Epigenetic regulation of planarian stem cells by the SET1/MLL family of histone methyltransferases

Chromatin regulation is a fundamental mechanism underlying stem cell pluripotency, differentiation, and the establishment of cell type-specific gene expression profiles. To examine the role of chromatin regulation in stem cells in vivo, we study regeneration in the freshwater planarian Schmidtea mediterranea. These animals possess a high concentration of pluripotent stem cells, which are capable of restoring any damaged or lost tissues after injury or amputation. Here, we identify the S. mediterranea homologs of the SET1/MLL family of histone methyltransferases and COMPASS and COMPASS-like complex proteins and investigate their role in stem cell function during regeneration. We identified six S. mediterranea homologs of the SET1/MLL family (set1, mll1/2, trr-1, trr-2, mll5–1 and mll5–2), characterized their patterns of expression in the animal, and examined their function by RNAi. All members of this family are expressed in the stem cell population and differentiated tissues. We show that set1, mll1/2, trr-1, and mll5–2 are required for regeneration and that set1, trr-1 and mll5–2 play roles in the regulation of mitosis. Most notably, knockdown of the planarian set1 homolog leads to stem cell depletion. A subset of planarian homologs of COMPASS and COMPASS-like complex proteins are also expressed in stem cells and implicated in regeneration, but the knockdown phenotypes suggest that some complex members also function in other aspects of planarian biology. This work characterizes the function of the SET1/MLL family in the context of planarian regeneration and provides insight into the role of these enzymes in adult stem cell regulation in vivo.     

Role of Saw1 in Rad1/Rad10 complex assembly at recombination intermediates in budding yeast

The Saccharomyces cerevisiae Rad1/Rad10 complex is a multifunctional, structure‐specific endonuclease that processes UV‐induced DNA lesions, recombination intermediates, and inter‐strand DNA crosslinks. However, we do not know how Rad1/Rad10 recognizes these structurally distinct target molecules or how it is incorporated into the protein complexes capable of incising divergent substrates. Here, we have determined the order and hierarchy of assembly of the Rad1/Rad10 complex, Saw1, Slx4, and Msh2/Msh3 complex at a 3′ tailed recombination intermediate. We found that Saw1 is a structure‐specific DNA binding protein with high affinity for splayed arm and 3′‐flap DNAs. By physical interaction, Saw1 facilitates targeting of Rad1 at 3′ tailed substrates in vivo and in vitro, and enhances 3′ tail cleavage by Rad1/Rad10 in a purified system in vitro. Our results allow us to formulate a model of Rad1/Rad10/Saw1 nuclease complex assembly and 3′ tail removal in recombination.     

Increased tRNA level in yeast cells with mutant translation termination factors eRF1 and eRF3

We have earlier characterized Saccharomyces cerevisiae strains with mutations of essential SUP45 and SUP35, which code for translation termination factors eRF1 and eRF3, respectively. In this work, the sup45 and sup35 nonsense mutants were compared with respect to the levels of eight tRNAs: tRNA^Tyr, tRNA^Gln, tRNA^Trp, tRNA^Leu, tRNA^Arg (described as potential suppressor tRNAs), tRNA^Pro, tRNA^His, and tRNA^Gly. The mutants did not display a selective increase in tRNAs, capable of a noncanonical read-through at stop codons. Most of the mutations increased the level of all tRNAs under study. The mechanisms providing for the viability of the sup45 and sup35 nonsense mutants are discussed.     

Modular assembly of yeast mitochondrial ATP synthase

The mitochondrial ATP synthase (F(1)-F(0) complex) of Saccharomces cerevisiae is a composite of different structural and functional units that jointly couple ATP synthesis and hydrolysis to proton transfer across the inner membrane. In organello, pulse labelling and pulse-chase experiments have enabled us to track the mitochondrially encoded Atp6p, Atp8p and Atp9p subunits of F(0) and to identify different assembly intermediates into which they are assimilated. Surprisingly, these core subunits of F(0) segregated into two different assembly intermediates one of which is composed of Atp6p, Atp8p, at least two stator subunits, and the Atp10p chaperone while the second consists of the F(1) ATPase and Atp9p ring. These studies show that assembly of the ATP synthase is not a single linear process, as previously thought, but rather involves two separate but coordinately regulated pathways that converge at the end stage.     

