Structural organization and sequence of the homeotic gene Antennapedia of Drosophila melanogaster

Antennapedia: The complexity of a master developmental transcription factor

Hox genes encode transcription factors that play an important role in establishing the basic body plan of animals. In Drosophila, Antennapedia is one of the five genes that make up the Antennapedia complex (ANT-C). Antennapedia determines the identity of the second thoracic segment, known as the mesothorax. Misexpression of Antennapedia at different developmental stages changes the identity of the mesothorax, including the muscles, nervous system, and cuticle. In Drosophila, Antennapedia has two distinct promoters highly regulated throughout development by several transcription factors. Antennapedia proteins are found with other transcription factors in different ANTENNAPEDIA transcriptional complexes to regulate multiple subsets of target genes. In this review, we describe the different mechanisms that regulate the expression and function of Antennapedia and the role of this Hox gene in the development of Drosophila.

Deciphering The Potential Role of Hox Genes in Pancreatic Cancer

The Hox gene family plays an important role in organogenesis and animal development. Currently, 39 Hox genes that are clustered in four chromosome regions have been identified in humans. Emerging evidence suggests that Hox genes are involved in the development of the pancreas. However, the expression of Hox genes in pancreatic tumor tissues has been investigated in only a few studies. In addition, whether specific Hox genes can promote or suppress cancer metastasis is not clear. In this article, we first review the recent progress in studies on the role of Hox genes in pancreatic cancer. By comparing the expression profiles of pancreatic cancer cells isolated from genetically engineered mice established in our laboratory with three different proliferative and metastatic abilities, we identified novel Hox genes that exhibited tumor-promoting activity in pancreatic cancer. Finally, a potential oncogenic mechanism of the Hox genes was hypothesized.

The regulation of Hox gene expression during animal development

Hox genes encode a family of transcriptional regulators that elicit distinct developmental programmes along the head-to-tail axis of animals. The specific regional functions of individual Hox genes largely reflect their restricted expression patterns, the disruption of which can lead to developmental defects and disease. Here, we examine the spectrum of molecular mechanisms controlling Hox gene expression in model vertebrates and invertebrates and find that a diverse range of mechanisms, including nuclear dynamics, RNA processing, microRNA and translational regulation, all concur to control Hox gene outputs. We propose that this complex multi-tiered regulation might contribute to the robustness of Hox expression during development.

My what big eyes you have: how the Drosophila retina grows

The compound eye of the fruit fly, Drosophila melanogaster, has for decades been used extensively to study a number of critical developmental processes including tissue development, pattern formation, cell fate specification, and planar cell polarity. To a lesser degree it has been used to examine the cell cycle and tissue proliferation. Discovering the mechanisms that balance tissue growth and cell death in developing epithelia has traditionally been the realm of those using the wing disc. However, over the last decade a series of observations has demonstrated that the eye is a suitable and maybe even preferable tissue for studying tissue growth. This review will focus on how growth of the retina is controlled by the genes and pathways that govern the specification of tissue fate, the division of the epithelium into dorsal-ventral compartments, the initiation, and progression of the morphogenetic furrow and the second mitotic wave.

Developmental RNA processing of 3'UTRs in Hox mRNAs as a context-dependent mechanism modulating visibility to microRNAs

The Drosophila Hox gene Ultrabithorax (Ubx) controls the development of thoracic and abdominal segments, allocating segment-specific features to different cell lineages. Recent studies have shown that Ubx expression is post-transcriptionally regulated by two microRNAs (miRNAs), miR-iab4 and miR-iab8, acting on target sites located in the 3' untranslated regions (UTRs) of Ubx mRNAs. Here, we show that during embryonic development Ubx produces mRNAs with variable 3'UTRs in different regions of the embryo. Analysis of the resulting remodelled 3'UTRs shows that each species harbours different sets of miRNA target sites, converting each class of Ubx mRNA into a considerably different substrate for miRNA regulation. Furthermore, we show that the distinct developmental distributions of Ubx 3'UTRs are established by a mechanism that is independent of miRNA regulation and therefore are not the consequence of miR-iab4/8-mediated RNA degradation acting on those sensitive mRNA species; instead, we propose that this is a hard-wired 3'UTR processing system that is able to regulate target mRNA visibility to miRNAs according to developmental context. We show that reporter constructs that include Ubx short and long 3'UTR sequences display differential expression within the embryonic central nervous system, and also demonstrate that mRNAs of three other Hox genes suffer similar and synchronous developmental 3'UTR processing events during embryogenesis. Our work thus reveals that developmental RNA processing of 3'UTR sequences is a general molecular strategy used by a key family of developmental regulators so that their transcripts can display different levels of visibility to miRNA regulation according to developmental cues.

In situ localization of the Antennapedia gene on the chromosomes of nine Drosophila species of the obscura group

The homeotic Antennapedia gene, cloned from the genomic DNA of D. subobscura, was localized on the polytene chromosomes of nine species of the Drosophila obscura group. In all of them, the probe used hybridized on chromosomes equivalent to the E element of Müller's terminology. These results are consistent with the idea that single copy genes do not move around the genome and that chromosomal elements have conserved their genetic identity during evolution.

Napin from Brassica juncea: thermodynamic and structural analysis of stability

The napin from Brassica juncea, oriental mustard, is highly thermostable, proteolysis resistant and allergenic in nature. It consists of two subunits - one small (29 amino acid residues) and one large (86 amino acids residues) - held together by disulfide bonds. The thermal unfolding of napin has been followed by differential scanning calorimetry (DSC) and circular dichroism (CD) measurements. The thermal unfolding is characterized by a three state transition with T(M1) and T(M2) at 323.5 K and 335.8 K, respectively; DeltaC(P1) and DeltaC(P2) are 2.05 kcal mol(-1) K(-1) and 1.40 kcal mol(-1) K(-1), respectively. In the temperature range 310-318 K, the molecule undergoes dimerisation. Isothermal equilibrium unfolding by guanidinium hydrochloride also follows a three state transition, N <_-_-> I <_-_-> U with DeltaG(1H2O) and DeltaG(2H2O) values of 5.2 kcal mol(-1) and 5.1 kcal mol(-1) at 300 K, respectively. Excess heat capacity values obtained, are similar to those obtained from DSC measurements. There is an increase in hydrodynamic radius from 20 A to 35.0 A due to unfolding by guanidinium hydrochloride. In silico alignment of sequences of napin has revealed that the internal repeats (40%) spanning residues 31 to 60 and 73 to 109 are conserved in all Brassica species. The internal repeats may contribute to the greater stability of napin. A thorough understanding of the structure and stability of these proteins is essential before they can be exploited for genetic improvements for nutrition.

