Engineered fatty acid catabolism for fuel and chemical production

Castration reshapes the liver by altering fatty acid composition and metabolism in male mice

Castration promotes subcutaneous fat deposition that may be associated with metabolic adaptations in the liver. However, fatty acid composition, abundance, and metabolic characteristics of the liver after castration are not fully understood. Our results showed that surgical castration significantly reduced water and food intake, reduced liver weight, and induced liver inflammation in mice. Transcriptome analyses revealed that castration enhanced fatty acid metabolism, particularly that of arachidonic and linoleic acids metabolism. Gas chromatography-mass spectrometry analysis revealed that castration altered the composition and relative abundance of fatty acids in the liver. The relative abundances of arachidonic and linoleic acids were significantly decreased in 4-week-old castrated mice. Analysis of fatty acid synthesis- and metabolism-related genes revealed that castration enhanced the transcription of fatty acid synthesis- and oxidation-related genes. Analyzing the level of key enzymes in the β-oxidation and tricarboxylic acid cycle pathways of fatty acids in mitochondria, we found that castration enhanced the β-oxidation of fatty acids in mitochondria, and also enhanced the protein level of the rate-limiting enzyme in the tricarboxylic acid cycle pathway, isocitrate dehydrogenase 2. These results comprehensively clarify metabolic changes in liver fatty acids after castration in mice of different ages and provide a reference for understanding castration-induced fat deposition from the perspective of liver fatty acid metabolism in male mice.

Biosynthesis pathways of expanding carbon chains for producing advanced biofuels

Because the thermodynamic property is closer to gasoline, advanced biofuels (C ≥ 6) are appealing for replacing non-renewable fossil fuels using biosynthesis method that has presented a promising approach. Synthesizing advanced biofuels (C ≥ 6), in general, requires the expansion of carbon chains from three carbon atoms to more than six carbon atoms. Despite some specific biosynthesis pathways that have been developed in recent years, adequate summary is still lacking on how to obtain an effective metabolic pathway. Review of biosynthesis pathways for expanding carbon chains will be conducive to selecting, optimizing and discovering novel synthetic route to obtain new advanced biofuels. Herein, we first highlighted challenges on expanding carbon chains, followed by presentation of two biosynthesis strategies and review of three different types of biosynthesis pathways of carbon chain expansion for synthesizing advanced biofuels. Finally, we provided an outlook for the introduction of gene-editing technology in the development of new biosynthesis pathways of carbon chain expansion.

Designing artificial pathways for improving chemical production

Metabolic engineering exploits manipulation of catalytic and regulatory elements to improve a specific function of the host cell, often the synthesis of interesting chemicals. Although naturally occurring pathways are significant resources for metabolic engineering, these pathways are frequently inefficient and suffer from a series of inherent drawbacks. Designing artificial pathways in a rational manner provides a promising alternative for chemicals production. However, the entry barrier of designing artificial pathway is relatively high, which requires researchers a comprehensive and deep understanding of physical, chemical and biological principles. On the other hand, the designed artificial pathways frequently suffer from low efficiencies, which impair their further applications in host cells. Here, we illustrate the concept and basic workflow of retrobiosynthesis in designing artificial pathways, as well as the most currently used methods including the knowledge- and computer-based approaches. Then, we discuss how to obtain desired enzymes for novel biochemistries, and how to trim the initially designed artificial pathways for further improving their functionalities. Finally, we summarize the current applications of artificial pathways from feedstocks utilization to various products synthesis, as well as our future perspectives on designing artificial pathways.

