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PubMed1999

The Berkeley Drosophila Genome Project gene disruption project: Single P-element insertions mutating 25% of vital Drosophila genes.

A fundamental goal of genetics and functional genomics is to identify and mutate every gene in model organisms such as Drosophila melanogaster. The Berkeley Drosophila Genome Project (BDGP) gene disruption project generates single P-element insertion strains that each mutate unique genomic open reading frames. Such strains strongly facilitate further genetic and molecular studies of the disrupted loci, but it has remained unclear if P elements can be used to mutate all Drosophila genes. We now report that the primary collection has grown to contain 1045 strains that disrupt more than 25% of the estimated 3600 Drosophila genes that are essential for adult viability. Of these P insertions, 67% have been verified by genetic tests to cause the associated recessive mutant phenotypes, and the validity of most of the remaining lines is predicted on statistical grounds. Sequences flanking >920 insertions have been determined to exactly position them in the genome and to identify 376 potentially affected transcripts from collections of EST sequences. Strains in the BDGP collection are available from the Bloomington Stock Center and have already assisted the research community in characterizing >250 Drosophila genes. The likely identity of 131 additional genes in the collection is reported here. Our results show that Drosophila genes have a wide range of sensitivity to inactivation by P elements, and provide a rationale for greatly expanding the BDGP primary collection based entirely on insertion site sequencing. We predict that this approach can bring >85% of all Drosophila open reading frames under experimental control.

Alleles↗
PubMed1999

An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: the Adh region.

A contiguous sequence of nearly 3 Mb from the genome of Drosophila melanogaster has been sequenced from a series of overlapping P1 and BAC clones. This region covers 69 chromosome polytene bands on chromosome arm 2L, including the genetically well-characterized "Adh region." A computational analysis of the sequence predicts 218 protein-coding genes, 11 tRNAs, and 17 transposable element sequences. At least 38 of the protein-coding genes are arranged in clusters of from 2 to 6 closely related genes, suggesting extensive tandem duplication. The gene density is one protein-coding gene every 13 kb; the transposable element density is one element every 171 kb. Of 73 genes in this region identified by genetic analysis, 49 have been located on the sequence; P-element insertions have been mapped to 43 genes. Ninety-five (44%) of the known and predicted genes match a Drosophila EST, and 144 (66%) have clear similarities to proteins in other organisms. Genes known to have mutant phenotypes are more likely to be represented in cDNA libraries, and far more likely to have products similar to proteins of other organisms, than are genes with no known mutant phenotype. Over 650 chromosome aberration breakpoints map to this chromosome region, and their nonrandom distribution on the genetic map reflects variation in gene spacing on the DNA. This is the first large-scale analysis of the genome of D. melanogaster at the sequence level. In addition to the direct results obtained, this analysis has allowed us to develop and test methods that will be needed to interpret the complete sequence of the genome of this species. Before beginning a Hunt, it is wise to ask someone what you are looking for before you begin looking for it. Milne 1926

Alcohol Dehydrogenase↗
PubMed1999

A direct screen identifies new flight muscle mutants on the Drosophila second chromosome.

An ethyl methanesulfonate mutagenesis of Drosophila melanogaster was undertaken, and >3000 mutagenized second chromosomes were generated. More than 800 homozygous viable lines were established, and adults were screened directly under polarized light for muscle defects. A total of 16 mutant strains in which the indirect flight muscles were reduced in volume or disorganized or were otherwise abnormal were identified. These fell into seven recessive and one semidominant complementation groups. Five of these eight complementation groups, including the semidominant mutation, have been mapped using chromosomal deficiencies and meiotic recombination. Two complementation groups mapped close to the Myosin heavy chain gene, but they are shown to be in different loci. Developmental analysis of three mutations showed that two of these are involved in the early stages of adult myogenesis while the other showed late defects. This is the first report of results from a systematic and direct screen for recessive flight muscle defects. This mutant screen identifies genes affecting the flight muscles, which are distinct from those identified when screening for flightlessness.

Animals↗
PubMed2000

Genetic analysis of the hybrid male rescue locus of Drosophila.

