d-Lactic acid production by metabolically engineered Saccharomyces cerevisiae

Transcriptional response of Saccharomyces cerevisiae to lactic acid enantiomers

The model yeast, Saccharomyces cerevisiae, is a popular object for both fundamental and applied research, including the development of biosensors and industrial production of pharmaceutical compounds. However, despite multiple studies exploring S. cerevisiae transcriptional response to various substances, this response is unknown for some substances produced in yeast, such as D-lactic acid (DLA). Here, we explore the transcriptional response of the BY4742 strain to a wide range of DLA concentrations (from 0.05 to 45 mM), and compare it to the response to 45 mM L-lactic acid (LLA). We recorded a response to 5 and 45 mM DLA (125 and 113 differentially expressed genes (DEGs), respectively; > 50% shared) and a less pronounced response to 45 mM LLA (63 DEGs; > 30% shared with at least one DLA treatment). Our data did not reveal natural yeast promoters quantitatively sensing DLA but provide the first description of the transcriptome-wide response to DLA and enrich our understanding of the LLA response. Some DLA-activated genes were indeed related to lactate metabolism, as well as iron uptake and cell wall structure. Additional analyses showed that at least some of these genes were activated only by acidic form of DLA but not its salt, revealing the role of pH. The list of LLA-responsive genes was similar to those published previously and also included iron uptake and cell wall genes, as well as genes responding to other weak acids. These data might be instrumental for optimization of lactate production in yeast and yeast co-cultivation with lactic acid bacteria. KEY POINTS: • We present the first dataset on yeast transcriptional response to DLA. • Differential gene expression was correlated with yeast growth inhibition. • The transcriptome response to DLA was richer in comparison to LLA.

Engineering of Saccharomyces cerevisiae for enhanced metabolic robustness and L-lactic acid production from lignocellulosic biomass

Metabolic engineering for high productivity and increased robustness is needed to enable sustainable biomanufacturing of lactic acid from lignocellulosic biomass. Lactic acid is an important commodity chemical used for instance as a monomer for production of polylactic acid, a biodegradable polymer. Here, rational and model-based optimization was used to engineer a diploid, xylose fermenting Saccharomyces cerevisiae strain to produce L-lactic acid. The metabolic flux was steered towards lactic acid through the introduction of multiple lactate dehydrogenase encoding genes while deleting ERF2, GPD1, and CYB2. A production of 93 g/L of lactic acid with a yield of 0.84 g/g was achieved using xylose as the carbon source. To increase xylose utilization and reduce acetic acid synthesis, PHO13 and ALD6 were also deleted from the strain. Finally, CDC19 encoding a pyruvate kinase was overexpressed, resulting in a yield of 0.75 g lactic acid/g sugars consumed, when the substrate used was a synthetic lignocellulosic hydrolysate medium, containing hexoses, pentoses and inhibitors such as acetate and furfural. Notably, modeling also provided leads for understanding the influence of oxygen in lactic acid production. High lactic acid production from xylose, at oxygen-limitation could be explained by a reduced flux through the oxidative phosphorylation pathway. On the contrast, higher oxygen levels were beneficial for lactic acid production with the synthetic hydrolysate medium, likely as higher ATP concentrations are needed for tolerating the inhibitors therein. The work highlights the potential of S. cerevisiae for industrial production of lactic acid from lignocellulosic biomass.

Genome engineering of Kluyveromyces marxianus for high D-( -)-lactic acid production under low pH conditions

Saccharomyces cerevisiae is the workhorse of fermentation industry. Upon engineering for D-lactate production by a series of gene deletions, this yeast had deficiencies in cell growth and D-lactate production at high substrate concentrations. Complex nutrients or high cell density were thus required to support growth and D-lactate production with a potential to increase medium and process cost of industrial-scale D-lactate production. As an alternative microbial biocatalyst, a Crabtree-negative and thermotolerant yeast Kluyveromyces marxianus was engineered in this study to produce high titer and yield of D-lactate at a lower pH without growth defects. Only pyruvate decarboxylase 1 (PDC1) gene was replaced by a codon-optimized bacterial D-lactate dehydrogenase (ldhA). Ethanol, glycerol, or acetic acid was not produced by the resulting strain, KMΔpdc1::ldhA. Aeration rate at 1.5 vvm and culture pH 5.0 at 30 °C provided the highest D-lactate titer of 42.97 ± 0.48 g/L from glucose. Yield and productivity of D-lactate, and glucose-consumption rate were 0.85 ± 0.01 g/g, 0.90 ± 0.01 g/(L·h), and 1.06 ± 0.00 g/(L·h), respectively. Surprisingly, D-lactate titer, productivity, and glucose-consumption rate of 52.29 ± 0.68 g/L, 1.38 ± 0.05 g/(L·h), and 1.22 ± 0.00 g/(L·h), respectively, were higher at 42 °C compared to 30 °C. Sugarcane molasses, a low-value carbon, led to the highest D-lactate titer and yield of 66.26 ± 0.81 g/L and 0.91 ± 0.01 g/g, respectively, in a medium without additional nutrients. This study is a pioneer work of engineering K. marxianus to produce D-lactate at the yield approaching theoretical maximum using simple batch process. Our results support the potential of an engineered K. marxianus for D-lactate production on an industrial scale. KEY POINTS: • K. marxianus was engineered by deleting PDC1 and expressing codon-optimized D-ldhA. • The strain allowed high D-lactate titer and yield under pH ranging from 3.5 to 5.0. • The strain produced 66 g/L D-lactate at 30 °C from molasses without any additional nutrients.

