Construction and characterization of ack knock-out mutants of Propionibacterium acidipropionici for enhanced propionic acid fermentation

The vast landscape of carbohydrate fermentation in prokaryotes

Fermentation is a type of metabolism carried out by organisms in environments without oxygen. Despite being studied for over 185 years, the diversity and complexity of this metabolism are just now becoming clear. Our review starts with the definition of fermentation, which has evolved over the years and which we help further refine. We then examine the range of organisms that carry out fermentation and their traits. Over one-fourth of all prokaryotes are fermentative, use more than 40 substrates, and release more than 50 metabolic end products. These insights come from studies analyzing records of thousands of organisms. Next, our review examines the complexity of fermentation at the biochemical level. We map out pathways of glucose fermentation in unprecedented detail, covering over 120 biochemical reactions. We also review recent studies coupling genomics and enzymology to reveal new pathways and enzymes. Our review concludes with practical applications for agriculture, human health, and industry. All these areas depend on fermentation and could be improved through manipulating fermentative microbes and enzymes. We discuss potential approaches for manipulation, including genetic engineering, electrofermentation, probiotics, and enzyme inhibitors. We hope our review underscores the importance of fermentation research and stimulates the next 185 years of study.

Expanding Pseudomonas taiwanensis VLB120's acyl-CoA portfolio: Propionate production in mineral salt medium

As one of the main precursors, acetyl-CoA leads to the predominant production of even-chain products. From an industrial biotechnology perspective, extending the acyl-CoA portfolio of a cell factory is vital to producing industrial relevant odd-chain alcohols, acids, ketones and polyketides. The bioproduction of odd-chain molecules can be facilitated by incorporating propionyl-CoA into the metabolic network. The shortest pathway for propionyl-CoA production, which relies on succinyl-CoA catabolism encoded by the sleeping beauty mutase operon, was evaluated in Pseudomonas taiwanensis VLB120. A single genomic copy of the sleeping beauty mutase genes scpA, argK and scpB combined with the deletion of the methylcitrate synthase PVLB_08385 was sufficient to observe propionyl-CoA accumulation in this Pseudomonas. The chassis' capability for odd-chain product synthesis was assessed by expressing an acyl-CoA hydrolase, which enabled propionate synthesis. Three fed-batch strategies during bioreactor fermentations were benchmarked for propionate production, in which a maximal propionate titre of 2.8 g L-1 was achieved. Considering that the fermentations were carried out in mineral salt medium under aerobic conditions and that a single genome copy drove propionyl-CoA production, this result highlights the potential of Pseudomonas to produce propionyl-CoA derived, odd-chain products.

Microbial production of odd-chain fatty acids

Odd-chain fatty acids (OcFAs) and their derivatives have attracted much attention due to their beneficial physiological effects and their potential to be alternatives to advanced fuels. However, cells naturally produce even-chain fatty acids (EcFAs) with negligible OcFAs. In the process of biosynthesis of fatty acids (FAs), the acetyl-CoA serves as the starter unit for EcFAs, and propionyl-CoA works as the starter unit for OcFAs. The lack of sufficient propionyl-CoA, the precursor, is usually regarded as the main restriction for large-scale bioproduction of OcFAs. In recent years, synthetic biology strategies have been used to modify several microorganisms to produce more propionyl-CoA that would enable an efficient biosynthesis of OcFAs. This review discusses several reported and potential metabolic pathways for propionyl-CoA biosynthesis, followed by advances in engineering several cell factories for OcFAs production. Finally, trends and challenges of synthetic biology driven OcFAs production are discussed.

Volatile fatty acids production from waste streams by anaerobic digestion: A critical review of the roles and application of enzymes

Volatile fatty acids (VFAs) produced from organic-rich wastewater by anaerobic digestion attract attention due to the increasing volatile fatty acids market, sustainability and environmentally friendly characteristics. This review aims to give an overview of the roles and applications of enzymes, a biocatalyst which plays a significant role in anaerobic digestion, to enhance volatile fatty acids production. This paper systematically overviewed: (i) the enzymatic pathways of VFAs formation, competition, and consumption; (ii) the applications of enzymes in VFAs production; and (iii) feasible measures to boost the enzymatic processes. Furthermore, this review presents a critical evaluation on the major obstacles and feasible future research directions for the better applications of enzymatic processes to promote VFAs production from wastewater.

A comprehensive review on current status and future perspectives of microbial volatile fatty acids production as platform chemicals

Volatile fatty acids (VFA), the secondary metabolite of microbial fermentation, are used in a wide range of industries for production of commercially valuable chemicals. In this review, the fermentative production of VFAs by both pure as well mixed microbial cultures is highlighted along with the strategies for enhancing the VFA production through innovations in existing approaches. Role of conventionally applied tools for the optimization of operational parameters such as pH, temperature, retention time, organic loading rate, and headspace pressure has been discussed. Furthermore, a comparative assessment of above strategies on VFA production has been done with alternate developments such as co-fermentation, substrate pre-treatment, and in situ removal from fermented broth. The review also highlights the applications of different bioreactor geometries in the optimum production of VFAs and how metagenomic tools could provide a detailed insight into the microbial communities and their functional attributes that could be subjected to metabolic engineering for the efficient production of VFAs.

Recent trends in microbial flavour Compounds: A review on Chemistry, synthesis mechanism and their application in food

Aroma and flavour represent the key components of food that improves the organoleptic characteristics of food and enhances the acceptability of food to consumers. Commercial manufacturing of aromatic and flavouring compounds is from the industry's microbial source, but since time immemorial, its concept has been behind human practices. The interest in microbial flavour compounds has developed in the past several decades because of its sustainable way to supply natural additives for the food processing sector. There are also numerous health benefits from microbial bioprocess products, ranging from antibiotics to fermented functional foods. This review discusses recent developments and advancements in many microbial aromatic and flavouring compounds, their biosynthesis and production by diverse types of microorganisms, their use in the food industry, and a brief overview of their health benefits for customers.

