A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes

Expanding the synthetic biology toolbox of Cupriavidus necator for establishing fatty acid production

The Gram-negative betaproteobacterium Cupriavidus necator is a chemolithotroph that can convert carbon dioxide into biomass. Cupriavidus necator has been engineered to produce a variety of high-value chemicals in the past. However, there is still a lack of a well-characterized toolbox for gene expression and genome engineering. Development and optimization of biosynthetic pathways in metabolically engineered microorganisms necessitates control of gene expression via functional genetic elements such as promoters, ribosome binding sites (RBSs), and codon optimization. In this work, a set of inducible and constitutive promoters were validated and characterized in C. necator, and a library of RBSs was designed and tested to show a 50-fold range of expression for green fluorescent protein (gfp). The effect of codon optimization on gene expression in C. necator was studied by expressing gfp and mCherry genes with varied codon-adaptation indices and was validated by expressing codon-optimized variants of a C12-specific fatty acid thioesterase to produce dodecanoic acid. We discuss further hurdles that will need to be overcome for C. necator to be widely used for biosynthetic processes.

Ketosynthase mutants enable short-chain fatty acid biosynthesis in E. coli

Cells build fatty acids in tightly regulated assembly lines, or fatty acid synthases (FASs), in which β-ketoacyl-acyl carrier protein (ACP) synthases (KSs) catalyze sequential carbon-carbon bond forming reactions that generate acyl-ACPs of varying lengths-precursors for a diverse set of lipids and oleochemicals. To date, most efforts to control fatty acid synthesis in engineered microbes have focused on modifying termination enzymes such as acyl-ACP thioesterases, which release free fatty acids from acyl-ACPs. Changes to the substrate specificity of KSs provide an alternative-and, perhaps, more generalizable-approach that focuses on controlling the acyl-ACPs available for downstream products. This study combines mutants of FabF and FabB, the two elongating KSs of the E. coli FAS, with in vitro and in vivo analyses to explore the use of KS mutants to control fatty acid synthesis. In vitro, single amino acid substitutions in the gating loop and acyl binding pocket of FabF shifted the product profiles of reconstituted FASs toward short chains and showed that KS mutants, alone, can cause large shifts in average length (i.e., 6.5-13.5). FabB, which is essential for unsaturated fatty acid synthesis, blunted this effect in vivo, but exogenously added cis-vaccenic acid (C18:1) enabled sufficient transcriptional repression of FabB to restore it. Strikingly, a single mutant of FabB afforded titers of octanoic acid as high as those generated by an engineered thioesterase. Findings indicate that fatty acid synthesis must be decoupled from microbial growth to resolve the influence of KS mutants on fatty acid profiles but show that these mutants offer a versatile approach for tuning FAS outputs.

Conformational Changes of Acyl Carrier Protein Switch the Chain Length Preference of Acyl-ACP Thioesterase ChFatB2

Microbial fatty acids are synthesized by Type II fatty acid synthase and could be tailored by acyl-ACP thioesterase. With the prospects of medium-chain fatty-acid-derivative biofuels, the selectivity of thioesterase has been studied to control the fatty acid product chain length. Here, we report an alternative approach by manipulating the acyl carrier protein portion of acyl-ACP to switch the chain length propensity of the thioesterase. It was demonstrated that ChFatB2 from Cuphea hookeriana preferred C10-ACP to C8-ACP with ACP from E. coli, while converting preference to C8-ACP with ACP from Cuphea lanceolate. Circular dichroism (CD) results indicated that the C8-EcACP encountered a 34.4% α-helix increment compared to C10-EcACP, which resulted in an approximate binding affinity decrease in ChFatB2 compared to C10-EcACP. Similarly, the C10-ClACP2 suffered a 45% decrease in helix content compared to C8–ClACP2, and the conformational changes resulted in an 18% binding affinity decline with ChFatB2 compared with C10-ClACP2. In brief, the study demonstrates that the ACP portion of acyl-ACP contributes to the selectivity of acyl-ACP thioesterase, and the conformational changes of EcACP and ClACP2 switch the chain length preference of ChFatB2 between C8 and C10. The result provides fundamentals for the directed synthesis of medium-chain fatty acids based on regulating the conformational changes of ACPs.

Evaluation of strategies to narrow the product chain-length distribution of microbially synthesized free fatty acids

The dominant strategy for tailoring the chain-length distribution of free fatty acids (FFA) synthesized by heterologous hosts is expression of a selective acyl-acyl carrier protein (ACP) thioesterase. However, few of these enzymes can generate a precise (greater than 90% of a desired chain-length) product distribution when expressed in a microbial or plant host. The presence of alternative chain-lengths can complicate purification in situations where blends of fatty acids are not desired. We report the assessment of several strategies for improving the dodecanoyl-ACP thioesterase from the California bay laurel to exhibit more selective production of medium-chain free fatty acids to near exclusivity. We demonstrated that matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS) was an effective library screening technique for identification of thioesterase variants with favorable shifts in chain-length specificity. This strategy proved to be a more effective screening technique than several rational approaches discussed herein. With this data, we isolated four thioesterase variants which exhibited a more selective FFA distribution over wildtype when expressed in the fatty acid accumulating E. coli strain, RL08. We then combined mutations from the MALDI isolates to generate BTE-MMD19, a thioesterase variant capable of producing free fatty acids consisting of 90% of C₁₂ products. Of the four mutations which conferred a specificity shift, we noted that three affected the shape of the binding pocket, while one occurred on the positively charged acyl carrier protein landing pad. Finally, we fused the maltose binding protein (MBP) from E. coli to the N - terminus of BTE-MMD19 to improve enzyme solubility and achieve a titer of 1.9 g per L of twelve-carbon fatty acids in a shake flask.

Determinants of substrate specificity in a catalytically diverse family of acyl-ACP thioesterases from plants

BACKGROUND

ACYL-LIPID THIOESTERASES (ALTs) are a subclass of plastid-localized, fatty acyl-acyl carrier protein (ACP) thioesterase enzymes from plants. They belong to the single hot dog-fold protein family. ALT enzymes generate medium-chain (C6-C14) and C16 fatty acids, methylketone precursors (β-keto fatty acids), and 3-hydroxy fatty acids when expressed heterologously in E. coli. The diverse substrate chain-length and oxidation state preferences of ALTs set them apart from other plant acyl-ACP thioesterases, and ALTs show promise as metabolic engineering tools to produce high-value medium-chain fatty acids and methylketones in bacterial or plant systems. Here, we used a targeted motif-swapping approach to explore connections between ALT protein sequence and substrate specificity. Guided by comparative motif searches and computational modelling, we exchanged regions of amino acid sequence between ALT-type thioesterases from Arabidopsis thaliana, Medicago truncatula, and Zea mays to create chimeric ALT proteins.

RESULTS

Comparing the activity profiles of chimeric ALTs in E. coli to their wild-type counterparts led to the identification of interacting regions within the thioesterase domain that shape substrate specificity and enzyme activity. Notably, the presence of a 31-CQH[G/C]RH-36 motif on the central α-helix was shown to shift chain-length specificity towards 12-14 carbon chains, and to be a core determinant of substrate specificity in ALT-type thioesterases with preference for 12-14 carbon 3-hydroxyacyl- and β-ketoacyl-ACP substrates. For an ALT containing this motif to be functional, an additional 108-KXXA-111 motif and compatible sequence spanning aa77-93 of the surrounding β-sheet must also be present, demonstrating that interactions between residues in these regions of the catalytic domain are critical to thioesterase activity. The behaviour of chimeric enzymes in E. coli also indicated that aa77-93 play a significant role in dictating whether an ALT will prefer ≤10-carbon or ≥ 12-carbon acyl chain-lengths, and aa91-96 influence selectivity for substrates of fully or partially reduced oxidation states. Additionally, aa64-67 on the hot dog-fold β-sheet were shown to be important for enabling an ALT to act on 3-hydroxy fatty acyl-ACP substrates.

