scholarly journals Expansion of antisense lncRNA transcriptomes in budding yeast species since the loss of RNAi

2016 ◽  
Vol 23 (5) ◽  
pp. 450-455 ◽  
Author(s):  
Eric A Alcid ◽  
Toshio Tsukiyama
Keyword(s):  
Yeast Species ◽  
Budding Yeast

scholarly journals Closely related budding yeast species respond to different ecological signals for spore activation

Yeast ◽  
2020 ◽  
Author(s):  
Samuel Plante ◽  
Christian R. Landry
Keyword(s):  
Yeast Species ◽  
Budding Yeast ◽  
Spore Activation

scholarly journals Either of the major H2A genes but not an evolutionarily conserved H2A.F/Z variant of Tetrahymena thermophila can function as the sole H2A gene in the yeast Saccharomyces cerevisiae.

1996 ◽  
Vol 16 (6) ◽  
pp. 2878-2887 ◽  
Author(s):  
X Liu ◽  
J Bowen ◽  
M A Gorovsky
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Tetrahymena Thermophila ◽  
Yeast Species ◽  
Budding Yeast ◽  
Yeast Cells ◽  
Ciliated Protozoan ◽  
Yeast Saccharomyces Cerevisiae ◽  
Evolutionarily Conserved ◽  
Cold Sensitive ◽  
Conserved Epitope

H2A.F/Z histones are conserved variants that diverged from major H2A proteins early in evolution, suggesting they perform an important function distinct from major H2A proteins. Antisera specific for hv1, the H2A.F/Z variant of the ciliated protozoan Tetrahymena thermophila, cross-react with proteins from Saccharomyces cerevisiae. However, no H2A.F/Z variant has been reported in this budding yeast species. We sought to distinguish among three explanations for these observations: (i) that S. cerevisiae has an undiscovered H2A.F/Z variant, (ii) that the major S. cerevisiae H2A proteins are functionally equivalent to H2A.F/Z variants, or (iii) that the conserved epitope is found on a non-H2A molecule. Repeated attempts to clone an S. cerevisiae hv1 homolog only resulted in the cloning of the known H2A genes yHTA1 and yHTA2. To test for functional relatedness, we attempted to rescue strains lacking the yeast H2A genes with either the Tetrahymena major H2A genes (tHTA1 or tHTA2) or the gene (tHTA3) encoding hv1. Although they differ considerably in sequence from the yeast H2A genes, the major Tetrahymena H2A genes can provide the essential functions of H2A in yeast cells, the first such case of trans-species complementation of histone function. The Tetrahymena H2A genes confer a cold-sensitive phenotype. Although expressed at high levels and transported to the nucleus, hv1 cannot replace yeast H2A proteins. Proteins from S. cerevisiae strains lacking yeast H2A genes fail to cross-react with anti-hv1 antibodies. These studies make it likely that S. cerevisiae differs from most other eukaryotes in that it does not have an H2A.F/Z homolog. A hypothesis is presented relating the absence of H2A.F/Z in S. cerevisiae to its function in other organisms.

scholarly journals Variation of the meiotic recombination landscape and properties over a broad evolutionary distance in yeasts

2017 ◽  
Author(s):  
Christian Brion ◽  
Sylvain Legrand ◽  
Jackson Peter ◽  
Claudia Caradec ◽  
David Pflieger ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Segregation ◽  
Meiotic Recombination ◽  
Yeast Species ◽  
Budding Yeast ◽  
Evolutionary Distance ◽  
Model Organisms ◽  
Model Species ◽  
Recombination Hotspots ◽  
Chromosome Arm