Thallium(I and III) exposure leads to liver damage and disorders of fatty acid metabolism in mice

Thallium (Tl), a highly toxic and priority pollutant heavy metal, exposure can damage mitochondria and disrupt their function. The liver is the central organ that controls lipid homeostasis and contains a large number of mitochondria. So far, there is no study investigating the effects of Tl exposure on hepatic fatty acid metabolism. Here, we showed that 10 ppm of Tl(I) and Tl(III) exposures for two weeks did not significantly affect the body weight and water/food intake in mice. However, it decreased the ratio of liver/weight and induced hepatic sinus congestion and hepatocyte necrosis. Inductively coupled plasma-mass spectrometry (ICP-MS) analysis revealed Tl accumulation in the liver. Gas chromatography-mass spectrometry (GC-MS) results showed that Tl(I) exposure significantly increased hepatic C18:0 concentration, while significantly decreased the concentrations of C16:1n-7, C20:1n-9, C18:3n-6, and C20:2n-9. Tl(III) exposure significantly reduced hepatic concentrations of C20:0, C22:0, C20:1n-9, C18:3n-6, and C20:3n-6. In addition, Tl(I) exposure upregulated the genes related to antioxidation (HO-1, GPX1, and GPX4), fatty acid synthesis (FADS2 and Elovl2), and fatty acid oxidation pathway (PPARα, ACADM, ACADVL, ACAA2, and CPT1A) in the liver. Tl(III) exposure did not significantly affect the transcript levels of liver antioxidative/metabolic enzymes and fatty acid synthesis-related genes, but upregulated fatty acid oxidation pathway-related genes (CYP4A10 and CPT1A). These results suggest that Tl(I) and Tl(III) exposures can cause liver damage and disrupt hepatic fatty acid metabolism, which provide new insights into Tl exposure-induced energy depletion from the perspective of fatty acid metabolism.

Evaluation of the Efficiency of Functional Reversal of Fatty Acid Β-Oxidation in Escherichia coli upon the Action of Various Native Acyl-CoA Dehydrogenases

Abstract

Using Escherichia coli strain MG1655 lacIQ, ∆ackA-pta, ∆poxB, ∆ldhA, ∆adhE, ∆fadE, PL‑SDφ10-atoB, Ptrc-ideal-4-SDφ10-fadB, PL-SDφ10-tesB, ∆yciA as a core strain, the efficiency of the reversal of fatty acid β-oxidation upon the action of native cellular enzymes capable of serving as acyl-CoA dehydrogenases was examined. Increased expression of fadE, fabI, and ydiO/ydiQRST genes encoding the corresponding enzymes was ensured in derivatives of the core strain by substituting their native regulatory regions with artificial regulatory element Ptrc-ideal-4-SDφ10. A three-turn reversal of the cycle in the engineered recombinants was demonstrated that was accompanied by considerable secretion of butyric, caproic, and caprylic acids. The highest level of six- and eight-carbon carboxylates production was achieved upon the overexpression of the fabI gene, while the lowest levels of secretion of the corresponding compounds were demonstrated by the strain with the enhanced expression of the ydiO and ydiQRST genes. The recombinant with the individually enhanced expression of ydiO did not produce detectable amounts of the derivatives of the complete and successful β-oxidation reversal.

Role of cytochrome P450 genes of Trichoderma atroviride T23 on the resistance and degradation of dichlorvos

The Trichoderma has been extensively used to degrade the xenobiotics. In the present study, thirty-nine open reading frames of cytochrome P450 genes from T. atroviride T23 genome was cloned and it was found to be distributed in 29 families under 21 clades. Among them, 21 cytochrome P450 genes were involved in the degradation of xenobiotics. The quantitative expression of P450 genes in the presence of dichlorvos at 24 h showed 7 different expression patterns in the presence of 100 μg/mL, 300 μg/mL, 500 μg/mL and 1000 μg/mL of dichlorvos. The relative expression of P450 genes belongs to the family of TaCyp548, TaCyp620, TaCyp52, TaCyp528, TaCyp504 were upregulated at least 1-fold compared to the control. Significantly, the deletion of TaCyp548-2 reduced the concentration of 2,2-dichloroethanol. Further, it was observed that TaCyp548-2 belongs to the ω-hydroxylase family was responsible for fatty acid oxidation and the production of acetic acid, propionic acid, isobutyric acid and dibutyric acid to convert the 2,2-dichloroethanol to 2,2-dichloroethanolacetate. This study evidenced the involvement of Trichoderma P450 genes on dichlorvos degradation as an environmentally significant Biological control agent for the sustainable agriculture.

