Overexpression of cytosolic malate dehydrogenase (MDH2) causes overproduction of specific organic acids in Saccharomyces cerevisiae

Recent advances in producing food additive L-malate: Chassis, substrate, pathway, fermentation regulation and application

In addition to being an important intermediate in the TCA cycle, L-malate is also widely used in the chemical and beverage industries. Due to the resulting high demand, numerous studies investigated chemical methods to synthesize L-malate from petrochemical resources, but such approaches are hampered by complex downstream processing and environmental pollution. Accordingly, there is an urgent need to develop microbial methods for environmentally-friendly and economical L-malate biosynthesis. The rapid progress and understanding of DNA manipulation, cell physiology, and cell metabolism can improve industrial L-malate biosynthesis by applying intelligent biochemical strategies and advanced synthetic biology tools. In this paper, we mainly focused on biotechnological approaches for enhancing L-malate synthesis, encompassing the microbial chassis, substrate utilization, synthesis pathway, fermentation regulation, and industrial application. This review emphasizes the application of novel metabolic engineering strategies and synthetic biology tools combined with a deep understanding of microbial physiology to improve industrial L-malate biosynthesis in the future.

Malic acid: fermentative production and applications

Microbial metabolites have gained lot of industrial interest. These are currently employed in various industries including pharmaceuticals, chemical, textiles, food etc. Organic acids are among the important microbial products. Production of microbial organic acids present numerous advantages like agro-industrial waste may be utilized as substrate, low production cost, natural in origin and production is environment friendly. Malic acid is an organic acid (C4 dicarboxylic acid) that can be produced by microbes. It is also useful in industrial sectors as food, chemicals, and pharmaceuticals etc. Production/extraction of malic acid has been reported from fruits, egg shells, microbes, via chemical synthesis, bio-transformation and from renewable sources. Microbial production of malic acid seems very promising due to various advantages and the approach is environment-friendly. In recent years, researchers have focused on fermentative microbial production of malic acid and possibility of using agro-industrial waste as raw substrates. In current article, malic acid production along with applications has been discussed with recent advances in the area.

Predicting Human Protein Subcellular Locations by Using a Combination of Network and Function Features

Given the limitation of technologies, the subcellular localizations of proteins are difficult to identify. Predicting the subcellular localization and the intercellular distribution patterns of proteins in accordance with their specific biological roles, including validated functions, relationships with other proteins, and even their specific sequence characteristics, is necessary. The computational prediction of protein subcellular localizations can be performed on the basis of the sequence and the functional characteristics. In this study, the protein-protein interaction network, functional annotation of proteins and a group of direct proteins with known subcellular localization were used to construct models. To build efficient models, several powerful machine learning algorithms, including two feature selection methods, four classification algorithms, were employed. Some key proteins and functional terms were discovered, which may provide important contributions for determining protein subcellular locations. Furthermore, some quantitative rules were established to identify the potential subcellular localizations of proteins. As the first prediction model that uses direct protein annotation information (i.e., functional features) and STRING-based protein-protein interaction network (i.e., network features), our computational model can help promote the development of predictive technologies on subcellular localizations and provide a new approach for exploring the protein subcellular localization patterns and their potential biological importance.

Microbial Biosynthesis of L-Malic Acid and Related Metabolic Engineering Strategies: Advances and Prospects

Malic acid, a four-carbon dicarboxylic acid, is widely used in the food, chemical and medical industries. As an intermediate of the TCA cycle, malic acid is one of the most promising building block chemicals that can be produced from renewable sources. To date, chemical synthesis or enzymatic conversion of petrochemical feedstocks are still the dominant mode for malic acid production. However, with increasing concerns surrounding environmental issues in recent years, microbial fermentation for the production of L-malic acid was extensively explored as an eco-friendly production process. The rapid development of genetic engineering has resulted in some promising strains suitable for large-scale bio-based production of malic acid. This review offers a comprehensive overview of the most recent developments, including a spectrum of wild-type, mutant, laboratory-evolved and metabolically engineered microorganisms for malic acid production. The technological progress in the fermentative production of malic acid is presented. Metabolic engineering strategies for malic acid production in various microorganisms are particularly reviewed. Biosynthetic pathways, transport of malic acid, elimination of byproducts and enhancement of metabolic fluxes are discussed and compared as strategies for improving malic acid production, thus providing insights into the current state of malic acid production, as well as further research directions for more efficient and economical microbial malic acid production.

