A complex genetic locus that controls of the first three steps of pyrimidine biosynthesis in Drosophila

Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase

The catalytic activities of enzymes can be described using Gene Ontology (GO) terms and Enzyme Commission (EC) numbers. These annotations are available from numerous biological databases and are routinely accessed by researchers and bioinformaticians to direct their work. However, enzyme data may not be congruent between different resources, while the origin, quality and genomic coverage of these data within any one resource are often unclear. GO/EC annotations are assigned either manually by expert curators or inferred computationally, and there is potential for errors in both types of annotation. If such errors remain unchecked, false positive annotations may be propagated across multiple resources, significantly degrading the quality and usefulness of these data. Similarly, the absence of annotations (false negatives) from any one resource can lead to incorrect inferences or conclusions. We are systematically reviewing and enhancing the functional annotation of the enzymes of Drosophila melanogaster, focusing on improvements within the FlyBase (www.flybase.org) database. We have reviewed four major enzyme groups to date: oxidoreductases, lyases, isomerases and ligases. Herein, we describe our review workflow, the improvement in the quality and coverage of enzyme annotations within FlyBase and the wider impact of our work on other related databases.

Metabolomic Studies in Drosophila

Metabolomic analysis provides a powerful new tool for studies of Drosophila physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in Drosophila, often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in Drosophila and highlight new directions for future research.

Interactions between enhancer of rudimentary and Notch and deltex reveal a regulatory function of enhancer of rudimentary in the Notch signaling pathway in Drosophila melanogaster

Enhancer of rudimentary, e(r), encodes a small nuclear protein, ER, that has been implicated in the regulation of pyrimidine metabolism, DNA replication, and cell proliferation. In Drosophila melanogaster, a new recessive Notch allele, N (nd-p) , was isolated as a lethal in combination with an e(r) allele, e(r) (p2) . Both mutants are viable as single mutants. N (nd-p) is caused by a P-element insertion in the 5' UTR, 378-bp upstream of the start of translation. Together the molecular and genetic data argue that N (nd-p) is a hypomorphic allele of N. The three viable notchoid alleles, N (nd-p) , N (nd-1) , and N (nd-3) , are lethal in combination with e(r) (-) alleles. Our present hypothesis is that e(r) is a positive regulator of the Notch signaling pathway and that the lethality of the N e(r) double mutants is caused by a reduction in the expression of the pathway. This is supported by the rescue of the lethality by a mutation in Hairless, a negative regulator of N, and by the synthetic lethality of dx e(r) double mutants. Further support for the hypothesis is a reduction in E(spl) expression in an e(r) (-) mutant. Immunostaining localizes ER to the nucleus, suggesting a nuclear function for ER. A role in the Notch signaling pathway, suggests that e(r) may be expressed in the nervous system. This turns out to be the case, as immunostaining of ER shows that ER is localized to the developing CNS.

Zebrafish mutations in gart and paics identify crucial roles for de novo purine synthesis in vertebrate pigmentation and ocular development

Although purines and purinergic signaling are crucial for numerous biochemical and cellular processes, their functions during vertebrate embryonic development have not been well characterized. We analyze two recessive zebrafish mutations that affect de novo purine synthesis, gart and paics. gart encodes phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamide synthetase, phosphoribosylaminoimidazole synthetase, a trifunctional enzyme that catalyzes steps 2, 3 and 5 of inosine monophosphate (IMP) synthesis. paics encodes phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazole succinocarboxamide synthetase, a bifunctional enzyme that catalyzes steps 6 and 7 of this process. Zygotic gart and paics mutants have pigmentation defects in which xanthophore and iridophore pigmentation is almost completely absent, and melanin-derived pigmentation is significantly decreased, even though pigment cells are present in normal amounts and distributions. Zygotic gart and paics mutants are also microphthalmic, resulting from defects in cell cycle exit of proliferative retinoblasts within the developing eye. Maternal-zygotic and maternal-effect mutants demonstrate a crucial requirement for maternally derived gart and paics; these mutants show more severe developmental defects than their zygotic counterparts. Pigmentation and eye growth phenotypes in zygotic gart and paics mutants can be ascribed to separable biosynthetic pathways: pigmentation defects and microphthalmia result from deficiencies in a GTP synthesis pathway and an ATP synthesis pathway, respectively. In the absence of ATP pathway activity, S phase of proliferative retinoblasts is prolonged and cell cycle exit is compromised, which results in microphthalmia. These results demonstrate crucial maternal and zygotic requirements for de novo purine synthesis during vertebrate embryonic development, and identify independent functions for ATP and GTP pathways in mediating eye growth and pigmentation, respectively.

