Systematically redesigning and optimizing the expression of D-lactate dehydrogenase efficiently produces high-optical-purity D-lactic acid in Saccharomyces cerevisiae

Factors Affecting D-Lactic Acid Production by Flocculant Saccharomyces cerevisiae Under Non-Neutralizing Conditions

Integrating heterogeneous genes is widely used in metabolic engineering to produce D-lactic acid (D-LA), an essential compound in bioplastics and pharmaceuticals. However, research on the effects of integrating various loci on gene expression, especially regarding flocculation behavior, remains limited. This study constructed Saccharomyces cerevisiae strains by incorporating a codon-optimized D-LDH gene from Leuconostoc pseudomesenteroides (LpDLDH) into the specific genomic loci of the CYB2, PDC1, MPC1, PDC6, ADH1, and PDC5 genes to redirect pyruvate toward lactic acid. Strains with the LpDLDH gene integrated at the PDC1 locus achieved the highest D-LA titers (51 g/L) with minimal ethanol byproduct, followed by strains with integrations into the CYB2 locus at 31.92 g/L, the MPC1 locus at 10 g/L, and the PDC6 locus at 0.026 g/L. In contrast, strains with LpDLDH integrated at the ADH1 and PDC5 loci failed to produce detectable levels of D-LA and exhibited a complete loss of flocculation. Gene expression analysis revealed a significant expression of genes related to flocculation (FLO5), stress adaptation (HSP150), and cell wall integrity (YGP1, SED1, and SCW11). The CYB2-integrating strain showed strong flocculant properties, contributing to its robustness. These findings highlight the influence of genomic locus selection on metabolic flux and stress adaptation, offering insights into optimizing D-LA production in flocculant S. cerevisiae yeast.

The advances in creating Crabtree-negative Saccharomyces cerevisiae and the application for chemicals biosynthesis

Saccharomyces cerevisiae is a promising microbial cell factory. However, the overflow metabolism, known as the Crabtree effect, directs the majority of the carbon source toward ethanol production, in many cases, resulting in low yields of other target chemicals and byproducts accumulation. To construct Crabtree-negative S. cerevisiae, the deletion of pyruvate decarboxylases and/or ethanol dehydrogenases is required. However, these modifications compromises the growth of the strains on glucose. This review discusses the metabolic engineering approaches used to eliminate ethanol production, the efforts to alleviate growth defect of Crabtree-negative strains, and the underlying mechanisms of the growth rescue. In addition, it summarizes the applications of Crabtree-negative S. cerevisiae in the synthesis of various chemicals such as lactic acid, 2,3-butanediol, malic acid, succinic acid, isobutanol, and others.

Enhancing D-lactic acid production by optimizing the expression of D-LDH gene in methylotrophic yeast Komagataella phaffii

BACKGROUND

Currently, efficient technologies producing useful chemicals from alternative carbon resources, such as methanol, to replace petroleum are in demand. The methanol-utilizing yeast, Komagataella phaffii, is a promising microorganism to produce chemicals from methanol using environment-friendly microbial processes. In this study, to achieve efficient D-lactic acid production from methanol, we investigated a combination of D-lactate dehydrogenase (D-LDH) genes and promoters in K. phaffii. The yeast strain was constructed by integrating a gene cassette containing the identified gene and promoter into the rDNA locus of K. phaffii, followed by post-transformational gene amplification. Subsequently, D-lactic acid production from methanol was evaluated.

RESULTS

Among the five D-LDH genes and eight promoters tested, the combination of LlDLDH derived from Leuconostoc lactis and CAT1 and FLD1 promoters was suitable for expression in K. phaffii. GS115_CFL/Z3/04, the best-engineered strain constructed via integration of LlDLDH linked to CAT1 and FLD1 promoters into the rDNA locus and post-transformational gene amplification, produced 5.18 g/L D-lactic acid from methanol. To the best of our knowledge, the amount of D-lactic acid from methanol produced by this engineered yeast is the highest reported value to date when utilizing methanol as the sole carbon source.

CONCLUSIONS

This study demonstrated the effectiveness of combining different enzyme genes and promoters using multiple promoters with different induction and repression conditions, integrating the genes into the rDNA locus, and further amplifying the genes after transformation in K. phaffii. Using our established method, other K. phaffii strains can be engineered to produce various useful chemicals in the future.

