Horizontal gene transfer in yeasts

Rampant Interkingdom Horizontal Gene Transfer in Pezizomycotina? An Updated Inspection of Anomalous Phylogenies

Horizontal gene transfer (HGT) is a significant source of diversity in prokaryotes and a key factor in their genome evolution. Although similar processes have been postulated for eukaryotes, the validity of HGT's impact remains contested, particularly between long-distance-related organisms like those from different kingdoms. Among eukaryotes, the fungal subphylum Pezizomycotina has been frequently cited in the literature for experiencing HGT events, with over 600 publications on the subject. The proteomes of 421 Pezizomycotina species were meticulously examined to identify potential instances of interkingdom HGT. Furthermore, the phylogenies of over 275 HGT candidates previously reported were revisited. Manual scrutiny of 521 anomalous phylogenies revealed that only 1.5% display patterns indicative of interkingdom HGT. Moreover, novel interkingdom HGT searches within Pezizomycotina yielded few new contenders, casting doubt on the prevalence of such events within this subphylum. Although the detailed examination of phylogenies suggested interkingdom HGT, the evidence for lateral gene transfer is not conclusive. The findings suggest that expanding the number of homologous sequences could uncover vertical inheritance patterns that have been misclassified as HGT. Consequently, this research supports the notion that interkingdom HGT may be an extraordinary occurrence rather than a significant evolutionary driver in eukaryotic genomes.

Transcriptional response of Saccharomyces cerevisiae during competition with S. kudriavzevii: Genetic expression variability and accelerated activation

Transcriptomic studies have become an essential tool to understand the response of yeast to stimuli. The present work analyses the reaction of eight Saccharomyces cerevisiae strains with varying competitive abilities against a competitor (CR85, Saccharomyces kudriavzevii) in co-cultured fermentations. RNA sequencing (RNAseq) was performed at three very early time points after strains coinoculation in fermentation to delimit exactly when S. cerevisiae's response is triggered. A rapid response to its competitor, including activation of the glycolytic pathway, ribosomal metabolism, and nucleotide synthesis, is crucial for the dominance of S. cerevisiae strain in mixed fermentations. Additionaly, the study highlights the necessity of investigating individual yeast strains rather than a holistic species view, as significant variations in responses are observed among strains of the same clade.

Optogenetic control of horizontally acquired genes prevent stuck fermentations in yeast

Nitrogen limitations in the grape must be the main cause of stuck fermentations during the winemaking process. In Saccharomyces cerevisiae, a genetic segment known as region A, which harbors 12 protein-coding genes, was acquired horizontally from a phylogenetically distant yeast species. This region is mainly present in the genome of wine yeast strains, carrying genes that have been associated with nitrogen utilization. Despite the putative importance of region A in yeast fermentation, its contribution to the fermentative process is largely unknown. In this work, we used a wine yeast strain to evaluate the contribution of region A to the fermentation process. To do this, we first sequenced the genome of the wine yeast strain using long-read sequencing and determined that region A is present in a single copy. We then implemented an optogenetic system in this wine yeast strain to precisely regulate the expression of each gene, generating a collection of 12 strains that allow for light-activated gene expression. To evaluate the role of these genes during fermentation, we assayed this collection using microculture and fermentation experiments in synthetic must with varying amounts of nitrogen concentration. Our results show that changes in gene expression for genes within this region can impact growth parameters and fermentation rate. We additionally found that the expression of various genes in region A is necessary to complete the fermentation process and prevent stuck fermentations under low nitrogen conditions. Altogether, our optogenetics-based approach demonstrates the importance of region A in completing fermentation under nitrogen-limited conditions.IMPORTANCEStuck fermentations due to limited nitrogen availability in grape must represent one of the main problems in the winemaking industry. Nitrogen limitation in grape must reduces yeast biomass and fermentation rate, resulting in incomplete fermentations with high levels of residual sugar, undesired by-products, and microbiological instability. Here, we used an optogenetic approach to demonstrate that expression of genes within region A is necessary to complete fermentations under low nitrogen availability. Overall, our results suggest that region A is a genetic signature for adaptation to low nitrogen conditions.