Several hybrid rescue mutations-alleles that restore the viability of normally lethal hybrids-have been discovered in Drosophila melanogaster and its relatives. Here we analyze one of these genes, Hybrid male rescue (Hmr), asking two questions about its role in hybrid inviability. (1) Does the wild-type allele from D. melanogaster (Hmr(mel)) cause hybrid embryonic inviability? (2) Does Hmr(mel) cause hybrid larval inviability? Our results show that the wild-type product of Hmr is neither necessary nor sufficient for hybrid embryonic inviability. Hmr(mel) does, however, appear to lower the viability of hybrid larvae. The data further suggest (though do not prove) that Hmr(mel) acts as a gain-of-function poison in hybrids. These findings support previous claims that hybrid embryonic and larval lethalities are genetically distinct and suggest that Hmr(mel) is at least one of the proximate causes of hybrid larval inviability.

Animals↗
PubMed2000

Deletion of a conserved regulatory element in the Drosophila Adh gene leads to increased alcohol dehydrogenase activity but also delays development.

In vivo levels of enzymatic activity may be increased through either structural or regulatory changes. Here we use Drosophila melanogaster alcohol dehydrogenase (ADH) in an experimental test for selective differences between these two mechanisms. The well-known ADH-Slow (S)/Fast (F) amino acid replacement leads to a twofold increase in activity by increasing the catalytic efficiency of the enzyme. Disruption of a highly conserved, negative regulatory element in the Adh 3' UTR also leads to a twofold increase in activity, although this is achieved by increasing in vivo Adh mRNA and protein concentrations. These two changes appear to be under different types of selection, with positive selection favoring the amino acid replacement and purifying selection maintaining the 3' UTR sequence. Using transgenic experiments we show that deletion of the conserved 3' UTR element increases adult and larval Adh expression in both the ADH-F and ADH-S genetic backgrounds. However, the 3' UTR deletion also leads to a significant increase in developmental time in both backgrounds. ADH allozyme type has no detectable effect on development. These results demonstrate a negative fitness effect associated with Adh overexpression. This provides a mechanism whereby natural selection can discriminate between alternative pathways of increasing enzymatic activity.

3' Untranslated Regions↗
PubMed2000

Targeted recovery of mutations in Drosophila.

Reverse genetic techniques will be necessary to take full advantage of the genomic sequence data for Drosophila and other experimental organisms. To develop a method for the targeted recovery of mutations, we combined an EMS chemical mutagenesis regimen with mutation detection by denaturing high performance liquid chromatography (DHPLC). We recovered mutant strains at the high rate of approximately 4.8 mutations/kb for every 1000 mutagenized chromosomes from a screen for new mutations in the Drosophila awd gene. Furthermore, we observed that the EMS mutational spectrum in Drosophila germ cells shows a strong preference for 5'-PuG-3' sites, and for G/C within a stretch of three or more G/C base pairs. Our method should prove useful for targeted mutagenesis screens in Drosophila and other genetically tractable organisms and for more precise studies of mutagenesis and DNA repair mechanisms.

Animals↗
PubMed2001

Positive and negative intronic regulatory elements control muscle-specific alternative exon splicing of Drosophila myosin heavy chain transcripts.

Alternative splicing of Drosophila muscle myosin heavy chain (MHC) transcripts is precisely regulated to ensure the expression of specific MHC isoforms required for the distinctive contractile activities of physiologically specialized muscles. We have used transgenic expression analysis in combination with mutagenesis to identify cis-regulatory sequences that are required for muscle-specific splicing of exon 11, which is encoded by five alternative exons that produce alternative "converter" domains in the MHC head. Here, we report the identification of three conserved intronic elements (CIE1, -2, and -3) that control splicing of exon 11e in the indirect flight muscle (IFM). Each of these CIE elements has a distinct function: CIE1 acts as a splice repressor, while CIE2 and CIE3 behave as splice enhancers. These CIE elements function in combination with a nonconsensus splice donor to direct IFM-specific splicing of exon 11e. An additional cis-regulatory element that is essential in coordinating the muscle-specific splicing of other alternative exon 11s is identified. Therefore, multiple interacting intronic and splice donor elements establish the muscle-specific splicing of alternative exon 11s.

Alternative Splicing↗
PubMed2003

Identification of trans-dominant modifiers of Prat expression in Drosophila melanogaster.

