sequence was established by Cestmir Vlcek (Institute of Molecular Genetics, Prag). Completion of the genome sequence, assembly and function-annotation is persued in Burger's laboratory.

  5. Nuclear genomes of primitive eukaryotes
  6. The protist group called jakobids is considered to include the most primitive (least derived or most ancestral) eukaryotes known. However, because of the deep divergences, phylogenetic reconstructions have sofar not been able to resolve with confidence which group the earliest offshoot of eukaryotes may be. To address this question, and also to understand the basic gene make-up of primitive eukaryotes, we are sequencing nuclear genomes from this group.

    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).

  7. Information processing in primitive eukaryotes
  8. In the initial transition phase from a symbiotic bacterium to an organelle, the proto-mitochondrial genome must have encoded more than a thousand genes specifying mitochondrial proteins, and adhered to bacterial conventions with respect to genome organization, RNA transcription and protein translation. However, in present-day mitochondria from animals, fungi and plants, gene organization and gene expression bear little traces of their bacterial past.

    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.

  9. Genomics of bacterial endosymbionts in eukaryotes
  10. CINAR PATHOBACTER is a European Union Research Project. In collaboration with four other universities in Europe and one in the USA, we are investigating ciliate-bacteria relationships at an ecological, functional and evolutionary-genomics level. The Montreal group (BF Lang & G Burger) is focussing on genome sequencing and annotation of Holospora bacteria.

Past Projects

  1. -Omics for Phytoremediation
  2. The GenoRem project aims at studing the inter-relationships between plants, fungi, and bacteria in the detoxification of soils that are contaminated with organic or inorganic compounds. The experimental approaches include genomics, transcriptomics, proteomics, and metabolomics. Bioinformatics methodologies assure thorough data management and analysis. This project is conducted by ~30 collaborating researchers of the Universite de Montreal and McGill University, and is financed by Genome Canada and Genome Quebec. Long-term goal is to select optimal combinations of plants and microorganisms for particular soil contaminations.

  3. Nuclear Genome Exploration
  4. The genome project "Unicorn" is a collaboration of seven research groups from Canada, UK, and USA, and endorsed by the National Human Genome Research Institute (NHGRI). This project aims at understanding how multicellularity first evolved. Genomic data are being generated from unicellular relatives of animals and fungi, i.e., choanflagellates, Ichthyosporea, Nuclearidae, chytrids, zygomycetes and apusozoa (outgroup) (see e.g., Ruiz-Trillo I et al, 2007).

  5. Organelle Genome Database (GOBASE)
  6. This comparative database ties together and unifies the various data on mitochondrial and chloroplast genomes and the organism which contain them, by making the information network-accessible to the scientific community. Data validation and addition of missing information is at the center of this project (O'Brien E et al 2007).

  7. EST Surveys
  8. The Protist EST Program ((PEP), a collaboration involving eight Canadian research groups, aims to determine the expressed portions of genomes from a taxonomically broad collection of mostly unicellular eukaryotes. The organismal group studied by myself and my collegues BF. Lang and MW. Gray are jakobid flagellates, which are believed to be amongst the most primitive extant eukaryotes. The goal of this project is to better understand early eukaryotic cell evolution (Keeling PJ et al, 2005). See also TBestDB below.

  9. Bioinformatics Development
  10. TBestDB organizes c-DNA and EST data from poorly-investigated protistan eukaryotes, generated by the pan-Canadian Protist EST program. Cross-referencing will be possible between the various PEP projects and with data from model organisms, including yeast, flatworm, but also cyanobacteria and alpha-proteobacteria, the ancestors of eukaryotic organelles. Interoparability with single-organism databases will be possible via the gene ontology framework (developped by the GO consortium). Released data are deposited into TBestDB for network access and download by the scientific community (O'Brien E et al, 2007).
    AutoFact is an automated pipeline to annotate EST sequences in a comprehensive and informative way. It is currently used to annotate PEP data, and available as open source.
    AnaBench, a web-based, integrated analysis environment, provides biologists access to diverse bioinformatics tools. The current prototype, which is accessible to the public, includes translation, Blast searches, multiple alignment, tRNA search, and more.
    Prediction of protein function and cellular localization. In typical genome projects, only ~50% of the protein-coding genes can be assigned to a function, and even less to a particular cellular location. This highlights the need of sensitive and efficient prediction methods. The main objective of this project is to apply machine learning methods (predictive data mining), to detect hidden signatures and patterns in integrated biological data, and to employ this new knowledge for deciphering genomic data at a large scale (Shen & Burger, 2008; Kannan & Burger, 2008a, b).

  11. Organelle Genome Megasequencing Program (OGMP)
  12. The OGMP is a collaborative project aiming at complete sequencing of mitochondrial and chloroplast genomes of a phylogenetically broad collection of mostly unicellular eukaryotes (Protista) (see Gray et al 2004, Annu Rev Genet).
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