TAL effectors: Function, structure, engineering and applications

Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N. A3-025, Seattle, WA 98109, United States.
Current Opinion in Structural Biology (Impact Factor: 7.2). 12/2012; 23(1). DOI: 10.1016/
Source: PubMed


TAL effectors are proteins secreted by bacterial pathogens into plant cells, where they enter the nucleus and activate expression of individual genes. TAL effectors display a modular architecture that includes a central DNA-binding region comprising a tandem array of nearly identical repeats that are almost all 34 residues long. Residue number 13 in each TAL repeat (one of two consecutive polymorphic amino acids that are termed 'repeat variable diresidues', or 'RVDs') specifies the identity of a single base; collectively the sequential repeats and their RVDs dictate the recognition of sequential bases along one of the two DNA strands. The modular architecture of TAL effectors has facilitated their extremely rapid development and application as artificial gene targeting reagents, particularly in the form of site-specific nucleases. Recent crystallographic and biochemical analyses of TAL effectors have established the structural basis of their DNA recognition properties and provide clear directions for future research.

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    • "Nucleotide specificity of each repeat is determined by the hypervariable positions 12 and 13, together known as the repeat variable diresidue (RVD) (Boch et al., 2009; Moscou and Bogdanove, 2009). Crystal structures showed that only the thirteenth residue interacts with the nucleotide, while the twelfth stabilizes the loop that projects the thirteenth residue into the major groove (Deng et al., 2012; Mak et al., 2012). And, while some amino acids at the twelfth position abolish or dramatically reduce binding affinity, RVDs that share the same thirteenth residue typically have similar binding specificities (Boch et al., 2009; Moscou and Bogdanove, 2009; Yang et al., 2014). "
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    ABSTRACT: Xanthomonas oryzae pv. oryzicola (Xoc) causes the increasingly important disease bacterial leaf streak of rice (BLS) in part by type III delivery of repeat-rich transcription activator-like (TAL) effectors to upregulate host susceptibility genes. By pathogen whole genome, single molecule, real-time sequencing and host RNA sequencing, we compared TAL effector content and rice transcriptional responses across 10 geographically diverse Xoc strains. TAL effector content is surprisingly conserved overall, yet distinguishes Asian from African isolates. Five TAL effectors are conserved across all strains. In a prior laboratory assay in rice cv. Nipponbare, only two contributed to virulence in strain BLS256 but the strict conservation indicates all five may be important, in different rice genotypes or in the field. Concatenated and aligned, TAL effector content across strains largely reflects relationships based on housekeeping genes, suggesting predominantly vertical transmission. Rice transcriptional responses did not reflect these relationships, and on average, only 28% of genes upregulated and 22% of genes downregulated by a strain are up- and down- regulated (respectively) by all strains. However, when only known TAL effector targets were considered, the relationships resembled those of the TAL effectors. Toward identifying new targets, we used the TAL effector-DNA recognition code to predict effector binding elements in promoters of genes upregulated by each strain, but found that for every strain, all upregulated genes had at least one. Filtering with a classifier we developed previously decreases the number of predicted binding elements across the genome, suggesting that it may reduce false positives among upregulated genes. Applying this filter and eliminating genes for which upregulation did not strictly correlate with presence of the corresponding TAL effector, we generated testable numbers of candidate targets for four of the five strictly conserved TAL effectors.
    Frontiers in Plant Science 08/2015; 6:536. DOI:10.3389/fpls.2015.00536 · 3.95 Impact Factor
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    • "mediate the binding of TAL effectors to the double - strand DNA in a sequence - specific manner with residue 12 stabilizing the overall interaction while residue 13 specifically contacts the DNA base ( reviewed in Mak et al . , 2013 ) . Functional differences between TAL effectors are therefore mainly due to the nature of the string of RVDs that determine the sequence of the so - called TAL effector binding element ( EBE ) in host promoters . TAL effectors can be found in most Xanthomonas species and related proteins are also present in Ralstonia solanacearum ( Rip"
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    ABSTRACT: Many plant-pathogenic xanthomonads rely on Transcription Activator-Like (TAL) effectors to colonize their host. This particular family of type III effectors functions as specific plant transcription factors via a programmable DNA-binding domain. Upon binding to the promoters of plant disease susceptibility genes in a sequence-specific manner, the expression of these host genes is induced. However, plants have evolved specific strategies to counter the action of TAL effectors and confer resistance. One mechanism is to avoid the binding of TAL effectors by mutations of their DNA binding sites, resulting in resistance by loss-of-susceptibility. This article reviews our current knowledge of the susceptibility hubs targeted by Xanthomonas TAL effectors, possible evolutionary scenarios for plants to combat the pathogen with loss-of-function alleles, and how this knowledge can be used overall to develop new pathogen-informed breeding strategies and improve crop resistance.
    Frontiers in Plant Science 07/2015; 6:535. DOI:10.3389/fpls.2015.00535 · 3.95 Impact Factor
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    • "TALEs (transcription activator-like effectors) are proteins secreted by plant bacterial pathogens in the genus Xanthomonas after host infection and contain a DNA-binding domain composed of a series of tandem repeats (Bogdanove et al., 2010; Mak et al., 2013). Each repeat contains a highly conserved 33–35 amino acid sequence with the exception of two residues at positions 12 and 13 which show hypervariability and are, thus, designated repeat variable diresidues or RVDs (Mak et al., 2013). In 2009, two independent groups showed that RVDs were responsible for the binding of specific nucleotides in the TALE target site following a simple code (Boch et al., 2009; Moscou and Bogdanove, 2009). "
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    ABSTRACT: CRISPR/Cas9 and TALEN are currently the two systems of choice for genome editing. We have studied the efficiency of the TALEN system in rice as well as the nature and inheritability of TALEN-induced mutations and found important features of this technology. The N287C230 TALEN backbone resulted in low mutation rates (0-6.6%), but truncations in its C-terminal domain dramatically increased efficiency to 25%. In most transgenic T0 plants, TALEN produced a single prevalent mutation accompanied by a variety of low-frequency mutations. For each independent T0 plant, the prevalent mutation was present in most tissues within a single tiller as well as in all tillers examined, suggesting that TALEN-induced mutations occurred very early in the development of the shoot apical meristem. Multigenerational analysis showed that TALEN-induced mutations were stably transmitted to the T1 and T2 populations in a normal Mendelian fashion. In our study, the vast majority of TALEN-induced mutations (~81%) affected multiple bases and ~70% of them were deletions. Our results contrast with published reports for the CRISPR/Cas9 system in rice, in which the predominant mutations affected single bases and deletions accounted for only 3.3% of the overall mutations. © 2015 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.
    Plant Biotechnology Journal 04/2015; DOI:10.1111/pbi.12372 · 5.75 Impact Factor
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