The effect of DNA replication on mutation of the Saccharomyces cerevisiae CDC8 gene

Summary Incubation in YPD medium under permissive conditions when DNA replication is going on, strongly stimulates the induction of cdc⁺ colonies of UV-irradiated cells of yeast strains HB23 (cdc8-1/cdc8-3), HB26 (cdc8-3/cdc8-3) and HB7 (cdc8-1/cdc8-1). Inhibition of DNA replication by hydroxyurea, araCMP, cycloheximide or caffeine or else by incubation in phosphate buffer pH 7.0, abolishes this stimulation. Thus the replication of DNA is strongly correlated with the high induction of cdc⁺ colonies by UV irradiation. It is postulated that these UV-induced cdc⁺ colonies arise as the result infidelity in DNA replication.     

The essential Schizosaccharomyces pombe cdc23 DNA replication gene shares structural and functional homology with the Saccharomyces cerevisiae DNA43 (MCM10) gene

The fission yeast cdc23 gene is required for correct DNA replication: cdc23 mutants show reduced rates of DNA synthesis and become elongated after cell-cycle arrest. We have cloned the Schizosaccharomyces pombe cdc23 gene by complementation of the temperature-sensitive phenotype of cdc23-M36 and confirmed the identity of the gene by integrative mapping. Analysis of the DNA sequence reveals that cdc23 can encode a protein of 593 amino acids (M_r=67 kDa) with 22% overall identity and many structural homologies with the product of the Saccharomyces cerevisiae DNA43 (MCM10) gene which is required for correct initiation of DNA synthesis at chromosomal origins of replication. Construction of a cdc23 null allele has established that the cdc23 gene is essential for viability, with cdc23 deletion mutant spores germinating but undergoing arrest with undivided nuclei in the first or second cell cycle. The S. pombe cdc23 gene on an expression plasmid is able to complement the S. cerevisiae dna43-1 mutant. These structural and functional homologies between two distantly related species suggest that cdc23 and DNA43 may represent genes for a conserved essential eukaryotic DNA replication function. Received: 12 April / 6 July 1998     

Cdm1, the smallest subunit of DNA polymerase d in the fission yeast Schizosaccharomyces pombe, is non-essential for growth and division

Highly purified DNA polymerase δ from the fission yeast Schizosaccharomyces pombe is a complex of at least four distinct subunits. Genes encoding three of these (pol3 ⁺ /cdc6 ⁺ , cdc1 ⁺ and cdc27 ⁺ ) have been characterised previously. Here we describe the isolation and characterisation of cdm1 ⁺ , the gene encoding the smallest (22kDa) subunit of the Pol δ complex. Over-expression of cdm1 ⁺ , which encodes a 160 amino-acid protein with no significant sequence similarity to proteins in current databases, is able to rescue cells carrying temperature-sensitive mutations in either pol3 ⁺ /cdc6 ⁺ , cdc1 ⁺ or cdc27 ⁺ . Cells deleted for cdm1 ⁺ are viable, indicating that cdm1 ⁺ is non-essential for mitotic growth, and are no more sensitive to a variety of DNA replication inhibitors and DNA damaging agents than are wild-type cells. In addition, over-expression of cdm1 ⁺ suppresses the temperature-sensitive cdc24-M38 mutant suggesting that cdc24 ⁺ may also have a role in DNA polymerase δ function. Received: 14 June / 10 August 1998     

Chemical mutagenesis and DNA synthesis in cdc8, a DNA replication mutant of Saccharomyces cerevisiae

Summary Incubation of cdc8 mutants of the yeast Saccharomyces cerevisiae in YPD under permissive conditions, when DNA replication is taking place, prior to transfer to restrictive conditions, strongly stimulates induction of cdc ⁺ colonies of ethyl methane sulphonate (EMS)- and methyl methane sulphonate (MMS)-treated yeast strains HB23 (cdc8-1/cdc8-3), HB26 (cdc8-3/cdc8-3) and HB7 (cdc8-1/cdc8-1). After diepoxybutane (DEB) treatment, both the induction of cdc ⁺ colonies and their stimulation after incubation in YPD under permissive conditions is low. The results obtained show that stimulation of induction of cdc ⁺ colonies under permissive conditions occurs not only after UV-treatment, but also after treatment with such mutagens as EMS and MMS.     