AbstractMeiotic recombination is a major factor of genome evolution, deeply characterized in only a few model species, notably the yeast Saccharomyces cerevisiae. Consequently, little is known about variations of its properties across species. In this respect, we explored the recombination landscape of Lachancea kluyveri, a protoploid yeast species that diverged from the Saccharomyces genus more than 100 million years ago and we found striking differences with S. cerevisiae. These variations include a lower recombination rate, a higher frequency of chromosomes segregating without any crossover and the absence of recombination on the chromosome arm containing the sex locus. In addition, although well conserved within the Saccharomyces clade, the S. cerevisiae recombination hotspots are not conserved over a broader evolutionary distance. Finally and strikingly, we found evidence of frequent reversion of meiotic commitment to mitotic growth allowing allele shuffling without meiosis completion. Identification of this major but underestimated evolutionary phenomenon illustrates the relevance of exploring non-model species.Author summaryMeiotic recombination promotes accurate chromosome segregation and genetic diversity. To date, the mechanisms and rules lying behind recombination were dissected using model organisms such as the budding yeast Saccharomyces cerevisiae. To assess the conservation and variation of this process over a broad evolutionary distance, we explored the meiotic recombination landscape in Lachancea kluyveri, a budding yeast species that diverged from S. cerevisiae more than 100 million years ago. The meiotic recombination map we generated revealed that the meiotic recombination landscape and properties significantly vary across distantly related yeast species, supporting that recombination hotspots conservation across yeast species is likely associated to the conservation of synteny. Finally, the frequent meiotic reversions we observed led us to re-evaluate their evolutionary importance.

scholarly journals Loss of inner kinetochore genes is associated with the transition to an unconventional point centromere in budding yeast

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e10085
Author(s):  
Nagarjun Vijay
Keyword(s):  
Gene Loss ◽  
Yeast Species ◽  
Budding Yeast ◽  
High Quality ◽  
Sequence Of Events ◽  
Intergenic Regions ◽  
Actual Sequence ◽  
Or Gene ◽  
Conserved Gene ◽  
Genome Assemblies

Background The genomic sequences of centromeres, as well as the set of proteins that recognize and interact with centromeres, are known to quickly diverge between lineages potentially contributing to post-zygotic reproductive isolation. However, the actual sequence of events and processes involved in the divergence of the kinetochore machinery is not known. The patterns of gene loss that occur during evolution concomitant with phenotypic changes have been used to understand the timing and order of molecular changes. Methods I screened the high-quality genomes of twenty budding yeast species for the presence of well-studied kinetochore genes. Based on the conserved gene order and complete genome assemblies, I identified gene loss events. Subsequently, I searched the intergenic regions to identify any un-annotated genes or gene remnants to obtain additional evidence of gene loss. Results My analysis identified the loss of four genes (NKP1, NKP2, CENPL/IML3 and CENPN/CHL4) of the inner kinetochore constitutive centromere-associated network (CCAN/also known as CTF19 complex in yeast) in both the Naumovozyma species for which genome assemblies are available. Surprisingly, this collective loss of four genes of the CCAN/CTF19 complex coincides with the emergence of unconventional centromeres in N. castellii and N. dairenensis. My study suggests a tentative link between the emergence of unconventional point centromeres and the turnover of kinetochore genes in budding yeast.

scholarly journals A model of actin-driven endocytosis explains differences of endocytic motility in budding and fission yeast

2021 ◽  
Author(s):  
Masoud M. Nickaeen ◽  
Julien Berro ◽  
Thomas D. Pollard ◽  
Boris M. Slepchenko
Keyword(s):  
Comparative Study ◽  
Fission Yeast ◽  
Yeast Species ◽  
Budding Yeast ◽  
Turgor Pressure ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Factors Affecting

A comparative study (Sun et al., eLife, 2019) showed that the abundance of proteins at sites of endocytosis in fission and budding yeast is more similar in the two species than previously thought, yet membrane invaginations in fission yeast elongate two-fold faster and are nearly twice as long as in budding yeast. Here we use a three-dimensional model of a motile endocytic invagination (Nickaeen et al., MBoC, 2019) to investigate factors affecting elongation of the invaginations. We found that differences in turgor pressure in the two yeast species can largely explain the paradoxical differences observed experimentally in endocytic motility.

scholarly journals Paralogs in the PKA Regulon Traveled Different Evolutionary Routes to Divergent Expression in Budding Yeast

