Cell, Vol. 70, 877, September
18, 1992, Copyright
0 1992 by Cell Press
Letter to the Editor
Is DNA Strand Transfer Protein a Also a Transcription Factot? The sequence has recently been published of a gene, designated DSTl (DNA strand transferase l), that encodes the Saccharomyces cerevisiae DNA strand transfer protein a, Stpa, which promotes homologous pairing of DNA in meiosis (Clark et al., 1991). The predicted Stpa sequence of 309 residues includes one zinc-finger domain (Berg, 1988) presumably involved in DNA binding. Nosimilarity was reported between the predicted sequence of Stpa and any known sequence. However, during analysis of an unrelated zinc-finger protein, I found that the C-terminal 128 residues of Stpa are identical to the predicted product of the yeast gene PPRP, which encodes a zincfinger transcription factor (PpR) that regulates the expression of the MA4 gene (Hubert et al., 1983). URA4 encodes dihydroorotase, an enzyme of the pyrimidine biosynthetic pathway. Alignment of DSTl and PPRP reveals 99% DNA sequence identity in a 954 bp overlap, indicating that DSTl and PPRP are the same gene, assuming the sequence differences represent errors or allelic/strain variation. Of the seven base substitutions (asterisks, Figure l), five are silent, and the other two result in conservative replacements, consistent with alleliclstrain variation. The remaining diff erences are due to nucleotide insertion or deletion (arrows, Figure 1) and may be sequencing errors. The reported PPRP sequence could encode the majority, but not all, of Stpa provided two frame shifts (corresponding to such insertions/deletions) are allowed (Figure 1). The DSTlIPPRP gene appears to be single-copy based on Southern blot analysis (Clark et al., 1991). Stpa is the product of this gene by several criteria (Clark et al., 1991) and the purified protein possesses DNA strand transfer activity in an invitro system (Sugino et al., 1988). However, the same gene can complement a ppr2 mutant (Hubert et al., 1983). Furthermore, the ppr2 mutant allele has been sequenced to reveal a nonsense (ochre) mutation in the DSTllPPRP gene, and the ppr2 phenotype is suppressed in an ochre suppressing strain (Hubert et al., 1983). Thus, the product of the DSTllPPRP gene appears to have two distinct functions: one as a DNA strand transfer protein, and the other as a transcription factor. (The highly unlikely alternate possibility is that DSTl is an extragenic suppressor of ppr2, and that the ppr2 mutant carries an ochre mutation in the bona fide PPRP gene in addition to a spurious ochre mutation in the DSTl gene.) Although these functions share the requirement for a DNA-binding capability that may be mediated by the zinc-finger domain, they are otherwise unrelated. A full-length Stpa protein is apparently not required for Ppr2 function, because the DNA fragment that complements the ppr2 mutation (Hubert et al., 1983) lacks the DSTl promoter and the first 23 codons of the open reading
frame. In addition to the full-length Stpa protein, an antiStpa antibody detects several smaller proteins that persist in a strain carrying the dstl-1 disruption allele, which retains the 128 residue Ppr2 open reading frame and 97 bp of its 5’ flanking region (Clark et al., 1991). The dstl-1 strain appears to be wild-type for pyrimidine biosynthesis, as judged by its ability to grow in the absence of uracil (Clarket al., 1991). Thus, one or more of the species recognized by the anti-Stpa antibody may represent a truncated Stpa protein(s), such as Ppr2. The mechanism of their synthesis is unclear, but may not be due to multiple transcripts from the DSTlIPPRP gene, as northern blot analysis with a DSTl probe detects a single transcript from this locus (Clark et al., 1991). (However, under the growth conditions studied, pyrimidine biosynthesis, and thus PPRP expression, may have been repressed.) It is possible that Ppr2 may exist naturally as a truncated version of Stpa due to initiation at internal methionines (Figure 1) or proteolytic processing. Thus, the DSTllPPRP gene either encodes a protein that can function both as a transcription factor and a DNA strand transfer protein, or alternatively, directs the expression of related polypeptides with different functions. It will be interesting to see if the dstl-1 mutant, or other dstl deletion alleles, are impaired in the regulation of pyrimidine biosynthesis, and whether a ppr2 mutant exhibits reduced meiotic recombination frequency. Rohan T. Baker Molecular Genetics Group The John Curtin School of Medical Research The Australian National University PO Box 334 Canberra, Australian Capital Territory 2801 Australia References
Berg, J. M. (1988). Clark, A. 6.. Dykstra, 2576-2582.
Proc.
Natl. Acad.
Sci. USA 85, 99-102
C. C., and Sugino,
A. (1991).
Mol. Cell Biol. 71,
Hubert, J.-C., Guyonvarch, A., Kammerer, B, Exinger, P., and Lacroute, F. (1983). EMBO J. 2, 2071-2073. Sugino, A., Nitiss, J., and Resnick. USA 85, 3883-3687.
Figure 1. Alignment Sequences.
of DSTf
M. A. (1988).
F., Liljelund,
Proc. Natl. Acad. Sci.
and PPRP DNA and Predicted
DNA sequences are shown as solid lines, encoded proteins boxes. Nucleotidesubstitutions(‘)and insertions/deletions cated in PPRP relative to DST7.
