Predicting promoters targeted by TAL effectors in plant genomes: from dream to reality

Laurent D Noël, Nicolas Denancé, Boris Szurek

Résumé:

Transcription Activator-Like (TAL) effectors from the plant pathogenic bacteria of the genus Xanthomonas are molecular weapons injected into eukaryotic cells to modulate the host transcriptome. Upon delivery, TAL effectors localize into the host cell nucleus and bind to the promoter of plant susceptibility (S) genes to activate their expression and thereby facilitate bacterial multiplication (Boch and Bonas, 2010; Schornack et al., 2013). In resistant plants, a few TAL effectors have been shown to bind to promoters of executor resistance (R) genes, resulting in localized cell death and preventing pathogen spread (reviewed in Doyle et al., 2013). Remarkably, TAL effectors harbor a novel type of DNA-binding domain with a unique modular architecture composed of 1.5–33.5 almost identical tandem repeats of 33–35 amino acids. Each repeat type specifies one or more bases through direct interaction with the second amino acid in a centrally located “Repeat Variable Diresidue” (RVD). The number and sequence of the RVDs across the whole repeat region of the TAL protein defines the DNA target. The code of DNA-binding specificity of Xanthomonas TAL effectors was inferred from experimental, computational and later on structural approaches (Boch et al., 2009; Moscou and Bogdanove, 2009; Deng et al., 2012; Mak et al., 2012). This new paradigm for protein-DNA interaction is now revolutionizing our perspectives for the understanding of TAL effectors roles during plant disease and defense since the identification of their plant targets is largely facilitated. A few algorithms are now available to predict in silico candidate genes of a given TAL effector. This Opinion gives an overview of the current tools and strategies that may be applied for finding targets of TAL effectors. We also raise limitations and pitfalls and emphasize what may be improved to gain in prediction accuracy. Finally, we also highlight several perspectives offered by these new tools.

Revue:

Frontiers in Plant Science

Lien:

www.ncbi.nlm.nih.gov/pmc/articles/PMC3759964/