The first committed step in the purine de novo synthesis pathway is performed by amidophosphoribosyltransferase (EC 2.4.2.14) or Prat. Drosophila melanogaster Prat is an essential gene with a promoter that lacks a TATA-box and initiator element and has multiple transcription start sites with a predominant start site. To study the regulation of Prat expression in the adult eye, we used the Prat:bw reporter gene, in which the Prat coding region was replaced with the brown (bw) coding region. The pale-orange eye color of a single copy of Prat:bw prompted us to use a multicopy array of Prat:bw that was derived using P transposase mutagenesis and produces a darker-orange eye color in a bw(D); st genetic background. We used a 13-copy array of Prat:bw as a tool to recover dominant EMS-induced mutations that affect the expression of the transgene. After screening 21,000 F(1)s for deviation from the orange eye color, we isolated 23 dominant modifiers: 21 suppressors (1 Y-linked, 5 X-linked, 4 2-linked, and 11 3-linked) and 2 enhancers (1 2-linked and 1 3-linked). Quantification of their effect on endogenous Prat gene expression, using RT-PCR in young adult fly heads, identifies a subset of modifiers that are candidates for genes involved in regulating Prat expression.

Amidophosphoribosyltransferase↗
PubMed2003

Distinguishing the hitchhiking and background selection models.

A simple method to distinguish hitchhiking and background selection is proposed. It is based on the observation that these models make different predictions about the average level of nucleotide diversity in regions of low recombination. The method is applied to data from Drosophila melanogaster and two highly selfing tomato species.

Animals↗
PubMed1999

Tumor-specific gene delivery using recombinant vaccinia virus in a rabbit model of liver metastases.

BACKGROUND: Several approaches to gene therapy for cancer have yielded promising results in rodent models. The translation of these results to the clinical realm has been delayed by the lack of tumor models in large animals. We investigated the pattern of transgene (i. e., foreign or introduced gene) expression and virus vector elimination after systemic gene delivery using a thymidine kinase-negative vaccinia virus in a rabbit model of disseminated liver metastases. METHODS: VX-2 rabbit carcinoma cells were maintained by serial transplantation in the thigh muscles of New Zealand White rabbits, and disseminated liver metastases were established by direct injection of tumor cells into the portal vein of the animals. Different doses of a recombinant thymidine kinase-negative vaccinia virus vector encoding the firefly luciferase reporter gene (i.e., transgene) were injected into tumor-bearing rabbits. Transgene activity in tumors and other organs was measured at multiple time points thereafter. The pattern of development of antibodies against the vaccinia virus vector was also examined. Two-tailed Student's paired t test was used for comparisons of transgene activity. RESULTS: Transgene expression was increased in tumors by at least 16-fold in comparison with expression in other tissues by day 4 after vector injection (all P<. 001) and was maintained for approximately 1 week, providing evidence of tumor-specific gene delivery in this model. Rapid elimination of the circulating vector by the host immune system was observed. Anti-vector antibodies were detectable in serum as early as day 6 and were maintained for more than 3 months. CONCLUSIONS: Tumor-specific gene delivery is possible after systemic injection of a thymidine kinase-negative vaccinia virus vector in a model of rabbit liver metastases. Although the period of transgene expression appears limited because of a rapid immune response, the therapeutic window might be sufficient for an enzyme/prodrug gene therapy approach in clinical application.

Animals↗
PubMed2006

Restrictive flamenco alleles are maintained in Drosophila melanogaster population cages, despite the absence of their endogenous gypsy retroviral targets.

The flamenco (flam) locus, located at 20A1-3 in the centromeric heterochromatin of the Drosophila melanogaster X chromosome, is a major regulator of the gypsy/mdg4 endogenous retrovirus. In restrictive strains, functional flam alleles maintain gypsy proviruses in a repressed state. By contrast, in permissive strains, proviral amplification results from infection of the female germ line and subsequent insertions into the chromosomes of the progeny. A restrictive/permissive polymorphism prevails in natural and laboratory populations. This polymorphism was assumed to be maintained by the interplay of opposite selective forces; on one hand, the increase of genetic load caused by proviral insertions would favor restrictive flam alleles because they make flies resistant to these gypsy replicative transpositions and, on the other, a hypothetical resistance cost would select against such alleles in the absence of the retrovirus. However, the population cage data presented in this paper do not fit with this simple resistance cost hypothesis because restrictive alleles were not eliminated in the absence of functional gypsy proviruses; on the contrary, using 2 independent flam allelic pairs, the restrictive frequency rose to about 90% in every experimental population, whatever the pair of alleles and the allelic proportions in the initial inoculum. These data suggest that the flam polymorphism is maintained by some strong balancing selection, which would act either on flam itself, independently of the deleterious effect of gypsy, or on a hypothetical flanking gene, in linkage disequilibrium with flam. Alternatively, restrictive flam alleles might also be resistant to some other retroelements that would be still present in the cage populations, causing a positive selection for these alleles. Whatever selective forces that maintain high levels of restrictive alleles independently of gypsy, this unknown mechanism can set up an interesting kind of antiviral innate immunity, at the population level.