Regulation of the Drosophila melanogaster protein, enhancer of rudimentary, by casein kinase II

The Drosophila melanogaster gene enhancer of rudimentary, e(r), encodes a conserved protein, ER. Most ER homologs share two casein kinase II (CKII) target sites. In D. melanogaster, these sites are T18 and S24. A third CKII site, T63, has been seen only in drosophilids. The conservation of these CKII sites, particularly T18 and S24, suggests a role for these residues in the function of the protein. To test this hypothesis, these positions were mutated either to alanine as a nonphosphorylated mimic or to glutamic acid as a phosphorylated mimic. The mutations were tested individually or in double or triple combinations for their ability to rescue either a wing truncation characteristic of the genotype e(r)(p1) r(hd1-12) or the synthetic lethal interaction between e(r)(p2) and the Notch allele N(nd-p). All of the substitutions as single mutations rescued both mutant phenotypes, arguing that individually the phosphorylation of the three residues does not affect ER activity. The double mutants T18A-S24A and T18E-S24E and the triple mutants T18A-S24A-T63A and T18E-S24E-T63E failed to rescue. Together the data support the following model for the regulation of ER by CKII. ER that is unphosphorylated at both T18A and S24 is inactive. CKII activates ER by phosphorylating either T18 or S24. Further phosphorylation to produce the doubly phosphorylated protein inactivates ER.

C. elegans pharyngeal morphogenesis requires both de novo synthesis of pyrimidines and synthesis of heparan sulfate proteoglycans

The C. elegans pharynx undergoes elongation and morphogenesis to its characteristic bi-lobed shape between the 2- and 3-fold stages of embryogenesis. During this period, the pharyngeal muscles and marginal cells forming the isthmus between the anterior and posterior pharyngeal bulbs elongate and narrow. We have identified the spontaneous mutant pyr-1(cu8) exhibiting defective pharyngeal isthmus elongation, cytoskeletal organization defects, and maternal effect lethality. pyr-1 encodes CAD, a trifunctional enzyme required for de novo pyrimidine synthesis, and pyr-1(cu8) mutants are rescued by supplying exogenous pyrimidines. Similar pharyngeal defects and maternal effect lethality were found in sqv-1, sqv-8, rib-1 and rib-2 mutants, which affect enzymes involved in heparan sulfate proteoglycan (HSPG) synthesis. rib-1 mutant lethality was enhanced in a pyr-1 mutant background, indicating that HSPG synthesis is very sensitive to decreased pyrimidine pools, and HS disaccharides are moderately decreased in both rib-1 and pyr-1 mutants. We hypothesize that HSPGs are necessary for pharyngeal isthmus elongation, and pyr-1 functions upstream of proteoglycan synthesizing enzymes by providing precursors of UDP-sugars essential for HSPG synthesis.

ATM activation and its recruitment to damaged DNA require binding to the C terminus of Nbs1

ATM has a central role in controlling the cellular responses to DNA damage. It and other phosphoinositide 3-kinase-related kinases (PIKKs) have giant helical HEAT repeat domains in their amino-terminal regions. The functions of these domains in PIKKs are not well understood. ATM activation in response to DNA damage appears to be regulated by the Mre11-Rad50-Nbs1 (MRN) complex, although the exact functional relationship between the MRN complex and ATM is uncertain. Here we show that two pairs of HEAT repeats in fission yeast ATM (Tel1) interact with an FXF/Y motif at the C terminus of Nbs1. This interaction resembles nucleoporin FXFG motif binding to HEAT repeats in importin-beta. Budding yeast Nbs1 (Xrs2) appears to have two FXF/Y motifs that interact with Tel1 (ATM). In Xenopus egg extracts, the C terminus of Nbs1 recruits ATM to damaged DNA, where it is subsequently autophosphorylated. This interaction is essential for ATM activation. A C-terminal 147-amino-acid fragment of Nbs1 that has the Mre11- and ATM-binding domains can restore ATM activation in an Nbs1-depleted extract. We conclude that an interaction between specific HEAT repeats in ATM and the C-terminal FXF/Y domain of Nbs1 is essential for ATM activation. We propose that conformational changes in the MRN complex that occur upon binding to damaged DNA are transmitted through the FXF/Y-HEAT interface to activate ATM. This interaction also retains active ATM at sites of DNA damage.

Overproduction, purification, crystallization and preliminary X-ray diffraction studies of the human transcription repressor ERH

The human gene coding for the enhancer of rudimentary homologue (ERH) protein was overexpressed in Escherichia coli. The ERH protein was purified by anion-exchange, hydrophobic interaction and gel-filtration chromatography. Well diffracting single crystals were obtained by the vapour-diffusion method in hanging drops. The crystals belong to the trigonal space group P3(1)21 or its enantiomorph P3(2)21, with unit-cell parameters a = b = 53.74, c = 67.45 A, alpha = beta = 90, gamma = 120 degrees. They diffract to at least 1.75 A. A selenomethionine derivative of the protein was prepared and crystallized for multiwavelength anomalous diffraction (MAD) phasing.

