Molecular analysis of Saccharomyces cerevisiae chromosome I. On the number of genes and the identification of essential genes using temperature-sensitive-lethal mutations

Previous analyses of Saccharomyces cerevisiae chromosome I have suggested that the majority (greater than 75%) of single-copy essential genes on this chromosome are difficult or impossible to identify using temperature-sensitive (Ts-) lethal mutations. To investigate whether this situation reflects intrinsic difficulties in generating temperature-sensitive proteins or constraints on mutagenesis in yeast, we subjected three cloned essential genes from chromosome I to mutagenesis in an Escherichia coli mutator strain and screened for Ts- lethal mutations in yeast using the "plasmid-shuffle" technique. We failed to obtain Ts- lethal mutations in two of the genes (FUN12 and FUN20), while the third gene yielded such mutations, but only at a low frequency. DNA sequence analysis of these mutant alleles and of the corresponding wild-type region revealed that each mutation was a single substitution not in the previously identified gene FUN19, but in the adjacent, newly identified essential gene FUN53. FUN19 itself proved to be non-essential. These results suggest that many essential proteins encoded by genes on chromosome I cannot be rendered thermolabile by single mutations. However, the results obtained with FUN53 suggest that there may also be significant constraints on mutagenesis in yeast. The 5046 base-pair interval sequenced contains the complete FUN19, FUN53 and FUN20 coding regions, as well as a portion of the adjacent non-essential FUN21 coding region. In all, 68 to 75% of this interval is open reading frame. None of the four predicted products shows significant homologies to known proteins in the available databases.

New molecular markers for the distal end of the t-complex and their relationships to mutations affecting mouse development

Many mutations affecting mouse development have been mapped to the t-complex of mouse chromosome 17. We have obtained 17 cosmid clones as molecular markers for this region by screening a hamster-mouse chromosome 17 and 18 cell hybrid cosmid library with mouse-specific repetitive elements and mapping positive clones via t-haplotype vs. C3H restriction fragment length polymorphism (RFLP) analysis. Twelve of the clones mapping distal to Leh66B in t-haplotypes are described here. Using standard RFLP analysis or simple sequence length polymorphism between t-haplotypes, exceptional partial t-haplotypes and nested sets of inter-t-haplotype recombinants, five cosmids have been mapped in or around In(17)3 and seven in the most distal inversion In17(4). More precise mapping of four of the cosmids from In(17)4 shows that they will be useful in the molecular identification of some of the recessive lethals mapped to the t-complex: two cosmids map between H-2K and Crya-1, setting a distal limit in t-haplotypes for the position of the tw5 lethal, one is inseparable from the tw12 lethal, and one maps distal to tf near the t0(t6) lethal and cld.

The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli

One of the most abundant modified nucleosides in tRNA is 5-methyluridine (m5U or rT, ribothymidine). The enzyme tRNA(m5U54)methyltransferase [S-adenosyl-L-methionine:tRNA (uracil-5-)-methyltransferase, EC 2.1.1.35] (the trmA gene product) catalyzes S-adenosylmethionine-dependent methylation of the uracil in position 54 (T psi C loop) in all Escherichia coli tRNAs to form m5U. Hitherto no modified nucleoside in tRNA has been shown to be essential for growth, although their importance in fine tuning the function of tRNA is well established. In this paper, we show that the structural gene trmA is essential for viability, although the known catalytic activity of the tRNA(m5U54)methyltransferase is not.

Blackpatch, a neural degeneration mutation that interacts with the Notch locus in Drosophila

We have identified a gene in Drosophila melanogaster that is involved in the development of the adult eye and optic lobe of the brain and that interacts with facet alleles at the Notch locus. We have named this locus Blackpatch (Bpt). Mutant alleles of Bpt produce a variety of abnormal phenotypes in the presence of facet alleles. These phenotypes include neural degeneration in the eye and in the optic lobe of the adult brain that begins 60 hr after pupariation and produces a dark, necrotic eye spot in the adult eye. Other phenotypes include recessive embryonic lethality, pharate adult lethality, and premature adult death. We have isolated and characterized 10 Bpt alleles, all of which yield the neural eye/brain degeneration phenotype in individuals who are also homozygous or hemizygous for facet mutations. Only some of the facet alleles interact with Bpt. Bpt mutations also interact with the split mutation but do not interact with other types of Notch mutation. Somatic mosaic analysis and imaginal disc transplantation experiments suggest that the optic lobe of the brain may be the focus of Bpt action. We conclude that the Notch and Bpt genes have important functions during the interaction between the retina and the optic lobe of the brain.