CONCLUSIONS

By revealing connections between thioesterase sequence and substrate specificity, this study is an advancement towards engineering recombinant ALTs with product profiles suited for specific applications.

Utilizing Alcohol for Alkane Biosynthesis by Introducing a Fatty Alcohol Dehydrogenase

Alkanes produced by microorganisms are expected to be an alternative to fossil fuels as an energy source. Microbial synthesis of alkanes involves the formation of fatty aldehydes via fatty acyl coenzyme A (acyl-CoA) intermediates derived from fatty acid metabolism, followed by aldehyde decarbonylation to generate alkanes. Advancements in metabolic engineering have enabled the construction of such pathways in various microorganisms, including Escherichia coli. However, endogenous aldehyde reductases in the host microorganisms are highly active in converting fatty aldehydes to fatty alcohols, limiting the substrate pool for alkane production. To reuse the alcohol by-product, a screening of fatty alcohol-assimilating microorganisms was conducted, and a bacterial strain, Pantoea sp. strain 7-4, was found to convert 1-tetradecanol to tetradecanal. From this strain, an alcohol dehydrogenase, PsADH, was purified and found to be involved in 1-tetradecanol-oxidizing reaction. Subsequent heterologous expression of the PsADH gene in E. coli was conducted, and recombinant PsADH was purified for a series of biochemical characterizations, including cofactors, optimal reaction conditions, and kinetic parameters. Furthermore, direct alkane production from alcohol was achieved in E. coli by coexpressing PsADH with a cyanobacterial aldehyde-deformylating oxygenase and a reducing system, including ferredoxin and ferredoxin reductase, from Nostoc punctiforme PCC73102. The alcohol-aldehyde-alkane synthetic route established in this study will provide a new approach to utilizing fatty alcohols for the production of alkane biofuel. IMPORTANCE Alcohol dehydrogenases are a group of enzymes found in many organisms. Unfortunately, studies on these enzymes mainly focus on their activities toward short-chain alcohols. In this study, we discovered an alcohol dehydrogenase, PsADH, from the bacterium Pantoea sp. 7-4, which can oxidize 1-tetradecanol to tetradecanal. The medium-chain aldehyde products generated by this enzyme can serve as the substrate of aldehyde-deformylating oxygenase to produce alkanes. The enzyme found in this study can be applied to the biosynthetic pathway involving the formation of medium-chain aldehydes to produce alkanes and other valuable compounds.

Combinatorial Metabolic Engineering Strategies for the Enhanced Production of Free Fatty Acids in Escherichia coli

In this study, we evaluated the effects of several metabolic engineering strategies in a systematic and combinatorial manner to enhance the free fatty acid (FFA) production in Escherichia coli. The strategies included (i) overexpression of mutant thioesterase I ('TesA^R64C) to efficiently release the FFAs from fatty acyl-ACP; (ii) coexpression of global regulatory protein FadR; (iii) heterologous expression of methylmalonyl-CoA carboxyltransferase and phosphoenolpyruvate carboxylase to synthesize fatty acid precursor molecule malonyl-CoA; and (iv) disruption of genes associated with membrane proteins (GusC, MdlA, and EnvR) to improve the cellular state and export the FFAs outside the cell. The synergistic effects of these genetic modifications in strain SBF50 yielded 7.2 ± 0.11 g/L FFAs at the shake flask level. In fed-batch cultivation under nitrogen-limiting conditions, strain SBF50 produced 33.6 ± 0.02 g/L FFAs with a productivity of 0.7 g/L/h from glucose, which is the maximum titer reported in E. coli to date. Combinatorial metabolic engineering approaches can prove to be highly useful for the large-scale production of FA-derived chemicals and fuels.

Ca:Mg ratio, medium-chain fatty acids, and the gut microbiome

BACKGROUND & AIMS

Ketogenic medium-chain fatty acids (MCFAs) with profound health benefits are commonly found in dairy products, palm kernel oil and coconut oil. We hypothesize that magnesium (Mg) supplementation leads to enhanced gut microbial production of MCFAs and, in turn, increased circulating MCFAs levels.

METHODS

We tested this hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (NCT01105169), a double-blind 2 × 2 factorial randomized controlled trial enrolling 240 participants. Six 24-h dietary recalls were performed for all participants at the baseline and during the intervention period. Based on the baseline 24-h dietary recalls, the Mg treatment used a personalized dose of Mg supplementation that would reduce the calcium (Ca): Mg intake ratio to around 2.3. We measured plasma MCFAs, sugars, ketone bodies and tricarboxylic acid cycle (TCA cycle) metabolites using the Metabolon's global Precision Metabolomics™ LC-MS platform. Whole-genome shotgun metagenomics (WGS) sequencing was performed to assess microbiota in stool samples, rectal swabs, and rectal biopsies.

RESULTS

Personalized Mg treatment (mean dose 205.58 mg/day with a range from 77.25 to 389.55 mg/day) significantly increased the plasma levels of C7:0, C8:0, and combined C7:0 and C8:0 by 18.45%, 25.28%, and 24.20%, respectively, compared to 14.15%, 10.12%, and 12.62% decreases in the placebo arm. The effects remain significant after adjusting for age, sex, race and baseline level (P = 0.0126, P = 0.0162, and P = 0.0031, respectively) and FDR correction at 0.05 (q = 0.0324 for both C7:0 and C8:0). Mg treatment significantly reduced the plasma level of sucrose compared to the placebo arm (P = 0.0036 for multivariable-adjusted and P = 0.0216 for additional FDR correction model) whereas alterations in daily intakes of sucrose, fructose, glucose, maltose and C8:0 from baseline to the end of trial did not differ between two arms. Mediation analysis showed that combined C7:0 and C8:0 partially mediated the effects of Mg treatment on total and individual ketone bodies (P for indirect effect = 0.0045, 0.0043, and 0.03, respectively). The changes in plasma levels of C7:0 and C8:0 were significantly and positively correlated with the alterations in stool microbiome α diversity (r = 0.51, p = 0.0023 and r = 0.34, p = 0.0497, respectively) as well as in stool abundance for the signatures of MCFAs-related microbiota with acyl-ACP thioesterase gene producing C7:0 (r = 0.46, p = 0.0067) and C8:0 (r = 0.49, p = 0.003), respectively, following Mg treatment.

CONCLUSIONS

Optimizing Ca:Mg intake ratios to around 2.3 through 12-week personalized Mg supplementation leads to increased circulating levels of MCFAs (i.e. C7:0 and C8:0), which is attributed to enhanced production from gut microbial fermentation and, maybe, sucrose consumption.

