Protein – DNA contacts in the structure of a homeodomain – DNA complex determined by nuclear magnetic resonance spectroscopy in solution

Otting, Gottfried; Yan, Qiu Qian; Billeter, Martin; Müller, Martin; Affolter, Markus; Gehring, Walter J.; Wüthrich, Kurt

doi:10.1142/9789812795830_0041

Cited by 46 publications

(69 citation statements)

References 20 publications

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“…In addition to the mutations affecting the third ␣-helix of the HD (residues A50, A51, K50, and H53), we introduced two mutations in the N terminus changing R5 into H5 or A5. R5, which is highly conserved in evolution, was shown to be critical in stabilizing the HD on DNA by binding to the minor groove (18). Thus, mutating this amino acid should result in a protein with reduced DNA-binding activity.…”

Section: Truncated Ey Proteins Are Able To Antagonize Antp-induced Eymentioning

confidence: 99%

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

Plaza

Prince

Adachi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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Homeotic Hox selector genes encode highly conserved transcriptional regulators involved in the differentiation of multicellular organisms. Ectopic expression of the Antennapedia (ANTP) homeodomain protein in Drosophila imaginal discs induces distinct phenotypes, including an antenna-to-leg transformation and eye reduction. We have proposed that the eye loss phenotype is a consequence of a negative posttranslational control mechanism because of direct protein-protein interactions between ANTP and Eyeless (EY). In the present work, we analyzed the effect of various ANTP homeodomain mutations for their interaction with EY and for head development. Contrasting with the eye loss phenotype, we provide evidence that the antenna-to-leg transformation involves ANTP DNA-binding activity. In a complementary genetic screen performed in yeast, we isolated mutations located in the N terminus of the ANTP homeodomain that inhibit direct interactions with EY without abolishing DNA binding in vitro and in vivo. In a bimolecular fluorescence complementation assay, we detected the ANTP-EY interaction in vivo, these interactions occurring through the paired domain and/or the homeodomain of EY. These results demonstrate that the homeodomain supports multiple molecular regulatory functions in addition to protein-DNA and protein-RNA interactions; it is also involved in protein-protein interactions. Drosophila ͉ antagonism ͉ regulation H omeotic Hox genes are selector genes that generate morphological diversity along the antero-posterior body axis during animal development (1). They encode highly conserved transcription factors defining various cellular identities in the body segments along the antero-posterior axis of the embryo (2, 3). Hox genes share a common sequence element of 180 bp, the homeobox, first isolated in Drosophila (4, 5), encoding a 60-aa homeodomain (HD) DNA-binding domain. The HD presents a stereotypical three ␣-helical structure, and its mode of interaction with DNA is largely invariant. The amino acid 50, a glutamine signature for the Hox proteins, plays a fundamental role in DNA-binding specificity (6). Hox factors have very similar DNA-binding properties (7). Therefore, the limited sequence selectivity of the HD is not sufficient to explain the diversity of cell types and the batteries of downstream genes under the control of Hox proteins. Consequently, elucidating the mechanisms of Hox protein function is critical for understanding development and the diversification of serially homologous structures. Several studies have indicated that Hox factors cooperate with signaling pathways and act with cofactors that modify DNA binding and activation/repression properties (8-10). To date, the best-known Hox cofactors are the Drosophila extradenticle (EXD/PBX) and homothorax (HTH/Meis) proteins. EXD was shown to modulate the DNA-binding specificity and the activity of Hox proteins (11-13), whereas HTH promotes EXD translocation into the nucleus where they participate in a DNA-bound HOX/EXD/HTH ternary complex (14). Altho...

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Section: Truncated Ey Proteins Are Able To Antagonize Antp-induced Eymentioning

confidence: 99%

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

Plaza

Prince

Adachi

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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“…Although the primary amino acid sequences show relatively low identity, 27%, highresolution structural studies of the homeodomains of Engrailed (En) and Antennapedia (Antp) and of u2 complexed with DNA have revealed nearly identical structures (Kissinger et al, 1990;Otting et al, 1990;Wolberger et al, 1991). The homeodomain of each protein contains three a-helices, although the third a-helix of ANTP is kinked and is therefore referred to as helices 3 and 4 (Qian et al, 1989).…”

Section: Introductionmentioning

confidence: 99%

Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes.

et al. 1994

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The homeobox of the knottedl (knl) gene was used to isolate 12 related sequences in maize. The homeodomains encoded by the knl-like genes are very similar, ranging from 55 to 89% amino acid identity. Differences outside the precisely conserved third helix allowed us to group the genes into two classes. The homeodomains of the seven class 1 genes share 73 to 89% identical residues with knl. The four class 2 genes share 55 to 58% identical residues with knl, although the conservation within the class is greater than 87%. Expression patterns were analyzed by RNA gel blot analysis. Class 1 genes were highly expressed in meristem-enriched tissues, such as the vegetative meristem and ear primordia. Expression was not detectable in leaves. The class 2 genes were expressed in all tissues, although one was abundantly expressed in roots. The genes were mapped using recombinant inbred populations. We determined that clusters of two to three linked genes are present on chromosomes 1 and 8; otherwise, the genes are distributed throughout the genome. Four pairs of genes, similar in both sequence and expression patterns, mapped within duplicated regions of the genome.

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“…Based on these expression patterns, KNOX genes are thought to be involved in the process of making lateral organs or the maintenance of stem cells in SAM (Smith et al, 1992). Typical HDs consist of a conserved 60 amino acid domain containing three α-helices that form a helix-turn-helix type DNA-binding motif (Desplan et al, 1988;Otting et al, 1990). On the other hand, there is a family of atypical HDs proteins containing three extra amino acid stretches between the first and second helices in their HD (Bürglin, 1997).…”

Section: Introductionmentioning

confidence: 99%

Mutations that cause amino acid substitutions at the invariant positions in homeodomain of OSH3 KNOX protein suggest artificial selection during rice domestication.

2001

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KNOX homeodomain (HD) proteins encoded by KNOTTED1-like homeobox genes (KNOX genes) are considered to work as important regulators for plant developmental and morphogenetic events. We found that OSH3, one of the KNOX genes isolated from a cultivar of Oryza sativa (Nipponbare), encodes a novel HD, which has two amino acid substitutions at invariant positions. Sequence analysis of OSH3 from various domesticated and wild species of rice has revealed that these substitutions are distributed only in Japonica and Javanica type of O. sativa, two groups of domesticated rice in Asia. Surprisingly, nucleotide sequences in the first intron are almost conserved in the rice strains that have the substitutions at the invariant amino acids. Overexpression studies revealed that these invariant amino acids are critical for the function of OSH3 in vivo. The facts that these substitutions occurred specifically at the functionally important amino acids and the sequences are conserved in intron where neutral mutations accumulate suggest the substitutions at the invariant positions of OSH3 have been fixed by artificial selections during domestication. Based on these observations, we hypothesize that OSH3 is responsible for one of the traits that are selectively introduced during the domestication of most of Japonica and a part of Javanica type of rice.

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Protein – DNA contacts in the structure of a homeodomain – DNA complex determined by nuclear magnetic resonance spectroscopy in solution

Cited by 46 publications

References 20 publications

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

Cross-regulatory protein–protein interactions between Hox and Pax transcription factors

Sequence analysis and expression patterns divide the maize knotted1-like homeobox genes into two classes.

Mutations that cause amino acid substitutions at the invariant positions in homeodomain of OSH3 KNOX protein suggest artificial selection during rice domestication.

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