Improving ribonucleic acid production in Saccharomyces pastorianus via in silico genome‐scale metabolic network model

Abstract

Ribonucleic acid (RNA) and its degradation products are important biomolecules widely used in the food and pharmaceutical industries for their flavoring and nutritional functions. In this study, we used a genome‐scale metabolic network model (GSMM) to explore genetic targets for nucleic acid synthesis in a Saccharomyces pastorianus strain (G03). Yeast 8.5.0 was used as the base model, which accurately predicted G03's growth. Using OptForce, we found that overexpression of ARO8 and ATP1 among six different strategies increased the RNA content of G03 by 58.0% and 74.8%, respectively. We also identified new metabolic targets for improved RNA production using a modified GSMM called TissueModel, constructed using the GIMME transcriptome constraint tool to remove low‐expressed reactions in the model. After running OptKnock, the RNA content of G03‐△BNA1 and G03‐△PMA1 increased by 44.6% and 39.8%, respectively, compared to G03. We suggest that ATP1, ARO8, BNA1, and PMA1 regulate cell fitness, which affects RNA content. This study is the first to identify strategies for RNA overproduction using GSMM and to report that regulation of ATP1, ARO8, BNA1, and PMA1 can increase RNA content in S. pastorianus. These findings also provide valuable knowledge on model reconstruction for S. pastorianus.

Development of a genome-scale metabolic model for the lager hybrid yeast S. pastorianus to understand the evolution of metabolic pathways in industrial settings

“…The Yeast Consensus Model (Yeast8) provides a highly curated and comprehensive representation of yeast metabolism ( 23 , 25 ) and has been used as a template to reconstruct the draft genome-scale metabolic model of S. pastorianus . The reactions in Yeast8 that are present/absent in S. pastorianus were identified based on the presence/absence of the genes that support these reactions.…”

“…Indeed, although the sequence of S. cerevisiae genome has been available for almost 30 years, only more recently the hybrid genomes of some S. pastorianus strains have been sequenced and annotated ( 10 , 12 , 18 – 22 ). It has been shown that S. pastorianus and S. cerevisiae exhibit significant differences in gene expression and metabolic levels, and that the Yeast8 model could not always accurately calculate the metabolic flux of S. pastorianus ( 23 ), hence the need to develop a model specific for S. pastorianus .…”

Proteomic analysis reveals that the co‐ordination of cytosolic and mitochondrial pathways is beneficial for sabinene biosynthesis in engineered Saccharomyces cerevisiae

“…Construction of efficient cell factories requires extensive rewiring cellular metabolism toward overproduction of target metabolites through enzyme and metabolic engineering. [ 6,10–12 ] Rational engineering the biosynthetic pathways is considered to be the first step to improve chemical production. [ 3–6,13 ] Recently, several advanced metabolic engineering strategies were developed to enhance the biosynthesis.…”

Biological autoluminescence enables effective monitoring of yeast cell electroporation

“…The extent of cell membrane disruption can be adjusted depending on the specific application, requiring reversible or irre-versible membrane disruption. For example, reversible electroporation is used in ribonucleic acid production (RNA) in yeast, [12] as well as a tool for cell electrofusion for the production of monoclonal antibodies. [13] The versatility of the electroporation technique renders it a potent tool in genetic engineering, the food industry, as well as in medical applications [14,15] .…”