Complete sequences of Schizosaccharomyces pombe subtelomeres reveal multiple patterns of genome variation.

Genome sequences have been determined for many model organisms; however, repetitive regions such as centromeres, telomeres, and subtelomeres have not yet been sequenced completely. Here, we report the complete sequences of subtelomeric homologous (SH) regions of the fission yeast Schizosaccharomyces pombe. We overcame technical difficulties to obtain subtelomeric repetitive sequences by constructing strains that possess single SH regions of a standard laboratory strain. In addition, some natural isolates of S. pombe were analyzed using previous sequencing data. Whole sequences of SH regions revealed that each SH region consists of two distinct parts with mosaics of multiple common segments or blocks showing high variation among subtelomeres and strains. Subtelomere regions show relatively high frequency of nucleotide variations among strains compared with the other chromosomal regions. Furthermore, we identified subtelomeric RecQ-type helicase genes, tlh3 and tlh4, which add to the already known tlh1 and tlh2, and found that the tlh1-4 genes show high sequence variation with missense mutations, insertions, and deletions but no severe effects on their RNA expression. Our results indicate that SH sequences are highly polymorphic and hot spots for genome variation. These features of subtelomeres may have contributed to genome diversity and, conversely, various diseases.

Schizosaccharomyces osmophilus sp. nov., an osmophilic fission yeast occurring in bee bread of different solitary bee species.

Eight yeast strains that asexually reproduce by cell fission were isolated from bee bread of different solitary bees in Germany. DNA sequence analysis revealed that the strains shared the same sequence in the D1/D2 domain of the nuclear large subunit (LSU) rRNA gene with a strain that was previously isolated from a fig snack from Spain. The closest related type strain was that of Schizosaccharomyces octosporus, which showed 98.2% sequence similarity (11 substitutions) with the new strains. By clone sequence analysis of the internal transcribed spacer (ITS) region (ITS1, 5.8S rDNA, and ITS2) a total of nine different copy types were identified. The new strains differed from S. octosporus by approximately 31% in the ITS region. Sequence analysis of the RNAse P gene further supported the description of a new species. The strains isolated during this study show some phenotypic characteristics that separate them from the closest related species, S. octosporus and S. cryophilus. Since all strains showed true osmophily the name of the new species is S. osmophilus (holotype: CBS 15793T; isotype: CLIB 3267 T = NCAIM Y.02225 T, MycoBank no.: MB829586).

Schizosaccharomyces pombe Isolation Protocol.

This chapter describes a methodology to isolate yeast strains from Schizosaccharomyces pombe species. The method is based on a selective-differential medium that notably facilitates the isolation of S. pombe. The main difficulty in isolating microorganisms from this genus is their extremely low incidence in nature when they are compared to other microorganisms. The proposed methodology allows isolating and selecting strains from this species for industrial purposes. Methodologies allows detecting the presence of those yeasts when they are considered spoilage microorganisms. Several selective-differential agents based on the basic physiological characteristics of S. pombe species are exposed during the chapter introduction and the use is properly justified. Some of those representative characteristics are its extraordinary resistance to high sugar concentrations, sulfur dioxide, sorbic acid, benzoic acid, acetic acid, or their unique malo-ethanolic fermentation ability. The proposed selective medium is mainly based on S. pombe resistance to the antibiotic actidione and the unusual tolerance to the inhibitory agent benzoic acid compared to possible microorganisms that could produce false-positive results during an isolation process. In addition, malic acid is proposed as the main differential factor due to the exclusive ability of this species to metabolize malic acid into ethanol. This fact allows the detection of malic acid degradation. Cloramphenicol is used to inhibit bacteria growth and liquid media to avoid fungi development.

Selecting Schizosaccharomyces pombe Diploids.

Here we describe procedures for the selection of diploid Schizosaccharomyces pombeade6-M210/ade6-M216 heteroallelic complementation is widely used to select for Ade+ diploids. Such diploids will readily sporulate when starved of nitrogen. For some investigations, stable diploids are preferable (e.g., for genetic complementation tests), and in these cases mating an h- strain with an h90 mat2-Pi-102 strain can be used to prevent sporulation. When ade6-M210/ade6-M216 mutations impact on, or show synthetic interactions with, the gene of interest, two different auxotrophic markers can be used to select complementation.