Mutual correction of faulty PCNA subunits in temperature-sensitive lethal mus209 mutants of Drosophila melanogaster

Proliferating cell nuclear antigen (PCNA) functions in DNA replication as a processivity factor for polymerases delta and epsilon, and in multiple DNA repair processes. We describe two temperature-sensitive lethal alleles (mus209(B1) and mus209(2735)) of the Drosophila PCNA gene that, at temperatures permissive for growth, result in hypersensitivity to DNA-damaging agents, suppression of position-effect variegation, and female sterility in which ovaries are underdeveloped and do not produce eggs. We show by mosaic analysis that the sterility of mus209(B1) is partly due to a failure of germ-line cells to proliferate. Strikingly, mus209(B1) and mus209(2735) interact to restore partial fertility to heteroallelic females, revealing additional roles for PCNA in ovarian development, meiotic recombination, and embryogenesis. We further show that, although mus209(B1) and mus209(2735) homozygotes are each defective in repair of transposase-induced DNA double-strand breaks in somatic cells, this defect is substantially reversed in the heteroallelic mutant genotype. These novel mutations map to adjacent sites on the three-dimensional structure of PCNA, which was unexpected in the context of this observed interallelic complementation. These mutations, as well as four others we describe, reveal new relationships between the structure and function of PCNA.

A mutation that uncouples allosteric regulation of carbamyl phosphate synthetase in Drosophila

In animals, UTP feedback inhibition of carbamyl phosphate synthetase II (CPSase) controls pyrimidine biosynthesis. Suppressor of black (Su(b) or rSu(b)) mutants of Drosophila melanogaster have elevated pyrimidine pools, and this mutation has been mapped to the rudimentary locus. We report that rSu(b) is a missense mutation resulting in a glutamate to lysine substitution within the second ATP binding site (i.e. CPS.B2 domain) of CPSase. This residue corresponds to Glu780 in the Escherichia coli enzyme (Glu1153 in hamster CAD) and is universally conserved among CPSases. When a transgene expressing the Glu-->Lys substitution was introduced into Drosophila lines homozygous for the black mutation, the resulting flies exhibited the Su(b) phenotype. Partially purified CPSase from rSu(b) and transgenic flies carrying this substitution exhibited a dramatic reduction in UTP feedback inhibition. The slight UTP inhibition observed with the Su(b) enzyme in vitro was due mainly to chelation of Mg2+ by UTP. However, the Km values for glutamate, bicarbonate, and ATP obtained from the Su(b) enzyme were not significantly different from wild-type values. From these experiments, we conclude that this residue plays an essential role in the UTP allosteric response, probably in propagating the response between the effector binding site and the ATP binding site. This is the first CPSase mutation found to abolish feedback inhibition without significantly affecting other enzyme catalytic parameters.

Modifier of rudimentary p1, mod(r)p1, a trans-acting regulatory mutation of rudimentary

Modifier of rudimentaryp1 (mod(r)p1) is a hybrid dysgenesis-induced mutation isolated as a suppressor of rhd1, a hypomorphic rudimentary(r) allele in Drosophila melanogaster.mod(r)p1 has opposite effects on two of the rudimentary mutant phenotypes. It suppresses the wing truncation associated with hypomorphic r alleles, which was the phenotype used to isolate it. On the other hand, it does not suppress the sterility of r females and in fact decreases the fertility of wild-type females. This infertility is associated with a drastic decrease in r expression in mod(r)p1 females. P elementagging was used to clone the mutant allele, mod(r)p1. Subsequently, 28 kb of genomic DNA encompassing the wild-type mod(r) gene in the chromosomal region 1B was cloned. mod(r) encodes a 1.3 kb transcript which is not detected in the mod(r)p1 mutant. The sequences of mod(r) cDNA clones reveal that the gene encodes a protein of 200 amino acids in length. When compared to sequences in GenBank, the amino acid sequence did not reveal any long sequences similarities. However, the structure of the protein reveals similarities to known transcription factors. The N-terminal half of the protein is very acidic, whereas the C-terminal half is basic. The basic domain suggests a possible DNA-binding domain, while the acidic domain suggests a transcriptional activation domain. Consistent with this possibility is the fact that mod(r) acts through the 5' control region of the rudimentary gene to control its expression.

The dominant mutation Suppressor of black indicates that de novo pyrimidine biosynthesis is involved in the Drosophila tan pigmentation pathway

A deficiency in the production of beta-alanine causes the black (b) phenotype of Drosophila melanogaster. This phenotype is normalized by a semi-dominant mutant gene Su(b) shown previously to be located adjacent to or within the rudimentary (r) locus. The r gene codes for three enzyme activities involved in de novo pyrimidine biosynthesis. Pyrimidines are known to give rise to beta-alanine. However, until recently it has been unclear whether de novo pyrimidine biosynthesis is directly coupled to beta-alanine synthesis during the tanning process. In this report we show that flies carrying Su(b) can exhibit an additional phenotype, resistance to toxic pyrimidine analogs (5-fluorouracil, 6-azathymine and 6-azauracil). Our interpretation of this observation is that the pyrimidine pool is elevated in the mutant flies. However, enzyme assays indicate that r enzyme activities are not increased in Su(b) flies. Genetic mapping of the Su(b) gene now places the mutation within the r gene, possibly in the carbamyl phosphate synthetase (CPSase) domain. The kinetics of CPSase activity in crude extracts has been studied in the presence of uridine triphosphate (UTP). While CPSase from wild-type flies was strongly inhibited by the end-product, UTP, CPSase from Su(b) was inhibited to a lesser extent. We propose that diminished end-product inhibition of de novo pyrimidine biosynthesis in Su(b) flies increases available pyrimidine and consequently the beta-alanine pool. Normalization of the black phenotype results.

