Transcriptional activation by the Antennapedia and fushi tarazu proteins in cultured Drosophila cells

zeste, a nonessential gene, potently activates Ultrabithorax transcription in the Drosophila embryo

The GAGA, NTF-1, and zeste proteins have been purified previously from Drosophila embryo extracts and shown to activate the Ultrabithorax (Ubx) promoter in vitro. Here, differently mutated Ubx-promoter constructs containing binding sites for none, one, or all three of these transcription factors have been introduced into Drosophila by P-element transformation. Binding sites for each factor activate dramatically different patterns of transcription. In zeste mutant embryos, the activation by zeste protein-binding sites is essentially abolished. These genetic data, when considered with our earlier biochemical experiments, demonstrate that zeste directly and potently activates Ubx transcription in vivo. Surprisingly, previous genetic experiments indicate that zeste is a nonessential gene shown only to act in a dispensable regulatory process termed transvection. In our transgenic experiments, zeste is not activating transcription by transvection. We propose that the function of zeste in Drosophila is much broader than assumed previously, and that it is a member of a redundant system of transcription factors that regulate and maintain the expression of Ubx and other Drosophila genes.

In vivo analysis of the helix-turn-helix motif of the fushi tarazu homeo domain of Drosophila melanogaster

We report a systematic mutational analysis of the helix-turn-helix motif (HTH) of the fushi tarazu (ftz) homeo domain (HD) of Drosophila. We started out by testing the function of chimeric ftz proteins containing either a part of the Sex combs reduced (Scr) or the muscle segment homeobox (msh) HDs. By complementation tests in transgenic flies, cotransfection assays in cultured Drosophila cells and in vitro DNA-binding assays, we have found that the ftz activity is retained in the ftz-Scr chimera but is lost in the ftz-msh chimera, which is defective in binding to an Antennapedia (Antp)-class target site. Further studies with a series of back-mutants of the ftz-msh chimera have revealed that a set of class-specific DNA backbone-contacting residues in the HTH, particularly Arg-28 and Arg-43, are required for efficient target site recognition and, hence, full ftz activity both in vitro and in vivo.

Homeodomain-independent activity of the fushi tarazu polypeptide in Drosophila embryos

The Drosophila segmentation gene fushi tarazu (ftz) encodes a homeodomain-containing protein, ftz, that can act as a DNA-binding activator of transcription. In the developing embryo, ftz is expressed in seven stripes which correspond to the even-numbered parasegments. These parasegments are missing in ftz- embryos. When ftz is expressed throughout blastoderm embryos under the control of a heat-shock promoter, the odd-numbered parasegments are lost. This 'anti-ftz' phenotype has been attributed to autoactivation of the endogenous ftz gene by the ectopically expressed protein. Here we show that the same phenotype is induced by ectopic expression of a ftz polypeptide containing a deletion in the homeodomain. Thus, ftz can alter gene expression without binding directly to DNA.

Cell type dependent transcription regulation by chick homeodomain proteins

Five chick homeodomain proteins (CHOXs), CHOX-1.7, -1.1, -1.4, -4.2 and -2.6, had different transcription-regulating activities in a chick cultured cell line, LMH. In particular, CHOX-1.7 highly activated transcription when NP6 was used as the target site whereas CHOX-1.4 did not. This was mainly due to differences in the activation domains since both proteins bound to NP with almost the same affinities in vitro. In LMH cells, they competitively acted on target gene transcription. Moreover, the strength of the CHOX-1.4 activation domain depended on the cell type. These findings suggest that the effect on a target gene is determined by a combination of CHOXs and cell types.

A transcriptional hierarchy involved in mammalian cell-type specification

Although transcriptional hierarchies have been extensively studied in invertebrates, their involvement in mammalian cell-type specification is poorly understood. Here we report a hepatocyte transcriptional cascade suggested by the expression patterns of hepatic transcription factors in dedifferentiated hepatomas and hepatocyte: fibroblast hybrids in which the liver phenotype was extinguished. These results indicated that the homeoprotein hepatocyte nuclear factor-1 alpha (HNF-1 alpha), and HNF-4, a member of the steroid hormone receptor superfamily, were regulated coordinately or in a hierarchy by a higher-order locus, independently of other hepatic transactivators. HNF-4 was implicated as an essential positive regulator of HNF-1 alpha, as deletion of an HNF-4 binding site in the HNF-1 alpha promoter abolished promoter activity, and HNF-4 potently transactivated the HNF-1 alpha promoter in cotransfection assays. Moreover, genetic complementation of dedifferentiated hepatomas with HNF-4 complementary DNA rescued expression of endogenous HNF-1 alpha messenger RNA and DNA-binding activity. Our studies therefore define an HNF-4----HNF-1 alpha (4----1 alpha) transcriptional hierarchy operative in differentiated hepatocytes but selectively inhibited by an extinguishing locus and somatic mutations which antagonize the liver phenotype.