Extra copy of the mitochondrial cytochrome-c peroxidase gene confers a pyruvate-underproducing characteristic of sake yeast through respiratory metabolism

The mechanism of pyruvate-underproduction of aneuploid sake yeast was investigated in this study. In our previous report, we revealed that an increase in chromosome XI decreases pyruvate productivity of sake yeast. In this report, we found that increased copy number of CCP1, which is located on chromosome XI and encodes cytochrome-c peroxidase, decreased the pyruvate productivity of sake yeasts. Introducing an extra copy of CCP1 activated respiratory metabolism governed by Hap4 and increased reactive oxygen species. Therefore, it was concluded that increased copy number of CCP1 on chromosome XI activated respiratory metabolism and decreased pyruvate levels in an aneuploid sake yeast. This is the first report that describes a mechanism underlying the improvement of brewery yeast by chromosomal aneuploidy.

Deep Ocean Water Concentrate Changes Physicochemical Characteristics, the Profile of Volatile Components and Consumer Acceptance for Taiwanese Rice Shochu

To study the effects of deep-ocean water concentrate (DOWC) on sake quality, Taichung No. 10 indica rice (Oryza sativa subsp. indica) and Tainan No. 11 japonica rice (O. sativa subsp. japonica) were used as raw materials, and basic physicochemical property parameters in shochu were analyzed differentially. Sake fermentation mash analysis results revealed that DOWC addition did not significantly affect the basic physicochemical properties during sake brewing, but it significantly reduced citric acid and malic acid contents in Taichung No. 10 indica rice sake sample by 52–66% and 73–93%, respectively. DOWC addition significantly increased citric acid content in Tainan No. 11 japonica rice sake sample by 32–202%. Rice shochu analysis results revealed that DOWC addition significantly increased isoamyl acetate, ethyl hexanoate, and ethyl octanoate contents in shochu made from japonica rice and indica rice, respectively. The results indicate that rice variety directly affects the types of volatile compounds in rice shochu. Principal component analysis and sensory evaluation results revealed that DOWC addition affected the composition of volatile compounds in the two types of rice shochu and resulted in differences in flavor evaluation. DOWC addition affects yeast metabolites and directly changes the volatile compound composition and flavor of rice shochu.

Recent progress on bio-based production of dicarboxylic acids in yeast

Dicarboxylic acids are widely used in fine chemical and food industries as well as the monomer for polymerisation of high molecular material. Given the problems of environmental contamination and sustainable development faced by traditional production of dicarboxylic acids based on petrol, new approaches such as bio-based production of dicarboxylic acids drew more attentions. The yeast, Saccharomyces cerevisiae, was regarded as an ideal organism for bio-based production of dicarboxylic acids with high tolerance to acidic and hyperosmotic environments, robust growth using a broad range of substrates, great convenience for genetic manipulation, stable inheritance via sub-cultivation, and food compatibility. In this review, the production of major dicarboxylates via S. cerevisiae was concluded and the challenges and opportunities facing were discussed.Key Points• Summary of current production of major dicarboxylic acids by Saccharomyces cerevisiae.• Discussion of influence factors on four-carbon dicarboxylic acids production by Saccharomyces cerevisiae.• Outlook of potential production of five- and six-carbon dicarboxylic acids by Saccharomyces cerevisiae.

