Section: New Results
Characterization of STAND protein families
Participants : David James Sherman, Pascal Durrens, Witold Dyrka [correspondant] .
In collaboration with Sven Saupe and Mathieu Paoletti from IBGC Bordeaux (ANR Mykimun), we worked on characterization of the STAND protein family in the fungal phylum. We established an in silico screen based on state-of-the-art bioinformatic tools, which – starting from experimentally studied sequences from Podospora anserina – allowed us to determine the first systematic picture of fungal STAND protein repertoire (ms. in preparation). Most notably, we found evidence of extensive modularity of domain associations, and signs of concerted evolution within the recognition domain  . Both results support the hypothesis that fungal STAND proteins, originally described in the context of vegetative incompatibility, are involved in a general fungal immune system. In addition, we investigated improved protein domain representations and elaborated a grammatical modelling method  , which will be used to elucidate mechanisms of formation and operation of the STAND proteins.
NLR domains identified in this work have been incorporated into the upcoming release of Pfam (http://pfam.xfam.org ).
To further explor the underlying mechanisms of repeat formation we implemented a stochastic string rewriting system that models the generation process of highly internally conserved repeats. The system is grounded in the biology of the process as it models transformation of repeats through the events of unequal crossing-over and mutation, which are believed to be main mechanisms that produce diversity in repeats. We confirmed that highly variable sites identified on the basis of entropy, are subject to selective pressure towards composition typical for binding sites, which is consistent with the suggested role of recognition epitopes.