Molecular cloning, analysis, and chromosomal localization of a mouse genomic sequence related to the human papillomavirus type 18 E5 region

The E5 open reading frame (ORF) from bovine papillomavirus type 1 (BPV 1) as well as the E5 ORFs from human papillomaviruses (HPV) type 6 and type 16 have been reported to transform immortalized rodent cells. In an analysis of murine and human tumors for the presence of putative papillomavirus-related sequences, we cloned amplified cellular sequences from the mouse cell line Eb that cross-hybridized with the E5 ORF of HPV 18. A 2.1-kb fragment termed HC1 was sequenced. In normal murine cells, it was present as a single-copy genomic sequence located on chromosome 8. A region of 213 nucleotides corresponded to the E5 gene (HC1 E5), based on the best alignments and on the presence of direct and inverted repeats bearing a central sequence motif. These structural elements are also present in the HPV 18 E5 ORF. HC1 E5 contained an ORF that was transcribed bidirectionally. The transcription in the E5 direction was enhanced in RNA obtained from organs and tumors from carcinogen-treated animals and C127 cells. The polypeptide deduced from the sequence was related to E5 proteins from genital papillomaviruses, to the putative product of the Q300 mouse gene, and to several viral and human growth factors. The data suggest that there may be several cellular counterparts to the viral E5 proteins.

Identification of 10 murine homeobox genes

In Drosophila a number of genes important in establishing segmentation patterns and in determining segment identities have been shown to carry the homeobox sequence. Over 30 murine homeobox genes have been cloned, many on the basis of sequence homology to Drosophila prototypes. Here we report the cloning and sequencing of 10 new and 6 previously known homeobox genes by screening a murine genomic library with a 768-fold degenerate oligonucleotide corresponding to the most conserved 8-amino acid motif in the recognition helix of the homeodomain. Eight of these new homeobox genes have been chromosomally mapped. Four genes do not belong to any of the known homeobox gene clusters but instead map to new locations on chromosome 1 (single gene) and chromosome 5 (three genes). Sequence comparisons indicate that two of these are very closely related and represent a distinct new category of homeobox genes. The remaining four mapped genes reside in previously established murine homeobox gene clusters. Specifically, two map to the cluster HOX-1 on chromosome 6 and one each to HOX-3 and HOX-4 on chromosome 15 and 2, respectively. The ratio of newly identified homeobox genes to the previously characterized murine homeobox genes suggests that there remain several uncharacterized homeobox genes in the murine genome.

Sequence requirements for embryonic transcriptional activation of a gastrula-specific actin gene in Xenopus laevis

Cytoskeletal actin genes undergo developmentally timed transcriptional activation at the gastrula stage of embryonic development in the amphibian Xenopus laevis. To study the regulation of this process, a molecularly marked cloned actin gene has been introduced into living embryos by microinjection, and levels of its transcripts (which are distinct from endogenous actin message) have been measured by RNase protection. In vitro mutagenesis of the marked gene, followed by microinjection and transcriptional analysis of various mutants, has been used to search for gene sequences that participate in accurate transcriptional initiation and developmental control. Deletion mutants containing only 90 nucleotides of upstream sequence undergo correct developmental regulation, while deletion to -33 prevents normal activation of the gene. In the presence of sufficient upstream sequence, an actin-globin fusion gene, containing only 564 nucleotides downstream of the actin gene transcription startsite, is correctly activated. Taken together, these results imply that all sequences necessary for correct temporal regulation reside between -90 and +564 nucleotides, with respect to the transcriptional start site of the actin gene. They further suggest that developmental activation of actin gene transcription may involve either (1) interaction of non-DNA binding proteins with basal transcription factors, or (2) the concerted action of ubiquitous promoter-binding factors and factors that interact with downstream regulatory regions.

Recombinant gene expression in cultured Drosophila melanogaster cells

Cultured Drosophila Schneider line 2 cells provide a versatile and efficient system for the expression of recombinant gene products that retain authentic properties. An efficient method now exists for the expression of large amounts of recombinant protein from continuous cell lines. In addition, Schneider line 2 cells have proven reliable as a background for in vivo studies of gene regulation and protein function.

Expression patterns of mouse Hox genes: clues to an understanding of developmental and evolutionary strategies

Expression patterns of Antennapedia-like homeogenes in the mouse embryo show many similarities o those of their homologues in Drosophila. It is argued here that homeogenes may regulate development of the body plan in mouse by mechanisms similar to those used in Drosophila. In particular, they may differentially specify positional address of cell groups within lineage compartments along the body axes. In vertebrates, a single ancestral homeogene cluster has become duplicated to give four separate clusters. Comparisons of homeogene expression patterns between different clusters of the mouse suggest ways in which duplication has permitted development of a more complex body plan. Cluster duplication may therefore have provided a selective advantage during vertebrate evolution.

