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A P-Element Insertion Screen Identified Mutations in 455 Novel Essential Genes in Drosophila
Su-Wan Oha, Tracy Kingsleya, Hyun-hee Shina, Zhiyu Zhenga, Hua-Wei Chena, Xiu Chena, Hong Wanga, Peizheng Ruana, Michelle Moodya, and Steven X. Houaa The Laboratory of Immunobiology, National Institutes of Health, National Cancer Institute, Frederick, Maryland 21702-1201
Corresponding author: Steven X. Hou, National Institutes of Health, National Cancer Institute, Frederick, MD 21702-1201., shou{at}mail.ncifcrf.gov (E-mail)
Communicating editor: T. SCHÜPBACH
| ABSTRACT |
|---|
With the completion of the nucleotide sequences of several complex eukaryotic genomes, tens of thousands of genes have been predicted. However, this information has to be correlated with the functions of those genes to enhance our understanding of biology and to improve human health care. The Drosophila transposon P-element-induced mutations are very useful for directly connecting gene products to their biological function. We designed an efficient transposon P-element-mediated gene disruption procedure and performed genetic screening for single P-element insertion mutations, enabling us to recover 2500 lethal mutations. Among these, 2355 are second chromosome mutations. Sequences flanking >2300 insertions that identify 850 different genes or ESTs (783 genes on the second chromosome and 67 genes on the third chromosome) have been determined. Among these, 455 correspond to genes for which no lethal mutation has yet been reported. The Drosophila genome is thought to contain
3600 vital genes; 1400 are localized on the second chromosome. Our mutation collection represents
56% of the second chromosome vital genes and
24% of the total vital Drosophila genes.
THE nucleotide sequences of several complex eukaryotic genomes, including those of Caenorhabditis elegans, Drosophila melanogaster, Arabidopsis thaliana, and Homo sapiens, have been completed (C. ELEGANS SEQUENCING CONSORTIUM 1998; ![]()
The combination of powerful genetic manipulations, excellent cytology, and sophisticated molecular biology tools available in Drosophila make it a powerful model in the study of conserved gene function. Drosophila and humans share many genes whose sequences and functions have been conserved. More importantly, many biological processes between humans and Drosophila are remarkably similar. Humans and Drosophila share pathways for intercellular signaling, developmental patterning, learning, and behavior, as well as for tumor formation and metastasis (![]()
Several large-scale genetic screens have been conducted in Drosophila to identify the maternal and zygotic gene products involved in specific events in pattern formation of the embryo. Maternal functions have been identified via screens for female sterility, while zygotic genes have been detected via screens for embryonic lethal mutations (![]()
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300 genes with functions in oogenesis and 140 patterning genes that are instrumental in controlling specific embryonic decisions. This is a small number of genes, considering that the Drosophila genome has been estimated to potentially code for
13,600 different genes (![]()
The above screens have two major drawbacks. First, mutations in these screens were generated by chemically induced mutagenesis. Identification of the open reading frame responsible for a mutant phenotype has varied widely and has frequently been a time-consuming and challenging task. Second, the assumption underlying these screens is that the expression of genes that encode "decisionmaking" functions is tightly restricted to the corresponding developmental stage. Indeed, some of the maternal gene functions could be missed if the gene products were used at multiple times during the development of the animal. Similarly, some zygotic gene functions important for embryonic patterning could be missed if the gene were also expressed maternally, because the maternal product can mask the zygotic requirement. Many genes involved in critical patterning events have not been identified because of their developmental pleiotropy; a screen to analyze the maternal effects of X-linked zygotic lethal mutations has been conducted (![]()
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The P-element insertional mutagenesis has many advantages over traditional mutagenesis procedures: It is usually possible to identify rapidly the transcription unit that an insertion has disrupted by sequencing the flanking sequences from one or both ends of the P-element insertion; remobilizing the inserted element can generate new alleles, and expression patterns can be characterized by lacZ staining of tissues. However, only a small number of existing P-element mutations are suitable for analyzing the maternal effects of the zygotic lethal mutations in a germline clonal (GLC) assay (![]()
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| MATERIALS AND METHODS |
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Strains:
A y w P-lacW stock (![]()
2-3), referred to as Sb
2-3, is the standard transposase source (![]()
P-element mutagenesis:
The basic genetic design involves crossing (en masse) males carrying transposase activity on the third chromosome, provided by the
2-3 P-element, which is inserted at 99B and apparently immobilized, to white females that were homozygous for a P-lacW insertion on the X chromosome (and therefore had pigmented eyes). Males that carried P-lacw on the X chromosome (maternally derived) and transposase on the third were recovered from this cross. The
2-3 transposase-producing chromosome was marked with the dominant Stubble bristle marker but could also be scored easily by the
2-3 transposase activity directly. Because the absence of the last intron in the
2-3 P-element causes expression of transposase in all tissues, rather than exclusively in the germline, flies that carry both P-lacW and
2-3 have eyes with patches of color mixed with white areas, a phenomenon known as somatic variegation.
