Pathway engineering of Propionibacterium jensenii for improved production of propionic acid

New biochemical pathways for forming short-chain fatty acids during fermentation in rumen bacteria

Short-chain fatty acids (SCFA) are essential to cattle as a source of energy and for other roles in metabolism. These molecules are formed during fermentation by microbes in the rumen, but even after decades of study, the biochemical pathways responsible for forming them are not always clear. Here we review recent advances in this area and their importance for improving animal productivity. Studies of bacterial genomes have pointed to unusual biochemical pathways in rumen organisms. One study found that 8% of rumen organisms forming acetate, a major SCFA, had genes for a pathway previously unknown in bacteria. The existence of this pathway was subsequently confirmed biochemically in propionibacteria. The pathway was shown to involve 2 enzymes that convert acetyl-coenzyme A to acetate. Similar studies have revealed new enzymatic steps for forming propionate and butyrate, other major SCFA. These new steps and pathways are significant for controlling fermentation. With more precise control over SCFA, cows can be fed more precisely and potentially reach higher productivity.

Engineering propionyl-CoA pools for de novo biosynthesis of odd-chain fatty acids in microbial cell factories

Odd-chain fatty acids (OcFAs) and their derivatives have attracted great interest due to their wide applications in the food, pharmaceutical and petrochemical industries. Microorganisms can naturally de novo produce fatty acids (FAs), where mainly, even-chain with acetyl-CoA instead of odd-chain with propionyl-CoA is used as the primer. Usually, the absence of the precursor propionyl-CoA is considered the main reason that limits the efficient production of OcFAs. It is thus crucial to explore/evaluate/identify promising propionyl-CoA biosynthetic pathways to achieve large-scale biosynthesis of OcFAs. This review discusses the latest advances in microbial metabolism engineering toward producing propionyl-CoA and considers future research directions and challenges toward optimized production of OcFAs.

HIVEP3 as a potential prognostic factor promotes the development of acute myeloid leukemia

Acute myeloid leukemia (AML) is a common malignancy worldwide. Human immune deficiency virus type 1 enhancer-binding protein 3 (HIVEP3) was verified to play a vital role in types of cancers. However, the functional role of HIVEP3 in AML was rarely reported. In this study, CCK-8, colony formation assay, flow cytometry, and Trans-well chamber experiments were applied for detecting cell proliferation, apoptosis, and invasion in AML cells. The expression of proteins related to TGF-β/Smad signaling pathway was determined by western blot. Our data showed that the expression level of HIVEP3 was closely related to the risk classification and prognosis of AML patients. Moreover, HIVEP3 was highly expressed in AML patients and cells. Knockdown of HIVEP3 significantly repressed cell proliferation invasion, and enhanced cell apoptosis in HL-60 and THP-1 cells. In addition, HIVEP3 donwreglation could inhibit the TGF-β/Smad signaling pathway. TGF-β overexpression could reverse the inhibition effects of HIVEP3 knockdown on AML development and the TGF-β/Smad signaling pathway. These findings indicated that HIVEP3 contributed to the progression of AML via regulating the TGF-β/Smad signaling pathway and had a prognostic value for AML.

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.

Fermentation strategies to improve propionic acid production with propionibacterium ssp.: a review

Propionic acid (PA) is a carboxylic acid applied in a variety of processes, such as food and feed preservative, and as a chemical intermediate in the production of polymers, pesticides and drugs. PA production is predominantly performed by petrochemical routes, but environmental issues are making it necessary to use sustainable processes based on renewable materials. PA production by fermentation with the Propionibacterium genus is a promising option in this scenario, due to the ability of this genus to consume a variety of renewable carbon sources with higher productivity than other native microorganisms. However, Propionibacterium fermentation processes present important challenges that must be faced to make this route competitive, such as: a high fermentation time, product inhibition and low PA final titer, which increase the cost of product recovery. This article summarizes the state of the art regarding strategies to improve PA production by fermentation with the Propionibacterium genus. Firstly, strategies associated with environmental fermentation conditions and nutrition requirements are discussed. Subsequently, advantages and disadvantages of various strategies proposed to improve process performance (high cell concentration by immobilization or recycle, co-culture fermentation, genome shuffling, evolutive and metabolic engineering, and in situ recovery) are evaluated.

