产肌醇酿酒酵母基因工程菌的构建

【目的】过表达酿酒酵母肌醇合成关键酶基因INO1,促进肌醇合成,构建能够分泌肌醇的基因工程菌株。【方法】构建r DNA介导的INO1基因多拷贝整合表达载体p URIH,电转化酿酒酵母Y01菌株,构建工程菌株YI2-1和YI2-2,荧光定量PCR方法分析INO1基因表达量。敲除Kan MX抗性基因,HPLC检测重组菌发酵液中肌醇含量。【结果】获得INO1基因过表达菌株YI2-1和YI2-2,YI2-1的INO1基因表达量是出发菌Y01的16.235倍。敲除Kan MX抗性基因的菌株命名为YI2-1△KP,初步检测YI2-1△KP产肌醇量为627 mg/L。【结论】r DNA介导的INO1基因多拷贝整合表达载体p URIH能够有效地过表达目的基因;过表达菌株合成的肌醇不仅能满足自身的需要,而且能够向胞外分泌,具有潜在的工业应用价值。     

Enhanced production of para-hydroxybenzoic acid by genetically engineered Saccharomyces cerevisiae

Saccharomyces cerevisiae is a popular organism for metabolic engineering; however, studies aiming at over-production of bio-replacement precursors for the chemical industry often fail to overcome proof-of-concept stage. When intending to show real industrial attractiveness, the challenge is twofold: formation of the target compound must be increased, while minimizing the formation of side and by-products to maximize titer, rate and yield. To tackle these, the metabolism of the organism, as well as the parameters of the process, need to be optimized. Addressing both we show that S. cerevisiae is well-suited for over-production of aromatic compounds, which are valuable in chemical industry and are particularly useful in space technology. Specifically, a strain engineered to accumulate chorismate was optimized for formation of para-hydroxybenzoic acid. Then a fed-batch bioreactor process was developed, which delivered a final titer of 2.9 g/L, a maximum rate of 18.625 mg_pHBA/(g_CDW × h) and carbon-yields of up to 3.1 mg_pHBA/g_glucose.

     

酿酒酵母产D-乳酸重组菌的构建与发酵

采用基因工程方法对酿酒酵母进行代谢改造,使酵母产生乳酸代谢途径。将来源于L.mesenteroides和E.coli的D-乳酸脱氢酶基因,分别插入带有G418抗性的酵母穿梭质粒p YX212-kan MX上,电转化酵母,得到2株生产D-乳酸的酿酒酵母重组菌S.cerevisiae WE1510和S.cerevisiae WB1186。进一步摇瓶发酵试验表明:重组菌S.cerevisiae WB1186在YEPD培养基、20 g/L糖、p H 5的条件下生长条件最好,并具有更好的产乳酸能力。经3 L发酵罐条件下验证,S.cerevisiae WB1186分批发酵96 h,最终乳酸积累量达到18.0 g/L;发酵条件为培养基YEPD,接种量10%,溶解氧(DO)30%,转速150 r/min,初始葡萄糖质量浓度10 g/L,控制pH 5.0,通气量3 L/min,OD600最大值转为厌氧发酵。     

Efficient production of S-adenosyl-l-methionine from dl-methionine in metabolic engineered Saccharomyces cerevisiae

S-Adenosyl-l -methionine (SAM) is an important small molecule compound widely used in treating various diseases. Although l -methionine is generally used, the low-cost dl -methionine is more suitable as the substrate for industrial production of SAM. However, d -methionine is inefficient for SAM formation due to the substrate-specificity of SAM synthetase. In order to increase the utilization efficiency of dl -methionine, intracellular conversion of d -methionine to l -methionine was investigated in the type strain Saccharomyces cerevisiae BY4741 and an industrial strain S. cerevisiae HDL. Firstly, via disruption of HPA3 encoding d -amino acid-N-acetyltransferase, d -methionine was accumulated in vivo and no N-acetyl-d -methionine production was observed. Further, codon-optimized d -amino acid oxidase (DAAO) gene from Trigonopsis variabilis (Genbank MK280686) and l -phenylalanine dehydrogenase gene (l -PheDH) from Rhodococcus jostii (Genbank MK280687) were introduced to convert d -methionine to l -methionine, SAM concentration and content was increased by 110% and 72.1% in BY4741 (plasmid borne) and increased by 38.2% and 34.1% in HDL (genome integrated), by feeding 0.5 g/L d -methionine. Using the recently developed CRISPR tools, the DAAO and l -PheDH expression cassettes were integrated into the HPA3 and SAH1 loci while SAM2 expression was integrated into the SPE2 and GLC3 loci of HDL, and the resultant strain HDL-R2 accumulated 289% and 192% more SAM concentration and content, respectively, by feeding 0.5 g/L dl -methionine. Further, in a 10 L fed-batch fermentation process, 10.3 g/L SAM were accumulated with the SAM content of 242 mg/g dry cell weight by feeding 16 g/L dl -methionine. The strategies used here provided a promising approach to enhance SAM production using low-cost dl -methionine.     

