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      QueTAL: a suite of tools to classify and compare TAL effectors functionally and phylogenetically

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          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.

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          Most cited references 40

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          Identification of common molecular subsequences.

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            The Bioperl toolkit: Perl modules for the life sciences.

            The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
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              Xanthomonas AvrBs3 family-type III effectors: discovery and function.

               Jens Boch,  Ulla Bonas (2009)
              Xanthomonads are bacterial plant pathogens that cause diseases on many plant species, including important crops. Key to pathogenicity of most Xanthomonas pathovars is a Hrp-type III secretion (T3S) system that translocates effector proteins into plant cells. Within the eukaryotic cell, the effectors are thought to perform a variety of tasks to support bacterial virulence, proliferation, and dissemination. We are only beginning to understand the host targets of different effectors. The largest effector family found in Xanthomonas spp. is the AvrBs3/PthA or TAL (transcription activator-like) family. TAL effectors act as transcriptional activators in the plant cell nucleus. Specificity of TAL effectors is determined by a novel modular DNA-binding domain. Here, we describe the discovery of TAL effectors and their structure, activity, and host targets.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                03 August 2015
                2015
                : 6
                Affiliations
                1UMR IPME, IRD-CIRAD-Université Montpellier Montpellier, France
                2UMR PVBMT, CIRAD-Université de la Réunion Saint-Pierre, France
                Author notes

                Edited by: Thomas Lahaye, Ludwig-Maximilians-University Munich, Germany

                Reviewed by: David John Studholme, University of Exeter, UK; Tina Britta Jordan, Eberhard Karls University Tübingen, Germany

                *Correspondence: Boris Szurek and Lionel Gagnevin, UMR IPME, IRD-CIRAD-UM, 911, Av. Agropolis BP 64501, 34394 Montpellier, France boris.szurek@ 123456ird.fr ; lionel.gagnevin@ 123456cirad.fr

                This article was submitted to Plant Biotic Interactions, a section of the journal Frontiers in Plant Science

                †These authors have contributed equally to this work.

                Article
                10.3389/fpls.2015.00545
                4522561
                Copyright © 2015 Pérez-Quintero, Lamy, Gordon, Escalon, Cunnac, Szurek and Gagnevin.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                Page count
                Figures: 8, Tables: 0, Equations: 0, References: 53, Pages: 16, Words: 11226
                Funding
                Funded by: Erasmus Mundus Action 2 PRECIOSA program of the European Community
                Funded by: Agence Nationale de la Recherche
                Award ID: ANR-14-CE19-0002
                Funded by: Fondation Agropolis
                Award ID: 1403-073
                Funded by: European Union's Seventh Framework Programme
                Award ID: 263958
                Categories
                Plant Science
                Methods

                Plant science & Botany

                ebe, tal effectors, functional convergence, xanthomonas, ralstonia, phylogeny

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