Production of mouse Hox-2.1 protein in Escherichia coli: characterisation of in vitro binding to DNA

The developmentally regulated mouse Hox-2.1 gene encodes a homeodomain-containing (Hox) protein which is likely to function as a transcription factor. We expressed the DNA coding for full-length Hox-2.1 protein in a T7 promoter-containing vector in bacteria, which produced low levels of protein showing weak DNA-binding activity. Synthesis of a truncated polypeptide lacking all the sequence upstream from the homeodomain enabled us to produce greater amounts of protein and demonstrate its sequence-dependent DNA binding. The tetranucleotide ATTA is necessary for binding, but a single copy is not by itself sufficient. Flanking sequences are important; in particular a cytosine immediately 5' to the ATTA enhances binding.

Functional dissection of Drosophila abdominal-B protein

The Abdominal-B gene is unique among homeotic Drosophila genes as it encodes two proteins m and r which confer different functions. The m protein corresponds to an r protein with a large N-terminal extension; the two proteins contain the same homeodomain. We have used a transient co-transfection assay, based on HeLa cells, to analyse the intrinsic function of m and r protein in activating transcription. We find two strong transcriptional activation domains in the common part of the two proteins. The m-specific exon contains additional transcriptional activation potential. Despite this, the m protein is a weaker transcriptional activator than the r protein. Apparently, there are inhibitory sequences in the m-specific exon which, in the embryo, may have a role in masking r function in the intact m protein.

DNA-binding specificity of the fushi tarazu homeodomain

The fushi tarazu (ftz) gene of Drosophila melanogaster encodes a homeodomain-containing transcription factor that functions in the formation of body segments. Here we report an analysis of the DNA-binding properties of the ftz homeodomain in vitro. We provide evidence that the homeodomain binds to DNA as a monomer, with an equilibrium dissociation constant of 2.5 x 10(-11) M for binding to a consensus binding site. A single ftz binding site occupies 10 to 12 bp, as judged by the ability of protein bound at one site to interfere with binding to an adjacent site. These experiments also demonstrated a lack of cooperative binding between ftz homeodomains. Analysis of single-nucleotide substitutions over an 11-bp sequence shows that a stretch of 6 bp is critical for binding, with an optimal sequence of 5'CTAATTA3'. These data correlate well with recent structural evidence for base-specific contact at these positions. In addition, we found that sequences flanking the region of direct contact have effects on DNA binding that could be of biological significance.

DNA-binding specificity of the fushi tarazu homeodomain

The fushi tarazu (ftz) gene of Drosophila melanogaster encodes a homeodomain-containing transcription factor that functions in the formation of body segments. Here we report an analysis of the DNA-binding properties of the ftz homeodomain in vitro. We provide evidence that the homeodomain binds to DNA as a monomer, with an equilibrium dissociation constant of 2.5 x 10(-11) M for binding to a consensus binding site. A single ftz binding site occupies 10 to 12 bp, as judged by the ability of protein bound at one site to interfere with binding to an adjacent site. These experiments also demonstrated a lack of cooperative binding between ftz homeodomains. Analysis of single-nucleotide substitutions over an 11-bp sequence shows that a stretch of 6 bp is critical for binding, with an optimal sequence of 5'CTAATTA3'. These data correlate well with recent structural evidence for base-specific contact at these positions. In addition, we found that sequences flanking the region of direct contact have effects on DNA binding that could be of biological significance.

A deficiency of the homeotic complex of the beetle Tribolium

In Drosophila, the establishment of regional commitments along most of the anterior/posterior axis of the developing embryo depends on two clusters of homeotic genes: the Antennapedia complex (ANT-C) and the bithorax complex (BX-C). The red flour beetle has a single complex (HOM-C) representing the homologues of the ANT-C and BX-C in juxtaposition. Beetles trans-heterozygous for two particular HOM-C mutations spontaneously generate a large deficiency, presumably by an exchange within the common region of two overlapping inversions. Genetic and molecular results indicate that this deficiency spans at least the interval between the Deformed and abdominal-A homologues. In deficiency homozygous embryos, all gnathal, thoracic and abdominal segments develop antennal appendages, suggesting that a gene(s) has been deleted that acts to distinguish trunk from head. There is no evidence that beetles have a homologue of the segmentation gene fushi tarazu of similar genomic location and function. On the basis of the genetic tractability, convenient genome size and organization of Tribolium, and its relatively long phylogenetic divergence from Drosophila (>300 million years), we have integrated developmental genetic and molecular analyses of the HOM-C. We isolated about 70 mutations in the complex representing at least six complementation groups. The homeotic phenotypes of adults and lethal embryos lead us to believe that these beetle genes are homologous with the Drosophila genes indicated in Fig. 1 (see text).

