Occurrence of FFZ genes in yeasts and correlation with fructophilic behaviour

Extensive remodeling of sugar metabolism through gene loss and horizontal gene transfer in a eukaryotic lineage

BACKGROUND

In yeasts belonging to the subphylum Saccharomycotina, genes encoding components of the main metabolic pathways, like alcoholic fermentation, are usually conserved. However, in fructophilic species belonging to the floral Wickerhamiella and Starmerella genera (W/S clade), alcoholic fermentation was uniquely shaped by events of gene loss and horizontal gene transfer (HGT).

RESULTS

Because HGT and gene losses were first identified when only eight W/S-clade genomes were available, we collected publicly available genome data and sequenced the genomes of 36 additional species. A total of 63 genomes, representing most of the species described in the clade, were included in the analyses. Firstly, we inferred the phylogenomic tree of the clade and inspected the genomes for the presence of HGT-derived genes involved in fructophily and alcoholic fermentation. We predicted nine independent HGT events and several instances of secondary loss pertaining to both pathways. To investigate the possible links between gene loss and acquisition events and evolution of sugar metabolism, we conducted phenotypic characterization of 42 W/S-clade species including estimates of sugar consumption rates and fermentation byproduct formation. In some instances, the reconciliation of genotypes and phenotypes yielded unexpected results, such as the discovery of fructophily in the absence of the cornerstone gene (FFZ1) and robust alcoholic fermentation in the absence of the respective canonical pathway.

CONCLUSIONS

These observations suggest that reinstatement of alcoholic fermentation in the W/S clade triggered a surge of innovation that goes beyond the utilization of xenologous enzymes, with fructose metabolism playing a key role.

Survey of the yeast ecology of dehydrated grapes and strain selection for wine fermentation

In this study we investigated the yeast population present on partially dehydrated Nebbiolo grapes destined for 'Sforzato di Valtellina', with the aim to select indigenous starters suitable for the production of this wine. Yeasts were enumerated, isolated, and identified by molecular methods (5.8S-ITS-RFLP and D1/D2 domain sequencing). A genetic, physiological (ethanol and sulphur dioxide tolerance, potentially useful enzymatic activities, hydrogen sulphide production, adhesive properties, and killer activity) and oenological (laboratory pure micro-fermentations) characterization was also carried out. Based on relevant physiological features, seven non-Saccharomyces strains were chosen for laboratory-scale fermentations, either in pure or in mixed-culture (simultaneous and sequential inoculum) with a commercial Saccharomyces cerevisiae strain. Finally, the best couples and inoculation strategy were further tested in mixed fermentations in winery. In both laboratory and winery, microbiological and chemical analyses were conducted during fermentation. The most abundant species on grapes were Hanseniaspora uvarum (27.4 % of the isolates), followed by Metschnikowia spp. (21.0 %) and Starmerella bacillaris (12.9 %). Technological characterization highlighted several inter- and intra-species differences. The best oenological aptitude was highlighted for species Starm. bacillaris, Metschnikowia spp., Pichia kluyveri and Zygosaccharomyces bailli. The best fermentation performances in laboratory-scale fermentations were found for Starm. bacillaris and P. kluyveri, due to their ability to reduce ethanol (-0.34 % v/v) and enhance glycerol production (+0.46 g/L). This behavior was further confirmed in winery. Results of this study contribute to the knowledge of yeast communities associated with a specific environment, like those of Valtellina wine region.

Metabolic profiles alteration of Southern Thailand traditional sweet pickled mango during the production process

Sweet pickled mango named Ma-Muang Bao Chae-Im (MBC), a delicacy from the Southern part of Thailand, has a unique aroma and taste. The employed immersion processes (brining 1, brining 2, and immersion in a hypertonic sugar solution, sequentially) in the MBC production process bring changes to the unripe mango, which indicate the occurrence of metabolic profiles alteration during the production process. This occurrence was never been explored. Thus, this study investigated metabolic profile alteration during the MBC production process. The untargeted metabolomics profiling method was used to reveal the changes in volatile and non-volatile metabolites. Headspace solid-phase micro-extraction tandem with gas chromatography quadrupole time of flight (GC/QTOF) was employed for the volatile analysis, while metabolites derivatization for non-volatile analysis. In conclusion, a total of 82 volatile and 41 non-volatile metabolites were identified during the production process. Terpenes, terpenoids, several non-volatile organic acids, and sugars were the major mango metabolites that presented throughout the process. Gamma-aminobutyric acid (GABA) was only observed during the brining processes, which suggested the microorganism’s stress response mechanism to an acidic environment and high chloride ions in brine. Esters and alcohols were abundant during the last immersion process, which had an important role in MBC flavor characteristics. The knowledge of metabolites development during the MBC production process would be beneficial for product development and optimization.

