VDE-initiated intein homing in Saccharomyces cerevisiae proceeds in a meiotic recombination-like manner

BACKGROUND: Inteins and group I introns found in prokaryotic and eukaryotic organisms occasionally behave as mobile genetic elements. During meiosis of the yeast Saccharomyces cerevisiae, the site-specific endonuclease encoded by VMA1 intein, VDE, triggers a single double-strand break (DSB) at an inteinless allele, leading to VMA1 intein homing. Besides the accumulating information on the in vitro activity of VDE, very little has been known about the molecular mechanism of intein homing in yeast nucleus. RESULTS: We developed an assay to detect the product of VMA1 intein homing in yeast genome. We analysed mutant phenotypes of RecA homologs, Rad51p and Dmc1p, and their interacting proteins, Rad54p and Tid1p, and found that they all play critical roles in intein inheritance. The absence of DSB end processing proteins, Sae2p and those in the Mre11-Rad50-Xrs2 complex, also causes partial reduction in homing efficiency. As with meiotic recombination, crossover events are frequently observed during intein homing. We also observed that the absence of premeiotic DNA replication caused by hydroxyurea (HU) or clb5delta clb6delta mutation reduces VDE-mediated DSBs. CONCLUSION: The repairing system working in intein homing shares molecular machinery with meiotic recombination induced by Spo11p. Moreover, like Spo11p-induced DNA cleavage, premeiotic DNA replication is a prerequisite for a VDE-induced DSB. VMA1 intein thus utilizes several host factors involved in meiotic and recombinational processes to spread its genetic information and guarantee its progeny through establishment of a parasitic relationship with the organism.     

Mih1/Cdc25 is negatively regulated by Pkc1 in Saccharomyces cerevisiae

Mitotic cyclin‐dependent kinase (CDK) is activated by Cdc25 phosphatase through dephosphorylation at the Wee1‐mediated phosphorylation site. In Saccharomyces cerevisiae, regulation of Mih1 (Cdc25 homologue) remains unclear because inactivation/degradation of Swe1 (Wee1 homologue) is the main trigger for G2/M transition. By deleting all mitotic cyclins except Clb2, a strain was created where Mih1 became essential for mitotic entry at high temperatures. Using this novel assay, the essential domain of Mih1 was identified and Mih1 regulation was characterized. Mih1(3E1D) with phosphomimetic substitutions of four putative PKC target residues in Mih1 had a reduced complementation activity, whereas Mih1(4A) with those nonphosphorylatable substitutions was active. The band pattern of Mih1 by SDS‐PAGE was similar to that of Mih1(4A) only after inactivation of Pkc1 in a pkc1^ts mutant. Over‐expression of GFP‐tagged Mih1 or GFP‐Mih1(4A) accumulated as dot‐like structures in the nucleus, whereas GFP‐Mih1(3E1D) was localized in the cytoplasm. Over‐expression of an active form of Pkc1 excluded GFP‐Mih1 from the nucleus, but had minimal effect on GFP‐Mih1(4A) localization. Furthermore, addition of ectopic nuclear localization signal to the Mih1(3E1D) sequence recovered complementation activity and nuclear localization. These results suggest that Mih1 is negatively regulated by Pkc1‐mediated phosphorylation, which excludes it from the nucleus under certain conditions.     

CM1 ligation initiates apoptosis in a caspase 8-dependent manner in Ramos cells and in a mitochondria-controlled manner in Raji cells

Burkitt lymphoma (BL) is a tumor with the characteristics of germinal center B cells. We previously reported that the CM1 (centrocyte/-blast marker 1) molecule is expressed only in germinal center B cells, specifically, in a subpopulation of centroblasts and centrocytes. In the present study, we investigated the apoptosis induced by anti-CM1 in the Ramos and Raji human BL cell lines. The Ramos is protected from apoptosis by the crosslinking of sIgM and the calcium ionophore by the ligation of CD40 with anti-CD40 monoclonal antibodies (mAb) or soluble CD40 ligand (sCD40L). In this investigation on the effect of CM1 on apoptosis in BL cell lines, we found that cellular signaling by CM1 induces apoptosis and decreases cell viability, in BL cell lines cultured for 24 hours with protein-G agarose beads conjugated anti-CM1 mAb. Stimulation by CD40 ligated with sCD40L protected Raji cells from CM1-induced apoptosis, but did not protect Ramos cells. Furthermore, after anti-CM1 mAb stimulation, CD95 expression was upregulated and CD40 expression was unaltered or slightly decreased in Ramos cells, whereas CD95 was downregulated and CD40 was slightly upregulated in Raji cells. The engagement of CD40 by sCD40L enhanced CD95 expression, but the level of CM1 expression was unchanged in Ramos. However, sCD40L downregulated both CD95 and CM1 expression in Raji. In addition, the caspase-8 specific inhibitor blocked CM1-induced apoptosis in Ramos cells, but not in Raji cells. Increased mitochondrial membrane permeabilization was observed only in Raji cells. Moreover, the effector caspase inhibitor, z-DEVD, blocked CM1-mediated apoptosis in both cell lines. We found that CM1-induced apoptosis is achieved via different initiation pathways, which are cell-type dependent.     