To carry out the experiment, we set crosses in several vials. In each cross we mated 20 female virgins that were homozygous for a P-lacW insertion X chromosome (line A) with 10 yw;
2-3, Sb/TM3, Ser males (Fig 1). After 2 days, we transferred the flies from vials to bottles. Flies were transferred daily for 5 days to assemble enough bottles with a large number of males that carry P-lacW on the X chromosome and transposase on the third. In the next generation, we collected males that carry P-lacW on the X chromosome and transposase on the third; flies that carry both P-lacW and
2-3, Sb have orange or red eyes (with patches of color mixed with white areas) and the dominant Stubble bristle phenotype. We set up 3000 vials per person [one cycle: 300 vials per day, 300 x 10 days (2 weeks or 10 work days)], each with two P-lacW;
2-3, Sb males crossed to three w/w; Sco/Cyo females. Male progeny from such a cross will inherit the w X chromosome from their mothers and will have white eyes unless the P-lacW in the father has jumped to an autosome, in which case the P-lacW element could segregate into both male and female offspring, resulting in pigmented eyes. One P-lacW male (Cyo without
2-3, Sb; the range of eye colors as a result of position effect in these transformed flies may vary from very light yellow to essentially wild-type red, with the bulk of insertions yielding an intermediate orange shade) were crossed to three w/w; Hs-hid SP/Cyo females. The flies were cultured at room temperature; we discharged the adult flies after 4 days and performed a 60-min incubation in a 37° water bath twice during the early larval stages (days 4 and 5 after cross). Induction of ectopic hid expression in this manner presumably causes massive cell death and results in embryonic/larval lethality. Progeny of these flies were checked. If there were white eye flies in the vial, it was a third chromosome insertion. If all flies were orange eye and Cyo, we transferred them to a fresh vial to produce the next generation. Progeny of the above flies then were examined. If P-lacW insertions were on the second chromosome and homozygous viable, the observer saw two kinds of flies: P-lacW/P-lacW and P-lacW/Cyo. Straight-wing flies (i.e., homozygous for P-lacW) have darker eyes (usually dull red) than those of Cyo flies (i.e., heterozygous for P-lacW). If P-lacW insertions are on the second chromosome and homozygously lethal, the observer will see one kind of fly: P-lacW/Cyo (one eye color and Cyo wing). We saved the lethal lines as permanent stocks.
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Germline clonal analysis:
Females carrying GLCs of P-lethal mutants were generated using the "FLP-DFS" technique (![]()
Genomic DNA preparation:
The fresh flies were grown on standard fly food (![]()
Digestions, ligations, and PCR:
A total of 20 µl of genomic DNA (
10 µg/µl) were taken and digested with Sau3A I or HinPI at 37° for 3 hr to overnight separately; then 30 µl of ligation mixture was added to the digested solution. The ligation mixture was incubated overnight at 4°. Ten microliters of ligates was used as a PCR template for both 5' end and 3' end PCR. PCR was performed on Gene Amp PCR system 9600 and 9700 using the following parameters: 1 time at 95°/5 min; 35 times at 95°/30 sec, 60°/2 min, 70°/2 min; and 1 time at 72°/10 min.