Reverse β-oxidation pathways for efficient chemical production

Microbial production of fuels, chemicals, and materials has the potential to reduce greenhouse gas emissions and contribute to a sustainable bioeconomy. While synthetic biology allows readjusting of native metabolic pathways for the synthesis of desired products, often these native pathways do not support maximum efficiency and are affected by complex regulatory mechanisms. A synthetic or engineered pathway that allows modular synthesis of versatile bioproducts with minimal enzyme requirement and regulation while achieving high carbon and energy efficiency could be an alternative solution to address these issues. The reverse β-oxidation (rBOX) pathways enable iterative non-decarboxylative elongation of carbon molecules of varying chain lengths and functional groups with only four core enzymes and no ATP requirement. Here, we describe recent developments in rBOX pathway engineering to produce alcohols and carboxylic acids with diverse functional groups, along with other commercially important molecules such as polyketides. We discuss the application of rBOX beyond the pathway itself by its interfacing with various carbon-utilization pathways and deployment in different organisms, which allows feedstock diversification from sugars to glycerol, carbon dioxide, methane, and other substrates.

Non-Photosynthetic CO2 Utilization to Increase Fatty Acid Production in Yarrowia lipolytica

Metabolic engineering of non-photosynthetic microorganisms to increase the utilization of CO₂ has been focused on as a green strategy to convert CO₂ into valuable products such as fatty acids. In this study, a CO₂ utilization pathway involving carbonic anhydrase and biotin carboxylase was formed to recycle CO₂ in the oleaginous yeast Yarrowia lipolytica, thereby increasing the production of fatty acids. In the recombinant strain in which the CO₂ utilization pathway was introduced, the production of fatty acids was 10.7 g/L, which was 1.5-fold higher than that of the wild-type strain. The resulting strain had a 1.4-fold increase in dry cell mass compared to the wild-type strain. In addition, linoleic acid was 47.7% in the fatty acid composition of the final strain, which was increased by 11.6% compared to the wild-type strain. These results can be applied as an essential technology for developing efficient and eco-friendly processes by directly utilizing CO₂.

Chemoenzymatic Production of Enantiocomplementary 2-Substituted 3-Hydroxycarboxylic Acids from L-α-Amino Acids

A two-enzyme cascade reaction plus in situ oxidative decarboxylation for the transformation of readily available canonical and non-canonical L-α-amino acids into 2-substituted 3-hydroxy-carboxylic acid derivatives is described. The biocatalytic cascade consisted of an oxidative deamination of L-α-amino acids by an L-α-amino acid deaminase from Cosenzaea myxofaciens, rendering 2-oxoacid intermediates, with an ensuing aldol addition reaction to formaldehyde, catalyzed by metal-dependent (R)- or (S)-selective carboligases namely 2-oxo-3-deoxy-l-rhamnonate aldolase (YfaU) and ketopantoate hydroxymethyltransferase (KPHMT), respectively, furnishing 3-substituted 4-hydroxy-2-oxoacids. The overall substrate conversion was optimized by balancing biocatalyst loading and amino acid and formaldehyde concentrations, yielding 36-98% aldol adduct formation and 91- 98% ee for each enantiomer. Subsequent in situ follow-up chemistry via hydrogen peroxide-driven oxidative decarboxylation afforded the corresponding 2-substituted 3-hydroxycarboxylic acid derivatives.

Opportunities and Challenges for Microbial Synthesis of Fatty Acid-Derived Chemicals (FACs)

Global warming and uneven distribution of fossil fuels worldwide concerns have spurred the development of alternative, renewable, sustainable, and environmentally friendly resources. From an engineering perspective, biosynthesis of fatty acid-derived chemicals (FACs) is an attractive and promising solution to produce chemicals from abundant renewable feedstocks and carbon dioxide in microbial chassis. However, several factors limit the viability of this process. This review first summarizes the types of FACs and their widely applications. Next, we take a deep look into the microbial platform to produce FACs, give an outlook for the platform development. Then we discuss the bottlenecks in metabolic pathways and supply possible solutions correspondingly. Finally, we highlight the most recent advances in the fast-growing model-based strain design for FACs biosynthesis.