Spore Analysis and Tetrad Dissection of Schizosaccharomyces pombe.

Here we describe the processing of Schizosaccharomyces pombe spores in batches (random spore analysis) or through tetrad dissections. Spores are usually prepared from matings between haploid strains (producing zygotic asci) or from sporulating diploids (producing azygotic asci). In random spore analysis, a snail enzyme preparation is used to digest the walls of asci to release free spores that are diluted and plated to form colonies. In tetrad dissection, a needle attached to a micromanipulator is used to pick asci and separate spores. Tetrad dissection has traditionally been the method of choice for genetic mapping and is very useful in the study of genetic interactions (e.g., suppressor analysis). It is also the preferred method for routine crosses because it ensures that every colony stems from a single spore. This can never be certain in random spore analysis.

Construction, Growth, and Harvesting of Fission Yeast Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) Strains.

Stable isotope labeling by amino acids in cell culture (SILAC) enables the relative quantification of protein amounts and posttranslational modifications in complex biological samples through the use of stable heavy isotope-labeled amino acids. Here we describe methods for the application of SILAC to fission yeast Schizosaccharomyces pombe using either labeled lysine or a combination of labeled lysine and labeled arginine. The latter approach is more complicated than the use of labeled lysine alone but may yield a more comprehensive (phospho)proteomic analysis. The protocol includes methods for construction of SILAC-compatible strains, growth of cultures in labeled medium, cell harvesting, and protein extraction.

Selection of appropriate Schizosaccharomyces strains for winemaking.

This paper describes the selection of Schizosaccharomyces yeasts with adequate oenological suitability and high capacity for the degradation of malic acid. Despite the almost non-existent number of commercial strains, the use of this yeast genus has recently been recommended by the International Organisation of Vine and Wine (OIV, in French). Thus, in the present study, a large number of Schizosaccharomyces strains were isolated using a selective differential medium. Initially, classic parameters of oenological interest for the use of fermentative strains of Saccharomyces cerevisiae (the most frequently used type of yeast) were assessed. Only five strains of moderate acetic acid production lower than 0.4 g/L were obtained at the end of fermentation. Other, more specific features of this yeast genus' physiology were also studied, including urease activity and the production of pyruvic acid and glycerol. Finally, oenological suitability was determined by comparing selected strains with other Schizosaccharomyces reference and S cerevisiae control strains. Schizosaccharomyces strains produced 80% less urea content, four times higher pyruvic acid levels and 1 g higher glycerol contents than the Saccharomyces reference strains. The results confirmed that it is possible to perform selective processes on microorganisms from the genus Schizosaccharomyces using methodology developed in this work to obtain strains of industrial interest.

gitter: a robust and accurate method for quantification of colony sizes from plate images.

Colony-based screens that quantify the fitness of clonal populations on solid agar plates are perhaps the most important source of genome-scale functional information in microorganisms. The images of ordered arrays of mutants produced by such experiments can be difficult to process because of laboratory-specific plate features, morphed colonies, plate edges, noise, and other artifacts. Most of the tools developed to address this problem are optimized to handle a single setup and do not work out of the box in other settings. We present gitter, an image analysis tool for robust and accurate processing of images from colony-based screens. gitter works by first finding the grid of colonies from a preprocessed image and then locating the bounds of each colony separately. We show that gitter produces comparable colony sizes to other tools in simple cases but outperforms them by being able to handle a wider variety of screens and more accurately quantify colony sizes from difficult images. gitter is freely available as an R package from http://cran.r-project.org/web/packages/gitter under the LGPL. Tutorials and demos can be found at http://omarwagih.github.io/gitter.

Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy.

Chromosomal rearrangements are mutations contributing to both within and between species variation; however their contribution to fitness is yet to be measured. Here we show that chromosomal rearrangements are pervasive in natural isolates of Schizosaccharomyces pombe and contribute to reproductive isolation. To determine the fitness effects of chromosome structure, we constructed two inversions and eight translocations without changing the coding sequence. We show that chromosomal rearrangements contribute to both reproductive success in meiosis and growth rate in mitosis with a strong genotype by environment interaction. These changes are accompanied by alterations in gene expression. Strikingly, we find several examples leading to antagonistic pleiotropy. Even though chromosomal rearrangements may have a deleterious effect during sexual reproduction, some compensate with a strong growth advantage in mitosis. Our results constitute the first quantification of fitness effects caused by de novo mutations that result in chromosomal rearrangement variation and suggest a mechanism for their maintenance in natural populations.