Current advance in biological production of malic acid using wild type and metabolic engineered strains

Malic acid (2-hydroxybutanedioic acid) is a four-carbon dicarboxylic acid, which has attracted great interest due to its wide usage as a precursor of many industrially important chemicals in the food, chemicals, and pharmaceutical industries. Several mature routes for malic acid production have been developed, such as chemical synthesis, enzymatic conversion and biological fermentation. With depletion of fossil fuels and concerns regarding environmental issues, biological production of malic acid has attracted more attention, which mainly consists of three pathways, namely non-oxidative pathway, oxidative pathway and glyoxylate cycle. In recent decades, metabolic engineering of model strains, and process optimization for malic acid production have been rapidly developed. Hence, this review comprehensively introduces an overview of malic acid producers and highlight some of the successful metabolic engineering approaches.

The mitochondrial malate dehydrogenase 1 gene GhmMDH1 is involved in plant and root growth under phosphorus deficiency conditions in cotton

Cotton, an important commercial crop, is cultivated for its natural fibers, and requires an adequate supply of soil nutrients, including phosphorus, for its growth. Soil phosporus exists primarily in insoluble forms. We isolated a mitochondrial malate dehydrogenase (MDH) gene, designated as GhmMDH1, from Gossypium hirsutum L. to assess its effect in enhancing P availability and absorption. An enzyme kinetic assay showed that the recombinant GhmMDH1 possesses the capacity to catalyze the interconversion of oxaloacetate and malate. The malate contents in the roots, leaves and root exudates was significantly higher in GhmMDH1-overexpressing plants and lower in knockdown plants compared with the wild-type control. Knockdown of GhmMDH1 gene resulted in increased respiration rate and reduced biomass whilst overexpression of GhmMDH1 gave rise to decreased respiration rate and higher biomass in the transgenic plants. When cultured in medium containing only insoluble phosphorus, Al-phosphorus, Fe-phosphorus, or Ca-phosphorus, GhmMDH1-overexpressing plants produced significantly longer roots and had a higher biomass and P content than WT plants, however, knockdown plants showed the opposite results for these traits. Collectively, our results show that GhmMDH1 is involved in plant and root growth under phosphorus deficiency conditions in cotton, owing to its functions in leaf respiration and P acquisition.

Microbial biosynthesis and secretion of l-malic acid and its applications

l-Malic acid has many uses in food, beverage, pharmaceutical, chemical and medical industries. It can be produced by one-step fermentation, enzymatic transformation of fumaric acid to l-malate and acid hydrolysis of polymalic acid. However, the process for one-step fermentation is preferred as it has many advantages over any other process. The pathways of l-malic acid biosynthesis in microorganisms are partially clear and three metabolic pathways including non-oxidative pathway, oxidative pathway and glyoxylate cycle for the production of l-malic acid from glucose have been identified. Usually, high levels of l-malate are produced under the nitrogen starvation conditions, l-malate, as a calcium salt, is secreted from microbial cells and CaCO3 can play an important role in calcium malate biosynthesis and regulation. However, it is still unclear how it is secreted into the medium. To enhance l-malate biosynthesis and secretion by microbial cells, it is very important to study the mechanisms of l-malic acid biosynthesis and secretion at enzymatic and molecular levels.

Metabolic engineering of biocatalysts for carboxylic acids production

Fermentation of renewable feedstocks by microbes to produce sustainable fuels and chemicals has the potential to replace petrochemical-based production. For example, carboxylic acids produced by microbial fermentation can be used to generate primary building blocks of industrial chemicals by either enzymatic or chemical catalysis. In order to achieve the titer, yield and productivity values required for economically viable processes, the carboxylic acid-producing microbes need to be robust and well-performing. Traditional strain development methods based on mutagenesis have proven useful in the selection of desirable microbial behavior, such as robustness and carboxylic acid production. On the other hand, rationally-based metabolic engineering, like genetic manipulation for pathway design, has becoming increasingly important to this field and has been used for the production of several organic acids, such as succinic acid, malic acid and lactic acid. This review investigates recent works on Saccharomyces cerevisiae and Escherichia coli, as well as the strategies to improve tolerance towards these chemicals.

