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Molecular Characterization of Mutant Alleles of the DNA Repair/Basal Transcription Factor haywire/ERCC3 in Drosophila
Leslie C. Mounkes1,a,b and Margaret T. Fullerba Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309
b Departments of Developmental Biology and Genetics, Stanford University School of Medicine, Stanford, California 94309
Corresponding author: Margaret T. Fuller, Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305-5427., fuller{at}cmgm.stanford.edu (E-mail)
Communicating editor: R. S. HAWLEY
| ABSTRACT |
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The haywire gene of Drosophila encodes a putative helicase essential for transcription and nucleotide excision repair. A haywire allele encoding a dominant acting poison product, lethal alleles, and viable but UV-sensitive alleles isolated as revertants of the dominant acting poison allele were molecularly characterized. Sequence analysis of lethal haywire alleles revealed the importance of the nucleotide-binding domain, suggesting an essential role for ATPase activity. The viable haync2 allele, which encodes a poison product, has a single amino acid change in conserved helicase domain VI. This mutation results in accumulation of a 68-kD polypeptide that is much more abundant than the wild-type haywire protein.
THE haywire locus of Drosophila encodes the fly homolog of ERCC3, a human gene associated with the DNA repair deficiency disease xeroderma pigmentosum group B (XP-B) (![]()
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The fly, yeast, and human ERCC3 homologs show hallmark conserved domains characteristic of the superfamily of DNA/RNA helicases (![]()
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The Drosophila ERCC3 homolog haywire was originally identified through an unusual mutant allele, haync2, that acted as a dominant enhancer of mutations in the testis-specific ß-tubulin B2t. Males heterozygous for either haync2 or B2tnull and wild type are fertile at 25°. However, flies transheterozygous for one copy of haync2 and one copy of B2tnull are male sterile at 25°. The genetic interaction between haync2 and B2tnull suggested the haync2 allele encoded a poison product because flies transheterozygous for B2t mutations and a deficiency of haywire were male fertile (![]()
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In this article, we report the molecular characterization of mutations that identify regions of haywire that are important either for viability or DNA repair. In addition, we show data indicating that the haync2 allele causes production of a 68-kD polypeptide that accumulates to much higher levels than wild-type haywire protein. Mutant haywire alleles that revert the genetic interaction between haync2 and B2tnull abrogate production of the stable, truncated protein, suggesting that the same defect causes accumulation of the 68-kD polypeptide and the poison product activity.
| MATERIALS AND METHODS |
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Fly strains and culture:
Fly stocks and crosses were maintained using standard fly media at 25°. Balancer chromosomes, visible markers, Df(1)w, B2tnull, and Df(3L)E(z)7e11 (67E1-4;67F1-3) are described in ![]()
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Sequencing of haywire alleles:
The coding region of haywire was divided into halves by two sets of PCR primers, each amplifying ~1.5-kb fragments from haywire. Primers used to amplify the 5' half of haywire were 5'-GGAAGCTTGCCATACGTGCTGTGTTAC-3', and 5'-CCAAGCTTCCAGCACCATGATGCCCC-3'. Primers used to amplify the 3' half of haywire were 5'-GGGCTGTGGAATTCTTGTGACCACATAC-3' and 5'-GGAAGCTTGGGTTACTGCAGTGGTAAAG-3'. For the viable alleles haync2 and haync2rv8, templates for the PCR reactions were genomic DNA made from flies heterozygous for the viable haywire allele and a deficiency for haywire, Df(3L)E(z)7e11. For lethal haywire alleles, template DNA for the PCR reactions was made from flies heterozygous for the lethal revertant allele and the parent chromosome, haync2. PCR products were purified and sequenced as described (![]()
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Northern analysis:
Total RNA was isolated by RNAzol extraction according to Cinna Scientific. RNA (30 µg) was run on 0.1 M sodium phosphate gels, blotted onto a Hybond membrane (Amersham, Arlington Heights, IL), and hybridized as described (![]()
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haywire antibody production and purification:
A 2.5-kb HindIII-NotI fragment from the haywire cDNA plasmid was treated with Klenow (![]()
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Western analysis:
Protein samples were made by grinding 20 adult flies in an Eppendorf tube in 0.15 ml of solution A (0.1 M Tris, pH 9.0, 0.1 M EDTA, 1% SDS, 0.5% DEPC) plus 1 mM PMSF. Samples were spun in the microfuge for 30 sec to pellet large body parts. Supernatants were transferred to a new tube, 10 µl each were brought to 1x sample buffer (![]()
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Germline transformations:
PCR mutagenesis of a 380-nucleotide BglII-SacI fragment of the 3' end of the haywire cDNA was performed to introduce the same C-to-T transition found in the haync2 allele. The mutagenic oligonucleotide had the sequence 5'-CCAGATCTCTTCGCATGGCGGCTCTTGTCGTCAGGAGG-3'. The mutagenized BglII-SacI fragment was subcloned into a 4.5-kb BamHI fragment of the 3' half of a genomic haywire clone (![]()
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23] (![]()
| RESULTS |
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Molecular lesion in the haync2 allele responsible for the dominant genetic interaction with B2t:
The original haync2 mutation caused replacement of arginine 652 with a cysteine (Table 1) in conserved helicase domain VI (Figure 1). This missense mutation was present in all the revertant alleles of haync2, as expected. As haync2 homozygotes are viable, arginine 652 is not absolutely required for haywire function in basal transcription, but it may be important in DNA repair since the haync2 allele is UV sensitive (![]()
