Structure of two genes at the gooseberry locus related to the paired gene and their spatial expression during Drosophila embryogenesis

Pax-8, a paired domain-containing protein, binds to a sequence overlapping the recognition site of a homeodomain and activates transcription from two thyroid-specific promoters

The Pax-8 gene, a member of the murine family of paired box-containing genes (Pax genes), is expressed in adult thyroid and in cultured thyroid cell lines. The Pax-8 protein binds, through its paired domain, to the promoters of thyroglobulin and thyroperoxidase, genes that are exclusively expressed in the thyroid. In both promoters, the binding site of Pax-8 overlaps with that of TTF-1, a homeodomain-containing protein involved in the activation of thyroid-specific transcription. Pax-8 activates transcription from cotransfected thyroperoxidase and thyroglobulin promoters, indicating that it may be involved in the establishment, control, or maintenance of the thyroid-differentiated phenotype. Thus, the promoters of thyroglobulin and thyroperoxidase represent the first identified natural targets for transcriptional activation by a paired domain-containing protein.

Pax-8, a paired domain-containing protein, binds to a sequence overlapping the recognition site of a homeodomain and activates transcription from two thyroid-specific promoters

The Pax-8 gene, a member of the murine family of paired box-containing genes (Pax genes), is expressed in adult thyroid and in cultured thyroid cell lines. The Pax-8 protein binds, through its paired domain, to the promoters of thyroglobulin and thyroperoxidase, genes that are exclusively expressed in the thyroid. In both promoters, the binding site of Pax-8 overlaps with that of TTF-1, a homeodomain-containing protein involved in the activation of thyroid-specific transcription. Pax-8 activates transcription from cotransfected thyroperoxidase and thyroglobulin promoters, indicating that it may be involved in the establishment, control, or maintenance of the thyroid-differentiated phenotype. Thus, the promoters of thyroglobulin and thyroperoxidase represent the first identified natural targets for transcriptional activation by a paired domain-containing protein.

Pax-5 encodes the transcription factor BSAP and is expressed in B lymphocytes, the developing CNS, and adult testis

BSAP has been identified previously as a transcription factor that is expressed at early, but not late, stages of B-cell differentiation. Biochemical purification and cDNA cloning has now revealed that BSAP belongs to the family of paired domain proteins. BSAP is encoded by the Pax-5 gene and has been highly conserved between human and mouse. An intact paired domain was shown to be both necessary and sufficient for DNA binding of BSAP. Binding studies with several BSAP recognition sequences demonstrated that the sequence specificity of BSAP differs from that of the distantly related paired domain protein Pax-1. During embryogenesis, the BSAP gene is transiently expressed in the mesencephalon and spinal cord with a spatial and temporal expression pattern that is distinct from that of other Pax genes in the developing central nervous system (CNS). Later, the expression of the BSAP gene shifts to the fetal liver where it correlates with the onset of B lymphopoiesis. BSAP expression persists in B lymphocytes and is also seen in the testis of the adult mouse. All of this evidence indicates that the transcription factor BSAP may not only play an important role in B-cell differentiation but also in neural development and spermatogenesis.

Hairless, a Drosophila gene involved in neural development, encodes a novel, serine rich protein

Hairless is a dominant loss of function mutation in Drosophila affecting the formation of adult sensory organs. In the mutants, neuronal precursor cells do not differentiate, suggesting that Hairless might be involved in specifying or realizing neuronal fate in the fly, similar to the 'pro-neural' genes of the achaete-scute complex. As highlighted by the manifold phenotypic interactions of Hairless with most of the neurogenic loci, the gene might play an important role in nervous system development. Therefore, we initiated a molecular analysis of the Hairless locus in order to elucidate the function of its gene product and gain insight into the biochemical nature of the observed genetic interactions in which it participates. Here, we report the molecular cloning of the Hairless locus, confirmed by breakpoint and transformation analysis. Unexpectedly, Hairless activity peaks during embryogenesis, where transcripts accumulate primarily in endo- and mesodermal cell layers, and is lowest during larval stages, the lethal phase of Hairless mutants. The putative Hairless protein deduced from DNA sequencing is extremely basic and highly enriched in serine residues. Hairless appears to encode a novel protein without compelling homology to other known proteins which function in specifying peripheral nervous system development in Drosophila.

The homeodomain: a new face for the helix-turn-helix?

The discovery of conserved protein domains found in many Drosophila and mammalian developmental gene products suggests that fundamental developmental processes are conserved throughout evolution. Our understanding of development has been enhanced by the discovery of the widespread role of the homeodomain (HD). The action of HD-containing proteins as transcriptional regulators is mediated through a helix-turn-helix motif which confers sequence specific DNA binding. Unexpectedly, the well conserved structural homology between the HD and the prokaryotic helix-turn-helix proteins contrasts with their divergent types of physical interaction with DNA. A C-terminal extension of the HD recognition helix has assumed the role that the N-terminus of the prokaryotic helix plays for specification of DNA binding preference. However, the HD appears also capable of recognizing DNA in an alternative way and its specificity in vivo may be modified by regions outside the helix-turn-helix motif. We propose that this intrinsic complexity of the HD, as well as its frequent association with other DNA binding domains, explains the functional specificity achieved by genes encoding highly related HDs.

