Escherichia coli as a fatty acid and biodiesel factory: current challenges and future directions

De novo biosynthesis of nylon 12 monomer ω-aminododecanoic acid

Nylon 12 is valued for its exceptional properties and diverse industrial applications. Traditional chemical synthesis of nylon 12 faces significant technical challenges and environmental concerns, while bioproduction from plant-extracted decanoic acid (DDA) raises issues related to deforestation and biodiversity loss. Here, we show the development of an engineered Escherichia coli cell factory capable of biosynthesizing the nylon 12 monomer, ω-aminododecanoic acid (ω-AmDDA), from glucose. We enable de novo biosynthesis of ω-AmDDA by introducing a thioesterase specific to C12 acyl-ACP and a multi-enzyme cascade converting DDA to ω-AmDDA. Through modular pathway engineering, redesign and dimerization enhancement of the rate-limiting P450, reconstruction of redox and energy homeostasis, and enhancement of oxidative stress tolerance, we achieve a production level of 471.5 mg/L ω-AmDDA from glucose in shake flasks. This work paves the way for sustainable nylon 12 production and offers insights for bioproduction of other fatty acid-derived products.

Recent advances in genetic technology development of oleaginous yeasts

As important chemical raw materials and potential nutritional supplements, microbial lipids play an important role in ensuring economic development, food security, and energy security. Compared with non-natural hosts, oleaginous yeasts exhibit obvious advantages in lipid yield and productivity and have great potential to be genetically engineered into an oil cell factory. The main bottleneck in the current oleaginous yeasts engineering is the lack of genetic manipulation tools. Fortunately, the rapid development of synthetic biology has provided numerous new approaches, resources, and ideas for the field. Most importantly, gene editing technology mediated by CRISPR/Cas systems has been successfully applied to some oleaginous yeasts, almost completely rewriting the development pattern of genetic manipulation technology applicable. This paper reviews recent progress in genetic technology with regard to oleaginous yeasts, with a special focus on transformation methods and genome editing tools, discussing the effects of some important genetic parts. KEY POINTS: •Contribution of microbiotechnology in food safety and biofuel by oleaginous yeasts. •Advancement of genetic manipulation and transformation for oleaginous yeasts.

Overview of the Cellular Stress Responses Involved in Fatty Acid Overproduction in E. coli

Research on microbial fatty acid metabolism started in the late 1960s, and till date, various developments have aided in elucidating the fatty acid metabolism in great depth. Over the years, synthesis of microbial fatty acid has drawn industrial attention due to its diverse applications. However, fatty acid overproduction imparts various stresses on its metabolic pathways causing a bottleneck to further increase the fatty acid yields. Numerous strategies to increase fatty acid titres in Escherichia coli by pathway modulation have already been published, but the stress generated during fatty acid overproduction is relatively less studied. Stresses like pH, osmolarity and oxidative stress, not only lower fatty acid titres, but also alter the cell membrane composition, protein expression and membrane fluidity. This review discusses an overview of fatty acid synthesis pathway and presents a panoramic view of various stresses caused due to fatty acid overproduction in E. coli. It also addresses how certain stresses like high temperature and nitrogen limitation can boost fatty acid production. This review paper also highlights the interconnections that exist between these stresses.

Enhanced Production of Fatty Acid Ethyl Ester with Engineered fabHDG Operon in Escherichia coli

Biodiesel, or fatty acid ethyl ester (FAEE), is an environmentally safe, next-generation biofuel. Conventionally, FAEE is produced by the conversion of oil/fats, obtained from plants, animals, and microorganisms, by transesterification. Recently, metabolic engineering of bacteria for ready-to-use biodiesel was developed. In Escherichia coli, it is produced by fatty acyl-carrier proteins and ethanol, with the help of thioesterase (TesB) and wax synthase (WS) enzymes. One of the foremost barriers in microbial FAEE production is the feedback inhibition of the fatty acid (FA) operon (fabHDG). Here, we studied the effect of biodiesel biosynthesis in E. coli with an engineered fabHDG operon. With a basic FAEE producing BD1 strain harboring tes and ws genes, biodiesel of 32 mg/L were produced. Optimal FAEE biosynthesis was achieved in the BD2 strain that carries an overexpressed operon (fabH, fabD, and fabG genes) and achieved up to 1291 mg/L of biodiesel, a 40-fold rise compared to the BD1 strain. The composition of FAEE obtained from the BD2 strain was 65% (C10:C2, decanoic acid ethyl ester) and 35% (C12:C2, dodecanoic acid ethyl ester). Our findings indicate that overexpression of the native FA operon, along with FAEE biosynthesis enzymes, improved biodiesel biosynthesis in E. coli.