2021 ◽  
Vol 2 ◽  
Author(s):  
Benjamin M. Heineike ◽  
Hana El-Samad
Keyword(s):  
Yeast Species ◽  
Budding Yeast ◽  
Kluyveromyces Lactis ◽  
Functional Divergence ◽  
Promoter Sequence ◽  
Duplicate Genes ◽  
Generating Functional ◽  
Basal Expression ◽  
Genes Expression ◽  
Paralog Gene

Functional divergence of duplicate genes, or paralogs, is an important driver of novelty in evolution. In the model yeast Saccharomyces cerevisiae, there are 547 paralog gene pairs that survive from an interspecies Whole Genome Hybridization (WGH) that occurred ~100MYA. In this work, we report that ~1/6th (110) of these WGH paralogs pairs (or ohnologs) are differentially expressed with a striking pattern upon Protein Kinase A (PKA) inhibition. One member of each pair in this group has low basal expression that increases upon PKA inhibition, while the other has moderate and unchanging expression. For these genes, expression of orthologs upon PKA inhibition in the non-WGH species Kluyveromyces lactis and for PKA-related stresses in other budding yeasts shows unchanging expression, suggesting that lack of responsiveness to PKA was likely the typical ancestral phenotype prior to duplication. Promoter sequence analysis across related budding yeast species further revealed that the subsequent emergence of PKA-dependence took different evolutionary routes. In some examples, regulation by PKA and differential expression appears to have arisen following the WGH, while in others, regulation by PKA appears to have arisen in one of the two parental lineages prior to the WGH. More broadly, our results illustrate the unique opportunities presented by a WGH event for generating functional divergence by bringing together two parental lineages with separately evolved regulation into one species. We propose that functional divergence of two ohnologs can be facilitated through such regulatory divergence.

scholarly journals A gene coevolution network provides insight into eukaryotic cellular and genomic structure and function

2021 ◽  
Author(s):  
Jacob L. Steenwyk ◽  
Megan A. Phillips ◽  
Feng Yang ◽  
Swapneeta S. Date ◽  
Todd Graham ◽  
...  
Keyword(s):  
Yeast Species ◽  
Budding Yeast ◽  
Genomic Structure ◽  
Structure And Function ◽  
Yeast Gene ◽  
Gene Pairs ◽  
Opportunistic Human Pathogen ◽  
And Function ◽  
Cellular Compartments ◽  
Insight Into

Gene coevolution - which refers to gene pairs whose evolutionary rates covary across speciation events - is often observed among functionally related genes. We present a comprehensive gene coevolution network inferred from the examination of nearly three million gene pairs from 332 budding yeast species spanning ~400 million years of eukaryotic evolution. Modules within the network provide insight into cellular and genomic structure and function, such as genetic pleiotropy, genes functioning in distinct cellular compartments, vesicle transport, and DNA replication. Examination of the phenotypic impact of network perturbation across 14 environmental conditions using deletion mutant data from the baker's yeast Saccharomyces cerevisiae suggests that fitness in diverse environments is impacted by gene neighborhood and gene connectivity. By mapping the network onto the chromosomes of S. cerevisiae and the opportunistic human pathogen Candida albicans, which diverged ~235 million years ago, we discovered that coevolving gene pairs are not clustered in either species; rather, they are most often located on different chromosomes or far apart on the same chromosome. The budding yeast gene coevolution network captures the hierarchy of eukaryotic cellular structure and function, provides a roadmap for genotype-to-phenotype discovery, and portrays the genome as an extensively linked ensemble of genes.

scholarly journals A model of actin-driven endocytosis explains differences of endocytic motility in budding and fission yeast

2021 ◽  
Author(s):  
Masoud Nickaeen ◽  
Julien Berro ◽  
Thomas D. Pollard ◽  
Boris M. Slepchenko
Keyword(s):  
Comparative Study ◽  
Fission Yeast ◽  
Yeast Species ◽  
Budding Yeast ◽  
Turgor Pressure ◽  
Three Dimensional ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Factors Affecting

