Improved production of fatty alcohols in cyanobacteria by metabolic engineering

Peroxisomal metabolic coupling improves fatty alcohol production from sole methanol in yeast

Methanol is an ideal feedstock for chemical and biological manufacturing. Constructing an efficient cell factory is essential for producing complex compounds through methanol biotransformation, in which coordinating methanol use and product synthesis is often necessary. In methylotrophic yeast, methanol utilization mainly occurs in peroxisomes, which creates challenges in driving the metabolic flux toward product biosynthesis. Here, we observed that constructing the cytosolic biosynthesis pathway resulted in compromised fatty alcohol production in the methylotrophic yeast Ogataea polymorpha. Alternatively, peroxisomal coupling of fatty alcohol biosynthesis and methanol utilization significantly improved fatty alcohol production by 3.9-fold. Enhancing the supply of precursor fatty acyl-CoA and cofactor NADPH in the peroxisomes by global metabolic rewiring further improved fatty alcohol production by 2.5-fold and produced 3.6 g/L fatty alcohols from methanol under fed-batch fermentation. We demonstrated that peroxisome compartmentalization is helpful for coupling methanol utilization and product synthesis, and with this approach, constructing efficient microbial cell factories for methanol biotransformation is feasible.

Production of Fatty Acids and Derivatives Using Cyanobacteria

Fatty acids and their derivatives are highly valuable chemicals that can be produced through chemical or enzymatic processes using plant lipids. This may compete with human food sources. Therefore, there has been an urge to create a new method for synthesizing these chemicals. One approach is to use microbial cells, specifically cyanobacteria, as a factory platform. Engineering may need to be implemented in order to allow a cost-competitive production and to enable a production of a variety of different fatty acids and derivatives. In this chapter, we explain in details the importance of fatty acids and their derivatives, including fatty aldehydes, fatty alcohols, hydrocarbons, fatty acid methyl esters, and hydroxy fatty acids. The production of these chemicals using cyanobacterial native metabolisms together with strategies to engineer them are also explained. Moreover, recent examples of fatty acid and fatty acid derivative production from engineered cyanobacteria are gathered and reported. Commercial opportunities to manufacture fatty acids and derivatives are also discussed in this chapter. Altogether, it is clear that fatty acids and their derivatives are important chemicals, and with recent advancements in genetic engineering, a cyanobacterial platform for bio-based production is feasible. However, there are regulations and guidelines in place for the use of genetically modified organisms (GMOs) and some further developments are still needed before commercialization can be reached.

Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria

Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.

Metabolic transformation of cyanobacteria for biofuel production

World-wide, an emerging demand is moving towards the biofuels to replace the fossil fuels. In alternative biofuel production strategies, cyanobacteria have unique characteristic of accumulating glycogen, lipid, and fuel molecules through natural mechanisms. Moreover, the cyanobacteria can be easily engineered to synthesis a plenty of fuel molecules from CO₂. To obtain the fuel molecule from cyanobacteria, various techniques were invented in which the metabolic engineering is found to be a prerequisite to develop an economically feasible process. The expression of indigenous or heterologous pathways plays an important role in developing successful production process. In addition, the engineering of photosynthetic apparatus, destruction of competitive pathways and improvement of tolerance were also proven to improve the product specific synthesis. Although various metabolic engineering approaches have been developed, there are certain obstacles when it comes to implementation for the production. In this review, the important biosynthetic pathways for biofuels, alteration of other genes to improve the actual pathway and possibilities of developing cyanobacterial fuel production have been elaborated.

α-Dioxygenases (α-DOXs): Promising biocatalysts for the environmentally friendly production of aroma compounds

Fatty aldehydes (FALs) can be derived from fatty acids (FAs) and related compounds and are frequently used as flavors and fragrances. Although chemical methods have been conventionally used, their selective biotechnological production aiming at more efficient and eco‐friendly synthetic routes is in demand. α‐Dioxygenases (α‐DOXs) are heme‐dependent oxidative enzymes biologically involved in the initial step of plant FA α‐oxidation during which molecular oxygen is incorporated into the C_α‐position of a FA (C_n) to generate the intermediate FA hydroperoxide, which is subsequently converted into the shortened corresponding FAL (C_n‐1). α‐DOXs are promising biocatalysts for the flavor and fragrance industries, they do not require NAD(P)H as cofactors or redox partner proteins, and they have a broad substrate scope. Here, we highlight recent advances in the biocatalytic utilization of α‐DOXs with emphasis on newly discovered cyanobacterial α‐DOXs as well as analytical methods to measure α‐DOX activity in vitro and in vivo.