A screen for upstream components of the yeast protein kinase C signal transduction pathway identifies the product of the SLG1 gene

We employed the constitutive BCK1-20 allele of the gene for the MAP kinase kinase kinase (MAPKKK) in the yeast Pkc signal transduction pathway to develop a genetic screen for mutants in genes encoding upstream components. Transposon mutagenesis yielded a mutant that was completely dependent on the active allele in the absence of osmotic stabilization. The transposon had integrated at the yeast SLG1 (HCS77) locus. This gene encodes a putative membrane protein. Haploid slg1 deletion strains are sensitive to caffeine, as expected for mutants in the Pkc pathway, as well as a variety of other drugs. The response to elevated temperatures and the dependence on osmotic stabilization depends on the genetic background. Thus, in the strain used for mutagenesis, disruption of SLG1 causes the cells to become non-viable in the absence of osmotic stabilization at both 30° C and 37° C. In a different genetic background this phenotype was not observed. Sensitivity of the haploid deletion mutants to caffeine can be partially suppressed by overexpression of genes for other components of the Pkc pathway, such as PKC1, SLT2, ROM2, and STE20. In addition, a SLG1-lacZ reporter construct shows higher expression in the presence of caffeine or magnesium chloride in a wild-type diploid background. Received: 2 December 1997 / Accepted: 15 December 1997     

Characterization of the PR domain of RIZ1 histone methyltransferase

RIZ1 (PRDM2) and PRDI-BF1 (PRDM1) are involved in B cell differentiation and the development of B cell lymphomas. These proteins are expressed in two forms that differ by the presence or absence of a PR domain. The protein product that retains the PR domain is anti-tumorigenic while the product that lacks the PR domain is oncogenic and over-expressed in tumor cells. The conserved PR domain is homologous to the SET domain from a family of histone methyltransferases. RIZ1 is also a histone methyltransferase and methylates lysine 9 in histone H3. This activity has been mapped to the PR domain. In the present study, deuterium exchange mass spectrometry was used to define the structural boundaries of the RIZ1 PR domain and to map sites of missense mutations that occur in human cancers and reduce methyltransferase activity. Flexible segments were selectively deleted to produce protein products that crystallize for structural studies. Segments at the carboxyl terminus of the PR domain that are involved in methylation of H3 were shown to be flexible, similar to SET domains, suggesting that the PR and SET methyltransferases may belong to an emerging class of proteins that contain mobile functional regions.     

敲除啤酒酵母fks1基因对啤酒酵母自溶性能的影响

以啤酒酵母G-03为模板,扩增得到铜抗性基因(cup 1)和β-葡聚糖合成酶基因(fks 1)。将fks 1连接pMD-18T Vector得到重组质粒pTK,重组质粒pTK和cup1经Bgl Ⅱ、Sal Ⅰ酶切后连接得到重组质粒pKC。Bam HI酶切重组质粒pKC得到以fks 1为整合位点包含cup1的基因片段fks 1::cup1。用此片段转化啤酒酵母工业菌株G-03,通过硫酸铜抗性筛选得到一株啤酒酵母工程菌G-03/C。工程菌连续传代10次后依然能在筛选平板上生长,遗传稳定性良好。主酵结束G-03/C和G-03的辛酸和癸酸含量基本相同。25℃诱导自溶20 d,G-03/C的辛酸、癸酸分别下降57.3%、81.8%,自溶性能减弱。G-03/C的死亡率、双乙酰、浊度及TBA均较原菌有所下降。G-03/C与G-03酿制成品啤酒的常规指标没有较大差别,品评结果表明,G-03/C风味更优。     

Functional differences between RSC1 and RSC2, components of a for growth essential chromatin-remodeling complex of Saccharomyces cerevisiae,during the sporulation process