Analysis of mutagenic DNA repair in a thermoconditional mutant of Saccharomyces cerevisiae

Summary A double mutant being thermoconditionally defective in mutation induction as well as in repair of pre-lethal UV-induced DNA damage (rev2 ^ts ) and deficient in excision repair (rad3-2) was studied in temperature-shift experiments. The influence of inhibitors of DNA replication (hydroxyurea, aphidicolin) was determined. Additionally, an analysis of the dose-response pattern of mutation induction (mutation kinetics) at several ochre alleles was carried out. It was concluded that the UV-inducible REV2 dependent mutagenic repair process is not induced in excision-deficient cells. In excision-deficient cells, REV2 dependent mutation fixation is slow and mostly postreplicative though not dependent on DNA replication. The REV2 mediated mutagenic process could be separated from the repair function.     

Cloning and manipulation of the Schizosaccharomyces pombe his7 +gene as a new selectable marker for molecular genetic studies

We have cloned the his7 ⁺ gene of the fission yeast Schizosaccharomyces pombe by complementation of the recessive mutant allele his7-366. The his7 ⁺ gene is able to complement a mutation of the Escherichia coli hisI gene, suggesting that his7 ⁺ encodes a phosphoribosyl-AMP cyclohydrase. Subcloning experiments localize the gene to a 1.9-kb XbaI-BglII fragment. We describe the construction of plasmids to facilitate the use of his7 ⁺ as a selectable marker in S. pombe studies. Plasmid pEA2 carries his7 ⁺ cloned into the pUC18 polylinker. From either pEA2 or the original his7 ⁺ clone, pMN1, fragments carrying his7 ⁺ can be isolated using a variety of restriction enzymes for the construction of gene disruptions. Plasmid pEA500 is a cloning vector that carries his7 ⁺ and ars1, yet retains the ability to use the blue/white color screen to identify recombinants.     

SV40 DNA replication: From the A gene to a nanomachine

Duplication of the simian virus 40 (SV40) genome is the best understood eukaryotic DNA replication process to date. Like most prokaryotic genomes, the SV40 genome is a circular duplex DNA organized in a single replicon. This small viral genome, its association with host histones in nucleosomes, and its dependence on the host cell milieu for replication factors and precursors led to its adoption as a simple and powerful model. The steps in replication, the viral initiator, the host proteins, and their mechanisms of action were initially defined using a cell-free SV40 replication reaction. Although our understanding of the vastly more complex host replication fork is advancing, no eukaryotic replisome has yet been reconstituted and the SV40 paradigm remains a point of reference. This article reviews some of the milestones in the development of this paradigm and speculates on its potential utility to address unsolved questions in eukaryotic genome maintenance.     

The DNA-binding subunit p140 of replication factor C is upregulated in cycling cells and associates with G1 phase cell cycle regulatory proteins

The DNA-binding subunit of replication factor C (RFCp140) plays an important role in both DNA replication and DNA repair. The mechanisms regulating activation of RFCp140 thereby controlling replication and cellular proliferation are largely unknown. We analyzed protein expression of RFCp140 during cell cycle progression and investigated the association of RFCp140 with cell cycle regulatory proteins in cell lines of various tissue origin and in primary hematopoietic cells. Western and Northern blot analyses of RFCp140 from synchronized cells showed downregulation of RFCp140 when cells enter a G₀-like quiescent state and upregulation of RFCp140 in cycling cells. Translocation from the cytoplasmic compartment to the nucleus did not account for the significant increase in RFCp140 protein levels observed in cycling cells. To investigate a potential association of RFCp140 with cell cycle regulatory proteins coimmunoprecipitation assays were performed. These studies demonstrated specific binding of RFCp140 to cdk4-kinase in hematopoietic and fibroblast cell lines. Additional coimmunoprecipitation studies revealed specific association of RFCp140 with cyclin D1, p21, proliferating cell nuclear antigen, and retinoblastoma protein. These findings link DNA replication and repair factor RFCp140 to G₁ phase cell cycle regulatory elements critically involved in cell cycle control. Received: 13 May 1998 / Accepted: 1 February 1999     