Fermentative production of propionic acid: prospects and limitations of microorganisms and substrates

Propionic acid is an important organic acid with wide industrial applications, especially in the food industry. It is currently produced from petrochemicals via chemical routes. Increasing concerns about greenhouse gas emissions from fossil fuels and a growing consumer preference for bio-based products have led to interest in fermentative production of propionic acid, but it is not yet competitive with chemical production. To improve the economic feasibility and sustainability of bio-propionic acid, fermentation performance in terms of concentration, yield, and productivity must be improved and the cost of raw materials must be reduced. These goals require robust microbial producers and inexpensive renewable feedstocks, so the present review focuses on bacterial producers of propionic acid and promising sources of substrates as carbon sources. Emphasis is placed on assessing the capacity of propionibacteria and the various approaches pursued in an effort to improve their performance through metabolic engineering. A wide range of substrates employed in propionic acid fermentation is analyzed with particular interest in the prospects of inexpensive renewable feedstocks, such as cellulosic biomass and industrial residues, to produce cost-competitive bio-propionic acid. KEY POINTS: • Fermentative propionic acid production emerges as competitor to chemical synthesis. • Various bacteria synthesize propionic acid, but propionibacteria are the best producers. • Biomass substrates hold promise to reduce propionic acid fermentation cost.

A New Pathway for Forming Acetate and Synthesizing ATP during Fermentation in Bacteria

Many bacteria and other organisms carry out fermentations forming acetate. These fermentations have broad importance for foods, agriculture, and industry. They also are important for bacteria themselves because they often generate ATP. Here, we found a biochemical pathway for forming acetate and synthesizing ATP that was unknown in fermentative bacteria. We found that the bacterium Cutibacterium granulosum formed acetate during fermentation of glucose. It did not use phosphotransacetylase or acetate kinase, enzymes found in nearly all acetate-forming bacteria. Instead, it used a pathway involving two different enzymes. The first enzyme, succinyl coenzyme A (succinyl-CoA):acetate CoA-transferase (SCACT), forms acetate from acetyl-CoA. The second enzyme, succinyl-CoA synthetase (SCS), synthesizes ATP. We identified the genes encoding these enzymes, and they were homologs of SCACT and SCS genes found in other bacteria. The pathway resembles one described in eukaryotes, but it uses bacterial, not eukaryotic, gene homologs. To find other instances of the pathway, we analyzed sequences of all biochemically characterized homologs of SCACT and SCS (103 enzymes from 64 publications). Homologs with similar enzymatic activity had similar sequences, enabling a large-scale search for them in genomes. We searched nearly 600 genomes of bacteria known to form acetate, and we found that 6% encoded homologs with SCACT and SCS activity. This included >30 species belonging to 5 different phyla, showing that a diverse range of bacteria encode the SCACT/SCS pathway. This work suggests the SCACT/SCS pathway is important for acetate formation in many branches of the tree of life. IMPORTANCE Pathways for forming acetate during fermentation have been studied for over 80 years. In that time, several pathways in a range of organisms, from bacteria to animals, have been described. However, one pathway (involving succinyl-CoA:acetate CoA-transferase and succinyl-CoA synthetase) has not been reported in prokaryotes. Here, we discovered enzymes for this pathway in the fermentative bacterium Cutibacterium granulosum. We also found >30 other fermentative bacteria that encode this pathway, demonstrating that it could be common. This pathway represents a new way for bacteria to form acetate from acetyl-CoA and synthesize ATP via substrate-level phosphorylation. It could be a target for controlling yield of acetate during fermentation, with relevance for foods, agriculture, and industry.

Propionic acid production from apple pomace in bioreactor using Propionibacterium freudenreichii: an economic analysis of the process

Propionic acid and its salts are widely used as food and feed preservative. Currently, these compounds are chemically produced, which is more profitable compared to biotechnological production using bacteria of the Propionibacterium genus. Appropriate steps can enable reducing the production costs; for example, cheap industrial byproducts can be used as culture media. One such cost-effective raw material is apple pomace, a low-value byproduct from the food industry. It contains sugars such as glucose and fructose which can serve as potential carbon sources for microorganisms. This paper discusses the possibility of using apple pomace in the production of propionic acid and presents an economic analysis of the production process. The tested strain produced 8.01 g/L of propionic acid (yield 0.40 g/g) and 2.29 g/L of acetic acid (yield 0.11 g/g) from apple pomace extract. The economic analysis showed that the production of 1 kg of propionic acid (considering only waste) from 1000 kg of apple pomace would cost approximately 1.25 USD. The manufacturing cost (consumables, including feedstock, labor, and utilities) would be approximately 2.35 USD/kg, and the total cost including taxes would be approximately 3.05 USD/kg. From the economic point of view, it is necessary to improve the production of propionic acid from apple pomace, to increase the yield of fermentation and thus decrease the total production costs. This can be achieved, for example, using industrial byproducts as nitrogen and vitamin sources, instead of high-cost substrates such as yeast extract or peptone.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-020-02582-x.