RSC, a for growth essential chromatin-remodeling complex of Saccharomyces cerevisiae, is composed of 15 subunits. Rsc1p and Rsc2p are highly homologous proteins and are contained in distinct RSC complexes. We found that both rsc1Delta and rsc2Delta homozygous diploids showed reduced sporulation with decreased expression of IME2 and that rsc1Delta, but not rsc2Delta, produced aberrant asci containing one to three spores. Overexpression of RSC2 in rsc1Delta recovered the sporulation efficiency but not the production of aberrant asci. In contrast, overexpression of RSC1 in rsc2Delta did not alleviate its sporulation defect. These results suggest that both Rsc1p and Rsc2p share overlapping functions on IME2 expression, with a prominent role for Rsc2p, whereas Rsc1p has an additional function in the late steps of the sporulation process.     

Absence of Gup1p in Saccharomyces cerevisiae results in defective cell wall composition, assembly, stability and morphology

Saccharomyces cerevisiae Gup1p and its homologue Gup2p, members of the superfamily of membrane-bound O-acyl transferases, were previously associated with glycerol-mediated salt-stress recovery and glycerol symporter activity. Several other phenotypes suggested Gup1p involvement in processes connected with cell structure organization and biogenesis. The gup1Delta mutant is also thermosensitive and exhibits an altered plasma membrane lipid composition. The present work shows that the thermosensitivity is independent of glycerol production and retention. Furthermore, the mutant grows poorly on salt, ethanol and weak carboxylic acids, suggestive of a malfunctioning membrane potential. Additionally, gup1Delta is sensitive to cell wall-perturbing agents, such as Calcofluor white, Zymolyase, lyticase and sodium dodecyl sulphate and exhibits a sedimentation/aggregation phenotype. Quantitative analysis of cell wall components yielded increased contents of chitin and beta-1,3-glucans and lower amounts of mannoproteins. Consistently, scanning electron microscopy showed a strikingly rough surface morphology of the mutant cells. These results suggest that the gup1Delta is affected in cell wall assembly and stability, although the Slt2p/MAP kinase from the PKC pathway was phosphorylated during hypo-osmotic shock to a normal extent. Results emphasize the pleiotropic nature of gup1Delta, and are consistent with a role of Gulp1p in connection with several pathways for cell maintenance and construction/remodelling.     

Severe reduction of superoxide dismutase activity in the yeast Saccharomyces cerevisae with the deletion or overexpression of GTS1

We report herein that the level of reactive oxygen species (ROS) observed using dihydrorhodamine is much higher in either GTS1-deleted (gts1Delta) or GTS1-overexpressing (TMpGTS1) transformants than in the wild-type and that the levels of protein carbonyls are increased and the glutathione levels are decreased in both transformants. Consistently, the activities of superoxide dismutases (SODs) in both gts1Delta and TMpGTS1 were severely weakened, while the protein levels of both Cu/Zn-SOD and Mn-SOD were not so changed. As the intracellular copper levels were significantly increased in both transformants, we hypothesized that, in either gts1Delta or TMpGTS1 cells, the imbalanced homeostasis of copper induced an accumulation of ROS which caused inactivation of SODs further increasing ROS levels.     

Histone acetylation facilitates association of nucleosomes with SET domain of ALL-1 methyltransferase in vitro

The inheritable methylation pattern of gene activity, created upon cell differentiation, is further maintained by the “SET” (methyltransferase)-domain proteins. However, it is still not clear how SET-proteins can decide on the required gene activity state and the way their chromatin association is maintained. Here we have found that high levels of histone acetylation - the hallmarks of active chromosome regions in vivo - can increase the affinity of reconstituted nucleosomes to the SET domain of ALL-1 histone methyltransferase in a defined system in vitro.     