Xylose assimilation enhances the production of isobutanol in engineered Saccharomyces cerevisiae

Bioconversion of xylose—the second most abundant sugar in nature—into high-value fuels and chemicals by engineered Saccharomyces cerevisiae has been a long-term goal of the metabolic engineering community. Although most efforts have heavily focused on the production of ethanol by engineered S. cerevisiae, yields and productivities of ethanol produced from xylose have remained inferior as compared with ethanol produced from glucose. However, this entrenched focus on ethanol has concealed the fact that many aspects of xylose metabolism favor the production of nonethanol products. Through reduced overall metabolic flux, a more respiratory nature of consumption, and evading glucose signaling pathways, the bioconversion of xylose can be more amenable to redirecting flux away from ethanol towards the desired target product. In this report, we show that coupling xylose consumption via the oxidoreductive pathway with a mitochondrially-targeted isobutanol biosynthesis pathway leads to enhanced product yields and titers as compared to cultures utilizing glucose or galactose as a carbon source. Through the optimization of culture conditions, we achieve 2.6 g/L of isobutanol in the fed-batch flask and bioreactor fermentations. These results suggest that there may be synergistic benefits of coupling xylose assimilation with the production of nonethanol value-added products.     

De novo production of the flavonoid naringenin in engineered Saccharomyces cerevisiae

Background

Specific strains of Lactobacillus plantarum are marketed as health-promoting probiotics. The role and interplay of cell-wall compounds like wall- and lipo-teichoic acids (WTA and LTA) in bacterial physiology and probiotic-host interactions remain obscure. L. plantarum WCFS1 harbors the genetic potential to switch WTA backbone alditol, providing an opportunity to study the impact of WTA backbone modifications in an isogenic background.

Results

Through genome mining and mutagenesis we constructed derivatives that synthesize alternative WTA variants. The mutants were shown to completely lack WTA, or produce WTA and LTA that lack D-Ala substitution, or ribitol-backbone WTA instead of the wild-type glycerol-containing backbone. DNA micro-array experiments established that the tarIJKL gene cluster is required for the biosynthesis of this alternative WTA backbone, and suggest ribose and arabinose are precursors thereof. Increased tarIJKL expression was not observed in any of our previously performed DNA microarray experiments, nor in qRT-PCR analyses of L. plantarum grown on various carbon sources, leaving the natural conditions leading to WTA backbone alditol switching, if any, to be identified. Human embryonic kidney NF-κB reporter cells expressing Toll like receptor (TLR)-2/6 were exposed to purified WTAs and/or the TA mutants, indicating that WTA is not directly involved in TLR-2/6 signaling, but attenuates this signaling in a backbone independent manner, likely by affecting the release and exposure of immunomodulatory compounds such as LTA. Moreover, human dendritic cells did not secrete any cytokines when purified WTAs were applied, whereas they secreted drastically decreased levels of the pro-inflammatory cytokines IL-12p70 and TNF-α after stimulation with the WTA mutants as compared to the wild-type.

Conclusions

The study presented here correlates structural differences in WTA to their functional characteristics, thereby providing important information aiding to improve our understanding of molecular host-microbe interactions and probiotic functionality.

     

Metabolic flux analysis of genetically engineered Saccharomyces cerevisiae that produces lactate under micro-aerobic conditions

In the present study, to elucidate mechanisms of growth suppression in YIBO-pdc1/5Δ, we performed carbon metabolic flux analysis under micro-aerobic conditions. Our results indicate that growth suppression of YIBO-pdc1/5Δ is caused by decreased flux to the pentose phosphate pathway, which supplies ribose-5-phosphate, a precursor for histidine synthesis in Sacchar omyces cerevisiae. In addition, significant accumulation of pyruvate was observed in the continuous culture.     