Construction of a machine-learning model to predict the optimal gene expression level for efficient production of D-lactic acid in yeast

The modification of gene expression is being researched in the production of useful chemicals by metabolic engineering of the yeast Saccharomyces cerevisiae. When the expression levels of many metabolic enzyme genes are modified simultaneously, the expression ratio of these genes becomes diverse; the relationship between the gene expression ratio and chemical productivity remains unclear. In other words, it is challenging to predict phenotypes from genotypes. However, the productivity of useful chemicals can be improved if this relationship is clarified. In this study, we aimed to construct a machine-learning model that can be used to clarify the relationship between gene expression levels and D-lactic acid productivity and predict the optimal gene expression level for efficient D-lactic acid production in yeast. A machine-learning model was constructed using data on D-lactate dehydrogenase and glycolytic genes expression (13 dimensions) and D-lactic acid productivity. The coefficient of determination of the completed machine-learning model was 0.6932 when using the training data and 0.6628 when using the test data. Using the constructed machine-learning model, we predicted the optimal gene expression level for high D-lactic acid production. We successfully constructed a machine-learning model to predict both D-lactic acid productivity and the suitable gene expression ratio for the production of D-lactic acid. The technique established in this study could be key for predicting phenotypes from genotypes, a problem faced by recent metabolic engineering strategies.

A synthetic C2 auxotroph of Pseudomonas putida for evolutionary engineering of alternative sugar catabolic routes

Acetyl-coenzyme A (AcCoA) is a metabolic hub in virtually all living cells, serving as both a key precursor of essential biomass components and a metabolic sink for catabolic pathways for a large variety of substrates. Owing to this dual role, tight growth-production coupling schemes can be implemented around the AcCoA node. Building on this concept, a synthetic C2 auxotrophy was implemented in the platform bacterium Pseudomonas putida through an in silico-informed engineering approach. A growth-coupling strategy, driven by AcCoA demand, allowed for direct selection of an alternative sugar assimilation route-the phosphoketolase (PKT) shunt from bifidobacteria. Adaptive laboratory evolution forced the synthetic P. putida auxotroph to rewire its metabolic network to restore C2 prototrophy via the PKT shunt. Large-scale structural chromosome rearrangements were identified as possible mechanisms for adjusting the network-wide proteome profile, resulting in improved PKT-dependent growth phenotypes. ¹³C-based metabolic flux analysis revealed an even split between the native Entner-Doudoroff pathway and the synthetic PKT bypass for glucose processing, leading to enhanced carbon conservation. These results demonstrate that the P. putida metabolism can be radically rewired to incorporate a synthetic C2 metabolism, creating novel network connectivities and highlighting the importance of unconventional engineering strategies to support efficient microbial production.

l-Lactic Acid Production Using Engineered Saccharomyces cerevisiae with Improved Organic Acid Tolerance

Lactic acid is mainly used to produce bio-based, bio-degradable polylactic acid. For industrial production of lactic acid, engineered Saccharomyces cerevisiae can be used. To avoid cellular toxicity caused by lactic acid accumulation, pH-neutralizing agents are used, leading to increased production costs. In this study, lactic acid-producing S. cerevisiae BK01 was developed with improved lactic acid tolerance through adaptive laboratory evolution (ALE) on 8% lactic acid. The genetic basis of BK01 could not be determined, suggesting complex mechanisms associated with lactic acid tolerance. However, BK01 had distinctive metabolomic traits clearly separated from the parental strain, and lactic acid production was improved by 17% (from 102 g/L to 119 g/L). To the best of our knowledge, this is the highest lactic acid titer produced by engineered S. cerevisiae without the use of pH neutralizers. Moreover, cellulosic lactic acid production by BK01 was demonstrated using acetate-rich buckwheat husk hydrolysates. Particularly, BK01 revealed improved tolerance against acetic acid of the hydrolysates, a major fermentation inhibitor of lignocellulosic biomass. In short, ALE with a high concentration of lactic acid improved lactic acid production as well as acetic acid tolerance of BK01, suggesting a potential for economically viable cellulosic lactic acid production.

Influence of Nitrogen Sources on D-Lactic Acid Biosynthesis by Sporolactobacillus laevolacticus DSM 442 Strain

The purpose of this study was to explore the possibility of replacing an expensive yeast extract contained in the fermentation medium for D-lactic acid (D-LA, R-lactic acid) biosynthesis with an alternative nitrogen source. The screening studies were conducted under stationary conditions and showed that pea seed hydrolysate was the most beneficial substrate in the process of D-LA biosynthesis by the strain Sporolactobacillus laevolacticus DSM 442 among the used inorganic and organic nitrogen sources, waste materials, food and agricultural products. After 96 h, 75.5 g/L D-LA was obtained in batch cultures in a medium containing pea seed hydrolysate, with an average productivity of 0.79 g/L/h, yield of 75.5%, and optical purity of 99.4%. In batch cultures fed once, in a medium with an analogous composition, 122.6 g/L D-LA was obtained after 120 h, and the average yield, productivity and optical purity were 87.6%, 1.021 g/L/h, and 99.6%, respectively. Moreover, the amount of D-LA obtained in the fermentation medium enriched with the above-mentioned cheap agricultural product was similar to the amounts obtained in the medium containing yeast extract in both stationary and bioreactor cultures. Our research shows that hydrolyzed pea seeds, which belong to the legume family, may be a promising nitrogen source for the production of D-LA on an industrial scale.