A Pan-Genome Guided Metabolic Network Reconstruction of Five Propionibacterium Species Reveals Extensive Metabolic Diversity

Propionibacteria have been studied extensively since the early 1930s due to their relevance to industry and importance as human pathogens. Still, their unique metabolism is far from fully understood. This is partly due to their signature high GC content, which has previously hampered the acquisition of quality sequence data, the accurate annotation of the available genomes, and the functional characterization of genes. The recent completion of the genome sequences for several species has led researchers to reassess the taxonomical classification of the genus Propionibacterium, which has been divided into several new genres. Such data also enable a comparative genomic approach to annotation and provide a new opportunity to revisit our understanding of their metabolism. Using pan-genome analysis combined with the reconstruction of the first high-quality Propionibacterium genome-scale metabolic model and a pan-metabolic model of current and former members of the genus Propionibacterium, we demonstrate that despite sharing unique metabolic traits, these organisms have an unexpected diversity in central carbon metabolism and a hidden layer of metabolic complexity. This combined approach gave us new insights into the evolution of Propionibacterium metabolism and led us to propose a novel, putative ferredoxin-linked energy conservation strategy. The pan-genomic approach highlighted key differences in Propionibacterium metabolism that reflect adaptation to their environment. Results were mathematically captured in genome-scale metabolic reconstructions that can be used to further explore metabolism using metabolic modeling techniques. Overall, the data provide a platform to explore Propionibacterium metabolism and a tool for the rational design of strains.

Improving propionic acid production from a hemicellulosic hydrolysate of sorghum bagasse by means of cell immobilization and sequential batch operation

Propionic acid (PA) is an important organic compound with extensive application in different industrial sectors and is currently produced by petrochemical processes. The production of PA by large-scale fermentation processes presents a bottleneck, particularly due to low volumetric productivity. In this context, the present work aimed to produce PA by a biochemical route from a hemicellulosic hydrolysate of sorghum bagasse using the strain Propionibacterium acidipropionici CIP 53164. Conditions were optimized to increase volumetric productivity and process efficiency. Initially, in simple batch fermentation, a final concentration of PA of 17.5 g⋅L^-1 was obtained. Next, fed batch operation with free cells was adopted to minimize substrate inhibition. Although a higher concentration of PA was achieved (38.0 g⋅L^-1 ), the response variables (Y_P/S = 0.409 g⋅g^-1 and Q_P = 0.198 g⋅L^-1 ⋅H^-1 ) were close to those of the simple batch experiment. Finally, the fermentability of the hemicellulosic hydrolysate was investigated in a sequential batch with immobilized cells. The PA concentration achieved a maximum of 35.3 g⋅L^-1 in the third cycle; moreover, the volumetric productivity was almost sixfold higher (1.17 g⋅L^-1 ⋅H^-1 ) in sequential batch than in simple batch fermentation. The results are highly promising, providing preliminary data for studies on scaling up the production of this organic acid.

Sequencing and Analysis of the Genome of Propionibacterium Freudenreichii T82 Strain: Importance for Industry

The genome of Propionibacterium freudenreichii ssp. freudenreichii T82, which has a chromosome containing 2,585,340 nucleotides with 67.3% GC content (guanine-cytosine content), is described in this paper. The total number of genes is 2308, of which 2260 are protein-coding genes and 48 are RNA genes. According to the genome analysis and the obtained results, the T82 strain can produce various compounds such as propionic acid, trehalose, glycogen, and B group vitamins (e.g., B6, B9, and B12). From protein-coding sequences (CDSs), genes related to stress adaptation, biosynthesis, metabolism, transport, secretion, and defense machinery were detected. In the genome of the T82 strain, sequences corresponding to the CRISPR loci (Clustered Regularly Interspaced Short Palindromic Repeats), antibiotic resistance, and restriction-modification system were found.

Disruption of the lactate dehydrogenase and acetate kinase genes in Klebsiella pneumoniae HD79 to enhance 2,3-butanediol production, and related transcriptomics analysis

OBJECTIVES

2,3-Butanediol (2,3-BD) is widely used in several chemical syntheses as well as the manufacture of plastics, solvents, and antifreeze formulations, and can be manufactured by microbial glucose fermentation. Conventional (2,3-BD) fermentation typically has low productivity, yield, and purity, and is expensive for commercial applications. We aimed to delete the lactate dehydrogenase and acetate kinase (ldhA and ack) genes in Klebsiella pneumoniae HD79 by using λRed homologous recombination technology, to eliminate by-products and thereby improve (2,3-BD) production. We also analyzed the resulting gene changes by using transcriptomics.

RESULTS

The yield of (2,3-BD) from the mutant Klebsiella strain was 46.21 g/L, the conversion rate was 0.47 g/g, and the productivity was 0.64 g/L·h, which represented increases of 54.9%, 20.5%, and 106.5% respectively, compared to (WT) strains. Lactate and acetate decreased by 48.2% and 62.8%, respectively. Transcriptomics analysis showed that 4628 genes were differentially expressed (404 significantly up-regulated and 162 significantly down-regulated). Moreover, the (2,3-BD) operon genes were differentially expressed.

CONCLUSION

Our data showed that the biosynthesis of (2,3-BD) was regulated by inducers (lactate and acetate), a regulator (BudR), and carbon flux. Elimination of acidic by-products by ldhA and ack knockdown significantly improved (2,3-BD) production. Our results provide a deeper understanding of the mechanisms underlying (2,3-BD) production, and form a molecular basis for the improvement this process by genetic modification in the future.