Alleles↗
PubMed1995

Tannic acid is not mutagenic in germ cells but weakly genotoxic in somatic cells of Drosophila melanogaster.

Tannic acid (TA) was tested for genotoxic activity in three different assays (1-3) in Drosophila melanogaster by feeding of larvae or adult flies. TA did not induce sex-linked recessive lethals (1) nor sex-chromosome loss, mosaicism or non-disjunction (2) in male germ cells. In the wing somatic mutation and recombination test (SMART) (3) TA was found to be toxic for larvae of the high bioactivation cross and produced a weak positive response. These results suggest that this compound, when administered orally to larvae or adults of D. melanogaster, is not mutagenic and clastogenic in male germ cells, but weakly genotoxic in somatic cells of the wing imaginal disk.

Animals↗
PubMed1997

Ectopic mitotic recombination in Drosophila probed with bacterial beta-galactosidase gene-based reporter transgenes.

Plasmids were constructed to investigate homologous mitotic recombination in Drosophila cells. Heteroalleles containing truncated but overlapping segments of the bacterial beta-galactosidase gene (lacZ) were positioned either on separate plasmids or as direct repeats on the same chromosome. Recombination reconstituted a functional lacZgene leading to expression of LacZ+activity detectable by histochemical staining. High extrachromosomal recombination (ECR) frequencies between unlinked heteroalleles were observed upon transient co-transfection into Drosophila melanogaster Schneider line 2 (S2) cells. Stably transfected cells containing the lacZ heteroalleles linked on a chromosome exhibited intrachromosomal recombination (ICR) frequencies two orders of magnitude lower than ECR frequencies. Recombination was inducible by exposing the cells to ethyl methanesulphonate or mitomycin C. Recombination products were characterized by multiplex PCR analysis and unequal sister chromatid recombination was found as the predominant mechanism reconstituting the lacZ gene. To investigate recombination in vivo imaginal disc cells from transgenic larvae carrying the reporter gene on the X chromosome were isolated and stained for LacZ+ activity. The presence of a few LacZ+ clones indicated that mitotic recombination events occurred at frequencies two orders of magnitude lower than the corresponding event in cultured cells and late during larval development.

Animals↗
PubMed1998

A contiguous 60 kb genomic stretch from barley reveals molecular evidence for gene islands in a monocot genome.

The contiguous DNA sequence of a 60 kb genomic interval of barley chromosome 4HL has been assembled. The region harbours a single and novel gypsy -like retrotransposon, designated BAGY-1. Only three genes appear to reside in the genomic stretch. One predicts a plant homologue of ribophorin I, a subunit of the oligosaccharyltransferase-protein complex located in the rough endoplasmatic reticulum. The second is similar to the Drosophila g1 gene encoding a ring finger protein involved in developmental processes. The observed gene density is approximately 5-fold lower than in the best characterized dicot genome of Arabidopsis but 6- to 10-fold higher than expected from an equidistant gene distribution in the complex barley genome. Our data suggest that the 60 kb genomic interval represents part of a gene island, a seemingly distinctive feature of grass genomes.

Amino Acid Sequence↗
PubMed2001

GST-PRIME: a genome-wide primer design software for the generation of gene sequence tags.

The availability of sequenced genomes has generated a need for experimental approaches that allow the simultaneous analysis of large, or even complete, sets of genes. To facilitate such analyses, we have developed GST-PRIME, a software package for retrieving and assembling gene sequences, even from complex genomes, using the NCBI public database, and then designing sets of primer pairs for use in gene amplification. Primers were designed by the program for the direct amplification of gene sequence tags (GSTs) from either genomic DNA or cDNA. Test runs of GST-PRIME on 2000 randomly selected Arabidopsis and Drosophila genes demonstrate that 93 and 88% of resulting GSTs, respectively, fulfilled imposed length criteria. GST-PRIME primer pairs were tested on a set of 1900 Arabidopsis genes coding for chloroplast-targeted proteins: 95% of the primer pairs used in PCRs with genomic DNA generated the correct amplicons. GST-PRIME can thus be reliably used for large-scale or specific amplification of intron-containing genes of multicellular eukaryotes.

