DYRKA, Witold; DURRENS, Pascal; PAOLETTI, Mathieu; SAUPE, Sven J; SHERMAN, David J

Métadonnées

Licence d’utilisation du document

DYRKA, Witold
Models and Algorithms for the Genome [ MAGNOME]

DURRENS, Pascal
Laboratoire Bordelais de Recherche en Informatique [LaBRI]
Models and Algorithms for the Genome [ MAGNOME]

PAOLETTI, Mathieu
Institut de biochimie et génétique cellulaires [IBGC]

Langue

Document de travail - Pré-publication

Résumé en anglais

The NLR family of receptors plays a key role in the innate immune system of animals, plants and fungi. In the latter two phyla NLRs adapt quickly to ever-changing pathogen-specific invasion markers thanks to their repeat-based architecture, which can pro-duce diversity of recognition epitopes through unequal crossing-over and mutation. Charac-terizing computationally the language of these pathogen recognition receptors can provide insight into the molecular mechanisms of immune response and describe the limits of the pathogen targets that can be recognized. In this work, we model generation and selection of the recognition epitopes as a stochastic string rewriting system with constraints, tuned by analysis of observed evolutionary processes and validated with regard to a large dataset of fungal NLRs. Among others, analyzing the feasible set of solutions revealed that the model explained the i/i + 2 periodicity observed in the repeat number distribution of a family of receptors. In addition, in exploring discrepancies between real and simulated data we discovered an overrepresented pattern which potentially has functional importance. The methodology developed in this work is general and therefore can be applied to any class of amino acid repeats generated by unequal crossing-over for which an equivalent high quality dataset is available.< Réduire

Mots clés en anglais

innate immune system

amino acid repeats

unequal crossing-over

string rewrit-ing system

formal languages

URI

https://oskar-bordeaux.fr/handle/20.500.12278/198953

Project ANR

Reconnaissance hétérospécifique chez les champignons filamenteux : Des récepteurs à la réponse cellulaire - ANR-11-BSV3-0019

Origine

Importé de hal

Unités de recherche

Laboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800