The homeobox gene GAX activates p21WAF1/CIP1 expression in vascular endothelial cells through direct interaction with upstream AT-rich sequences

Tumors secrete pro-angiogenic factors to induce the ingrowth of blood vessels from the surrounding stroma, the end targets of which are vascular endothelial cells (ECs). The homeobox gene GAX inhibits angiogenesis and induces p21(WAF1/CIP1) expression in vascular ECs. To elucidate the mechanism through which GAX activates p21(WAF1/CIP1) expression, we constructed GAX cDNAs with deletions of the N-terminal domain, the homeodomain, or the C-terminal domain and then assessed these constructs for their ability to activate p21(WAF1/CIP1). There was an absolute requirement for the homeodomain, whereas deleting the C-terminal domain decreased but did not abolish transactivation of the p21(WAF1/CIP1) promoter by GAX. Deleting the N-terminal domain did abolish transactivation. Next, we performed chromatin immunoprecipitation and found, approximately 15 kb upstream of the p21(WAF1/CIP1) ATG codon, an ATTA-containing GAX-binding site (designated A6) with a sequence similar to that of other homeodomain-binding sites. GAX was able to bind to A6 in a homeodomain-dependent manner and thereby activate the expression of a reporter gene coupled to this sequence, and this activation was abolished by mutating specific residues in this sequence. On the basis of the sequence of A6, we were then able to locate other ATTA-containing sequences that also bound GAX and activated transcription in reporter constructs. Finally, we found that the ability of these GAX deletions to induce G(0)/G(1) arrest correlates with their ability to transactivate the p21(WAF1/CIP1) promoter. We conclude that GAX activates p21(WAF1/CIP1) through multiple upstream AT-rich sequences. Given the multiple biological activities of GAX in regulating EC function, identification of a putative GAX-binding site will allow the study of how GAX activates or represses other downstream targets to inhibit angiogenesis.

Nerfin-1 is required for early axon guidance decisions in the developing Drosophila CNS

Many studies have focused on the mechanisms of axon guidance; however, little is known about the transcriptional control of the navigational components that carryout these decisions. This report describes the functional analysis of Nerfin-1, a nuclear regulator of axon guidance required for a subset of early pathfinding events in the developing Drosophila CNS. Nerfin-1 belongs to a highly conserved subfamily of Zn-finger proteins with cognates identified in nematodes and man. We show that the neural precursor gene prospero is essential for nerfin-1 expression. Unlike nerfin-1 mRNA, which is expressed in many neural precursor cells, the encoded Nerfin-1 protein is only detected in the nuclei of neuronal precursors that will divide just once and then transiently in their nascent neurons. Although nerfin-1 null embryos have no discernible alterations in neural lineage development nor in neuronal or glial identities, CNS pioneering neurons require nerfin-1 function for early axon guidance decisions. Furthermore, nerfin-1 is required for the proper development of commissural and connective axon fascicles. Our studies also show that Nerfin-1 is essential for the proper expression of robo2, wnt5, derailed, G-oalpha47A, Lar, and futsch, genes whose encoded proteins participate in these early navigational events.

Hox genes and kidney patterning

PURPOSE OF REVIEW

Hox gene activity is essential for proper organization or pattern of the vertebrate body plan and is necessary for organogenesis. Sequence conservation within this family of genes is high yet they are involved in very diverse developmental processes. How this family functions in these processes is a challenging question, but is important for the understanding of renal organogenesis. Multiple Hox genes are expressed in the kidney and mutation in at least one group of paralogous genes results in severe renal defects.

RECENT FINDINGS

Recent studies in mice with targeted Hox gene mutations and in kidney cell lines demonstrate that these genes have evolved to control tissue specific functions through their ability to regulate the expression of renal morphogens. The studies also demonstrate that Hox gene activity is not only restricted by the domain of expression but also by the specificity of the DNA binding homeodomain. Interestingly, these conserved homeodomains are not wholly interchangeable for normal renal organogenesis while they do appear to be interchangeable for axial skeleton development.

SUMMARY

It is clear that Hox genes regulate important interactions between the ureteric bud and metanephric mesenchyme. Nevertheless, much work remains to define the expression patterns of multiple Hox genes during kidney development, to better determine the functional relationships of the encoded proteins, and to identify additional Hox downstream targets.

Sequence of the Tribolium castaneum homeotic complex: the region corresponding to the Drosophila melanogaster antennapedia complex

The homeotic selector genes of the red flour beetle, Tribolium castaneum, are located in a single cluster. We have sequenced the region containing the homeotic selector genes required for proper development of the head and anterior thorax, which is the counterpart of the ANTC in Drosophila. This 280-kb interval contains eight homeodomain-encoding genes, including single orthologs of the Drosophila genes labial, proboscipedia, Deformed, Sex combs reduced, fushi tarazu, and Antennapedia, as well as two orthologs of zerknüllt. These genes are all oriented in the same direction, as are the Hox genes of amphioxus, mice, and humans. Although each transcription unit is similar to its Drosophila counterpart in size, the Tribolium genes contain fewer introns (with the exception of the two zerknüllt genes), produce shorter mRNAs, and encode smaller proteins. Unlike the ANTC, this region of the Tribolium HOMC contains no additional genes.