Reconstruction and optimization of a Pseudomonas putida-Escherichia coli microbial consortium for mcl-PHA production from lignocellulosic biomass

The demand for non-petroleum-based, especially biodegradable plastics has been on the rise in the last decades. Medium-chain-length polyhydroxyalkanoate (mcl-PHA) is a biopolymer composed of 6–14 carbon atoms produced from renewable feedstocks and has become the focus of research. In recent years, researchers aimed to overcome the disadvantages of single strains, and artificial microbial consortia have been developed into efficient platforms. In this work, we reconstructed the previously developed microbial consortium composed of engineered Pseudomonas putida KT∆ABZF (p2-a-J) and Escherichia coli ∆4D (ACP-SCLAC). The maximum titer of mcl-PHA reached 3.98 g/L using 10 g/L glucose, 5 g/L octanoic acid as substrates by the engineered P. putida KT∆ABZF (p2-a-J). On the other hand, the maximum synthesis capacity of the engineered E. coli ∆4D (ACP-SCLAC) was enhanced to 3.38 g/L acetic acid and 0.67 g/L free fatty acids (FFAs) using 10 g/L xylose as substrate. Based on the concept of “nutrient supply-detoxification,” the engineered E. coli ∆4D (ACP-SCLAC) provided nutrient for the engineered P. putida KT∆ABZF (p2-a-J) and it acted to detoxify the substrates. Through this functional division and rational design of the metabolic pathways, the engineered P. putida-E. coli microbial consortium could produce 1.30 g/L of mcl-PHA from 10 g/L glucose and xylose. Finally, the consortium produced 1.02 g/L of mcl-PHA using lignocellulosic hydrolysate containing 10.50 g/L glucose and 10.21 g/L xylose as the substrate. The consortium developed in this study has good potential for mcl-PHA production and provides a valuable reference for the production of high-value biological products using inexpensive carbon sources.

A dual cellular-heterogeneous catalyst strategy for the production of olefins from glucose

Living systems provide a promising approach to chemical synthesis, having been optimized by evolution to convert renewable carbon sources, such as glucose, into an enormous range of small molecules. However, a large number of synthetic structures can still be difficult to obtain solely from cells, such as unsubstituted hydrocarbons. In this work, we demonstrate the use of a dual cellular-heterogeneous catalytic strategy to produce olefins from glucose using a selective hydrolase to generate an activated intermediate that is readily deoxygenated. Using a new family of iterative thiolase enzymes, we genetically engineered a microbial strain that produces 4.3 ± 0.4 g l^-1 of fatty acid from glucose with 86% captured as 3-hydroxyoctanoic and 3-hydroxydecanoic acids. This 3-hydroxy substituent serves as a leaving group that enables heterogeneous tandem decarboxylation-dehydration routes to olefinic products on Lewis acidic catalysts without the additional redox input required for enzymatic or chemical deoxygenation of simple fatty acids.

Machine learning-guided acyl-ACP reductase engineering for improved in vivo fatty alcohol production

Alcohol-forming fatty acyl reductases (FARs) catalyze the reduction of thioesters to alcohols and are key enzymes for microbial production of fatty alcohols. Many metabolic engineering strategies utilize FARs to produce fatty alcohols from intracellular acyl-CoA and acyl-ACP pools; however, enzyme activity, especially on acyl-ACPs, remains a significant bottleneck to high-flux production. Here, we engineer FARs with enhanced activity on acyl-ACP substrates by implementing a machine learning (ML)-driven approach to iteratively search the protein fitness landscape. Over the course of ten design-test-learn rounds, we engineer enzymes that produce over twofold more fatty alcohols than the starting natural sequences. We characterize the top sequence and show that it has an enhanced catalytic rate on palmitoyl-ACP. Finally, we analyze the sequence-function data to identify features, like the net charge near the substrate-binding site, that correlate with in vivo activity. This work demonstrates the power of ML to navigate the fitness landscape of traditionally difficult-to-engineer proteins.

Recent Progress and Trends in the Development of Microbial Biofuels from Solid Waste—A Review

This review covers the recent progress in the design and application of microbial biofuels, assessing the advancement of genetic engineering undertakings and their marketability, and lignocellulosic biomass pretreatment issues. Municipal solid waste (MSW) is a promising sustainable biofuel feedstock due to its high content of lignocellulosic fiber. In this review, we compared the production of fatty alcohols, alkanes, and n-butanol from residual biogenic waste and the environmental/economic parameters to that of conventional biofuels. New synthetic biology tools can be used to engineer fermentation pathways within micro-organisms to produce long-chain alcohols, isoprenoids, long-chain fatty acids, and esters, along with alkanes, as substitutes to petroleum-derived fuels. Biotechnological advances have struggled to address problems with bioethanol, such as lower energy density compared to gasoline and high corrosive and hygroscopic qualities that restrict its application in present infrastructure. Biofuels derived from the organic fraction of municipal solid waste (OFMSW) may have less environmental impacts compared to traditional fuel production, with the added benefit of lower production costs. Unfortunately, current advanced biofuel production suffers low production rates, which hinders commercial scaling-up efforts. Microbial-produced biofuels can address low productivity while increasing the spectrum of produced bioenergy molecules.

Analytical methods in fatty acid analysis for microbial applications: the recent trends

Fatty acids are among the most important components of many biological systems and have been highlighted in many research fields in recent decades. In the food industry, it is important to check the amount and types of fatty acids in edible oils, beverages and other foods products, and checking the fatty acids parameters are among the quality control parameters for those products. In medical applications, investigation of fatty acids in biological samples and comparing imbalances in them can help to diagnose some diseases. On the other hand, the development of cell factories for the production of biofuels and other valuable chemicals requires the accurate analysis of fatty acids, which serve as precursors in development of those products. As a result, given all these different applications of fatty acids, rapid and accurate methods for characterization and quantification of fatty acids are essential. In recent years, various methods for the analysis of fatty acids have been proposed, which according to the specific purpose of the analysis, some of them can be used with consideration of speed, accuracy and cost. In this article, the available methods for the analysis of fatty acids are reviewed with a special emphasis on the analysis of microbial samples to pave the way for more widespread metabolic engineering research.

Genome-scale target identification in Escherichia coli for high-titer production of free fatty acids

To construct a superior microbial cell factory for chemical synthesis, a major challenge is to fully exploit cellular potential by identifying and engineering beneficial gene targets in sophisticated metabolic networks. Here, we take advantage of CRISPR interference (CRISPRi) and omics analyses to systematically identify beneficial genes that can be engineered to promote free fatty acids (FFAs) production in Escherichia coli. CRISPRi-mediated genetic perturbation enables the identification of 30 beneficial genes from 108 targets related to FFA metabolism. Then, omics analyses of the FFAs-overproducing strains and a control strain enable the identification of another 26 beneficial genes that are seemingly irrelevant to FFA metabolism. Combinatorial perturbation of four beneficial genes involving cellular stress responses results in a recombinant strain ihfA^L−-aidB⁺-ryfA^M−-gadA^H−, producing 30.0 g L⁻¹ FFAs in fed-batch fermentation, the maximum titer in E. coli reported to date. Our findings are of help in rewiring cellular metabolism and interwoven intracellular processes to facilitate high-titer production of biochemicals.

Identification of gene targets is one of the major challenges to construct superior microbial cell factory for chemical synthesis. Here, the authors employ CRISPRi and omics analyses for genome-scale target genes identification for high-titer production of free fatty acids in E. coli.

The Role of Metabolic Engineering Technologies for the Production of Fatty Acids in Yeast

Simple Summary

Metabolic engineering involves the sustainable production of high-value products. E. coli and yeast, in particular, are used for such processes. Using metabolic engineering, the biosynthetic pathways of these cells are altered to obtain a high production of desired products. Fatty acids (FAs) and their derivatives are products produced using metabolic engineering. However, classical methods used for engineering yeast metabolic pathways for the production of fatty acids and their derivatives face problems such as the low supply of key precursors and product tolerance. This review introduces the different ways FAs are being produced in E. coli and yeast and the genetic manipulations for enhanced production of FAs. The review also summarizes the latest techniques (i.e., CRISPR–Cas and synthetic biology) for developing FA-producing yeast cell factories.