Microbial engineering to produce fatty alcohols and alkanes

Owing to their high energy density and composition, fatty acid-derived chemicals possess a wide range of applications such as biofuels, biomaterials, and other biochemical, and as a consequence, the global annual demand for products has surpassed 2 million tons. With the exhausting petroleum reservoirs and emerging environmental concerns on using petroleum feedstock, it has become indispensable to shift to a renewable-based industry. With the advancement in the field of synthetic biology and metabolic engineering, the use of microbes as factories for the production of fatty acid-derived chemicals is becoming a promising alternative approach for the production of these derivatives. Numerous metabolic approaches have been developed for conditioning the microbes to improve existing or develop new methodologies capable of efficient oleochemical production. However, there still exist several limitations that need to be addressed for the commercial viability of the microbial cell factory production. Though substantial advancement has been made toward successfully producing these fatty acids derived chemicals, a considerable amount of work needs to be done for improving the titers. In the present review, we aim to address the roadblocks impeding the heterologous production, the engineering pathway strategies implemented across the range of microbes in a detailed manner, and the commercial readiness of these molecules of immense application.

Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications

Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.

Biosynthesis of Fatty Alcohols in Engineered Microbial Cell Factories: Advances and Limitations

Concerns about climate change and environmental destruction have led to interest in technologies that can replace fossil fuels and petrochemicals with compounds derived from sustainable sources that have lower environmental impact. Fatty alcohols produced by chemical synthesis from ethylene or by chemical conversion of plant oils have a large range of industrial applications. These chemicals can be synthesized through biological routes but their free forms are produced in trace amounts naturally. This review focuses on how genetic engineering of endogenous fatty acid metabolism and heterologous expression of fatty alcohol producing enzymes have come together resulting in the current state of the field for production of fatty alcohols by microbial cell factories. We provide an overview of endogenous fatty acid synthesis, enzymatic methods of conversion to fatty alcohols and review the research to date on microbial fatty alcohol production. The primary focus is on work performed in the model microorganisms, Escherichia coli and Saccharomyces cerevisiae but advances made with cyanobacteria and oleaginous yeasts are also considered. The limitations to production of fatty alcohols by microbial cell factories are detailed along with consideration to potential research directions that may aid in achieving viable commercial scale production of fatty alcohols from renewable feedstock.

Determination of Volatile Organic Compounds and Antibacterial Activity of the Amazonian Cyanobacterium Synechococcus sp. Strain GFB01

Cyanobacteria exhibit great biotechnological potential due to their capacity to produce compounds with various applicability. Volatile organic compounds (VOCs) possess low molecular weight and high vapor pressure. Many volatiles produced by microorganisms have biotechnological potential, including antimicrobial activity. This study aimed to investigate the VOCs synthesized by cyanobacterium Synechococcus sp. strain GFB01, and the influence of nitrate and phosphate on its antibacterial potential. The strain was isolated from the surface of the freshwater lagoon Lagoa dos Índios, Amapá state, in Northern Brazil. After cultivation, the VOCs were extracted by a simultaneous distillation-extraction process, using a Likens-Nickerson apparatus (2 h), and then identified by GC-MS. The extracts did not display inhibitory activity against the Gram-positive bacteria tested by the disk-diffusion agar method. However, the anti-Salmonella property in both extracts (methanol and aqueous) was detected. The main VOCs identified were heptadecane (81.32%) and octadecyl acetate (11.71%). To the best of our knowledge, this is the first study of VOCs emitted by a cyanobacterium from the Amazon that reports the occurrence of 6-pentadecanol and octadecyl acetate in cyanobacteria.

Effect of ozone stress on the intracellular metabolites from Cobetia marina

A GCxGC-MS system was employed with a non-polar × mid-polar column set for the metabolic non-target analysis of Cobetia marina, the model bacteria for marine biofouling. C. marina was treated with ozone to investigate the intracellular metabolic state change under oxidative stress. A minimal inhibitory concentration test was involved to guarantee that the applied ozone dosages were not lethal for the cells. In this study, non-target analyses were performed to identify the metabolites according to the NIST database. As a result, over 170 signals were detected under normal living conditions including 35 potential metabolites. By the comparison of ozone-treated and non-treated samples, five compounds were selected to describe observed trends of signals in the contour plots. Oleic acid exhibited a slight growth by increasing ozone dosage. In contrast, other metabolites such as the amino acid L-proline showed less abundance after ozone treatment, which was more evident once ozone dosage was raised. Thus, this work could provide a hint for searching for up/downregulating factors in such environmental stress conditions for C. marina. Graphical abstract.