The<Emphasis Type="Italic"> Neurospora crassa mus-19</Emphasis> gene is identical to the<Emphasis Type="Italic"> qde-3</Emphasis> gene,which encodes a RecQ homologue and is involved in recombination repair and postreplication repair

An allele called mus-19 was identified by screening temperature-sensitive and mutagen-sensitive mutants of Neurospora crassa. The mus-19 gene was genetically mapped to a region near the end of the right arm of linkage group I, where a RecQ homologue called qde-3 had been physically mapped in the Neurospora database. Complementation tests between the mus-19 mutant and the qde-3 ^RIP mutant showed that mus-19 and qde-3 were the same gene. The qde-3 genes of both mutants were cloned and sequenced; and the results showed that they have mutation(s) in their qde-3 genes. The original mus-19 and qde-3 ^RIP mutants are defective in quelling, as reported for other qde-3 mutants. The mutants show high sensitivity to methyl methanesulfonate, ethyl methanesulfonate, N-methyl-N-nitro-N-nitrosoguanidine, tert-butyl hydroperoxide, 4-nitroquinoline-1-oxide, hydroxyurea and histidine. Epistasis analysis indicated that the qde-3 gene belongs both to the uvs-6 recombination repair pathway and the uvs-2 postreplication repair pathway. The qde-3 mutation has no effect on the integration of a plasmid carrying the mtr gene by homologous recombination. In homozygous crosses, the qde-3 mutant is defective in ascospore production.Communicated by U. Kück     

Identification of a 450-bp region of human papillomavirus type 1 that promotes episomal replication in Saccharomyces cerevisiae

Human papillomaviruses (HPVs) replicate as nuclear plasmids in infected cells. Since the DNA replication machinery is generally conserved between humans and Saccharomyces cerevisiae, we studied whether HPV-1 DNA can replicate in yeast. Plasmids containing a selectable marker (with or without a yeast centromere) and either the full-length HPV-1 genome or various regions of the viral long control region (LCR) and the 3' end of the L1 gene were introduced into S. cerevisiae and their ability to replicate episomally was investigated. Our results show that HPV-1 sequences promote episomal replication of plasmids although the yeast centromere is required for plasmid retention. We have mapped the autonomously replicating sequence activity of HPV-1 DNA to a 450 base-pair sequence (HPV-1 nt 6783-7232) that includes 293 nucleotides from the 5' region of the viral LCR and 157 nucleotides from the 3' end of the L1 gene. The HPV-1 ARS does not include the binding sites for the viral E1 and E2 proteins, and these proteins are dispensable for replication in S. cerevisiae.     

Occurrence of C3 nephritic factor and C4 nephritic factor in membranoproliferative glomerulonephritis (MPGN).

One hundred patients diagnosed with hypocomplementaemic MPGN (C3 < 40%) were studied to determine the presence of C3 nephritic factor (C3NeF) and/or C4 nephritic factor (C4NeF). Of those studied, 12 were C3NeF-positive, nine were C4NeF-positive and 10 were positive for both C3NeF and C4NeF. In the 10 patients both C3NeF- and C4NeF-positive, a marked decrease in C3 and C5 levels and a decrease in levels of late components from C6 to C9 were observed. This observation was in contrast to that seen in patients who were either C3NeF- or C4NeF-positive. Patients positive for both C3NeF and C4NeF continued to exhibit hypocomplementaemia after therapy. Immunofluorescent findings revealed heavy C3 immunoglobulin deposits in the 10 patients who were both C3NeF- and C4NeF-positive, whereas no such deposits were found in those patients who were either C3NeF- or C4NeF-positive only. When those patients who were both C3NeF- and C4NeF-positive were compared with those who were either C3NeF- or C4NeF-positive, nephritic syndrome and a poor prognosis were observed more frequently. This study demonstrates a correlation between clinical outcome and hypocomplementaemic MPGN. Further investigations of MPGN as an autoimmune disease are necessary.     

