Yeast最新文献

Trichosporon asahii is a pathogenic yeast that cause trichosporonosis. T. asahii exhibits several colony morphologies, such as white (W)- or off-white (O)-type, which may affect virulence. In this study, we compared the expression pattern of heparin-binding proteins in various colony morphologies and identified heparin-binding protein in T. asahii. Surface plasmon resonance analysis revealed that cell surface molecules attached more strongly to heparin in W- than O-type cells. We purified and identified a heparin-binding protein strongly expressed in W-type cells using heparin-Sepharose beads, named it heparin-binding protein 1 (HepBP1), and expressed Flag-tagged HepBP1 in mammalian cells. The heparin-binding ability of Flag-tagged HepBP1 was confirmed by pulldown assay using heparin-Sepharose beads. Thus, HepBP1 is a heparin-binding protein on T. asahii cell surface. These results suggest that several T. asahii cell surface proteins interact with glycosaminoglycans; therefore, they could contribute to infection.

Yeast-insect interactions are one of the most interesting long-standing relationships whose research has contributed to our understanding of yeast biodiversity and their industrial applications. Although insect-derived yeast strains are exploited for industrial fermentations, only a limited number of such applications has been documented. The search for novel yeasts from insects is attractive to augment the currently domesticated and commercialized production strains. More specifically, there is potential in tapping the insects native to southern Africa. Southern Africa is home to a disproportionately high fraction of global biodiversity with a cluster of biomes and a broad climate range. This review presents arguments on the roles of the mutualistic relationship between yeasts and insects, the presence of diverse pristine environments and a long history of spontaneous food and beverage fermentations as the potential source of novelty. The review further discusses the recent advances in novelty of industrial strains of insect origin, as well as various ancient and modern-day industries that could be improved by use yeasts from insect origin. The major focus of the review is on the relationship between insects and yeasts in southern African ecosystems as a potential source of novel industrial yeast strains for modern bioprocesses.

Transcription presents challenges to genome stability both directly, by altering genome topology and exposing single-stranded DNA to chemical insults and nucleases, and indirectly by introducing obstacles to the DNA replication machinery. Such obstacles include the RNA polymerase holoenzyme itself, DNA-bound regulatory factors, G-quadruplexes and RNA-DNA hybrid structures known as R-loops. Here, we review the detrimental impacts of transcription on genome stability in budding yeast, as well as the mitigating effects of transcription-coupled nucleotide excision repair and of systems that maintain DNA replication fork processivity and integrity. Interactions between DNA replication and transcription have particular potential to induce mutation and structural variation, but we conclude that such interactions must have only minor effects on DNA replication by the replisome with little if any direct mutagenic outcome. However, transcription can significantly impair the fidelity of replication fork rescue mechanisms, particularly Break Induced Replication, which is used to restart collapsed replication forks when other means fail. This leads to de novo mutations, structural variation and extrachromosomal circular DNA formation that contribute to genetic heterogeneity, but only under particular conditions and in particular genetic contexts, ensuring that the bulk of the genome remains extremely stable despite the seemingly frequent interactions between transcription and DNA replication.