Molecular characterization of the 5' end of the rudimentary gene in Drosophila and analysis of three P element insertions

A detailed analysis of the 5' end of the rudimentary gene of Drosophila melanogaster is presented. Rudimentary transcripts are heterogeneous at their 5' ends indicating that transcription is initiated at multiple sites within a region of approximately 50 bp. These transcription initiation sites are within a region that is preferentially susceptible to nuclease cleavage in isolated nuclei. Additional nuclease hypersensitive regions were found within the first exon and the first intron. Within these internal nuclease hypersensitive regions are the insertion sites for previously identified P element transposons which disrupt rudimentary expression. One of these P element insertions, located in the first intron, is removed from the rudimentary transcript with the splicing of this intron. Another P element insertion, within the first exon, is removed from the rudimentary transcript by novel first intron splicing involving a cryptic splice donor site, located 5' to the insertion, and either the normal acceptor site or a cryptic splice acceptor site within the second exon.

Functions of maternal mRNA in early development

In this review, the types of mRNAs found in oocytes and eggs of several animal species, particularly Drosophila, marine invertebrates, frogs, and mice, are described. The roles that proteins derived from these mRNAs play in early development are discussed, and connections between maternally inherited information and embryonic pattern are sought. Comparisons between genetically identified maternally expressed genes in Drosophila and maternal mRNAs biochemically characterized in other species are made when possible. Regulation of the meiotic and early embryonic cell cycles is reviewed, and translational control of maternal mRNA following maturation and/or fertilization is discussed with regard to specific mRNAs.

Molecular cloning of the UMP synthase gene rudimentary-like from Drosophila melanogaster

The rudimentary-like locus encodes UMP synthase, a bienzyme protein containing the last two enzyme activities of de novo pyrimidine biosynthesis: orotate phosphoribosyltransferase and orotidylate decarboxylase. This locus lies within chromosome region 93B. New mutations have been used to refine the 93B cytogenetic map and a chromosome walk has been executed to clone DNA from this region. DNA encoding UMP synthase was identified using mixed oligonucleotides which were based on sequences derived from conserved peptide tracts of the protein in other species. cDNA clones of the embryonic UMP synthase mRNA have been isolated and used to define the extent of genomic DNA sequences which encode the transcript. The embryonic RNA is approximately 1.75 kb in length.

Mammalian dihydroorotase: nucleotide sequence, peptide sequences, and evolution of the dihydroorotase domain of the multifunctional protein CAD

Mammalian DHOase (S-dihydroorotate amidohydrolase, EC 3.5.2.3) is part of a large multifunctional protein called CAD, which also has a carbamoyl-phosphate synthetase [carbon-dioxide: L-glutamine amido-ligase (ADP-forming, carbamate-phosphorylating), EC 6.3.5.5] and aspartate transcarbamoylase (carbamoyl-phosphate: L-aspartate carbamoyltransferase, EC 2.1.3.2) activities. We sequenced selected restriction fragments of a Syrian hamster CAD cDNA. The deduced amino acid sequence agreed with the sequence of tryptic peptides and the amino acid composition of the DHOase domain isolated by controlled proteolysis of CAD. Escherichia coli transformed with a recombinant plasmid containing the cDNA segment 5' to the aspartate transcarbamoylase coding region expressed a polypeptide recognized by DHOase domain-specific antibodies. Thus, the order of domains within the polypeptide is NH2-carbamoyl-phosphate synthetase-DHO-aspartate transcarbamoylase-COOH. The 334-residue DHOase domain has a molecular weight of 36,733 and a pI of 6.1. A fragment of CAD having DHOase activity that was isolated after trypsin digestion has extensions on both the NH2 (18 residues) and COOH (47-65 residues) termini of this core domain. Three of five conserved histidines are within short, highly conserved regions that may participate in zinc binding. Phylogenetic analysis clustered the monofunctional and fused DHOases separately. Although these families may have arisen by convergent evolution, we favor a model involving DHOase gene duplication and insertion into an ancestral bifunctional locus.