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.

Mechanisms underlying lactic acid tolerance and its influence on lactic acid production in Saccharomyces cerevisiae

One of the major bottlenecks in lactic acid production using microbial fermentation is the detrimental influence lactic acid accumulation poses on the lactic acid producing cells. The accumulation of lactic acid results in many negative effects on the cell such as intracellular acidification, anion accumulation, membrane perturbation, disturbed amino acid trafficking, increased turgor pressure, ATP depletion, ROS accumulation, metabolic dysregulation and metal chelation. In this review, the manner in which Saccharomyces cerevisiae deals with these issues will be discussed extensively not only for lactic acid as a singular stress factor but also in combination with other stresses. In addition, different methods to improve lactic acid tolerance in S. cerevisiae using targeted and non-targeted engineering methods will be discussed.

Microbial engineering for the production of C2-C6 organic acids

Covering: up to the end of 2020Organic acids, as building block compounds, have been widely used in food, pharmaceutical, plastic, and chemical industries. Until now, chemical synthesis is still the primary method for industrial-scale organic acid production. However, this process encounters some inevitable challenges, such as depletable petroleum resources, harsh reaction conditions and complex downstream processes. To solve these problems, microbial cell factories provide a promising approach for achieving the sustainable production of organic acids. However, some key metabolites in central carbon metabolism are strictly regulated by the network of cellular metabolism, resulting in the low productivity of organic acids. Thus, multiple metabolic engineering strategies have been developed to reprogram microbial cell factories to produce organic acids, including monocarboxylic acids, hydroxy carboxylic acids, amino carboxylic acids, dicarboxylic acids and monomeric units for polymers. These strategies mainly center on improving the catalytic efficiency of the enzymes to increase the conversion rate, balancing the multi-gene biosynthetic pathways to reduce the byproduct formation, strengthening the metabolic flux to promote the product biosynthesis, optimizing the metabolic network to adapt the environmental conditions and enhancing substrate utilization to broaden the substrate spectrum. Here, we describe the recent advances in producing C₂-C₆ organic acids by metabolic engineering strategies. In addition, we provide new insights as to when, what and how these strategies should be taken. Future challenges are also discussed in further advancing microbial engineering and establishing efficient biorefineries.

Lactic acid production - producing microorganisms and substrates sources-state of art

Lactic acid is an organic compound produced via fermentation by different microorganisms that are able to use different carbohydrate sources. Lactic acid bacteria are the main bacteria used to produce lactic acid and among these, Lactobacillus spp. have been showing interesting fermentation capacities. The use of Bacillus spp. revealed good possibilities to reduce the fermentative costs. Interestingly, lactic acid high productivity was achieved by Corynebacterium glutamicum and E. coli, mainly after engineering genetic modification. Fungi, like Rhizopus spp. can metabolize different renewable carbon resources, with advantageously amylolytic properties to produce lactic acid. Additionally, yeasts can tolerate environmental restrictions (for example acidic conditions), being the wild-type low lactic acid producers that have been improved by genetic manipulation. Microalgae and cyanobacteria, as photosynthetic microorganisms can be an alternative lactic acid producer without carbohydrate feed costs. For lactic acid production, it is necessary to have substrates in the fermentation medium. Different carbohydrate sources can be used, from plant waste as molasses, starchy, lignocellulosic materials as agricultural and forestry residues. Dairy waste also can be used by the addition of supplementary components with a nitrogen source.

Catabolic Division of Labor Enhances Production of D-Lactate and Succinate From Glucose-Xylose Mixtures in Engineered Escherichia coli Co-culture Systems

Although biological upgrading of lignocellulosic sugars represents a promising and sustainable route to bioplastics, diverse and variable feedstock compositions (e.g., glucose from the cellulose fraction and xylose from the hemicellulose fraction) present several complex challenges. Specifically, sugar mixtures are often incompletely metabolized due to carbon catabolite repression while composition variability further complicates the optimization of co-utilization rates. Benefiting from several unique features including division of labor, increased metabolic diversity, and modularity, synthetic microbial communities represent a promising platform with the potential to address persistent bioconversion challenges. In this work, two unique and catabolically orthogonal Escherichia coli co-cultures systems were developed and used to enhance the production of D-lactate and succinate (two bioplastic monomers) from glucose-xylose mixtures (100 g L-1 total sugars, 2:1 by mass). In both cases, glucose specialist strains were engineered by deleting xylR (encoding the xylose-specific transcriptional activator, XylR) to disable xylose catabolism, whereas xylose specialist strains were engineered by deleting several key components involved with glucose transport and phosphorylation systems (i.e., ptsI, ptsG, galP, glk) while also increasing xylose utilization by introducing specific xylR mutations. Optimization of initial population ratios between complementary sugar specialists proved a key design variable for each pair of strains. In both cases, ∼91% utilization of total sugars was achieved in mineral salt media by simple batch fermentation. High product titer (88 g L-1 D-lactate, 84 g L-1 succinate) and maximum productivity (2.5 g L-1 h-1 D-lactate, 1.3 g L-1 h-1 succinate) and product yield (0.97 g g-total sugar-1 for D-lactate, 0.95 g g-total sugar-1 for succinate) were also achieved.