Arabidopsis Proteins↗
PubMedDate not supplied

Chromosome extraction and revision of linkage group 2 in Tribolium castaneum.

We used a balancer chromosome to recover ethylmethanesulfonate-induced recessive mutations in a targeted region of the genome of the red flour beetle (Tribolium castaneum) by the technique of chromosome extraction. The experiments reported herein constitute the first successful application of this powerful technique in the order Coleoptera. Using the balancer chromosome maxillopedia-Dachs3 (mxpDch-3), we recovered seven recessive visible variants representing seven distinct loci and several dozen recessive lethal variants representing at least five distinct loci after screening 1,607 EMS-mutagenized chromosomes. A subset of the mxpDch-3-extracted mutations were positioned on the map of the second linkage group by a series of two-, three-, and four-point crosses. The orientation of the homeotic gene complex (HOM-C) on this linkage group was also determined. With the advent of better and more varied balancer chromosomes and the concomitant improvement of chromosome extraction procedures for genetic analysis of T. castaneum, saturation mutagenesis of targeted regions of the genome is now feasible in this species.

Animals↗
PubMed1999

Retrotransposons and retroviruses: analysis of the envelope gene.

Retroviruses and long terminal repeat (LTR) retrotransposons share a common structural organization. The main difference between these retroelements is the presence of a functional envelope (env) gene in retroviruses, which is absent or nonfunctional in LTR retrotransposons. Several similarities between these two groups of retroelements have been detected for the reverse transcriptase, gag, and integrase domains. Assuming that each of these domains shares a common ancestral sequence, several hypotheses could account for the emergence of retroviruses from LTR retrotransposons. In this context, the positions of elements such as gypsy and the members of the Ty3 subfamily are not clear, since they are classified as retroviruses but phylogenetically they are assigned to the LTR retrotransposon group. We compared the env gene products of these retroelements and identified two similar motifs in retroviruses and LTR retrotransposons. These two regions do not occur in the same order. If we assume that they are derived from the same ancestral sequence, this could result from independent acquisition of the various domains rather than the single acquisition of the whole env gene. However, we cannot exclude the possibility that the env gene was reorganized after being acquired. Trees based on these regions show that these two groups of elements are clearly distinguished. These trees are similar to those obtained from reverse transcriptase or integrase. In trees based on reverse transcriptase, the retroviruses with complete or partial env genes can be distinguished from the other LTR retrotransposons.

Amino Acid Sequence↗
PubMed1999

Current concepts on lung development.

Recent molecular genetic and embryonic organ culture studies have implicated several novel regulatory processes in the coordination of lung development. Failure of pulmonary initiation results from interruptions of the sonic hedgehog/patched/Gli and Nkx 2.1 signaling pathways. Sonic hedgehog null mutants and Gli2/Gli3 compound null mutants each exhibited failed tracheoesophageal septation. However, proximodistal epithelial differentiation is disrupted by compound Gli mutation, but is preserved in sonic hedgehog mutants. Null mutation of Nkx 2.1 also abrogates tracheoesophageal septation in association with thyroid and pituitary agenesis. Primary tracheal branching is regulated by fibroblast growth factor-10 signaling; in the murine fibroblast growth factor-10 null phenotype, the lung fails to separate from the foregut and morphogenesis is arrested distal to the trachea. Several genes in the fibroblast growth factor-10 pathway have homologous roles in fruit fly tracheal organogenesis, and corresponding Drosophila mutations yield strikingly similar phenotypes. Recent data also indicate that airway branching can be regulated by vascular endothelial growth factor, suggesting mutual regulation of airway and vascular development. The bases of pulmonary left-right asymmetry and laterality have also been investigated. The transforming growth factor-beta superfamily members Lefty-1, Lefty-2, and nodal comprise a regulatory pathway whose function is required for the development of left-right asymmetry, whereas left-right laterality is dependent on regulation of dynein expression by the transcription factor hepatocyte nuclear factor-4. Terminal lung differentiation is modulated by yet another set of signals. Hoxa5 null mutants exhibit tracheal occlusion and surfactant protein deficiency, whereas fibroblast growth factor receptor-2 and -4 compound null phenotypes include abrogated neonatal alveolization, perturbed alveolar myofibroblast differentiation, and persistent neonatal elastin deposition. These new contributions represent substantial advances toward a comprehensive molecular model of pulmonary development.

Animals↗