The genotoxicity of the anti-cancer drug mitoxantrone in somatic and germ cells of Drosophila melanogaster

The novel antineoplastic drug mitoxantrone was studied for its genotoxic effects in Drosophila melanogaster. In male germ cells, the clinical preparation Novantrone, the dihydrochloride salt of mitoxantrone, did not induce sex-linked recessive lethal mutations in feeding and injection experiments with adult flies, although statistically the results were inconclusive rather than truly negative. However, the free base mitoxantrone was weakly, but significantly genotoxic in this test (0.14% lethals/mM exposure concentration); this is most probably the result of prolonged exposure. On the other hand, both forms of mitoxantrone assayed were clearly genotoxic in the somatic mutation and recombination test of the wing. This test assays the cells of the proliferating imaginal wing discs of larvae. Depending on the feeding method used, the overall clone induction frequency was in the range of about 2-6 x 10(-5) per cell and cell generation and per mM exposure dose. Correction of these frequencies according to mean clone size led to slightly higher estimates (by about 5-25% higher). Although the majority of the clone induction events are due to mitotic recombination, a significant proportion can be attributed to mutational events (gene and chromosome mutations). The genotoxicity of mitoxantrone seems to depend mainly on impaired DNA synthesis in cycling cells owing to the compound's ability to inhibit topoisomerase II by intercalation into DNA.

Interspecific comparison of the transformer gene of Drosophila reveals an unusually high degree of evolutionary divergence

The transformer (tra) gene of Drosophila melanogaster occupies an intermediate position in the regulatory pathway controlling all aspects of somatic sexual differentiation. The female-specific expression of this gene's function is regulated by the Sex lethal (Sxl) gene, through a mechanism involving sex-specific alternative splicing of tra pre-mRNA. The tra gene encodes a protein that is thought to act in conjunction with the transformer-2 (tra-2) gene product to control the sex-specific processing of doublesex (dsx) pre-mRNA. The bifunctional dsx gene carries out opposite functions in the two sexes, repressing female differentiation in males and repressing male differentiation in females. Here we report the results from an evolutionary approach to investigate tra regulation and function, by isolating the tra-homologous genes from selected Drosophila species, and then using the interspecific DNA sequence comparisons to help identify regions of functional significance. The tra-homologous genes from two Sophophoran subgenus species, Drosophila simulans and Drosophila erecta, and two Drosophila subgenus species, Drosophila hydei and Drosophila virilis, were cloned, sequenced and compared to the D. melanogaster tra gene. This comparison reveals an unusually high degree of evolutionary divergence among the tra coding sequences. These studies also highlight a highly conserved sequence within intron one that probably defines a cis-acting regulator of the sex-specific alternative splicing event.

A dominant negative allele of p34cdc2 shows altered phosphoamino acid content and sequesters p56cdc13 cyclin

The cdc2 gene product, a 34-kDa phosphoprotein with serine/threonine protein kinase activity, has been implicated as the key component in the regulation of the eucaryotic cell cycle. Activation of the cdc2 protein kinase is regulated by its phosphorylation state and by interaction with other proteins. We have mutagenized the fission yeast cdc2 gene to obtain conditionally dominant negative alleles. One of these mutants, named DL2, is characterized in this report. Overexpression of the mutant protein in a wild-type cdc2 background is lethal and leads to arrest in the G2 phase of the cell cycle. The mutant phenotype is the result of a single amino acid change in the GDSEID motif of the protein, a region of identity in all cdc2 homologs, and results in a nonfunctional protein that shows an altered content of phosphothreonine. Multicopy suppressors of the dominant negative phenotype have been isolated, and one of these has been shown to encode the cdc13 cyclin B gene product.