Activation of the L1 late H2B histone gene in blastula-stage sea urchin embryos by Antennapedia-class homeoprotein

The L1 late H2B histone gene of the sea urchin Strongylocentrotus purpuratus is transcriptionally activated in late blastula stage embryos by a mechanism that depends on an enhancer element located 3' of the gene (Zhao et al., 1990). A protein factor, designated H2B abp 1, binds this element at a site that resembles the consensus recognition sequence of Antennapedia-class homeodomain proteins. We demonstrate here that Antennapedia (Antp) and Hbox4 proteins, members of the Antennapedia class of homeoproteins from Drosophila and sea urchin respectively, bind the L1 H2B abp 1 site, and that the Drosophila Antp protein acts through this site to trans-activate the L1 H2B gene, in vivo. In addition, RNA gel blot analysis demonstrated that Hbox4 transcripts accumulate in developing embryos with a time course that closely resembles that of H2B adp 1 DNA binding activity and the activity and the transcription rate of the L1 late H2B gene. Finally, we show that antibody prepared against the sea urchin Hbox4 protein, a member of the Abd-B subclass of the Antennapedia class, specifically inhibits binding of the H2B abp 1 factor to the L1 H2B enhancer, suggesting that H2B abp 1 is encoded by Hbox4 or a closely related gene.

Activation and repression of transcription by the gap proteins hunchback and Krüppel in cultured Drosophila cells

We have studied the ability of the Drosophila gap proteins Krüppel and hunchback to function as transcriptional regulators in cultured cells. Both proteins bind to specific sites in a 100-bp DNA fragment located upstream of the segment polarity gene engrailed, which also contains functional binding sites for a number of homeo box proteins. The hunchback protein is a strikingly concentration-dependent activator of transcription, capable of functioning both by itself and also synergistically with the pair-rule proteins fushi tarazu and paired. In contrast, Krüppel is a transcriptional repressor that can block transcription induced either by hunchback or by several different homeo box proteins. While repression of the homeo box protein activators requires a Krüppel-binding site on the DNA, repression of hunchback can occur efficiently in the absence of a Krüppel-binding site. We discuss the possible molecular mechanisms underlying these activities, as well as the potential significance of these results with respect to segmentation in Drosophila.

High-affinity binding sites for the Deformed protein are required for the function of an autoregulatory enhancer of the Deformed gene

The homeotic selector gene Deformed (Dfd) is required to specify the identity of head segments during Drosophila development. Previous experiments have shown that for the Dfd segmental identity function to operate in epidermal cells, the Dfd gene must be persistently expressed. One mechanism that provides persistent embryonic expression of Dfd is an autoregulatory circuit. Here, we show that the control of this autoregulatory circuit is likely to be directly mediated by the binding of Dfd protein to an upstream enhancer in Dfd locus DNA. In a 25-kb region around the Dfd transcription unit, restriction fragments with the highest binding affinity for Dfd protein map within the limits of the upstream autoregulatory element at approximately -5 kb. A minimal autoregulatory element, within a 920-bp segment of upstream DNA, has four moderate- to high-affinity binding sites for Dfd protein, with the two highest affinity sites sharing an ATCATTA consensus sequence. Site-specific mutagenesis of these four sites results in an element that has low affinity for Dfd protein when assayed in vitro and is nonfunctional when assayed in embryos.

Activation of a late H2B histone gene in blastula-stage sea urchin embryos by an unusual enhancer element located 3' of the gene

In the sea urchin embryo, late histone genes are transcribed at low levels during cleavage and blastula formation and at substantially higher levels in later stages of embryogenesis. To investigate the molecular basis of the stage-specific expression of a late H2B histone gene, we injected mutant genes lacking portions of 5'- and 3'-flanking regions into Lytechinus pictus embryos and monitored their expression by RNase protection. A 200-bp region located 489 bp downstream of the mRNA 3' terminus was necessary for the increase in transcription of the late H2B gene at the mid-blastula stage of development. DNase I and methylation interference footprint analyses located only one factor-binding site in this region, and gel mobility shift experiments showed that the DNA-binding activity of this factor (designated H2B abp 1) paralleled the transcriptional activity of the L1 H2B gene. Additional mutagenesis and microinjection experiments located the activator element to a 32-bp DNA segment that includes the H2B abp 1-binding site. These experiments also showed that the 32-bp fragment functions independently of position and orientation and therefore has the hallmarks of an enhancer. That this fragment contains most or all of the L1 H2B gene transcription-stimulatory activity makes it unusual among enhancerlike elements, which generally consist of several clustered factor-binding sites that act additively or cooperatively to affect transcription. The nucleotide sequence of the L1 H2B enhancer element suggests that the trans-acting factor that interacts with it is a member of the antennapedia or engrailed class of homeodomain proteins.