The anterior determinant bicoid of Drosophila is a derived Hox class 3 gene

The Drosophila gene bicoid functions as the anterior body pattern organizer of Drosophila. Embryos lacking maternally expressed bicoid fail to develop anterior segments including head and thorax. In wild-type eggs, bicoid mRNA is localized in the anterior pole region and the bicoid protein forms an anterior-to-posterior concentration gradient. bicoid activity is required for transcriptional activation of zygotic segmentation genes and the translational suppression of uniformly distributed maternal caudal mRNA in the anterior region of the embryo. caudal genes as well as other homeobox genes or members of the Drosophila segmentation gene cascade have been found to be conserved in animal evolution. In contrast, bicoid homologs have been identified only in close relatives of the schizophoran fly Drosophila. This poses the question of how the bicoid gene evolved and adopted its unique function in organizing anterior-posterior polarity. We have cloned bicoid from a basal cyclorrhaphan fly, Megaselia abdita (Phoridae, Aschiza), and show that the gene originated from a recent duplication of the direct homolog of the vertebrate gene Hox3, termed zerknüllt, which specifies extraembryonic tissues in insects.

Cloning of the multipartite promoter of the sodium-calcium exchanger gene NCX1 and characterization of its activity in vascular smooth muscle cells

The sodium-calcium exchange activity is mediated by proteins encoded in a small gene family, of which the gene NCX1 is ubiquitously expressed in mammalian tissues. In this study, the multipartite promoter of this gene was analyzed in the human and rat genomes by means of DNA cloning, reverse transcriptase-polymerase chain reaction, and transient transfection of fusion constructs with the firefly luciferase gene into cultured rat aortic smooth muscle cells. The gene-proximal promoter, located 30 kilobase pairs (kb) away from the first coding exon 2, has features of a GC-rich housekeeping promoter and is apparently always active; in specific tissues, however, it is augmented by one or two additional promoters, located either within 1.5 kb upstream of it, or 35 kb upstream. The gene proximal promoter shows the highest activity in aortic smooth muscle cells. In mammalian species transcripts from all three promoters undergo splicing via an intermediate, containing two noncoding exons, of which the downstream one is normally not present in the terminal splicing product.

RNA editing and alternative splicing generate mRNA transcript diversity from the Drosophila 4f-rnp locus

Extensive sequencing of genomic 4f-rnp and 15 cDNA clones isolated from libraries of 0-4-h embryos, pupae, and adult heads from Drosophila melanogaster has enabled identification of factors resulting in transcript sequence diversity. The 4f-rnp gene contains eight small introns. Among non-edited cDNAs, one transcript class potentially encodes a 943-amino-acid protein, within which several motifs are predicted, including a single C-terminal RNA-binding domain. Intron 5 is retained in all cDNAs examined except for a pupal cDNA, where it is excised. This potentially introduces an in-frame stop codon and predicts a truncated protein of 639 amino acids. One adult head transcript class is edited, some 31% of As being converted to Gs exclusive of edits within introns. An edit site in intron 4 changes a canonical 3'-terminal AG to GG, which interferes with splicing and is predicted to introduce a stop codon. A potential editing substrate recognition element in 4f-rnp contains the weak consensus sequence: 5'-G-G-G-N-A-A-G-3', which may interact with double-stranded RNA adenosine deaminase following pairing of 4f-rnp mRNA with an antisense transcript. It is possible that extensive editing in 4f-rnp destabilizes transcripts and thus provides a novel mechanism for post-transcriptional control of gene expression, although resolution of this point will require study of additional edited transcripts.

Characterization of a gene encoding a DNA-binding protein that interacts in vitro with vascular specific cis elements of the phenylalanine ammonia-lyase promoter

A study of the expression of a bean phenylalanine ammonia-lyase (PAL) promoter/beta-glucuronidase gene fusion in transgenic tobacco has shown that the PAL2 promoter has a modular organization. Expression of the PAL2 promoter in the vascular system involves positive and negative regulatory cis elements. Among these elements is an AC-rich motif implicated in xylem expression and a suppressing cis element for phloem expression. Using radiolabelled complementary oligonucleotides bearing the AC-rich motif, a cDNA clone encoding a DNA-binding protein has been isolated from a tobacco lambda gt11 expression library. This factor, named AC-rich binding factor (ACBF), showed binding specificity to the AC-rich region. The specificity of ACBF for the AC-rich region was also shown using a gel retardation assay with an ACBF recombinant protein extract. The deduced amino acid sequence from ACBF contains a long repeat of glutamine residues as found in well characterized transcription factors. Interestingly, ACBF shared sequence similarity to conserved amino acid motifs found in RNA-binding proteins. Genomic gel blot analysis indicated the presence of a small gene family of sequences related to ACBF within the tobacco nuclear genome. Analysis of tobacco mRNA using the ACBF cDNA as probe showed that while ACBF mRNA was present in all tissues examined, the highest transcript accumulation occurred in stem tissues. The functional characteristics of the AC-rich sequence were examined in transgenic tobacco. A heptamer of the AC-rich sequence, in front of a minimal 35S promoter from cauliflower mosaic virus (-46 to +4), conferred specific expression in xylem.

Regulation of osteoblast-specific factor-1 (OSF-1) mRNA expression by dual promoters as revealed by RT-PCR

OSF-1 (osteoblast-specific factor-1), which is also referred to as p18, HBBM, HB-GAM, HBGF-8, HARP, HBNF, and pleiotrophin, is a 121-amino acid polypeptide that can induce neurite outgrowth in vitro and is highly expressed in several tissues during fetal development but exhibits expression restricted to brain and bone tissues in adults. We have reported the genomic structure of mouse OSF-1 gene, in which the open reading frame spans four exons and at least two additional 5'-UTR exons (upstream exon U2 and downstream exon U1) exist. From analysis of isolated cDNAs, two types of cDNAs were identified: one has a sequence for U1 and U2 and the other has a sequence for an intron (present between U1 and U2) and U1. This suggests that the OSF-1 gene utilizes two alternative promoters, a distal and a proximal promoter, designated promoters II and I, respectively, for the translation initiation site (ATG). Promoter II is thought to exist upstream of the intron, while promoter I is present in the intron. RT-PCR was employed to examine which OSF-1 promoters are used during development and in various cell lines. In adult mice (aged 2 months), usage of promoter I was predominant, and OSF-1 mRNAs were expressed in many organs including brain and bone. At one fetal stage (E-19), promoter I was active in the major organs including brain, liver, kidney, and intestine, while promoter II was active only in the brain. In the cell lines examined, usage of promoter I was frequent, while promoter II was active only in a few cell lines such as MC3T3-E1 (cultured for 7 days) and C3H10T1/2. These findings suggest that OSF-1 may play fundamental roles in differentiation, growth and maintenance of adult organs as well as in embryogenesis, and indicate that the expression of OSF-1 is regulated, at least in part, by the usage of different promoters in the mouse.

