The evolution and role of the periplasmic asparaginase Asp3 in yeast

Abstract

The study of nitrogen assimilation in yeast is of interest from genetic, evolutionary, and biotechnological perspectives. Over the course of evolution, yeasts have developed sophisticated control mechanisms to regulate nitrogen metabolism, with domesticated lineages sometimes displaying particular specialisation. The focus of this study was on assimilation of asparagine, which is a significant nutritional source for some alcoholic fermentations. We were particularly interested in ASP3, which encodes a periplasmic asparaginase and that was proposed to have been acquired relatively recently in S. cerevisiae by horizontal gene transfer. We examined 1680 S. cerevisiae genome assemblies to evaluate the distribution and evolutionary trajectory of ASP3. Our findings suggest an alternative hypothesis that ASP3 is an ancient Saccharomyces gene that has generally been lost over the course of evolution but has been retained in certain fermentative environments. As asparagine is the major nitrogen source in apple juice, we explored whether the presence of ASP3 would confer a growth advantage. Interestingly, we found that although ASP3 enhances growth when asparagine is the sole nitrogen source, the same effect is not seen in apple juice. These data indicate that growth in pure culture may not reflect the original selective environment for ASP3+ strains and highlight the role that complex regulation may play in optimising nitrogen assimilation in yeasts.

The growth and metabolome of Saccharomyces uvarum in wine fermentations are strongly influenced by the route of nitrogen assimilation

“…The relatively better growth of S. uvarum on methionine suggests higher efficiency of the transaminases Aro8p and Aro9p or more fine-tuned regulation of the enzymes in this species. Regarding asparagine, the better growth of S. cerevisiae could possibly be attributed to the presence of ASP3 in some strains, but that cannot be the full explanation since, like S. uvarum, S. cerevisiae EC1118 lacks this gene (Coral-Medina et al, 2022 ; League et al, 2012 ). It is also noteworthy that outliers to these species-level findings can be observed at the strain level.…”

Systematic Profiling of Ale Yeast Protein Dynamics across Fermentation and Repitching

“…Our genetic characterization of Wyeast 3068 showed deletions of many genes as expected for ale yeast: flocculation genes vary between brewing strains 43 and can be lost in aged brewing yeast 44 , less efficient carbohydrate transporters are lost in some brewing strains 45 , ASP3 has been lost in many S. cerevisiae isolates 46 , and transposition events and copy number variations of Ty elements are common in industrial yeast strains 47 . Previous studies have demonstrated that genome evolution in brewing yeast strains does occur across the repitching process as selected populations have adapted to the fermentation environment 19 .…”

Mosaic Genome of a British Cider Yeast

“…It encodes an L-asparaginase that catalyzes the hydrolysis of asparagine to aspartic acid releasing ammonia [ 47 ]. This could be of adaptive value in cider yeasts as asparagine is an abundant amino acid in apple must [ 48 , 49 ].…”