Malic Enzyme Facilitates d-Lactate Production through Increased Pyruvate Supply during Anoxic Dark Fermentation in Synechocystis sp. PCC 6803

d-Lactate is one of the most valuable compounds for manufacturing biobased polymers. Here, we have investigated the significance of endogenous malate dehydrogenase (decarboxylating) (malic enzyme, ME), which catalyzes the oxidative decarboxylation of malate to pyruvate, in d-lactate biosynthesis in the cyanobacterium Synechocystis sp. PCC6803. d-Lactate levels were increased by 2-fold in ME-overexpressing strains, while levels in ME-deficient strains were almost equivalent to those in the host strain. Dynamic metabolomics revealed that overexpression of ME led to increased turnover rates in malate and pyruvate metabolism; in contrast, deletion of ME resulted in increased pool sizes of glycolytic intermediates, probably due to sequential feedback inhibition, initially triggered by malate accumulation. Finally, both the loss of the acetate kinase gene and overexpression of endogenous d-lactate dehydrogenase, concurrent with ME overexpression, resulted in the highest production of d-lactate (26.6 g/L) with an initial cell concentration of 75 g-DCW/L after 72 h fermentation.

Co-culture of Lactobacillus delbrueckii and engineered Lactococcus lactis enhances stoichiometric yield of D-lactic acid from whey permeate

D-Lactic acid (D-LA) is an enantiomer of lactic acid, which has a niche application in synthesis of poly-lactic acid based (PLA) polymer owing to its contribution to the thermo-stability of stereo-complex PLA polymer. Utilization of renewable substrates such as whey permeate is pivotal to economically viable production of D-LA. In present work, we have demonstrated D-LA production from whey permeate by Lactobacillus delbrueckii and engineered Lactococcus lactis. We observed that lactose fermentation by a monoculture of L. delbrueckii yields D-LA and galactose as major products. The highest yield of D-LA obtained was 0.48 g g^-1 when initial lactose concentration was 30 g L^-1. Initial lactose concentration beyond 20 g L^-1 resulted in accumulation of glucose and galactose, and hence, reduced the stoichiometric yield of D-LA. L. lactis naturally produces L-lactic acid (L-LA), so a mutant strain of L. lactis (L. lactis Δldh ΔldhB ΔldhX) was used to prevent L-LA production and engineer it for D-LA production. Heterologous over-expression of D-lactate dehydrogenase (ldhA) in the recombinant strain L. lactis TSG1 resulted in 0.67 g g^-1 and 0.44 g g^-1 of D-LA yield from lactose and galactose, respectively. Co-expression of galactose permease (galP) and α-phosphoglucomutase (pgmA) with ldhA in the recombinant strain L. lactis TSG3 achieved a D-LA yield of 0.92 g g^-1 from galactose. A co-culture batch process of L. delbrueckii and L. lactis TSG3 achieved an enhanced stoichiometric yield of 0.90 g g^-1 and ~45 g L^-1D-LA from whey permeate (lactose). This is the highest reported yield of D-LA from lactose substrate, and the titres can be improved further by a suitably designed fed-batch co-culture process.

Microbial production of d-lactic acid from dried distiller's grains with solubles

d-Lactic acid production is gaining increasing attention due to the thermostable properties of its polymer, poly-d-lactic acid . In this study, Lactobacillus coryniformis subsp. torquens, was evaluated for its ability to produce d-lactic acid using Dried Distiller's Grains with Solubles (DDGS) hydrolysate as the substrate. DDGS was first subjected to alkaline pretreatment with sodium hydroxide to remove the hemicellulose component and the generated carbohydrate-rich solids were then subjected to enzymatic hydrolysis using cellulase mixture Accellerase® 1500. When comparing separate hydrolysis and fermentation and simultaneous saccharification and fermentation (SSF) of L. coryniformis on DDGS hydrolysate, the latter method demonstrated higher d-lactic acid production (27.9 g/L, 99.9% optical purity of d-lactic acid), with a higher glucose to d-lactic acid conversion yield (84.5%) compared to the former one (24.1 g/L, 99.9% optical purity of d-lactic acid). In addition, the effect of increasing the DDGS concentration in the fermentation system was investigated via a fed-batch SSF approach, where it was shown that the d-lactic acid production increased to 38.1 g/L and the conversion yield decreased to 70%. In conclusion, the SSF approach proved to be an efficient strategy for the production of d-lactic acid from DDGS as it reduced the overall processing time and yielded high d-lactic acid concentrations.

Catalytic, Computational, and Evolutionary Analysis of the d-Lactate Dehydrogenases Responsible for d-Lactic Acid Production in Lactic Acid Bacteria

d-Lactate dehydrogenase (d-LDH) catalyzes the reversible reaction pyruvate + NADH + H⁺ ↔ lactate + NAD⁺, which is a principal step in the production of d-lactate in lactic acid bacteria. In this study, we identified and characterized the major d-LDH (d-LDH1) from three d-LDHs in Leuconostoc mesenteroides, which has been extensively used in food processing. A molecular simulation study of d-LDH1 showed that the conformation changes during substrate binding. During catalysis, Tyr101 and Arg235 bind the substrates by hydrogen bonds and His296 acts as a general acid/base for proton transfer. These residues are also highly conserved and have coevolved. Point mutations proved that the substrate binding sites and catalytic site are crucial for enzyme activity. Network and phylogenetic analyses indicated that d-LDH1 and the homologues are widely distributed but are most abundant in bacteria and fungi. This study expands the understanding of the functions, catalytic mechanism, and evolution of d-LDH.