Complex gene organization of synaptic protein SNAP-25 in Drosophila melanogaster

The evolutionarily conserved protein SNAP-25 (synaptosome-associated protein 25 kDa (kilodaltons)) is a component of the protein complex involved in the docking and/or fusion of synaptic vesicles in nerve terminals. We report here that the SNAP-25 gene (Snap) in the fruit fly Drosophila melanogaster has a complex organization with eight exons spanning more than 120 kb (kilobases). The exon boundaries coincide with those of the chicken SNAP-25 gene (Bark, 1993). Only a single exon 5 has been found in Drosophila, whereas human, rat, chicken, zebrafish and goldfish have two alternatively spliced versions of this exon. In situ hybridization and immunocytochemistry to whole mount embryos show that SNAP-25 mRNA and protein are detected in stage 14 and later developmental stages, and are mainly localized to the ventral nerve cord. Thus, Snap has an evolutionarily conserved and complex gene organization, and its onset of expression in Drosophila melanogaster correlates with a time in neuronal development when synapses begin to be formed and when other synapse-specific genes are switched on.

Multicellular ascomycetous fungal genomes contain more than 8000 genes

Fungi comprise a large monophyletic group of uni- and multicellular eukaryotic organisms in which many species are of economic or medical importance. Fungal genomes are variable in size (13-42 Mb), and multicellular species support true spatial and temporal cell-type-specific regulation of gene expression. In a 38.8-kb Aspergillus nidulans contiguous genomic DNA region, a transposable element and 12 potential genes were identified, 7 similar to genes in other organisms. This observation is consistent with the prediction that multicellular ascomycetous fungi harbor 8000-9000 genes in a 36-Mb average genome. Thus, the genomic DNA sequence of filamentous fungi will provide substantial amounts of genetic and functional information that is not available in yeast, for the human and other metazoan minimal gene complement.

A role for phosphorylation by casein kinase II in modulating Antennapedia activity in Drosophila

We present evidence that the in vivo activity of the HOX protein Antennapedia (ANTP) is modified because of phosphorylation by the serine/threonine kinase casein kinase II (CKII). Using an in vivo assay a form of ANTP that has alanine substitutions at its CKII target sites has, in addition to wild-type ANTP functions, the ability to alter severely thoracic and abdominal development. The novel functions of this protein suggest that this form of ANTP is not suppressed phenotypically by the more posterior homeotic proteins. In contrast, the in vivo activity of a form of ANTP that contains acidic amino acid substitutions at its CKII target sites, thereby mimicking a constitutively phosphorylated ANTP protein, is greatly reduced. This hypoactive form of ANTP, but not the alanine-substituted form, is also reduced in its ability to bind to DNA cooperatively with the homeodomain protein Extradenticle. Our results suggest that phosphorylation of ANTP by CKII is important for preventing inappropriate activities of this homeotic protein during embryogenesis.

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1

We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints," whereas the conformations of nonhomologous regions of the unknown protein are defined only by the potential energy function. A full energy function (excluding explicit solvent) is employed to ensure that the calculated structures have good conformational energies and are physically reasonable. As in NMR structure determinations, information on the consistency of the structure prediction is obtained by superposition of the resulting family of protein structures. In this paper, our homology modeling algorithm is described and compared with related homology modeling methods using spatial constraints derived from the structures of homologous proteins. The software is then used to predict the DNA-bound structures of three homeodomain proteins from the X-ray crystal structure of the engrailed homeodomain protein (Kissinger CR et al., 1990, Cell 63:579-590). The resulting backbone and side-chain conformations of the modeled yeast Mat alpha 2 and D. melanogaster Antennapedia homeodomains are excellent matches to the corresponding published X-ray crystal (Wolberger C et al., 1991, Cell 67:517-528) and NMR (Billeter M et al., 1993, J Mol Biol 234:1084-1097) structures, respectively. Examination of these structures of Msx-1 reveals a network of highly conserved surface salt bridges that are proposed to play a role in regulating protein-protein interactions of homeodomains in transcription complexes.

Positive cross-regulation and enhancer sharing: two mechanisms for specifying overlapping Hox expression patterns

Vertebrate Hox genes display nested and overlapping patterns of expression. During mouse hindbrain development, Hoxb3 and Hoxb4 share an expression domain caudal to the boundary between rhombomeres 6 and 7. Transgenic analysis reveals that an enhancer (CR3) is shared between both genes and specifies this domain of overlap. Both the position of CR3 within the complex and its sequence are conserved from fish to mammals, suggesting it has a common role in regulating the vertebrate HoxB complex. CR3 mediates transcriptional activation by multiple Hox genes, including Hoxb4, Hoxd4, and Hoxb5 but not Hoxb1. It also functions as a selective HOX response element in Drosophila, where activation depends on Deformed, Sex combs reduced, and Antennapedia but not labial. Taken together, these data show that a Deformed/Hoxb4 autoregulatory loop has been conserved between mouse and Drosophila. In addition, these studies reveal the existence of positive cross-regulation and enhancer sharing as two mechanisms for reinforcing the overlapping expression domains of vertebrate Hox genes. In contrast, Drosophila Hox genes do not appear to share enhancers and where they overlap in expression, negative cross-regulatory interactions are observed. Therefore, despite many well documented aspects of Hox structural and functional conservation, there are mechanistic differences in Hox complex regulation between arthropods and vertebrates.