Photosynthetic Conversion of Carbon Dioxide to Oleochemicals by Cyanobacteria: Recent Advances and Future Perspectives

Sustainable production of biofuels and biochemicals has been broadly accepted as a solution to lower carbon dioxide emissions. Besides being used as lubricants or detergents, oleochemicals are also attractive biofuels as they are compatible with existing transport infrastructures. Cyanobacteria are autotrophic prokaryotes possessing photosynthetic abilities with mature genetic manipulation systems. Through the introduction of exogenous or the modification of intrinsic metabolic pathways, cyanobacteria have been engineered to produce various bio-chemicals and biofuels over the past decade. In this review, we specifically summarize recent progress on photosynthetic production of fatty acids, fatty alcohols, fatty alk(a/e)nes, and fatty acid esters by genetically engineered cyanobacteria. We also summarize recent reports on fatty acid and lipid metabolisms of cyanobacteria and provide perspectives for economic cyanobacterial oleochemical production in the future.

Cyanobacteria: Review of Current Potentials and Applications

Continual increases in the human population and growing concerns related to the energy crisis, food security, disease outbreaks, global warming, and other environmental issues require a sustainable solution from nature. One of the promising resources is cyanobacteria, also known as blue-green algae. They require simple ingredients to grow and possess a relatively simple genome. Cyanobacteria are known to produce a wide variety of bioactive compounds. In addition, cyanobacteria’s remarkable growth rate enables its potential use in a wide range of applications in the fields of bioenergy, biotechnology, natural products, medicine, agriculture, and the environment. In this review, we have summarized the potential applications of cyanobacteria in different areas of science and development, especially related to their use in producing biofuels and other valuable co-products. We have also discussed the challenges that hinder such development at an industrial level and ways to overcome such obstacles.

Enhancing production of microalgal biopigments through metabolic and genetic engineering

The versatile use of biopigments in food, feed, cosmetic, pharmaceutical and analytical industries emphasized to find different and renewable sources of biopigments. Microalgae, including cyanobacteria, are becoming a potential candidate for pigment production as these have fast-growing ability, high pigment content, highly variable and also have "Generally recognized as safe" status. These algal groups are known to produce different metabolites that include hormones, vitamins, biopolythene and biochemicals. We discuss here the potential use of microalgal biopigments in our daily life as well as in food and cosmetic industries. Pigment like carotenoids has many health benefits such as antioxidant, anti-inflammatory properties and also provide photo-protection against UV radiation. This review details the effect of various abiotic and biotic factors such as temperature, light, nutrition on maximizing the pigment content in the microalgal cell. This review also highlights the potential of microalgae, whether in present native or engineered strain including the many metabolic strategies which are used or can be used to produce a higher amount of these valuable biopigments. Additionally, future challenges in the context of pigment production have also been discussed.

Synthetic Biology Approaches to the Sustainable Production of p-Coumaric Acid and Its Derivatives in Cyanobacteria

The photosynthetic cyanobacteria are promising candidates for the sustainable production of a plethora of plant secondary metabolites, which are beneficial to human health but are difficult to produce and purify in other systems. This chapter focuses on genetic engineering of Synechocystis PCC 6803 for production of p-coumaric acid and its derivatives. Cyanobacterial engineering approaches are briefly reviewed. Strategies to increase production yield are discussed, including codon optimization of genes expressing enzymatic proteins and a laccase-coding gene knockout from Synechocystis genome which degrades polyphenols.

Membrane physical state and stress regulation in Synechocystis: fluidizing alcohols repress fatty acid desaturation

Cyanobacteria are prokaryotic photosynthetic organisms widely used in biotechnology, photosynthesis and abiotic stress research. There are several cyanobacterial strains modified to produce biofuels, but the influence of alcohols on cyanobacterial cell physiology is poorly understood. Here, we conducted a systematic study of the effects of nine primary aliphatic alcohols and an aromatic benzyl alcohol on both membrane physical state and the expression of genes for fatty acid desaturases (FADs) in a model cyanobacterium Synechocystis sp. strain PCC 6803. Hexan-1-ol was found to have the most membrane fluidizing action among all alcohols studied, with its efficiency correlating with both duration of treatment and alcohol concentration. A prolonged exposure to alcohol results in a continuous loss of unsaturated fatty acids (FAs) followed by cell death, an undesired challenge that should be considered in cyanobacterial biotechnology. We suggest that membrane fluidization is the key component in alcohol stress causing inactivation of FADs and resulting in a lethal depletion of unsaturated FAs. Due to the most pronounced effects of alcohol- and heat-induced membrane fluidization on desB encoding a terminal ω3-FAD, we propose to call desB a 'viscosity gene' in analogy to heat-induced 'fluidity gene' hspA.