Genome-scale model guided design of Propionibacterium for enhanced propionic acid production

Production of propionic acid by fermentation of propionibacteria has gained increasing attention in the past few years. However, biomanufacturing of propionic acid cannot compete with the current oxo-petrochemical synthesis process due to its well-established infrastructure, low oil prices and the high downstream purification costs of microbial production. Strain improvement to increase propionic acid yield is the best alternative to reduce downstream purification costs. The recent generation of genome-scale models for a number of Propionibacterium species facilitates the rational design of metabolic engineering strategies and provides a new opportunity to explore the metabolic potential of the Wood-Werkman cycle. Previous strategies for strain improvement have individually targeted acid tolerance, rate of propionate production or minimisation of by-products. Here we used the P. freudenreichii subsp. shermanii and the pan-Propionibacterium genome-scale metabolic models (GEMs) to simultaneously target these combined issues. This was achieved by focussing on strategies which yield higher energies and directly suppress acetate formation. Using P. freudenreichii subsp. shermanii, two strategies were assessed. The first tested the ability to manipulate the redox balance to favour propionate production by over-expressing the first two enzymes of the pentose-phosphate pathway (PPP), Zwf (glucose-6-phosphate 1-dehydrogenase) and Pgl (6-phosphogluconolactonase). Results showed a 4-fold increase in propionate to acetate ratio during the exponential growth phase. Secondly, the ability to enhance the energy yield from propionate production by over-expressing an ATP-dependent phosphoenolpyruvate carboxykinase (PEPCK) and sodium-pumping methylmalonyl-CoA decarboxylase (MMD) was tested, which extended the exponential growth phase. Together, these strategies demonstrate that in silico design strategies are predictive and can be used to reduce by-product formation in Propionibacterium. We also describe the benefit of carbon dioxide to propionibacteria growth, substrate conversion and propionate yield.

Propionic acid production from soy molasses by Propionibacterium acidipropionici: Fermentation kinetics and economic analysis

Propionic acid (PA) is a specialty chemical; its calcium salt is widely used as food preservative. Soy molasses (SM), a low-value byproduct from soybean refinery, contains sucrose and raffinose-family oligosaccharides (RFO), which are difficult to digest for most animals and industrial microorganisms. The feasibility of using SM for PA production by P. acidipropionici, which has genes encoding enzymes necessary for RFO hydrolysis, was studied. With corn steep liquor as the nitrogen source, stable long-term PA production from SM was demonstrated in sequential batch fermentations, achieving PA productivity of >0.8 g/L h and yield of 0.42 g/g sugar at pH 6.5. Economic analysis showed that calcium propionate as the main component (63.5%) in the product could be produced at US $1.55/kg for a 3000-MT plant with a capital investment of US $10.82 million. At $3.0/kg for the product, the process offers attractive 40% return of investment and is promising for commercial application.

Propionibacterium spp.-source of propionic acid, vitamin B12, and other metabolites important for the industry

Bacteria from the Propionibacterium genus consists of two principal groups: cutaneous and classical. Cutaneous Propionibacterium are considered primary pathogens to humans, whereas classical Propionibacterium are widely used in the food and pharmaceutical industries. Bacteria from the Propionibacterium genus are capable of synthesizing numerous valuable compounds with a wide industrial usage. Biomass of the bacteria from the Propionibacterium genus constitutes sources of vitamins from the B group, including B12, trehalose, and numerous bacteriocins. These bacteria are also capable of synthesizing organic acids such as propionic acid and acetic acid. Because of GRAS status and their health-promoting characteristics, bacteria from the Propionibacterium genus and their metabolites (propionic acid, vitamin B12, and trehalose) are commonly used in the cosmetic, pharmaceutical, food, and other industries. They are also used as additives in fodders for livestock. In this review, we present the major species of Propionibacterium and their properties and provide an overview of their functions and applications. This review also presents current literature concerned with the possibilities of using Propionibacterium spp. to obtain valuable metabolites. It also presents the biosynthetic pathways as well as the impact of the genetic and environmental factors on the efficiency of their production.

Construction of a novel anaerobic pathway in Escherichia coli for propionate production

Background

Propionate is widely used as an important preservative and important chemical intermediate for synthesis of cellulose fibers, herbicides, perfumes and pharmaceuticals. Biosynthetic propionate has mainly been produced by Propionibacterium, which has various limitations for industrial application.

Results

In this study, we engineered E. coli by combining reduced TCA cycle with the native sleeping beauty mutase (Sbm) cycle to construct a redox balanced and energy viable fermentation pathway for anaerobic propionate production. As the cryptic Sbm operon was over-expressed in E. coli MG1655, propionate titer reached 0.24 g/L. To increase precursor supply for the Sbm cycle, genetic modification was made to convert mixed fermentation products to succinate, which slightly increased propionate production. For optimal expression of Sbm operon, different types of promoters were examined. A strong constitutive promoter Pbba led to the highest titer of 2.34 g/L. Methylmalonyl CoA mutase from Methylobacterium extorquens AM1 was added to strain T110(pbba-Sbm) to enhance this rate limiting step. With optimized expression of this additional Methylmalonyl CoA mutase, the highest production strain was obtained with a titer of 4.95 g/L and a yield of 0.49 mol/mol glucose.

Conclusions

With various metabolic engineering strategies, the propionate titer from fermentation achieved 4.95 g/L. This is the reported highest anaerobic production of propionate by heterologous host. Due to host advantages, such as non-strict anaerobic condition, mature engineering and fermentation techniques, and low cost minimal media, our work has built the basis for industrial propionate production with E. coli chassis.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-017-0354-5) contains supplementary material, which is available to authorized users.

Current advances in biological production of propionic acid

Propionic acid and its derivatives are considered "Generally Recognized As Safe" food additives and are generally used as an anti-microbial and anti-inflammatory agent, herbicide, and artificial flavor in diverse industrial applications. It is produced via biological pathways using Propionibacterium and some anaerobic bacteria. However, its commercial chemical synthesis from the petroleum-based feedstock is the conventional production process bit results in some environmental issues. Novel biological approaches using microorganisms and renewable biomass have attracted considerable recent attention due to economic advantages as well as great adaptation with the green technology. This review provides a comprehensive overview of important biotechnological aspects of propionic acid production using recent technologies such as employment of co-culture, genetic and metabolic engineering, immobilization technique and efficient bioreactor systems.

