Isolation and characterization of the nuclei fromSaccharomyces cerevisiae

Nuclear magnetic resonance footprint of Wharton Jelly mesenchymal stem cells death mechanisms and distinctive in‐cell biophysical properties in vitro

The importance of the biophysical characterization of mesenchymal stem cells (MSCs) was recently pointed out for supporting the development of MSC‐based therapies. Among others, tracking MSCs in vivo and a quantitative characterization of their regenerative impact by nuclear magnetic resonance (NMR) demands a full description of MSCs’ MR properties. In the work, Wharton Jelly MSCs are characterized in a low magnetic field (LF) in vitro by using different approaches. They encompass various settings: MSCs cultured in a Petri dish and cell suspensions; experiments‐ 1D‐T₁, 1D‐T₂, 1D diffusion, 2D T₁‐T₂ and D‐T₂; devices‐ with a bore aperture and single‐sided one. Complex NMR analysis with the aid of random walk simulations allows the determination of MSCs T₁ and T₂ relaxation times, cells and nuclei sizes, self‐diffusion coefficients of the nucleus and cytoplasm. In addition, the influence of a single layer of cells on the effective diffusion coefficient of water is detected with the application of a single‐sided NMR device. It also enables the identification of apoptotic and necrotic cell death and changed diffusional properties of cells suspension caused by compressing forces induced by the subsequent cell layers. The study delivers MSCs‐specific MR parameters that may help tracking MSCs in vivo.

Evidence for DNA cleavage caused directly by a transfer RNA-targeting toxin

The killer yeast species Pichiaacaciae produces a heteromeric killer protein, PaT, that causes DNA damage and arrests the cell cycle of sensitive Saccharomyces cerevisiae in the S phase. However, the mechanism by which DNA damage occurs remains elusive. A previous study has indicated that Orf2p, a subunit of PaT, specifically cleaves an anticodon loop of an S. cerevisiae transfer RNA (tRNA^Gln_mcm5s2UUG). This finding raised a question about whether the DNA damage is a result of the tRNA cleavage or whether Orf2p directly associates with and cleaves the genomic DNA of sensitive yeast cells. We showed that Orf2p cleaves genomic DNA in addition to cleaving tRNA in vitro. This DNA cleavage requires the same Orf2p residue as that needed for tRNA cleavage, His299. The expression of Orf2p, in which His299 was substituted to alanine, abolished the cell cycle arrest of the host cell. Moreover, the translation impairment induced by tRNA cleavage enabled Orf2p to enter the nucleus, thereby inducing histone phosphorylation.

Identification and purification of CREB like protein in Candida albicans

cAMP response element binding protein (CREB) belongs to ATF/CREB family of transcription factors, which are bonafide targets of cAMP-PKA signalling pathway in mammalian cells. CREB is known to regulate the genes involved in transcription, cell cycle, cell survival, neurotransmitter, growth factors and immune regulation. But there is no evidence of presence of ATF/CREB family members in Candida albicans. In the present study, CREB like transcription factor has been identified and purified in C. albicans. The putative CREB was observed to have different molecular mass (47 kDa) as compared to its mammalian counterpart (43 kDa). Both forms of CREB (CREB and phosphorylated CREB) were detected in C. albicans and phosphorylation of CREB was found to be a function of cAMP levels and protein kinase A activity within this organism. CREB protein was purified by sequence-specific CRE-DNA affinity chromatography. Purified CREB exhibited characteristic CRE binding activity as revealed by electrophoretic mobility shift assay and gave reactivity with CREB antibodies. CREB protein was phosphorylated by purified catalytic subunit of PKA under in vitro conditions. To the best of our knowledge, this study reports for the first time identification of CREB like protein as an important component of cAMP signalling pathway in C. albicans.

Cell cycle effects of the phenothiazines: trifluoperazine and chlorpromazine in Candida albicans

The study demonstrates the in vitro effectiveness of phenothiazine compounds, i.e. chlorpromazine and trifluoperazine against Candida albicans. Anticandidal effect of these drugs is suggested to be because of their interaction with Ca(2+)/calmodulin dependent protein phosphorylation. 3H-thymidine uptake studies revealed that both these compounds affect the DNA synthesis along with decrease in activities of nuclear calmodulin (CaM) and Ca(2+)/calmodulin dependent protein kinase (CaMPK). Failure in cell growth was due to defect in CaM mediated cell cycle arrest. Flow cytometric analysis showed that progression through G(1) and mitotic phase was affected when cells after alpha-factor arrest were grown in the presence of chlorpromazine or trifluoperazine. These drugs also produced significant decline in the cellular lipids and phospholipids. 14C-acetate incorporation studies further substantiated these results. We suggest that chlorpromazine or trifluoperazine affect the cell cycle through DNA synthesis (S phase) and cell division phases which are governed by calmodulin and Ca(2+)/calmodulin dependent protein phosphorylation and lipids and phospholipids appear to be additional targets of phenothiazine compounds in C. albicans. These results will have important significance in the development of new anticandidal compounds.