Dilute sulfuric acid fractionation of Korean food waste for ethanol and lactic acid production by yeast

Fermentation of food waste biomass can be used to produce biochemicals such as lactic acid and ethanol in a cost-effective manner. Korean food waste (KFW) dewatered by a screw press contains 23.1% glucan on a dry basis and is a potential raw material for the production of ethanol and lactic acid through fermentation. This study was conducted to optimize the dilute acid fractionation conditions for KFW fermentation with respect to the H₂SO₄ concentration (0-0.8% w/v), temperature (130-190 °C), and residence time (1-128 min) using response surface methodology. Dilute sulfuric acid fractionation was carried out using a 30-mL stainless steel reactor under conditions, and then the dilute acid fractionation was scaled-up in 1-L and 7-L stainless steel reactors under the optimal conditions. The hydrolysate was concentrated, liquid-liquid extracted and neutralized for lactic acid and ethanol production. The highest concentration of glucose obtained from the KFW was 26.4 g/L using fractionation with 0.37% w/v H₂SO₄ at 156 °C for 123.6 min. Using recombinant Saccharomyces cerevisiae containing a codon-optimized lactate dehydrogenase, the yield of lactic acid and ethanol was 77% of the theoretical yield for 17.4 g/L of fermentable sugar at pH 5.5. Additionally, the yield of ethanol produced by Issatchenkia orientalis was 89% of the theoretical yield for 25 g/L of fermentable sugar at pH 3.

Advancement of Biotechnology by Genetic Modifications

One of the greatest sources of metabolic and enzymatic diversity are microorganisms. In recent years, emerging recombinant DNA and genomic techniques have facilitated the development of new efficient expression systems, modification of biosynthetic pathways leading to new metabolites by metabolic engineering, and enhancement of catalytic properties of enzymes by directed evolution. Complete sequencing of industrially important microbial genomes is taking place very rapidly, and there are already hundreds of genomes sequenced. Functional genomics and proteomics are major tools used in the search for new molecules and development of higher-producing strains.

Non-sterilized fermentation of high optically pure D-lactic acid by a genetically modified thermophilic Bacillus coagulans strain

Background

Optically pure d-lactic acid (≥ 99%) is an important precursor of polylactic acid. However, there are relatively few studies on d-lactic acid fermentation compared with the extensive investigation of l-lactic acid production. Most lactic acid producers are mesophilic organisms. Optically pure d-lactic acid produced at high temperature not only could reduce the costs of sterilization but also could inhibit the growth of other bacteria, such as l-lactic acid producers.

Results

Thermophilic Bacillus coagulans is an excellent producer of l-lactic acid with capable of growing at 50 °C. In our previous study, the roles of two l-lactic acid dehydrogenases have been demonstrated in B. coagulans DSM1. In this study, the function of another annotated possible l-lactate dehydrogenase gene (ldhL3) was verified to be leucine dehydrogenase with an activity of 0.16 units (μmol/min) per mg protein. Furthermore, the activity of native d-lactate dehydrogenase was too low to support efficient d-lactic acid production, even under the control of strong promoter. Finally, an engineered B. coagulans D-DSM1 strain with the capacity for efficient production of d-lactic acid was constructed by deletion of two l-lactate dehydrogenases genes (ldhL1 and ldhL2) and insertion of the d-lactate dehydrogenase gene (LdldhD) from Lactobacillus delbrueckii subsp. bulgaricus DSM 20081 at the position of ldhL1.

Conclusions

This genetically engineered strain produced only d-lactic acid under non-sterilized condition, and finally 145 g/L of d-lactic acid was produced with an optical purity of 99.9% and a high yield of 0.98 g/g. This is the highest optically pure d-lactic acid titer produced by a thermophilic strain.

Electronic supplementary material

The online version of this article (10.1186/s12934-017-0827-1) contains supplementary material, which is available to authorized users.

Production of D-lactate from glucose using Klebsiella pneumoniae mutants

Background

d-Lactate is a valued chemical which can be produced by some bacteria including Klebsiella pneumoniae. However, only a few studies have focused on K. pneumoniae for d-lactate production with a significant amount of by-products, which complicated the purification process and decreased the yield of d-lactate.

Results

Based on the redirection of carbon towards by-product formation, the effects of single-gene and multiple-gene deletions in K. pneumoniae on d-lactate production from glucose via acetolactate synthase (budB), acetate kinase (ackA), and alcohol dehydrogenase (adhE) were tested. Klebsiella pneumoniae mutants had different production behaviours. The accumulation of the main by-products was decreased in the mutants. The triple mutant strain had the most powerful ability to produce optically pure d-lactate from glucose, and was tested with xylose and arabinose as carbon sources. Fed-batch fermentation was also carried out under various aeration rates, and the strain accumulated 125.1 g/L d-lactate with a yield of 0.91 g/g glucose at 2.5 vvm.

Conclusions

Knocking out by-product synthesis genes had a remarkable influence on the production and yield of d-lactate. This study demonstrated, for the first time, that K. pneumoniae has great potential to convert monosaccharides into d-lactate. The results provide new insights for industrial production of d-lactate by K. pneumoniae.