Mutations occurring at the human minisatellite MS1 integrated in haploid yeast are similar to MS1 mutations in humans

MS1 is one of the most variable minisatellites so far isolated from the human genome. We have previously reported an MS1 length-mutant frequency of 29.6% in overnight cultures of haploid yeast cells carrying a 1.35 kb MS1 allele. Here we present data on the instability of alleles with lengths ranging from 0.15 kb to 2.05 kb, which revealed a threshold of 0.75 kb, at and below which MS1 alleles were entirely stable. Larger alleles exhibited a length-related increase in mutation frequency. Chromosomal integration of various MS1 alleles, isolated from bacterial transformants, in haploid yeast cells also revealed a threshold for the onset of instability and a higher degree of mutability for longer alleles. DNA sequencing of alleles showed that the length changes were due to mutational events involving repeat units in the central region of MS1 which is composed of two variant repeat units only. The similarity between MS1 mutations in yeast and humans argues that yeast represents a suitable model organism for mechanistic studies on mutations occurring in human minisatellites. Received: 1 July 1996 / Accepted: 11 October 1996     

The immunosuppressant leflunomide blocks the yeast Saccharomyces cerevisiae cell cycle at the G1 phase

Abstract Leflunomide is a novel immunomodulatory drug representing a new small molecule class of substances which are structurally unrelated to previously described immunomodulatory/immunosuppressive compounds. The effect of leflunomide on the cell cycle of Saccharomyces cerevisiae was investigated to elucidate the molecular mechanism of its action in eukaryotic organisms. When yeast cells were treated with leflunomide, unbudded cells were accumulated, suggesting that leflunomide may arrest the cell cycle in the G☎ase. When leflunomide-treated cells were subjected to heat shock treatment, the cells became resistant to heat shock treatment, implying that leflunomide-mediated block to cell division results in entry from the proliferative cycle into the alternative developmental g₀ phase.     

Nuclear exopolyphosphatase of Saccharomyces cerevisiae is not encoded by the PPX1 gene encoding the major yeast exopolyphosphatase

Intact nuclei from a parental strain CRY and a PPX1-mutant CRX of Saccharomyces cerevisiae were isolated and found to be essentially free of cytoplasmic, mitochondrial and vacuolar marker enzymes. The protein-to-DNA ratios of the nuclei were 22 and 30 for CRY and CRX nuclei, respectively. An exopolyphosphatase (exopolyPase) with molecular mass of approximately 57 kDa and a pyrophosphatase (PPase) of approximately 41 kDa were detected in the parental strain CRY. Inactivation of PPX1 encoding a major exopolyPase (PPX1) in S. cerevisiae did not result in considerable changes in the content and properties of nuclear exopolyPase as compared to the parental strain of S. cerevisiae. Consequently, the nuclear exopolyPase was not encoded by PPX1. In the CRX strain, the exopolyPase was stimulated by bivalent metal cations. Co2+, the best activator, stimulated it by approximately 2.5-fold. The exopolyPase activity was nearly the same with polyphosphate (polyP) chain lengths ranging from 3 to 208 orthophosphate when measured with Mg2+. With Co 2+, the exopolyPase activity increased along with the increase in polymerization degree of the substrate.     

Formic acid induces Yca1p-independent apoptosis-like cell death in the yeast Saccharomyces cerevisiae

Formic acid disrupts mitochondrial electron transport and sequentially causes cell death in mammalian ocular cells by an unidentified molecular mechanism. Here, we show that a low concentration of formic acid induces apoptosis-like cell death in the budding yeast Saccharomyces cerevisiae, with several morphological and biochemical changes that are typical of apoptosis, including chromatin condensation, DNA fragmentation, externalization of phosphatidylserine, reactive oxygen species (ROS) production, loss of mitochondrial membrane potential and mitochondrion destruction. This process may not be dependent on the activation of Yca1p, the yeast caspase counterpart. In addition, the cell death induced by formic acid is associated with ROS burst,while intracellular ROS accumulate more rapidly and to a higher level in the YCA1 disruptant than in the wild-type strain during the progression of cell death. Our data indicate that formic acid induces yeast apoptosis via an Yca1p-independent pathway and it could be used as an extrinsic inducer for identifying the regulators downstream of ROS production in yeast.