Deciphering the language of fungal pathogen recognition receptors
| hal.structure.identifier | Models and Algorithms for the Genome [ MAGNOME] | |
| dc.contributor.author | DYRKA, Witold | |
| hal.structure.identifier | Laboratoire Bordelais de Recherche en Informatique [LaBRI] | |
| hal.structure.identifier | Models and Algorithms for the Genome [ MAGNOME] | |
| dc.contributor.author | DURRENS, Pascal | |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | PAOLETTI, Mathieu | |
| hal.structure.identifier | Institut de biochimie et génétique cellulaires [IBGC] | |
| dc.contributor.author | SAUPE, Sven J | |
| hal.structure.identifier | Laboratoire Bordelais de Recherche en Informatique [LaBRI] | |
| hal.structure.identifier | Models and Algorithms for the Genome [ MAGNOME] | |
| dc.contributor.author | SHERMAN, David J | |
| dc.date.accessioned | 2024-04-15T09:57:52Z | |
| dc.date.available | 2024-04-15T09:57:52Z | |
| dc.date.created | 2014-10-19 | |
| dc.identifier.uri | https://oskar-bordeaux.fr/handle/20.500.12278/198953 | |
| dc.description.abstractEn | 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. | |
| dc.description.sponsorship | Reconnaissance hétérospécifique chez les champignons filamenteux : Des récepteurs à la réponse cellulaire - ANR-11-BSV3-0019 | |
| dc.language.iso | en | |
| dc.subject.en | innate immune system | |
| dc.subject.en | amino acid repeats | |
| dc.subject.en | unequal crossing-over | |
| dc.subject.en | string rewrit-ing system | |
| dc.subject.en | formal languages | |
| dc.title.en | Deciphering the language of fungal pathogen recognition receptors | |
| dc.type | Document de travail - Pré-publication | |
| dc.subject.hal | Informatique [cs]/Bio-informatique [q-bio.QM] | |
| bordeaux.hal.laboratories | Laboratoire Bordelais de Recherche en Informatique (LaBRI) - UMR 5800 | * |
| bordeaux.institution | Université de Bordeaux | |
| bordeaux.institution | Bordeaux INP | |
| bordeaux.institution | CNRS | |
| hal.identifier | hal-01083421 | |
| hal.version | 1 | |
| hal.origin.link | https://hal.archives-ouvertes.fr//hal-01083421v1 | |
| bordeaux.COinS | ctx_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.au=DYRKA,%20Witold&DURRENS,%20Pascal&PAOLETTI,%20Mathieu&SAUPE,%20Sven%20J&SHERMAN,%20David%20J&rft.genre=preprint |
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