Identification and characterization of nuclear calmodulin-binding proteins of Saccharomyces cerevisiae

Nuclear calmodulin-binding proteins of the yeast Saccharomyces cerevisiae were investigated. The soluble fractions after serial treatments of the isolated nuclei with buffers containing the nonionic detergent NP-40 (F1), 0.5 M KCl (F2) and 2.0 M KCl (F3) in this order, and the residual proteins (F4) were obtained. The calmodulin-binding proteins of the nucleus and nuclear subfractions were identified using the gel overlay method using 125I-calmodulin. Each subnuclear fraction contained a large number of components that bound calmodulin in a Ca(2+)-dependent or -independent manners. The calmodulin-binding proteins were isolated from F1 and F2 subnuclear fractions by affinity chromatography. The affinity-purified proteins bound calmodulin in a Ca(2+)-dependent manner when analyzed using the gel overlay method. The major calmodulin-binding components of F1 were 44, 42, 36, 32 and 29 kDa proteins, and those of F2 were 200, 100, 40, 42, 36, 34 and 32 kDa proteins. The isolated proteins also contained several Coomassie-blue stained proteins that did not bind calmodulin and, therefore, may represent the proteins associated with the calmodulin-binding proteins. Antisera raised against the affinity-purified preparation of F1 and F2 recognized almost all of the calmodulin-binding proteins present in the fraction and several other proteins of the nucleus. The presence of Ca(2+)-dependent protein phosphatase (type 2B) in the nucleus was demonstrated by Western blotting. The enzyme was localized predominantly in F1 and F4.

cDNA cloning of a calcineurin B homolog in Saccharomyces cerevisiae

We have isolated a cDNA clone encoding a homolog of mammalian calcineurin B (the regulatory subunit of calmodulin-dependent protein phosphatase) by screening a cDNA expression library of Saccharomyces cerevisiae with antiserum against bovine calcineurin B. The yeast calcineurin B homolog (YCNB) is composed of 175 amino acids with a calculated molecular mass of 19,639 daltons and contains four putative Ca(2+)-binding domains. The amino-acid alignment of YCNB with human calcineurin B demonstrates 53% sequence identity and 82% homology. Southern blot analysis indicates that the gene for YCNB is a single-copy gene. Thus, yeast calmodulin-dependent protein phosphatase apparently has a heterodimeric structure similar to that of the enzyme in mammalians.

Calmodulin-binding proteins of Saccharomyces cerevisiae

The subcellular distribution of calmodulin-binding proteins in the soluble, plasma membrane, and nuclear fractions of Saccharomyces cerevisiae was analyzed with a gel binding assay using 125I-labeled calmodulin. Over 20 binding proteins were detected. The calmodulin-binding protein profiles were markedly different among the fractions. Calmodulin-binding proteins were most abundant in the nuclear fraction, followed by the membrane fraction and the soluble fraction in decreasing order. The amounts of certain calmodulin-binding proteins increased after treatment with alpha-mating factor.

Identification of a wheat germ agglutinin-sensitive ATPase in yeast nuclei

We have found that wheat germ agglutinin (WGA), a lectin that specifically binds to N-acetylglucosamine residues inhibits the in vitro transport of plasmid DNA, pJDB219, into yeast nuclei. Histochemical staining of the isolated nuclei with biotinylated WGA and streptavidin-biotinylated peroxidase complex revealed the presence of WGA-binding materials around the nuclear pore under an electron microscope. Using WGA-agarose column chromatography of yeast nuclear extracts, a novel Mg2+-dependent ATPase was isolated. Its activity was highly sensitive to WGA and stimulated by Nonidet P-40 or phosphatidylserine. We suggest that the WGA-sensitive ATPase plays a role in yeast nuclear transport of DNA.

Characterization of a DNA uptake reaction through the nuclear membrane of isolated yeast nuclei

Isolated yeast nuclei were able to incorporate 3H-labeled pJDB219 DNA in vitro in the presence of ATP and Mg2+. The number of plasmid molecules incorporated into each nucleus was calculated to be 60 under the conditions we used. Enzyme-histochemical staining of the incorporated biotinylated pJDB219 with streptavidin-biotinylated-peroxidase complex indicated a uniform distribution of the incorporated plasmids within each nucleus. After intranuclear incorporation, substrate pJDB219 DNAs (open and closed circular forms) were changed to the linear form and were weakly digested over the longer incubation period (over 60 min). Facile release of the once-incorporated plasmid DNA was never observable; discharge of the incorporated [3H]pJDB219 during a 60-min incubation was less than 5%. The addition of adenylyl-imidodiphosphate, N,N'-dicyclohexylcarbodiimide (DCCD), or quercetin inhibited in vitro DNA uptake reaction. DCCD and quercetin inhibited the nuclear ATPase and apparent protein kinase, respectively; hence, the involvement of these enzymes in the nuclear DNA transport system was suggested.

Selection by genetic transformation of a Saccharomyces cerevisiae mutant defective for the nuclear uracil-DNA-glycosylase

A coliphage M13 chimer containing the Saccharomyces cerevisiae TRP1 gene and ARS1 replication origin (mPY2) was grown on an ung- dut- strain of Escherichia coli. The resulting single-stranded phage DNA had 13% of thymine residues substituted by uracil. This DNA failed to transform a delta trp1 yeast strain to prototrophy. However, when a mutagenized yeast stock was transformed with uracil-containing single-stranded mPY2 DNA, unstable transformants were obtained. After plasmid segregation, about half of these were retransformed at a high frequency by uracil-containing single-stranded mPY2 DNA. In vitro, these mutants were defective for uracil-DNA-glycosylase activity. They were designated ung1. Strains containing the ung1 mutation have an increased sensitivity to sodium bisulfite and sodium nitrite but a wild-type sensitivity to methyl methanesulfonate, UV light, and drugs that cause depletion of the thymidylate pool. They have a moderate mutator phenotype for nuclear but not for mitochondrial genes. A low mitochondrial uracil-DNA-glycosylase activity was demonstrated in the mutant strains.