Scalable nano-bioprobes with sub-cellular resolution for cell detection.

Here we present a carbon nanotube based device to noninvasively and quickly detect mobile single cells with the potential to maintain a high degree of spatial resolution. The device utilizes standard complementary metal oxide semiconductor (CMOS) technologies for fabrication, allowing it to be easily scalable (down to a few nanometers). Nanotubes are deposited using electrophoresis after fabrication in order to maintain CMOS compatibility. The devices are spaced by 6 µm which is the same size or smaller than a single cell. To demonstrate its capability to detect cells, we performed impedance spectroscopy on mobile human embryonic kidney (HEK) cells, neurons cells from mice, and yeast cells (S. pombe). Measurements were performed with and without cells and with and without nanotubes. Nanotubes were found to be crucial to successfully detect the presence of cells. The devices are also able to distinguish between cells with different characteristics.

A fast and inexpensive method for random spore analysis in Schizosaccharomyces pombe.

Random spore analysis is a fundamental tool of yeast genetics for determining gene linkage and the generation of recombinant progeny by genetic crosses. Experimentally it involves treatment of a mating mix with enzymes, such as zymolyase or lyticase, that selectively lyse the cell wall of vegetative cells rather than the spores. Here, we describe a method whereby the relative refractory nature of the spores to treatment with elevated temperature and repeated freeze-thawing facilitates random spore analysis at low cost in fission yeast Schizosaccharomyces pombe. Because of similar properties of spores in budding yeast, this method should prove to be useful for random spore analysis in both budding and fission yeasts.

New insights into galactose metabolism by Schizosaccharomyces pombe: isolation and characterization of a galactose-assimilating mutant.

The fission yeast Schizosaccharomyces pombe cannot use galactose as a carbon or energy source, and little is known about galactose metabolism in this species. Here we report isolation of a galactose-assimilating mutant that grows on a medium containing galactose as a sole carbon source through use of a proofreading-deficient DNA polymerase δ variant encoded by cdc6-1. Based on comparative analysis of gene expression profiles in the wild-type and the mutant (FG2-8), we found that SPBPB2B2.10c (gal7+), SPBPB2B2.12c (gal10+) and SPBPB2B2.13 (gal1+), homologous to Saccharomyces cerevisiae GAL7, GAL10 and GAL1, respectively, and SPBPB2B2.08, SPBPB2B2.09c, and SPBPB2B2.11 that localize close to the gal genes, were highly expressed and dramatically induced by addition of galactose. The gal7Δ strain, carrying an integrated ura4+ marker at the gal7+ locus, grew on 5-fluoroorotic acid (5-FOA)-containing medium. In contrast, the FG2-8 gal7Δ strain could not grow on 5-FOA medium. In addition, expression of gal7+, SPBPB2B2.13, gal10+ and gal1+ genes increased in the wild-type strain when carried on a vector, and these transformants grew on galactose medium. We suggest that gal7+, gal10+, and gal1+ are localized close to a chromosomal terminal repressed by gene silencing in S. pombe. In contrast, gene silencing was defective in the FG2-8 strain making galactose assimilation possible.

Isolation and characterization of ethanol-producing Schizosaccharomyces pombe CHFY0201.

Ethanol-producing yeast strain, CHFY0201 was isolated from soil in South Korea using an enrichment technique in a yeast peptone dextrose medium supplemented with 5% (w/v) ethanol at 30 degrees C. The phenotypic and physiological characteristics, as well as molecular phylogenetic analysis based on the D1/D2 domains of the large subunit (26S) rDNA gene and the internally transcribed spacer (ITS) 1+2 regions suggested that the CHFY0201 was novel strain of Schizosaccharomyces pombe. During shaking flask cultivation, the highest ethanol productivity and theoretical yield of S. pombe CHFY0201 in YPD media containing 9.5% total sugars was 0.59 +/- 0.01 g/l/h and 88.4 +/- 0.91%, respectively. Simultaneous saccharification and fermentation for ethanol production was carried out using liquefied cassava (Manihot esculenta) powder in a 5 l lab-scale jar fermenter at 32 degrees C for 66 h with an agitation speed of 120 rpm. Under these conditions, S. pombe CHFY0201 yielded a final ethanol concentration of 72.1 +/- 0.27 g/l and a theoretical yield of 82.7 +/- 1.52% at a maximum ethanol productivity of 1.16 +/- 0.07 g/l/h. These results suggest that S. pombe CHFY0201 is a potential producer for industrial bioethanol production.