Evolution of the insect body plan as revealed by the Sex combs reduced expression pattern

The products of the HOM/Hox homeotic genes form a set of evolutionarily conserved transcription factors that control elaborate developmental processes and specify cell fates in many metazoans. We examined the expression of the ortholog of the homeotic gene Sex combs reduced (Scr) of Drosophila melanogaster in insects of three divergent orders: Hemiptera, Orthoptera and Thysanura. Our data reflect how the conservation and variation of Scr expression has affected the morphological evolution of insects. Whereas the anterior epidermal expression of Scr, in a small part of the posterior maxillary and all of the labial segment, is found to be in common among all four insect orders, the posterior (thoracic) expression domains vary. Unlike what is observed in flies, the Scr orthologs of other insects are not expressed broadly over the first thoracic segment, but are restricted to small patches. We show here that Scr is required for suppression of wings on the prothorax of Drosophila. Moreover, Scr expression at the dorsal base of the prothoracic limb in two other winged insects, crickets (Orthoptera) and milkweed bugs (Hemiptera), is consistent with Scr acting as a suppressor of prothoracic wings in these insects. Scr is also expressed in a small patch of cells near the basitarsal-tibial junction of milkweed bugs, precisely where a leg comb develops, suggesting that Scr promotes comb formation, as it does in Drosophila. Surprisingly, the dorsal prothoracic expression of Scr is also present in the primitively wingless firebrat (Thysanura) and the leg patch is seen in crickets, which have no comb. Mapping both gene expression patterns and morphological characters onto the insect phylogenetic tree demonstrates that in the cases of wing suppression and comb formation the appearance of expression of Scr in the prothorax apparently precedes these specific functions.

Molecular cloning of a myoD-like gene from the parasitic nematode, Trichinella spiralis

The infective larval stage of the nematode Trichinella spiralis is an intracellular parasite of skeletal muscle cells. Infection with T. spiralis results in dedifferentiation of the host cell and the formation of a host/parasite complex. A gene encoding a T. spiralis Helix-Loop-helix (HLH) protein with homology to the myogenic transcription factor, MyoD, and to the Caenorhabditis elegans protein, CeMyoD, has been identified and partially characterized. The tsmyd-1 gene is expressed constitutively during the muscle-larval and adult stages. A purified recombinant Tsmyd-1 protein, expressed in Escherichia coli, binds to a high affinity mouse MyoD DNA binding site in vitro. The present study describes the first HLH gene to be identified in Trichinella.

Position-effect variegation in Drosophila depends on dose of the gene encoding the E2F transcriptional activator and cell cycle regulator

A dominant mutation due to the insertion of a P-element at 93E on the third chromosome of Drosophila melanogaster enhances position-effect variegation. The corresponding gene was cloned by transposon tagging and the sequence of the transcript revealed that it corresponds to the gene encoding the transcriptional activator and cell cycle regulator dE2F. The transposon-tagged allele is homozygous viable, and the insertion of the transposon in an intron correlates with a strong reduction in the amount of transcript. A homozygous lethal null allele was found to behave as a strong enhancer when heterozygous. Overexpression of the gene in transgenic flies has the opposite effect of suppressing variegation. A link is established here, and discussed, between the dose of a transcriptional activator, which controls the cell cycle, and epigenetic silencing of chromosomal domains in Drosophila.

RNA recognition and translational regulation by a homeodomain protein

In Drosophila, the primary determinant of anterior pattern is the gradient morphogen bicoid (bcd), a homeodomain protein that binds DNA and transcriptionally activates target genes at different threshold concentrations. Here we present evidence that bcd also binds RNA and acts as a translational repressor to generate an opposing gradient of the homeodomain protein caudal (cad). RNA binding by bcd seems to involve direct interactions between the bcd homeodomain and discrete target sequences within the 3' untranslated region of the cad messenger RNA and to block the initiation of cad translation.

Structure and function of the HOX A1 human homeobox gene cDNA

Homeobox genes code for transcription factors and are arranged in clusters, named A, B, C and D, found on four separate chromosomes in vertebrates. They contain a homeobox DNA sequence which codes for the homeodomain, a region of amino acids responsible for the DNA binding exhibited by these proteins. During embryonic development, the homeobox genes are both spatially and temporally regulated. In teratocarcinoma cell cultures, homeobox genes are regulated by retinoic acid (RA). The cDNAs from the first gene in the human HOX A cluster, HOX A1 (1.6), were cloned and the nucleotide sequence of a full-length cDNA was determined. It is highly homologous to its murine counterpart. Another HOX A1 cDNA was cloned, corresponding to an alternatively spliced form. In vitro translation of the full-length cDNA clone gave rise to a protein of 36 kDa. In PA-1 human teratocarcinoma cells HOX A1 is the earliest HOX A gene to be expressed after treatment with RA. To test whether HOX A1 could function as a early regulator of other HOX A cluster genes, we cotransfected into PA-1 human teratocarcinoma cells sense and antisense HOX A1 cDNAs expressed from an SV40 promoter with a 5.4-kb RA-sensitive HOX A4 (1.4) promoter-cat reporter. We found no effect of HOX A1 on the HOX A4 promoter. However, cotransfection of HOX A5 (1.3) was able to inhibit the HOX A4 promoter activity.

Polar zippers: their role in human disease

Ascaris hemoglobin consists of eight subunits, each of which contains a C-terminal peptide with the sequence Glu-Glu-Lys-His repeated four times. When plotted on a beta-strand, this sequence leads to alternate lysines and glutamates on one side of the strand, and alternate glutamates and histidines on the other side, suggestive of a polar zipper which links the subunits together. A computer search of the protein database showed that the same or similar sequences also occur in other proteins. Some contain long repeats of Asp-Arg or Glu-Arg, among them the small nuclear ribonucleo-U1 70K protein which is an autoantigen in Systemic Lupus Erythematosis. These repeats appear to constitute the dominant epitopes in the autoimmune reaction. Single chains with Asp-Arg repeats may form alpha-helices in which alternate positively charged ridges and negatively charged grooves compensate each other. Several separate chains with Asp-Arg repeats could compensate each other's charges optimally by zipping together to beta-sheets. Several homeodomains of Drosophila as well as the human transcription factor SP1 contain repeats of glutamines. Molecular modelling, circular dichroism, electron and X-ray diffraction studies of a synthetic poly(L-glutamine) showed that it forms beta-sheets held together by hydrogen bonds between the main chain and side chain amides. Published data suggest that the function of these glutamine repeats consists in joining essential transcription factors bound to distant segments of DNA. The study of the structure and function of glutamine repeats has assumed medical importance with the discovery that Huntington's Disease and four other dominantly inherited diseases are associated with a lengthening of glutamine repeats in the proteins coded for by the affected genes.