Abstract

Metabolic engineering is a cutting-edge field that aims to produce simple, readily available, and inexpensive biomolecules by applying different genetic engineering and molecular biology techniques. Fatty acids (FAs) play an important role in determining the physicochemical properties of membrane lipids and are precursors of biofuels. Microbial production of FAs and FA-derived biofuels has several advantages in terms of sustainability and cost. Conventional yeast Saccharomyces cerevisiae is one of the models used for FA synthesis. Several genetic manipulations have been performed to enhance the citrate accumulation and its conversation into acetyl-CoA, a precursor for FA synthesis. Success has been achieved in producing different chemicals, including FAs and their derivatives, through metabolic engineering. However, several hurdles such as slow growth rate, low oleaginicity, and cytotoxicity are still need to be resolved. More robust research needs to be conducted on developing microbes capable of resisting diverse environments, chemicals, and cost-effective feed requirements. Redesigning microbes to produce FAs with cutting-edge synthetic biology and CRISPR techniques can solve these problems. Here, we reviewed the technological progression of metabolic engineering techniques and genetic studies conducted on S. cerevisiae, making it suitable as a model organism and a great candidate for the production of biomolecules, especially FAs.

Animal Fatty Acid Synthase: A Chemical Nanofactory

Fatty acids are crucial molecules for most living beings, very well spread and conserved across species. These molecules play a role in energy storage, cell membrane architecture, and cell signaling, the latter through their derivative metabolites. De novo synthesis of fatty acids is a complex chemical process that can be achieved either by a metabolic pathway built by a sequence of individual enzymes, such as in most bacteria, or by a single, large multi-enzyme, which incorporates all the chemical capabilities of the metabolic pathway, such as in animals and fungi, and in some bacteria. Here we focus on the multi-enzymes, specifically in the animal fatty acid synthase (FAS). We start by providing a historical overview of this vast field of research. We follow by describing the extraordinary architecture of animal FAS, a homodimeric multi-enzyme with seven different active sites per dimer, including a carrier protein that carries the intermediates from one active site to the next. We then delve into this multi-enzyme's detailed chemistry and critically discuss the current knowledge on the chemical mechanism of each of the steps necessary to synthesize a single fatty acid molecule with atomic detail. In line with this, we discuss the potential and achieved FAS applications in biotechnology, as biosynthetic machines, and compare them with their homologous polyketide synthases, which are also finding wide applications in the same field. Finally, we discuss some open questions on the architecture of FAS, such as their peculiar substrate-shuttling arm, and describe possible reasons for the emergence of large megasynthases during evolution, questions that have fascinated biochemists from long ago but are still far from answered and understood.

Improved Bioproduction of 1-Octanol Using Engineered Synechocystis sp. PCC 6803

1-Octanol has gained interest as a chemical precursor for both high and low value commodities including fuel, solvents, surfactants, and fragrances. By harnessing the power from sunlight and CO₂ as carbon source, cyanobacteria has recently been engineered for renewable production of 1-octanol. The productivity, however, remained low. In the present work, we report efforts to further improve the 1-octanol productivity. Different N-terminal truncations were evaluated on three thioesterases from different plant species, resulting in several candidate thioesterases with improved activity and selectivity toward octanoyl-ACP. The structure/function trials suggest that current knowledge and/or state-of-the art computational tools are insufficient to determine the most appropriate cleavage site for thioesterases in Synechocystis. Additionally, by tuning the inducer concentration and light intensity, we further improved the 1-octanol productivity, reaching up to 35% (w/w) carbon partitioning and a titer of 526 ± 5 mg/L 1-octanol in 12 days. Long-term cultivation experiments demonstrated that the improved strain can be stably maintained for at least 30 days and/or over ten times serial dilution. Surprisingly, the improved strain was genetically stable in contrast to earlier strains having lower productivity (and hence a reduced chance of reaching toxic product concentrations). Altogether, improved enzymes and environmental conditions (e.g., inducer concentration and light intensity) substantially increased the 1-octanol productivity. When cultured under continuous conditions, the bioproduction system reached an accumulative titer of >3.5 g/L 1-octanol over close to 180 days.

Biosynthesis of Commodity Chemicals From Oil Palm Empty Fruit Bunch Lignin

Lignin is one of the most abundant natural resources that can be exploited for the bioproduction of value-added commodity chemicals. Oil palm empty fruit bunches (OPEFBs), byproducts of palm oil production, are abundant lignocellulosic biomass but largely used for energy and regarded as waste. Pretreatment of OPEFB lignin can yield a mixture of aromatic compounds that can potentially serve as substrates to produce commercially important chemicals. However, separation of the mixture into desired individual substrates is required, which involves expensive steps that undermine the utility of OPEFB lignin. Here, we report successful engineering of microbial hosts that can directly utilize heterogeneous mixtures derived from OPEFB lignin to produce commodity chemicals, adipic acid and levulinic acid. Furthermore, the corresponding bioconversion pathway was placed under a genetic controller to autonomously activate the conversion process as the cells are fed with a depolymerized OPEFB lignin mixture. This study demonstrates a simple, one-pot biosynthesis approach that directly utilizes derivatives of agricultural waste to produce commodity chemicals.

Metabolic Engineering for Unusual Lipid Production in Yarrowia lipolytica

Using microorganisms as lipid-production factories holds promise as an alternative method for generating petroleum-based chemicals. The non-conventional yeast Yarrowia lipolytica is an excellent microbial chassis; for example, it can accumulate high levels of lipids and use a broad range of substrates. Furthermore, it is a species for which an array of efficient genetic engineering tools is available. To date, extensive work has been done to metabolically engineer Y. lipolytica to produce usual and unusual lipids. Unusual lipids are scarce in nature but have several useful applications. As a result, they are increasingly becoming the targets of metabolic engineering. Unusual lipids have distinct structures; they can be generated by engineering endogenous lipid synthesis or by introducing heterologous enzymes to alter the functional groups of fatty acids. In this review, we describe current metabolic engineering strategies for improving lipid production and highlight recent researches on unusual lipid production in Y. lipolytica.

Undecane production by cold-adapted bacteria from Antarctica

In the last decades, efforts to reduce the use of fossil fuels have increased the search for alternative sustainable sources of renewable energy. In this scenario, hydrocarbons derived from fatty acids are among the compounds that have been drawing attention. The intracellular production of hydrocarbons by bacteria derived from cold environments such as the Antarctic continent is currently poorly investigated, as extremophilic microorganisms provide a great range of metabolic capabilities and may represent a key tool in the production of biofuels. The aim of this study was to explore the ability of bacterial cells derived from extreme environments to produce hydrocarbons with potential for further use as biofuels. Seven bacteria isolated from Antarctic samples were evaluated for hydrocarbon production using GC-MS approaches. Two isolates, identified as Arthrobacter livingstonensis 593 and Pseudoalteromonas arctica 628, were able to produce the hydrocarbon undecane (CH3-(CH2)₉-CH3) in concentrations of 1.39 mg L^-1 and 1.81 mg L^-1, respectively. Results from the present work encourage further research focusing on the optimization of hydrocarbon production by the isolates identified as producers, which may be used in further aircraft biofuel production. This is the first report on the production of the undecane compound by bacteria isolated from waterlogged soil and sponge from Antarctica.

Isobutanol production freed from biological limits using synthetic biochemistry

Cost competitive conversion of biomass-derived sugars into biofuel will require high yields, high volumetric productivities and high titers. Suitable production parameters are hard to achieve in cell-based systems because of the need to maintain life processes. As a result, next-generation biofuel production in engineered microbes has yet to match the stringent cost targets set by petroleum fuels. Removing the constraints imposed by having to maintain cell viability might facilitate improved production metrics. Here, we report a cell-free system in a bioreactor with continuous product removal that produces isobutanol from glucose at a maximum productivity of 4 g L⁻¹ h⁻¹, a titer of 275 g L⁻¹ and 95% yield over the course of nearly 5 days. These production metrics exceed even the highly developed ethanol fermentation process. Our results suggest that moving beyond cells has the potential to expand what is possible for bio-based chemical production.