Yeast identification in grape juice concentrates from Argentina.

AIMS: The purpose of this study was to identify yeast species present in spoiled and unspoiled grape juice concentrates from Argentine industries. METHODS AND RESULTS: Osmophilic and osmotolerant yeasts were isolated from spoiled--visually effervescent--and unspoiled--without any visible damage--grape juice concentrates by the spread-plate technique in two culture media. Yeast identification was done by classical and molecular methods. Zygosaccharomyces rouxii was the only species isolated from spoiled grape juice concentrates. In unspoiled samples, five different species were identified: Z. rouxii was isolated at a higher frequency, followed in decreasing order by Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia anomala and Kluyveromyces delphensis. CONCLUSIONS: Yeasts isolated from grape juice concentrates were characterized by a limited taxonomic diversity, where Z. rouxii was the main species isolated. SIGNIFICANCE AND IMPACT OF THE STUDY: Grape production in Argentina is mainly devoted to the industry where wine and grape juice concentrates represent major types of commercial products. Little information on common yeast contaminants is available for grape juice concentrates. This study constitutes the first report of osmophilic yeast species present in spoiled and unspoiled grape juice concentrates elaborated in Argentina.

Fingerprinting fission yeast: polymorphic markers for molecular genetic analysis of Schizosaccharomyces pombe strains.

The fission yeast Schizosaccharomyces pombe is widely used as a model eukaryote for cell and molecular studies but little is known of natural genetic variation in this species. In order to obtain informative molecular markers, imperfect tandem repeats, identified through bioinformatic methods, were tested for length polymorphism in six wild-type strains of Sch. pombe isolated from different substrates and geographical locations in Africa, America, Asia and Europe. Of 26 loci tested, 21 were multi-allelic, consistent with tandem repeat copy number variation. Eleven of these polymorphic tandem repeats are in regions encoding intracellular proteins. Most of the protein-coding repeats are not sited within structured domains but have non-regular predicted structure; one has a repeat unit length corresponding to integer turns of a predicted amphipathic alpha-helix secondary structure, suggesting that this repeat may be tolerated because copy number mutations change alpha-helix length but not orientation within the protein structure. In contrast to the differences observed between natural isolates of Sch. pombe, genetic strains were found to be essentially isogenic: only two polymorphic loci were detected out of 26 minisatellites and five microsatellites tested in 16 strains, including a hypervariable microsatellite in the med15 gene. The polymorphic tandem repeat markers identified in this study will prove useful for DNA fingerprinting and molecular analysis of natural genetic variation in Sch. pombe isolates.

Scw1p antagonizes the septation initiation network to regulate septum formation and cell separation in the fission yeast Schizosaccharomyces pombe.

Cytokinesis in the fission yeast Schizosaccharomyces pombe is regulated by a signaling pathway termed the septation initiation network (SIN). The SIN is essential for initiation of actomyosin ring constriction and septum formation. In a screen to search for mutations that can rescue the sid2-250 SIN mutant, we obtained scw1-18. Both the scw1-18 mutant and the scw1 deletion mutant (scw1Delta mutant), have defects in cell separation. Both the scw1-18 and scw1Delta mutations rescue the growth defects of not just the sid2-250 mutant but also the other temperature-sensitive SIN mutants. Other cytokinesis mutants, such as those defective for actomyosin ring formation, are not rescued by scw1Delta. scw1Delta does not seem to rescue the SIN by restoring SIN signaling defects. However, scw1Delta may function downstream of the SIN to promote septum formation, since scw1Delta can rescue the septum formation defects of the cps1-191beta-1,3-glucan synthase mutant, which is required for synthesis of the primary septum.

Isolation and characterisation of nuclear mutants with enhanced mitochondrial mutability in the fission yeast Schizosaccharomyces pombe.