Protein
as stippled (f)are indi-
18, 1992, Copyright
0 1992 by Cell Press
Letter to the Editor
Is DNA Strand Transfer Protein a Also a Transcription Factot? The sequence has recently been published of a gene, designated DSTl (DNA strand transferase l), that encodes the Saccharomyces cerevisiae DNA strand transfer protein a, Stpa, which promotes homologous pairing of DNA in meiosis (Clark et al., 1991). The predicted Stpa sequence of 309 residues includes one zinc-finger domain (Berg, 1988) presumably involved in DNA binding. Nosimilarity was reported between the predicted sequence of Stpa and any known sequence. However, during analysis of an unrelated zinc-finger protein, I found that the C-terminal 128 residues of Stpa are identical to the predicted product of the yeast gene PPRP, which encodes a zincfinger transcription factor (PpR) that regulates the expression of the MA4 gene (Hubert et al., 1983). URA4 encodes dihydroorotase, an enzyme of the pyrimidine biosynthetic pathway. Alignment of DSTl and PPRP reveals 99% DNA sequence identity in a 954 bp overlap, indicating that DSTl and PPRP are the same gene, assuming the sequence differences represent errors or allelic/strain variation. Of the seven base substitutions (asterisks, Figure l), five are silent, and the other two result in conservative replacements, consistent with alleliclstrain variation. The remaining diff erences are due to nucleotide insertion or deletion (arrows, Figure 1) and may be sequencing errors. The reported PPRP sequence could encode the majority, but not all, of Stpa provided two frame shifts (corresponding to such insertions/deletions) are allowed (Figure 1). The DSTlIPPRP gene appears to be single-copy based on Southern blot analysis (Clark et al., 1991). Stpa is the product of this gene by several criteria (Clark et al., 1991) and the purified protein possesses DNA strand transfer activity in an invitro system (Sugino et al., 1988). However, the same gene can complement a ppr2 mutant (Hubert et al., 1983). Furthermore, the ppr2 mutant allele has been sequenced to reveal a nonsense (ochre) mutation in the DSTllPPRP gene, and the ppr2 phenotype is suppressed in an ochre suppressing strain (Hubert et al., 1983). Thus, the product of the DSTllPPRP gene appears to have two distinct functions: one as a DNA strand transfer protein, and the other as a transcription factor. (The highly unlikely alternate possibility is that DSTl is an extragenic suppressor of ppr2, and that the ppr2 mutant carries an ochre mutation in the bona fide PPRP gene in addition to a spurious ochre mutation in the DSTl gene.) Although these functions share the requirement for a DNA-binding capability that may be mediated by the zinc-finger domain, they are otherwise unrelated. A full-length Stpa protein is apparently not required for Ppr2 function, because the DNA fragment that complements the ppr2 mutation (Hubert et al., 1983) lacks the DSTl promoter and the first 23 codons of the open reading
frame. In addition to the full-length Stpa protein, an antiStpa antibody detects several smaller proteins that persist in a strain carrying the dstl-1 disruption allele, which retains the 128 residue Ppr2 open reading frame and 97 bp of its 5’ flanking region (Clark et al., 1991). The dstl-1 strain appears to be wild-type for pyrimidine biosynthesis, as judged by its ability to grow in the absence of uracil (Clarket al., 1991). Thus, one or more of the species recognized by the anti-Stpa antibody may represent a truncated Stpa protein(s), such as Ppr2. The mechanism of their synthesis is unclear, but may not be due to multiple transcripts from the DSTlIPPRP gene, as northern blot analysis with a DSTl probe detects a single transcript from this locus (Clark et al., 1991). (However, under the growth conditions studied, pyrimidine biosynthesis, and thus PPRP expression, may have been repressed.) It is possible that Ppr2 may exist naturally as a truncated version of Stpa due to initiation at internal methionines (Figure 1) or proteolytic processing. Thus, the DSTllPPRP gene either encodes a protein that can function both as a transcription factor and a DNA strand transfer protein, or alternatively, directs the expression of related polypeptides with different functions. It will be interesting to see if the dstl-1 mutant, or other dstl deletion alleles, are impaired in the regulation of pyrimidine biosynthesis, and whether a ppr2 mutant exhibits reduced meiotic recombination frequency. Rohan T. Baker Molecular Genetics Group The John Curtin School of Medical Research The Australian National University PO Box 334 Canberra, Australian Capital Territory 2801 Australia References
Berg, J. M. (1988). Clark, A. 6.. Dykstra, 2576-2582.
Proc.
Natl. Acad.
Sci. USA 85, 99-102
C. C., and Sugino,
A. (1991).
Mol. Cell Biol. 71,
Hubert, J.-C., Guyonvarch, A., Kammerer, B, Exinger, P., and Lacroute, F. (1983). EMBO J. 2, 2071-2073. Sugino, A., Nitiss, J., and Resnick. USA 85, 3883-3687.
Figure 1. Alignment Sequences.
of DSTf
M. A. (1988).
F., Liljelund,
Proc. Natl. Acad. Sci.
and PPRP DNA and Predicted
DNA sequences are shown as solid lines, encoded proteins boxes. Nucleotidesubstitutions(‘)and insertions/deletions cated in PPRP relative to DST7.
Protein
as stippled (f)are indi-