Evaluation of gene modification strategies for the development of low-alcohol-wine yeasts

Saccharomyces cerevisiae has evolved a highly efficient strategy for energy generation which maximizes ATP energy production from sugar. This adaptation enables efficient energy generation under anaerobic conditions and limits competition from other microorganisms by producing toxic metabolites, such as ethanol and CO(2). Yeast fermentative and flavor capacity forms the biotechnological basis of a wide range of alcohol-containing beverages. Largely as a result of consumer demand for improved flavor, the alcohol content of some beverages like wine has increased. However, a global trend has recently emerged toward lowering the ethanol content of alcoholic beverages. One option for decreasing ethanol concentration is to use yeast strains able to divert some carbon away from ethanol production. In the case of wine, we have generated and evaluated a large number of gene modifications that were predicted, or known, to impact ethanol formation. Using the same yeast genetic background, 41 modifications were assessed. Enhancing glycerol production by increasing expression of the glyceraldehyde-3-phosphate dehydrogenase gene, GPD1, was the most efficient strategy to lower ethanol concentration. However, additional modifications were needed to avoid negatively affecting wine quality. Two strains carrying several stable, chromosomally integrated modifications showed significantly lower ethanol production in fermenting grape juice. Strain AWRI2531 was able to decrease ethanol concentrations from 15.6% (vol/vol) to 13.2% (vol/vol), whereas AWRI2532 lowered ethanol content from 15.6% (vol/vol) to 12% (vol/vol) in both Chardonnay and Cabernet Sauvignon juices. Both strains, however, produced high concentrations of acetaldehyde and acetoin, which negatively affect wine flavor. Further modifications of these strains allowed reduction of these metabolites.

Production of fumaric acid by fermentation

Fermentative fumaric acid production from renewable resources may become competitive with petrochemical production. This will require very efficient processes. So far, using Rhizopus strains, the best fermentations reported have achieved a fumaric acid titer of 126 g/L with a productivity of 1.38 g L(-1) h(-1) and a yield on glucose of 0.97 g/g. This requires pH control, aeration, and carbonate/CO(2) supply. Limitations of the used strains are their pH tolerance, morphology, accessibility for genetic engineering, and partly, versatility to alternative carbon sources. Understanding of the mechanism and energetics of fumaric acid export by Rhizopus strains will be a success factor for metabolic engineering of other hosts for fumaric acid production. So far, metabolic engineering has been described for Escherichia coli and Saccharomyces cerevisiae.

Isolation and characterization of an apple cytosolic malate dehydrogenase gene reveal its function in malate synthesis

Cytosolic NAD-dependent malate dehydrogenase (cyMDH) is an enzyme crucial for malate synthesis in the cytosol. The apple MdcyMDH gene (GenBank Accession No. DQ221207) encoding the cyMDH enzyme in apple was cloned and functionally characterized. The protein was subcellularly localized to the cytoplasm and plasma membrane. Based on kinetic parameters, it mainly catalyzes the reaction from oxalacetic acid (OAA) to malate in vitro. The expression level of MdcyMDH was positively correlated with malate dehydrogenase (MDH) activity throughout fruit development, but not with malate content, especially in the ripening apple fruit. MdcyMDH overexpression contributed to malate accumulation in the apple callus and tomato. Taken together, our results support the involvement of MdcyMDH directly in malate synthesis and indirectly in malate accumulation through the regulation of genes/enzymes associated with malate degradation and transportation, gluconeogenesis and the tricarboxylic acid cycle.

The functions of an apple cytosolic malate dehydrogenase gene in growth and tolerance to cold and salt stresses

It is well-known that cytosolic NAD-dependent malate dehydrogenase (cyMDH; l-malate:NAD-oxidoreductase; EC 1.1.1.37) is an enzyme crucial for malic acid synthesis in the cytosol. Nothing is known about cyMDH in growth and stress tolerance. Here we characterised the role of the apple cyMDH gene (MdcyMDH, GenBank ID: DQ221207) in growth and tolerance to cold and salt stresses. MdcyMDH transcripts were highly accumulated in vigorously growing apple tissues, organs and suspension cells. In addition, MdcyMDH was sensitive to cold and salt stresses. MdcyMDH overexpression favourably contributed to cell and plant growth and conferred stress tolerance both in the apple callus and tomato. Taken together, our results indicated that MdcyMDH is involved in plant and cell growth as well as the tolerance to cold and salt stresses.