Mosquito sex and mycobiota contribute to fructose metabolism in the Asian tiger mosquito Aedes albopictus

BACKGROUND

Plant floral nectars contain natural sugars such as fructose, which are a primary energy resource for adult mosquitoes. Despite the importance of carbohydrates for mosquito metabolism, a limited knowledge is available about the pathways involved in sugar assimilation by mosquitoes and their associated microbiota. To this end, we used 13C-metabolomic and stable isotope probing approaches coupled to high-throughput sequencing to reveal fructose-related mosquito metabolic pathways and the dynamics of the active gut microbiota following fructose ingestion.

RESULTS

Our results revealed significant differences in metabolic pathways between males and females, highlighting different modes of central carbon metabolism regulation. Competitive and synergistic interactions of diverse fungal taxa were identified within the active mycobiota following fructose ingestion. In addition, we identified potential cross-feeding interactions between this. Interestingly, there is a strong correlation between several active fungal taxa and the presence of fructose-derived metabolites.

CONCLUSIONS

Altogether, our results provide novel insights into mosquito carbohydrate metabolism and demonstrate that dietary fructose as it relates to mosquito sex is an important determinant of mosquito metabolism; our results also further highlight the key role of active mycobiota interactions in regulating the process of fructose assimilation in mosquitoes. This study opens new avenues for future research on mosquito-microbiota trophic interactions related to plant nectar-derived sugars. Video abstract.

D-Fructose Assimilation and Fermentation by Yeasts Belonging to Saccharomycetes: Rediscovery of Universal Phenotypes and Elucidation of Fructophilic Behaviors in Ambrosiozyma platypodis and Cyberlindnera americana

The purpose of this study was to investigate the ability of ascomycetous yeasts to assimilate/ferment d-fructose. This ability of the vast majority of yeasts has long been neglected since the standardization of the methodology around 1950, wherein fructose was excluded from the standard set of physiological properties for characterizing yeast species, despite the ubiquitous presence of fructose in the natural environment. In this study, we examined 388 strains of yeast, mainly belonging to the Saccharomycetes (Saccharomycotina, Ascomycota), to determine whether they can assimilate/ferment d-fructose. Conventional methods, using liquid medium containing yeast nitrogen base +0.5% (w/v) of d-fructose solution for assimilation and yeast extract-peptone +2% (w/v) fructose solution with an inverted Durham tube for fermentation, were used. All strains examined (n = 388, 100%) assimilated d-fructose, whereas 302 (77.8%) of them fermented d-fructose. In addition, almost all strains capable of fermenting d-glucose could also ferment d-fructose. These results strongly suggest that the ability to assimilate/ferment d-fructose is a universal phenotype among yeasts in the Saccharomycetes. Furthermore, the fructophilic behavior of Ambrosiozyma platypodis JCM 1843 and Cyberlindnera americana JCM 3592 was characterized by sugar consumption profiles during fermentation.

Comparative genome analysis proposes three new Aureobasidium species isolated from grape juice

Aureobasidium pullulans is the most abundant and ubiquitous species within the genus and is also considered a core component of the grape juice microflora. So far, a small number of other Aureobasidium species have been reported, that in contrast to A. pullulans, appear far more constrained to specific habitats. It is unknown whether grape juice is a reservoir of novel Aureobasidium species, overlooked in the course of conventional morphological and meta-barcoding analyses. In this study, eight isolates from grape juice taxonomically classified as Aureobasidium through ITS sequencing were subjected to whole-genome phylogenetic, synteny and nucleotide identity analyses, which revealed three isolates to likely represent newly discovered Aureobasidium species. Analyses of ITS and metagenomic sequencing datasets show that these species can be present in grape juice samples from different locations and vintages. Functional annotation revealed the Aureobasidium isolates possess the genetic potential to support growth on the surface of plants and grapes. However, the loss of several genes associated with tolerance to diverse environmental stresses suggest a more constrained ecological range than A. pullulans.