Several splicing variants of isl-1 like genes in the chinook salmon (Oncorhynchus tschawytscha) encode truncated transcription factors containing a complete LIM domain

Several novel cDNA clones have been isolated from a chinook salmon pituitary cDNA library. Sequence analysis of these clones indicates that they are closely related to the rat LIM domain homeobox gene, isl-1. Due to differential splicing, several of the clones encode truncated polypeptides containing a complete copy of the LIM domain without the homeodomain and C-terminal activation domain. The roles of these truncated polypeptides are discussed.

Studies on transcription activation by the multimeric CCAAT-binding factor CBF

The CCAAT-binding factor CBF is a heteromeric transcription factor that specifically binds to CCAAT sequences in many eukaryotic genes. CBF consists of three subunits, CBF-A, CBF-B, and CBF-C, all three of which are necessary for DNA binding. In this study we examined the transcription activation function of CBF by two different approaches. We first used a heterologous system in which a series of deletion mutations of CBF-B, fused to the bacterial LexA DNA binding domain, were transfected into HeLa cells together with a reporter gene driven by a minimal promoter containing LexA binding sites. These experiments showed that CBF-B needed both a glutamine-rich domain and an adjacent serine/threonine-rich domain to activate the reporter gene optimally. The glutamine-rich domain by itself activated transcription only modestly. We also set up an in vitro transcription reconstituted system in which trans-activation by CBF occurred through a physiological CCAAT motif. Nuclear extracts from NIH 3T3 cells were first depleted of CBF and then complemented with recombinant CBF-B and a highly purified fraction containing native CBF-A and CBF-C. Recombinant full-length CBF-B together with CBF-A and CBF-C activated transcription of several alpha 2(I) collagen gene promoter constructs. We then tested whether in this system the glutamine- and serine/threonine-rich domains of CBF-B were needed for trans-activation by CBF. We generated a truncated form of CBF-B that was still able to bind DNA in the presence of CBF-A and CBF-C. Even in the absence of the glutamine- and serine/threonine-rich domains of CBF-B, reconstituted CBF did activate transcription, suggesting that CBF transcriptional activation can also be mediated by the other subunits of CBF or by another transcription factor present in the nuclear extracts that interacts with CBF. Taken together our results suggest a model in which CBF has the potential to activate transcription either through the glutamine- and serine/threonine-rich domains of CBF-B or through the other subunits of CBF or through another component recruited by CBF.

ovo, a Drosophila gene required for ovarian development, is specifically expressed in the germline and shares most of its coding sequences with shavenbaby, a gene involved in embryo patterning

Genetic analyses of Drosophila oogenesis have revealed the central role of ovo, a gene required for differentiation of the female germline. A number of recessive ovo mutations also affect the shavenbaby (svb) function required for late embryo patterning, suggesting a tight structural link between ovo and svb. By using various genomic probes for in situ hybridization to wild type and mutant embryos, we show that ovo indeed shares most of its coding sequences with svb. svb expression is detected early in the presumptive head region and later in each segment. It requires control elements located upstream of the ovo genomic region. ovo expresses abundant maternal RNAs which are uniformly distributed in early cleavage embryos. A fraction that lacks an alternative ovo-specific protein coding region (ORF 2b) is detected in pole cells. Expression of an ovo-specific lacZ reporter gene (ovoB) shows that ovo encodes a nuclear protein present in the germline of both sexes. Zygotic ovoB expression is first detected in embryos at around stage 17 and persists up to the adult stage. Our data show that the germline specific expression of ovo in females correlates with its function in oogenesis. This expression, however, is also observed in males in which ovo is not required.

The Drosophila homeotic mutation Nasobemia (AntpNs) and its revertants: an analysis of mutational reversion

The homeotic gene Antennapedia (Antp) controls determination of many different cell types in the thorax and abdomen of Drosophila melanogaster. The spontaneous mutant allele Nasobemia (AntpNs) and its revertants have been widely used to infer normal Antp gene function but have not themselves been thoroughly characterized. Our analysis reveals that AntpNs consists of an internal 25-kb partial duplication of the Antp gene as well as a complex insertion of > 40 kb of new DNA including two roo transposons. The duplication gives the mutant gene three Antp promoters, and transcripts from each of these are correctly processed to yield functional ANTP proteins. At least two of the promoters are ectopically active in the eye-antenna imaginal discs, leading to homeotic transformation of the adult head. A molecular and genetic description of several AntpNs revertants shows them to be diverse in structure and activity, including a restoration of the wild type, rearrangements separating two of the AntpNs promoters from the coding sequences, and protein nulls and hypomorphs affecting expression from all three of the promoters. Finally, one revertant has a suppressing lesion in the osa locus far away from Antp. These features explain the unusual homozygous viable nature of AntpNs, suggest a mechanism by which its homeotic transformation occurs, and exemplify the diversity of ways in which mutational reversion can take place.