L-malate production by metabolically engineered Escherichia coli

Escherichia coli strains (KJ060 and KJ073) that were previously developed for succinate production have now been modified for malate production. Many unexpected changes were observed during this investigation. The initial strategy of deleting fumarase isoenzymes was ineffective, and succinate continued to accumulate. Surprisingly, a mutation in fumarate reductase alone was sufficient to redirect carbon flow into malate even in the presence of fumarase. Further deletions were needed to inactivate malic enzymes (typically gluconeogenic) and prevent conversion to pyruvate. However, deletion of these genes (sfcA and maeB) resulted in the unexpected accumulation of D-lactate despite the prior deletion of mgsA and ldhA and the absence of apparent lactate dehydrogenase activity. Although the metabolic source of this D-lactate was not identified, lactate accumulation was increased by supplementation with pyruvate and decreased by the deletion of either pyruvate kinase gene (pykA or pykF) to reduce the supply of pyruvate. Many of the gene deletions adversely affected growth and cell yield in minimal medium under anaerobic conditions, and volumetric rates of malate production remained low. The final strain (XZ658) produced 163 mM malate, with a yield of 1.0 mol (mol glucose(-1)), half of the theoretical maximum. Using a two-stage process (aerobic cell growth and anaerobic malate production), this engineered strain produced 253 mM malate (34 g liter(-1)) within 72 h, with a higher yield (1.42 mol mol(-1)) and productivity (0.47 g liter(-1) h(-1)). This malate yield and productivity are equal to or better than those of other known biocatalysts.

Organic chemicals from bioprocesses in China

Over the last 20 years, China has successfully established a modern biotechnology industry from almost nothing. Presently, China is a major producer of a vast array of products involving bioprocesses, for some China is even the world's top producer. The ever-increasing list of products includes organic acids, amino acids, antibiotics, solvents, chiral chemicals, biopesticides, and biopolymers. Herein, the research and development of bioprocesses in China will be reviewed briefly. We will concentrate on three categories of products: small molecules produced via fermentation, biopolymers produced via fermentation and small chemicals produced by enzyme-catalyzed reactions. In comparison with the traditional chemical process, in which, nonrenewable mineral resources are generally used, products in the first and second categories noted above can use renewable bioresources as raw materials. The bioprocesses are generally energy saving and environmentally benign. For products developed via the third category, although the raw materials still need to be obtained from mineral resources, the biocatalysts are more effective with higher selectivity and productivity, and the bioprocesses occur under ambient temperature and pressure, therefore, these are "green processes." Most of the products such as citric acid, xanthan and acrylamide etc., discussed in this paper have been in large-scale commercial production in China. Also introduced herein are three scientists, Prof. Shen Yinchu, Prof. Ouyang Pingkai and Prof. Chen Guoqiang, and six enterprises, Anhui Fengyuan Biochemical Co. Ltd., Shandong Hiland Biotechnology Co. Ltd., Shandong Fufeng Fermentation Co. Ltd., Shandong Bausch & Lomb-Freda Pharmaceutical Co. Ltd., Zhejiang Hangzhou Xinfu Pharmaceutical Co. Ltd., and Changzhou Changmao Biochemical Engineering Co. Ltd.; they have all contributed a great deal to research and development in the commercialization of bioprocesses.