Evolutionary engineering of Saccharomyces cerevisiae for anaerobic growth on xylose

Xylose utilization is of commercial interest for efficient conversion of abundant plant material to ethanol. Perhaps the most important ethanol-producing organism, Saccharomyces cerevisiae, however, is incapable of xylose utilization. While S. cerevisiae strains have been metabolically engineered to utilize xylose, none of the recombinant strains or any other naturally occurring yeast has been able to grow anaerobically on xylose. Starting with the recombinant S. cerevisiae strain TMB3001 that overexpresses the xylose utilization pathway from Pichia stipitis, in this study we developed a selection procedure for the evolution of strains that are capable of anaerobic growth on xylose alone. Selection was successful only when organisms were first selected for efficient aerobic growth on xylose alone and then slowly adapted to microaerobic conditions and finally anaerobic conditions, which indicated that multiple mutations were necessary. After a total of 460 generations or 266 days of selection, the culture reproduced stably under anaerobic conditions on xylose and consisted primarily of two subpopulations with distinct phenotypes. Clones in the larger subpopulation grew anaerobically on xylose and utilized both xylose and glucose simultaneously in batch culture, but they exhibited impaired growth on glucose. Surprisingly, clones in the smaller subpopulation were incapable of anaerobic growth on xylose. However, as a consequence of their improved xylose catabolism, these clones produced up to 19% more ethanol than the parental TMB3001 strain produced under process-like conditions from a mixture of glucose and xylose.     

Improving biobutanol production in engineered Saccharomyces cerevisiae by manipulation of acetyl-CoA metabolism

Recently, butanols (1-butanol, 2-butanol and iso-butanol) have generated attention as alternative gasoline additives. Butanols have several properties favorable in comparison to ethanol, and strong interest therefore exists in the reconstruction of the 1-butanol pathway in commonly used industrial microorganisms. In the present study, the biosynthetic pathway for 1-butanol production was reconstructed in the yeast Saccharomyces cerevisiae. In addition to introducing heterologous enzymes for butanol production, we engineered yeast to have increased flux toward cytosolic acetyl-CoA, the precursor metabolite for 1-butanol biosynthesis. This was done through introduction of a plasmid-containing genes for alcohol dehydrogenase (ADH2), acetaldehyde dehydrogenase (ALD6), acetyl-CoA synthetase (ACS), and acetyl-CoA acetyltransferase (ERG10), as well as the use of strains containing deletions in the malate synthase (MLS1) or citrate synthase (CIT2) genes. Our results show a trend to increased butanol production in strains engineered for increased cytosolic acetyl-CoA levels, with the best-producing strains having maximal butanol titers of 16.3 mg/l. This represents a 6.5-fold improvement in butanol titers compared to previous values reported for yeast and demonstrates the importance of an improved cytosolic acetyl-CoA supply for heterologous butanol production by this organism.     

Dynamics of anaerobic growth of Saccharomyces cerevisiae in the chemostat.

A kinetic Monod model has been used to describe the dynamic response of a continuous stirred tank fermentor (CSTF) to changes in dilution rate. A general analytical solution of a linearized model was obtained. Experimental results (Vairo et al. 1977) of continuous anaerobic culture of Saccharomyces cerevisiae have verified the model quantitatively. For step disturbances on the dilution rate the responses of biomass concentration and the outlet substrate concentration were calculated on a digital computer and compared with the experimental data.     

Ethanol production from xylose in engineered Saccharomyces cerevisiae strains: current state and perspectives

Bioethanol production from xylose is important for utilization of lignocellulosic biomass as raw materials. The research on yeast conversion of xylose to ethanol has been intensively studied especially for genetically engineered Saccharomyces cerevisiae during the last 20 years. S. cerevisiae, which is a very safe microorganism that plays a traditional and major role in industrial bioethanol production, has several advantages due to its high ethanol productivity, as well as its high ethanol and inhibitor tolerance. However, this yeast cannot ferment xylose, which is the dominant pentose sugar in hydrolysates of lignocellulosic biomass. A number of different strategies have been applied to engineer yeasts capable of efficiently producing ethanol from xylose, including the introduction of initial xylose metabolism and xylose transport, changing the intracellular redox balance, and overexpression of xylulokinase and pentose phosphate pathways. In this review, recent progress with regard to these studies is discussed, focusing particularly on xylose-fermenting strains of S. cerevisiae. Recent studies using several promising approaches such as host strain selection and adaptation to obtain further improved xylose-utilizing S. cerevisiae are also addressed.     