Polar zippers: their role in human disease

Ascaris hemoglobin consists of 8 subunits, each of which contains a C-terminal peptide with the sequence Glu-Glu-Lys-His repeated 4 times. When plotted on a beta-strand, this sequence leads to alternate lysines and glutamates on one side of the strand, and alternate glutamates and histidines on the other side, suggestive of a polar zipper that links the subunits together. A computer search of the protein database showed that the same or similar sequences also occur in other proteins. Some contain long repeats of Asp-Arg or Glu-Arg, among them the small nuclear ribonucleo-U1 70K protein, which is an autoantigen in systemic lupus erythematosis. These repeats appear to constitute the dominant epitopes in the autoimmune reaction. Single chains with Asp-Arg repeats may form alpha-helices in which alternate positively charged ridges and negatively charged grooves compensate each other. Several separate chains with Asp-Arg repeats could compensate each other's charges optimally by zipping together to beta-sheets. Several homeodomains of Drosophila, as well as the human transcription factor SP1, contain repeats of glutamines. Molecular modeling, circular dichroism, and electron and X-ray diffraction studies of a synthetic poly(L-glutamine) showed that it forms beta-sheets held together by hydrogen bonds between the main-chain and side-chain amides. Published data suggest that the function of these glutamine repeats consists of joining essential transcription factors bound to distant segments of DNA.(ABSTRACT TRUNCATED AT 250 WORDS)

Dax, a locust Hox gene related to fushi-tarazu but showing no pair-rule expression

We describe an unusual Antennapedia class homeobox gene from the grasshopper Schistocerca gregaria (Orthoptera, African Plague Locust). Its sequence is not sufficiently similar to that of any other insect Hom-Hox gene to identify it unambiguously, but short conserved elements suggest a relationship to the segmentation gene fushi-tarazu, (ftz). We term it Sg Dax (divergent Antennapedia class homeobox gene). Antibodies raised against the protein encoded by this gene reveal two phases of expression during embryogenesis. In the early embryo, it is a marker for the posterior part of the forming embryonic primordium, and subsequently for the posterior part of the growing germ band. In older embryos, it labels a subset of neural precursor cells in each trunk segment, very similar to that defined by the expression of fushi tarazu (ftz) in Drosophila. We suggest that Schistocerca Dax and Drosophila ftz are homologous members of a gene family whose members are diverging relatively rapidly, both in terms of sequence and role in early development.

Transcriptional activation modulated by homopolymeric glutamine and proline stretches

Many transcription factors contain proline- or glutamine-rich activation domains. Here it is shown that simple homopolymeric stretches of these amino acids can activate transcription when fused to the DNA binding domain of GAL4 factor. In vitro, activity increased with polymer length, whereas in cell transfection assays maximal activity was achieved by 10 to 30 glutamines or about 10 prolines. Similar results were obtained when glutamine stretches were placed within a [GAL4]-VP16 chimeric protein. Because these stretches are encoded by rapidly evolving triplet repeats (microsatellites), they may be the main cause for modulation of transcription factor activity and thus result in subtle or overt genomic effects.

Mapping Polycomb-repressed domains in the bithorax complex using in vivo formaldehyde cross-linked chromatin

The Polycomb group (Pc-G) proteins are responsible for keeping developmental regulators, like homeotic genes, stably and inheritably repressed during Drosophila development. Several similarities to a protein class involved in heterochromatin formation suggest that the Pc-G exerts its function at the higher order chromatin level. Here we have mapped the distribution of the Pc protein in the homeotic bithorax complex (BX-C) of Drosophila tissue culture cells. We have elaborated a method, based on the in vivo formaldehyde cross-linking technique, that allows a substantial enrichment for Pc-interacting sites by immunoprecipitation of the cross-linked chromatin with anti-Pc antibodies. We find that the Pc protein quantitatively covers large regulatory regions of repressed BX-C genes. Conversely, we find that the Abdominal-B gene is active in these cells and the region devoid of any bound Pc protein.

Effects of transposable elements on the expression of the forked gene of Drosophila melanogaster

The products of the forked gene are involved in the formation and/or maintenance of a temporary fibrillar structure within the developing bristle rudiment of Drosophila melanogaster. Mutations in the forked locus alter this structure and result in aberrant development of macrochaetae, microchaetae and trichomes. The locus has been characterized at the molecular level by walking, mutant characterization and transcript analysis. Expression of the six forked transcripts is temporally restricted to mid-late pupal development. At this time, RNAs of 6.4, 5.6, 5.4, 2.5, 1.9 and 1.1 kilobases (kb) are detected by Northern analysis. The coding region of these RNAs has been found to be within a 21-kb stretch of genomic DNA. The amino terminus of the proteins encoded by the 5.4- and 5.6-kb forked transcripts contain tandem copies of ankyrin-like repeats that may play an important role in the function of forked-encoded products. The profile of forked RNA expression is altered in seven spontaneous mutations characterized during this study. Three forked mutations induced by the insertion of the gypsy retrotransposon contain a copy of this element inserted into an intron of the gene. In these mutants, the 5.6-, 5.4- and 2.5-kb forked mRNAs are truncated via recognition of the polyadenylation site in the 5' long terminal repeat of the gypsy retrotransposon. These results help explain the role of the forked gene in fly development and further our understanding of the role of transposable elements in mutagenesis.

Structure and chromosomal assignment of a gene encoding the major protein of rat sperm outer dense fibres

Outer dense fibres are located on the outside of the axoneme in the midpiece and principal piece of the mammalian sperm tail and may help to maintain the passive elastic structures and elastic recoil of the sperm tail. Here we describe the isolation and genomic organization of a rat gene encoding a cysteine-proline-rich outer dense fibre protein. The cDNA sequence of rts 5/1 and its expression pattern have already been published [Burfeind, P. & Hoyer-Fender, S. (1991) Dev. Biol. 148, 195-204]. There exist two different genes in the rat genome, rts 5/1 major and rts 5/1 minor. Rts 5/1 major consists of two exons interrupted by one intron of about 3.8 kb. Exon 1 and rts 5/1 minor contains a deletion of 120 bp, without destroying the open reading frame, which is flanked by short direct repeats, 15 bp in length. The first two nucleotides of the intronic sequence were identified as GA and, therefore, do not agree with the donor consensus sequence. From the analysis of mouse x rat cell hybrids, the rts 5/1 major gene has been assigned to chromosome 7. By immunoblotting and immunocytochemistry, it was demonstrated that the isolated gene encodes a major protein of rat sperm outer dense fibres.

