A simple cipher governs DNA recognition by TAL effectors

Department of Plant Pathology and Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA.
Science (Impact Factor: 33.61). 10/2009; 326(5959):1501. DOI: 10.1126/science.1178817
Source: PubMed


TAL effectors of plant pathogenic bacteria in the genus Xanthomonas bind host DNA and activate genes that contribute to disease or turn on defense. Target specificity depends on an effector-variable number of typically 34 amino acid repeats, but the mechanism of recognition is not understood. We show that a repeat-variable pair of residues specifies the nucleotides in the target site, one pair to one nucleotide, with no apparent context dependence. Our finding represents a previously unknown mechanism for protein-DNA recognition that explains TAL effector specificity, enables target site prediction, and opens prospects for use of TAL effectors in research and biotechnology.

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Available from: Matthew J Moscou, Mar 11, 2015
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    • "Proximal to the N - terminal portion of the repetitive domain are non - canonical repeats that mediate pairing with an initial 5 ′ thymine ( Boch et al . , 2009 ; Moscou and Bogdanove , 2009 ) . E gene expression occurs upon cognate effector binding to a compatible effector binding element in the respective promoter ( Figure 1A ) . "
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    ABSTRACT: Transcription activator-like (TAL) effectors are bacterial type III secretion proteins that function as transcription factors in plants during Xanthomonas/plant interactions, conditioning either host susceptibility and/or host resistance. Three types of TAL effector associated resistance (R) genes have been characterized-recessive, dominant non-transcriptional, and dominant TAL effector-dependent transcriptional based resistance. Here, we discuss the last type of R genes, whose functions are dependent on direct TAL effector binding to discrete effector binding elements in the promoters. Only five of the so-called executor R genes have been cloned, and commonalities are not clear. We have placed the protein products in two groups for conceptual purposes. Group 1 consists solely of the protein from pepper, BS3, which is predicted to have catalytic function on the basis of homology to a large conserved protein family. Group 2 consists of BS4C-R, XA27, XA10, and XA23, all of which are relatively short proteins from pepper or rice with multiple potential transmembrane domains. Group 2 members have low sequence similarity to proteins of unknown function in closely related species. Firm predictions await further experimentation on these interesting new members to the R gene repertoire, which have potential broad application in new strategies for disease resistance.
    Frontiers in Plant Science 09/2015; 6:641. DOI:10.3389/fpls.2015.00641 · 3.95 Impact Factor
    • "In contrast, no chromocenter was evident in Stella-null embryos (Fig. 1A). We then investigated the localization of major satellite repeats, which were important for CF, in more detail using TALE technology [21] [22]. Visualization of major satellite dynamics by TALEmClover_MajSat was reported in ES cells and confirmed in Stelladeficient ES cells [18] (Supplemental Fig. S2). "
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    ABSTRACT: In mammals, the structure of the pericentromeric region alters from a ring structure to a dot-like structure during the 2-cell stage. This structural alteration is termed chromocenter formation (CF) and is required for preimplantation development. Although reverse transcripts of major satellite repeats at pericentromeric regions are known to play roles in CF, its underlying mechanism is not fully understood. We previously reported that Stella (also known as PGC7 and Dppa3) deficiency led to developmental arrest at the preimplantation stage, accompanied by frequent chromosome segregation. In this study, we further investigated the effect of Stella deficiency on chromatin reorganization. The Stella-null embryos exhibited impaired CF and reduced expression of the reverse strand of major satellite repeats. In addition, the accumulation of H3.3, a histone H3 variant associated with transcriptional activation, at the pericentromeric regions and expression of the H3.3-specific chaperone Daxx were reduced in Stella-null embryos. These abnormalities were restored by the enforced expression of Daxx in Stella-null embryos. Thus, Stella controls the expression of Daxx and ensures chromatin reorganization in early embryos. Copyright © 2015 Elsevier Inc. All rights reserved.
    Biochemical and Biophysical Research Communications 08/2015; DOI:10.1016/j.bbrc.2015.08.106 · 2.30 Impact Factor
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    • "Theprogramincludespre-processingofanyTALsequence,and alignmentofrepeatsequencesbasedontheARLEMprogram (Abouelhodaetal.,2010).Webelievethistoolnotonlyismore reliableatcomparingandclassifyingTALeffectorsaccording totheirphylogenybutwillalsoofferprecioushelpforfuture experimentalandmodelingworksonTALeffectorevolution. AnimportantfeatureofTALeffectorsisthattheirfunction can,tosomeextent,bepredictedfromtheirRVDssequence thankstotheirmodularandspecificinteractionwithDNA (Bochetal.,2009;MoscouandBogdanove,2009).Indeed toolsalreadyexisttopredictcandidateEBEsinplantgenomes (Doyleetal.,2012;Grauetal.,2013;Perez-Quinteroetal., 2013).AsmoreTALeffectorsarediscovered,notablythrough sequencingofentireTALomes(e.g.,Wilkinsetal.,2015),itis essentialtoclassifythemaccordingtowhatcanbehypothesized abouttheirfunction.Thesecondmainoutputofthisstudy isthedesignofatoolforcomparingTALeffectorsthrough theirEBEs,whichwillfacilitatetheidentificationofcasesof functionalconvergencesandthereforecandidatesusceptibility hubs.FuncTALcalculatescorrelationsbetweenpotentialTAL effectorbindingsitesbytranslatingRVDsequencesintoPWMs accordingtotheRVD-DNAcode.Theprogramsuccessfully "
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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
    Frontiers in Plant Science 08/2015; 6:545. DOI:10.3389/fpls.2015.00545 · 3.95 Impact Factor
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