An Ancient Chinese Herbal Decoction Containing Angelicae Sinensis Radix, Astragali Radix, Jujuba Fructus, and Zingiberis Rhizoma Recens Stimulates the Browning Conversion of White Adipocyte in Cultured 3T3-L1 Cells

Background

Abnormal storage of white adipocyte tissue (WAT) is the major factor causing obesity. The promising strategies for obesity treatment are building up the brown adipocyte tissue (BAT) and/or expedite fatty acid catabolism. Traditional Chinese Medicine (TCM) sheds light on preventing obesity. Ginger is one of the most effective herbs for antiobesity by accelerating browning WAT. To fortify the antiobesity effect of ginger, an ancient Chinese herbal decoction composed of four herbs, Angelicae Sinensis Radix (ASR), Astragali Radix (AR), Jujuba Fructus (JF), and Zingiberis Rhizoma Recens (ZRR; ginger), was tested here: this herbal formula was written in AD 1155, named as Danggui Buxue Tang (DBT₁₁₅₅). Therefore, the antiobesity function of this ancient herbal decoction was revealed in vitro by cultured 3T3-L1 cells.

Materials and Method

The lipid accumulation was detected by Oil Red O staining. Furthermore, the underlying working mechanisms of antiobesity functions of DBT₁₁₅₅ were confirmed in 3T3-L1 cells by confocal microscopy, western blot, and RT-PCR.

Results

DBT₁₁₅₅ was able to actuate brown fat-specific gene activations, which included (i) expression of PPARγ, UCP1, and PCG1α and (ii) fatty acid oxidation genes, i.e., CPT1A and HSL. The increase of browning WAT, triggered by DBT₁₁₅₅, was possibly mediated by a Ca²⁺-AMPK signaling pathway, because the application of Ca²⁺ chelator, BAMPTA-AM, reversed the effect.

Conclusion

These findings suggested that the herbal mixture DBT₁₁₅₅ could potentiate the antiobesity functions of ginger, which might have potential therapeutic implications.

Biocatalytic Oxidative Cascade for the Conversion of Fatty Acids into α-Ketoacids via Internal H2 O2 Recycling

The functionalization of bio-based chemicals is essential to allow valorization of natural carbon sources. An atom-efficient biocatalytic oxidative cascade was developed for the conversion of saturated fatty acids to α-ketoacids. Employment of P450 monooxygenase in the peroxygenase mode for regioselective α-hydroxylation of fatty acids combined with enantioselective oxidation by α-hydroxyacid oxidase(s) resulted in internal recycling of the oxidant H2 O2 , thus minimizing degradation of ketoacid product and maximizing biocatalyst lifetime. The O2 -dependent cascade relies on catalytic amounts of H2 O2 and releases water as sole by-product. Octanoic acid was converted under mild conditions in aqueous buffer to 2-oxooctanoic acid in a simultaneous one-pot two-step cascade in up to >99 % conversion without accumulation of hydroxyacid intermediate. Scale-up allowed isolation of final product in 91 % yield and the cascade was applied to fatty acids of various chain lengths (C6:0 to C10:0).

Enantioselective biocatalytic formal α-amination of hexanoic acid to l-norleucine

A three-step one-pot biocatalytic cascade enabled the enantioselective formal α-amination of hexanoic acid to l-norleucine in >97% ee.

Designing and Creating a Synthetic Omega Oxidation Pathway in Saccharomyces cerevisiae Enables Production of Medium-Chain α, ω-Dicarboxylic Acids