All colonies of CHO-K1 cells surviving gamma-irradiation contain non-viable cells

This paper addresses the problem of the production of defective cells within clones arising from irradiated progenitor cells and is specifically aimed at answering the question of whether lethal mutations result from a generalised effect which lowers the ability of all the progeny to divide successfully or whether it represents a late expressed but unique lethal defect induced by radiation which occurs in some cells only and which causes those cells only to cease dividing. The results obtained from autoradiographic analysis of cells within individual surviving colonies (i.e. containing more than 150 cells) suggests that some cells in all clones are not synthesizing DNA over a 9-h period and that the proportion of non-synthesising cells rises with increasing dose of radiation from less than 3% in the controls to 80-85% after a progenitor dose of 12.5 Gy. Because of the possibility that cells had longer division times post irradiation, these results were repeated using Ki67 antibody labelling, a technique which identifies cells which are in cycle. The results were similar. This suggests the non-labelled cells were not reproducing. Both techniques were also used to look at the % labelling of morphologically abnormal cells in the colonies. The results suggested that up to 35% of these abnormal cells were actively cycling and about 20% were synthesising DNA. Abnormal cells did not appear in subcultures of survivor progeny suggesting that they may have failed to replate successfully and may contribute to the lethally mutated population. The idea that radiation induces a general instability in the cell population was supported by experiments where growth and the plating efficiency of irradiated progeny was measured daily. This revealed that the growth curves deviated from the control by a constant factor suggesting a division probability of about 70% of the control level after a progenitor dose of 10 Gy. The results are discussed in the context of their significance for survival curve analysis and for radiotherapy and radiation protection results.

Genetic and molecular analysis of the dpy-14 region in Caenorhabditis elegans

Essential genes have been identified in the 1.5 map unit (m.u.) dpy-14-unc-29 region of chromosome 1 in Caenorhabditis elegans. Previous work defined nine genes with visible mutant phenotypes and nine genes with lethal mutant phenotypes. In this study, we have identified an additional 28 essential genes with 97 lethal mutations. The mutations were mapped using eleven duplication breakpoints, eight deficiencies and three-factor recombination experiments. Genes required for the early stages of development were common, with 24 of the 37 essential genes having mutant phenotypes arresting at an early larval stage. Most mutants of a gene have the same time of arrest; only four of the 20 essential genes with multiple alleles have alleles with different phenotypes. From the analysis of complementing alleles of let-389, alleles with the same time-of-arrest phenotype were classified as either hypomorphic or amorphic. Mutants of let-605, let-534 and unc-37 have both uncoordinated and lethal phenotypes, suggesting that these genes are required for the coordination of movement and for viability. The physical and genetic maps in the dpy-14 region were linked by positioning two N2/BO polymorphisms with respect to duplications in the region, and by localizing the right breakpoint of the deficiency hDf8 on the physical map. Using cross-species hybridization to C. briggsae, ten regions of homology have been identified, eight of which are known to be coding regions, based on Northern analysis and/or the isolation of cDNA clones.

Overproduction and functional analysis of DNA primase subunits from yeast and mouse

Eukaryotic DNA primases are composed of two distinct subunits of 48-50 and 58-60 kDa. The amino acid sequences derived from the nucleotide sequences of the cloned genes are known only for the yeast and mouse polypeptides, and the extensive homology between the corresponding mouse and yeast subunits suggests conservation of functional domains. We were able to express in Saccharomyces cerevisiae the homologous and mouse primase-encoding genes under the control of both the constitutive ADH1 and the inducible GAL1 strong promoters, thus obtaining strains producing relevant amounts of the different polypeptides. In vivo complementation studies showed that neither one of the wild-type mouse primase-encoding genes was able to rescue the lethal or temperature-sensitive phenotype caused by mutations in the yeast PRI1 or PRI2 genes, indicating that these proteins, even if structurally and functionally very similar, might be involved in critical species-specific interactions during DNA replication.

Caenorhabditis elegans gene ced-9 protects cells from programmed cell death

The gene ced-9 of the nematode Caenorhabditis elegans acts to protect cells from programmed cell death. A mutation that abnormally activates ced-9 prevents the cell deaths that occur during normal C. elegans development. Conversely, mutations that inactivate ced-9 cause cells that normally live to undergo programmed cell death; these mutations result in embryonic lethality, indicating that ced-9 function is essential for development. The ced-9 gene functions by negatively regulating the activities of other genes that are required for the process of programmed cell death.

