FEMS yeast research最新文献

Here we report the draft genome sequence of Naganishia friedmannii (formerly Cryptococcus friedmannii) isolate, a Basidiomycota yeast commonly found in some of the most extreme environments of the Earth's cryosphere. We isolated N. friedmannii strain Llullensis from soils at 6000 m above sea level on Volcán Llullaillaco, Argentina. The genome was 22.2 Mb with 6251 identified protein coding genes. Proteins known to be associated with thermal, osmotic, and radiation stress were identified in the genome. Comparative analysis with seven other Naganishia genomes revealed unique features underlying its polyextremophilic lifestyle. Naganishia friedmannii showed an expansion of genes involved in breaking down plant-derived carbohydrates, supporting the hypothesis that it survives at high elevations by metabolizing wind-deposited organic matter. Surprisingly, many genes involved in cell-cycle checkpoints and DNA repair were missing, as in several other Naganishia species. This extensive loss may be adaptive in extreme environments prone to abiotic stress, where a high mutation rate could generate advantageous traits, and reduced cell-cycle control may allow for faster reproduction that would be advantageous for rapid growth during brief periods of soil wetting following rare snow events.

Nakaseomyces glabratus (Candida glabrata) is an opportunistic human fungal pathogen of high priority that shares an ancestor with the non-pathogenic yeast Saccharomyces cerevisiae. Candida glabrata causes infections of the mucosal surfaces as well as fatal deep-seated tissue infections in immunocompromised individuals. The co-resistance to two commonly used antifungal drug classes, azoles and echinocandins, is increasingly being reported in clinical isolates of C. glabrata all over the world, which poses a significant threat to the successful treatment of C. glabrata infections. Acquisition of drug resistance in hospital settings is a complex multifaceted process that is governed by various factors including antimicrobial stewardship. This review summarizes both the key clinical antifungal resistance mechanisms, and the contribution of cellular stress signaling pathways to drug resistance acquisition in C. glabrata. Specifically, we discuss the emerging concepts regarding the role of mitochondrial functions, epigenetic modifications, and the host niche in the development of drug resistance. Lastly, we outline some potential areas for future research that will enable us to better understand the drug evolutionary dynamics of this important human fungal pathogen.

Ribosome-associated noncoding RNAs, particularly tRNA-derived fragments (tDRs), have emerged as key regulators of translation, especially under stress conditions. In Saccharomyces cerevisiae, tDRs interact with small ribosomal subunits to modulate protein biosynthesis, yet methods to quantitatively assess these interactions have been lacking. Here, we present tDR-quant, a robust technique for in vivo quantification of tDR/ribosome associations using electroporation of radiolabeled tDRs into yeast spheroplasts, followed by polysome profiling and radioactivity detection. We show that tDR interactions with ribosomes are stress- and dose-dependent, primarily associating with the 40S subunit but also with 60S, monosomes, and polysomes under specific conditions. Translation assays revealed that increased tDR levels inhibit protein synthesis without altering polysome profiles. Northern blot and quantitative real-time PCR (qRT-PCR) validated tDR-quant results, confirming its reliability. Stress-specific association patterns suggest that tDRs dynamically regulate translation by interacting with different ribosomal components in response to environmental cues. Importantly, these interactions do not correlate directly with tDR abundance, indicating selective ribosome binding. This study provides the first comprehensive method to quantify tDR-ribosome interactions in vivo and demonstrates that tDRs act as regulatory elements fine-tuning translation during cellular stress in yeast.

Global transcription machinery engineering (gTME) is a strategy for optimizing complex phenotypes in microbes by manipulating transcription factors (TFs) and their downstream transcriptional regulatory networks (TRN). In principle, gTME leads to a focused but comprehensive optimization of a microbe, also enabling the engineering of nonpathway functionalities, like stress resistance, protein expression, or growth rate. A link between a TF and a desired phenotype is to be established for a rationally designed gTME. For use in a high-throughput format with extensive libraries of TRN-engineered clones tested under multiple conditions, well-developed culturing and analytical protocols are needed, to reveal the pleiotropic effects of the TFs. This mini-review summarizes the gTME strategies and TFs described under different contexts in Yarrowia lipolytica. The outcomes of the gTME strategy application are also addressed, demonstrating its effectiveness in engineering complex, industrially relevant traits in Y. lipolytica.

A large variety of synthetic biology toolkits for the introduction of multiple expression cassettes is available for Saccharomyces cerevisiae. Unfortunately, none of these tools is designed to allow the modification - exchange or removal - of the cassettes already integrated into the genome in a standardized way. The application of the modularity principle therefore ends to the steps preceding the final host engineering, making microbial cell factories construction stiff and strictly sequential. In this work, we describe a system that easily allows CRISPR-mediated swapping or removal of previously integrated cassettes, thus bringing the modularity to the strain level, enhancing the possibility of modifying existing strains with a reduced number of steps. In the system, each cassette is tagged with specific barcodes, which can be used as targets for CRISPR nucleases (Cas9 and Cas12a), allowing the excision of the construct from the genome and its substitution with another expression cassette or the restoration of the wild type locus in one single standardized step. The system has been applied to the previously developed Easy-MISE toolkit and tested by swapping fluorescent protein expression cassettes with an efficiency of ∼90% quantified by PCR and flow cytometry.