The Drosophila sloppy paired locus encodes two proteins involved in segmentation that show homology to mammalian transcription factors

The sloppy paired locus is involved in the establishment of the metameric body plan of the Drosophila embryo. We have cloned the sloppy paired locus by P-element-mediated enhancer detection. The locus is composed of two genes, slp1 and slp2, that are structurally and functionally related. They belong to a novel class of putative transcription factors containing a fork head domain that has also been found in mammalian hepatocyte transcription factors. The spatial expression patterns of the two transcripts are very similar, suggesting common regulation of the two genes. We recovered additional sloppy paired alleles by remobilization of an enhancer detector transposon. Genetic analysis suggests that both genes contribute to the segmentation phenotype that has characteristics of both, pair-rule and segment polarity genes, and that they interact functionally. The two genes appear to share an enhancer element situated upstream of slp1 that acts on both the proximal slp1 promoter and the distal slp2 promoter.

The paired box gene pox neuro: A determiant of poly-innervated sense organs in Drosophila

This study describes the structure and function of pox neuro (poxn), a gene previously isolated by virtue of a conserved domain, the paired box, which it shares with the segmentation genes paired and gooseberry. Its expression pattern has been analyzed, particularly during development of the PNS. We propose that poxn is a "neuroblast identity" gene acting in both the PNS and the CNS on the basis of the following evidence. Its expression is restricted to four neuronal precursors in each hemisegment: two neuronal stem cells (neuroblasts) in the CNS, and two sensory mother cells (SMCs) in the PNS. The SMCs that express poxn produce the poly-innervated external sense organs of the larva. In poxn- embryos, poly-innervated sense organs are transformed into mono-innervated. Conversely, ectopic expression of poxn in embryos transformed with a heat-inducible poxn gene can switch mono-innervated to poly-innervated sense organs. Expression of poxn in the wing disc is restricted to the SMCs of the poly-innervated sense organs, suggesting that poxn also determines the lineage of poly-innervated adult sense organs.

Molecular cloning and developmental expression of the catalytic and 65-kDa regulatory subunits of protein phosphatase 2A in Drosophila

cDNA clones encoding the catalytic subunit and the 65-kDa regulatory subunit of protein phosphatase 2A (PR65) from Drosophila melanogaster have been isolated by homology screening with the corresponding human cDNAs. The Drosophila clones were used to analyze the spatial and temporal expression of the transcripts encoding these two proteins. The Drosophila PR65 cDNA clones contained an open reading frame of 1773 nucleotides encoding a protein of 65.5 kDa. The predicted amino acid sequence showed 75 and 71% identity to the human PR65 alpha and beta isoforms, respectively. As previously reported for the mammalian PR65 isoforms, Drosophila PR65 is composed of 15 imperfect repeating units of approximately 39 amino acids. The residues contributing to this repeat structure show also the highest sequence conservation between species, indicating a functional importance for these repeats. The gene encoding Drosophila PR65 was located at 29B1,2 on the second chromosome. A major transcript of 2.8 kilobase (kb) encoding the PR65 subunit and two transcripts of 1.6 and 2.5 kb encoding the catalytic subunit could be detected throughout Drosophila development. All of these mRNAs were most abundant during early embryogenesis and were expressed at lower levels in larvae and adult flies. In situ hybridization of different developmental stages showed a colocalization of the PR65 and catalytic subunit transcripts. The mRNA expression is high in the nurse cells and oocytes, consistent with a high equally distributed expression in early embryos. In later embryonal development, the expression remains high in the nervous system and the gonads but the overall transcript levels decrease. In third instar larvae, high levels of mRNA could be observed in brain, imaginal discs, and in salivary glands. These results indicate that protein phosphatase 2A transcript levels change during development in a tissue and in a time-specific manner.

PBX2 and PBX3, new homeobox genes with extensive homology to the human proto-oncogene PBX1

Two new homeobox genes, PBX2 and PBX3, were isolated on the basis of their extensive homology to PBX1, a novel human homeobox gene involved in t(1;19) translocation in acute pre-B-cell leukemias. The predicted Pbx2 and Pbx3 proteins are 92 and 94% identical to Pbx1 over a large region of 266 amino acids within and flanking their homeodomains, but all three proteins diverge significantly near their amino and carboxy termini. Chromosome in situ hybridizations demonstrated that the PBX genes are not clustered but map to separate chromosomal loci: PBX1, 1q23; PBX2, 3q22-23; PBX3, 9q33-34. Expression of PBX2 or PBX3 was not restricted to particular states of differentiation or development, as mRNA transcripts of these genes were detected in most fetal and adult tissues and all cell lines, unlike PBX1, which is not expressed in lymphoid cell lines. Similar to PBX1 RNA, PBX3 RNA is alternatively spliced to yield two translation products with different carboxy termini, a feature not observed for PBX2. Their extensive sequence similarity and widespread expression suggest a generalized, overlapping role for Pbx proteins in most cell types. Differences in their amino and carboxy termini may modulate their activities, mediated in part by differential splicing and, for PBX1, protein fusion following t(1;19) chromosomal translocation.