A novel multilayer antimicrobial urinary catheter material with antimicrobial properties

Urinary catheters are commonly used in medical practice to drain and monitor urine of patients. However, urinary catheterisation is associated with the risk of developing catheter-associated urinary tract infections (CAUTIs), which can result in life-threatening sepsis that requires antibiotics for treatment. Using the layer-by-layer (LbL) technique, we assembled a multilayer catheter comprising nine quadruple layers (9QL) of alginate, chlorhexidine (CHX), alginate and poly(β-amino ester) (PBAE) built upon an amino-functionalised silicone. The prepared catheter materials were tested for pre-packaged storage conditions and sterilisation techniques. The daily release of CHX was measured at pH 7.4 and pH 5 and simulated urine at 37 °C, which was used to determine the antimicrobial affect. CHX release was detected for a minimum of 14 days in PBS (pH 7.4), pH 5 release media, and simulated urine for the samples tested against storage conditions and sterilisation techniques. Incubation of the prepared material with bacterial cultures for 24 hours restricted bacterial growth compared to incubation with the standard material. The minimum inhibition concentration of CHX for clinically isolated urinary tract infection (UTI) bacterial strains was in the range of 19.4-77.4 µM, at which the released CHX could indirectly prevent bacterial growth for up to 14 days. Based on the daily CHX release from the samples, the hydrolysis of PBAE at pH 5 was gradual, resulting in a greater number of days of preventing bacterial growth, followed by pH 7.4 and then simulated urine. To the best of our knowledge, this is the first report on the use of PBAE in association with a urinary catheter material for the release of an antimicrobial drug.

Uneven distribution of prokaryote-derived horizontal gene transfer in fungi: a lifestyle-dependent phenomenon

Horizontal gene transfer (HGT) in fungi is less understood despite its significance in prokaryotes. In this study, we systematically searched for HGT events in 829 representative fungal genomes. Using a combination of sequence similarity and phylogeny-based approaches, we detected 20,093 prokaryotic-derived transferred genes across 750 fungal genomes, via 8,815 distinct HGT events. Notably, our analysis revealed that eight lifestyle-related traits significantly influence HGT diversity in fungi. For instance, parasites exhibited the highest estimated number of HGT-acquired genes, followed by saprotrophs, with symbionts showing the lowest. HGT-acquired genes were predominantly associated with metabolism and cellular functions and underwent purifying selection. Moreover, horizontally transferred genes with introns have significantly higher expression levels compared to intron-lacking genes, suggesting a probable role of intron gains in the adaptation of HGT-acquired genes. Overall, our findings highlight the influence of lifestyle on HGT diversity in fungi and underscore the substantial contribution of HGT to fungal adaptation.

IMPORTANCE

This study sheds new light on the role of horizontal gene transfer (HGT) in fungi, an area that has remained relatively unexplored compared to its well-established prevalence in bacteria. By analyzing 829 fungal genomes, we identified over 20,000 genes that fungi acquired from prokaryotes, revealing the significant impact of HGT on fungal evolution. Our findings highlight that fungal lifestyle traits, such as being parasitic or saprotrophic, play a key role in determining the extent of HGT, with parasites showing the highest gene acquisition rates. We also uncovered unique patterns of HGT occurrence based on fungal morphology and reproduction. Importantly, genes with introns, which are more highly expressed, appear to play a crucial role in fungal adaptation. This research deepens our understanding of how HGT contributes to the metabolic diversity and ecological success of fungi, and it underscores the broader significance of gene transfer in shaping fungal evolution.

Reticulate evolution: Detection and utility in the phylogenomics era

Phylogenomics has enriched our understanding that the Tree of Life can have network-like or reticulate structures among some taxa and genes. Two non-vertical modes of evolution - hybridization/introgression and horizontal gene transfer - deviate from a strictly bifurcating tree model, causing non-treelike patterns. However, these reticulate processes can produce similar patterns to incomplete lineage sorting or recombination, potentially leading to ambiguity. Here, we present a brief overview of a phylogenomic workflow for inferring organismal histories and compare methods for distinguishing modes of reticulate evolution. We discuss how the timing of coalescent events can help disentangle introgression from incomplete lineage sorting and how horizontal gene transfer events can help determine the relative timing of speciation events. In doing so, we identify pitfalls of certain methods and discuss how to extend their utility across the Tree of Life. Workflows, methods, and future directions discussed herein underscore the need to embrace reticulate evolutionary patterns for understanding the timing and rates of evolutionary events, providing a clearer view of life's history.