Vestigial mutants of Drosophila melanogaster live better in the presence of aminopterin: increased level of dihydrofolate reductase in a mutant

Vestigial (vg) mutants of Drosophila melanogaster are characterized by atrophied wings. In this paper we show that: (1) aminopterin an inhibitor of dihydrofolate reductase (DHFR) and fluorodeoxyuridine (FUdR), an inhibitor of thymidylate synthetase induce nicks in the wings of wild-type flies and phenocopies of the vg mutant phenotype when vg/+ and vgB/+ flies are reared on these substances (vgB is a deficiency of the vg locus). Only thymidine and thymidylate can rescue the flies from the effect of aminopterin. We propose that the vg phenotype is due to a decrease in the dTMP pool in the wings. (2) Mutant vg strains yield more offspring on medium containing aminopterin than on normal medium. The resistance of vg larvae to the inhibitor seems specific to the gene. This is the first case of aminopterin resistance in living eucaryotes. In contrast sensitivity of the vg larvae to FUdR is observed. (3) An increase in the activity and amount of DHFR is observed in mutant strains as compared with the wild-type flies. Our data suggest that the vg+ gene is a regulatory gene acting on the DHFR gene or a structural gene involved in the same metabolic pathway.

The rudimentary gene of Drosophila melanogaster encodes four enzymic functions

We have determined the 7168 nucleotide DNA sequence corresponding to the messenger RNA of the rudimentary gene of Drosophila melanogaster. By sequence comparison with genes involved in the pyrimidine pathway of prokaryotes and lower eukaryotes, we conclude that the rudimentary gene encodes four enzymically different functions. Each function is restricted to a specific coding domain but in an order different from that previously defined by genetic data. We have found that the corresponding mammalian gene, the CAD gene, exhibits a similar functional organization, and we propose schemes for the evolution of the corresponding coding sequences.

Genetic programming of development: a model

Genetic programming of the developmental processes in multicellular organisms is proposed to be so intricate and vitally important that a large set of genes is dedicated solely to this end. It is further proposed that this set can be compartmentalized into subsets on the basis of the changes in gene activities that occur during ontogenesis, and that the genes in each subset transiently control the epigenetic activities of a small group of cells. Automatic subset activation is achieved by the product of a gene in each subset that transfers activity specifically to the subset next in the developmental sequence. This device can generate a unidirectional series of activations that cascade hierarchically through development like toppling dominoes. The model provides a basis for developmental phenomena, such as pattern formation, morphogenesis, and regeneration, and it makes testable predictions at the molecular level.

Two Drosophila melanogaster mutations block successive steps of de novo purine synthesis

Drosophila melanogaster purine auxotrophs ade2(1) and ade3(1) have been characterized biochemically. The ade2(1) strain is deficient in the fourth step of the de novo purine synthetic pathway catalyzed by phosphoribosylglycinamidine synthase (phosphoribosylformylglycinamide amidotransferase). The ade3(1) strain is deficient in the previous step catalyzed by phosphoribosylglycinamide formyltransferase (GART). The mutation responsible for the slightly leaky ade3(1) phenotype was characterized further. First, the mutant GART polypeptide was found to be of normal size and present at normal levels. Second, the GART-encoding region of the mutant was cloned, inserted into a yeast-Escherichia coli shuttle vector, and used to transform mutant yeast. Transformants showed very slight in vivo activity when compared to wild type, verifying that the mutation is in the GART coding sequence. Lastly, the region of the gene encoding GART activity from mutant and inbred parental strain flies was completely sequenced. A single base transition was found, leading to the substitution of a serine for a highly conserved glycine. These two mutations provide examples of blocks in the de novo purine synthetic pathway in a whole animal.

Molecular organization of the rudimentary gene of Drosophila melanogaster

We have determined the molecular structure of the rudimentary gene of Drosophila melanogaster. The transcription unit, which extends over 14,000 bases, is split into seven exons and six introns. Sequences presenting homologies with a TATA box and a CAT box are located upstream from the transcription initiation site, and there is a consensus polyadenylation signal in the vicinity of the 3' end of the messenger RNA coding sequence. Short intronic sequences fit well with consensus signals found in other eukaryotic genes and involved in the splicing of the precursor messenger RNA. Partial genomic and complementary DNA sequencing has revealed stretches of amino acid sequence homologies with the corresponding enzymes in Saccharomyces cerevisiae and Escherichia coli. This is in good agreement with the genetic map of the locus, which indicates that the enzymic activities encoded by the gene are organized linearly along the DNA.

Organization of transcription units around the Drosophila melanogaster rudimentary locus and temporal pattern of expression

The molecular organization of 90 kb of DNA derived from a region of the X chromosome that encompasses the rudimentary locus of D. melanogaster is presented. This segment spans the cytogenetic region 14F2-3 to 15A1-2, and there are, in addition to the rudimentary gene several transcription units present, whose functions are still unknown. We have determined the pattern of expression of all these genes at several stages of development, and found that they all show a different temporal modulation of their activity. The accumulation of the r product correlates well with the enzymatic activity determined for the protein product of the gene, being highest in very early embryos and adult females.