Safflower Biodiesel: Improvement of its Oxidative Stability by Using BHA and TBHQ

Biodiesel is gaining more and more importance due to environmental issues. This way, alternative and sustainable crops as new biofuel sources are demanded. Safflower could be a sustainable raw material for biodiesel production, showing one disadvantage (as many biodiesels from vegetable oils), that is, a short oxidative stability. Consequently, the use of antioxidants to increase this parameter is mandatory. The aim of this research work was to assess the effect of two antioxidants (butylated hydroxyanisole, BHA, and tert-butylhydroquinone, TBHQ) on the oxidative stability of safflower biodiesel, which was characterized paying attention to its fatty acid methyl ester profile. For oxidative stability, the Rancimat method was used, whereas for fatty acid profile gas chromatography was selected. For the remaining parameters, the methods were followed according to the UNE-EN 14214 standard. The overall conclusion was that safflower biodiesel could comply with the standard, thanks to the use of antioxidants, with TBHQ being more effective than BHA. On the other hand, the combined use of these antioxidants did not show, especially at low concentrations, a synergic or additive effect, which makes the mixture of these antioxidants unsuitable to improve the oxidative stability.

Amaranth seeds (Amaranthus palmeri L.) as novel feedstock for biodiesel production by oleaginous yeast

The potential of lipid accumulation by oleaginous yeast Cryptococcus vishniaccii grown on amaranth seed aqueous extract (AAE) media was assessed. Maximum cell biomass productivity of 104 mg/L/h, lipid productivity of 54 mg/L/h, and lipid content of 52.31% were recorded on AAE when carbon to nitrogen (C:N) ratio increased from 134 to 147 after removal of ammonia nitrogen. The lipid droplet (LD) size (2.32 ± 0.38 μm) was visualized by fluorescence microscopy using Nile red stain indicating maximum accumulated triacylglycerol (TAG) at C:N 147. Fatty acid methyl ester (FAME) profile obtained after transesterification of extracted lipid revealed the presence of palmitic acid (16:0), palmitoleic acid (16:1), stearic acid (18:0), oleic acid (18:1), and linoleic acid (18:2). Data showed the presence of high monounsaturated fatty acid (MUFA) content (68.17%) depicting improved winter operating conditions of biodiesel. Various quality parameters of biodiesel were evaluated and compared to the American and European biodiesel standards specifications. Based on the lipid productivity, distribution of fatty acids, and evaluated properties obtained; the lipid accumulation by C. vishniaccii utilizing amaranth seeds as substrate could serve as a feasible feedstock for biodiesel production.

Monitoring of nutrient limitation in growing E. coli: a mathematical model of a ppGpp-based biosensor

Background

E. coli can be used as bacterial cell factories for production of biofuels and other useful compounds. The efficient production of the desired products requires careful monitoring of growth conditions and the optimization of metabolic fluxes. To avoid nutrient depletion and maximize product yields we suggest using a natural mechanism for sensing nutrient limitation, related to biosynthesis of an intracellular messenger - guanosine tetraphosphate (ppGpp).

Results

We propose a design for a biosensor, which monitors changes in the intracellular concentration of ppGpp by coupling it to a fluorescent output. We used mathematical modelling to analyse the intracellular dynamics of ppGpp, its fluorescent reporter, and cell growth in normal and fatty acid-producing E. coli lines. The model integrates existing mechanisms of ppGpp regulation and predicts the biosensor response to changes in nutrient state. In particular, the model predicts that excessive stimulation of fatty acid production depletes fatty acid intermediates, downregulates growth and increases the levels of ppGpp-related fluorescence.

Conclusions

Our analysis demonstrates that the ppGpp sensor can be used for early detection of nutrient limitation during cell growth and for testing productivity of engineered lines.

Electronic supplementary material

The online version of this article (10.1186/s12918-017-0490-5) contains supplementary material, which is available to authorized users.