Metabolic engineering of Propionibacterium freudenreichii subsp. shermanii for xylose fermentation

Propionibacterium freudenreichii cannot use xylose, the second most abundant sugar in lignocellulosic biomass. Although Propionibacterium acidipropionici can use xylose as a carbon source, it is difficult to genetically modify, impeding further improvement through metabolic engineering. This study identified three xylose catabolic pathway genes encoding for xylose isomerase (xylA), xylose transporter (xylT), and xylulokinase (xylB) in P. acidipropionici and overexpressed them in P. freudenreichii subsp. shermanii via an expression plasmid pKHEM01, enabling the mutant to utilize xylose efficiently even in the presence of glucose without glucose-induced carbon catabolite repression. The mutant showed similar fermentation kinetics with glucose, xylose, and the mixture of glucose and xylose, respectively, as carbon source, and with or without the addition of antibiotic for selection pressure. The engineered P. shermanii thus can provide a novel cell factory for industrial production of propionic acid and other value-added products from lignocellulosic biomass.

Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels

Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

Metabolic engineering of acid resistance elements to improve acid resistance and propionic acid production of Propionibacterium jensenii

Propionic acid (PA) and its salts are widely used in the food, pharmaceutical, and chemical industries. Microbial production of PA by propionibacteria is a typical product-inhibited process, and acid resistance is crucial in the improvement of PA titers and productivity. We previously identified two key acid resistance elements-the arginine deaminase and glutamate decarboxylase systems-that protect propionibacteria against PA stress by maintaining intracellular pH homeostasis. In this study, we attempted to improve the acid resistance and PA production of Propionibacterium jensenii ATCC 4868 by engineering these elements. Specifically, five genes (arcA, arcC, gadB, gdh, and ybaS) encoding components of the arginine deaminase and glutamate decarboxylase systems were overexpressed in P. jensenii. The activities of the five enzymes in the engineered strains were 26.7-489.0% higher than those in wild-type P. jensenii. The growth rates of the engineered strains decreased, whereas specific PA production increased significantly compared with those of the wild-type strain. Among the overexpressed genes, gadB (encoding glutamate decarboxylase) increased PA resistance and yield most effectively; the PA resistance of P. jensenii-gadB was more than 10-fold higher than that of the wild-type strain, and the production titer, yield, and conversion ratio of PA reached 10.81 g/L, 5.92 g/g cells, and 0.56 g/g glycerol, representing increases of 22.0%, 23.8%, and 21.7%, respectively. We also investigated the effects of introducing these acid resistance elements on the transcript levels of related enzymes. The results showed that the expression of genes in the engineered pathways affected the expression of the other genes. Additionally, the intracellular pools of amino acids were altered as different genes were overexpressed, which may further contribute to the enhanced PA production. This study provides an effective strategy for improving PA production in propionibacteria; this strategy may be useful for the production of other organic acids. Biotechnol. Bioeng. 2016;113: 1294-1304. © 2015 Wiley Periodicals, Inc.

Improved production of propionic acid in Propionibacterium jensenii via combinational overexpression of glycerol dehydrogenase and malate dehydrogenase from Klebsiella pneumoniae

Microbial production of propionic acid (PA), an important chemical building block used as a preservative and chemical intermediate, has gained increasing attention for its environmental friendliness over traditional petrochemical processes. In previous studies, we constructed a shuttle vector as a useful tool for engineering Propionibacterium jensenii, a potential candidate for efficient PA synthesis. In this study, we identified the key metabolites for PA synthesis in P. jensenii by examining the influence of metabolic intermediate addition on PA synthesis with glycerol as a carbon source under anaerobic conditions. We also further improved PA production via the overexpression of the identified corresponding enzymes, namely, glycerol dehydrogenase (GDH), malate dehydrogenase (MDH), and fumarate hydratase (FUM). Compared to those in wild-type P. jensenii, the activities of these enzymes in the engineered strains were 2.91- ± 0.17- to 8.12- ± 0.37-fold higher. The transcription levels of the corresponding enzymes in the engineered strains were 2.85- ± 0.19- to 8.07- ± 0.63-fold higher than those in the wild type. The coexpression of GDH and MDH increased the PA titer from 26.95 ± 1.21 g/liter in wild-type P. jensenii to 39.43 ± 1.90 g/liter in the engineered strains. This study identified the key metabolic nodes limiting PA overproduction in P. jensenii and further improved PA titers via the coexpression of GDH and MDH, making the engineered P. jensenii strain a potential industrial producer of PA.

Metabolic engineering of carbon and redox flow in the production of small organic acids

The review describes efforts toward metabolic engineering of production of organic acids. One aspect of the strategy involves the generation of an appropriate amount and type of reduced cofactor needed for the designed pathway. The ability to capture reducing power in the proper form, NADH or NADPH for the biosynthetic reactions leading to the organic acid, requires specific attention in designing the host and also depends on the feedstock used and cell energetic requirements for efficient metabolism during production. Recent work on the formation and commercial uses of a number of small mono- and diacids is discussed with redox differences, major biosynthetic precursors and engineering strategies outlined. Specific attention is given to those acids that are used in balancing cell redox or providing reduction equivalents for the cell, such as formate, which can be used in conjunction with metabolic engineering of other products to improve yields. Since a number of widely studied acids derived from oxaloacetate as an important precursor, several of these acids are covered with the general strategies and particular components summarized, including succinate, fumarate and malate. Since malate and fumarate are less reduced than succinate, the availability of reduction equivalents and level of aerobiosis are important parameters in optimizing production of these compounds in various hosts. Several other more oxidized acids are also discussed as in some cases, they may be desired products or their formation is minimized to afford higher yields of more reduced products. The placement and connections among acids in the typical central metabolic network are presented along with the use of a number of specific non-native enzymes to enhance routes to high production, where available alternative pathways and strategies are discussed. While many organic acids are derived from a few precursors within central metabolism, each organic acid has its own special requirements for high production and best compatibility with host physiology.