Comparative responses of flocculating and nonflocculating yeasts to cell density and chemical stress in lactic acid fermentation

While flocculation has demonstrated its efficacy in enhancing yeast robustness and ethanol production, its potential application for lactic acid fermentation remains largely unexplored. Our study examined the differences between flocculating and nonflocculating Saccharomyces cerevisiae strains in terms of their metabolic dynamics when incorporating an exogenous lactic acid pathway, across varying cell densities and in the presence of lignocellulose-derived byproducts. Comparative gene expression profiles revealed that cultivating a nonflocculant strain at higher cell density yielded a substantial upregulation of genes associated with glycolysis, energy metabolism, and other key pathways, resulting in elevated levels of fermentation products. Meanwhile, the flocculating strain displayed an inherent ability to sustain high glycolytic activity regardless of the cell density. Moreover, our investigation revealed a significant reduction in glycolytic activity under chemical stress, potentially attributable to diminished ATP supply during the energy investment phase. Conversely, the formation of flocs in the flocculating strain conferred protection against toxic chemicals present in the medium, fostering more stable lactic acid production levels. Additionally, the distinct flocculation traits observed between the two examined strains may be attributed to variations in the nucleotide sequences of the flocculin genes and their regulators. This study uncovers the potential of flocculation for enhanced lactic acid production in yeast, offering insights into metabolic mechanisms and potential gene targets for strain improvement.

Systematic engineering of Saccharomyces cerevisiae for D-lactic acid production with near theoretical yield

D-lactic acid is a chiral three-carbon organic acid that can improve the thermostability of polylactic acid. Here, we systematically engineered Saccharomyces cerevisiae to produce D-lactic acid from glucose, a renewable carbon source, at near theoretical yield. Specifically, we screened D-lactate dehydrogenase (DLDH) variants from lactic acid bacteria in three different genera and identified the Leuconostoc pseudomesenteroides variant (LpDLDH) as having the highest activity in yeast. We then screened single-gene deletions to minimize the production of the side products ethanol and glycerol as well as prevent the conversion of D-lactic acid back to pyruvate. Based on the results of the DLDH screening and the single-gene deletions, we created a strain called ASc-d789M which overexpresses LpDLDH and contains deletions in glycerol pathway genes GPD1 and GPD2 and lactate dehydrogenase gene DLD1, as well as downregulation of ethanol pathway gene ADH1 using the L-methionine repressible promoter to minimize impact on growth. ASc-d789M produces D-lactic acid at a titer of 17.09 g/L in shake-flasks (yield of 0.89 g/g glucose consumed or 89% of the theoretical yield). Fed-batch fermentation resulted in D-lactic acid titer of 40.03 g/L (yield of 0.81 g/g glucose consumed). Altogether, our work represents progress towards efficient microbial production of D-lactic acid.

Rewiring yeast metabolism to synthesize products beyond ethanol

Saccharomyces cerevisiae, Baker's yeast, is the industrial workhorse for producing ethanol and the subject of substantial metabolic engineering research in both industry and academia. S. cerevisiae has been used to demonstrate production of a wide range of chemical products from glucose. However, in many cases, the demonstrations report titers and yields that fall below thresholds for industrial feasibility. Ethanol synthesis is a central part of S. cerevisiae metabolism, and redirecting flux to other products remains a barrier to industrialize strains for producing other molecules. Removing ethanol producing pathways leads to poor fitness, such as impaired growth on glucose. Here, we review metabolic engineering efforts aimed at restoring growth in non-ethanol producing strains with emphasis on relieving glucose repression associated with the Crabtree effect and rewiring metabolism to provide access to critical cellular building blocks. Substantial progress has been made in the past decade, but many opportunities for improvement remain.

Enzymological characterization of a novel d-lactate dehydrogenase from Lactobacillus rossiae and its application in d-phenyllactic acid synthesis

A novel lactate dehydrogenase gene, named lrldh, was cloned from Lactobacillus rossiae and heterologously expressed in Escherichia coli. The lactate dehydrogenase LrLDH is NADH-dependent with a molecular weight of approximately 39 kDa. It is active at 40 °C and pH 6.5 and stable in a neutral to alkaline environment below 35 °C. The kinetic constants, including maximal reaction rate (V _max), apparent Michaelis-Menten constant (K _m), turnover number (K _cat) and catalytic efficiency (K _cat/K _m) for phenylpyruvic acid were 1.95 U mg^-1, 2.83 mM, 12.29 s^-1, and 4.34 mM^-1 s^-1, respectively. Using whole cells of recombinant E. coli/pET28a-lrldh, without coexpression of a cofactor regeneration system, 20.5 g l^-1 d-phenyllactic acid with ee above 99% was produced from phenylpyruvic acid in a fed-batch biotransformation process, with a productivity of 49.2 g l^-1 d^-1. Moreover, LrLDH has broad substrate specificity to a range of ketones, keto acids and ketonic esters. Taken together, LrLDH is a promising biocatalyst for the efficient synthesis of d-phenyllactic acid and other fine chemicals.