Crude glycerol as feedstock for the sustainable production of p-hydroxybenzoate by Pseudomonas putida S12

Enhanced production of microbial levulinic acid through deletion of the levulinic acid transcriptional regulator (lvaR) in engineered Pseudomonas putida KT2440

Levulinic acid (LA) is a platform compound regarded as a promising organic intermediate for the synthesis of various chemicals such as fuel additives, plasticizers, solvents, and pharmaceuticals. Traditionally, LA is produced via acid-catalyzed dehydration and hydrolysis of lignocellulosic biomass, but this process involves challenges such as high temperatures and pressures, the use of strong acids, byproducts formation, and limitations in recovery and purification. To provide an alternative for chemical synthesis, we previously designed an integrated process to produce LA from glucose using genetically engineered Pseudomonas putida KT2440. However, as the consumption of the produced LA could not be completely prevented, its overall yield was limited. Therefore, in this study we constructed P. putida strains with additional knock-out of the lva operon genes (lvaAB, lvaE, and lvaR) in a pcaIJ knock-out strain, and introduced the aroG, asbF, and adc genes to design an LA production pathway. The pcaIJ, lvaR double knock-out strain P. putida HP205 produced 20.42 mM of LA from glycerol, and culture condition including temperature, glucose concentration, and nitrogen source were optimized. Under optimal conditions, P. putida HP205 produced 73.9 mM (8.58 g/L) LA in fed-batch fermentation. When crude glycerol was used as the substrate, both LA production and cell growth were enhanced. This study presents the impact of the LA transcriptional regulator and demonstrates a strategy for enhanced LA production in P. putida.

The Application of Multiple Strategies to Enhance Methylparaben Synthesis Using the Engineered Saccharomyces cerevisiae

Methylparaben (MP) is an important member of the paraben family of aromatic compounds, which is under great demand in the industrial market as an antibacterial agent, preservative, and feed additive, and also has potential application value in the preparation of bio-based polyetherester materials. However, the current chemical production method of MP has various problems, such as serious environmental pollution, its dependence on petrochemical resources, and the generation of different types of waste. It is of great significance to develop an environmentally friendly MP synthesis method via synthetic biology. In this work, Saccharomyces cerevisiae was used as the host to construct the biosynthetic pathway of MP and various metabolic engineering strategies were applied to break the bottlenecks in the synthesis process, including the regulation of the rate-limiting steps in the endogenous shikimate pathway, the enhancement of central carbon flux via knocking out competitive pathways and promoting precursors synthesis, and the improvement of the exogenous enzyme expression using promoter engineering. The final engineered S. cerevisiae could produce 68.59 mg/L MP in shake flasks, which was the highest titer of MP synthesized by S. cerevisiae so far. It was indicated that the strategies applied in our work were effective in promoting the synthesis of MP, which not only laid an important foundation for the industrial production of MP, but also provided a platform for the synthesis of other aromatic compounds.

Metabolic engineering of Pseudomonas chlororaphis P3 for high-level and directed production of phenazine-1,6-dicarboxylic acid from crude glycerol

Phenazine-1,6-dicarboxylic acid (PDC) is a precursor of complex substituted phenazines used as pesticides and pharmaceuticals. The PDC biosynthesis exists the low production and the high proportion of by-products phenazine-1-carboxylic acid (PCA) derivatives in Pseudomonas P3△A. Herein, PDC production were improved by systematic metabolic engineering and synthetic regulation. The directed PDC biosynthesis was achieved by introducing the isozymes of PhzF', and PCA derivatives was barely detectable. Subsequently, a high-level PDC-producing strain P3FK2E-aF'EC was obtained by co-overexpression of aroE, phzE, phzC, and aphzF' in a multi-knockout strain. Through scale-up culture, the highest PDC production and proportion reached 6,447.05 mg/L and 99.68 %, with the productivity of 89.54 mg/L·h using KB. Economically, PDC production achieved 5,584.35 mg/L accounting for 99.43 % with the highest productivity of 108.32 mg/L·h from crude glycerol. This study first achieved the directed high-level production of PDC from renewable energy, and presented a potential biosynthesis platform for PDC derivatives in Pseudomonas.