Polyadenylation occurs at numerous sites within 3'-untranslated regions (3'-UTRs) but rarely within coding regions. How does Pol II travel through long coding regions without generating poly(A) sites, yet then permits promiscuous polyadenylation once it reaches the 3'-UTR? The cleavage/polyadenylation (CpA) machinery preferentially associates with 3'-UTRs, but it is unknown how its recruitment is restricted to 3'-UTRs during Pol II elongation. Unlike coding regions, 3'-UTRs have long AT-rich stretches of DNA that may be important for restricting polyadenylation to 3'-UTRs. Recognition of the 3'-UTR could occur at the DNA (AT-rich), RNA (AU-rich), or RNA:DNA hybrid (rU:dA- and/or rA:dT-rich) level. Based on the nucleic acid critical for 3'-UTR recognition, there are three classes of models, not mutually exclusive, for how the CpA machinery is selectively recruited to 3'-UTRs, thereby restricting where polyadenylation occurs: (1) RNA-based models suggest that the CpA complex directly (or indirectly through one or more intermediary proteins) binds long AU-rich stretches that are exposed after Pol II passes through these regions. (2) DNA-based models suggest that the AT-rich sequence affects nucleosome depletion or the elongating Pol II machinery, resulting in dissociation of some elongation factors and subsequent recruitment of the CpA machinery. (3) RNA:DNA hybrid models suggest that preferential destabilization of the Pol II elongation complex at rU:dA- and/or rA:dT-rich duplexes bridging the nucleotide addition and RNA exit sites permits preferential association of the CpA machinery with 3'-UTRs. Experiments to provide evidence for one or more of these models are suggested.

N⁶-methyladenosine (m6A) is a highly abundant and evolutionarily conserved messenger RNA (mRNA) modification. This modification is installed on RRACH motifs on mRNAs by a hetero-multimeric holoenzyme known as m6A methyltransferase complex (MTC). The m6A mark is then recognised by a group of conserved proteins known as the YTH domain family proteins which guide the mRNA for subsequent downstream processes that determine its fate. In yeast, m6A is installed on thousands of mRNAs during early meiosis by a conserved MTC and the m6A-modified mRNAs are read by the YTH domain-containing protein Mrb1/Pho92. In this review, we aim to delve into the recent advances in our understanding of the regulation and roles of m6A in yeast meiosis. We will discuss the potential functions of m6A in mRNA translation and decay, unravelling their significance in regulating gene expression. We propose that yeast serves as an exceptional model organism for the study of fundamental molecular mechanisms related to the function and regulation of m6A-modified mRNAs. The insights gained from yeast research not only expand our knowledge of mRNA modifications and their molecular roles but also offer valuable insights into the broader landscape of eukaryotic posttranscriptional regulation of gene expression.

Yeasts are naturally diverse, genetically tractable, and easy to grow such that researchers can investigate any number of genotypes, environments, or interactions thereof. However, studies of yeast transcriptomes have been limited by the processing capabilities of traditional RNA sequencing techniques. Here we optimize a powerful, high-throughput single-cell RNA sequencing (scRNAseq) platform, SPLiT-seq (Split Pool Ligation-based Transcriptome sequencing), for yeasts and apply it to 43,388 cells of multiple species and ploidies. This platform utilizes a combinatorial barcoding strategy to enable massively parallel RNA sequencing of hundreds of yeast genotypes or growth conditions at once. This method can be applied to most species or strains of yeast for a fraction of the cost of traditional scRNAseq approaches. Thus, our technology permits researchers to leverage "the awesome power of yeast" by allowing us to survey the transcriptome of hundreds of strains and environments in a short period of time and with no specialized equipment. The key to this method is that sequential barcodes are probabilistically appended to cDNA copies of RNA while the molecules remain trapped inside of each cell. Thus, the transcriptome of each cell is labeled with a unique combination of barcodes. Since SPLiT-seq uses the cell membrane as a container for this reaction, many cells can be processed together without the need to physically isolate them from one another in separate wells or droplets. Further, the first barcode in the sequence can be chosen intentionally to identify samples from different environments or genetic backgrounds, enabling multiplexing of hundreds of unique perturbations in a single experiment. In addition to greater multiplexing capabilities, our method also facilitates a deeper investigation of biological heterogeneity, given its single-cell nature. For example, in the data presented here, we detect transcriptionally distinct cell states related to cell cycle, ploidy, metabolic strategies, and so forth, all within clonal yeast populations grown in the same environment. Hence, our technology has two obvious and impactful applications for yeast research: the first is the general study of transcriptional phenotypes across many strains and environments, and the second is investigating cell-to-cell heterogeneity across the entire transcriptome.