Linking gene and function by comparative genomics: examples from deazapurine metabolism reveal cross-talks between RNA and DNA modifications

Identifying the function of every gene in all sequenced organisms is the major challenge of the post-genomic era and an obligate step for any systems biology approach. This objective is far from reached. By various estimates, at least 30-50% of the genes of any given organism are of unknown function, incorrectly annotated, or have only a generic annotation such as “ATPase”. Moreover, with ~15,000 complete and ~300,000 incomplete bacterial genomes sequenced (http://www.genomeson.line.org), the numbers of unknown genes are increasing, and annotation errors are proliferating rapidly. For some gene families, 40% of the annotations are wrong. On the other side of the coin, there are still ~1,900 known enzyme activities for which no corresponding gene has been identified and these numbers are also increasing. This biochemical knowledge is yet to be captured in genome annotations. Using mainly a comparative genomic approach, we have linked gene and function for around 60 gene families related mainly to the fields of coenzyme metabolism, tRNA modification, protein modification and more recently metabolite repair. This approach integrates several types of data and uses filters, sieves, and associations to make predictions that can then be tested experimentally. An unknown gene’s function may thus be predicted from those of its associates: the ‘guilt by association’ principle. Associations that can be derived from whole genome datasets include: gene clustering, gene fusion events, phylogenetic occurrence profiles or signatures and shared regulatory sites. Post-genomic experimental sources such as protein interaction networks, gene expression profiles and phenomics data can also be used to find associations. In practice it is often ‘guilt by multiple association’ as genes can be associated in several ways and analyzing more than one of these improves the accuracy of predictions.

We have applied these methods to decipher the synthesis and salvage pathways for two deazapurine modifications of tRNA, Queuosine (Q) and Archaeosine (G+), made from the same precursor molecule PreQ0. This has led to the discovery of many novel enzymes, chemistry and pathways that will be discussed. These include: 1) the discovery of novel bacterial queuine base in human pathogens; 2) to the detection of 7-deazapurine derivatives in bacterial and phage DNA that play key roles in the war between bacteria and phages.

Fungal cell-wall polysaccharides, exploiting their translational potential

Annually, invasive fungal infections (IFI) kill >1.6-million people globally, a number greater than the deaths caused by malaria, and equal to tuberculosis/HIV. Despite available antifungal treatment, the population at risk for IFI is on the rise. One of the reasons for that is our poor knowledge on virulence strategies of pathogenic fungi. Amongst virulence arms, the cell-wall of fungal pathogens play a crucial role. Fungal cell-wall is composed of different polysaccharides. Although their composition has been determined by biochemical methods, the organization of cell-wall polysaccharides in situ had never been explored. While poor immunogenicity, insolubility and aggregating property are the limiting factors of fungal cell-wall polysaccharides for their translational application. Using biophysical, biochemical, and immunological techniques, and working on Aspergillus fumigatus as a model pathogen, we have made attempts in filling these research gaps, which will be the topic of my presentation.