Maternal-effect selfish genes in flour beetles

A previously unknown class of dominant, maternal-effect lethal M factors was found to be widespread in natural populations of the flour beetle, Tribolium castaneum, collected on several continents. Such factors are integrated into the host chromosomes at variable locations and show the remarkable property of self-selection by maternal-effect lethality to all hatchlings that do not inherit a copy of the factor itself. Offspring are rescued by either paternally or maternally inherited copies. The M-bearing chromosome is thereby perpetuated at the expense of its non-M homolog. M factors that map to different regions of the genome do not rescue one another's maternal-effect lethality. Factors expressing these properties are predicted to spread in a population, even in the absence of any additional selective advantage. Similar factors also occur in the related species T. confusum.

Induction of recessive lethal and specific locus mutations in the zebrafish with ethyl nitrosourea

Recessive lethal mutations and mutations at the gol-1 locus were induced in the zebrafish by exposure of mature sperm to the alkylating agent ethyl nitrosourea (ENU). Embryonic lethal phenotypes were recognized among the parthenogenetic progeny of mutagenized animals or among the progeny of daughters of mutagenized animals. Novel specific locus mutations were identified by the failure of mutagenized chromosomes to complement pre-existing mutant alleles at the gol-1 locus. Each mutagenized individual harboured approximately 10 embryonic lethal mutations in its germ line and about 1 in 500 mutagenized animals harboured a new mutation at the gol-1 locus. Three lines of evidence indicate that the majority of mutations that were recovered following treatment of mature sperm with ENU were probably point mutations. First, the soma and germ lines of mutagenized animals were mosaic, as expected following simple alkylation of sperm DNA. Second, mutations induced by ENU at the gol-1 locus affected pigmentation but not viability, unlike the majority of mutations induced at this locus with gamma-irradiation. Third, the ratio of specific locus:recessive lethal mutations induced by ENU was approximately 50-fold lower than the ratio observed following mutagenesis with gamma-rays. Comparison of the incidence with which embryonic recessive lethal mutations were induced with the incidence with which specific locus mutations arose indicates that there are greater than 5000 genes essential to the development and viability of the zebrafish embryo.

Studies of a spontaneous lethal mutation at the albino locus in SELH/Bc mice

We report a new mutation at the albino locus in SELH/Bc mice. The mutation arose spontaneously in a male mouse that appeared to be a somatic and germ line mosaic for a new albino (c) allele, provisionally named cBc. The mutation is a recessive lethal, causing embryonic death soon after implantation. We have shown that there is no detectable activity of the Mod-2 allele in cis with the mutation and conclude that the mutation is probably a deletion that includes the c locus, the Mod-2 locus, the intervening 2 cM, and at least one locus essential for postimplantation embryonic survival, either proximal to the c locus or distal to the Mod-2 locus. This new mutation is similar to most previously reported spontaneous mutations at the albino locus in that it arose in a somatic and germ line mosaic mutant animal but differs from them in that it is an embryonic lethal when homozygous and is apparently a deletion. SELH/Bc mice appear to have a high mutation rate. This lethal albino mutation that appears to be a postmeiotic deletion should be useful in the search for the mechanism of mutagenesis in SELH/Bc mice. It may also be useful in mapping essential genes in the c-locus region.

Molecular analysis of the lethal(1)B214 region at the base of the X chromosome of Drosophila melanogaster

