Perez-Quintero A. L., Rodriguez L. M., Dereeper Alexis, Lopez C., Koebnik Ralf, Szurek Boris, Cunnac Sébastien. (2013). An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains. Plos One, 8 (7), p. e68464. ISSN 1932-6203.
Titre du document
An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains
Perez-Quintero A. L., Rodriguez L. M., Dereeper Alexis, Lopez C., Koebnik Ralf, Szurek Boris, Cunnac Sébastien
Source
Plos One, 2013,
8 (7), p. e68464 ISSN 1932-6203
Transcription Activators-Like Effectors (TALEs) belong to a family of virulence proteins from the Xanthomonas genus of bacterial plant pathogens that are translocated into the plant cell. In the nucleus, TALEs act as transcription factors inducing the expression of susceptibility genes. A code for TALE-DNA binding specificity and high-resolution three-dimensional structures of TALE-DNA complexes were recently reported. Accurate prediction of TAL Effector Binding Elements (EBEs) is essential to elucidate the biological functions of the many sequenced TALEs as well as for robust design of artificial TALE DNA-binding domains in biotechnological applications. In this work a program with improved EBE prediction performances was developed using an updated specificity matrix and a position weight correction function to account for the matching pattern observed in a validation set of TALE-DNA interactions. To gain a systems perspective on the large TALE repertoires from X. oryzae strains, this program was used to predict rice gene targets for 99 sequenced family members. Integrating predictions and available expression data in a TALE-gene network revealed multiple candidate transcriptional targets for many TALEs as well as several possible instances of functional convergence among TALEs.
Plan de classement
Sciences fondamentales / Techniques d'analyse et de recherche [020]
;
Sciences du monde végétal [076]
;
Biotechnologies [084]