Engineering propionibacteria as versatile cell factories for the production of industrially important chemicals: advances, challenges, and prospects

Propionibacteria are actinobacteria consisting of two principal groups: cutaneous and dairy. Cutaneous propionibacteria are considered primary pathogens to humans, whereas dairy propionibacteria are widely used in the food and pharmaceutical industries. Increasing attention has been focused on improving the performance of dairy propionibacteria for the production of industrially important chemicals, and significant advances have been made through strain engineering and process optimization in the production of flavor compounds, nutraceuticals, and antimicrobial compounds. In addition, genome sequencing of several propionibacteria species has been completed, deepening understanding of the metabolic and physiological features of these organisms. However, the metabolic engineering of propionibacteria still faces several challenges owing to the lack of efficient genome manipulation tools and the existence of various types of strong restriction-modification systems. The emergence of systems and synthetic biology provides new opportunities to overcome these bottlenecks. In this review, we first introduce the major species of propionibacteria and their properties and provide an overview of their functions and applications. We then discuss advances in the genome sequencing and metabolic engineering of these bacteria. Finally, we discuss systems and synthetic biology approaches for engineering propionibacteria as efficient and robust cell factories for the production of industrially important chemicals.

Engineering Propionibacterium freudenreichii subsp. shermanii for enhanced propionic acid fermentation: effects of overexpressing propionyl-CoA:Succinate CoA transferase

Propionibacterium freudenreichii subsp. shermanii naturally forms propionic acid as the main fermentation product with acetate and succinate as two major by-products. In this study, overexpressing the native propionyl-CoA:succinate CoA transferase (CoAT) in P. shermanii was investigated to evaluate its effects on propionic acid fermentation with glucose, glycerol, and their mixtures as carbon source. In general, the mutant produced more propionic acid, with up to 10% increase in yield (0.62 vs. 0.56g/g) and 46% increase in productivity (0.41 vs. 0.28g/Lh), depending on the fermentation conditions. The mutant also produced less acetate and succinate, with the ratios of propionate to acetate (P/A) and succinate (P/S) in the final product increased 50% and 23%, respectively, in the co-fermentation of glucose/glycerol. Metabolic flux analysis elucidated that CoAT overexpression diverted more carbon fluxes toward propionic acid, resulting in higher propionic acid purity and a preference for glycerol over glucose as carbon source.

Vitamin B12 biosynthesis over waste frying sunflower oil as a cost effective and renewable substrate

Statistical experimental designs were used to develop a medium based on waste frying sunflower oil (WFO) and other nutrient sources for production of vitamin B12 (VB12) by Propionibacterium freudenreichii subsp. freudenreichii PTCC 1674. The production of acetic acid and propionic acid were also evaluated using the same microorganism. The amount of WFO in the media was initially optimized. The amount of 4 % w/v of oil found to be an appropriate amount for production of VB12. A Plackett Burman design was then employed to identify nutrients that have significant effect on the production of VB12 in the WFO media. Dimethylbenzimidazolyl (DMB), cobalt chloride, ferrous sulfate, and calcium chloride were the most important compounds. The level optimization of nutrients as the significant factors was finally performed using response surface methodology based on a central composite design. The model predicted that a medium containing 35.56 mg/L DMB, 14.69 mg/L CoCl2.6H2O, 5.82 mg/L FeSO4.7H2O, and 11.41 mg/L CaCl2.2H2O gives the maximum VB12 production of 2.60 mg/L. The optimized medium provides a final concentration of vitamin 170 % higher than that by the original medium. This study offers valuable insights on a cost-effective carbon source for industrial production of food-grade VB12.

Development of an industrializable fermentation process for propionic acid production

Propionic acid (PA) is a short-chain fatty acid with wide industrial application including uses in pharmaceuticals, herbicides, cosmetics, and food preservatives. As a three-carbon building block, PA also has potential as a precursor for high-volume commodity chemicals such as propylene. Currently, most PA is manufactured through petrochemical routes, which can be tied to increasing prices and volatility due to difficulty in demand forecasting and feedstock availability. Herein described are research advancements to develop an industrially feasible, renewable route to PA. Seventeen Propionibacterium strains were screened using glucose and sucrose as the carbon source to identify the best platform strain. Propionibacterium acidipropionici ATCC 4875 was selected as the platform strain and subsequent fermentation optimization studies were performed to maximize productivity and yield. Fermentation productivity was improved three-fold to exceed 2 g/l/h by densifying the inoculum source. Byproduct levels, particularly lactic and succinic acid, were reduced by optimizing fermentor headspace pressure and shear. Following achievement of commercially viable productivities, the lab-grade medium components were replaced with industrial counterparts to further reduce fermentation costs. A pure enzymatically treated corn mash (ECM) medium improved the apparent PA yield to 0.6 g/g (PA produced/glucose consumed), but it came at the cost of reduced productivity. Supplementation of ECM with cyanocobalamin restored productivity to near lab-grade media levels. The optimized ECM recipe achieved a productivity of 0.5 g/l/h with an apparent PA yield of 0.60 g/g corresponding to a media cost <1 USD/kg of PA. These improvements significantly narrow the gap between the fermentation and incumbent petrochemical processes, which is estimated to have a manufacturing cost of 0.82 USD/kg in 2017.