Metabolic engineering of Schizosaccharomyces pombe via CRISPR-Cas9 genome editing for lactic acid production from glucose and cellobiose

Modification of the Schizosaccharomyces pombe genome is often laborious, time consuming due to the lower efficiency of homologous recombination. Here, we constructed metabolically engineered S. pombe strains using a CRISPR-Cas9 system and also demonstrated D-lactic acid (D-LA) production from glucose and cellobiose. Genes encoding two separate pyruvate decarboxylases (PDCs), an L-lactic acid dehydrogenase (L-LDH), and a minor alcohol dehydrogenase (SPBC337.11) were disrupted, thereby attenuating ethanol production. To increase the cellular supply of acetyl-CoA, an important metabolite for growth, we introduced genes encoding bacterial acetylating acetaldehyde dehydrogenase enzymes (Escherichia coli MhpF and EutE). D-LA production by the resulting strain was achieved by expressing a Lactobacillus plantarum gene encoding D-lactate dehydrogenase. The engineered strain efficiently consumed glucose and produced D-LA at 25.2 g/L from 35.5 g/L of consumed glucose with a yield of 0.71 g D-LA / g glucose. We further modified this strain by expressing beta-glucosidase by cell surface display; the resulting strain produced D-LA at 24.4 g/L from 30 g/L of cellobiose in minimal medium, with a yield of 0.68 g D-LA / g glucose. To our knowledge, this study represents the first report of a S. pombe strain that was metabolically engineered using a CRISPR-Cas9 system, and demonstrates the possibility of engineering S. pombe for the production of value-added chemicals.

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Schizosaccharomyces pombe were metabolically engineered using a CRISPR-Cas9 system.

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D-lactic acid (D-LA) producing Schizosaccharomyces pombe strains were constructed.

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25.2 g/L of D-LA was produced with a yield of 0.71 g-D-LA / g-glucose.

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Beta-glucosidase was expressed on this engineered S. pombe strain.

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D-LA was produced at 24.4 g/L from 30 g/L of cellobiose directly.

Engineered biosynthesis of biodegradable polymers

Advances in science and technology have resulted in the rapid development of biobased plastics and the major drivers for this expansion are rising environmental concerns of plastic pollution and the depletion of fossil-fuels. This paper presents a broad view on the recent developments of three promising biobased plastics, polylactic acid (PLA), polyhydroxyalkanoate (PHA) and polybutylene succinate (PBS), well known for their biodegradability. The article discusses the natural and recombinant host organisms used for fermentative production of monomers, alternative carbon feedstocks that have been used to lower production cost, different metabolic engineering strategies used to improve product titers, various fermentation technologies employed to increase productivities and finally, the different downstream processes used for recovery and purification of the monomers and polymers.

Carbon Flux Trapping: Highly Efficient Production of Polymer-Grade d-Lactic Acid with a Thermophilic d-Lactate Dehydrogenase

High production of polymer-grade d-lactic acid is urgently required, particularly for the synthesis of polylactic acid. High-temperature fermentation has multiple advantages, such as lower equipment requirement and energy consumption, which are essential for lowering operating costs. We identified and introduced a unique d-lactate dehydrogenase into a thermotolerant butane-2,3-diol-producing strain. Carbon flux "trapping" was achieved by a "trapping point" created by combination of the introduced enzyme and the host efflux pump, which afforded irreversible transport of d-lactic acid. The overall carbon flux of the engineered strain was significantly enhanced and was redistributed predominantly to d-lactic acid. Under optimized conditions at 50 °C, d-lactic acid reached the highest titer (226.6 g L(-1) ) reported to date. This discovery allows us to extend the carbon flux trapping strategy to engineering complex metabolic networks.

Enhanced D-lactic acid production from renewable resources using engineered Lactobacillus plantarum

D-lactic acid is used as a monomer in the production of poly-D-lactic acid (PDLA), which is used to form heat-resistant stereocomplex poly-lactic acid. To produce cost-effective D-lactic acid by using all sugars derived from biomass efficiently, xylose-assimilating genes encoding xylose isomerase and xylulokinase were cloned into an L-lactate-deficient strain, Lactobacillus plantarum. The resulting recombinant strain, namely L. plantarum NCIMB 8826 ∆ldhL1-pLEM-xylAB, was able to produce D-lactic acid (at optical purity >99 %) from xylose at a yield of 0.53 g g(-1). Simultaneous utilization of glucose and xylose to produce D-lactic acid was also achieved by this strain, and 47.2 g L(-1) of D-lactic acid was produced from 37.5 g L(-1) glucose and 19.7 g L(-1) xylose. Corn stover and soybean meal extract (SBME) were evaluated as cost-effective medium components for D-lactic acid production. Optimization of medium composition using response surface methodology resulted in 30 % reduction in enzyme loading and 70 % reduction in peptone concentration. In addition, we successfully demonstrated D-lactic acid fermentation from corn stover and SBME in a fed-batch fermentation, which yielded 61.4 g L(-1) D-lactic acid with an overall yield of 0.77 g g(-1). All these approaches are geared to attaining high D-lactic acid production from biomass sugars to produce low-cost, highly thermostable biodegradable plastics.