A cell free or synthetic biochemistry approach offers a way to circumvent the many constraints of living cells. Here, the authors demonstrate, via enzyme and process enhancements, the production of isobutanol with the metrics exceeding highly developed ethanol fermentation.

IPRO+/-: Computational Protein Design Tool Allowing for Insertions and Deletions

Insertions and deletions (indels) in protein sequences alter the residue spacing along the polypeptide backbone and consequently open up possibilities for tuning protein function in a way that is inaccessible by amino acid substitution alone. We describe an optimization-based computational protein redesign approach centered around predicting beneficial combinations of indels along with substitutions and also obtain putative substrate-docked structures for these protein variants. This modified algorithmic capability would be of interest for enzyme engineering and broadly inform other protein design tasks. We highlight this capability by (1) identifying active variants of a bacterial thioesterase enzyme ('TesA) with experimental corroboration, (2) recapitulating existing active TEM-1 β-Lactamase sequences of different sizes, and (3) identifying shorter 4-Coumarate:CoA ligases with enhanced in vitro activities toward non-native substrates. A separate PyRosetta-based open-source tool, Indel-Maker (http://www.maranasgroup.com/software.htm), has also been created to construct computational models of user-defined protein variants with specific indels and substitutions.

Production of 1-octanol in Escherichia coli by a high flux thioesterase route

1-octanol is a valuable molecule in the chemical industry, where it is used as a plasticizer, as a precursor in the production of linear low-density polyethylene (LLDPE), and as a growth inhibitor of tobacco plant suckers. Due to the low availability of eight-carbon acyl chains in natural lipid feedstocks and the selectivity challenges in petrochemical routes to medium-chain fatty alcohols,1-octanol sells for the highest price among the fatty alcohol products. As an alternative, metabolic engineers have pursued sustainable 1-octanol production via engineered microbes. Here, we report demonstration of gram per liter titers in the model bacterium Escherichia coli via the development of a pathway composed of a thioesterase, an acyl-CoA synthetase, and an acyl-CoA reductase. In addition, the impact of deleting fermentative pathways was explored E. coli K12 MG1655 strain for production of octanoic acid, a key octanol precursor. In order to overcome metabolic flux barriers, bioprospecting experiments were performed to identify acyl-CoA synthetases with high activity towards octanoic acid and acyl-CoA reductases with high activity to produce 1-octanol from octanoyl-CoA. Titration of expression of key pathway enzymes was performed and a strain with the full pathway integrated on the chromosome was created. The final strain produced 1-octanol at 1.3 g/L titer and a >90% C₈ specificity from glycerol. In addition to the metabolic engineering efforts, this work addressed some of the technical challenges that arise when quantifying 1-octanol produced from cultures grown under fully aerobic conditions where evaporation and stripping are prevalent.

A bacterial biosynthetic pathway for methylated furan fatty acids

Fatty acids play many important roles in cells and also in industrial processes. Furan fatty acids (FuFAs) are present in the lipids of some plant, fish, and microbial species and appear to function as second messengers in pathways that protect cells from membrane-damaging agents. We report here the results of chemical, genetic, and synthetic biology experiments to decipher the biosynthesis of the monomethylated FuFA, methyl 9-(3-methyl-5-pentylfuran-2-yl) nonanoate (9M5-FuFA), and its dimethyl counterpart, methyl 9-(3,4-dimethyl-5-pentylfuran-2-yl) nonanoate (9D5-FuFA), in two α-proteobacteria. Each of the steps in FuFA biosynthesis occurs on pre-existing phospholipid fatty acid chains, and we identified pathway intermediates and the gene products that catalyze 9M5-FuFA and 9D5-FuFA synthesis in Rhodobacter sphaeroides 2.4.1 and Rhodopseudomonas palustris CGA009. One previously unknown pathway intermediate was a methylated diunsaturated fatty acid, (10E,12E)-11-methyloctadeca-10,12-dienoic acid (11Me-10t,12t-18:2), produced from (11E)-methyloctadeca-11-enoic acid (11Me-12t-18:1) by a newly identified fatty acid desaturase, UfaD. We also show that molecular oxygen (O₂) is the source of the oxygen atom in the furan ring of 9M5-FuFA, and our findings predict that an O₂-derived oxygen atom is incorporated into 9M5-FuFA via a protein, UfaO, that uses the 11Me-10t,12t-18:2 fatty acid phospholipid chain as a substrate. We discovered that R. palustris also contains a SAM-dependent methylase, FufM, that produces 9D5-FuFA from 9M5-FuFA. These results uncover the biochemical sequence of intermediates in a bacterial pathway for 9M5-FuFA and 9D5-FuFA biosynthesis and suggest the existence of homologs of the enzymes identified here that could function in FuFA biosynthesis in other organisms.

Metabolic engineering of β-oxidation to leverage thioesterases for production of 2-heptanone, 2-nonanone and 2-undecanone

Medium-chain length methyl ketones are potential blending fuels due to their cetane numbers and low melting temperatures. Biomanufacturing offers the potential to produce these molecules from renewable resources such as lignocellulosic biomass. In this work, we designed and tested metabolic pathways in Escherichia coli to specifically produce 2-heptanone, 2-nonanone and 2-undecanone. We achieved substantial production of each ketone by introducing chain-length specific acyl-ACP thioesterases, blocking the β-oxidation cycle at an advantageous reaction, and introducing active β-ketoacyl-CoA thioesterases. Using a bioprospecting approach, we identified fifteen homologs of E. coli β-ketoacyl-CoA thioesterase (FadM) and evaluated the in vivo activity of each against various chain length substrates. The FadM variant from Providencia sneebia produced the most 2-heptanone, 2-nonanone, and 2-undecanone, suggesting it has the highest activity on the corresponding β-ketoacyl-CoA substrates. We tested enzyme variants, including acyl-CoA oxidases, thiolases, and bi-functional 3-hydroxyacyl-CoA dehydratases to maximize conversion of fatty acids to β-keto acyl-CoAs for 2-heptanone, 2-nonanone, and 2-undecanone production. In order to address the issue of product loss during fermentation, we applied a 20% (v/v) dodecane layer in the bioreactor and built an external water cooling condenser connecting to the bioreactor heat-transferring condenser coupling to the condenser. Using these modifications, we were able to generate up to 4.4 g/L total medium-chain length methyl ketones.

Impact of feedstocks and downstream processing technologies on the economics of caproic acid production in fermentation by Megasphaera elsdenii T81

Caproic acid (CA) was produced by Megasphaera elsdenii T81 with Jerusalem artichoke tubers (JA) as a feedstock. More CA was produced under the medium with the acid hydrolysate of JA than the comparative medium with a carbon composition similar to that of JA. CA was produced up to 13.0 g/L and 0.52 g/L/h with extractive fermentation using a mixed solvent of alamine 336 in oleyl alcohol at 37 °C. The JA cost to produce 1 ton of CA is only 505 USD, which is much lower than that required for purchasing sucrose (860 USD) in CA production. As a result of the analysis performed using SuperPro Designer, including the cost of distillation to obtain pure CA, the estimated production cost for CA from dry JA is 1869 USD/ton CA at the production scale of 2000 ton/year, which is lower than the current market price for petroleum-derived CA (~2500 USD/ton).