A coordinate relationship between the GALK and the TK1 genes of the Chinese hamster

Chinese hamster cells in culture were treated with various concentrations of thymidine, 5-bromodeoxyuridine, trifluorothymidine, and 2-deoxy-D-galactose. Selection was made for deficiencies in the activities of galactokinase and thymidine kinase. Selection in the presence of thymidine, 5-bromodeoxyuridine, and trifluorothymidine was expected to produce clones deficient in thymidine kinase only, whereas those deficient in galactokinase were expected to be selected in the presence of 2-deoxy-D-galactose. However, it was found that clones growing in the presence of these inhibitors were frequently deficient in both enzymes. Or if a clone was deficient in only one, the deficiency frequently was not expected according to the selection procedure. This indicates some sort of coordinate relationship between the two gene loci, GALK and TK1, which specify galactokinase and thymidine kinase, respectively. GALK and TK1 are linked in all primates and rodents in which linkage determinations have been made. It is therefore probable that this linkage has been conserved for a long period of time. It is suggested that the apparent relationship between the two genes shown by the data presented here, as well as by others, supports the conclusion that linkage has been conserved by natural selection and is therefore not fortuitous.

Three purine auxotrophic loci on the second chromosome of Drosophila melanogaster

Mutations at three second-chromosomal loci of Drosophila melanogaster have been isolated, mapped, and shown to be purine nucleoside auxotrophs. Two of the loci, adenosine2 and adenosine3, located at map positions 18.4 and 20, respectively, produce mutations which are supplementable with adenine, adenosine, and inosine. Guanosine supplements mutations at the burgundy locus (55.7); this locus was described previously through a pteridine eye-color defect but identified as an auxotrophic locus after the isolation of a new allele, burgua2-1. The mutation ade2-1 also has defective pteridine metabolism.

Gene expression during Drosophila melanogaster oogenesis: analysis by in situ hybridization to tissue sections

The pattern of gene expression for specific genes during oogenesis has been examined by in situ hybridization to RNA in sectioned ovarian preparations. The accumulation (1) of RNA complementary to heat-shock genes, both before and after heat shock; (2) of RNA complementary to three lambda phage recombinants which contain sequences expressed during oogenesis; and (3) of RNA complementary to the rudimentary gene have been analyzed. Gene expression in the ovaries is found to be dependent on both the cell type and the developmental stage of the ovarian chamber. In the nurse cells, the onset of vitellogenesis (stages 8-11) appears to be accompanied by a substantial activation of many different genes and there is a pronounced increase in the level of accumulation of complementary RNAs. Moreover, much of the RNA synthesized in nurse cells during vitellogenesis is ultimately transported into the growing oocyte where it accumulates. It is likely that this accumulation of RNA provides a source of gene products, either as message or proteins, for embryogenesis.

The rudimentary locus of Drosophila melanogaster

In the studies reported here, we have examined the molecular organization of the rudimentary gene of Drosophila melanogaster. rudimentary encodes a 220,000 Mr polypeptide catalyzing the first three steps in pyrimidine biosynthesis: carbamyl phosphate synthetase, aspartate transcarbamylase and dihydroorotase. We have determined the direction of transcription of the gene relative to the genetic map of the locus. The 5' end maps to the distal end of the locus (relative to the centromere) and transcription proceeds through the domains encoding dihydroorotase, carbamyl phosphate synthetase and finally aspartate transcarbamylase. The rudimentary transcription unit spans a DNA segment of 13.2 X 10(3) base-pairs and encodes a mature messenger RNA of 7.3 X 10(3) base-pairs. Three intervening sequences have been identified, one of which is over 4 X 10(3) base-pairs in length. Finally, we have compared the DNA sequence organization of the Drosophila rudimentary gene with the corresponding loci of yeast and hamster.

A DNA sequence from Dictyostelium discoideum complements ura3 and ura5 mutations of Saccharomyces cerevisiae

A 3.7 kilobase fragment of Dictyostelium discoideum genomic DNA has been cloned by its ability to complement a yeast ura3 mutation affecting the activity of orotidine-5'-phosphate carboxy-lyase (EC 4.1.1.23). This fragment also complements a yeast ura5 mutation that leads to a defect in orotate phosphoribosyl transferase (EC 2.4.2.10). The orotidine-5'-phosphate carboxy-lyase and the orotate phosphoribosyl transferase activities that result from Dictyostelium gene expression in yeast have been detected. The size of the DNA required for both complementations has been localised to a segment of less than 2 kb. A unique Dictyostelium RNA species of 1,600 base pairs hybridizes to this fragment. In vitro deletions in this fragment lead to the simultaneous loss of the two activities. The two enzymatic activities coelute as a protein of 120,000 daltons during gel filtration of a Dictyostelium extract. These results favour the existence, on the cloned Dictyostelium DNA fragment, of a unique structural gene which codes for a bifunctional enzyme carrying the two activities, orotidine-5'-phosphate carboxy-lyase and orotate phosphoribosyl transferase.