Medium-chain (C8–C14) α, ω-dicarboxylic acids (α, ω-DCAs), which have numerous applications as raw materials for producing various commodities and polymers in chemical industry, are mainly produced from chemical or microbial conversion of petroleum-derived alkanes or plant-derived fatty acids at present. Recently, significant attention has been gained to microbial production of medium-chain α, ω-DCAs from simple renewable sugars. Here, we designed and created a synthetic omega oxidation pathway in Saccharomyces cerevisiae to produce C10 and C12 α, ω-DCAs from renewable sugars and fatty acids by introducing a heterogeneous cytochrome P450 CYP94C1 and cytochrome reductase ATR1. Furthermore, the deletion of fatty acyl-CoA synthetase genes FAA1 and FAA4 increased the production of medium-chain α, ω-DCAs from 4.690 ± 0.088 mg/L to 12.177 ± 0.420 mg/L and enabled the production of C14 and C16 α, ω-DCAs at low percentage. But blocking β-oxidation pathway by deleting fatty-acyl coenzyme A oxidase gene POX1 and overexpressing different thioesterase genes had no significant impact on the production and the composition of α, ω-dicarboxylic acids. Overall, our study indicated the potential of microbial production of medium-chain α, ω-DCAs from renewable feedstocks using engineered yeast.

Engineering modular polyketide synthases for production of biofuels and industrial chemicals

Polyketide synthases (PKSs) are one of the most profound biosynthetic factories for producing polyketides with diverse structures and biological activities. These enzymes have been historically studied and engineered to make un-natural polyketides for drug discovery, and have also recently been explored for synthesizing biofuels and industrial chemicals due to their versatility and customizability. Here, we review recent advances in the mechanistic understanding and engineering of modular PKSs for producing polyketide-derived chemicals, and provide perspectives on this relatively new application of PKSs.

Improving Escherichia coli membrane integrity and fatty acid production by expression tuning of FadL and OmpF

Background

Construction of microbial biocatalysts for the production of biorenewables at economically viable yields and titers is frequently hampered by product toxicity. Membrane damage is often deemed as the principal mechanism of this toxicity, particularly in regards to decreased membrane integrity. Previous studies have attempted to engineer the membrane with the goal of increasing membrane integrity. However, most of these works focused on engineering of phospholipids and efforts to identify membrane proteins that can be targeted to improve fatty acid production have been unsuccessful.

Results

Here we show that deletion of outer membrane protein ompF significantly increased membrane integrity, fatty acid tolerance and fatty acid production, possibly due to prevention of re-entry of short chain fatty acids. In contrast, deletion of fadL resulted in significantly decreased membrane integrity and fatty acid production. Consistently, increased expression of fadL remarkably increased membrane integrity and fatty acid tolerance while also increasing the final fatty acid titer. This 34% increase in the final fatty acid titer was possibly due to increased membrane lipid biosynthesis. Tuning of fadL expression showed that there is a positive relationship between fadL abundance and fatty acid production. Combinatorial deletion of ompF and increased expression of fadL were found to have an additive role in increasing membrane integrity, and was associated with a 53% increase the fatty acid titer, to 2.3 g/L.

Conclusions

These results emphasize the importance of membrane proteins for maintaining membrane integrity and production of biorenewables, such as fatty acids, which expands the targets for membrane engineering.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-017-0650-8) contains supplementary material, which is available to authorized users.

Photosynthetic CO2 Conversion to Fatty Acid Ethyl Esters (FAEEs) Using Engineered Cyanobacteria

Metabolic engineering of cyanobacteria has received attention as a sustainable strategy to convert carbon dioxide to fatty acid-derived chemicals that are widely used in the food and chemical industries. Herein, Synechococcus elongatus PCC 7942, a model cyanobacterium, was engineered for the first time to produce fatty acid ethyl esters (FAEEs) from CO₂. Due to the lack of an endogenous ethanol production pathway and wax ester synthase (AftA) activity in the wild-type cyanobacterium, we metabolically engineered S. elongatus PCC 7942 by expressing heterologous AftA and introducing the ethanol pathway, resulting in detectable peaks of FAEEs. To enhance FAEE production, a heterologous phosphoketolase pathway was introduced in the FAEE-producing strain to supply acetyl-CoA. Subsequent optimization of the cyanobacterial culture with a hexadecane overlay resulted in engineered S. elongatus PCC 7942 that produced photosynthetic FAEEs (10.0 ± 0.7 mg/L/OD₇₃₀) from CO₂. This paper is the first report of photosynthetic production of FAEEs from CO₂ in cyanobacteria.