Functional analysis of the mouse homeobox gene HoxB9 in Drosophila development

Mammalian genomes contain clusters of homeobox genes (Hox-C, HOX-C) which are structurally similar to the homeotic genes of the Drosophila HOM complex. One method for assessing the functional similarity of particular Drosophila HOM and mammalian Hox genes is to test the ability of Hox genes to induce homeotic phenotypes when expressed in developing Drosophila. Here we describe such functional tests using mouse HoxB9 (formerly Hox-2.5), whose closest structural relative in Drosophila is Abdominal-B. When expressed from a heat shock promoter, HoxB9 induces transformations of head towards more posterior identities in Drosophila larvae and adults. These transformations share some similarities with the phenotypic effects produced by ectopically expressed Abdominal-B, but are also similar to the transformations induced by Antennapedia and mouse HoxB6 (Hox-2.2), suggesting that HoxB9 specifies a positional identity that is intermediate between Antennapedia and Abdominal-B.

The mouse Hox-1.3 gene is functionally equivalent to the Drosophila Sex combs reduced gene

To test whether the mouse Hox-1.3 gene is a cognate of the Drosophila Sex combs reduced (Scr) gene, we inserted a hsp 70-Hox-1.3 fusion gene into the Drosophila genome. Transgenic flies displayed Scr-like homeotic transformations after ectopic expression of Hox-1.3 induced by heat shock. In larvae, the thoracic segments T2 and T3 are transformed toward T1. In adults, head structures are dramatically disrupted, including transformation of antenna towards leg. Transformations are not the result of ectopic activation of the endogenous Scr gene. Rather, Hox-1.3 appears to directly regulate Scr target genes, as demonstrated by the ectopic activation of fork head by Hox-1.3. The results suggest that mouse Hox-1.3 cannot only substitute functionally for Drosophila Scr in the determination of external structures but also can participate in the regulatory hierarchy of insect organogenesis.

HOM/Hox genes of Artemia: implications for the origin of insect and crustacean body plans

BACKGROUND

Insects and crustaceans are generally assumed to derive from a segmented common ancestor that had a distinct head but uniform, undifferentiated trunk segments. The subdivision of the body into functionally distinct regions (e.g. thorax and abdomen) is thought to have evolved independently in these two lineages. In insects, the differences between segments in the trunk are controlled by the Antennapedia-like genes of the homeotic gene clusters. Study of these genes in crustaceans should provide a basis for comparing body plans and assessing their evolutionary origin.

RESULTS

Using a polymerase chain reaction (PCR) / inverse PCR strategy, we have isolated six genes of the HOM/Hox family from the crustacean Artemia franciscana. Five of these are clearly identifiable as specific homologues of the insect homeotic genes Dfd, Scr, Antp, Ubx and abdA. The sixth appears to have no close counterpart in insects.

CONCLUSION

All the homeotic genes that specify middle body regions in insects originated before the divergence of the insect and crustacean lineages, probably not later than the Cambrian (about 500 million years ago). A commonly derived groundplan may underlie segment diversity in these two groups.

Expression of Cnox-2, a HOM/HOX homeobox gene in hydra, is correlated with axial pattern formation

Cnox-2 is a HOM/HOX homeobox gene that we have identified in the simple metazoan Hydra vulgaris (Cnidaria: Hydrozoa). Cnox-2 is most closely related to anterior members of the Antennapedia gene complex from Drosophila, with the greatest similarity to Deformed. The Cnox-2 protein is expressed in the epithelial cells of adult hydra polyps in a region-specific pattern along the body axis, at a low level in the head and at a high level in the body column and the foot. The expression pattern of Cnox-2 is consistent with a role in axial pattern formation. Alteration of hydra axial patterning by treatment with diacylglycerol (DAG) results in an increase of head activation down the body column and in a coordinate reduction of Cnox-2 expression in epithelial cells in ‘head-like’ regions. These results suggest that Cnox-2 expression is negatively regulated by a signaling pathway acting through protein kinase C (PKC), and that the varying levels of expression of Cnox-2 along the body axis have the potential to result in differential gene expression which is important for hydra pattern formation.

Homeotic gene Antennapedia mRNA contains 5'-noncoding sequences that confer translational initiation by internal ribosome binding

The Antennapedia (Antp) homeotic gene of Drosophila melanogaster has two promoters, P1 and P2. The resulting Antp mRNAs contain 1512-nucleotide (P1) and 1727-nucleotide (P2) 5'-noncoding regions, composed of exons A, B, D, and E (P1) or exons C, D, and E (P2), respectively. Multiple AUG codons are present in exons A, B, and C. We have found that 252-nucleotide exon D, common to mRNAs from both transcription units and devoid of AUG codons, can mediate initiation of translation by internal ribosome binding in cultured cells. Many mRNAs in Drosophila contain long 5'-noncoding regions with apparently unused AUG codons, suggesting that internal ribosome binding may be a common mechanism of translational initiation, and possibly its regulation, in Drosophila.

Clox, a mammalian homeobox gene related to Drosophila cut, encodes DNA-binding regulatory proteins differentially expressed during development

We report the isolation of a cDNA encoding a mammalian homeoprotein related to the Drosophila cut gene product, called Clox, for Cut like homeobox. In addition to the homeodomain, three 73-amino acid repeats, the so-called cut repeats, are also conserved between Cut and the mammalian counterpart described here. This conservation suggests that the cut repeat motif may define a new class of homeoproteins. Both cloned and endogenous Clox proteins are nuclear DNA-binding proteins with very similar sequence specificity. Western blot analysis revealed several distinct Clox protein species in a variety of tissues and cell types. The relative abundance of these proteins is regulated during mouse development and cell differentiation in culture. Interestingly, approximately 180–190 × 10(3) M(r) Clox proteins predominate in early embryos and are upregulated in committed myoblasts and chondrocytes, but downregulated upon terminal differentiation. Clox DNA-binding activity is correlated with the abundance of these proteins. In contrast, larger Clox protein species (approximately 230–250 × 10(3) M(r)) are detected mainly in adult tissues and in terminally differentiated cells. Cotransfection experiments show that Clox proteins can function as repressors of tissue-specific gene transcription. Thus, Clox, like their Drosophila counterparts, are candidate regulators of cell-fate specification in diverse differentiation programs.