Approximately 50 kb of genomic DNA was isolated from polytene chromosome bands 19F1 and 2 of Drosophila melanogaster. Bands 19F1 and 2 are in the immediate vicinity of the beta-heterochromatin at the base of the X chromosome and encompass the little fly-like and lethal(1)B214 complementation groups. The cloned DNA consists of an approximately 21 kb stretch of unique or low copy number sequence that is bounded by repetitive elements interspersed with further unique sequences. The presence of repeated sequences is characteristic of regions within and adjacent to beta-heterochromatin. At least part of a tRNA gene cluster is present within the 50 kb of cloned DNA. The cloned region also produces at least 18 discrete size classes of developmentally regulated poly(A)+ RNA species. A 2 kb EcoRI fragment (E10), which lies in the 21 kb stretch of unique sequence, generates seven of these transcripts (of sizes 3.5, 3.35, 2.1, 2.0, 1.5, 1.2 and 1.0 kb) in wild-type flies. However, a small deletion of approximately 75 bp in E10 in a lethal(1)B214 mutant allele is associated with alterations in the production or processing of all seven of these transcripts. These data identify E10 sequences as belonging to the lethal(1)B214 gene and suggest that the wild-type lethal(1)B214 gene encodes multiple transcripts. Furthermore, no transcripts of the same size and having the same developmental profile as those generated by the wild-type E10 fragment were identified by probes covering the remainder of the cloned region. This suggests that at least the larger transcripts hybridizing to E10 are partly transcribed from sequences located outside the cloned region, which indicates that the lethal(1)B214 gene extends for more than 20 kb and contains other transcriptionally active sequences within it.

Isolation and phenotypic analysis of conditional-lethal, linker-insertion mutations in the gene encoding the largest subunit of RNA polymerase II in Saccharomyces cerevisiae

Linker-insertion mutagenesis was used to isolate mutations in the Saccharomyces cerevisiae gene encoding the largest subunit of RNA polymerase II (RPO21, also called RPB1). The mutant rpo21 alleles carried on a plamid were introduced into a haploid yeast strain that conditionally expresses RPO21 from the inducible promoter pGAL10. Growth of this strain on medium containing glucose is sustained only if the plasmid-borne rpo21 allele encodes a functional protein. Of nineteen linker-insertion alleles tested, five (rpo21-4 to -8) were found that impose a temperature-sensitive (ts) lethal phenotype on yeast cells. Four of these five ts alleles encode mutant proteins in which the site of insertion lies near one of the regions of the largest subunit that have been conserved during evolution. Two of the ts mutants (rpo21-4 and rpo21-7) display pleiotropic phenotypes, including an auxotrophy for inositol and a decreased proliferation rate at the permissive temperature. The functional relationship between RPO21 and RPO26, the gene encoding the 17.9 kDa subunit shared by RNA polymerases I, II, and III was investigated by determining the ability of increased dosage of RPO26 to suppress the ts phenotype imposed by rpo21-4 to -8. Suppression of the ts defect was specific for the rpo21-4 allele and was accompanied by co-suppression of the inositol auxotrophy. These results suggest that mutations in the largest subunit of RNA polymerase II can have profound effects on the expression of specific subsets of genes, such as those involved in the metabolism of inositol. In the rpo21-4 mutant, these pleiotropic phenotypes can be attributed to a defective interaction between the largest subunit and the RPO26 subunit of RNA polymerase II.

Induction of mutations in the zebrafish with ultraviolet light

Recessive lethal germline and specific locus somatic mutations were induced efficiently in the zebrafish by exposure of mature sperm to UV light. Mutagenesis of sperm yielded mosaic individuals: clones bearing novel mutations represented approximately 12-25% of the haploid germ cells and 25-50% of the somatic tissue. Simple methods are described for the reliable identification and propagation of newly arising developmental mutations in zebrafish.

Five novel elements involved in the regulation of mitosis in fission yeast

Five new elements of the mitotic control in the fission yeast Schizosaccharomyces pombe were isolated from gene libraries as multicopy suppressors of the conditional lethal phenotype of win1-1 wee1ts cdc25ts triple mutant strains. These genes were designated wis1(+)-wis5+ for win suppressing, and do not correspond to win1+ or any of the previously characterised mitotic control genes. None of the wis genes is capable of suppressing the cdc phenotype of cdc25ts strains, suggesting that their effect is not simply to reverse the effect of loss of cdc25 function. wis1+ has been previously reported to encode a putative serine/threonine protein kinase that acts as a dosage-dependent inducer of mitosis. wis4+ appears to be a specific suppressor of the win1-1 mutation. wis2+ and wis3+ are capable of suppressing a wide range of cdc phenotypes arising from the combination of various mutations with wee1ts and cdc25ts, suggesting that the wis2+ and wis3+ products may interact with elements central to the mitotic control.