Positional cloning and characterization of a paired box- and homeobox-containing gene from the aniridia region

Based on the map location of the aniridia (AN) locus in human chromosomal band 11p13, we have cloned a candidate AN cDNA (D11S812E) that is completely or partially deleted in two patients with AN. The less than 70 kb smallest region of overlap between the two deletions encompasses the 3' coding region of the cDNA. This cDNA, which spans over 50 kb of genomic DNA, detects a 2.7 kb message specifically within all tissues affected in AN. The predicted polypeptide product possesses a paired domain, a homeodomain, and a serine/threonine-rich carboxy-terminal domain, structural motifs characteristic of certain transcription factors. The concordance between expression and pathology, map location, structure, and predicted function argues that the cDNA corresponds to the AN gene.

Characterization of two Drosophila POU domain genes, related to oct-1 and oct-2, and the regulation of their expression patterns

We have characterized two genes from Drosophila melanogaster that encode proteins with POU domains showing a high degree of identity with the human Oct-1 and Oct-2 transcription factors. These POU domain genes, pdm-1 and pdm-2, are expressed at high levels during early embryogenesis and at lower levels throughout the rest of development. Both genes are expressed as two stripes in the presumptive abdominal region during the blastoderm stage, followed by thirteen stripes in the germ band extended stage. This pattern of expression is altered in mutants for a gap gene (hunchback) and a pair-rule gene (fushi tarazu). In later stage embryos, both pdm-1 and pdm-2 are expressed in selected neuroblasts in the ventral nervous system, with higher levels in the three thoracic segments and lower levels in the abdominal segments. The low level of expression in the abdominal segments is maintained by the genes within the bithorax complex (BX-C). We have also identified the cells in the dorsal and lateral clusters of the peripheral nervous system that express pdm-1 and pdm-2, and show that some of these cells derive from lineages that require BX-C functions. Together, these results suggest that previously characterized members of the embryonic regulatory hierarchy specify the patterns of the POU domain gene expression, which, in turn, function during neurogenesis and perhaps in earlier stages.

PBX2 and PBX3, new homeobox genes with extensive homology to the human proto-oncogene PBX1

Two new homeobox genes, PBX2 and PBX3, were isolated on the basis of their extensive homology to PBX1, a novel human homeobox gene involved in t(1;19) translocation in acute pre-B-cell leukemias. The predicted Pbx2 and Pbx3 proteins are 92 and 94% identical to Pbx1 over a large region of 266 amino acids within and flanking their homeodomains, but all three proteins diverge significantly near their amino and carboxy termini. Chromosome in situ hybridizations demonstrated that the PBX genes are not clustered but map to separate chromosomal loci: PBX1, 1q23; PBX2, 3q22-23; PBX3, 9q33-34. Expression of PBX2 or PBX3 was not restricted to particular states of differentiation or development, as mRNA transcripts of these genes were detected in most fetal and adult tissues and all cell lines, unlike PBX1, which is not expressed in lymphoid cell lines. Similar to PBX1 RNA, PBX3 RNA is alternatively spliced to yield two translation products with different carboxy termini, a feature not observed for PBX2. Their extensive sequence similarity and widespread expression suggest a generalized, overlapping role for Pbx proteins in most cell types. Differences in their amino and carboxy termini may modulate their activities, mediated in part by differential splicing and, for PBX1, protein fusion following t(1;19) chromosomal translocation.

Apical localization of pair-rule transcripts requires 3' sequences and limits protein diffusion in the Drosophila blastoderm embryo

The peripheral cytoplasm (periplasm) of the Drosophila blastoderm embryo is subdivided into apical and basal compartments by a layer of nuclei. We have demonstrated three classes of periplasmic transcript localization: apical, basal, and unlocalized (apical and basal), each of which depends on 3' sequences. We define 3' apical localization signals within the even-skipped, fushi tarazu, and hairy pair-rule segmentation genes and the alpha 1-tubulin and bicoid genes. 3' human alpha-globin sequences direct transcripts basally. Transcript destination depends on transcript structure, not on transcript stability or chromosomal location. Apical transcripts direct apical compartmentalization of cytoplasmic protein. We propose that apical localization of pair-rule transcripts restricts lateral protein diffusion, thereby allowing pair-rule proteins to define sharp boundaries and precise spatial domains.

The molecular basis of the undulated/Pax-1 mutation

The murine paired box gene Pax-1 has been associated with the mouse developmental mutant undulated (un), which exhibits malformations in the vertebral column. In un mice, a point mutation leading to a Gly-Ser exchange in a conserved part of the paired domain of Pax-1 is present. Here we show that Pax-1 encodes a DNA-binding protein with transcriptional activating properties. The DNA-binding specificity of the Pax-1 protein has been extensively analyzed in gel shift assays, and in conjunction with binding interference experiments, a DNA-binding core motif was defined. Comparison of the DNA-binding properties of wild-type and un Pax-1 proteins demonstrates that the Gly-Ser replacement at position 15 within the paired domain dramatically decreases the DNA-binding affinity of the un Pax-1 protein and alters its DNA-binding specificity. These results decipher the molecular basis of the un mutation.