Induced cellular resistance to ultraviolet light in Saccharomyces cerevisiae is not accompanied by increased repair of plasmid DNA

Summary Many reports show that resistance of Saccharomyces cerevisiae to a large UV dose can be enhanced by pre-induction with a smaller one given some hours before. This work tests if such increased cell survival is associated with increased DNA repair on UV damaged plasmid transformed into yeast. There was no change in transformation efficiency of UV-damaged plasmid DNA under conditions where RAD cell survival increased 5-fold, and where rad1-1 and rad6-1 survival increased 2-fold. It is concluded that DNA repair activity involving the RAD6 and RAD3 pathways is either not inducible or is unable to work on plasmid DNA. It is suggested that the enhancement of cellular survival detected may be based on changes in cell-cycle behaviour which permit cells generally proficient in repair a greater chance to recover.     

The gene DIS2S1 is essential in Saccharomyces cerevisiae and is involved in glycogen phosphorylase activation

Summary S. cerevisiae gene DIS2S1, which codes for a protein very similar to the catalytic subunit of mammalian protein phosphatase 1, was disrupted in vitro. Diploid yeast cells were transformed and sporulated. Tetrad analysis demonstrated that disruption of DIS2S1 is lethal for the cell. Glycogen phosphorylase a and glycogen synthase activity ratio were measured in diploids carrying a disrupted allele of the gene. Phosphorylase was dramatically activated in mutant cells but, under the same conditions, glycogen synthase activity was essentially identical in both mutant and wild-type cells.     

An α-specific gene,SAG1 is required for sexual agglutination in Saccharomyces cerevisiae

Summary Seven -specific mutants specifically defective in sexual agglutinability were isolated. The other mating functions exhibited by these mutants, designated sag mutants, such as the production of pheromone and response to a mating pheromone, were normal. While the MAT sag1 cells did not agglutinate with wild-type a cells, the MAT sag1 cells did, indicating that the SAG1 gene is expressed only in cells. The mutations were semi-dominant and fell into a single complementation group, SAG1, which was mapped near met3 on chromosome X. Complementation analysis showed that sag1 and aga1, the latter being a previously reported -specific mutation, were mutations in the same gene.     

A role for KEM1 at the START of the cell cycle in Saccharomyces cerevisiae

KEM1 is a Saccharomyces cerevisiae gene, conserved in all eukaryotes, whose deletion leads to pleiotropic phenotypes. For the most part, these phenotypes are thought to arise from Kem1p’s role in RNA turnover, because Kem1p is a major 5′–3′ cytoplasmic exonuclease. For example, the exonuclease-dependent role of Kem1p is involved in the exit from mitosis, by degrading the mRNA of the mitotic cyclin CLB2. Here, we describe the identification of a KEM1 truncation, KEM1 ^1-975 , that accelerated the G1 to S transition and initiation of DNA replication when over-expressed. Interestingly, although this truncated Kem1p lacked exonuclease activity, it could efficiently complement another function affected by the loss of KEM1, microtubule-dependent nuclear migration. Taken together, the results we report here suggest that Kem1p might have a previously unrecognized role at the G1 to S transition, but not through its exonuclease activity. Our findings also support the notion that Kem1p is a multifunctional protein with distinct and separable roles.     

The Tup1-Ssn6 general repressor is involved in repression of IME1 encoding a transcriptional activator of meiosis in Saccharomyces cerevisiae

Ime1 plays a pivotal role in the initiation of meiosis in a/α diploid cells of Saccharomyces cerevisiae. In the absence of glucose and nitrogen, IME1 expression is greater in a/α cells than in either a or α cells and therefore only a/α, but not a/a or α/α, cells are committed to sporulation. It is known that IME1 expression is positively regulated by Mck1, Rim1, Ime4 and the Swi-Snf complex but other factors may also be involved. In addition, Rme1 is assumed to repress IME1 expression. To provide more details of the repression of expression of IME1, we have isolated mutants in which the IME1p-PHO5 fusion gene integrated at the ura3 locus is expressed in α cells under nutritionally rich conditions. We found that mutations occurred in TUP1, SSN6, SIN4 and RGR1, among which TUP1 and SSN6 were identified for the first time as negative regulators of IME1 expression. Deletion of the Rme1-binding site from the IME1 promoter did not result in activation of the expression of IME1 under nutritionally rich conditions, suggesting that Rme1 does not function as a DNA-binding protein with the Tup1-Ssn6 repression complex. We also demonstrated that the 294-bp fragment from nucleotide position –914 to –621 and the 301-bp fragment from nucleotide position –1215 to –915 of the IME1 promoter region contain elements acting as URS and UAS in TUP1 ⁺ and tup1 mutant cells, respectively. These findings indicate that IME1 is negatively regulated by the Tup1-Ssn6 repressor complex through two distinct upstream regions in conjunction with unidentified DNA-binding proteins. Received: 14 November 1997 / 12 January 1998     