Chirality Matters: Synthesis and Consumption of the d-Enantiomer of Lactic Acid by Synechocystis sp. Strain PCC6803

Both enantiomers of lactic acid, l-lactic acid and d-lactic acid, can be produced in a sustainable way by a photosynthetic microbial cell factory and thus from CO2, sunlight, and water. Several properties of polylactic acid (a polyester of polymerized lactic acid) depend on the controlled blend of these two enantiomers. Recently, cyanobacterium Synechocystis sp. strain PCC6803 was genetically modified to allow formation of either of these two enantiomers. This report elaborates on the d-lactic acid production achieved by the introduction of a d-specific lactate dehydrogenase from the lactic acid bacterium Leuconostoc mesenteroides into Synechocystis. A typical batch culture of this recombinant strain initially shows lactic acid production, followed by a phase of lactic acid consumption, until production "outcompetes" consumption at later growth stages. We show that Synechocystis is able to use d-lactic acid, but not l-lactic acid, as a carbon source for growth. Deletion of the organism's putative d-lactate dehydrogenase (encoded by slr1556), however, does not eliminate this ability with respect to d-lactic acid consumption. In contrast, d-lactic acid consumption does depend on the presence of glycolate dehydrogenase GlcD1 (encoded by sll0404). Accordingly, this report highlights the need to match a product of interest of a cyanobacterial cell factory with the metabolic network present in the host used for its synthesis and emphasizes the need to understand the physiology of the production host in detail.

Metabolic engineering and adaptive evolution for efficient production of D-lactic acid in Saccharomyces cerevisiae

There is an increasing demand for microbial production of lactic acid (LA) as a monomer of biodegradable poly lactic acid (PLA). Both optical isomers, D-LA and L-LA, are required to produce stereocomplex PLA with improved properties. In this study, we developed Saccharomyces cerevisiae strains for efficient production of D-LA. D-LA production was achieved by expressing highly stereospecific D-lactate dehydrogenase gene (ldhA, LEUM_1756) from Leuconostoc mesenteroides subsp. mesenteroides ATCC 8293 in S. cerevisiae lacking natural LA production activity. D-LA consumption after glucose depletion was inhibited by deleting DLD1 encoding D-lactate dehydrogenase and JEN1 encoding monocarboxylate transporter. In addition, ethanol production was reduced by deleting PDC1 and ADH1 genes encoding major pyruvate decarboxylase and alcohol dehydrogenase, respectively, and glycerol production was eliminated by deleting GPD1 and GPD2 genes encoding glycerol-3-phosphate dehydrogenase. LA tolerance of the engineered D-LA-producing strain was enhanced by adaptive evolution and overexpression of HAA1 encoding a transcriptional activator involved in weak acid stress response, resulting in effective D-LA production up to 48.9 g/L without neutralization. In a flask fed-batch fermentation under neutralizing condition, our evolved strain produced 112.0 g/L D-LA with a yield of 0.80 g/g glucose and a productivity of 2.2 g/(L · h).

Hydrophilic compounds in liquids of enzymatic hydrolyzed spruce and pine biomass

Organic acids are used for starting compounds in material sciences and in biorefinery, food, fuel, pharmaceutical, and medical industry. Here, we provide the data from a biochemical approach made to investigate production of organic acids and isolation of metals from wood, which is the most abundant biomass. Spruce and bark, phloem, and heartwood from pine were fermented with either microbes of oyster mushroom (Pleurotus ostreatus), baker's yeast, or lactic acid bacteria to improve selective fermentation. Using capillary electrophoresis and liquid chromatography techniques, we identified 14 different organic acids and phenolic acids with good yields. With inductively coupled plasma atomic emission spectroscopy 11 metals were quantified and further detailed analysis/results from these data are available in Sirén et al. (2015) [1].

Microbial production of lactic acid

Lactic acid is an important commodity chemical having a wide range of applications. Microbial production effectively competes with chemical synthesis methods because biochemical synthesis permits the generation of either one of the two enantiomers with high optical purity at high yield and titer, a result which is particularly beneficial for the production of poly(lactic acid) polymers having specific properties. The commercial viability of microbial lactic acid production relies on utilization of inexpensive carbon substrates derived from agricultural or waste resources. Therefore, optimal lactic acid formation requires an understanding and engineering of both the competing pathways involved in carbohydrate metabolism, as well as pathways leading to potential by-products which both affect product yield. Recent research leverages those biochemical pathways, while researchers also continue to seek strains with improved tolerance and ability to perform under desirable industrial conditions, for example, of pH and temperature.

Production of optically pure d-lactate from glycerol by engineered Klebsiella pneumoniae strain

In this study, glycerol was used to produce optically pure d-lactate by engineered Klebsiella pneumoniae strain. In the recombinant strain, d-lactate dehydrogenase LdhA was overexpressed, and two genes, dhaT and yqhD for biosynthesis of main byproduct 1,3-propanediol, were knocked out. To further improve d-lactate production, the culture condition was optimized and the results demonstrated that aeration rate played an important role in d-lactate production. In microaerobic fed-batch fermentation, the engineered strain accumulated 142.1g/L optically pure d-lactate with a yield of 0.82g/g glycerol, which represented the highest d-lactate production from glycerol so far. This study showed that K. pneumoniae strain has high efficiency to convert glycerol into d-lactate and high potentiality in utilization of crude glycerol from biodiesel industry.