Sequencing and database search:
The PCR products were purified with an enzymatic clean-up method using SAP/ExoI and a 96-well PCR purification kit (QIAGEN). Two microliters of purified PCR product was used as a sequencing template. The sequencing reaction was performed using a Gene Amp PCR system 9700 with an ABI Big dye mixture. The sequencing reaction was applied onto an ABI Prism gene analyzer and ABI 3700 automatic sequencer. Vectors were cut from the raw sequence data and the vector-pilled sequences were blasted; the Berkeley Drosophila Genome Project (BDGP) database (http://www.fruitfly.org/) was used to identify the probable disrupted gene.
Stock distribution:
At present, lines from this collection are maintained at Dr. Steven Hou's laboratory and are available (limited to five lines) upon request to shou{at}mail.ncifcrf.gov. The entire collection will be sent to the Bloomington Stock Center later. Return information from further study of any line is welcome.
| RESULTS |
|---|
Isolation of P-insertion mutants:
A large-scale single P-element mutagenesis was performed to saturate the second chromosome with recessive lethal insertion using the high transposition frequency of the P-lacW construct. The genetic scheme used to mobilize P-lacW to autosomal sites from the X chromosome is shown in Fig 1.
Approximately 50,000 individual vials were set up, each with two P-lacW,
2-3 males crossed to three white females carrying the second chromosome balancer Cyo. Male progeny from such a cross will inherit the white X chromosome from their mothers and will have white eyes unless the P-lacW in the father has jumped to an autosome, in which case, the P-lacW element could segregate into both male and female offspring, resulting in pigmented eyes. In 43,000 vials (86%), at least one w+ male was recovered (i.e., a P-lacW transposition to an autosome). The range of eye colors as a result of position effect in these transformed flies varied from very light yellow to essentially wild-type red, with the bulk of insertions yielding an intermediate orange shade. One w+ F1 male from each vial was used for crosses to generate balanced mutant stocks. Of the 17,635 P insertions in the second chromosome, 2962 (
16.8%) proved to be lethal or semilethal. To reduce the multiple P-insertion lines, we discharged 142 lines that have near wild-type red eyes. We further eliminated 465 semilethal lines. A total of 2355 independently derived second chromosome strains was retained for further characterization. We also analyzed 160 third chromosome lethal strains.
Characterizing insertions using flanking DNA sequences:
The genomic DNA sequence flanking the insertion sites in the collection lines was needed to associate lines with specific genes. We attempted to recover genomic DNA adjacent to the 5', 3', or both sides of the P-element from all collection lines. We used an inverse PCR method that was carried out in a 96-well format (![]()
Associating primary collection lines with genes:
Our final collection contains 854 independent strains. To identify as many genes as possible, the P-element flank sequences were used to blast the completed Drosophila sequences in the BDGP database. Mutation-causing P elements are known to preferentially cluster in the 5' region of the affected genes (see ![]()
|
P-element selectivity:
This screen identified most genes that are hotspots for P-element insertion on the autosomes (Table S1 at http://www.genetics.org/supplemental/ and Table 2). However, in comparison with the previously published BDGP primary collection (![]()
|
We also considered whether strong preferences exist for insertion within certain classes of genes among all those disrupted in our collection. In the BDGP collection (![]()
50% of all autosomal genes known to be involved in the EGFR, dpp, ras, wg, hh, or N signaling pathways). The posterior group genes are also well represented (46% of autosomal posterior group genes are disrupted), but only 14% of the ribosomal protein genes were disrupted. In our collection, all classes of genes are generally evenly represented (Table S1 at http://www.genetics.org/supplemental/ and Table 1).
In our collection, only four P elements are not associated with a protein-coding gene. In the BDGP collection, a number of P elements are inserted into locations that are not associated with protein-coding genes. It remains unclear whether these differences are due to the BDGP search using an incomplete Drosophila sequence database or whether our search has pushed to link each P element with a gene.