Enhanced canavanine uptake is associated with nucleotide permeability in a thymidylate auxotroph of Saccharomyces cerevisiae

Summary The recovery of spontaneous canavanine-resistant mutants is reduced dramatically in a strain of Saccharomyces cerevisiae that carries a suppressed can1–100 allele and is permeable to and auxotrophic for thymidylate. This effect does not occur in an isogenic strain that neither takes up nor requires the nucleotide. However, it is observed for another isogenic strain which is permeable to but not auxotrophic for thymidylate, indicating that the effect is related to thymidylate permeability. Apparently, increased sensitivity of the permeable cells to growth inhibition by canavanine accounts for the diminished mutant recovery. In turn, enhanced uptake of canavanine in these cells seems to be responsible for the increased sensitivity. The experimental findings suggest that the elevated transport of canavanine in the thymidylate auxotroph is unlikely to be due to enhanced suppression of the can1–100 allele or to activation of the yeast general amino acid permease.     

CTD kinase large subunit is encoded by CTK1, a gene required for normal growth of Saccharomyces cerevisiae

We previously purified a yeast protein kinase that specifically hyperphosphorylates the carboxyl-terminal repeat domain (CTD) of RNA polymerase II largest subunit and showed that this CTD kinase consists of three subunits of 58, 38, and 32 kDa. We have now cloned, sequenced, and characterized CTK1, the gene encoding the 58 kDa alpha subunit. The CTK1 gene product contains a central domain homologous to catalytic subunits of other protein kinases, notably yeast CDC28, suggesting that the 58 kDa subunit is catalytic. Cells that carry a disrupted version of the CTK1 gene lack the characterized CTD kinase activity, grow slowly and are cold-sensitive, demonstrating that the CTK1 gene product is essential for CTD kinase activity and normal growth. While ctk1 mutant cells do contain phosphorylated forms of the RNA polymerase II largest subunit, these forms differ from those found in wild type cells, implicating CTK1 as a component of the physiologically significant CTD phosphorylating machinery. As befitting an enzyme with a nuclear function, the N-terminal region of the CTK1 protein contains a nuclear targeting signal.     

Glucose-dependent cell size is regulated by a G protein-coupled receptor system in yeast Saccharomyces cerevisiae

In the yeast, Saccharomyces cerevisiae, cell size is affected by the kind of carbon source in the medium. Here, we present evidence that the Gpr1 receptor and Gpa2 Galpha subunit are required for both maintenance and modulation of cell size in response to glucose. In the presence of glucose, mutants lacking GPR1 or GPA2 gene showed smaller cells than the wild-type strain. Physiological studies revealed that protein synthesis rate was reduced in the mutant strains indicating that reduced growth rate, while the level of mRNAs for CLN1, 2 and 3 was not affected in all strains. Gene chip analysis also revealed a down-regulation in the expression of genes related to biosynthesis of not only protein but also other cellular component in the mutant strains. We also show that GPR1 and GPA2 are required for a rapid increase in cell size in response to glucose. Wild-type cells grown in ethanol quickly increased in size by addition of glucose, while little change was observed in the mutant strains, in which glucose-dependent cell cycle arrest caused by CLN1 repression was somewhat alleviated. Our study indicates that the yeast G-protein coupled receptor system consisting of Gpr1 and Gpa2 regulates cell size by affecting both growth rate and cell division.     

The DLP1 mutant of the yeast Saccharomyces cerevisiae with an increased copy number of the 2micron plasmid shows a shortened lifespan

We isolated and characterized a recessive mutant, named dlp1, which shows the Dlp phenotype (delayed loss of proliferation activity) during the autophagic death of cdc28. The dip1 mutant was found to consist of two subtypes of cells based on colony morphology. One subtype with the Dlp phenotype, named dlp1-1, became large, red, and nibbled during the incubation, suggesting that the cells on the surface of the colonies were dying. The other without the Dlp phenotype, named dlp1-s, retained small, white colonies even after a prolonged incubation and was found to be a petite mutant. The change from dlp1-1 to dlp1-s (petite) occurred much more frequently (about 15%) than that from the wild-type to petite mutant (less than 1%). The lifespan of both subtypes of cells was severely shortened. The copy number of the endogenous 2micron plasmid of dlp1-1 was 68-fold that of the original cdc28, and decreased by half after the conversion to dlp1-s (petite). A 4.0-kbp fragment of the 2micron plasmid containing REP2 decreased the copy number of the endogenous 2micron plasmid to 8-fold that of the original cdc28 cells and partially rescued the shortened lifespan, in addition to resulting in the complete complementation of the Dlp and nibbled-colony phenotypes. These results suggest that DLP1 is a chromosomal gene that regulates the copy number of the 2micron plasmid, and that the shortening of the lifespan and other effects of the dlp1 mutation are likely caused by the increased copy number of the endogenous 2micron plasmid.