Comparative Transcriptome Analysis of Recombinant Industrial Saccharomyces cerevisiae Strains with Different Xylose Utilization Pathways

Combination of mutagenesis and adaptive evolution to engineer salt-tolerant and aroma-producing yeast for soy sauce fermentation

BACKGROUND

The moromi fermentation of high-salt liquid-state fermentation (HLF) soy sauce is usually performed in high-brine solution (17-20%, w/w), which decreases the metabolic activity of aroma-producing yeast. To enhance the soy sauce flavors, increasing the salt tolerance of aroma-producing yeasts is very important for HLF soy sauce fermentation.

RESULTS

In the present study, atmospheric and room-temperature plasma (ARTP) was first used to mutate the aroma-producing yeast Wickerhamomyces anomalus, and the salt tolerant strains were obtained by selection of synthetic medium with a sodium chloride concentration of 18% (w/w). Furthermore, adaptive laboratory evolution (ALE) was used to improve the salt tolerance of the mutant strains. The results obtained indicated that the combination use of ARTP and ALE markedly increased the NaCl tolerance of the yeast by increasing the cellular accumulation of K+ and removal of cytosolic Na+ , in addition to promoting the production of glycerin and strengthening the integrity of the cell membrane and cell wall. In soy sauce fermentation, the engineered strains improved the physicochemical parameters of HLF soy sauce compared to those produced by the wild-type strain, and the engineered strains also increased the alcohol, acid and aldehyde production, and enriched the types of esters in the soy sauce.

CONCLUSION

The results of the present study indicated that the combination of ARTP mutagenesis and ALE significantly improved the salt tolerance of the aroma-producing yeast, and also enhanced the production of volatiles of HLF soy sauce. © 2021 Society of Chemical Industry.

Metabolic and transcriptional analysis of recombinant Saccharomyces?cerevisiae for xylose fermentation: a feasible and efficient approach

Lignocellulose is an abundant xylose-containing biomass found in agricultural wastes, and has arisen as a suitable alternative to fossil fuels for the production of bioethanol. Although Saccharomyces cerevisiae has been thoroughly used for the production of bioethanol, its potential to utilize lignocellulose remains poorly understood. In this work, xylose-metabolic genes of Pichia stipitis and Candida tropicalis, under the control of different promoters, were introduced into S. cerevisiae. RNA-seq analysis was use to examine the response of S. cerevisiae metabolism to the introduction of xylose-metabolic genes. The use of the PGK1 promoter to drive xylitol dehydrogenase (XDH) expression, instead of the TEF1 promoter, improved xylose utilization in ?XR-pXDH? strain by overexpressing xylose reductase (XR) and XDH from C. tropicalis, enhancing the production of xylitol (13.66 ? 0.54 g/L after 6 days fermentation). Overexpression of xylulokinase and XR/XDH from P. stipitis remarkably decreased xylitol accumulation (1.13 ? 0.06 g/L and 0.89 ? 0.04 g/L xylitol, respectively) and increased ethanol production (196.14% and 148.50% increases during the xylose utilization stage, respectively), in comparison with the results of XR-pXDH. This result may be produced due to the enhanced xylose transport, Embden?Meyerhof and pentose phosphate pathways, as well as alleviated oxidative stress. The low xylose consumption rate in these recombinant strains comparing with P. stipitis and C. tropicalis may be explained by the insufficient supplementation of NADPH and NAD+. The results obtained in this work provide new insights on the potential utilization of xylose using bioengineered S. cerevisiae strains.

Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae

Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.

Different transcriptional responses of haploid and diploid S. cerevisiae strains to changes in cofactor preference of XR

Background

Xylitol accumulation is a major barrier for efficient ethanol production through heterologous xylose reductase-xylitol dehydrogenase (XR-XDH) pathway in recombinant Saccharomyces cerevisiae. Mutated NADH-preferring XR is usually employed to alleviate xylitol accumulation. However, it remains unclear how mutated XR affects the metabolic network for xylose metabolism. In this study, haploid and diploid strains were employed to investigate the transcriptional responses to changes in cofactor preference of XR through RNA-seq analysis during xylose fermentation.

Results

For the haploid strains, genes involved in xylose-assimilation (XYL1, XYL2, XKS1), glycolysis, and alcohol fermentation had higher transcript levels in response to mutated XR, which was consistent with the improved xylose consumption rate and ethanol yield. For the diploid strains, genes related to protein biosynthesis were upregulated while genes involved in glyoxylate shunt were downregulated in response to mutated XR, which might contribute to the improved yields of biomass and ethanol. When comparing the diploids with the haploids, genes involved in glycolysis and MAPK signaling pathway were significantly downregulated, while oxidative stress related transcription factors (TFs) were significantly upregulated, irrespective of the cofactor preference of XR.

Conclusions

Our results not only revealed the differences in transcriptional responses of the diploid and haploid strains to mutated XR, but also provided underlying basis for better understanding the differences in xylose metabolism between the diploid and haploid strains.