Association of newly induced recessive lethality with the new P insertion:
To ensure that the newly induced recessive lethality is directly attributable to the new P insertion, we performed the following experiments. First, the P element in line l(2)2276, which inserted into a gene (CG8902) for which no mutation had previously been described, was remobilized by the
2-3 transposase. Among 200 white-eye P-jump-out lines, 158 lines were homozygously viable, indicating that no second lethality exists in the l(2)2276 line. Second, we analyzed seven new alleles of kis in a germline clonal assay; all of them developed the kis-type segmentation defects (data not shown), suggesting that the P's indeed disrupted only the kis gene. Finally, we isolated nine new zip alleles; all of them developed the "dorsal open" phenotype as expected, implying that no second lethalities are in these lines. In another experiment, we recombined 700 new P lines onto FRT chromosomes; 20 lines (
3%) lost lethality after recombination, suggesting that the lethality in these 20 lines is not associated with the P elements. From these data we conclude that most lethal mutations (>90%) are attributed to the P insertions.
Suitability of the P elements for GLC analysis:
We tested 133 of our P-element mutants for performing germline clonal analysis, which also served as means to verify the quality of the P-element mutants, because our previous experiences taught us that only one mutant on each chromosome arm is suitable for performing a GLC assay. Most of the Kiss lines (![]()
We recombined the 133 P lines onto the FRT chromosome and performed a GLC assay (see Table 3). Among the 133 P lines, 18 (14%) did not lay eggs, 67 (50%) laid eggs and the embryos hatched, and 48 (36%) laid abnormal eggs or had embryos that died before hatching and showed cuticles with patterning defects. This result is better than the one obtained in Perrimon's study (![]()
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|
| DISCUSSION |
|---|
Features of this screen:
This P-element-mediated gene disruption screen has several distinct advantages. First, screen efficiency is widely variable in the generation of single P-element-induced mutations (![]()
![]()
![]()
All remaining genes are within 5 kb:
This screen generated P-element insertion mutations for 850 autosomal vital genes. Among them, 783 are on the second chromosome and 67 are on the third chromosome. The Drosophila genome is thought to contain
3600 vital genes. Among them, 1400 are localized on the second chromosome. Our mutation collection represents 56% of second chromosome vital genes and 24% of total vital Drosophila genes. In combination with the previously published BDGP collection (![]()
80% of second chromosome vital genes and
30% of total vital Drosophila genes. Furthermore, we checked the remaining second chromosome genes and found that most of them are within 5 kb of a nearby P-element insertion. The deletion mutations for these genes can be easily generated by imprecise excision of the nearby P element. Theoretically, this makes it possible to generate an entire chromosome's gene mutation, which will be the first time this has been done in any of the widely used models of multi-cellular eukaryotes, including Arabidopsis, C. elegans, zebrafish, and mice.
Genes:
This screen identified all classes of genes involved in important biological processes (Table 1): 12 genes may regulate apoptosis; 12 belong to cell adhesion molecules; 8 are cell cycle regulators; 24 are cytoskeleton molecules; 114 are enzymes; 31 are involved in DNA replication, DNA repair, and other chromosomal functions; 61 are involved in transcription or gene regulation; 64 are involved in RNA processing or translation regulation; 91 are signal transduction components; 28 are channel and transporter molecules; 77 are involved in other cellular processes; and 274 are novel molecules.
The signal transduction molecules are richly represented in this collection. Our P-element collection disrupted 91 genes involved in signal transduction. Among them, 32 correspond to genes for which no lethal mutation had yet been reported.
Some predicted genes may be inaccurate:
In linking a P-element insertion to a gene, we followed the rule that most P elements insert into the 5' portion of the transcription units (![]()
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| ACKNOWLEDGMENTS |
|---|
We are grateful to Jasmine Young, Cristina Chuang, Robin Deniker, Gregory Szeto, Katie Renn, Amy Lin, Kelly Jacobs, and Jim Wang for their help in the experimental work. We thank Yuh Nung Jan and Ruth Lehmann for providing fly strains. This work is supported in part by a grant from the U.S. Army (award number: DAMD17-00-1-0356) to S.X.H.
Manuscript received July 24, 2002; Accepted for publication October 15, 2002.
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