The Dhod locus of Drosophila: mutations and interrelationships with other loci controlling de novo pyrimidine biosynthesis

Mutations at the Dhod locus have been isolated following ethylmethanesulfonate mutagenesis. These mutants express those phenotypes common to other mutations of the de novo pyrimidine pathway: specific wing and leg defects and female sterility. Dihydroorotate dehydrogenase activity is severely reduced in all Dhod mutants, whereas levels of the other pathway enzymes are largely unaffected. The twelve Dhod mutations described here comprise a single complementation group. All of these mutations are nonlethal and the collection includes apparent amorphic as well as hypomorphic alleles. These results are discussed relative to the properties of the complex loci that encode the other steps of de novo pyrimidine biosynthesis.

Partial cDNA sequence to a hamster gene corrects defect in Escherichia coli pyrB mutant

The first three enzymes of pyrimidine biosynthesis (carbamoyl-phosphate synthetase, aspartate carbamoyl-transferase, and dihydro-orotase) are carried on a multifunctional protein in mammalian cells and are on separate proteins in bacteria. A plasmid containing a cDNA sequence corresponding to 80% of a hamster mRNA for this protein was transformed into Escherichia coli mutants lacking aspartate carbamoyltransferase (pyrB) or dihydro-orotase (pyrC). Only pyrB transformants were able to grow in the absence of uracil. Plasmid recovered from primary transformants was similar in size to the original plasmid and could yield prototrophs after secondary transformation of E. coli pyrB mutants. When cell extracts were prepared from pyrB transformants, high levels of aspartate carbamoyltransferase activity were found, and the enzyme had properties identical to the mammalian enzyme, including lack of allosteric regulation, precipitation by antiserum specific to the hamster multifunctional protein, and presence of a strong aggregation center. These results demonstrate that (i) a partial hamster protein can complement E. coli defective in pyrimidine biosynthesis, (ii) the order of the enzyme domains of the multifunctional protein is likely to be NH2-dihydro-orotase-carbamoyl-phosphate synthetase-aspartate carbamoyltransferase-COOH, and (iii) the enzyme domains appear to be self-contained at the DNA and protein levels. The protocol described here may be a general means for studying the domains of multifunctional proteins and for isolating other mammalian genes for which bacterial mutants have been prepared. It also permits study of the structure and function of the same gene in both prokaryotic and eukaryotic cells and may provide new insight into the evolution of complex genes.

Purine-resistant Drosophila melanogaster result from mutations in the adenine phosphoribosyltransferase structural gene

Mutants of Drosophila melanogaster selected for resistance to purine killing are deficient in adenine phosphoribosyltransferase (APRT; E.C. 2.4.2.7) activity. Genetic mapping and complementation analysis demonstrate that purine resistance, deficiency of APRT activity, and differences in the isoelectric point of APRT result from alterations at a single locus, Aprt (map position, 3:3.03). The level of APRT activity shows gene dose dependence in Aprt heterozygotes and in flies that are haploid for different Aprt alleles. Drosophila APRT is a dimer composed of apparently identical 23,000-dalton subunits. These results suggest that Aprt contains the structural gene for APRT.

Analysis of the phenotypes exhibited by rudimentary-like mutants of Drosophila melanogaster

Flies mutant for one or both of the last two enzymes of de novo pyrimidine biosynthesis express a number of phenotypes that are also expressed by mutants of the first four pathway enzymes (r and Dhod-null mutants). However, r-1 flies also express two phenotypes, mottled eyes and poor viability, that are not usually expressed by r and Dhod-null flies. Chemical determinations show that orotic acid, a substrate for the fifth pathway enzyme, accumulates in r-1 individuals but not in r and wild-type individuals. Moreover, flies simultaneously mutant for r and r-1 do not express the mottled-eye phenotype, showing that r is epistatic to r-1 for this r-1-specific phenotype. When genotypically wild-type flies are cultured on a medium containing 6-azauracil, the base of a potent inhibitor of the last enzyme of de novo pyrimidine biosynthesis, phenocopies are obtained that include the mottled-eye as well as the wing phenotypes of r-1 flies. These results support hypotheses that the phenotypes common to r, Dhod-null, and r-1 flies are consequences of uridylic acid deficiency, whereas the r-1-specific phenotypes result from orotic acid accumulation in flies lacking either or both of the last two enzymes of de novo pyrimidine biosynthesis.

Genetic and biochemical properties of revertants at the rudimentary locus in Drosophila melanogaster

The rudimentary (r) locus of Drosophila melanogaster encodes the first three enzymes for the de novo synthesis of pyrimidines: carbamyl phosphate synthase (CPSase), aspartyl transcarbamylase (ATCase), and dihydroorotase (DHOase). Revertants of leaky r mutants deficient in CPSase have been recovered. Of those examined, most (28/30) appear to result from reversion of the original mutation or a second site mutation in the mutant gene: They map to the r locus, have levels of CPSase and Km's for glutamine similar to wild type, and have comparatively little change in ATCase and DHOase activity. Two of the revertants appear to involve regulatory mutations that lead to an increase in defective CPSase molecules: They map to the r locus, have Km's for glutamine like that of the CPSase in the progenitor stock, and lead to relatively small increases in CPSase activity that are roughly paralleled by increases in ATCase and DHOase. The recovery of these putative regulatory mutations increasing the activity of the three enzymes supports the conclusion that the three activities are part of a trifunctional polypeptide or that their genes are transcribed together as parts of a multicistronic transcript.