Whole animal cell sorting of Drosophila embryos

Use of primary culture cells has been limited by the inability to purify most types of cells, particularly cells from early developmental stages. In whole animal cell sorting (WACS), live cells derived from animals harboring a lacZ transgene are purified according to their level of beta-galactosidase expression with a fluorogenic beta-galactosidase substrate and fluorescence-activated cell sorting. With WACS, incipient posterior compartment cells that express the engrailed gene were purified from early Drosophila embryos. Neuronal precursor cells were also purified, and they differentiated into neurons with high efficiency in culture. Because there are many lacZ strains, it may be possible to purify most types of Drosophila cells. The same approach is also applicable to other organisms for which germ-line transformation is possible.

Activation of a late H2B histone gene in blastula-stage sea urchin embryos by an unusual enhancer element located 3' of the gene

In the sea urchin embryo, late histone genes are transcribed at low levels during cleavage and blastula formation and at substantially higher levels in later stages of embryogenesis. To investigate the molecular basis of the stage-specific expression of a late H2B histone gene, we injected mutant genes lacking portions of 5'- and 3'-flanking regions into Lytechinus pictus embryos and monitored their expression by RNase protection. A 200-bp region located 489 bp downstream of the mRNA 3' terminus was necessary for the increase in transcription of the late H2B gene at the mid-blastula stage of development. DNase I and methylation interference footprint analyses located only one factor-binding site in this region, and gel mobility shift experiments showed that the DNA-binding activity of this factor (designated H2B abp 1) paralleled the transcriptional activity of the L1 H2B gene. Additional mutagenesis and microinjection experiments located the activator element to a 32-bp DNA segment that includes the H2B abp 1-binding site. These experiments also showed that the 32-bp fragment functions independently of position and orientation and therefore has the hallmarks of an enhancer. That this fragment contains most or all of the L1 H2B gene transcription-stimulatory activity makes it unusual among enhancerlike elements, which generally consist of several clustered factor-binding sites that act additively or cooperatively to affect transcription. The nucleotide sequence of the L1 H2B enhancer element suggests that the trans-acting factor that interacts with it is a member of the antennapedia or engrailed class of homeodomain proteins.

Mouse Hox-2.2 specifies thoracic segmental identity in Drosophila embryos and larvae

The mouse genome has a number of homeobox genes that are structurally similar to the Drosophila Antenapedia (Antp) gene. We find that one of the mouse Antp-like genes, Hox-2.2, when expressed in developing Drosophila cells under control of a heat shock promoter, can induce homeotic transformations that are nearly identical to those caused by ectopic expression of Antp. In larvae, the Hox-2.2-induced transformations include thoracic denticle belts in place of head structures; in adults, the Hox-2.2 transformations include thoracic legs in place of antennae. The phenotypic effects of Hox-2.2 do not depend on the endogenous Antp gene, whose spatial limits of expression are unaffected by Hox-2.2 expression. Thus, in the Drosophila embryo, Hox-2.2 can substitute for some of the segmental identity functions of Antp, presumably by regulating the same set of downstream genes.

Targets of homeotic gene control in Drosophila

The homeotic gene Ultrabithorax (Ubx) encodes homeodomain-containing transcription factors that determine segmental identity in Drosophila. Here, an immunopurification procedure is described that enriches for embryonic chromatin fragments containing binding sites for Ubx protein. In two cases these binding sites are located near embryonic transcription units regulated by the Ubx locus in vivo. Thus, these transcripts may correspond to Ubx target genes involved in elaborating segment-specific developmental pathways.

Molecular interactions within the ecdysone regulatory hierarchy: DNA binding properties of the Drosophila ecdysone-inducible E74A protein

The E74 early ecdysone-inducible gene plays a key role in the regulatory hierarchy activated by ecdysone at the onset of Drosophila metamorphosis. We show here that E74A protein binds to three adjacent sites in the middle of the E74 gene. The consensus sequence for E74A protein binding, determined by random-sequence oligonucleotide selection, contains an invariant purine-rich core sequence, C/AGGAA. This sequence is also present in the binding sites of two mammalian proteins that, like E74A, are related to the ets oncoprotein. Antibody staining of larval salivary gland polytene chromosomes revealed that E74A protein binds to both early and late ecdysone-inducible puffs. This study supports Ashburner's proposal that the early puffs encode site-specific DNA binding proteins that directly interact with the early and late ecdysone-inducible puffs.