Functional dissection of the paired segmentation gene in Drosophila embryos

An ectopic expression assay in Drosophila embryos was used to investigate the roles of pair-rule segmentation genes in the spatial regulation of the segment-polarity gene, engrailed (en). It is hypothesized that the regions of overlap in expression of two genes, paired (prd) and even-skipped (eve), define the odd-numbered en expression stripes. Consistent with this combinatorial model, ectopic expression of prd caused these en stripes to be expanded posteriorly. Surprisingly, however, ectopic expression of a prd gene with a deletion of the conserved paired box resulted in loss of these odd-numbered en stripes. This dominant negative effect is a phenocopy of en expression in prd embryos and suggests that the paired box is necessary for normal prd- function. A similar deletion of odd-numbered en stripes was also observed after ectopic expression of a chimeric fushi tarazu (ftz) gene containing a substituted prd gene homeo box; in addition, in these embryos, the even-numbered en stripes were expanded anteriorly, as observed when the unaltered ftz gene is ectopically expressed. These effects suggest that the chimeric protein may have DNA or protein targets of both the normal Ftz and Prd proteins.

Interactions between segment polarity genes and the generation of the segmental pattern in Drosophila

Although mutations in the segment polarity genes wingless, engrailed, hedgehog, gooseberry and cubitus-interruptusD all affect the region of naked cuticle within each segment of the Drosophila larva, subtle phenotypic differences suggest that these genes play different roles in segmental patterning. In this paper, the regulative interactions between these genes are analysed. They have revealed that the products of most of these genes accomplish more than one function during embryogenesis. Whereas early on a positive feed-back loop involving wg, en and hh maintains the expression of wg and en in the extremes of each parasegment, later on wg and en become independent from each other. en appears to regulate the expression of hh and ptc, while wg depends on gsb and ciD.

Segment polarity genes and cell patterning within the Drosophila body segment

The formation of complex structures in any multicellular organism requires cooperative behaviour within cell populations. Genetic and molecular analysis of pattern formation in the Drosophila embryo is providing us with new insights into the cellular basis of this process, implicating a diversity of molecules, some familiar, others novel, in intercellular communication.

The oncofetal gene Pem specifies a divergent paired class homeodomain

The polypeptide sequence predicted from the Pem oncofetal gene cDNA contains a homeodomain most closely related to the paired class. Pem, paired class member orthodenticle, and the bicoid maternal gene product homeodomains all have lysine residues at a recognition helix position implicated in DNA-binding specificity. The Pem recognition helix also has an isoleucine residue replacing an invariant asparagine residue and shares an asparagine residue at a third position with two other vertebrate homeoproteins, at least one of which binds to DNA only as a dimer.

Epithelial synthesis of tenascin at tips of growing bronchi and graded accumulation in basement membrane and mesenchyme

The extracellular matrix protein, tenascin, has been proposed as mediator in epithelial-mesenchymal interactions because of its characteristic distribution during embryogenesis. Here we compared the accumulation of tenascin and laminin in the early chicken lung bud. Laminin is deposited in the basement membrane, starting at the tips and increasing along the shafts of growing primary and secondary bronchi. In contrast, tenascin accumulation is highest in basement membranes and mesenchyme at sites where new bronchial branches are formed. By in situ hybridization, tenascin mRNA was found to be produced exclusively by the epithelium at sites of active growth of bronchial tubes.

The prospero gene specifies cell fates in the Drosophila central nervous system

The molecular mechanisms used to generate neuronal diversity are largely unknown. To identify genes controlling cell fate in the Drosophila central nervous system, we screened for mutations that alter expression of homeobox genes in the developing central nervous system (indicating changes in cell fates). We also screened "enhancer trap" lines to identify genes expressed in neuronal stem cells (neuroblasts). The prospero gene was discovered in both screens. prospero is expressed in a subset of neuroblasts, sensory neuron precursors, and identified glial precursors. It is not expressed in neurons. Neuroblasts lacking prospero function generate abnormal cell lineages, producing incorrectly specified progeny that differentiate into neurons showing axon pathfinding defects. prospero is therefore a novel type of gene expressed in neuroblasts and known to specify neuronal fate.

The paired box encodes a second DNA-binding domain in the paired homeo domain protein

The homeo box, which encodes the DNA-binding homeo domain, is a DNA sequence motif present in several Drosophila developmental genes; it has been used to identify many homologous genes involved in mammalian development. The paired box is another conserved sequence motif, first identified in the paired (prd) and gooseberry (gsb) Drosophila homeo domain genes. It encodes a 128-amino-acid domain, the paired domain, which has since been found in other fly and mouse gene products, in association with the homeo domain or in its absence. We show that the paired box of the prd gene encodes a DNA-binding activity, independent of the DNA-binding activity of the Paired (Prd) homeo domain and with a different sequence specificity. The amino-terminal region of the paired domain, including one of the three predicted alpha-helices, is necessary and sufficient for binding. We investigate the binding of the Prd protein to two sites in the even-skipped promoter, which are composed of overlapping sequences bound by the homeo domain and by the paired domain. We also show that a mutation in the paired box of Prd, corresponding to the mutation in the paired box of the mouse Pax-1 gene thought to cause the undulated skeletal phenotype, destroys the ability of the Prd protein to bind to the paired domain-specific site. This supports the view that the undulated phenotype results from the inactivation of the DNA-binding activity of the paired domain of Pax-1.