Fatty Acyl Synthetases and Thioesterases in Plant Lipid Metabolism: Diverse Functions and Biotechnological Applications

Plants use fatty acids to synthesize acyl lipids for many different cellular, physiological, and defensive roles. These roles include the synthesis of essential membrane, storage, or surface lipids, as well as the production of various fatty acid-derived metabolites used for signaling or defense. Fatty acids are activated for metabolic processing via a thioester linkage to either coenzyme A or acyl carrier protein. Acyl synthetases metabolically activate fatty acids to their thioester forms, and acyl thioesterases deactivate fatty acyl thioesters to free fatty acids by hydrolysis. These two enzyme classes therefore play critical roles in lipid metabolism. This review highlights the surprisingly complex and varying roles of fatty acyl synthetases in plant lipid metabolism, including roles in the intracellular trafficking of fatty acids. This review also surveys the many specialized fatty acyl thioesterases characterized to date in plants, which produce a great diversity of fatty acid products in a tissue-specific manner. While some acyl thioesterases produce fatty acids that clearly play roles in plant-insect or plant-microbial interactions, most plant acyl thioesterases have yet to be fully characterized both in terms of their substrate specificities and their functions. The biotechnological applications of plant acyl thioesterases and synthetases are also discussed, as there is significant interest in these enzymes as catalysts for the sustainable production of fatty acids and their derivatives for industrial uses.

Revisiting metabolic engineering strategies for microbial synthesis of oleochemicals

Microbial production of oleochemicals from renewable feedstocks remains an attractive route to produce high-energy density, liquid transportation fuels and high-value chemical products. Metabolic engineering strategies have been applied to demonstrate production of a wide range of oleochemicals, including free fatty acids, fatty alcohols, esters, olefins, alkanes, ketones, and polyesters in both bacteria and yeast. The majority of these demonstrations synthesized products containing long-chain fatty acids. These successes motivated additional effort to produce analogous molecules comprised of medium-chain fatty acids, molecules that are less common in natural oils and therefore of higher commercial value. Substantial progress has been made towards producing a subset of these chemicals, but significant work remains for most. The other primary challenge to producing oleochemicals in microbes is improving the performance, in terms of yield, rate, and titer, of biocatalysts such that economic large-scale processes are feasible. Common metabolic engineering strategies include blocking pathways that compete with synthesis of oleochemical building blocks and/or consume products, pulling flux through pathways by removing regulatory signals, pushing flux into biosynthesis by overexpressing rate-limiting enzymes, and engineering cells to tolerate the presence of oleochemical products. In this review, we describe the basic fundamentals of oleochemical synthesis and summarize advances since 2013 towards improving performance of heterotrophic microbial cell factories.

Recent trends in integrated bioprocesses: aiding and expanding microbial biofuel/biochemical production

Microbial biosynthesis of fuels and chemicals represents a promising route for their renewable production. Product toxicity, however, represents a common challenge limiting the efficacy of this approach. Integrated bioprocesses incorporating in situ product separation are poised to help address this intrinsic problem, but suffer their own unique shortcomings. To improve and expand the utility of this versatile bioprocessing strategy, recent innovations have focused on developing more effective separation materials and novel process configurations, as well as adapting designs to accommodate semi-continuous modes of operation. As a result, integrated bioprocesses are finding new applications to aid the biosynthesis of an ever-growing list of bioproducts. Emerging applications, meanwhile, are exploring the further expansion of such designs to interface microbial and chemical catalysts, leading to new and versatile routes for the one-pot synthesis of an even greater diversity of renewable products.

Production of long-chain free fatty acids from metabolically engineered Rhodobacter sphaeroides heterologously producing periplasmic phospholipase A2 in dodecane-overlaid two-phase culture

Background

Long-chain free fatty acids (FFAs) are a type of backbone molecule that can react with alcohol to produce biodiesels. Various microorganisms have become potent producers of FFAs. Efforts have focused on increasing metabolic flux to the synthesis of either neutral fat or fatty acyl intermediates attached to acyl carrier protein (ACP), which are the source of FFAs. Membrane lipids are also a source of FFAs. As an alternative way of producing FFAs, exogenous phospholipase may be used after heterologous production and localization in the periplasmic space. In this work, we examined whether Rhodobacter sphaeroides, which forms an intracytoplasmic membrane, can be used for long-chain FFA production using phospholipase.

Results

The recombinant R. sphaeroides strain Rs-A2, which heterologously produces Arabidopsis thaliana phospholipase A2 (PLA2) in the periplasm, excretes FFAs during growth. FFA productivity under photoheterotrophic conditions is higher than that observed under aerobic or semiaerobic conditions. When the biosynthetic enzymes for FA (β-ketoacyl-ACP synthase, FabH) and phosphatidate (1-acyl-sn-glycerol-3-phosphate acyltransferase, PlsC) were overproduced in Rs-A2, the FFA productivity of the resulting strain Rs-HCA2 was elevated, and the FFAs produced mainly consisted of long-chain FAs of cis-vaccenate, stearate, and palmitate in an approximately equimolar ratio. The high-cell-density culture of Rs-HCA2 with DMSO in two-phase culture with dodecane resulted in an increase of overall carbon substrate consumption, which subsequently leads to a large increase in FFA productivity of up to 2.0 g L⁻¹ day⁻¹. Overexpression of the genes encoding phosphate acyltransferase (PlsX) and glycerol-3-phosphate acyltransferase (PlsY), which catalyze the biosynthetic steps immediately upstream from PlsC, in Rs-HCA2 generated Rs-HXYCA2, which grew faster than Rs-HCA2 and showed an FFA productivity of 2.8 g L⁻¹ day⁻¹ with an FFA titer of 8.5 g L⁻¹.

Conclusion

We showed that long-chain FFAs can be produced from metabolically engineered R. sphaeroides heterologously producing PLA2 in the periplasm. The FFA productivity was greatly increased by high-cell-density culture in two-phase culture with dodecane. This approach provides highly competitive productivity of long-chain FFAs by R. sphaeroides compared with other bacteria. This method may be applied to FFA production by other photosynthetic bacteria with similar differentiated membrane systems.

Electronic supplementary material

The online version of this article (10.1186/s12934-019-1070-8) contains supplementary material, which is available to authorized users.

New coculture system of Clostridium spp. and Megasphaera hexanoica using submerged hollow-fiber membrane bioreactors for caproic acid production

In this study, a coculture bioprocess was developed with Clostridium strains producing butyric acid and Megasphaera hexanoica producing caproic acid from the butyric acid. The two bacterial strains were each cultivated in two submerged hollow-fiber membrane bioreactors (s-HF/MBRs), separately. Each fermentation broth was filtered through the membrane modules, and the filtered broth was either interchanged on another reactor or obtained sequentially through. Using s-HF/MBRs, the caproic acid concentration increased to 10.08 g L^-1, with the fastest productivity of 0.69 g L^-1 h^-1, which higher than that previously reported.

Fatty acid biosynthesis is enhanced in Escherichia coli strains with deletion in genes encoding the PII signaling proteins

The committed and rate-limiting step in fatty acid biosynthesis is catalyzed by acetyl-CoA carboxylase (ACC). In previous studies we showed that ACC activity is inhibited through interactions with the PII signaling proteins in vitro. Here we provide in vivo support for that model; we noted that PII proteins are able to reduce malonyl-CoA levels in vivo in Escherichia coli. Furthermore, we show that fatty acid biosynthesis is strongly enhanced in E. coli strains carrying deletions in PII coding genes. Given that PII proteins act as conserved negative regulators of ACC in Bacteria, our findings may be explored to engineer other prokaryotes to improve fatty acid yields, thereby turning microbial biofuel production economically competitive in the future.