Engineering of the metabolism of Saccharomyces cerevisiae for anaerobic production of mannitol

Under anaerobic conditions, Saccharomyces cerevisiae uses NADH-dependent glycerol-3-phosphate dehydrogenase (Gpd1p and Gpd2p) to re-oxidize excess NADH, yielding substantial amounts of glycerol. In a Deltagpd1 Deltagpd2 double-null mutant, the necessary NAD+ regeneration through glycerol production is no longer possible, and this mutant does not grow under anaerobic conditions. The excess NADH formed can potentially be used to drive other NADH-dependent reactions or pathways. To investigate this possibility, a double-null mutant was transformed with a heterologous gene (mtlD) from Escherichia coli, coding for NADH-dependent mannitol-1-phosphate dehydrogenase. Expression of this gene in S. cerevisiae should result in NADH oxidation by the NADH-requiring formation of mannitol-1-phosphate from fructose-6-phosphate. The strain was characterized using step-change experiments, in which, during the exponential growth phase, the inlet gas was changed from air to nitrogen. It was found that the mutant produced mannitol only under anaerobic conditions. However, anaerobic growth was not regained, which was probably due to the excessive accumulation of mannitol in the cells.     

Homofermentative production of d-lactic acid from sucrose by a metabolically engineered Escherichia coli

Escherichia coli W, a sucrose-positive strain, was engineered for the homofermentative production of d-lactic acid through chromosomal deletion of the competing fermentative pathway genes (adhE, frdABCD, pta, pflB, aldA) and the repressor gene (cscR) of the sucrose operon, and metabolic evolution for improved anaerobic cell growth. The resulting strain, HBUT-D, efficiently fermented 100?g?sucrose?l^?1 into 85?g?d-lactic acid?l^?1 in 72–84?h in mineral salts medium with a volumetric productivity of ~1?g?l^?1?h^?1, a product yield of 85?% and d-lactic acid optical purity of 98.3?%, and with a minor by-product of 4?g?acetate?l^?1. HBUT-D thus has great potential for production of d-lactic acid using an inexpensive substrate, such as sugar cane and/or beet molasses, which are primarily composed of sucrose.     

Enhanced butanol production by eukaryotic Saccharomyces cerevisiae engineered to contain an improved pathway

Compared with ethanol, butanol has more advantageous physical properties as a fuel, and biobutanol is thus considered a promising biofuel material. Biobutanol has often been produced by Clostridium species; however, because they are strictly anaerobic microorganisms, these species are challenging to work with. We attempted to introduce the butanol production pathway into yeast Saccharomyces cerevisiae, which is a well-known microorganism that is tolerant to organic solvents. 1-Butanol was found to be produced at very low levels when the butanol production pathway of Clostridium acetobutylicum was simply introduced into S. cerevisiae. The elimination of glycerol production pathway in the yeast contributed to the enhancement of 1-butanol production. In addition, by the use of trans-enoyl-CoA reductase in the engineered pathway, 1-butanol production was markedly enhanced to yield 14.1 mg/L after 48 h of cultivation.     

L-lactate production in engineered Saccharomyces cerevisiae using a multistage multiobjective automated design framework

The design of alternative biodegradable polymers has the potential of severely reducing the environmental impact, cost and production time currently associated with the petrochemical industry. In fact, growing demand for renewable feedstock has recently brought to the fore synthetic biology and metabolic engineering. These two interdependent research areas focus on the study of microbial conversion of organic acids, with the aim of replacing their petrochemical-derived equivalents with more sustainable and efficient processes. The particular case of Lactic acid (LA) production has been the subject of extensive research because of its role as an essential component for developing an eco-friendly biodegradable plastic—widely used in industrial biotechnological applications. Because of its resistance to acidic environments, among the many LA-producing microbes, Saccharomyces cerevisiae has been the main focus of research into related biocatalysts. In this study, we present an extensive in silico investigation of S. cerevisiae cell metabolism (modeled with Flux Balance Analysis) with the overall aim of maximizing its LA production yield. We focus on the yeast 8.3 steady-state metabolic model and analyze it under the impact of different engineering strategies including: gene knock-in, gene knock-out, gene regulation and medium optimization; as well as a comparison between results in aerobic and anaerobic conditions. We designed ad-hoc constrained multiobjective evolutionary algorithms to automate the engineering process and developed a specific postprocessing methodology to analyze the genetic manipulation results obtained. The in silico results reported in this paper empirically show that our method is able to automatically select a small number of promising genetic and metabolic manipulations, deriving competitive strains that promise to impact microorganisms design in the production of sustainable chemicals.