Genomics of fungal DNA repair

All organisms operate many proteins that protect their chromosomes from the continuous damage they suffer every day. Most of what we know about DNA damage response in fungi comes from model organisms like Saccharomyces cerevisiae; it is unknown to what extent the data obtained in model organisms is relevant to the entire fungal kingdom. We compared 100 DNA damage response genes across the genomes of ascomycete fungi and found significant divergent from the current dogma. First, while the MRE11 gene is highly conserved its partner at the MRX complex RAD50 is far less conserved at least in the classes of Saccharomycotina, Sordariomycetes and Dothideomycetes. Second, the major recombinase of the eukaryotic world Rad51 is far less conserved than its paralog Rad55 in the orders of Sordariomycetes and Dothideomycetes, suggesting that Rad55 can act as a standalone recombinase. Third, on one hand Dothideomycetes lack the conserved holiday junction resolvase MUS81, on the other hand they show high degree of conservation of SRS2. This combination suggests that the balance between crossover and non-crossover is tilted towards the latter. We also examined the transcription response of Fusarium oxysporum to DNA damage. Surprisingly, the nucleotide excision repair machinery, UVDE or PHR1 are not stimulated by UV. Moderate degree of stimulation of other DNA repair genes by UV is observed in fungi exposed to 50J but not 200J. Interestingly UV repair genes are induced during the transition of conidia to germilings. In contrast to UV, there is a massive transcriptional response to MMS in Fusarium oxysporum. Most interesting is the over expression of nucleotide repair genes. In summary, our DNA damage response analysis is the most comprehensive one ever done in filamentous fungi. We show significant divergence of the response from the one described in model organisms such as Saccharomyces cerevisiae.