TAL effector: Difference between revisions

<!--[[Image:Positions_of_the_mutations_in_PR_variants_used_for_structural_studies.jpg|left|320px|thumb| Fig.2 Positions of the mutations in PR variants used for structural studies. -->

<br>[[Image:sanjana.png|left|400px|thumb|Fig.1]]<br>

'''Figure 1''': Natural structure of TALEs derived from Xanthomonas sp. Each DNA-binding module consists of 34 amino acids, where the RVDs in the 12th and 13th amino acid positions of each repeat specify the DNA base being targeted according to the cipher NG = T, HD = C, NI = A, and NN = G or A. The DNA-binding modules are flanked by nonrepetitive N and C termini, which carry the translocation, nuclear localization (NLS) and transcription activation (AD) domains. A cryptic signal within the N terminus specifies a thymine as the first base of the target site.<ref> PMID:022223736 </ref>

<br>[[Image:Mak_An.png|right|400px|thumb|Fig.2]]<br>

'''Figure 2''': Domain organization of PthXo1 and structure of a single TAL effector repeat

TAL effectors contain N-terminal signals for bacterial type III secretion, tandem repeats that specify the target nucleotide sequence, nuclear localization signals, and a C-terminal region that is required for transcriptional activation. PthXo1 contains 23.5 canonical repeats (color coded to match Figure 2) that contact the DNA target found in the promoter of the rice Os8N3 gene (17). Blue bases correspond to positions in the target where the match between protein and DNA differs from the optimal match specified by the recognition code (3,4). Arrows indicate the start and end of the crystallized protein construct. In the structure, repeats 22 to 23.5 are poorly ordered, as are the C-termini of the two N-terminal cryptic repeats. The sequence and structure of a representative repeat (#14) is shown; RVD residues (HD) that recognize cytosine are red.<ref> PMID:22222791 </ref>

<br>[[Image:nihms396484f3.jpg|left|400px|thumb|Fig.3]]<br>

'''Figure 3''': All of the repeats in the DNA-bound PthXo1 structure form highly similar two-helix bundles (Figure 1c). The helices span positions 3 to 11 and 14 to 33, locating the RVD in a loop between them. A proline located at position 27, creates a kink in the second helix that appears to be critical for the sequential packing and association of tandem repeats with the DNA double helix. The packing of consecutive helices within and between individual repeats is left-handed, in contrast to the right-handed packing of helices found in TPR proteins (10). The modular architecture of the TAL effector repeats is reminiscent of the mitochondrial transcription terminator [http://www.proteopedia.org/wiki/index.php/3n6s mTERF] (11) and the [http://www.proteopedia.org/wiki/index.php/TRAP RNA-binding attenuation protein TRAP] (12).

<br>[[Image:crypticrepeats.jpg|right|500px|thumb|Fig.4]]<br>

N-terminal to the canonical repeats, the PthXo1 structure reveals two degenerate repeat folds that appear to cooperate to specify the conserved thymine that precedes the RVD-specified sequence (Figure 4). We have designated these as the 0th and -1st repeats. Residues 221 to 239 and residues 256 to 273 each form a helix and an adjoining loop that resembles helix 1 and the RVD loop in the canonical repeats; the remaining residues in each region are poorly ordered. Those two N-terminal regions converge near the 5′ thymine base, with the indole ring of tryptophan 232 (in the -1st repeat) making a van der Waals contact with the methyl group of that base. Mutation of the thymine reduces TAL effector activity at the target (3, 15). Tryptophan 232, as well as the surrounding residues, is highly conserved across available, intact TAL effector sequences.