The specificities of Sex combs reduced and Antennapedia are defined by a distinct portion of each protein that includes the homeodomain

The sequence requirements for distinguishing the functional specificities of two homeodomain proteins, Antennapedia and Sex combs reduced, involved in the specification of segmental identities in Drosophila, have been determined. A series of deletions and hybrid proteins was generated and assayed for their function in vivo after heat shock-induced ectopic expression during development. A distinct portion of each protein, including the residues within and adjacent to both ends of the homeodomain, has been found to almost entirely determine its functional specificity as measured by diagnostic cuticular transformations of embryonic and adult head structures. The remaining sequences contribute to the potency with which the proteins act in different cells and are to a limited extent functionally transferable from one protein to the other.

A homeo domain protein reveals the metameric nature of the developing chick hindbrain

The segmented embryonic hindbrain of vertebrates develops by sequential constriction of the neural tube into eight metameric units known as rhombomeres. The cellular and molecular basis of this segmentation process is largely unknown. Using an antibody, we analyzed the expression pattern of the chick homeo domain-containing protein Ghox-lab in the developing chick hindbrain. At the neural plate stage, prior to the appearance of rhombomeres, Ghox-lab is expressed within a single domain that extends anteriorly up to the site where rhombomere 4 will later form. After rhombomere 4 has appeared and as hindbrain segmentation progresses, the level of Ghox-lab protein increases significantly within the fourth rhombomere. This intensification, accompanied by the elimination of Ghox-lab protein in rhombomeres 5 and 6, eventually results in the formation of a distinct island of expression in rhombomere 4. All cells in the newly formed rhombomere 4 express Ghox-lab, except for the cells of the floor plate. In addition, neural crest cells migrating from the fourth rhombomere are also Ghox-lab-positive. These data raise the possibility that Ghox-lab protein might be one of the factors involved in the specification of the metameric pattern of the vertebrate hindbrain.

Analysis of the ftz upstream element: germ layer-specific enhancers are independently autoregulated

The Drosophila fushi tarazu (ftz) upstream element is an enhancer-like element that is required for the correct expression of ftz in developing embryos and that directs transcription from a minimal promoter in a ftz-like seven-striped pattern. Using a deletion analysis, we have identified several independent cis-regulatory elements in the upstream element. A distal enhancer directs fusion gene expression in seven stripes primarily in the mesoderm. A more complex proximal enhancer contains a mesodermally active element and a second element with which it interacts to generate seven stripes in the ectoderm. Striped expression directed by each enhancer is ftz-dependent, and each contains binding sites for purified ftz homeo domain. We suggest that ftz protein acts in combination with germ layer-restricted transcription factors directly and positively to regulate the transcription of its own gene.

Mutations in the Drosophila gene extradenticle affect the way specific homeo domain proteins regulate segmental identity

We characterized a gene, extradenticle, which seems to interact with a specific subset of Drosophila homeo domain proteins, possibly affecting their target specificity. This interpretation is based on an examination of the zygotic and maternal effect phenotypes of extradenticle mutations. In embryos with reduced levels of extradenticle gene product, anterior and posterior segmental transformations occur. Segmental identity in Drosophila is mediated by the products of the Antennapedia and bithorax complexes. These homeo domain proteins are thought to regulate different target genes specifically in each segment, resulting in different morphologies. extradenticle alters segmental identity without affecting the pattern of expression of homeotic genes. Genetic tests demonstrate that in extradenticle mutants, the homeotic proteins are functional and act in their normal segmental domains, yet segmental identities are altered. Even when homeotic proteins are ectopically expressed under the control of a heterologous promoter, extradenticle mutations affect their consequences. Thus, in the absence of sufficient extradenticle product, altered segmental morphology results from alteration of the functional consequences of specific homeo domain proteins, possibly through alterations in their target gene specificity. extradenticle is also expressed maternally. Complete removal of extradenticle, maternally and zygotically, leads to specific alterations in segmentation, many of which result from failure to maintain the expression of the homeo domain protein engrailed.

The POU-specific domain of Pit-1 is essential for sequence-specific, high affinity DNA binding and DNA-dependent Pit-1-Pit-1 interactions

Pit-1 is a member of a family of transcription factors sharing two regions of homology: a highly conserved POU-specific (POUS) domain and a more divergent homeodomain (POUHD). Analysis of mutant Pit-1 proteins suggests that, while the POUHD is required and sufficient for low affinity DNA binding, the POUS domain is necessary for high affinity binding and accurate recognition of natural Pit-1 response elements. Pit-1 is monomeric in solution but associates as a dimer on its DNA response element, exhibiting DNA-dependent protein-protein interactions requiring the POUS domain. Analysis of alpha-helical domains and conserved structures in Pit-1 suggests that POU domain proteins interact with their DNA recognition sites differently than classic homeodomain proteins, with both the POUHD and the POUS domain contacting DNA. Transcriptional activity of Pit-1 on enhancer elements is conferred primarily by a Ser- and Thr-rich N-terminal region unrelated to other known transcription-activating motifs.

