Annamaria Merico

Fermentative lifestyle in yeasts belonging to the Saccharomyces complex

The yeast Saccharomyces cerevisiae is characterized by its ability to: (a) degrade glucose or fructose to ethanol, even in the presence of oxygen (Crabtree effect); (b) grow in the absence of oxygen; and (c) generate respiratory‐deficient mitochondrial mutants, so‐called petites. How unique are these properties among yeasts in the Saccharomyces clade, and what is their origin? Recent progress in genome sequencing has elucidated the phylogenetic relationships among yeasts in the Saccharomyces complex, providing a framework for the understanding of the evolutionary history of several modern traits. In this study, we analyzed over 40 yeasts that reflect over 150 million years of evolutionary history for their ability to ferment, grow in the absence of oxygen, and generate petites. A great majority of isolates exhibited good fermentation ability, suggesting that this trait could already be an intrinsic property of the progenitor yeast. We found that lineages that underwent the whole‐genome duplication, in general, exhibit a fermentative lifestyle, the Crabtree effect, and the ability to grow without oxygen, and can generate stable petite mutants. Some of the pre‐genome duplication lineages also exhibit some of these traits, but a majority of the tested species are petite‐negative, and show a reduced Crabtree effect and a reduced ability to grow in the absence of oxygen. It could be that the ability to accumulate ethanol in the presence of oxygen, a gradual independence from oxygen and/or the ability to generate petites were developed later in several lineages. However, these traits have been combined and developed to perfection only in the lineage that underwent the whole‐genome duplication and led to the modern Saccharomyces cerevisiae yeast.

Physiological and oenological traits of different Dekkera/Brettanomyces bruxellensis strains under wine‐model conditions

Contamination of wine by Dekkera/Brettanomyces bruxellensis is mostly due to the production of off-flavours identified as vinyl- and especially ethyl-phenols, but these yeasts can also produce several other spoiling metabolites, such as acetic acid and biogenic amines. Little information is available about the correlation between growth, viability and off-flavour and biogenic amine production. In the present work, five strains of Dekkera bruxellensis isolated from wine were analysed over 3 months in wine-like environment for growth, cell survival, carbon source utilization and production of volatile phenols and biogenic amines. Our data indicate that the wine spoilage potential of D. bruxellensis is strain dependent, being strictly associated with the ability to grow under oenological conditions. 4-Ethyl-phenol and 4-ethyl-guaiacol production ranged between 0 and 2.7 and 2 mg L(-1), respectively, depending on the growth conditions. Putrescine, cadaverine and spermidine were the biogenic amines found.

Genetic diversity and physiological traits of Brettanomyces bruxellensis strains isolated from Tuscan Sangiovese wines

Eighty four isolates of Brettanomyces bruxellensis, were collected during fermentation of Sangiovese grapes in several Tuscan wineries and characterized by restriction analysis of 5.8S-ITS and species-specific PCR. The isolates were subsequently analysed, at strain level, by the combined use of the RAPD-PCR assay with primer OPA-02 and the mtDNA restriction analysis with the HinfI endonuclease. This approach showed a high degree of polymorphism and allowed to identify seven haplotypes, one of them being the most represented and widely distributed (72 isolates, 85.7%). Physiological traits of the yeasts were investigated under a wine model condition. Haplotypes clustered into two groups according to their growth rates and kinetics of production of 4-ethylphenol and 4-ethylguaiacol. Hexylamine was the biogenic amine most produced (up to 3.92 mg l(-1)), followed by putrescine and phenylethylamine. Formation of octapamine was detected by some haplotypes, for the first time.

A Second Pathway to Degrade Pyrimidine Nucleic Acid Precursors in Eukaryotes.

Pyrimidine bases are the central precursors for RNA and DNA, and their intracellular pools are determined by de novo, salvage and catabolic pathways. In eukaryotes, degradation of uracil has been believed to proceed only via the reduction to dihydrouracil. Using a yeast model, Saccharomyces kluyveri, we show that during degradation, uracil is not reduced to dihydrouracil. Six loci, named URC1-6 (for uracil catabolism), are involved in the novel catabolic pathway. Four of them, URC3,5, URC6, and URC2 encode urea amidolyase, uracil phosphoribosyltransferase, and a putative transcription factor, respectively. The gene products of URC1 and URC4 are highly conserved proteins with so far unknown functions and they are present in a variety of prokaryotes and fungi. In bacteria and in some fungi, URC1 and URC4 are linked on the genome together with the gene for uracil phosphoribosyltransferase (URC6). Urc1p and Urc4p are therefore likely the core components of this novel biochemical pathway. A combination of genetic and analytical chemistry methods demonstrates that uridine monophosphate and urea are intermediates, and 3-hydroxypropionic acid, ammonia and carbon dioxide the final products of degradation. The URC pathway does not require the presence of an active respiratory chain and is therefore different from the oxidative and rut pathways described in prokaryotes, although the latter also gives 3-hydroxypropionic acid as the end product. The genes of the URC pathway are not homologous to any of the eukaryotic or prokaryotic genes involved in pyrimidine degradation described to date.

