The modification of Gat1p in nitrogen catabolite repression to enhance non-preferred nitrogen utilization in Saccharomyces cerevisiae

Nitrogen signaling factor triggers a respiration-like gene expression program in fission yeast

Microbes have evolved intricate communication systems that enable individual cells of a population to send and receive signals in response to changes in their immediate environment. In the fission yeast Schizosaccharomyces pombe, the oxylipin nitrogen signaling factor (NSF) is part of such communication system, which functions to regulate the usage of different nitrogen sources. Yet, the pathways and mechanisms by which NSF acts are poorly understood. Here, we show that NSF physically interacts with the mitochondrial sulfide:quinone oxidoreductase Hmt2 and that it prompts a change from a fermentation- to a respiration-like gene expression program without any change in the carbon source. Our results suggest that NSF activity is not restricted to nitrogen metabolism alone and that it could function as a rheostat to prepare a population of S. pombe cells for an imminent shortage of their preferred nutrients.

Formation and hazard of ethyl carbamate and construction of genetically engineered Saccharomyces cerevisiae strains in Huangjiu (Chinese grain wine)

Huangjiu, a well-known conventional fermented Chinese grain wine, is widely consumed in Asia for its distinct flavor. Trace amounts of ethyl carbamate (EC) may be generated during the fermentation or storage process. The International Agency for Research on Cancer elevated EC to a Class 2A carcinogen, so it is necessary to regulate EC content in Huangjiu. The risk of intake of dietary EC is mainly assessed through the margin of exposure (MOE) recommended by the European Food Safety Authority, with a smaller MOE indicating a higher risk. Interventions are necessary to reduce EC formation. As urea, one of the main precursors of EC formation in Huangjiu, is primarily produced by Saccharomyces cerevisiae through the catabolism of arginine, the construction of dominant engineered fermentation strains is a favorable trend for the future production and application of Huangjiu. This review summarized the formation and carcinogenic mechanism of EC from the perspectives of precursor substances, metabolic pathways after ingestion, and risk assessment. The methods of constructing dominant S. cerevisiae strains in Huangjiu by genetic engineering technology were reviewed, which provided an important theoretical basis for reducing EC content and strengthening practical control of Huangjiu safety, and the future research direction was prospected.

The impact of carbon and nitrogen catabolite repression in microorganisms

Organisms have cellular machinery that is focused on optimum utilization of resources to maximize growth and survival depending on various environmental and developmental factors. Catabolite repression is a strategy utilized by various species of bacteria and fungi to accommodate changes in the environment such as the depletion of resources, or an abundance of less-favored nutrient sources. Catabolite repression allows for the rapid use of certain substrates like glucose over other carbon sources. Effective handling of carbon and nitrogen catabolite repression in microorganisms is crucial to outcompete others in nutrient limiting conditions. Investigations into genes and proteins linked to preferential uptake of different nutrients under various environmental conditions can aid in identifying regulatory mechanisms that are crucial for optimum growth and survival of microorganisms. The exact time and way bacteria and fungi switch their utilization of certain nutrients is of great interest for scientific, industrial, and clinical reasons. Catabolite repression is of great significance for industrial applications that rely on microorganisms for the generation of valuable bio-products. The impact catabolite repression has on virulence of pathogenic bacteria and fungi and disease progression in hosts makes it important area of interest in medical research for the prevention of diseases and developing new treatment strategies. Regulatory networks under catabolite repression exemplify the flexibility and the tremendous diversity that is found in microorganisms and provides an impetus for newer insights into these networks.

Comparisons of urea or ammonium on growth and fermentative metabolism of Saccharomyces cerevisiae in ethanol fermentation

This work was mainly about the understanding of how urea and ammonium affect growth, glucose consumption and ethanol production of S. cerevisiae, in particular regarding the basic physiology of cell. The basic physiology of cell included intracellular pH, ATP, NADH and enzyme activity. Results showed that fermentation time was reduced by 19% when using urea compared with ammonium. The maximal ethanol production rate using urea was 1.14 g/L/h, increasing 30% comparing with the medium prepared with ammonium. Moreover, urea could decrease the synthesis of glycerol from glucose by 26% comparing with ammonium. The by-product of acetic acid yields decreased from 40 mmol/mol of glucose (with urea) to 24 mmol/mol of glucose (with ammonium). At the end of ethanol fermentation, cell number and pH were greater with urea than ammonium. Comparing with urea, ammonium decreased the intracellular pH by 14% (from 7.1 to 6.1). Urease converting urea into ammonia resulted in a more than 50% lower of ATP when comparing with ammonium. The values of NADH/DCW were 0.21 mg/g and 0.14 mg/g respectively with urea and ammonium, suggesting a 33% lower NADH. The enzyme activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) was 0.0225 and 0.0275 U/mg protein respectively with urea and ammonium, which was consistent with the yields of glycerol.