The segment polarity gene armadillo encodes a functionally modular protein that is the Drosophila homolog of human plakoglobin

The Drosophila segment polarity gene armadillo is required for pattern formation within embryonic segments and imaginal discs. We have found that armadillo is highly conserved during evolution; it is 63% identical to human plakoglobin, a protein found in adhesive junctions joining epithelial and other cells. We have examined arm protein localization in a number of larval tissues and found that arm protein accumulation within cells shares many features with the accumulation of plakoglobin. We have compared the phenotype and molecular lesions responsible for the different arm mutations. Surprisingly, severely truncated proteins retain some function; the degree of function is strictly correlated with the length of the truncated protein, suggesting that the internally repetitive arm protein is modular in function. We present a possible model for the cellular role of arm.

Network of interactions among pair-rule genes regulating paired expression during primordial segmentation of Drosophila

A model of the trans-regulation of the Drosophila pair-rule segmentation gene, paired (prd), has been derived from the observed alterations in the distribution of prd transcripts during early embryogenesis in single and double pair-rule mutants. Important aspects of the model include the following features and implications: (i) The regulation of prd is subject to a regulatory hierarchy among pair-rule genes. In particular, it shows that prd is at the bottom of this hierarchy, mediating the transition from pair-rule to segment-polarity genes. The transition of the early 'pair-rule' to the 'segment-polarity' pattern of prd expression is regulated by the secondary pair-rule genes opa and odd. The model predicts the distributions of pair-rule gene products regulating prd at late syncytial blastoderm, e.g., that of opa. (ii) The initial activation of prd is independent of pair-rule genes. (iii) The regulation of prd is combinatorial and hence probably cooperative. Combination of one pair-rule gene product with different pair-rule proteins may lead to opposite regulatory effects on prd. Furthermore, we discuss a two-step conversion of the initial analogue specification of position along the anteroposterior axis into a digital code specified by combinations of active segment-polarity and homeotic genes.

The murine paired box gene, Pax7, is expressed specifically during the development of the nervous and muscular system

Eight murine paired box-containing (Pax) genes have been isolated so far. The gene described here, Pax7, contains not only a paired box, but also an octapeptide and a paired-type homeobox. As shown by Northern and in situ analysis, Pax7 is expressed from day 8 to 17 p.c. during embryogenesis. At early stages Pax7 transcripts are present in a subset of cells throughout the entire brain, but later in development expression is limited to the mesencephalon. In the developing neural tube Pax7 is restricted to the dorsal ventricular zone along the entire antero-posterior axis, suggesting a role for Pax7 in the formation of certain parts of the CNS. Additionally Pax7 expression can be followed during myogenesis from the dermamyotome of the somites to the skeletal muscle tissues.

Homeobox containing genes in the nematode Caenorhabditis elegans

We designed a unique 36-mer oligonucleotide probe, based on the most highly conserved amino acid sequences of Antennapedia-like homeodomains and the codon bias of Caenorhabditis elegans. This probe was then used to isolate four classes of genes from a C. elegans genomic library. Sequencing reveals that we have isolated three new homeobox genes, designated ceh-1, ceh-9 and ceh-10. The fourth homeobox gene, ceh-11, has recently been described by Schaller et al (Nucleic Acids Res. 18, 2033-2036). The amino acid sequence of ceh-1 is 87% similar to the honeybee H40 homeodomain, 85% similar to the Drosophila NK-1 homeodomain and 82% similar to the chicken CHox3 homeodomain. The sequence ceh-10 appears to be a member of the paired class of homeodomains. The other two sequences, ceh-9 and ceh-11, remain unclassified. Three of the four sequences have at least one intron within the homeobox region. Transcripts of ceh-10 and ceh-11 are present in embryonic RNA but are greatly diminished in later developmental stages. Three of the four new genes have been placed on the C. elegans genomic map.

An early embryonic product of the gene shaggy encodes a serine/threonine protein kinase related to the CDC28/cdc2+ subfamily

The product(s) of the gene shaggy (sgg) is required for seemingly unrelated events during the development of Drosophila melanogaster. In embryos, maternal and zygotically derived sgg products are required initially to construct a normal syncytial blastoderm and later for normal segmentation. Furthermore, in mutant animals a process of intercellular communication that is required for the segregation of the neural and epidermal lineage during the formation of the central nervous system and the adult peripheral nervous system is disrupted. Here we describe a transcription unit of approximately 40 kb lying within the cloned chromosomal interval 3B1, and provide evidence that it encodes the sgg+ function. Of seven developmentally regulated transcripts that are partially generated by alternative splicing, two seem to be responsible for early sgg activity. Sequence analysis of corresponding cDNA(s) predicts a protein of 514 amino acids with a canonical catalytic domain found in serine/threonine specific protein kinases, linked to an unusual region rich in Gly, Ala and Ser. A search for homologies as well as a comparative study of the kinase catalytic domain with that of other proteins, revealed that the protein kinase domain of sgg is distantly related to the members of the CDC28/cdc2+ subfamily of protein kinases, all of which play cardinal roles in the regulation of the yeast and mammalian cell cycles. Ubiquitous expression of sgg transcripts was found during embryonic stages. A possible role of the sgg protein in a signal transduction pathway necessary for intercellular communication at different stages of development is discussed.