Genome sequence of the non-conventional wine yeast Hanseniaspora guilliermondii UTAD222 unveils relevant traits of this species and of the Hanseniaspora genus in the context of wine fermentation

Hanseanispora species, including H. guilliermondii, are long known to be abundant in wine grape-musts and to play a critical role in vinification by modulating, among other aspects, the wine sensory profile. Despite this, the genetics and physiology of Hanseniaspora species remains poorly understood. The first genomic sequence of a H. guilliermondii strain (UTAD222) and the discussion of its potential significance are presented in this work. Metabolic reconstruction revealed that H. guilliermondii is not equipped with a functional gluconeogenesis or glyoxylate cycle, nor does it harbours key enzymes for glycerol or galactose catabolism or for biosynthesis of biotin and thiamine. Also, no fructose-specific transporter could also be predicted from the analysis of H. guilliermondii genome leaving open the mechanisms underlying the fructophilic character of this yeast. Comparative analysis involving H. guilliermondii, H. uvarum, H. opuntiae and S. cerevisiae revealed 14 H. guilliermondii-specific genes (including five viral proteins and one β-glucosidase). Furthermore, 870 proteins were only found within the Hanseniaspora proteomes including several β-glucosidases and decarboxylases required for catabolism of biogenic amines. The release of H. guilliermondii genomic sequence and the comparative genomics/proteomics analyses performed, is expected to accelerate research focused on Hanseniaspora species and to broaden their application in the wine industry and in other bio-industries in which they could be explored as cell factories.

Use of Nonconventional Yeasts for Modulating Wine Acidity

In recent years, in line with consumer preferences and due to the effects of global climate change, new trends have emerged in wine fermentation and wine technology. Consumers are looking for wines with less ethanol and fruitier aromas, but also with a good balance in terms of acidity and mouthfeel. Nonconventional yeasts contain a wide range of different genera of non-Saccharomyces. If in the past they were considered spoilage yeasts, now they are used to enhance the aroma profile of wine or to modulate wine composition. Recent publications highlight the role of non-Saccharomyces as selected strains for controlling fermentations mostly in cofermentation with Saccharomyces. In this article, I have reviewed the ability of some bacteria and non-Saccharomyces strains to modulate wine acidity.

Physiological Genomics of the Highly Weak-Acid-Tolerant Food Spoilage Yeasts of Zygosaccharomyces bailii sensu lato

Zygosaccharomyces bailii and two closely related species, Z. parabailii and Z. pseudobailii ("Z. bailii species complex", "Z. bailii sensu lato" or simply "Z. bailii (s.l.)"), are frequently implicated in the spoilage of acidified preserved foods and beverages due to their tolerance to very high concentrations of weak acids used as food preservatives. The recent sequencing and annotation of these species' genomes have clarified their genomic organization and phylogenetic relationship, which includes events of interspecies hybridization. Mechanistic insights into their adaptation and tolerance to weak acids (e.g., acetic and lactic acids) are also being revealed. Moreover, the potential of Z. bailii (s.l.) to be used in industrial biotechnological processes as interesting cell factories for the production of organic acids, reduction of the ethanol content, increase of alcoholic beverages aroma complexity, as well as of genetic source for increasing weak acid resistance in yeast, is currently being considered. This chapter includes taxonomical, ecological, physiological, and biochemical aspects of Z. bailii (s.l.). The focus is on the exploitation of physiological genomics approaches that are providing the indispensable holistic knowledge to guide the effective design of strategies to overcome food spoilage or the rational exploitation of these yeasts as promising cell factories.

Evidence for loss and reacquisition of alcoholic fermentation in a fructophilic yeast lineage

Fructophily is a rare trait that consists of the preference for fructose over other carbon sources. Here, we show that in a yeast lineage (the Wickerhamiella/Starmerella, W/S clade) comprised of fructophilic species thriving in the high-sugar floral niche, the acquisition of fructophily is concurrent with a wider remodeling of central carbon metabolism. Coupling comparative genomics with biochemical and genetic approaches, we gathered ample evidence for the loss of alcoholic fermentation in an ancestor of the W/S clade and subsequent reinstatement through either horizontal acquisition of homologous bacterial genes or modification of a pre-existing yeast gene. An enzyme required for sucrose assimilation was also acquired from bacteria, suggesting that the genetic novelties identified in the W/S clade may be related to adaptation to the high-sugar environment. This work shows how even central carbon metabolism can be remodeled by a surge of HGT events.