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The haync2 mutation resulted in accumulation of a polypeptide that migrated on SDS polyacrylamide gels as 68 kD, cross-reacted with anti-haywire antisera, and was present at much higher levels in the mutant than in the wild type (Figure 2). The 68-kD apparent molecular weight polypeptide was 26 kD less than expected for the full-length protein, suggesting the possibility that the haync2 allele results in accumulation of a shortened form of the haywire protein. Although truncation at the site of the haync2 mutation (Arg652-to-Cys) would produce a predicted 68-kD N-terminal peptide, the region of haywire protein present in the 68-kD polypeptide is not known. It is also formally possible that the 68-kD polypeptide does not correspond to a fragment of the haywire protein, but instead is an unrelated polypeptide that is overproduced specifically in the haync2 mutant background and that cross-reacts with the anti-haywire antisera. The 68-kD polypeptide did not accumulate in either the wild-type background strain (red e, Figure 2) or in flies carrying revertant alleles of haync2 (Figure 2), indicating that accumulation of the 68-kD product results from the haync2 allele. The affinity-purified, anti-haywire antibodies recognized many bands smaller than the expected wild-type size in Western blots. Although some of these smaller peptides could be proteins with cross-reacting epitopes, some could also be degradation products of haywire.
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To demonstrate that the Arg652-to-Cys mutation was responsible for the production of the 68-kD polypeptide in haync2 animals, we constructed a transgenic animal with the haync2 C-to-T transition introduced into an otherwise wild-type haywire genomic fragment. The mutated haywire gene was introduced into a background wild type for haywire, and the resulting transformants were tested for production of the truncated haync2 product. Several transformant lines established from a single Go fly all made and accumulated the 68-kD polypeptide seen in the original haync2 flies (Figure 3).
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Transformants carrying the Arg652-to-Cys change also showed the genetic interaction with B2tnull characteristic of the original haync2 mutation. One copy of the altered gene carried on the insert plus one wild-type endogenous copy of haywire resulted in male sterility in flies heterozygous for the B2tnull allele (Table 2, line 5). (The flies shown in Table 2, line 5, have one of the two endogenous copies of haywire deleted.) One copy of the altered transgene also caused reduced male fertility in B2tnull/+ heterozygotes, even in the presence of two wild-type endogenous copies of haywire (Table 2, line 7), although these flies were not as sterile as haync2 +/+ B2tnull. Thus, the genetic interaction appeared to be sensitive to the ratio between mutant and wild-type haywire (Table 2, compare lines 5 and 7). Similar behavior was observed in the failure of a missense mutation in
-tubulin to complement B2tnull (![]()
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The high levels of the 68-kD possible fragment of haywire accumulating in the haync2 mutant did not appear to result from increased transcription or stability of the haywire mRNA encoded by haync2. Northern blot analysis of all the alleles sequenced revealed relatively normal levels of haywire transcript in all cases (Figure 4), with the possible exception of the haync2rv3 and haync2rv7 alleles. haync2rv3/TM3 and haync2rv7/TM3 flies appeared to have reduced levels of haywire mRNA compared to other alleles tested over the same balancer chromosome. As both of these alleles introduce stop codons early in the haywire protein-coding region (below), they may cause destabilization of the mRNA encoding the mutant allele (![]()
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Lethal alleles isolated as revertants of haync2:
Several mutations that revert the failure of haync2 to complement mutations in B2t introduce stop codons into the haywire coding region, supporting the hypothesis that haync2 fails to complement B2t because of the production of a poison product (Table 1). haync2rv1 introduces a stop codon in helicase domain VI, haync2rv3 results in a stop codon in the conserved nucleotide-binding domain, and haync2rv7 has a stop codon six amino acids before the predicted magnesium-binding domain (helicase domain II, Figure 1). These nonsense mutations are all lethal, supporting an essential role in flies for the haywire gene product, probably in basal transcription.
A missense mutation (haync2rv2) and small rearrangement (haync2rv12) indicate that the nucleotide-binding domain of haywire is essential for viability. The haync2rv2 mutation replaced cysteine 377 with a tyrosine residue (Table 1). This cysteine, which lies eight amino acids downstream of the P loop (![]()
A viable revertant of haync2:
The haync2rv8 viable mutation changed glutamic acid 278 to lysine, introducing a charge change and possibly affecting protein structure or stability. haync2rv8 homozygotes are viable, indicating that glutamic acid 278 is not essential for basal transcription. Glu278 could be important for the repair of UV damage, since this allele also showed UV sensitivity (![]()
Altered amino acids encoded by wild-type haywire alleles:
The sequences of three wild-type alleles from different genetic backgrounds revealed regions of haywire/ERCC3 that are not essential (Figure 1). A wild-type cDNA from a dp cn bn strain and two different wild-type genomic sequences (red e and e11) differed at several positions within the amino acid coding region. Alanine residues at positions 238 and 244 in the dp cn bn and red e backgrounds were changed to threonine and proline, respectively, in wild-type haywire from the e11 chromosome. Amino acid 663 was a methionine in the e11 strain but a leucine in both the red e and dp cn bn strains. In addition, the e11 wild-type allele of haywire had a four-amino-acid deficiency at positions 253256 compared with haywire on both the red e and dp cn bn chromosomes. The four consecutive amino acids missing in the e11 background are valine/valine/alanine/alanine. Most of the wild-type polymorphisms occur in regions that are poorly conserved between the Drosophila, yeast, and mammalian homologs, and may identify residues of haywire not essential for function.