Transcriptomics and Proteomics Analyses of the Responses of Propionibacterium acidipropionici to Metabolic and Evolutionary Manipulation

We first performed a combination of metabolic engineering (deletion of ldh and poxB and overexpression of mmc) with evolutionary engineering (selection under oxygen stress, acid stress and osmotic stress) in Propionibacterium acidipropionici. The results indicated that the mutants had superior physiological activity, especially the mutant III obtained from P. acidipropionici-Δldh-ΔpoxB+mmc by evolutionary engineering, with 1.5-3.5 times higher growth rates, as well as a 37.1% increase of propionic acid (PA) titer and a 37.8% increase PA productivity compared to the wild type. Moreover, the integrative transcriptomics and proteomics analyses revealed that the differentially expressed genes (DEGs) and proteins (DEPs) in the mutant III were involved in energy metabolism, including the glycolysis pathway and tricarboxylic acid cycle (TCA cycle). These genes were up-regulated to supply increased amounts of energy and precursors for PA synthesis compared to the wild type. In addition, the down-regulation of fatty acid biosynthesis and fatty acid metabolism may indicate that the repressed metabolic flux was related to the production of PA. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was performed to verify the differential expression levels of 16 selected key genes. The results offer deep insights into the mechanism of high PA production, which provides the theoretical foundation for the construction of advanced microbial cell factories.

Microbial response to acid stress: mechanisms and applications

Microorganisms encounter acid stress during multiple bioprocesses. Microbial species have therefore developed a variety of resistance mechanisms. The damage caused by acidic environments is mitigated through the maintenance of pH homeostasis, cell membrane integrity and fluidity, metabolic regulation, and macromolecule repair. The acid tolerance mechanisms can be used to protect probiotics against gastric acids during the process of food intake, and can enhance the biosynthesis of organic acids. The combination of systems and synthetic biology technologies offers new and wide prospects for the industrial applications of microbial acid tolerance mechanisms. In this review, we summarize acid stress response mechanisms of microbial cells, illustrate the application of microbial acid tolerance in industry, and prospect the introduction of systems and synthetic biology to further explore the acid tolerance mechanisms and construct a microbial cell factory for valuable chemicals.

Bioengineering of anaerobic digestion for volatile fatty acids, hydrogen or methane production: A critical review

Anaerobic digestion (AD) is a well-established technology used for producing biogas or biomethane alongside the slurry used as biofertilizer. However, using a variety of wastes and residuals as substrate and mixed cultures in the bioreactor makes AD as one of the most complicated biochemical processes employing hydrolytic, acidogenic, hydrogen-producing, acetate-forming bacteria as well as acetoclastic and hydrogenoclastic methanogens. Hydrogen and volatile fatty acids (VFAs) including acetic, propionic, isobutyric, butyric, isovaleric, valeric and caproic acid and other carboxylic acids such as succinic and lactic acids are formed as intermediate products. As these acids are important precursors for various industries as mixed or purified chemicals, the AD process can be bioengineered to produce VFAs alongside hydrogen and therefore biogas plants can become biorefineries. The current review paper provides the theory and means to produce and accumulate VFAs and hydrogen, inhibit their conversion to methane and to extract them as the final products. The effects of pretreatment, pH, temperature, hydraulic retention time (HRT), organic loading rate (OLR), chemical methane inhibitions, and heat shocking of the inoculum on VFAs accumulation, hydrogen production, VFAs composition, and the microbial community were discussed. Furthermore, this paper highlights the possible techniques for recovery of VFAs from the fermentation media in order to minimize product inhibition as well as to supply the carboxylates for downstream procedures.