From degrader to producer: reversing the gallic acid metabolism of Pseudomonas putida KT2440

Gallic acid is a powerful antioxidant with multiple therapeutic applications, usually obtained from the acidic hydrolysis of tannins produced by many plants. As this process generates a considerable amount of toxic waste, the use of tannases or tannase-producing microorganisms has become a greener alternative over the last years. However, their high costs still impose some barriers for industrial scalability, requiring solutions that could be both greener and cost-effective. Since Pseudomonas putida KT2440 is a powerful degrader of gallic acid, its metabolism offers pathways that can be engineered to produce it from cheap and renewable carbon sources, such as the crude glycerol generated in biodiesel units. In this study, a synthetic operon with the heterologous genes aroG4, quiC and pobA* was developed and expressed in P. putida, based on an in silico analysis of possible metabolic routes, resulting in no production. Then, the sequences pcaHG and galTAPR were deleted from the genome of this strain to avoid the degradation of gallic acid and its main intermediate, the protocatechuic acid. This mutant was transformed with the vector containing the synthetic operon and was finally able to convert glycerol into gallic acid. Production assays in shaker showed a final concentration of 346.7 ± 0.004 mg L^-1 gallic acid after 72 h.

Advances and Prospects of Phenolic Acids Production, Biorefinery and Analysis

Biotechnological production of phenolic acids is attracting increased interest due to their superior antioxidant activity, as well as other antimicrobial, dietary, and health benefits. As secondary metabolites, primarily found in plants and fungi, they are effective free radical scavengers due to the phenolic group available in their structure. Therefore, phenolic acids are widely utilised by pharmaceutical, food, cosmetic, and chemical industries. A demand for phenolic acids is mostly satisfied by utilising chemically synthesised compounds, with only a low quantity obtained from natural sources. As an alternative to chemical synthesis, environmentally friendly bio-based technologies are necessary for development in large-scale production. One of the most promising sustainable technologies is the utilisation of microbial cell factories for biosynthesis of phenolic acids. In this paper, we perform a systematic comparison of the best known natural sources of phenolic acids. The advances and prospects in the development of microbial cell factories for biosynthesis of these bioactive compounds are discussed in more detail. A special consideration is given to the modern production methods and analytics of phenolic acids.

Lignin valorization meets synthetic biology

Lignin, an abundant renewable resource in nature, is a highly heterogeneous biopolymer consisting of phenylpropanoid units. It is essential for sustainable utilization of biomass to convert lignin to value-added products. However, there are technical obstacles for lignin valorization due to intrinsic heterogeneity. The emerging of synthetic biology technologies brings new opportunities for lignin breakdown and utilization. In this review, we discussed the applications of synthetic biology on lignin conversion, especially the production of value-added products, such as aromatic chemicals, ring-cleaved chemicals from lignin-derived aromatics and bio-active substances. Synthetic biology will offer new potential strategies for lignin valorization by optimizing lignin degradation enzymes, building novel artificial converting pathways, and improving the chassis of model microorganisms.

Production of methylparaben in Escherichia coli

Since the 1930s, parabens have been employed widely as preservatives in food, pharmaceutical, and personal care products. These alkyl esters of benzoic acid occur naturally in a broad range of plant species, where they are thought to enhance overall fitness through disease resistance and allelopathy. Current manufacture of parabens relies on chemical synthesis and the processing of 4-hydroxybenzoate as a precursor. A variety of bio-based production platforms have targeted 4-hydroxybenzoate for a greener alternative to chemical manufacturing, but parabens have yet to be made in microbes. Here, we deploy the plant enzyme benzoic acid carboxyl methyltransferase together with four additional recombinant enzymes to produce methylparaben in Escherichia coli. The feasibility of a tyrosine-dependent route to methylparaben is explored, establishing a framework for linking paraben production to emerging high-tyrosine E. coli strains. However, our use of a unique plant enzyme for bio-based methylparaben biosynthesis is potentially applicable to any microbial system engineered for the manufacture of 4-hydroxybenzoate.