| DISCUSSION |
|---|
The single nucleotide mutation in the haync2 allele that causes an arginine-to-cysteine change is responsible for both the production of a shortened polypeptide associated with the haync2 allele and the genetic interaction observed between haync2 and B2t mutations. Several molecular mechanisms of reverting the genetic interaction between haync2 and B2tnull are suggested by sequence analysis of the haywire alleles obtained as revertants of haync2. Destruction of the P loop of the nucleotide-binding domain reverted the genetic interaction between haync2 and B2tnull (haync2rv12, Table 1) possibly by destroying the ATP-binding or helicase function of the haync2 primary product. Two other revertant alleles, haync2rv2 and haync2rv8, caused missense mutations that could alter protein conformation or stability. haync2rv2, which caused a change from a cysteine to tyrosine, altered a potential disulfide bond partner. haync2rv8, which caused a change from a glutamic acid to lysine, caused a change from a negatively charged residue to a positively charged residue. Finally, nonsense mutations haync2rv1, haync2rv3, and haync2rv7 reverted the genetic interaction between haync2 and Bt2null. The finding that at least four out of six revertants of haync2 (the three stop codons and the P-loop mutation) are mutations that should knock out haywire function supports the idea that the original haync2 allele encodes a poison product.
The shortened polypeptide that accumulates in haync2 flies is likely to be either responsible for or a direct result of the poison nature of the haync2 allele, as the 68-kD polypeptide no longer accumulated in six out of six mutants that reverted the dominant enhancer effect of haync2 (Figure 2). The 68-kD polypeptide that accumulates in haync2 flies is not likely to be caused by a simple truncation of the haywire protein near the site of the nc2 mutation. The stop codon mutation in haync2rv1 (Table 1) suggests that a simple truncation event near amino acid 652 results in neither production of a poison product nor accumulation of the 68-kD polypeptide (Figure 2). Furthermore, the haync2rv1 allele is lethal, perhaps because of truncation of the protein within the last conserved helicase domain, whereas the haync2 allele is viable (Table 1).
The haync2 allele encodes a product that must contain at least some wild-type function, as haync2/Df(hay) flies were fully viable. As the mutation responsible for causing accumulation of the truncated product is not a stop codon, full-length haywire protein could be initially expressed from the haync2 allele. It is possible that this full-length but mutant haywire protein could provide sufficient haywire function for viability when initially expressed. However, defects in functioning or processing of the defective protein because of the Arg652-to-Cys mutation could alter or disrupt normally occurring processing of the full-length haywire protein, resulting in accumulation of a shortened form of the protein in haync2. The observation that the 68-kD shortened polypeptide accumulated to much higher levels than the wild-type haywire product also suggests the possibility of turnover of haywire/ERCC3 as a normal part of its function. We would like to raise the possibility that the haywire protein might normally be degraded as part of the functional cycle of TFIIH in transcription initiation. It is also possible that the 68-kD polypeptide that accumulates in haync2 flies is the product of some other gene that is upregulated in this particular mutant background. If so, however, the product of this hypothetical upregulated gene would have to cross-react with the affinity-purified, anti-haywire antiserum. In addition, upregulation of the other hypothetical gene appears to depend strictly on the poison product effect of the haync2 allele, as the polypeptide was not detected in any of the six revertants of haync2.
The haync2 allele genetically interacts with mutations in the B2t locus (![]()
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| FOOTNOTES |
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1 Present address: California Pacific Medical Center Research Institute, Stern Building, 2330 Clay St., San Francisco, CA 94115. ![]()
| ACKNOWLEDGMENTS |
|---|
We thank Barbara Robertson and Kim Schuske, who conducted genetic screens to identify new revertant alleles of haync2, and Cricket Wood for technical assistance. We thank Stig Hansen and Robert Tjian for help and advice in producing affinity-purified antibodies to the haywire protein. We acknowledge the protein and nucleic acid (PAN) facility, Stanford University, for synthesizing oligonucleotides used in this work. This work was supported by National Institutes of Health grants HD-18127 and HD-29194 to M.T.F.
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T transition introduced into an otherwise wild-type haywire genomic fragment; w; ScO/CyO, genetic background in which the transgene was propagated; P[A, ry+], wild-type copy of haywire introduced into flies. Note: Both P[A3, w+] and P[A, ry+] have two wild-type endogenous copies of haywire.



