Characterization and DNA-Binding Specificities of Ralstonia TAL-Like Effectors

Li, Lixin; Atef, Ahmed; Piatek, Agnieszka Anna; Ali, Zahir; Piatek, Marek J.; Aouida, Mustapha; Sharakuu, Altanbadralt; Mahjoub, Ali Ridha; Wang, Guangchao; Khan, Mohammad Suhail; Fedoroff, Nina V.; Zhu, Jian‐Kang; Mahfouz, Magdy M.

doi:10.1093/mp/sst006

Cited by 56 publications

(51 citation statements)

References 40 publications

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“…The crystal structure of a natural TALE protein suggests that there is a cryptic repeat domain in the N-terminus of the protein that specifically recognizes thymine (51,52). Novel TALE architectures have been developed to overcome this requirement by engineering this region of the TALE N-terminus to recognize alternative bases at this position (56,57) or by utilizing TALE-like domains from related plant pathogens (77,78) that naturally recognize guanine at the N0 position. However, DNA-binding activity of these TALE architectures may be reduced, especially for targets with adenosine and cytosine bases at the N0 position.…”

Section: Development Of Talensmentioning

confidence: 99%

The Development of TALE Nucleases for Biotechnology

Ousterout

Gersbach

2016

Methods in Molecular Biology

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The development of a facile genome engineering technology based on transcription activator-like effector nucleases (TALENs) has led to significant advances in diverse areas of science and medicine. In this review, we provide a broad overview of the development of TALENs and the use of this technology in basic science, biotechnology, and biomedical applications. This includes the discovery of DNA recognition by TALEs, engineering new TALE proteins to diverse targets, general advances in nuclease-based editing strategies, and challenges that are specific to various applications of the TALEN technology. We review examples of applying TALENs for studying gene function and regulation, generating disease models, and developing gene therapies. The current status of genome editing and future directions for other uses of these technologies are also discussed.

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Section: Development Of Talensmentioning

confidence: 99%

The Development of TALE Nucleases for Biotechnology

Ousterout

Gersbach

2016

Methods in Molecular Biology

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“…These Ralstonia TAL like-effectors (RTLs) harbor repeats of 35 amino acids and contain RVDs rarely or not observed in Xanthomonas . The RTL repeats, artificially substituted into a Xanthomonas TAL effector, mediate specific DNA recognition, with target sites corresponding to their RVD sequence [ 32 ]. Recently, wildtype RTLs were shown to be active on artificial promoters [ 33 ].…”

Section: The Natural Role Of Tal Effectorsmentioning

confidence: 99%

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins

Doyle

Stoddard

Voytas

et al. 2013

Trends in Cell Biology

120

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Transcription activator-like (TAL) effectors are transcription factors injected into plant cells by pathogenic bacteria in the genus Xanthomonas. They function as virulence factors by activating host genes important for disease, or as avirulence factors by turning on genes that provide resistance. DNA binding specificity is encoded by polymorphic repeats in each protein that correspond one-to-one with different nucleotides. This code has facilitated target identification and opened new avenues for engineering disease resistance. It has also enabled TAL effector customization for targeted gene control, genome editing, and other applications. This article reviews the structural basis for TAL effector-DNA specificity, the impact of the TAL effector-DNA code on plant pathology and engineered resistance, and recent accomplishments and future challenges in TAL effector-based DNA targeting.

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“…Several cloning methods have been developed that enable individual researchers to rapidly assemble custom repeat arrays into various structural contexts, including the native TAL effector backbone and derivatives fused to other protein domains [9–13]. High-throughput, automatable methods based on solid-state assembly have also been developed [14–16].…”

Section: Introductionmentioning

confidence: 99%

Tools for TAL effector design and target prediction

Booher

Bogdanove

2014

Methods

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TAL effectors are transcription factors injected into plant cells by pathogenic bacteria during infection. They find their specific DNA targets via a string of contiguous, structural repeats that individually recognize single nucleotides (with some degeneracy) by virtue of polymorphisms at residue 13. The number of repeats and sequence of the amino acids at position 13 determine the nucleotide sequence of the DNA target. Due to this modularity, TAL effectors are readily engineered and have been used alone or as molecular fusions for targeted gene activation, gene repression, chromatin modification, chromatin tagging, and most broadly, for genome editing as TAL effector nucleases (TALENs). Several moderate and high-throughput cloning methods are in place for assembling TAL effector-based genetic constructs. Targeting is complicated to an extent by a general requirement for thymine to precede the DNA target, a requirement of TALENs to bind paired opposing sites separated by a defined range of distances, differential contributions of different repeat types to overall affinity, and a polarity to mismatch tolerance. Several computational tools are available online to aid in design and the identification of candidate off-target binding sites, as well as assembly and implementation. These tools vary in their approaches, capabilities, and relative utility for different types of TAL effector applications. Accuracy of off-target prediction is not well characterized yet for any of the tools and will require a better understanding of the qualitative and quantitative variation in the nucleotide preferences of individual repeats.

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Characterization and DNA-Binding Specificities of Ralstonia TAL-Like Effectors

Cited by 56 publications

References 40 publications

The Development of TALE Nucleases for Biotechnology

The Development of TALE Nucleases for Biotechnology

TAL effectors: highly adaptable phytobacterial virulence factors and readily engineered DNA-targeting proteins

Tools for TAL effector design and target prediction

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