Production of D-lactic acid in a continuous membrane integrated fermentation reactor by genetically modified Saccharomyces cerevisiae: enhancement in D-lactic acid carbon yield

Poly d-lactic acid is an important polymer because it improves the thermostability of poly l-lactic acid by stereo complex formation. To demonstrate potency of continuous fermentation using a membrane-integrated fermentation reactor (MFR) system, continuous fermentation using genetically modified Saccharomyces cerevisiae which produces d-lactic acid was performed at the low pH and microaerobic conditions. d-Lactic acid continuous fermentation using the MFR system by genetically modified yeast increased production rate by 11-fold compared with batch fermentation. In addition, the carbon yield of d-lactic acid in continuous fermentation was improved to 74.6 ± 2.3% compared to 39.0 ± 1.7% with batch fermentation. This dramatic improvement in carbon yield could not be explained by a reduction in carbon consumption to form cells compared to batch fermentation. Further detailed analysis at batch fermentation revealed that the carbon yield increased to 76.8% at late stationary phase. S. cerevisiae, which exhibits the Crabtree-positive effect, demonstrated significant changes in metabolic activities at low sugar concentrations (Rossignol et al., Yeast, 20, 1369-1385, 2003). Moreover, lactate-producing S. cerevisiae requires ATP supplied not only from the glycolytic pathway but also from the TCA cycle (van Maris et al., Appl. Environ. Microbiol., 70, 2898-2905, 2004). Our finding was revealed that continuous fermentation, which can maintain the conditions of both a low sugar concentration and air supply, results in Crabtree-positive and lactate-producing S. cerevisiae for suitable conditions of d-lactic acid production with respect to redox balance and ATP generation because of releasing the yeast from the Crabtree effect.

Fermentative production of lactic acid from renewable materials: recent achievements, prospects, and limits

The development and implementation of renewable materials for the production of versatile chemical resources have gained considerable attention recently, as this offers an alternative to the environmental problems caused by the petroleum industry and the limited supply of fossil resources. Therefore, the concept of utilizing biomass or wastes from agricultural and industrial residues to produce useful chemical products has been widely accepted. Lactic acid plays an important role due to its versatile application in the food, medical, and cosmetics industries and as a potential raw material for the manufacture of biodegradable plastics. Currently, the fermentative production of optically pure lactic acid has increased because of the prospects of environmental friendliness and cost-effectiveness. In order to produce lactic acid with high yield and optical purity, many studies focus on wild microorganisms and metabolically engineered strains. This article reviews the most recent advances in the biotechnological production of lactic acid mainly by lactic acid bacteria, and discusses the feasibility and potential of various processes.

Metabolic engineering of Saccharomyces cerevisiae to improve succinic acid production based on metabolic profiling

We performed metabolic engineering on the budding yeast Saccharomyces cerevisiae for enhanced production of succinic acid. Aerobic succinic acid production in S. cerevisiae was achieved by disrupting the SDH1 and SDH2 genes, which encode the catalytic subunits of succinic acid dehydrogenase. Increased succinic acid production was achieved by eliminating the ethanol biosynthesis pathways. Metabolic profiling analysis revealed that succinic acid accumulated intracellularly following disruption of the SDH1 and SDH2 genes, which suggests that enhancing the export of intracellular succinic acid outside of cells increases succinic acid production in S. cerevisiae. The mae1 gene encoding the Schizosaccharomyces pombe malic acid transporter was introduced into S. cerevisiae, and as a result, succinic acid production was successfully improved. Metabolic profiling analysis is useful in producing chemicals for metabolic engineering of microorganisms.

Silencing the glycerol-3-phosphate dehydrogenase gene in Saccharomyces cerevisiae results in more ethanol being produced and less glycerol

Transcription of the gene coding for glycerol-3-phosphate dehydrogenase (GPD1) was repressed in an industrial strain of Saccharomyces cerevisiae using a silencing vector. A fusion fragment containing GPD1 and Kan MX genes was generated by overlap extension PCR, then, the vector, pYES2.0 GPD1/Kan MX, was constructed by inserting the fusion fragment into the S. cerevisiae plasmid, pYES2.0. pYES2.0 GPD1/Kan MX, was linearized by KpnI, transformed into S. cerevisiae using the PEG/LiAc/ssDNA method, and integrated into the S. cerevisiae chromosome. GPD1 silencing gave 20 % less glycerol-3-phosphate dehydrogenase activity, 19 % lower glycerol production, and 9.7 % higher ethanol production compared with the original strain. These findings further the development of industrial S. cerevisiae strains with improved ethanol production and reduced glycerol content for the efficient production of bio-ethanol.

Efficient production of polymer-grade D-lactate by Sporolactobacillus laevolacticus DSM442 with agricultural waste cottonseed as the sole nitrogen source

In this study, we show that Sporolactobacillus laevolacticus DSM442 can produce d-lactate by using cottonseed as the sole nitrogen source. The cottonseed was enzymatically hydrolyzed and simultaneously utilized during d-lactate fermentation. Under optimal conditions, a high d-lactic acid concentration (144.4 g/L) was obtained in a fed-batch fermentation within 35 h, with an average productivity of 4.13 g/(Lh) and a yield of 0.96 g/g glucose. The optical purity of d-lactic acid in the broth was 99.3%, which meets the requirement for use in lactic acid polymerization. Our study represents a cost-effective method for polymer-grade d-lactate production using cheap agricultural wastes.