Enhanced production of para-hydroxybenzoic acid by genetically engineered Saccharomyces cerevisiae

Saccharomyces cerevisiae is a popular organism for metabolic engineering; however, studies aiming at over-production of bio-replacement precursors for the chemical industry often fail to overcome proof-of-concept stage. When intending to show real industrial attractiveness, the challenge is twofold: formation of the target compound must be increased, while minimizing the formation of side and by-products to maximize titer, rate and yield. To tackle these, the metabolism of the organism, as well as the parameters of the process, need to be optimized. Addressing both we show that S. cerevisiae is well-suited for over-production of aromatic compounds, which are valuable in chemical industry and are particularly useful in space technology. Specifically, a strain engineered to accumulate chorismate was optimized for formation of para-hydroxybenzoic acid. Then a fed-batch bioreactor process was developed, which delivered a final titer of 2.9 g/L, a maximum rate of 18.625 mg_pHBA/(g_CDW × h) and carbon-yields of up to 3.1 mg_pHBA/g_glucose.

Global transcriptional response of solvent-sensitive and solvent-tolerant Pseudomonas putida strains exposed to toluene

Pseudomonas putida strains are generally recognized as solvent tolerant, exhibiting varied sensitivity to organic solvents. Pan-genome analysis has revealed that 30% of genes belong to the core-genome of Pseudomonas. Accessory and unique genes confer high degree of adaptability and capabilities for the degradation and synthesis of a wide range of chemicals. For the use of these microbes in bioremediation and biocatalysis, it is critical to understand the mechanisms underlying these phenotypic differences. In this study, RNA-seq analysis compared the short- and long-term responses of the toluene-sensitive KT2440 strain and the highly tolerant DOT-T1E strain. The sensitive strain activates a larger number of genes in a higher magnitude than DOT-T1E. This is expected because KT2440 bears one toluene tolerant pump, while DOT-T1E encodes three of these pumps. Both strains activate membrane modifications to reduce toluene membrane permeability. The KT2440 strain activates the TCA cycle to generate energy, while avoiding energy-intensive processes such as flagellar biosynthesis. This suggests that KT2440 responds to toluene by focusing on survival mechanisms. The DOT-T1E strain activates toluene degradation pathways, using toluene as source of energy. Among the unique genes encoded by DOT-T1E is a 70 kb island composed of genes of unknown function induced in response to toluene.

Quantitative 'Omics Analyses of Medium Chain Length Polyhydroxyalkanaote Metabolism in Pseudomonas putida LS46 Cultured with Waste Glycerol and Waste Fatty Acids