A gene encoding a putative tyrosine phosphatase suppresses lethality of an N-end rule-dependent mutant

The N-end rule relates the in vivo half-life of a protein to the identity of its N-terminal residue. In the yeast Saccharomyces cerevisiae, mutational inactivation of the N-end rule pathway is neither lethal nor phenotypically conspicuous. We have used a "synthetic lethal" screen to isolate a mutant that requires the N-end rule pathway for viability. An extragenic suppressor of this mutation was cloned and found to encode a 750-residue protein with strong sequence similarities to protein phosphotyrosine phosphatases. This heat-inducible gene was named PTP2. Null ptp2 mutants grow slowly, are hypersensitive to heat, and are viable in either the presence or absence of the N-end rule pathway. We discuss possible connections between dephosphorylation of phosphotyrosine in proteins and the N-end rule pathway of protein degradation.

Microphthalmia-4: a sex-influenced inherited eye condition of the chicken

A new mutation of the chicken that causes a reduction in eyeball size is described. Eyeball size reduction is extreme in over 80% of affected individuals. Two-thirds of affected chickens have bilateral expression, while the rest are unilaterally affected. The trait appears to affect liveability beyond that which might be expected of blind individuals. Embryonic mortality was increased five-fold among microphthalmic individuals, and all but two of the 35 microphthalmic chicks that hatched died within a week. Data from various crosses indicate that this condition is inherited as an autosomal recessive with expression being limited primarily to females. The name microphthalmia-4 and the gene symbol mi-4 are proposed for this trait.

The genetic analysis of snf: a Drosophila sex determination gene required for activation of Sex-lethal in both the germline and the soma

Our analysis demonstrates that snf is a positive regulator of Sex-lethal in both the germline and the soma. In the germline, unregulated expression of Sex-lethal can bypass the requirement for snf+ gene function, implying that snf is required for Sex-lethal activity in the germline. This conclusion is supported by the finding that the Sex-lethal transcription pattern is abnormal in a snf mutant background. In the soma, activation of Sex-lethal appears to be sensitive to snf gene dosage only when the probability of Sex-lethal activation has been otherwise reduced. We also show that the activity of one of the constitutive Sex-lethal alleles (SxlM1) is sensitive to snf gene dosage, demonstrating that, in spite of its constitutive behavior in some assays, SxlM1 is still subject to some regulation. In spite of snf's role in the somatic activation of Sex-lethal, no lethal alleles of snf were isolated in a screen of approximately 25,000 chromosomes. The observation that the existing snf mutations present a lethal phenotype only in certain genetic backgrounds suggests that snf is required, but is not essential, for the activation of Sex-lethal in the soma. In contrast, snf does appear to be essential for activation of Sex-lethal in the germline, as evidenced by its female-sterile phenotype.

Developmental arrest and ecdysteroid deficiency resulting from mutations at the dre4 locus of Drosophila

Loss-of-function mutations of the dre4 gene of Drosophila melanogaster caused stage-specific developmental arrest, the stages of arrest coinciding with periods of ecdysteroid (molting hormone) regulated development. Nonconditional mutations resulted in the arrest of larval development in the first instar; embryogenesis was not impaired, and mutant larvae were behaviorally normal and long-lived. At 31 degrees the temperature-sensitive dre4e55 allele caused the arrest of larval development in the first or second instars. When upshifted to 31 degrees at various times during development, dre4e55 mutants exhibited nonpupariation of third-instar larvae, failure of pupal head eversion, failure of adult differentiation, or noneclosion of pharate adults. Under some temperature regimens second-instar larvae pupariated precociously without entering the normally intervening third-instar. Nonpupariation and defects in metamorphosis were associated with the reduction or elimination of ecdysteroid peaks normally associated with late-larval, prepupal, pupal and pharate adult development. Ecdysteroid production by larval ring glands from dre4e55 hemizygous larvae was suppressed after 2 hr of incubation in vitro at 31 degrees, indicating autonomous expression of the dre4 gene in the ring gland. We postulate that the dre4 gene is required for ecdysteroid production at multiple stages of Drosophila development and that the pathologies observed in dre4 mutants reflect developmental consequences of ecdysteroid deficiency.