Malic acid production by Saccharomyces cerevisiae: engineering of pyruvate carboxylation, oxaloacetate reduction, and malate export

Malic acid is a potential biomass-derivable "building block" for chemical synthesis. Since wild-type Saccharomyces cerevisiae strains produce only low levels of malate, metabolic engineering is required to achieve efficient malate production with this yeast. A promising pathway for malate production from glucose proceeds via carboxylation of pyruvate, followed by reduction of oxaloacetate to malate. This redox- and ATP-neutral, CO(2)-fixing pathway has a theoretical maximum yield of 2 mol malate (mol glucose)(-1). A previously engineered glucose-tolerant, C(2)-independent pyruvate decarboxylase-negative S. cerevisiae strain was used as the platform to evaluate the impact of individual and combined introduction of three genetic modifications: (i) overexpression of the native pyruvate carboxylase encoded by PYC2, (ii) high-level expression of an allele of the MDH3 gene, of which the encoded malate dehydrogenase was retargeted to the cytosol by deletion of the C-terminal peroxisomal targeting sequence, and (iii) functional expression of the Schizosaccharomyces pombe malate transporter gene SpMAE1. While single or double modifications improved malate production, the highest malate yields and titers were obtained with the simultaneous introduction of all three modifications. In glucose-grown batch cultures, the resulting engineered strain produced malate at titers of up to 59 g liter(-1) at a malate yield of 0.42 mol (mol glucose)(-1). Metabolic flux analysis showed that metabolite labeling patterns observed upon nuclear magnetic resonance analyses of cultures grown on (13)C-labeled glucose were consistent with the envisaged nonoxidative, fermentative pathway for malate production. The engineered strains still produced substantial amounts of pyruvate, indicating that the pathway efficiency can be further improved.

Malo-ethanolic fermentation in Saccharomyces and Schizosaccharomyces

Yeast species are divided into the K(+) or K(-) groups, based on their ability or inability to metabolise tricarboxylic acid (TCA) cycle intermediates as sole carbon or energy source. The K(-) group of yeasts includes strains of Saccharomyces, Schizosaccharomyces pombe and Zygosaccharomyces bailii, which is capable of utilising TCA cycle intermediates only in the presence of glucose or other assimilable carbon sources. Although grouped together, these yeasts have significant differences in their abilities to degrade malic acid. Typically, strains of Saccharomyces are regarded as inefficient metabolisers of extracellular malic acid, whereas strains of Sch. pombe and Z. bailii can effectively degrade high concentrations of malic acid. The ability of a yeast strain to degrade extracellular malic acid is dependent on both the efficient transport of the dicarboxylic acid and the efficacy of the intracellular malic enzyme. The malic enzyme converts malic acid into pyruvic acid, which is further metabolised to ethanol and carbon dioxide under fermentative conditions via the so-called malo-ethanolic (ME) pathway. This review focuses on the enzymes involved in the ME pathway in Sch. pombe and Saccharomyces species, with specific emphasis on the malate transporter and the intracellular malic enzyme.

FUNCTION AND MECHANISM OF ORGANIC ANION EXUDATION FROM PLANT ROOTS

The rhizosphere is the zone of soil immediately surrounding plant roots that is modified by root activity. In this critical zone, plants perceive and respond to their environment. As a consequence of normal growth and development, a large range of organic and inorganic substances are exchanged between the root and soil, which inevitably leads to changes in the biochemical and physical properties of the rhizosphere. Plants also modify their rhizosphere in response to certain environmental signals and stresses. Organic anions are commonly detected in this region, and their exudation from plant roots has now been associated with nutrient deficiencies and inorganic ion stresses. This review summarizes recent developments in the understanding of the function, mechanism, and regulation of organic anion exudation from roots. The benefits that plants derive from the presence of organic anions in the rhizosphere are described and the potential for biotechnology to increase organic anion exudation is highlighted.

Production of multifunctional organic acids from renewable resources

Recently, the microbial production of multifunctional organic acid has received interest due to their increased use in the food industry and their potential as raw materials for the manufacture of biodegradable polymers. Certain species of microorganisms produce significant quantities of organic acids in high yields under specific cultivation conditions from biomass-derived carbohydrates. The accumulation of some acids, such as fumaric, malic and succinic acid, are believed to involve CO2-fixation which gives high yields of products. The application of special fermentation techniques and the methods for downstream processing of products are described. Techniques such as simultaneous fermentation and product recovery and downstream processing are likely to occupy an important role in the reduction of production costs. Finally, some aspects of process design and current industrial production processes are discussed.