Chinese Yellow Rice Wine Processing with Reduced Ethyl Carbamate Formation by Deleting Transcriptional Regulator Dal80p in Saccharomyces cerevisiae

Ethyl carbamate (EC) is a potential carcinogen that forms spontaneously during Chinese rice wine fermentation. The primary precursor for EC formation is urea, which originates from both external sources and arginine degradation. Urea degradation is suppressed by nitrogen catabolite repression (NCR) in Saccharomyces cerevisiae. The regulation of NCR is mediated by two positive regulators (Gln3p, Gat1p/Nil1p) and two negative regulators (Dal80p/Uga43p, Deh1p/Nil2p/GZF3p). DAL80 revealed higher transcriptional level when yeast cells were cultivated under nitrogen-limited conditions. In this study, when DAL80-deleted yeast cells were compared to wild-type BY4741 cells, less urea was accumulated, and genes involved in urea utilization were up-regulated. Furthermore, Chinese rice wine fermentation was conducted using dal80Δ cells; the concentrations of urea and EC were both reduced when compared to the BY4741 and traditional fermentation starter. The findings of this work indicated Dal80p is involved in EC formation possibly through regulating urea metabolism and may be used as the potential target for EC reduction.

Regulation and metabolic engineering strategies for permeases of Saccharomyces cerevisiae

Microorganisms have evolved permeases to incorporate various essential nutrients and exclude harmful products, which assists in adaptation to different environmental conditions for survival. As permeases are directly involved in the utilization of and regulatory response to nutrient sources, metabolic engineering of microbial permeases can predictably influence nutrient metabolism and regulation. In this mini-review, we have summarized the mechanisms underlying the general regulation of permeases, and the current advancements and future prospects of metabolic engineering strategies targeting the permeases in Saccharomyces cerevisiae. The different types of permeases and their regulatory mechanisms have been discussed. Furthermore, methods for metabolic engineering of permeases have been highlighted. Understanding the mechanisms via which permeases are meticulously regulated and engineered will not only facilitate research on regulation of global nutrition and yeast metabolic engineering, but can also provide important insights for future studies on the synthesis of valuable products and elimination of harmful substances in S. cerevisiae.

Metabolic Engineering of Four GATA Factors to Reduce Urea and Ethyl Carbamate Formation in a Model Rice Wine System

Urea is the most important precursor of ethyl carbamate (EC), a harmful carcinogenic product, in fermented wines. In this study, the effects of four GATA transcriptional factors (Gln3p, Gat1p, Dal80p ,and Gzf3p) on extracellular urea and EC formation and transcriptional changes in urea degradation related genes ( DUR1,2 and DUR3) were examined. Compared to the WT strain, the Δ gzf3 mutant showed 18.7% urea reduction and exhibited synergistic effects with overexpressed Gln3p_1-653 and Gat1p_1-375 on extracellular urea reduction. Moreover, Δ gzf3+Gln3p_1-653 and Δ gzf3+Gat1p_1-375 showed significant 38.7% and 43.7% decreases in urea concentration and 41.7% and 48.5% decreases in EC concentration, respectively, in a model rice wine system. These results provide a promising way to reduce urea and EC formation during wine fermentation and raise some cues for the regulations of the four GATA transcriptional factors on the expression of individual nitrogen catabolite repression sensitive genes and their related metabolism pathway.

Adaptive Evolution Relieves Nitrogen Catabolite Repression and Decreases Urea Accumulation in Cultures of the Chinese Rice Wine Yeast Strain Saccharomyces cerevisiae XZ-11

Urea is the major precursor of ethyl carbamate in Chinese rice wine. Although efforts have been made to decrease urea accumulation, few methods can be applied to industrial food production due to potential safety concerns. In this study, adaptive laboratory evolution (ALE) followed by high-throughput screening was used to identify low urea-accumulating strains derived from the industrial Chinese rice wine yeast strain Saccharomyces cerevisiae XZ-11. Three evolved strains were obtained that had 47.9%, 16.6%, and 12.4% lower urea concentrations than the wild-type strain. Comparative genomics analysis revealed that genes involved in carbon and nitrogen metabolism evolved quickly. Transcription levels of genes involved in urea metabolism were dramatically upregulated after ALE. This work describes a novel and safe strategy to improve nitrogen utilization of industrial yeast strains involved in food fermentation. The identified genomic variations may also help direct rational genetic engineering of nitrogen metabolism processes to achieve other goals.

Complete genome sequence and analysis of the industrial Saccharomyces cerevisiae strain N85 used in Chinese rice wine production

Chinese rice wine is a popular traditional alcoholic beverage in China, while its brewing processes have rarely been explored. We herein report the first gapless, near-finished genome sequence of the yeast strain Saccharomyces cerevisiae N85 for Chinese rice wine production. Several assembly methods were used to integrate Pacific Bioscience (PacBio) and Illumina sequencing data to achieve high-quality genome sequencing of the strain. The genome encodes more than 6,000 predicted proteins, and 238 long non-coding RNAs, which are validated by RNA-sequencing data. Moreover, our annotation predicts 171 novel genes that are not present in the reference S288c genome. We also identified 65,902 single nucleotide polymorphisms and small indels, many of which are located within genic regions. Dozens of larger copy-number variations and translocations were detected, mainly enriched in the subtelomeres, suggesting these regions may be related to genomic evolution. This study will serve as a milestone in studying of Chinese rice wine and related beverages in China and in other countries. It will help to develop more scientific and modern fermentation processes of Chinese rice wine, and explore metabolism pathways of desired and harmful components in Chinese rice wine to improve its taste and nutritional value.