Aerobic sugar metabolism in the spoilage yeast Zygosaccharomyces bailii

Despite the importance of some Zygosaccharomyces species as agents causing spoilage of food, the carbon and energy metabolism of most of them is yet largely unknown. This is the case with Zygosaccharomyces bailii. In this study the occurrence of the Crabtree effect in the petite-negative yeast Z. bailii ATCC 36947 was investigated. In this yeast the aerobic ethanol production is strictly dependent on the carbon source utilised. In glucose-limited continuous cultures a very low level of ethanol was produced. In fructose-limited continuous cultures ethanol was produced at a higher level and its production increased with the dilution rate. As a consequence, on fructose the onset of respiro-fermentative metabolism caused a reduction in biomass yield. An immediate aerobic alcoholic fermentation in Z. bailii was observed during the transition from sugar limitation to sugar excess, both on glucose and on fructose. The analysis of some key enzymes of the fermentative metabolism showed a high level of acetyl-CoA synthetase in Z. bailii growing on fructose. At high dilution rates, the activities of glucose- and fructose-phosphorylating enzymes, as well as of pyruvate decarboxylase and alcohol dehydrogenase, were higher in cells during growth on fructose than on glucose.

The oxygen level determines the fermentation pattern in Kluyveromyces lactis

Yeasts belonging to the lineage that underwent whole-genome duplication (WGD) possess a good fermentative potential and can proliferate in the absence of oxygen. In this study, we analyzed the pre-WGD yeast Kluyveromyces lactis and its ability to grow under oxygen-limited conditions. Under these conditions, K. lactis starts to increase the glucose metabolism and accumulates ethanol and glycerol. However, under more limited conditions, the fermentative metabolism decreases, causing a slow growth rate. In contrast, Saccharomyces cerevisiae and Saccharomyces kluyveri in anaerobiosis exhibit almost the same growth rate as in aerobiosis. In this work, we showed that in K. lactis, under oxygen-limited conditions, a decreased expression of RAG1 occurred. The activity of glucose-6-phosphate dehydrogenase also decreased, likely causing a reduced flux in the pentose phosphate pathway. Comparison of related and characterized yeasts suggests that the behavior observed in K. lactis could reflect the lack of an efficient mechanism to maintain a high glycolytic flux and to balance the redox homeostasis under hypoxic conditions. This could be a consequence of a recent specialization of K. lactis toward living in a niche where the ethanol accumulation at high oxygen concentrations and the ability to survive at a low oxygen concentration do not represent an advantage.

Generation of an evolved Saccharomyces cerevisiae strain with a high freeze tolerance and an improved ability to grow on glycerol

Glycerol is a residue generated during biodiesel production and represents around 10% of the total product output. Biodiesel production is currently having a significant impact on glycerol price, leading to an increased interest in the use of glycerol as a cheap substrate for fermentation processes. We have analysed the growth kinetics of two wild-type strains of Saccharomyces cerevisiae grown on synthetic media containing glycerol as the sole carbon and energy source. Both strains were initially unable to grow when cultivated under these conditions, and an unusually long lag phase was necessary prior to the appearance of slow-growing cells. Following the application of an “evolutionary engineering” approach, we obtained S. cerevisiae strains with an improved ability to grow on glycerol. We report here the isolation of an evolved strain that exhibits a reduction of the lag phase, a threefold increase of the specific growth rate and a higher glycerol consumption rate compared to wild-type strains. The evolved strain has retained its fermentative activity, producing ethanol at the same rate and yield as the wild type. Interestingly, the yeast biomass obtained by cultivating the evolved strain on synthetic glycerol-based media also showed a high viability after prolonged storage at −20°C. The strategy adopted in our study could be easily applied to obtain S. cerevisiae strains with new industrially relevant traits, such as an improved ability to use cheap substrates and high resistance to freeze and thaw procedures.

Catabolism of pyrimidines in yeast : a tool to understand degradation of anticancer drugs

The pyrimidine catabolic pathway is of crucial importance in cancer patients because it is involved in degradation of several chemotherapeutic drugs, such as 5-fluorouracil; it also is important in plants, unicellular eukaryotes, and bacteria for the degradation of pyrimidine-based biocides/antibiotics. During the last decade we have developed a yeast species, Saccharomyces kluyveri, as a model and tool to study the genes and enzymes of the pyrimidine catabolic pathway. In this report, we studied degradation of uracil and its putative degradation products in 38 yeasts and showed that this pathway was present in the ancient yeasts but was lost approximately 100 million years ago in the S. cerevisiae lineage.

Isolation and sequence analysis of the gene encoding triose phosphate isomerase from Zygosaccharomyces bailii

The ZbTPI1 gene encoding triose phosphate isomerase (TIM) was cloned from a Zygosaccharomyces bailii genomic library by complementation of the Saccharomyces cerevisiae tpi1 mutant strain. The nucleotide sequence of a 1.5 kb fragment showed an open reading frame (ORF) of 746 bp, encoding a protein of 248 amino acid residues. The deduced amino acid sequence shares a high degree of homology with TIMs from other yeast species, including some highly conserved regions. The analysis of the promoter sequence of the ZbTPI1 revealed the presence of putative motifs known to have regulatory functions in S. cerevisiae. The GenBank Accession No. of ZbTPI1 is AF325852. Copyright

Effects of the loss of triose phosphate isomerase activity on carbon metabolism in Kluyveromyces lactis

The effect of the loss of triose phosphate isomerase activity on carbon metabolism in Kluyveromyces lactis was studied in batch and in continuous cultures. The Kltpi1 mutant was able to grow on media containing glucose as the sole carbon source both in batch and in continuous culture, unlike the corresponding S. cerevisiae mutant. In K. lactis tpi1 mutant no glycerol production was detected in chemostat cultivations. DHAP accumulation triggers glycerol production only when glucose is the sole carbon source in excess. The analysis of the activities of some key enzymes of carbon metabolism shows that in chemostat cultivations on mixed-substrates the activities of enzymes involved in ethanol assimilation are higher both in K. lactis wild type and mutant strains than in S. cerevisiae.