Highly Active C8-Acyl-ACP Thioesterase Variant Isolated by a Synthetic Selection Strategy

Microbial metabolism is an attractive route for producing medium chain length fatty acids, e.g., octanoic acid, used in the oleochemical industry. One challenge to this strategy is the lack of enzymes that are both highly active in a microbial host and selective toward substrates with desired chain length. Of the many steps in fatty acid biosynthesis, the thioesterase is the most widely used enzyme for controlling chain length. Thioesterases hydrolyze the thioester bond between fatty acids and the acyl-carrier protein (ACP) or coenzyme A (CoA) cofactor. The functional role of thioesterases varies between organisms ( i.e., bacteria vs plant) and therefore so do the substrate specificities. As a result, microbial biocatalysts that utilize a heterologous thioesterase either produce high titers of fatty acids with mixed chain lengths or low titers of products with a narrow chain length distribution. To search for highly active enzymes that selectively hydrolyze octanoyl-ACP, we developed a genetic selection based on the lipoic acid requirement of Escherichia coli. We used the selection to identify variants in a randomly mutagenized library of the C₈-specific Cuphea palustris FatB1 thioesterase. After optimizing expression of the thioesterase, E. coli cultures produced 1.7 g/L of octanoic acid with >90% specificity from a single chromosomal copy of this thioesterase. In vitro studies confirmed the mutant thioesterase possessed a 15-fold increase in k_cat compared to its native sequence. The high level of specific activity allowed for low levels of expression while maintaining fatty acid titer. The low expression requirement will allow metabolic engineers to use more cellular resources to address other limitations in the pathway and maximize overall productivity.

Biodiesels from microbial oils: Opportunity and challenges

Although biodiesel has been extensively explored as an important renewable energy source, the raw materials-associated cost poses a serious challenge on its large-scale commercial production. The first and second generations of biodiesel are mainly produced from usable raw materials, e.g. edible oils, crops etc. Such a situation inevitably imposes higher demands on land and water usage, which in turn compromise future food and water supply. Obviously, there is an urgent need to explore alternative feedstock, e.g. microbial oils which can be produced by many types of microorganisms including microalgae, fungi and bacteria with the advantages of small footprint, high lipid content and efficient uptake of carbon dioxide. Therefore, this review offers a comprehensive picture of microbial oil-based technology for biodiesel production. The perspectives and directions forward are also outlined for future biodiesel production and commercialization.

A novel and rapid method for fatty acid preparation by the lipase-catalyzed hydrolysis of Phoenix tree seeds

Fatty acids are the precursors for the production of fuels, oleochemicals and special health care products. In this study, a novel rapid method for fatty acid (FA) preparation by the enzymatic hydrolysis of Phoenix tree seed, an undeveloped woody oil seed, was developed. High-temperature GC with flame ionization detector (FID) and the hydrolysis ratio were used to monitor reaction progress. Enzyme screening and the effect of reaction variables on the hydrolysis of seeds were evaluated and optimized by response surface methodology. The results showed that among the tested enzymes, Lipozyme TLIM showed the greatest amount of hydrolysis of Phoenix tree seed. FAs can be rapidly prepared by one-step hydrolysis of Phoenix tree seeds using Lipozyme TLIM as the biocatalyst. Under the optimized conditions (6% enzyme load, 1:8 mass ratio of seed to water, 47.7 °C and 16 min), the maximum hydrolysis ratio (96.4 ± 1.1%) can be achieved. The effect of reaction variables on the hydrolysis decreased in the following order: reaction time > enzyme load > substrate ratio of seed to water > reaction temperature. This work provides a novel and rapid method for FA preparation from oil seeds.

Differences in substrate specificity of V. cholerae FabH enzymes suggest new approaches for the development of novel antibiotics and biofuels

Vibrio cholerae, the causative pathogen of the life-threatening infection cholera, encodes two copies of β-ketoacyl-acyl carrier protein synthase III (vcFabH1 and vcFabH2). vcFabH1 and vcFabH2 are pathogenic proteins associated with fatty acid synthesis, lipid metabolism, and potential applications in biofuel production. Our biochemical assays characterize vcFabH1 as exhibiting specificity for acetyl-CoA and CoA thioesters with short acyl chains, similar to that observed for FabH homologs found in most gram-negative bacteria. vcFabH2 prefers medium chain-length acyl-CoA thioesters, particularly octanoyl-CoA, which is a pattern of specificity rarely seen in bacteria. Structural characterization of one vcFabH1 and six vcFabH2 structures determined in either apo form or in complex with acetyl-CoA/octanoyl-CoA indicate that the substrate-binding pockets of vcFabH1 and vcFabH2 are of different sizes, accounting for variations in substrate chain-length specificity. An unusual and unique feature of vcFabH2 is its C-terminal fragment that interacts with both the substrate-entrance loop and the dimer interface of the enzyme. Our discovery of the pattern of substrate specificity of both vcFabH1 and vcFabH2 can potentially aid the development of novel antibacterial agents against V. cholerae. Additionally, the distinctive substrate preference of FabH2 in V. cholerae and related facultative anaerobes conceivably make it an attractive component of genetically engineered bacteria used for commercial biofuel production.

Transcriptome remodeling of Pseudomonas putida KT2440 during mcl-PHAs synthesis: effect of different carbon sources and response to nitrogen stress

Bacterial response to environmental stimuli is essential for survival. In response to fluctuating environmental conditions, the physiological status of bacteria can change due to the actions of transcriptional regulatory machinery. The synthesis and accumulation of polyhydroxyalkanoates (PHAs) are one of the survival strategies in harsh environments. In this study, we used transcriptome analysis of Pseudomonas putida KT2440 to gain a genome-wide view of the mechanisms of environmental-friendly biopolymers accumulation under nitrogen-limiting conditions during conversion of metabolically different carbon sources (sodium gluconate and oleic acid). Transcriptomic data revealed that phaG expression is associated with medium-chain-length-PHAs' synthesis not only on sodium gluconate but also on oleic acid, suggesting that PhaG may play a role in this process, as well. Moreover, genes involved in the β-oxidation pathway were induced in the PHAs production phase when sodium gluconate was supplied as the only carbon and energy source. The transition from exponential growth to stationary phase caused a significant expression of genes involved in nitrogen metabolism, energy supply, and transport system. In this study, several molecular mechanisms, which drive mcl-PHAs synthesis, have been investigated. The identified genes may provide valuable information to improve the efficiency of this bioprocess and make it more economically feasible.

Engineering of E. coli inherent fatty acid biosynthesis capacity to increase octanoic acid production

BACKGROUND

As a versatile platform chemical, construction of microbial catalysts for free octanoic acid production from biorenewable feedstocks is a promising alternative to existing petroleum-based methods. However, the bio-production strategy has been restricted by the low capacity of E. coli inherent fatty acid biosynthesis. In this study, a combination of integrated computational and experimental approach was performed to manipulate the E. coli existing metabolic network, with the objective of improving bio-octanoic acid production.