Improved propionic acid production from glycerol with metabolically engineered Propionibacterium jensenii by integrating fed-batch culture with a pH-shift control strategy

Propionic acid (PA) production with metabolically engineered Propionibacterium jensenii (pZGX04-gldA) was improved by integrating fed-batch culture with a two-stage pH control strategy in a 3-L fermenter. The following two-stage pH control strategy was used: the pH was controlled at 5.9 for 0-36 h and shifted to 6.5 after 36 h. The PA titer was increased to 21.43 g/L. On the basis of pH control, the influence of fed-batch culture on PA production was further investigated and the maximum PA production (34.62 g/L) was obtained when glycerol was fed at a constant rate of 3.33 mL/h from 60 to 132 h with an initial glycerol concentration of 25 g/L. Crude glycerol was then used to produce PA using the optimized strategies, and maximal PA production reached 37.26 g/L. The strategies may be useful for the production of PA by other propionibacteria species.

Propionic acid production in glycerol/glucose co-fermentation by Propionibacterium freudenreichii subsp. shermanii

Propionibacterium freudenreichii subsp. shermanii can ferment glucose and glycerol to propionic acid with acetic and succinic acids as two by-products. Propionic acid production from glucose was relatively fast (0.19 g/Lh) but gave low product yield (~0.39 g/g) and selectivity (P/A: ~2.6; P/S: ~4.8). In contrast, glycerol with a more reduced state gave a high propionic acid yield (~0.65 g/g) and selectivity (P/A: ~31; P/S: ~11) but low productivity (0.11 g/L h). On the other hand, co-fermentation of glycerol and glucose at an appropriate mass ratio gave both a high yield (0.54-0.65 g/g) and productivity (0.18-0.23 g/L h) with high product selectivity (P/A: ~14; P/S: ~10). The carbon flux distributions in the co-fermentation as affected by the ratio of glycerol/glucose were investigated. Finally, co-fermentation with cassava bagasse hydrolysate and crude glycerol in a fibrous-bed bioreactor was demonstrated, providing an efficient way for economic production of bio-based propionic acid.

Development of a Propionibacterium-Escherichia coli shuttle vector for metabolic engineering of Propionibacterium jensenii, an efficient producer of propionic acid

Propionic acid (PA) is an important chemical building block and is widely applied for organic synthesis, food, feedstuff, and pharmaceuticals. To date, the strains that can efficiently produce PA have included Propionibacterium thoenii, P. freudenreichii, and P. acidipropionici. In this report, we show that P. jensenii ATCC 4868 is also able to produce PA in much higher yields than the previously reported strains. To further improve the production capacity, a P. jensenii-Escherichia coli shuttle vector was developed for the metabolic engineering of P. jensenii. Specifically, a 6.9-kb endogenous plasmid, pZGX01, was isolated from P. acidipropionici ATCC 4875 and sequenced. Since the sequencing analysis indicated that pZGX01 could encode 11 proteins, the transcriptional levels of the corresponding genes were also investigated. Then, a P. jensenii-Escherichia coli shuttle vector was constructed using the pZGX01 plasmid, the E. coli pUC18 plasmid, and a chloramphenicol resistance gene. Interestingly, not only could the developed shuttle vector be transformed into P. jensenii ATCC 4868 and 4870, but it also could be transformed into freudenreichii ATCC 6207 subspecies of P. freudenreichii. Finally, the glycerol dehydrogenase gene (gldA) from Klebsiella pneumoniae was expressed in P. jensenii ATCC 4868 with the constructed shuttle vector. In a 3-liter batch culture, the PA production by the engineered P. jensenii ATCC 4868 strain reached 28.23 ± 1.0 g/liter, which was 26.07% higher than that produced by the wild-type strain (22.06 ± 1.2 g/liter). This result indicated that the constructed vector can be used a useful tool for metabolic engineering of P. jensenii.

Metabolic engineering of Propionibacterium freudenreichii for n-propanol production

Propionibacteria are widely used in industry for manufacturing of Swiss cheese, vitamin B₁₂, and propionic acid. However, little is known about their genetics and only a few reports are available on the metabolic engineering of propionibacteria aiming at enhancing fermentative production of vitamin B12 and propionic acid. n-Propanol is a common solvent, an intermediate in many industrial applications, and a promising biofuel. To date, no wild-type microorganism is known to produce n-propanol in sufficient quantities for industrial application purposes. In this study, a bifunctional aldehyde/alcohol dehydrogenase (adhE) was cloned from Escherichia coli and expressed in Propionibacterium freudenreichii. The mutants expressing the adhE gene converted propionyl- coenzyme A, which is the precursor for propionic acid biosynthesis, to n-propanol. The production of n-propanol was limited by NADH availability, which was improved significantly by using glycerol as the carbon source. Interestingly, the improved propanol production was accompanied by a significant increase in propionic acid productivity, indicating a positive effect of n-propanol biosynthesis on propionic acid fermentative production. To our best knowledge, this is the first report on producing n-propanol by metabolically engineered propionibacteria, which offers a novel route to produce n-propanol from renewable feedstock, and possibly a new way to boost propionic acid fermentation.