A comparative study (Sun et al., eLife, 2019) showed that the abundance of proteins at sites of endocytosis in fission and budding yeast is more similar in the two species than previously thought, yet membrane invaginations in fission yeast elongate two-fold faster and are nearly twice as long as in budding yeast. Here we use a three-dimensional model of a motile endocytic invagination (Nickaeen et al., MBoC, 2019) to investigate factors affecting elongation of the invaginations. We found that differences in turgor pressure in the two yeast species can largely explain the paradoxical differences observed experimentally in endocytic motility.

scholarly journals Closely related budding yeast species respond to different ecological signals for spore activation

2020 ◽  
Author(s):  
Samuel Plante ◽  
Christian R Landry
Keyword(s):  
North American ◽  
Inorganic Phosphate ◽  
Species Complex ◽  
Yeast Species ◽  
Culture Media ◽  
Budding Yeast ◽  
Reproductive Barriers ◽  
The North ◽  
Spore Activation ◽  
Biochemical Signals

AbstractSpore activation is one of the most important developmental decisions in fungi as it initiates the transition from dormant and stress resistant cells to vegetative cells. Because in many species mating follows spore activation and germination, signals that trigger this developmental transition can also contribute to species reproductive barriers. Here we examine the biochemical signals triggering spore activation in a natural species complex of budding yeast, Saccharomyces paradoxus (lineages SpA, SpB, SpC and SpC*). We first demonstrate that we can quantitatively monitor spore activation in these closely related lineages. Second, we dissect the composition of culture media to identify components necessary and/or sufficient to activate spores in the four lineages. We show that, contrary to expectation, glucose is necessary but not sufficient to trigger spore activation. We also show that two of the North American lineages (SpC and SpC*) diverge from the other North American (SpB) and European (SpA) lineages in terms of germination signal as their spore activation requires inorganic phosphate. Our results show that the way budding yeast interpret environmental conditions during spore activation diverged among closely related and incipient species, which means that it may play a role in their ecological differentiation and reproductive isolation.

scholarly journals Growth and division mode plasticity by cell density in marine-derived black yeasts

2021 ◽  
Author(s):  
Gohta Goshima
Keyword(s):  
Cell Division ◽  
Cell Density ◽  
Marine Fungi ◽  
Yeast Species ◽  
Budding Yeast ◽  
Black Yeast ◽  
Black Yeasts ◽  
Intermediate Cell ◽  
The Pacific ◽  
Random Site

The diversity and ecological contribution of the fungus kingdom in the marine environment remain under-studied. A recent survey in the Atlantic (Woods Hole, MA, USA) brought to light the diversity and unique biological features of marine fungi. The study revealed that black yeast species undergo an unconventional cell division cycle, which has not been documented in conventional model yeast species such as Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast). The prevalence of this unusual property is unknown. Inspired by the findings in Woods Hole, I collected and identified >50 marine fungi species across 40 genera from the ocean surface, sediment, and macroalgal surface in the Pacific (Sugashima, Toba, Japan). The Sugashima collection largely did not overlap with the Woods Hole collection and included several unidentifiable species, further illustrating the diversity of marine fungi. Three black yeast species were isolated, two of which were commonly found in Woods Hole (Aureobasidium pullulans, Hortaea werneckii). Surprisingly, I observed that their cell division mode was dependent on cell density, and the previously reported unconventional division mode was reproduced only at a certain cell density. For all three black yeast species, cells underwent filamentous growth with septations at low cell density and immediately formed buds at high cell density. At intermediate cell density, two black yeasts showed rod cells undergoing septation at the cell equator, in a manner similar to S. pombe. In contrast, all eight budding yeast species showed a consistent division pattern regardless of cell density. In five budding yeast species, the mother cell formed a single bud at a time at an apparently random site, similar to S. cerevisiae. The other three budding yeast species possessed a fixed budding site. This study illustrates the plastic nature of the growth/division mode of marine-derived black yeast.

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