A homology domain shared between Drosophila optomotor-blind and mouse Brachyury is involved in DNA binding (original) (raw)
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Nucleic Acids Research, 2003
The bric a Á brac (bab) locus is composed of two paralogous genes, bab1 and bab2, in Drosophila melanogaster. Bab1 and Bab2 are nuclear proteins that contain a broad complex, tramtrack, bric a Á brac/ poxviruses and zinc-®nger (BTB/POZ) domain. Many BTB/POZ proteins are transcriptional regulators of which the majority contain C 2 H 2 zinc-®nger motifs. There is no detectable zinc-®nger motif in either Bab protein. However, they share the Bab conserved domain (BabCD) that is highly conserved between Bab1 and Bab2, and the Bab proteins of several other species, e.g. Anopheles gambiae, Apis mellifera and Drosophila virilis. Here we show that Bab2 binds to several discrete sites on polytene chromosomes including the bab locus, and that the BabCD of both Bab1 and Bab2 binds in vitro to the cis-regulatory regions of bab1 and bab2. Our results indicate that the BabCD binds to A/T-rich regions and that its optimum binding sites contain TA or TAA repeats. The BabCD is a composite DNA binding domain with a psq motif and an AT-Hook motif; both motifs are required for DNA binding activity. Structural similarities suggest that the BabCD may bind to DNA in a similar manner as some prokaryotic recombinases.
Genetic and molecular characterization of the optomotor-blind locus in Drosophila melanogaster
Genetics
The Drosophila gene optomotor-blind (omb) is involved in the development of a set of giant neurons in the optic lobes and possibly other structures in the imaginal brain. Adult flies have discrete defects in optomotor behavior. The gene has previously been mapped in chromomeres 4C5-6, together with three other genes, bijid, Quadroon and lacqueredg'". We have localized the gene in a genomic walk of 340 kb of DNA. By mapping seven chromosome breakpoints with om6 phenotype we determined its minimum size to about 80 kb. From this region more than 20 RNAs of different size and temporal expression pattern are transcribed. Three of them (T3, T7 and T7') stem from primary transcripts of 40-80 kb in length. In its distal part the om6 gene overlaps in at least 19 kb with four other complementation units, bijid, l(I)bijid, Quadroon and lacqueredg". The three nonlethals affect the external appearance of the fly and seem to be unrelated to brain development.
THE PLANT CELL ONLINE, 1992
The sequence element of box II (GTGTGGTTAATATG) is a regulatory component of a light-responsive element present within the upstream region of pea rbcS-3A. The nuclear protein GT-1 was defined previously as a DNA binding activity that interacts with box II. Here, we describe the isolation and characterization of cDNA sequences that encode a DNA binding protein with specificity for this element. The recombinant protein, tobacco GT-la, shows similar sequence requirements for DNA binding to nuclear GT-1, as assayed by its ability to interact with previously defined 2-bp scanning mutations of box II, and is shown to be immunologically related to nuclear GT-1. The predicted structure of the 43-kD protein derived from the cDNA sequence suggests the presence of a nove1 helix-helix-turn-helix (HHTH) motif. Comparison between the predicted protein sequence encoded by the tobacco GT-la cDNA and that of another GT binding protein, rice GT-2, reveals strong amino acid conservation over the HHTH region; this motif appears to be involved in the interaction between the recombinant protein and box II. Genomic DNA gel blot analysis indicated the presence of a small gene family of related sequences within the tobacco nuclear genome. RNA gel blot analysis of tobacco mRNA using the isolated cDNA as a probe showed that transcripts are present in several tissues, including both light-grown and dark-adapted leaves.
Genetic and molecular characterization of the optomotor-blind gene locus in Drosophila melanogaster
Genetics, 1990
The Drosophila gene optomotor-blind (omb) is involved in the development of a set of giant neurons in the optic lobes and possibly other structures in the imaginal brain. Adult flies have discrete defects in optomotor behavior. The gene has previously been mapped in chromomeres 4C5-6, together with three other genes, bifid, Quadroon and lacqueredgls. We have localized the gene in a genomic walk of 340 kb of DNA. By mapping seven chromosome breakpoints with omb phenotype we determined its minimum size to about 80 kb. From this region more than 20 RNAs of different size and temporal expression pattern are transcribed. Three of them (T3, T7 and T7') stem from primary transcripts of 40-80 kb in length. In its distal part the omb gene overlaps in at least 19 kb with four other complementation units, bifid, l(1)bifid, Quadroon and lacqueredgls. The three nonlethals affect the external appearance of the fly and seem to be unrelated to brain development.