Transcriptomes and proteomes of Pseudomonas putida LS46 cultured with biodiesel-derived waste glycerol or waste free fatty acids, as sole carbon sources, were compared under conditions that were either permissive or non-permissive for synthesis of medium chain length polyhydroxyalkanoates (mcl-PHA). The objectives of this study were to elucidate mechanisms that influence activation of biopolymer synthesis, intra-cellular accumulation, and monomer composition, and determine if these were physiologically specific to the carbon sources used for growth of P. putida LS46. Active mcl-PHA synthesis by P. putida LS46 was associated with high expression levels of key mcl-PHA biosynthesis genes and/or gene products including monomer-supplying proteins, PHA synthases, and granule-associated proteins. 'Omics data suggested that expression of these genes were regulated by different genetic mechanisms in P. putida LS46 cells in different physiological states, when cultured on the two waste carbon sources. Optimal polymer production by P. putida LS46 was primarily limited by less efficient glycerol metabolism during mcl-PHA synthesis on waste glycerol. Mapping the 'Omics data to the mcl-PHA biosynthetic pathway revealed significant variations in gene expression, primarily involved in: 1) glycerol transportation; 2) enzymatic reactions that recycle reducing equivalents and produce key mcl-PHA biosynthesis pathway intermediates (e.g. NADH/NADPH, acetyl-CoA). Active synthesis of mcl-PHAs was observed during exponential phase in cultures with waste free fatty acids, and was associated with the fatty acid beta-oxidation pathway. A putative Thioesterase in the beta-oxidation pathway that may regulate the level of fatty acid beta-oxidation intermediates, and thus carbon flux to mcl-PHA biosynthesis, was highly up-regulated. Finally, the data suggested that differences in expression of selected fatty acid metabolism and mcl-PHA monomer-supplying enzymes may play a role in determining the monomer composition of mcl-PHA polymers. Understanding the relationships between genome content, gene and gene product expression, and how these factors influence polymer synthesis, will aid in optimization of mcl-PHA production by P. putida LS46 using biodiesel waste streams.

Effects of impurities in biodiesel-derived glycerol on growth and expression of heavy metal ion homeostasis genes and gene products in Pseudomonas putida LS46

Biodiesel production-derived waste glycerol (WG) was previously investigated as potential carbon source for medium chain length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida LS46. In this study, we evaluated the effect of impurities in the WG on P. putida LS46 physiology during exponential growth and corresponding changes in transcription and protein expression profiles compared with cells grown on pure, reagent grade glycerol. High concentration of metal ions, such as Na(+), and numbers of heavy metals ion, such as copper, ion, zinc, were detected in biodiesel-derived WG. Omics analysis from the corresponding cultures suggested altered expression of genes involved in transport and metabolism of ammonia and heavy metal ions. Expression of three groups of heavy metal homeostasis genes was significantly changed (mostly upregulated) in WG cultures and included the following: copper-responded cluster 1 and 2 genes, primarily containing cusABC; two copies of copAB and heavy metal translocating P-type ATPase; Fur-regulated, TonB-dependent siderophore receptor; and several cobalt/zinc/cadmium transporters. Expression of these genes suggests regulation of intracellular concentrations of heavy metals during growth on biodiesel-derived glycerol. Finally, a number of genes involved in adapting to, or metabolizing free fatty acids and other nonheavy metal contaminants, such as Na(+), were also upregulated in P. putida LS46 grown on biodiesel-derived glycerol.

Evaluation of medium-chain-length polyhydroxyalkanoate production by Pseudomonas putida LS46 using biodiesel by-product streams

Medium-chain-length polyhydroxyalkanoate (mcl-PHA) production by Pseudomonas putida LS46 was analyzed in shake-flask-based batch reactions, using pure chemical-grade glycerol (PG), biodiesel-derived "waste" glycerol (WG), and biodiesel-derived "waste" free fatty acids (WFA). Cell growth, substrate consumption, mcl-PHA accumulation within the cells, and the monomer composition of the synthesized biopolymers were monitored. The patterns of mcl-PHA synthesis in P. putida LS46 cells grown on PG and WG were similar but differed from that of cells grown with WFA. Polymer accumulation in glycerol-based cultures was stimulated by nitrogen limitation and plateaued after 48 h in both PG and WG cultures, with a total accumulation of 17.9% cell dry mass and 16.3% cell dry mass, respectively. In contrast, mcl-PHA synthesis was independent of nitrogen concentration in P. putida LS46 cells cultured with WFA, which accumulated to 29% cell dry mass. In all cases, the mcl-PHAs synthesized consisted primarily of 3-hydroxyoctanoate (C(8)) and 3-hydroxydecanoate (C(10)). WG and WFA supported similar or greater cell growth and mcl-PHA accumulation than PG under the experimental conditions used. These results suggest that biodiesel by-product streams could be used as low-cost carbon sources for sustainable mcl-PHA production.