Acidic organic compounds in beverage, food, and feed production

Organic acids and their derivatives are frequently used in beverage, food, and feed production. Acidic additives may act as buffers to regulate acidity, antioxidants, preservatives, flavor enhancers, and sequestrants. Beneficial effects on animal health and growth performance have been observed when using acidic substances as feed additives. Organic acids could be classified in groups according to their chemical structure. Each group of organic acids has its own specific properties and is used for different applications. Organic acids with low molecular weight (e.g. acetic acid, lactic acid, and citric acid), which are part of the primary metabolism, are often produced by fermentation. Others are produced more economically by chemical synthesis based on petrochemical raw materials on an industrial scale (e.g. formic acid, propionic and benzoic acid). Biotechnology-based production is of interest due to legislation, consumer demand for natural ingredients, and increasing environmental awareness. In the United States, for example, biocatalytically produced esters for food applications can be labeled as "natural," whereas identical conventional acid catalyst-based molecules cannot. Natural esters command a price several times that of non-natural esters. Biotechnological routes need to be optimized regarding raw materials and yield, microorganisms, and recovery methods. New bioprocesses are being developed for organic acids, which are at this time commercially produced by chemical synthesis. Moreover, new organic acids that could be produced with biotechnological methods are under investigation for food applications.

The genome sequence of Propionibacterium acidipropionici provides insights into its biotechnological and industrial potential

BACKGROUND

Synthetic biology allows the development of new biochemical pathways for the production of chemicals from renewable sources. One major challenge is the identification of suitable microorganisms to hold these pathways with sufficient robustness and high yield. In this work we analyzed the genome of the propionic acid producer Actinobacteria Propionibacterium acidipropionici (ATCC 4875).

RESULTS

The assembled P. acidipropionici genome has 3,656,170 base pairs (bp) with 68.8% G + C content and a low-copy plasmid of 6,868 bp. We identified 3,336 protein coding genes, approximately 1000 more than P. freudenreichii and P. acnes, with an increase in the number of genes putatively involved in maintenance of genome integrity, as well as the presence of an invertase and genes putatively involved in carbon catabolite repression. In addition, we made an experimental confirmation of the ability of P. acidipropionici to fix CO2, but no phosphoenolpyruvate carboxylase coding gene was found in the genome. Instead, we identified the pyruvate carboxylase gene and confirmed the presence of the corresponding enzyme in proteome analysis as a potential candidate for this activity. Similarly, the phosphate acetyltransferase and acetate kinase genes, which are considered responsible for acetate formation, were not present in the genome. In P. acidipropionici, a similar function seems to be performed by an ADP forming acetate-CoA ligase gene and its corresponding enzyme was confirmed in the proteome analysis.

CONCLUSIONS

Our data shows that P. acidipropionici has several of the desired features that are required to become a platform for the production of chemical commodities: multiple pathways for efficient feedstock utilization, ability to fix CO2, robustness, and efficient production of propionic acid, a potential precursor for valuable 3-carbon compounds.

Multifaceted attributes of dairy propionibacteria: a review

Dairy propionibacteria are Generally Recognized as Safe (GRAS) status microorganisms which have been traditionally used for the manufacture of Swiss type cheeses. In the last two decades various added features and functionalities have been discovered and developed from these bacteria. Propionibacteria are robust organisms with remarkable adaptability to technological and physiological stress conditions. Besides, they also display a multitude of health promoting properties like modulation of gut microbiota, improved gut physiology and immunomodulation suggesting their promising probiotic potential. Propionibacteria produce an interestingly wide range of functional biomolecules like B group vitamins, trehalose, conjugated linoleic acid, propionic acid, bacteriocins, bifidogenic factors etc. These bacteria are thus now being explored for designing novel functional foods as well as for industrial production of nutraceuticals. Growing interest in these bacteria is fueled by the first whole genome sequencing of a Propionibacterium freudenreichii strain providing a platform for better understanding of various pathways and further improvement in related process technologies.

Microbial production of propionic acid from propionibacteria: current state, challenges and perspectives

Propionic acid (PA) is an important building block chemical and finds a variety of applications in organic synthesis, food, feeding stuffs, perfume, paint and pharmaceutical industries. Presently, PA is mainly produced by petrochemical route. With the continuous increase in oil prices, public concern about environmental pollution, and the consumers' desire for bio-based natural and green ingredients in foods and pharmaceuticals, PA production from propionibacteria has attracted considerable attention, and substantial progresses have been made on microbial PA production. However, production of PA by propionibacteria is facing challenges such as severe inhibition of end-products during cell growth and the formation of by-products (acetic acid and succinic acid). The integration of reverse metabolic engineering and systematic metabolic engineering provides an opportunity to significantly improve the acid tolerance of propionibacteria and reduce the formation of by-products, and makes it feasible to strengthen the commercial competition of biotechnological PA production from propionibacteria to be comparable to the petrochemical route.

Microbial production of propionic acid with Propionibacterium freudenreichii using an anion exchanger-based in situ product recovery (ISPR) process with direct and indirect contact of cells

The recovery of an inhibiting product from a bioreactor soon after its formation is an important issue in industrial bioprocess development. In the present study, the potential of the anion exchanger-based in situ product recovery (ISPR) technique for the biocatalytic production of propionic acid was discussed. The focus of the current work was the selection of a suitable configuration of metabolically active cells for application in propionic acid production. Accumulation of propionic acid in fermentation broth caused feedback inhibition of the growth and biotransformation activity of Propionibacterium freudenreichii CICC 10019. Relevant product inhibition kinetics was discussed, and the results showed that keeping the aqueous propionic acid concentration below 10.02 g L⁻¹ was an essential prerequisite for ISPR process. A batch study, in which three ISPR configuration mode designs were compared, was conducted. The comparison indicated that employing an external direct mode had significant advantages over other modes in terms of increased productivity and product yield, with a corresponding decrease in the number of downstream processing steps, as well as in substrate consumption. The fed-batch culture using an external direct mode for the continuous accumulation of propionic acid resulted in a cumulative propionic acid concentration of 62.5 g L⁻¹, with a corresponding product yield of 0.78 g propionic acid/g glucose.