Cells build their components, such as the molecular machinery that helps them obtain energy from their environment, by following the instructions contained in genes. This genetic information is usually transferred from parents to offspring. Over the course of several generations, genes can accumulate small changes and the molecules they code for can acquire new roles: yet, this process is normally slow. However, certain organisms can also obtain completely new genes by ‘stealing’ them from other species. For example, yeasts, such as the ones used to make bread and beer, can take genes from nearby bacteria. This ‘horizontal gene transfer’ helps organisms to rapidly gain new characteristics, which is particularly useful if the environment changes quickly.

One way that yeasts get the energy they need is by breaking down sugars through a process called alcoholic fermentation. To do this, most yeast species prefer to use a sugar called glucose, but a small group of ‘fructophilic’ species instead favors a type of sugar known as fructose. Scientists do not know exactly how fructophilic yeasts came to be, but there is some evidence horizontal gene transfers may have been involved in the process.

Now, Gonçalves et al. have compared the genetic material of fructophilic yeasts with that of other groups of yeasts . Comparing genetic material helps scientists identify similarities and differences between species, and gives clues about why specific genetic features first evolved.

The experiments show that, early in their history, fructophilic yeasts lost the genes that allowed them to do alcoholic fermentation, probably since they could obtain energy in a different way. However, at a later point in time, these yeasts had to adapt to survive in flower nectar, an environment rich in sugar. They then favored fructose as their source of energy, possibly because this sugar can compensate more effectively for the absence of alcoholic fermentation. Later, the yeasts acquired a gene from nearby bacteria, which allowed them to do alcoholic fermentation again: this improved their ability to use the other sugars present in flower nectars.

When obtaining energy, yeasts and other organisms produce substances that are relevant to industry. Studying natural processes of evolution can help scientists understand how organisms can change the way they get their energy and adapt to new challenges. In turn, this helps to engineer yeasts into ‘cell factories’ that produce valuable chemicals in environmentally friendly and cost-effective ways.

Transcriptional Response to Lactic Acid Stress in the Hybrid Yeast Zygosaccharomyces parabailii

Lactic acid has a wide range of applications starting from its undissociated form, and its production using cell factories requires stress-tolerant microbial hosts. The interspecies hybrid yeast Zygosaccharomyces parabailii has great potential to be exploited as a novel host for lactic acid production, due to high organic acid tolerance at low pH and a fermentative metabolism with a high growth rate. Here we used mRNA sequencing (RNA-seq) to analyze Z. parabailii's transcriptional response to lactic acid added exogenously, and we explore the biological mechanisms involved in tolerance. Z. parabailii contains two homeologous copies of most genes. Under lactic acid stress, the two genes in each homeolog pair tend to diverge in expression to a significantly greater extent than under control conditions, indicating that stress tolerance is facilitated by interactions between the two gene sets in the hybrid. Lactic acid induces downregulation of genes related to cell wall and plasma membrane functions, possibly altering the rate of diffusion of lactic acid into cells. Genes related to iron transport and redox processes were upregulated, suggesting an important role for respiratory functions and oxidative stress defense. We found differences in the expression profiles of genes putatively regulated by Haa1 and Aft1/Aft2, previously described as lactic acid responsive in Saccharomyces cerevisiae. Furthermore, formate dehydrogenase (FDH) genes form a lactic acid-responsive gene family that has been specifically amplified in Z. parabailii in comparison to other closely related species. Our study provides a useful starting point for the engineering of Z. parabailii as a host for lactic acid production.

IMPORTANCE Hybrid yeasts are important in biotechnology because of their tolerance to harsh industrial conditions. The molecular mechanisms of tolerance can be studied by analyzing differential gene expression under conditions of interest and relating gene expression patterns to protein functions. However, hybrid organisms present a challenge to the standard use of mRNA sequencing (RNA-seq) to study transcriptional responses to stress, because their genomes contain two similar copies of almost every gene. Here we used stringent mapping methods and a high-quality genome sequence to study the transcriptional response to lactic acid stress in Zygosaccharomyces parabailii ATCC 60483, a natural interspecies hybrid yeast that contains two complete subgenomes that are approximately 7% divergent in sequence. Beyond the insights we gained into lactic acid tolerance in this study, the methods we developed will be broadly applicable to other yeast hybrid strains.