The priority of yeast to select among various DNA options to repair genome breaks by homologous recombination

BACKGROUND

Horizontal gene transfer (HGT) is considered an important mechanism to contribute to the evolution of bacteria, plants, and animals by allowing the movement of genetic material between organisms, in difference to vertical inheritance. Thereby it can also play a significant role in spreading traits like antibiotic resistance among bacteria and virulence factors between pathogens. During the HGT, organisms take up free DNA from the environment and incorporate it into their genomes. Although HGT is known to be carried out by many organisms, there is limited information on how organisms select which genetic material for horizontal transfer. Here we have investigated the preference priority of Saccharomyces cerevisiae between different options of gene source presented under certain stress conditions to repair a double-strand break (DSB) in DNA via HR.

RESULTS

Each genetic module was designed with appropriate sequences being homologous for two sides of the DSB, which is important for yeast to repair the fracture with HR. S. cerevisiae made a random selection between two heterologous T1 (44%) and T2 (56%) modules to repair DSB. Interestingly, yeast corrected the DNA break only with the T3 module (almost 100%) when the homologous T3 module was an option for the selection. It seems that S. cerevisiae tends to prefer T3 over alternatives to fix DSBs when it exists among the options.

CONCLUSIONS

It seems that S. cerevisiae have a preference for priority to select a particular one under certain conditions when it has various DNA options to repair a DSB in its genome, further studies are required to support our findings.

Biocontainment Techniques and Applications for Yeast Biotechnology

Biocontainment techniques for genetically modified yeasts (GMYs) are pivotal due to the importance of these organisms for biotechnological processes and also due to the design of new yeast strains by using synthetic biology tools and technologies. Due to the large genetic modifications that many yeast strains display, it is highly desirable to avoid the leakage of GMY cells into natural environments and, consequently, the spread of synthetic genes and circuits by horizontal or vertical gene transfer mechanisms within the microorganisms. Moreover, it is also desirable to avoid patented yeast gene technologies spreading outside the production facility. In this review, the different biocontainment technologies currently available for GMYs were evaluated. Interestingly, uniplex-type biocontainment approaches (UTBAs), which rely on nutrient auxotrophies induced by gene mutation or deletion or the expression of the simple kill switches apparatus, are still the major biocontainment approaches in use with GMY. While bacteria such as Escherichia coli account for advanced biocontainment technologies based on synthetic biology and multiplex-type biocontainment approaches (MTBAs), GMYs are distant from this scenario due to many reasons. Thus, a comparison of different UTBAs and MTBAs applied for GMY and genetically engineered microorganisms (GEMs) was made, indicating the major advances of biocontainment techniques for GMYs.

Opportunities and Challenges of Understanding Community Assembly in Spontaneous Food Fermentation

Spontaneous fermentations that do not rely on backslopping or industrial starter cultures were especially important to the early development of society and are still practiced around the world today. While current literature on spontaneous fermentations is observational and descriptive, it is important to understand the underlying mechanism of microbial community assembly and how this correlates with changes observed in microbial succession, composition, interaction, and metabolite production. Spontaneous food and beverage fermentations are home to autochthonous bacteria and fungi that are naturally inoculated from raw materials, environment, and equipment. This review discusses the factors that play an important role in microbial community assembly, particularly focusing on commonly reported yeasts and bacteria isolated from spontaneously fermenting food and beverages, and how this affects the fermentation dynamics. A wide range of studies have been conducted in spontaneously fermented foods that highlight some of the mechanisms that are involved in microbial interactions, niche adaptation, and lifestyle of these microorganisms. Moreover, we will also highlight how controlled culture experiments provide greater insight into understanding microbial interactions, a modest attempt in decoding the complexity of spontaneous fermentations. Further research using specific in vitro microbial models to understand the role of core microbiota are needed to fill the knowledge gap that currently exists in understanding how the phenotypic and genotypic expression of these microorganisms aid in their successful adaptation and shape fermentation outcomes. Furthermore, there is still a vast opportunity to understand strain level implications on community assembly. Translating these findings will also help in improving other fermentation systems to help gain more control over the fermentation process and maintain consistent and superior product quality.