Cloning and characterization of the segment polarity gene cubitus interruptus Dominant of Drosophila

The segment polarity mutation, cubitus interruptus Dominant (ciD), of Drosophila melanogaster causes defects in the posterior half of every embryonic segment. We cloned sequences from the ciD region on the proximal fourth chromosome by "tagging" the gene with the transposable element P. Genetic and molecular evidence indicates that the P-element insertions, which all occurred within the same restriction fragment, are in 5'-regulatory regions of the ciD gene within 3 kb of the first exon of its transcript. The putative ciD transcript was identified on the basis of its absence in homozygous ciD embryos. Its spatial pattern of expression during development is unusual in that, unlike most other segmentation genes, it exhibits uniform expression throughout cellular blastoderm and gastrulation and does not resolve into a periodic pattern until the end of the fast phase of germ-band elongation when it is present in 15 broad segmentally repeating stripes along the anterior-posterior axis of the embryo. Registration of the ciD stripes of expression relative to the stripes of other segment polarity genes shows that ciD is expressed in the anterior three-quarters of every segment. This registration does not correlate with the pattern defects observed in ciD mutants. Sequence analysis indicates that the protein encoded by the ciD transcript contains a domain of five tandem amino acid repeats that have sequence similarity to the zinc-finger repeats of the Xenopus transcription factor TFIIIA and that share the highest degree of identity with the human zinc-finger protein GLI, which has been found to be amplified in several human glioblastomas.

The Drosophila patched gene encodes a putative membrane protein required for segmental patterning

The patched (ptc) gene is one of several segment polarity genes required for correct patterning within every segment of Drosophila. The absence of ptc gene function causes a transformation of the fate of cells in the middle part of each segment so that they form pattern elements characteristic of cells positioned around the segment border. Analysis of the mutant phenotype demonstrates that both segment and parasegment borders are included in the duplicated pattern of ptc mutants. We have cloned the ptc gene and deduced that the product is a 1286 amino acid protein with at least seven putative transmembrane alpha helices. ptc RNA is expressed in embryos in broad stripes of segmental periodicity that later split into two stripes per segment primordium. The pattern of expression does not directly predict the transformation seen in ptc mutant embryos, suggesting that ptc participates in cell interactions that establish pattern within the segment.

Isolation of two tissue-specific Drosophila paired box genes, Pox meso and Pox neuro

Two new paired domain genes of Drosophila, Pox meso and Pox neuro, are described. In contrast to the previously isolated paired domain genes, paired and gooseberry, which contain both a paired and a homeo-domain (PHox genes), Pox meso and Pox neuro possess no homeodomain. Evidence suggesting that the new genes encode tissue-specific transcriptional factors and belong to the same regulatory cascade as the other paired domain genes includes (i) tissue-specific expression of Pox meso in the somatic mesoderm and of Pox neuro in the central and peripheral nervous system, (ii) nuclear localization of their proteins, (iii) dependence on prd activity and (iv) presence of the paired domain in genes of known regulatory activity. While no mutant phenotypes of Pox meso and Pox neuro have yet been discovered, a murine gene with a paired domain closely homologous to that of Pox meso has recently been identified with the undulated mutant. Both Pox meso and undulated are expressed in tissues derived from the somatic mesoderm. The five known Drosophila paired domains fall into three classes: (i) the prd,gsb-class, (ii) the Pox meso, undulated-class and (iii) the Pox neuro-class which probably includes the paired domain of the murine gene Pax 2.

A protein with several possible membrane-spanning domains encoded by the Drosophila segment polarity gene patched

The patterning of cells in insect segments requires the exchange of information between cells, which in Drosophila depends on the activity of members of the segment-polarity class of genes. Here we report the molecular characterization of one such gene, patched. We find that patched encodes a large protein with several possible membrane-spanning domains and is expressed in a complex pattern during embryogenesis.

Drosophila NK-homeobox genes

Four Drosophila melanogaster homeobox genes were found by screening a genomic DNA library with oligodeoxynucleotides that correspond to a conserved amino acid sequence that is part of the putative of homeobox proteins that recognizes nucleotide sequences in DNA. The amino acid sequences of NK-2, NK-3, and NK-4 homeoboxes are more closely related to one another (59-66% homology) than they are to other Drosophila homeoboxes (28-54% homology), whereas the homeobox of NK-1 is most closely related, in order of decreasing homology, to muscle segment homeobox, zerknüllt-1, NK-3, and distal-less homeoboxes. Three of the genes, NK-1, NK-3, and NK-4, comprise a cluster of homeobox genes located in the 93E1-5 region of the right arm of the third chromosome, whereas the fourth homeobox gene, NK-2, is located in the 1C1-5 region of the X chromosome.