RESULTS

First, a customized OptForce methodology was run to predict a set of four genetic interventions required for production of octanoic acid at 90% of the theoretical yield. Subsequently, all the ten candidate proteins associated with the predicted interventions were regulated individually, as well as in contrast to the combination of interventions as suggested by the OptForce strategy. Among these enzymes, increased production of 3-hydroxy-acyl-ACP dehydratase (FabZ) resulted in the highest increase (+ 45%) in octanoic acid titer. But importantly, the combinatorial application of FabZ with the other interventions as suggested by OptForce further improved octanoic acid production, resulting in a high octanoic acid-producing E. coli strain +fabZ ΔfadE ΔfumAC ΔackA (TE10) (+ 61%). Optimization of TE10 expression, medium pH, and C:N ratio resulted in the identified strain producing 500 mg/L of C8 and 805 mg/L of total FAs, an 82 and 155% increase relative to wild-type MG1655 (TE10) in shake flasks. The best engineered strain produced with high selectivity (> 70%) and extracellularly (> 90%) up to 1 g/L free octanoic acid in minimal medium fed-batch culture.

CONCLUSIONS

This work demonstrates the effectiveness of integration of computational strain design and experimental characterization as a starting point in rewiring metabolism for octanoic acid production. This result in conjunction with the results of other studies using OptForce in strain design demonstrates that this strategy may be also applicable to engineering E. coli for other customized bioproducts.

The influence of fatty acid supply and aldehyde reductase deletion on cyanobacteria alkane generating pathway in Escherichia coli

Cyanobacteria alkane synthetic pathway has been heterologously constructed in many microbial hosts. It is by far the most studied and reliable alkane generating pathway. Aldehyde deformylating oxygenase (i.e., ADO, key enzyme in this pathway) obtained from different cyanobacteria species showed diverse catalytic abilities. This work indicated that single aldehyde reductase deletions were beneficial to Nostoc punctiforme ADO-depended alkane production in Escherichia coli even better than double deletions. Fatty acid metabolism regulator (FadR) overexpression and low temperature increased C18:1 fatty acid supply, and in turn stimulated C18:1-derived heptadecene production, suggesting that supplying ADO with preferred substrate was important to overall alkane yield improvement. Using combinational methods, 1 g/L alkane was obtained in fed-batch fermentation with heptadecene accounting for nearly 84% of total alkane.

Inhibition of Cyanobacterial Growth on a Municipal Wastewater Sidestream Is Impacted by Temperature

Cyanobacteria are viewed as promising platforms to produce fuels and/or high-value chemicals as part of so-called “biorefineries.” Their integration into wastewater treatment systems is particularly interesting because removal of the nitrogen and phosphorus in many wastewater streams is an expensive but necessary part of wastewater treatment. In this study, we evaluated strategies for cultivating Synechococcus sp. strain PCC 7002 on media comprised of two wastewater streams, i.e., treated secondary effluent supplemented with the liquid fraction extracted from sludge following anaerobic digestion. This strain is commonly used for metabolic engineering to produce a variety of valuable chemical products and product precursors (e.g., lactate). However, initial attempts to grow PCC 7002 under otherwise-standard conditions of light and temperature failed. We thus systematically evaluated alternative cultivation conditions and then used multiple methods to dissect the apparent toxicity of the media under standard cultivation conditions.

Sidestreams in wastewater treatment plants can serve as concentrated sources of nutrients (i.e., nitrogen and phosphorus) to support the growth of photosynthetic organisms that ultimately serve as feedstock for production of fuels and chemicals. However, other chemical characteristics of these streams may inhibit growth in unanticipated ways. Here, we evaluated the use of liquid recovered from municipal anaerobic digesters via gravity belt filtration as a nutrient source for growing the cyanobacterium Synechococcus sp. strain PCC 7002. The gravity belt filtrate (GBF) contained high levels of complex dissolved organic matter (DOM), which seemed to negatively influence cells. We investigated the impact of GBF on physiological parameters such as growth rate, membrane integrity, membrane composition, photosystem composition, and oxygen evolution from photosystem II. At 37°C, we observed an inverse correlation between GBF concentration and membrane integrity. Radical production was also detected upon exposure to GBF at 37°C. However, the dose-dependent relationship between the GBF concentration and the lack of membrane integrity was abolished at 27°C. Immediate resuspension of strains in high levels of GBF showed markedly reduced oxygen evolution rates relative to those seen with the control. Taken together, the data indicate that one mechanism responsible for GBF toxicity to Synechococcus is the interruption of photosynthetic electron flow and subsequent phenomena. We hypothesize that this is likely due to the presence of phenolic compounds within the DOM.

IMPORTANCE Cyanobacteria are viewed as promising platforms to produce fuels and/or high-value chemicals as part of so-called “biorefineries.” Their integration into wastewater treatment systems is particularly interesting because removal of the nitrogen and phosphorus in many wastewater streams is an expensive but necessary part of wastewater treatment. In this study, we evaluated strategies for cultivating Synechococcus sp. strain PCC 7002 on media comprised of two wastewater streams, i.e., treated secondary effluent supplemented with the liquid fraction extracted from sludge following anaerobic digestion. This strain is commonly used for metabolic engineering to produce a variety of valuable chemical products and product precursors (e.g., lactate). However, initial attempts to grow PCC 7002 under otherwise-standard conditions of light and temperature failed. We thus systematically evaluated alternative cultivation conditions and then used multiple methods to dissect the apparent toxicity of the media under standard cultivation conditions.

Microbial synthesis of medium-chain chemicals from renewables

Linear, medium-chain (C8-C12) hydrocarbons are important components of fuels as well as commodity and specialty chemicals. As industrial microbes do not contain pathways to produce medium-chain chemicals, approaches such as overexpression of endogenous enzymes or deletion of competing pathways are not available to the metabolic engineer; instead, fatty acid synthesis and reversed β-oxidation are manipulated to synthesize medium-chain chemical precursors. Even so, chain lengths remain difficult to control, which means that purification must be used to obtain the desired products, titers of which are typically low and rarely exceed milligrams per liter. By engineering the substrate specificity and activity of the pathway enzymes that generate the fatty acyl intermediates and chain-tailoring enzymes, researchers can boost the type and yield of medium-chain chemicals. Development of technologies to both manipulate chain-tailoring enzymes and to assay for products promises to enable the generation of g/L yields of medium-chain chemicals.

Introduction of an acetyl-CoA carboxylation bypass into Escherichia coli for enhanced free fatty acid production

This study investigated the effect of the methylmalonyl-CoA carboxyltransferase (MMC) of Propionibacterium freudenreichii on production of free fatty acid (FFA) in Escherichia coli. Overexpression of the MMC exhibited a 44% increase in FFA titer. Co-overexpression of MMC and phosphoenolpyruvate carboxylase (PPC), which supplies the MMC precursor, further improved the titer by 40%. Expression of malic enzyme (MaeB) led to a 23% increase in FFA titer in the acetyl-CoA carboxylase (ACC)-overexpressing cells, but no increase in the MMC-overexpressing cells. The highest FFA production in the MMC-overexpressing strain was achieved through the addition of aspartic acid, which can be converted into oxaloacetate (OAA), resulting in a 120% increased titer compared with that in the ACC-overexpressing strain. These findings demonstrate that MMC provides an alternative pathway for malonyl-CoA synthesis and increases fatty acid 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.

Recent advances in the production of value added chemicals and lipids utilizing biodiesel industry generated crude glycerol as a substrate - Metabolic aspects, challenges and possibilities: An overview

One of the major ecological concerns associated with biodiesel production is the generation of waste/crude glycerol during the trans-esterification process. Purification of this crude glycerol is not economically viable. In this context, the development of an efficient and economically viable strategy would be biotransformation reactions converting the biodiesel derived crude glycerol into value added chemicals. Hence the process ensures the sustainability and waste management in biodiesel industry, paving a path to integrated biorefineries. This review addresses a waste to wealth approach for utilization of crude glycerol in the production of value added chemicals, current trends, challenges, future perspectives, metabolic approaches and the genetic tools developed for the improved synthesis over wild type microorganisms were described.