Autophagy is required for sulfur dioxide tolerance in Saccharomyces cerevisiae

The distribution of beneficial mutational effects between two sister yeast species poorly explains natural outcomes of vineyard adaptation

Domesticated strains of Saccharomyces cerevisiae have adapted to resist copper and sulfite, two chemical stressors commonly used in winemaking. S. paradoxus, has not adapted to these chemicals despite being consistently present in sympatry with S. cerevisiae in vineyards. This contrast represents a case of apparent evolutionary constraints favoring greater adaptive capacity in S. cerevisiae. In this study, we used a comparative mutagenesis approach to test whether S. paradoxus is mutationally constrained with respect to acquiring greater copper and sulfite resistance. For both species, we assayed the rate, effect size, and pleiotropic costs of resistance mutations and sequenced a subset of 150 mutants isolated from our screen. We found that the distributions of mutational effects displayed by the two species were very similar and poorly explained the natural pattern. We also found that chromosome VIII aneuploidy and loss of function mutations in PMA1 confer copper resistance in both species, whereas loss of function mutations in REG1 were only a viable route to copper resistance in S. cerevisiae. We also observed a single de novo duplication of the CUP1 gene in S. paradoxus but none in S. cerevisiae. For sulfite, loss of function mutations in RTS1 and KSP1 confer resistance in both species, but mutations in RTS1 have larger average effects in S. paradoxus. Our results show that even when the distributions of mutational effects are largely similar, species can differ in the adaptive paths available to them. They also demonstrate that assays of the distribution of mutational effects may lack predictive insight concerning adaptive outcomes.

Novel insight into the role of sulfur dioxide in fruits and vegetables: Chemical interactions, biological activity, metabolism, applications, and safety

Sulfur dioxide (SO₂) are a category of chemical compounds widely used as additives in food industry. So far, the use of SO₂ in fruit and vegetable industry has been indispensable although its safety concerns have been controversial. This article comprehensively reviews the chemical interactions of SO₂ with the components of fruit and vegetable products, elaborates its mechanism of antimicrobial, anti-browning, and antioxidation, discusses its roles in regulation of sulfur metabolism, reactive oxygen species (ROS)/redox, resistance induction, and quality maintenance in fruits and vegetables, summarizes the application technology of SO₂ and its safety in human (absorption, metabolism, toxicity, regulation), and emphasizes the intrinsic metabolism of SO₂ and its consequences for the postharvest physiology and safety of fresh fruits and vegetables. In order to fully understand the benefits and risks of SO₂, more research is needed to evaluate the molecular mechanisms of SO₂ metabolism in the cells and tissues of fruits and vegetables, and to uncover the interaction mechanisms between SO₂ and the components of fruits and vegetables as well as the efficacy and safety of bound SO₂. This review has important guiding significance for adjusting an applicable definition of maximum residue limit of SO₂ in food.

Retromer Complex and PI3K Complex II-Related Genes Mediate the Yeast (Saccharomyces cerevisiae) Sodium Metabisulfite Resistance Response

Sodium metabisulfite (Na₂S₂O₅) is widely used as a preservative in the food and wine industry. However, it causes varying degrees of cellular damage to organisms. In order to improve our knowledge regarding its cyto-toxicity, a genome-wide screen using the yeast single deletion collection was performed. Additionally, a total of 162 Na₂S₂O₅-sensitive strains and 16 Na₂S₂O₅-tolerant strains were identified. Among the 162 Na₂S₂O₅ tolerance-related genes, the retromer complex was the top enriched cellular component. Further analysis demonstrated that retromer complex deletion leads to increased sensitivity to Na₂S₂O₅, and that Na₂S₂O₅ can induce mislocalization of retromer complex proteins. Notably, phosphatidylinositol 3-monophosphate kinase (PI3K) complex II, which is important for retromer recruitment to the endosome, might be a potential regulator mediating retromer localization and the yeast Na₂S₂O₅ tolerance response. Na₂S₂O₅ can decrease the protein expressions of Vps34, which is the component of PI3K complex. Therefore, Na₂S₂O₅-mediated retromer redistribution might be caused by the effects of decreased Vps34 expression levels. Moreover, both pharmaceutical inhibition of Vps34 functions and deletions of PI3K complex II-related genes affect cell tolerance to Na₂S₂O₅. The results of our study provide a global picture of cellular components required for Na₂S₂O₅ tolerance and advance our understanding concerning Na₂S₂O₅-induced cytotoxicity effects.