Red-Brown Pigmentation of Acidipropionibacterium jensenii Is Tied to Haemolytic Activity and cyl-Like Gene Cluster

The novel Acidipropionibacterium genus encompasses species of industrial importance but also those associated with food spoilage. In particular, Acidipropionibacterium acidipropionici, Acidipropionibacterium thoenii, and Acidipropionibacterium jensenii play an important role in food fermentation, as biopreservatives, or as potential probiotics. Notably, A. jensenii and A. thoenii can cause brown spot defects in Swiss-type cheeses, which have been tied to the rhamnolipid pigment granadaene. In the pathogenic bacterium Streptococcus agalactiae, production of granadaene depends on the presence of a cyl gene cluster, an important virulence factor linked with haemolytic activity. Here, we show that the production of granadaene in pigmented Acidipropionibacterium, including A. jensenii, A. thoenii, and Acidipropionibacterium virtanenii, is tied to haemolytic activity and the presence of a cyl-like gene cluster. Furthermore, we propose a PCR-based test, which allows pinpointing acidipropionibacteria with the cyl-like gene cluster. Finally, we present the first two whole genome sequence analyses of the A. jensenii strains as well as testing phenotypic characteristics important for industrial applications. In conclusion, the present study sheds light on potential risks associated with the presence of pigmented Acidipropionibacterium strains in food fermentation. In addition, the results presented here provide ground for development of a quick and simple diagnostic test instrumental in avoiding potential negative effects of Acidipropionibacterium strains with haemolytic activity on food quality.

Engineering Escherichia coli for propionic acid production through the Wood-Werkman cycle

Native to propionibacteria, the Wood-Werkman cycle enables propionate production via succinate decarboxylation. Current limitations in engineering propionibacteria strains have redirected attention toward the heterologous production in model organisms. Here, we report the functional expression of the Wood-Werkman cycle in Escherichia coli to enable propionate and 1-propanol production. The initial proof-of-concept attempt showed that the cycle can be used for production. However, production levels were low (0.17 mM). In silico optimization of the expression system by operon rearrangement and ribosomal-binding site tuning improved performance by fivefold. Adaptive laboratory evolution further improved performance redirecting almost 30% of total carbon through the Wood-Werkman cycle, achieving propionate and propanol titers of 9 and 5 mM, respectively. Rational engineering to reduce the generation of byproducts showed that lactate (∆ldhA) and formate (∆pflB) knockout strains exhibit an improved propionate and 1-propanol production, while the ethanol (∆adhE) knockout strain only showed improved propionate production.

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.

Production of acrylic acid and propionic acid by constructing a portion of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula in Escherichia coli

Acrylic acid and propionic acid are important chemicals requiring affordable, renewable production solutions. Here, we metabolically engineered Escherichia coli with genes encoding components of the 3-hydroxypropionate/4-hydroxybutyrate cycle from Metallosphaera sedula for conversion of glucose to acrylic and propionic acids. To construct an acrylic acid-producing pathway in E. coli, heterologous expression of malonyl-CoA reductase (MCR), malonate semialdehyde reductase (MSR), 3-hydroxypropionyl-CoA synthetase (3HPCS), and 3-hydroxypropionyl-CoA dehydratase (3HPCD) from M. sedula was accompanied by overexpression of succinyl-CoA synthetase (SCS) from E. coli. The engineered strain produced 13.28 ± 0.12 mg/L of acrylic acid. To construct a propionic acid-producing pathway, the same five genes were expressed, with the addition of M. sedula acryloyl-CoA reductase (ACR). The engineered strain produced 1430 ± 30 mg/L of propionic acid. This approach can be expanded to synthesize many important organic chemicals, creating new opportunities for the production of chemicals by carbon dioxide fixation.

Efficient production of propionic acid through high density culture with recycling cells of Propionibacterium acidipropionici

The aim of this study was to explore propionic acid production via high density culture of Propionibacterium acidipropionici and recycling of cells. Results showed that final cells of P. acidipropionici from high density culture still had high metabolic activity for reuse. Using our process, 75.9gl(-1) propionic acid was produced, which was 1.84-fold of that in fed-batch fermentation with low cell density (41.2gl(-1)); the corresponding productivity was 100.0% higher than that in fed-batch fermentation with low cell density (0.16gl(-1)h(-1)). This bioprocess may have potential for the industrial production of propionic acid.