Searching for pattern and mutation in the Drosophila genome with a P-lacZ vector

A P-element vector has been constructed and used to generate lines of flies with single autosomal P-element insertions. The lines were analyzed in two ways: (1) the identification of cis-acting patterning information within the Drosophila genome, as revealed by a lacZ reporter gene within the P element, and (2) the isolation of lethal mutations. We examined 3768 independent lines for the expression of lacZ in embryos and looked among these lines for lethal mutations affecting embryonic neurogenesis. This type of screen appears to be an effective way to find new loci that may play a role in the development of the Drosophila nervous system.

The role of segment polarity genes during Drosophila neurogenesis

Segment polarity genes in Drosophila are required for the proper formation of epidermal pattern within each segment. Here we show that certain segment polarity genes are also critical for the determination of specific neuronal identities in the developing central nervous system (CNS) of the Drosophila embryo. For several mutants, however, the pattern defects do not simply parallel their cuticular phenotypes. In fused, armadillo, and cubitus interruptus Dominant mutants, much of the CNS appears relatively normal. In hedgehog mutants, the CNS is highly disorganized, but this disruption may occur secondary to the initial events of neurogenesis. The specific cellular defects in patched mutants suggests that this gene specifies a subset of neuroblasts and neural progeny underlying the region of epidermal pattern defect. gooseberry mutants display a complex series of alterations in neuronal identity both underlying and outside of the region of epidermal modification. Neuronal identities of a set of cells along the midline appear to be changed in Cell mutants. The phenotype of wingless mutants is the most restricted and may be due to improper communication between sibling neurons. Thus, in addition to their functions in epidermal pattern formation, at least four of the segment polarity genes (gooseberry, patched, Cell, and wingless) appear to have specific roles in the control of cell fates during neurogenesis.

The homeotic gene fork head encodes a nuclear protein and is expressed in the terminal regions of the Drosophila embryo

The region-specific homeotic gene fork head (fkh) promotes terminal as opposed to segmental development in the Drosophila embryo. We have cloned the fkh region by chromosomal walking. P element-mediated germ-line transformation and sequence comparison of wild-type and mutant alleles identify the fkh gene within the cloned region. fkh is expressed in the early embryo in the two terminal domains that are homeotically transformed in fkh mutant embryos. The nuclear localization of the fkh protein suggests that fkh regulates the transcription of other, subordinate, genes. The fkh gene product, however, does not contain a known protein motif, such as the homeodomain or the zinc fingers, nor is it similar in sequence to any other known protein.

SPXX, a frequent sequence motif in gene regulatory proteins

A new DNA-binding unit, composed of four amino acid residues and common in gene regulatory proteins, is proposed. The occurrences of the sequences Ser-Pro-X-X (SPXX) and Thr-Pro-X-X (TPXX) in gene regulatory proteins are compared with those in general proteins. These sequences are found more frequently in gene regulatory proteins including homoeotic gene products, segmentation gene products, steroid hormone receptors and certain oncogene products, than they are in DNA-binding proteins that are not directly involved in gene regulation, such as the core histones, or in general proteins. It is therefore suggested that these sequences contribute to DNA-binding in a manner important for gene regulation. Amino acid residues characteristic of the types of proteins are found as the variable residues X: basic residues, Lys and Arg, in histones, H1 and sea urchin spermatogenous H2B; Tyr in RNA polymerase II; and Ser, Thr, Ala, Leu and Pro in other gene regulatory proteins S(T)PXX sequences are located on either side of other DNA-recognizing units such as Zn fingers, helix-turn-helices, and cores of histones. The structure of a S(T)PXX sequence is presumed to be a beta-turn I stabilized by two hydrogen bonds, and its potential mode of DNA-binding is discussed.

Conservation of the paired domain in metazoans and its structure in three isolated human genes

Sequences homologous to the paired domain of Drosophila melanogaster have been conserved in species as distantly related as nematodes, sea urchins, or man. In particular, paired domains of three human genes, HuP1, HuP2 and HuP48, have been isolated and sequenced. Together with four Drosophila paired domains, they fall into two separate paired domain classes named according to their Drosophila members, paired--gooseberry and P29 class. The P29 class includes the mouse Pax 1 and the human HuP48 gene which are nearly identical in their sequenced portions and hence might be true homologues. In addition to the paired domain, the two human genes HuP1 and HuP2 share the highly conserved octapeptide HSIAGILG with the two gooseberry genes of Drosophila. Possible functions of the paired domain are discussed in the light of a predicted helix-turn-helix structure in its carboxy-terminal portion.

Isolation, structure, and expression of labial, a homeotic gene of the Antennapedia Complex involved in Drosophila head development

The labial (lab) gene of Drosophila melanogaster is necessary for the proper development of the embryonic (larval) and adult head. We have identified the lab transcription unit within the proximal portion of the Antennapedia Complex (ANT-C) by mapping the molecular lesions associated with chromosomally rearranged lab alleles. We present its molecular structure, nucleotide sequence, and temporal pattern of expression. In addition, using antibodies generated against a fusion protein, we show that in the embryo the lab protein is distributed in neural and epidermal cells of the procephalic lobe; in a discrete loop of the midgut; and in specific progenitor sensory cells of the clypeolabrum, thoracic segments, and tail region. The regions of lab expression in the developing cephalon represent nonsegmented domains that are anterior to and largely nonoverlapping with the domains of expression of the Deformed (Dfd) and proboscipedia (pb) genes, two other homeotic loci of the ANT-C that also function to direct the development of head structures. Furthermore, lab head expression is associated with the complex cellular movements of head involution, a process that not only is defective in lab embryos, but the failure of which appears to be largely responsible for the defects observed in mutant embryos. Finally, we suggest that lab head expression provides a molecular marker for an intercalary segment, an ancestral segment that has become morphologically indistinct during the evolution of the insect head.