Stimulation of transcription by an Ultrabithorax protein in vitro

The Ultrabithorax (Ubx) gene of Drosophila melanogaster encodes a family of UBX proteins that are thought to specify the developmental fates of segments in the posterior thorax and anterior abdomen by controlling the expression of a set of target genes. UBX proteins bind DNA in vitro, and they activate or repress different natural and synthetic target promoters in cultured cells. Here it is shown that a purified UBX protein can stimulate transcription of a synthetic target gene in extracts of cultured D. melanogaster cells. Stimulation is dependent on the presence of upstream, promoter-region binding sites but is independent of binding site orientation. A naturally occurring binding site cluster and a binding site consensus sequence consisting of TAA trinucleotide repeats can mediate this activation. A minimal promoter fused to such sites is activated by UBX, suggesting that transcriptional stimulation could result from an interaction between the promoter-bound protein and the general transcriptional machinery.

Binding site-dependent direct activation and repression of in vitro transcription by Drosophila homeodomain proteins

Fushi tarazu and engrailed are two of the genes required for proper segmentation of the Drosophila embryo. Their protein products Fushi tarazu and Engrailed (Ftz and En) each contain a homeodomain and have been shown to act as transcriptional regulators in transient expression experiments in a Drosophila cell culture system. We used an in vitro transcription system to test whether the effects of Ftz and En on transcription were direct or indirect. Purified Ftz directly activates in vitro transcription by binding to homeodomain binding sites inserted upstream of the TATA box of the Drosophila hsp70 promoter. Equimolar amounts of purified En repress this activation by competition with Ftz for binding to these sites. These results indicate that Ftz and En act directly as transcription factors and suggest that such homeodomain proteins regulate development by combinatorial transcriptional control.

Specific DNA binding of the two chicken Deformed family homeodomain proteins, Chox-1.4 and Chox-a

The cDNA clones encoding two chicken Deformed (Dfd) family homeobox containing genes Chox-1.4 and Chox-a were isolated. Comparison of their amino acid sequences with another chicken Dfd family homeodomain protein and with those of mouse homologues revealed that strong homologies are located in the amino terminal regions and around the homeodomains. Although homologies in other regions were relatively low, some short conserved sequences were also identified. E. coli-made full length proteins were purified and used for the production of specific antibodies and for DNA binding studies. The binding profiles of these proteins to the 5'-leader and 5'-upstream sequences of Chox-1.4 and Chox-a coding regions were analyzed by immunoprecipitation and DNase I footprint assays. These two Chox proteins bound to the same sites in the 5'-flanking sequences of their coding regions with various affinities and their binding affinities to each site were nearly the same. The consensus sequences of the high and low affinity binding sites were TAATGA(C/G) and CTAATTTT, respectively. A clustered binding site was identified in the 5'-upstream of the Chox-a gene, suggesting that this clustered binding site works as a cis-regulatory element for auto- and/or cross-regulation of Chox-a gene expression.

A sequence-specific DNA-binding protein that activates fushi tarazu segmentation gene expression

The Drosophila segmentation gene fushi tarazu (ftz) is expressed at the cellular blastoderm stage in a pattern of seven transverse stripes; the stripes lie out of register with the segmental primordia, spanning alternate segmental boundaries. The zebra element, a 740-bp DNA sequence upstream of the ftz translational start, directs striped expression of lacZ when introduced into the fly genome. We have purified to homogeneity a sequence-specific DNA-binding factor, FTZ-F1, that binds to two sites located within the zebra element and to two sites within the ftz protein-coding sequence. FTZ-F1 DNA-binding activity is first detected in extracts of 1.5- to 4-hr embryos, coincident with the time of ftz expression in stripes; the activity then diminishes before reappearing during late embryo, larval, and adult stages. When one of the FTZ-F1-binding sequences in the zebra element is mutated by 2- or 4-base substitutions, the binding to FTZ-F1 is disrupted in vitro, and the intensity of lacZ expression is reduced in transformed embryos, especially in stripes 1, 2, 3, and 6. The results suggest that FTZ-F1 is a transcriptional activator necessary for the proper expression of the ftz gene.

