Response to Cold: A Comparative Transcriptomic Analysis in Eight Cold-Adapted Yeasts

Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure

Codon usage bias (CUB) has been described in viruses, prokaryotes, and eukaryotes and has been linked to several cellular and environmental factors, such as the organism's growth temperature, gene expression levels, and regulation of protein synthesis and folding. Most of the studies in this area have been conducted in bacteria and higher eukaryotes, in some cases with different results. In this study, a comparative analysis of CUB in yeasts isolated from cold and template environments was performed in order to evaluate the correlation of CUB with yeast optimal temperature of growth (OTG), gene expression levels, cellular function, and structure of encoded proteins. Among the main findings, highly expressed ORFs tend to have a more similar CUB within and between yeasts, and a direct correlation between codons ending in C and expression level was generally found. A low correspondence between CUB and OTG was observed, with an inverse correlation for some codons ending in C. The clustering of yeasts based on their CUB partially aligns with their OTG, being more consistent for yeasts with lower OTG. In most yeasts, the abundance of preferred codons was generally lower at the 5' end of ORFs, higher in segments encoding beta strand, lower in segments encoding extracellular and transmembrane regions, and higher in "translation" and "energy metabolism" pathways, especially in highly expressed ORFs. Based on our findings, it is suggested that the abundance and distribution of preferred and non-preferred codons along mRNAs contribute to proper protein folding and functionality by regulating protein synthesis rates, becoming a more important factor under conditions that require faster protein synthesis in yeasts.

Screening low-methanol and high-aroma produced yeasts for cider fermentation by transcriptive characterization

The commercial active dry yeast strains used for cider production in China are far behind the requirements of the cider industry development in recent decades. In this study, eight yeasts, including Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia bruneiensis, and Pichia kudriavzevii, were screened and assessed by growth performance, methanol production, aroma analysis, and their transcriptive characterization. Saccharomyces cerevisiae strains WFC-SC-071 and WFC-SC-072 were identified as promising alternatives for cider production. Strains WFC-SC-071 and WFC-SC-072 showed an excellent growth capacity characterized by 91.6 and 88.8% sugar utilization, respectively. Methanol production by both strains was below 200 mg/L. Key aroma compounds imparting cider appreciably characteristic aroma increased in cider fermented by strains WFC-SC-071 and WFC-SC-072. RT-qPCR analysis suggested that most genes associated with growth capacity, carbohydrate uptake, and aroma production were upregulated in WFC-SC-071 and WFC-SC-072. Overall, two Saccharomyces cerevisiae strains are the optimal starters for cider production to enable the diversification of cider, satisfy the differences in consumer demand, and promote cider industry development.

A genomic approach to analyze the cold adaptation of yeasts isolated from Italian Alps

Microorganisms including yeasts are responsible for mineralization of organic matter in cold regions, and their characterization is critical to elucidate the ecology of such environments on Earth. Strategies developed by yeasts to survive in cold environments have been increasingly studied in the last years and applied to different biotechnological applications, but their knowledge is still limited. Microbial adaptations to cold include the synthesis of cryoprotective compounds, as well as the presence of a high number of genes encoding the synthesis of proteins/enzymes characterized by a reduced proline content and highly flexible and large catalytic active sites. This study is a comparative genomic study on the adaptations of yeasts isolated from the Italian Alps, considering their growth kinetics. The optimal temperature for growth (OTG), growth rate (Gr), and draft genome sizes considerably varied (OTG, 10°C–20°C; Gr, 0.071–0.0726; genomes, 20.7–21.5 Mpb; %GC, 50.9–61.5). A direct relationship was observed between calculated protein flexibilities and OTG, but not for Gr. Putative genes encoding for cold stress response were found, as well as high numbers of genes encoding for general, oxidative, and osmotic stresses. The cold response genes found in the studied yeasts play roles in cell membrane adaptation, compatible solute accumulation, RNA structure changes, and protein folding, i.e., dihydrolipoamide dehydrogenase, glycogen synthase, omega-6 fatty acid, stearoyl-CoA desaturase, ATP-dependent RNA helicase, and elongation of very-long-chain fatty acids. A redundancy for several putative genes was found, higher for P-loop containing nucleoside triphosphate hydrolase, alpha/beta hydrolase, armadillo repeat-containing proteins, and the major facilitator superfamily protein. Hundreds of thousands of small open reading frames (SmORFs) were found in all studied yeasts, especially in Phenoliferia glacialis. Gene clusters encoding for the synthesis of secondary metabolites such as terpene, non-ribosomal peptide, and type III polyketide were predicted in four, three, and two studied yeasts, respectively.