Progressively restricted expression of a homeo box gene within the aboral ectoderm of developing sea urchin embryos

A homeo box-containing gene, Hbox1 is expressed in an unusual and highly conserved spatial pattern in embryos of two different species of sea urchin, Tripneustes gratilla and Strongylocentrotus purpuratus. Hybridization in situ shows that this mRNA accumulates initially throughout the aboral ectoderm; however, between blastula and pluteus stages, the region containing Hbox1 mRNA retracts gradually until only a small area around the vertex is labeled in pluteus larvae. Aboral ectoderm appears cytologically uniform and also accumulates uniform levels of other tissue-specific mRNAs. Therefore, the Hbox1 pattern reveals a previously unsuspected heterogeneity of aboral ectoderm cells and a polarity within this tissue. In S. purpuratus, the Hbox1 gene product probably is not involved in initial specification of cell fate, as this message does not achieve a significant fraction of its peak abundance until almost hatching blastula stage, well after the time aboral ectoderm cells have initiated a tissue-specific program of gene expression. RNA blot and RNase protection analyses revealed low levels of Hbox1 mRNA in all adult tissues examined. However, this message was not detectable in mature eggs, suggesting that the Hbox1 gene does not have a maternal function. In addition to highly conserved spatial and temporal patterns of expression, the homeo box genes of these two urchin species also are conserved highly in sequences outside the homeo domain, despite the divergence of these two species (30-45 my). Two notable features of the protein shared with several vertebrate homeo proteins are a short conserved sequence encoded by an exon upstream of that encoding the homeo domain and a large region of high serine and proline content.

Molecular analysis of the armadillo locus: uniformly distributed transcripts and a protein with novel internal repeats are associated with a Drosophila segment polarity gene

During Drosophila embryogenesis, the segment polarity genes are required for the formation of specific pattern domains within each segment. Mutations in the armadillo (arm) gene primarily affect the posterior part of the segment and lead to the production of anterior structures within this region. To examine the molecular basis for these effects, we have cloned the arm region and identified the gene by germ-line transformation. The arm gene produces two types of very abundant 3.2-kb transcripts that differ only in their first exons. These RNAs appear to be formed by independent transcriptional initiation but have similar patterns of expression throughout development. Both arm transcripts are present in virtually all of the cell types contained in embryos, third-instar larvae, and adult ovaries, suggesting that arm may be required in all cells. In addition, the arm transcripts are uniformly distributed in embryonic segments, so the regional pattern defects associated with its embryonic phenotype may result from interactions between arm and other localized factors. Both arm RNAs encode the same 91-kD polypeptide. This protein has no probable secretory or membrane-spanning regions and contains a series of novel internal repeats that are conserved in sequence, length, and spacing. Considering these results and previous genetic observations, we discuss potential roles for the arm gene in pattern formation processes.

The C. elegans cell lineage and differentiation gene unc-86 encodes a protein with a homeodomain and extended similarity to transcription factors

Mutations in the gene unc-86 affect development of the nematode C. elegans by altering cell lineages and cell differentiation. We molecularly cloned unc-86 by chromosomal walking from linked polymorphic genetic loci, and identified the gene by locating polymorphisms specific for unc-86 alleles. A transcript containing a 467 amino acid open reading frame was inferred from the DNA sequence of a genomic clone. The unc-86 transcript encodes a protein containing a 158 amino acid sequence, referred to as the pou ("pow") domain, which is strikingly similar to sequences found in three mammalian transcription factors. Within this conserved region, there is a homeodomain related to but distinct from homeodomains previously identified in Drosophila and other organisms. These findings suggest that unc-86 encodes a transcription factor, and that the related mammalian transcription factors may function to control cell fates and cell differentiation.

Requirements for hedgehog, a segmental polarity gene, in patterning larval and adult cuticle of Drosophila

Mutations of the hedgehog gene are generally embryonic lethal, resulting in a lawn of denticles on the ventral surface. In strong alleles, no segmentation is obvious and the anteroposterior polarity of ventral denticles is lost. Temperature shift analysis of a temperature-sensitive allele indicates an embryonic activity period for hedgehog between 2.5 and 6 hr of embryonic development (at 25 degrees) and a larval/pupal period from 4 to 7 days of development (at 25 degrees). Mosaic analysis of hedgehog mutations in the adult cuticle indicates a series of defined defects associated with the failure of appropriate hedgehog expression. In particular, defects in the distal portions of the legs and antenna occur in association with homozygous hedgehog clones in the posterior compartment of those structures. Because the defects are associated with homozygous clones, but are not co-extensive, a type of "domineering" nonautonomy is proposed for the activity of the hedgehog gene.