Identification and functional analysis of a Kluyveromyces lactis homologue of the SPT4 gene of Saccharomyces cerevisiae

Sequence analysis of a DNA fragment containing the KlCOX18 gene originating from chromosome II of the yeast Kluyveromyces lactis revealed the presence of an adjacent open reading frame (ORF) for a protein exhibiting 78.4% identity with the Saccharomyces cerevisiae Spt4p. Based on the identical length (102 aa) and the conservation of the zinc-finger motif found in Spt4p we named this ORF KlSPT4. When expressed in S. cerevisiae the KlSPT4 gene complemented all spt4 mutant phenotypes. It is proposed that KlSpt4p, like its S. cerevisiae counterpart is a protein involved in the establishment or maintenance of the chromatin structure that influences the expression of many yeast genes. Received: 15 June / 31 August 1998     

A direct study of the relative synthesis of petite and grande mitochondrial DNA in zygotes from crosses involving suppressive petite mutants of Saccharomyces cerevisiae

Summary Work in recent years has produced indirect evidence to support the view that the phenomenon of suppressiveness in yeast is the result of the ability of the petite mtDNA to out-replicate the wild-type genome. We have developed a method, based on fluorography of gels containing restriction fragments of radioactively labelled zygotic mtDNA, by which it has been possible to follow directly the incorporation of label into the two mtDNA species and hence their relative synthesis. Four petite isolates of 70%, 43%, 23% and 12% suppressiveness were tested by this method in crosses with a grande strain. Only the mtDNA from the 70% suppressive petite showed a replicative advantage over the grande mtDNA. The mtDNA from the 43% and 23% suppressive actually appeared to undergo, if anything, less replication in the zygote than the grande mtDNA. It is concluded that while some petites may exhibit suppressiveness as a result of enhanced replicative efficiency of their mtDNA, this cannot be the explanation for all suppressive petite strains.     

Localization of a r-protein gene within the chloroplast DNA replication origin of Chlamydomonas

Summary In our previous study of chloroplast (Cp) DNA replication in Chlamydomonas reinhardtii, one D-loop site with its flanking regions was cloned and sequenced. The D-loop site mapped by electron mircroscopy (EM) overlaps with an open reading frame (ORF) potentially coding for a polypeptide of 136 amino acids. In this report, the corresponding D-loop isolated from another species of Chlamydomonas was sequenced. An ORF was also detected. Sequence comparison indicated that most conserved sequences between these two cloned origins are located within the ORE Amino acid sequences of these two ORFs are highly conserved. The corresponding sequence for this ORF in the tobacco Cp genome was located by a Southern blotting analysis. Since the complete sequence data of Cp DNAs from a liverwort and from tobacco have been determined in 2 Japanese laboratories recently, it has been possible for us to show that this ORF encodes a protein homologous to the Cp ribosomal protein (r-protein) L16, by sequence comparison.     

The primary structure of the leul + gene of Schizosaccharomyces pombe

Summary A DNA fragment which carries the leul gene encoding beta-isopropylmalate dehydrogenase in Schizosaccharomyces pombe has been isolated by complementation of an E. coli leuB mutation. This 1.5 kb DNA fragment complements not only the S. pombe leul mutation, but also the S. cerevisiae leu2 mutation. The nucleotide sequence of the essential part of the leul gene and its flanking regions was determined. This sequence contains an open reading frame of 371 codons, from which a protein having a Mr = 39,732 can be predicted. The deduced amino acid sequence and its codon usage were compared with those of the S. cerevisiae LEU2 protein. The cloned DNA will be a useful marker when transforming S pombe.