Functional dissection of Ultrabithorax proteins in D. melanogaster

Expression of Ultrabithorax (UBX) proteins via a heat-inducible promoter generated homeotic transformations of segmental identities in the embryonic cuticle and peripheral nervous system (PNS) of Drosophila and transformed antennae into legs in the adult. The embryonic transformations were used to determine the identity functions of members of the UBX family and UBX mutant forms. Whereas UBX forms I and IV each induced the cuticle transformations, only form I induced the PNS transformations. Analysis of the transformations generated by UBX deletions and by a chimeric Ultrabithorax-Antennapedia protein demonstrated that the majority of the UBX identity information is contained within the C-terminal, homeodomain-containing portion of the protein. Implications of these results for how homeotic proteins select particular metameric identities are discussed.

A single amino acid can determine the DNA binding specificity of homeodomain proteins

Many Drosophila developmental genes contain a DNA binding domain encoded by the homeobox. This homeodomain contains a region distantly homologous to the helix-turn-helix motif present in several prokaryotic DNA binding proteins. We investigated the nature of homeodomain-DNA interactions by making a series of mutations in the helix-turn-helix motif of the Drosophila homeodomain protein Paired (Prd). This protein does not recognize sequences bound by the homeodomain proteins Fushi tarazu (Ftz) or Bicoid (Bcd). We show that changing a single amino acid at the C-terminus of the recognition helix is both necessary and sufficient to confer the DNA binding specificity of either Ftz or Bcd on Prd. This simple rule indicates that the amino acids that determine the specificity of homeodomains are different from those mediating protein-DNA contacts in prokaryotic proteins. We further show that Prd contains two DNA binding activities. The Prd homeodomain is responsible for one of them while the other is not dependent on the recognition helix.

A homeodomain substitution changes the regulatory specificity of the deformed protein in Drosophila embryos

Homeodomain proteins are believed to direct developmental pathways during Drosophila embryogenesis by the specific regulation of other genes. An unresolved issue is whether it is the homeodomain or the other regions of such proteins that confer target specificity. To test the role of the homeodomain in determining target specificity, we replaced the homeobox of Deformed with the homeobox of Ultrabithorax. The resulting chimeric protein cannot activate transcription from the Deformed gene, as does the normal Deformed protein. Instead, the chimeric protein activates ectopic transcription of Antennapedia, a gene normally regulated by Ultrabithorax. Our results indicate that in the context of the developing embryo, even closely related homeodomain sequences have different target specificities.

Transcription factors and the control of Drosophila development

Drosophila is a uniquely advantageous system for carrying out both biochemical and genetic analyses of proteins that regulate spatial and temporal patterns of transcription. Here we discuss what is known about the mechanisms of action and biological functions of transcription factors that act on genes controlling Drosophila embryogenesis.

A purified Drosophila homeodomain protein represses transcription in vitro

even-skipped (eve) is a homeodomain-encoding gene that is a genetically defined repressor of Ultrabithorax (Ubx), fushi-tarazu (ftz), and wingless (wg). Here we report that purified eve protein represses transcription in vitro at the Ubx promoter, in a DNA binding site-dependent manner. eve protein represses transcription when bound either upstream or downstream of the RNA start site or when DNA binding sites are in either orientation. We also show that eve represses expression from the Ubx promoter in Drosophila tissue culture cells, again in a binding site-dependent manner. Deletion of eve DNA binding sites does not alter transcription in the absence of eve, and so repression is not likely to be the result of eve competitively inhibiting an activator protein from binding to the same DNA element. Instead, we propose that eve protein is probably interfering with the function of proteins bound at other locations in the promoter. The biochemical demonstration that a Drosophila homeodomain protein can directly regulate RNA synthesis strengthens the view that this class of regulators act as transcription factors to control development.

Transcriptional activation and repression by Ultrabithorax proteins in cultured Drosophila cells

Homeotic genes of Drosophila melanogaster such as Ultrabithorax (Ubx) and Antennapedia (Antp) have long been thought to select metameric identity during development by controlling the expression of various target genes. Here we describe a cotransfection assay in cultured D. melanogaster cells that is used to demonstrate that Ubx proteins (UBX) can repress an Antp promoter fusion and activate a Ubx promoter fusion, activities predicted from genetic studies. We show (a) that UBX proteins regulated the level of accurately initiated Antp P1 and Ubx transcripts, (b) that activation of the Ubx promoter required a downstream cluster of UBX binding sites, and (c) that binding site sequences were sufficient to confer regulation on a heterologous promoter, regardless of their orientation or precise position. We conclude that UBX proteins are transcriptional repressors and activators, and that their actions are mediated by binding to promoter region sequences. Each member of the UBX protein family has similar regulatory abilities, but the properties of synthetic mutant forms suggest that UBX proteins may have a modular design similar to other transcriptional regulators.