Abstract
Transcription Activator-Like (TAL) effectors from Xanthomonas plant pathogenic bacteria can bind to the promoter region of plant genes and induce their expression. DNA-binding specificity is governed by a central domain made of nearly identical repeats, each determining the recognition of one base pair via two amino acid residues (a.k.a. Repeat Variable Di-residue, or RVD). Knowing how TAL effectors differ from each other within and between strains would be useful to infer functional and evolutionary relationships, but their repetitive nature precludes reliable use of traditional alignment methods. The suite QueTAL was therefore developed to offer tailored tools for comparison of TAL effector genes. The program DisTAL considers each repeat as a unit, transforms a TAL effector sequence into a sequence of coded repeats and makes pair-wise alignments between these coded sequences to construct trees. The program FuncTAL is aimed at finding TAL effectors with similar DNA-binding capabilities. It calculates correlations between position weight matrices of potential target DNA sequence predicted from the RVD sequence, and builds trees based on these correlations. The programs accurately represented phylogenetic and functional relationships between TAL effectors using either simulated or literature-curated data. When using the programs on a large set of TAL effector sequences, the DisTAL tree largely reflected the expected species phylogeny. In contrast, FuncTAL showed that TAL effectors with similar binding capabilities can be found between phylogenetically distant taxa. This suite will help users to rapidly analyse any TAL effector genes of interest and compare them to other available TAL genes and should improve our understanding of TAL effectors evolution. It is available at http://bioinfo-web.mpl.ird.fr/cgi-bin2/quetal/quetal.cgi.
Highlights
Transcription activator-like (TAL) effectors are Xanthomonas proteins that are translocated into the plant cell through the type III secretion system and directed to the nucleus where they commandeer the cell metabolism by activating plant genes (Bogdanove et al, 2010)
QueTAL: DisTAL, A Program for the Phylogenetic Classification of TAL Effector Repeat Regions The overall strategy to compare TAL effectors based on the sequence of their central repeat region consists in considering each repeat as a separate unit, and comparing the TAL effectors according to the nature and order of these units
In order to understand how TAL effectors or other related proteins differ from each other within and between strains of one or several pathovars, current approaches mainly rely on the evaluation of genetic distances through the alignment of the Nterminal and/or C-terminal regions, excluding the central region due its repetitive nature
Summary
Transcription activator-like (TAL) effectors are Xanthomonas proteins that are translocated into the plant cell through the type III secretion system and directed to the nucleus where they commandeer the cell metabolism by activating plant genes (Bogdanove et al, 2010) In several pathovars they were demonstrated to be major aggressiveness determinants responsible for symptoms. Comparing and classifying TAL effectors of action has been detailed and their most outstanding feature is their central repeat domain, which is responsible for their highly specific attachment to DNA in regions known as EBE (effector binding elements). This domain contains 1.5–33.5 repeats of 33– 35 amino acids. This may help to develop new tools to breed resistant plants, either by escaping susceptibility or by introgressing executor resistance genes (Bogdanove et al, 2010; Boch et al, 2014)
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