The action of the notch locus in Drosophila melanogaster. I. Effects of the notch8 deficiency on mitochondrial enzymes

It is shown that the Notch8 deficiency in Drosophila melanogaster affects a number of enzyme activities localized in the mitochondria, such as NADH oxidase (activity of the complete respiratory chain), NADH dehydrogenase (the first step in the respiratory chain before transfer to ubiquinone), Succinate dehydrogenase and alpha-glycerophosphate dehydrogenase. The experiments reported here do not exclude the possibility of involvement of other genes in the deficiency. The effect of duplications of the Notch locus on NADH oxidase and NADH dehydrogenase suggest that the locus determines the enzyme activities. The dosage effects of the Notch locus on activity suggest that this locus contains the structural genes for these enzymes.

Isolation and characterization of deficiencies exposing the rudimentary locus of Drosophila melanogaster

Therudimentarylocus ofDrosophila melanogastercontains the structural information for the first three enzymes of thede novopyrimidine pathway. Two newrudimentary (r)mutants have been isolated following mutagenesis with ICR-170. From complementation analysis and cyto-genetical observation both were shown to be deficiencies which expose therlocus.Df(1)r19is deleted from band 14D1 to 15D1 andDf(1)r1Dfrom band 14B6 to 15A2. These deficiencies were combined with several characterizedralleles each giving a single enzymatic defect in one of the first three enzymes of the pyrimidine pathway. An unusual semilethaltranseffect was observed in some but not all the combinations. The effect was not observed with a third smaller deficiency which also exposes therudimentarylocus.

A small genetic region that controls dihydroorotate dehydrogenase in Drosophila melanogaster

A locus is described that controls levels of mitochondrial dihydroorotate dehydrogenase (EC 1.3.3.1) in Drosophila melanogaster. The effects of alleles of the locus, Dhod, are manifest in preparations from whole organisms as well as in partially purified mitochondrial preparations; however, other mitochondrial functions do not appear to be appreciably affected by Dhod genotypes. The locus maps near p in the proximal portion of the right arm of chromosome 3. Flies trisomic for a chromosome segment including that region display elevated enzyme levels, implying that an enzyme structural gene is in that vicinity. Furthermore, Dhod alleles are semidominant in heterozygotes, suggesting that the dosage-sensitive element detected in the trisomics is actually the Dhod locus. These findings are discussed relative to the role of dihydroorotate dehydrogenase in the de novo pyrimidine biosynthetic pathway and relative to other pathway mutants that have been described in Drosophila.

cis-Interacting genes in the S region of the murine major histocompatibility complex

Insight into the control of gene expression may be gained by analysing genetic systems marked by both regulatory and structural variants. In such systems one can determine whether a regulatory element controls structural genes on both chromosomes or only on the chromosome to which it is linked. The latter may be detected in individuals heterozygous at both the regulatory and structural loci, in which case the effect of each regulatory allele is seen to be exerted only on the cis-located structural allele. In prokaryotic organisms, the identification of cis interaction of this sort has allowed elucidation of many features of genetic regulation, first for the lac operon and subsequently for a variety of other systems. In higher organisms, however, there have been few opportunities to observe cis-interacting genes. The most thoroughly characterized mammalian system in this regard is the murine beta-glucuronidase locus described by Paigen and his colleagues, in which cis interaction has been shown to occur between two closely linked genetic elements-the beta-glucuronidase structural gene itself and an androgen-activated regulatory gene which controls the quantity of beta-glucuronidase expressed. We report here that cis-interacting genetic elements are also found in the S region of the mouse major histocompatibility complex H-2.

Characterization of an autosomal rudimentary-shaped wing mutation in Drosophila melanogaster that affects pyrimidine synthesis

A new autosomal mutation, rudimental (ral), which causes rudimentary-shaped wings in Drosophila melanogaster, has been isolated following ethyl methanesulfonate (EMS) mutagenesis. The wing phenotype of rudimental is identical to that of the X-linked rudimentary (r) mutation, which affects the first three enzymes in the pyrimidine biosynthetic pathway. The autosomal mutant maps very close to ebony (3-70.7) at 70.42 on the right arm of chromosome 3. Analysis of the enzyme activities of orotate phosphoribosyltransferase (OPRTase) and orotidylate decarboxylase (ODCase) indicates that the rala26a allele has less than wild-type activity for both enzymes. This result is discussed in light of the fact that the OPRTase and ODCase activities are part of an enzyme complex, as are the carbamyl phosphate synthetase (CPSase), aspartate transcarbamylase (ATCase) and dihydroorotase (DHOase) activities, which are encoded by the complex rudimentary locus. We suggest that rudimental is also a complex lucus.