Proceedings of the National Academy of Sciences, 1997
We report here a method for the in vivo dissection of the regulatory region of a gene in the Drosophila genome. Our system includes (i) the reporter genes lacZ and white to detect transcriptional enhancer and silencer activities in a target gene, (ii) an efficient way to induce integration of gypsy elements in the genome, and (iii) unidirectional blocking of regulatory activities by the gypsy element, which is dependent on the su(Hw) protein. The optomotor-blind (omb) gene was analyzed. In the omb P1 line, a P[lacW] construct is inserted about 1.4 kb upstream of the omb transcription start site. The lacZ reporter gene within P[lacW] exhibits the same expression pattern as omb. The white reporter gene is expressed in a ''bipolar'' pattern. We induced high frequency gypsy mobilization in omb P1 and identified two lines (D11 and D13-1) with altered eye pigmentation pattern, which is dependent on su(Hw) activity. A gypsy element was found inserted in the first intron of omb in D13-1 and in P[lacW] in D11. These results indicate that it is the blocking of regulatory activities by gypsy that caused the changes in the white reporter gene expression. The effect of these gypsy insertions on the expression patterns allowed us to predict several aspects of the organization of the regulatory elements in the omb locus. MATERIALS AND METHODS Drosophila Stocks. w omb P1 was previously described (21). cm ct 6 sn 4 ; su(Hw) f TM6͞su(Hw) 2 sbd, FM3͞y v f mal flam 1 , and C(1)Dx, y f͞y w v f mal flam 1 were kindly provided by Alain Bucheton (Centre de Genetique Moleculaire, Centre National The publication costs of this article were defrayed in part by page charge payment. This article must therefore be hereby marked ''advertisement'' in accordance with 18 U.S.C. §1734 solely to indicate this fact.
Journal of Biochemistry, 2003
The protein DSP1 belongs to the group of HMG-box proteins, which share the common structural feature of the HMG-box. This approximately 80 amino acid long motif binds DNA via the minor groove. DSP1 was discovered as a transcriptional co-repressor of Dorsal in Drosophila melanogaster and then was shown to participate to the remodeling of chromatin. By means of sequence alignment and gene organization, DSP1 was classified as the fly homologue of the vertebrate proteins HMGB1/2. DSP1 contains two HMG boxes flanked by two glutamine-rich domains at the N-terminus. In addition, the HMG domain of DSP1 displays two differences in its primary sequence as compared to the vertebrate HMGB1: a shorter acidic tail and a linker between the two boxes longer by 6 amino acids. By comparing several functional parameters of DSP1 with those of HMGB1, the present study establishes the functional equivalence of both proteins in terms of DNA recognition. The major structural difference between the two proteins, the glutamine-rich N-terminal tail of DSP1, which does not exist in HMGB1, did not interfere with any of the studied DNA-binding properties of the proteins.
Structure of the Retinal Determination Protein Dachshund Reveals a DNA Binding Motif
Structure, 2002
There are multiple vertebrate homologs for each of the fly retinal determination genes; these are the Pax Division of Developmental Biology 3333 Burnet Avenue genes (ey homologs), the Eya genes (eya homologs), the Six genes (so homologs) and the Dach genes (dac Cincinnati, Ohio 45229 2 Structural Biology Program homologs). Drosophila toy, which is thought to have arisen by duplication of an early Pax6 gene, is unique to Skirball Institute New York University Medical Center the holometabolous insects. A crossregulatory system analogous to the one in flies is believed to exist in mam-New York, New York 10016 3 Departments of Ophthalmology, Visual Sciences, malian eye development (schematized in Figure 1A) [13, 14]. Furthermore, there is accumulating evidence that and Molecular Genetics Albert Einstein College of Medicine different combinations of these genes may function in other contexts, including vertebrate muscle [15], ear, Bronx, New York 10461 4 Structure Biology Center and kidney [16] development. The protein products of the retinal determination Argonne National Laboratories 9700 South Cass Avenue genes participate in physical interactions mediated by conserved domains. eya interacts with either dac or so, Argonne, Illinois 60439 and these complexes crossregulate, as well as regulate other downstream targets [7, 10, 15]. Models proposed for the molecular interactions among these proteins are Summary
Nucleic Acids Research, 1989
We have cloned, following an immunological screen of an expression library, five cDNA clones encoding the modulo antigen, a DNA-binding protein differentially expressed during Drosophila development. In addition a series of overlapping cDNA and genomic clones were also isolated. This protein is the product of a 2.2 kb mRNA that is encoded by a single genetic locus (IOOF). Analysis of the complete 544 amino-acid sequence, deduced from nucleotide sequence of cDNAs, shows that the polypeptide exhibits a primary structure with distinct charged regions, a modular structure found in several eukaryotic nuclear proteins, either transcription regulators or structural factors. The amino and carboxyl termini are rich in basic residues. The first third of the sequence contains a long domain comprised almost entirely of glutamic and aspartic acid residues. A typical cAMP dependent phosphorylation site and five potential glycosylation sites have been detected in the amino-acid sequence. Computer searches fail to reveal any significant homology with known proteins.