In this paper we report the isolation and preliminary characterisation of nuclear mutants with increased mitochondrial mutability in fission yeast. Screening of about 2000 clones after nitrosoguanidine mutagenesis led to the isolation of ten mutator mutants. For one of them (mut-1) we show that the mutation is chromosomally encoded. The activity of the mutator is restricted to the mitochondrial genome, since it increases the mutation rate to mitochondrially encoded drug resistance considerably, whereas the mutability of nuclear genes is not altered.

Identification of novel temperature-sensitive lethal alleles in essential beta-tubulin and nonessential alpha 2-tubulin genes as fission yeast polarity mutants.

We have screened for temperature-sensitive (ts) fission yeast mutants with altered polarity (alp1-15). Genetic analysis indicates that alp2 is allelic to atb2 (one of two alpha-tubulin genes) and alp12 to nda3 (the single beta-tubulin gene). atb2(+) is nonessential, and the ts atb2 mutations we have isolated are dominant as expected. We sequenced two alleles of ts atb2 and one allele of ts nda3. In the ts atb2 mutants, the mutated residues (G246D and C356Y) are found at the longitudinal interface between alpha/beta-heterodimers, whereas in ts nda3 the mutated residue (Y422H) is situated in the domain located on the outer surface of the microtubule. The ts nda3 mutant is highly sensitive to altered gene dosage of atb2(+); overexpression of atb2(+) lowers the restrictive temperature, and, conversely, deletion rescues ts. Phenotypic analysis shows that contrary to undergoing mitotic arrest with high viability via the spindle assembly checkpoint as expected, ts nda3 mutants execute cytokinesis and septation and lose viability. Therefore, it appears that the ts nda3 mutant becomes temperature lethal because of irreversible progression through the cell cycle in the absence of activating the spindle assembly checkpoint pathway.

Isolation and characterization of fission yeast sns mutants defective at the mitosis-to-interphase transition.

pim1-d1ts was previously identified in a visual screen for fission yeast mutants unable to complete the mitosis-to-interphase transition. pim1+ encodes the guanine nucleotide exchange factor (GEF) for the spi1 GTPase. Perturbations of this GTPase system by either mutation or overproduction of its regulatory proteins cause cells to arrest with postmitotic condensed chromosomes, an unreplicated genome, and a wide medial septum. The septation phenotype of pim1-d1ts was used as the basis for a more extensive screen for this novel class of sns (septated, not in S-phase) mutants. Seventeen mutants representing 14 complementation groups were isolated. Three strains, sns-A3, sns-A5, and sns-A6, representing two different alleles, are mutated in the pim1+ gene. Of the 13 non-pim1ts sns complementation groups, 11 showed genetic interactions with the spi1 GTPase system. The genes mutated in 10 sns strains were synthetically lethal with pim1-d1, and six sns strains were hypersensitive to overexpression of one or more of the known components of the spil GTPase system. Epistasis analysis places the action of the genes mutated in nine of these strains downstream of pim1+ and the action of one gene upstream of pim1+. Three strains, sns-A2, sns-B1, and sns-B9, showed genetic interaction with the spil GTPase system in every test performed. sns-B1 and sns-B9 are likely to identify downstream targets, whereas sns-A2 is likely to identify upstream regulators of the spi1 GTPase system that are required for the mitosis-to-interphase transition.

The Ste16 WD-repeat protein regulates cell-cycle progression under starvation through the Rum1 protein in Schizosaccharomyces pombe.

The haploid cells of the fission yeast, Schizosaccharomyces pombe, are arrested in the G1-phase by nitrogen starvation and are committed to sexual reproduction (mating and sporulation). We isolated the sterile mutants which were defective in G1 arrest following nitrogen starvation. Genetic analysis of these mutants defined a single locus designated as ste16. The nucleotide sequence revealed that ste16+ encodes an 82-kDa protein containing eight WD40-repeats in its carboxy terminal half. The ste16 disruptant was viable, but arrested the cell cycle in the G2-phase after the nutritional down-shift. When transferred to fresh growth medium, the G2-arrested ste16Delta haploids resumed the mitotic cycle from the S-phase, resulting in diploidization. This diploidization phenomenon was completely suppressed by the null mutation of rum1 encoding the inhibitor of Cdc2 kinase. As the Rum1 protein level was remarkably elevated in the ste16Delta, the Ste16 protein negatively controls the Rum1 level. The loss of function of ste16 disturbs the cell-cycle progression and impairs the mechanism for the maintenance of ploidy.