An improved method for TAL effectors DNA-binding sites prediction reveals functional convergence in TAL repertoires of Xanthomonas oryzae strains

PLoS One. 2013 Jul 15;8(7):e68464. doi: 10.1371/journal.pone.0068464. Print 2013.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Arabidopsis / genetics
  • Bacterial Proteins / chemistry*
  • Bacterial Proteins / genetics
  • Bacterial Proteins / physiology
  • Binding Sites
  • Gene Regulatory Networks
  • Oryza / genetics
  • Software*
  • Transcription Factors / chemistry*
  • Transcription Factors / genetics
  • Transcription Factors / physiology
  • Xanthomonas / genetics*

Substances

  • Bacterial Proteins
  • Transcription Factors

Grant support

This work was supported by the French Agence Nationale de la Recherche [ANR-2010-GENM-013] and Programme ECOS Nord. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.