Adaptive evolution of sulfite tolerance in Brettanomyces bruxellensis

Brettanomyces bruxellensis is considered one of the most problematic microbes associated with wine production. Sulfur dioxide is commonly used to inhibit the growth of B. bruxellensis and limit the potential wine spoilage. Brettanomyces bruxellensis wine isolates can grow at higher concentrations of this preservative than isolates from other sources. Thus, it has been suggested that the use of sulfite may have selected for B. bruxellensis strains better adapted to survive in the winemaking environment. We utilized laboratory adaptive evolution to determine the potential for this to occur. Three B. bruxellensis strains, representative of known genetic variation within the species, were subjected to increasing sublethal sulfur dioxide concentrations. Individual clones isolated from evolved populations displayed enhanced sulfite tolerance, ranging from 1.6 to 2.5 times higher than the corresponding parental strains. Whole-genome sequencing of sulfite-tolerant clones derived from two of the parental strains revealed structural variations affecting 270 genes. The region containing the sulfite efflux pump encoding gene, SSU1, showed clear copy number variants in all sequenced clones. Regardless of parental strain genetic background, SSU1 copy number changes were reproducibly associated with one SSU1 haplotype. This work clearly demonstrates adaptive evolution of B. bruxellensis when exposed to sublethal sulfites and suggests that, similar to Saccharomyces cerevisiae wine yeast, the mechanism responsible involves the gene SSU1.

Diverse function and regulation of CmSnf1 in entomopathogenic fungus Cordyceps militaris

SNF1/AMPK protein kinases play important roles in fungal development and activation of catabolite-repressed genes. In this study, we characterized the role of SNF1 ortholog in Cordyceps militaris (CmSnf1). The vegetative growth of a CmSnf1 deletion mutant was (ΔCmSnf1) reduced by 42.2% with arabinose as a sole carbon source. Most strikingly, the ΔCmSnf1 produced only a few conidia and exhibited delayed conidial germination. We found that CmSnf1 was necessary for mycelium to penetrate the insect cuticle to form the fruiting body on silkworm pupae, consistent with the down-regulation of chitinase- and protease-encoding genes in ΔCmSnf1. However, cordycepin content increased by more than 7 times in culture supernatants. Correspondingly, the relative expression levels of cordycepin gene cluster members were also elevated. In particular, the expression of cns4 associated with cordycepin transfer was up-regulated >10-fold. Furthermore, transcriptional analysis showed that CmSnf1 regulated the expression of genes involved in cell autophagy and oxidative stress tolerance. We speculated that under environmental stress, both the ATG and SNF1 pathways might collaborate to sustain adverse environments. Our study provides an initial framework to probe the diverse function and regulation of CmSnf1 in C. militaris, which will shed more light on the direction of molecular improvement of medicinal fungi.

Autophagic Proteome in Two Saccharomyces cerevisiae Strains During Second Fermentation for Sparkling Wine Elaboration

A correlation between autophagy and autolysis has been proposed in order to acceleratethe acquisition of wine organoleptic properties during sparkling wine elaboration. In this context, aproteomic analysis was carried out in two industrial Saccharomyces cerevisiae strains (P29,conventional sparkling wine strain and G1, implicated in sherry wine elaboration) with the aim ofstudying the autophagy-related proteome and comparing the effect of CO2 overpressure duringsparkling wine elaboration. In general, a detrimental effect of pressure and second fermentationdevelopment on autophagy-related proteome was observed in both strains, although it was morepronounced in flor yeast strain G1. Proteins mainly involved in autophagy regulation andautophagosome formation in flor yeast G1, and those required for vesicle nucleation and expansionin P29 strain, highlighted in sealed bottle. Proteins Sec2 and Sec18 were detected 3-fold underpressure conditions in P29 and G1 strains, respectively. Moreover, 'fingerprinting' obtained frommultivariate data analysis established differences in autophagy-related proteome between strainsand conditions. Further research is needed to achieve more solid conclusions and design strategiesto promote autophagy for an accelerated autolysis, thus reducing cost and time production, as wellas acquisition of good organoleptic properties.

Autophagy is required for sulfur dioxide tolerance in Saccharomyces cerevisiae

Sulfiting agents are among the most widely used preservatives in the food and beverages industries, including winemaking, and one of their main functions is inhibition of spoilage microorganisms. We have used a whole genome quantitative fitness analysis in order to improve our knowledge on yeast tolerance to sulfites. Apart from the contribution of sulfite efflux to tolerance, results point to vesicle‐mediated transport, autophagy and vacuolar activity as the main cellular functions required to survive sulfite challenges. The involvement of autophagic and vacuolar functions in sulfite tolerance was further confirmed by pairwise competition using a newly constructed atg2‐defective strain, as well as by showing induction of ATG8 expression by sulfite. Autophagy is required for the turnover of proteins and subcellular structures damaged by sulfite. In addition, the requirement for vacuolar functions might be related to its role in intracellular pH homeostasis. Finally, the involvement of the sulfite pump Ssu1 and the transcription factor Fzf1 in sulfite tolerance by Saccharomyces cerevisiae was confirmed; a result that validates the experimental approach used in this work. These findings have relevance for understanding sulfite toxicity and tolerance, as well as for the eventual design of strategies aiming to control yeast spoilage.