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The genomic basis of emerging fungal pathogenicity

Final Report Summary - FUNGI-PATHNCODE (The genomic basis of emerging fungal pathogenicity)


Marie Curie Final Report

FUNGI-PATHnCode contacts gabriela.aguileta@crg.es toni.gabaldon@crg.cat

Intra-European Fellowships (IEF) Call: FP7-PEOPLE-2010-IEF

1. FINAL PUBLISHABLE SUMMARY REPORT

When people are asked to think of microorganisms causing infections they are more likely to think about viruses and bacteria than fungi. However, fungal pathogens represent important threats to human welfare either by severely affecting crops for human consumption or by becoming able to infect us. In recent times, due to globalized trade, we have created the conditions that allow different fungal species to come together and mingle thereby providing the opportunity for new pathogenic species to emerge. Indeed, fungi have proven to be excellent opportunistic pathogens that can readily exchange genetic material and hybridize. Fungal cells are, as it were, fast evolution laboratories where new chemical weapons are constantly being crated and tried on different hosts. Typically, fungi attack plants more easily than animals but we have recently witnessed an increasing number of fungal pathogens that are able to infect animal cells, including humans.

Our proposed project “FUNGI-PATHnCode” aimed at understanding the genetic basis of the acquired ability of fungal species to become effective pathogens. We wanted to know if pathogenic fungi possessed a shared genetic “toolbox” that allowed them to infect a host. We also asked whether this collection of genes would differ between plant and animal fungal pathogens. Finally, we were interested in determining which genetic differences were more relevant for pathogenicity, whether those that involved changes in the genes themselves, or those that affected regulatory regions. In order to answer these questions, we used a comparative genomics approach in an evolutionary context. We therefore compared whole genomes of different fungal species, some of them were pathogenic and others, although closely related, were not. For each genome, we built one phylogenetic tree per gene and analyzed how all these gene trees combined represented the evolutionary interrelationships of all genes in all the analyzed species. This is what we call a phylome, from which we can infer the history of gene duplication and speciation events. A phylome will also inform us about the genes that are shared by all species, as well as the genes that are species-specific. In this way we were able to establish which was the genetic toolbox shared by fungal pathogens as opposed to non-pathogens. Furthermore, we were able to determine which families of genes had expanded in specific pathogens, for instance, in plant- relative to animal-pathogens.

Knowing which genes were used by different pathogens and how many copies of these genes were present in different species is an indication of which gene functions are necessary to infect host cells. Another indication comes from the pressure exerted by natural selection on different genes. Typically, following gene duplication some gene copies will accumulate substitutions more rapidly than others and, often, these changes prove advantageous and are thus maintained in the population. This process is referred to as positive selection. Genes with new functions can thus emerge from pre-existing genes. Because we were interested in predicting which genes (and gene functions) were important for pathogenicity, we investigated the selective pressure affecting the evolution of different genes in pathogen and non-pathogen fungal species. We hypothesized that the genes that were evolving rapidly in fungal pathogens relative to non-pathogen fungi could be good candidates for genes that were important for pathogenicity.

We used the described methods in three sets of species: 1) the group of fungi including the well-known pathogens Candida albicans and Candida glabrata, and 2) a complex of fungal species called Microbotryum that affect the Cariophyllaceae plant family, and 3) we are currently working on a similar analysis of the Magnaporthe oryzae group of fungi, among which, is an important pathogen of rice. The overall results from these three studies suggests that: 1) gene family expansions by gene duplication, followed by episodes of adaptive evolution often driven by positive selection, is a general trend in the evolution of pathogenic strains and species among fungi, 2) expansion of different gene families, involving different and specific gene functions that are particular depending on the target host are key for effective pathogenicity, 3) adaptive evolution in pathogenic fungi can occur rapidly (in an evolutionary scale), in the space of a few million years. In the case of the Candida group of species, the pathogenic species were closely related to non-pathogenic species, suggesting a rapid adaptation towards acquiring infective capabilities. Not only did these species became pathogenic but they were also able to shift ecological niche by invading new hosts, plants and animals, including humans. We believe we have identified a number of genes that may explain the acquired capacity for these fungal parasites to infect human cells. In the case of Microbotryum, the complex of species adapted to the plant host, we observe rapid evolution among closely related species which gave rise to host-specialization that eventually resulted in the emergence of new species (the process called speciation). Once the new, highly-specialized species emerged, a pattern of slow, conservative evolution ensued. Finally, what we observe in the ongoing project about Magnaporthe oryzae, is that the different strains share a very high proportion of genes coding for secreted-proteins, which play a key role in infection. This suggests that these genes are of capital importance for the strains in this species and that is why they are conserved relative to other gene families that are more variable. It remains to be determined, whether the differences in the pattern of gene expression are more important than the changes observed on the genes themselves.

We believe the FUNGI-PATHnCode project has been successful in tackling the objectives originally proposed. Only one aspect remains to be fully answered and it is the relative importance of the genetic versus the regulatory changes in the evolution of these groups of fungal pathogens. So far we have focused on the genetic changes but we are waiting for the data coming from our sequencing project which will hopefully help us to provide more answers soon. This work will continue beyond the fellowship framework. Also, additional to the main objectives of the FUNGI-PATHnCode project, we conducted a study on the variability of mitochondrial gene order among fungi. This work helped us to understand the important role played by repetitive elements, mostly in non-coding regions of the mitochondrial genome, in favoring recombination. These results could have implications in terms of fungal specialization to specific environments (respiratory adaptations) and in terms of driving mating sexual system evolution in fungi (as there is high selective pressure to avoid genomic conflict between the mitochondrial and nuclear genomes).

We believe the results of our project can make a difference in the way we understand the emergence of fungal pathogenicity and could potentially provide clues as to which gene functions are of relevance for infection, host-specialization, niche-shifts and possible targets for drug design.