Co-overexpression of native phospholipid-biosynthetic genes plsX and plsC enhances lipid production in Synechocystis sp. PCC 6803

The overexpression of native plsX and plsC genes involving in fatty acid/phospholipid synthesis first timely-reported the significantly enhanced lipid contents in Synechocystis sp. PCC 6803. Growth rate, intracellular pigment contents including chlorophyll a and carotenoids, and oxygen evolution rate of all overexpressing (OX) strains were normally similar as wild type. For fatty acid compositions, saturated fatty acid, in particular palmitic acid (16:0) was dominantly increased in OX strains whereas slight increases of unsaturated fatty acids were observed, specifically linoleic acid (18:2) and alpha-linolenic acid (18:3). The plsC/plsX-overexpressing (OX + XC) strain produced high lipid content of about 24.3%w/dcw under normal condition and was further enhanced up to 39.1%w/dcw by acetate induction. This OX + XC engineered strain was capable of decreasing phaA transcript level which related to poly-3-hydroxybutyrate (PHB) synthesis under acetate treatment. Moreover, the expression level of gene transcripts revealed that the plsX- and plsC/plsX-overexpression strains had also increased accA transcript amounts which involved in the irreversible carboxylation of acetyl-CoA to malonyl-CoA. Altogether, these overexpressing strains significantly augmented higher lipid contents when compared to wild type by partly overcoming the limitation of lipid production.

BioPS: System for screening and assessment of biofuel-production potential of cyanobacteria

Background

Cyanobacteria are one of the target groups of organisms explored for production of free fatty acids (FFAs) as biofuel precursors. Experimental evaluation of cyanobacterial potential for FFA production is costly and time consuming. Thus, computational approaches for comparing and ranking cyanobacterial strains for their potential to produce biofuel based on the characteristics of their predicted proteomes can be of great importance.

Results

To enable such comparison and ranking, and to assist biotechnology developers and researchers in selecting strains more likely to be successfully engineered for the FFA production, we developed the Biofuel Producer Screen (BioPS) platform (http://www.cbrc.kaust.edu.sa/biops). BioPS relies on the estimation of the predicted proteome makeup of cyanobacterial strains to produce and secrete FFAs, based on the analysis of well-studied cyanobacterial strains with known FFA production profiles. The system links results back to various external repositories such as KEGG, UniProt and GOLD, making it easier for users to explore additional related information.

Conclusion

To our knowledge, BioPS is the first tool that screens and evaluates cyanobacterial strains for their potential to produce and secrete FFAs based on strain’s predicted proteome characteristics, and rank strains based on that assessment. We believe that the availability of such a platform (comprising both a prediction tool and a repository of pre-evaluated stains) would be of interest to biofuel researchers. The BioPS system will be updated annually with information obtained from newly sequenced cyanobacterial genomes as they become available, as well as with new genes that impact FFA production or secretion.

Cyanobacterial Enzymes for Bioalkane Production

Cyanobacterial biosynthesis of alkanes is an attractive way of producing substitutes for petroleum-based fuels. Key enzymes for bioalkane production in cyanobacteria are acyl-ACP reductase (AAR) and aldehyde-deformylating oxygenase (ADO). AAR catalyzes the reduction of the fatty acyl-ACP/CoA substrates to fatty aldehydes, which are then converted into alkanes/alkenes by ADO. These enzymes have been widely used for biofuel production by metabolic engineering of cyanobacteria and other organisms. However, both proteins, particularly ADO, have low enzymatic activities, and their catalytic activities are desired to be improved for use in biofuel production. Recently, progress has been made in the basic sciences and in the application of AAR and ADO in alkane production. This chapter provides an overview of recent advances in the study of the structure and function of AAR and ADO, protein engineering of these enzymes for improving activity and modifying substrate specificities, and examples of metabolic engineering of cyanobacteria and other organisms using AAR and ADO for biofuel production.

Diversion of the long-chain acyl-ACP pool in Synechocystis to fatty alcohols through CRISPRi repression of the essential phosphate acyltransferase PlsX

Fatty alcohol production in Synechocystis sp. PCC 6803 was achieved through heterologous expression of the fatty acyl-CoA/ACP reductase Maqu2220 from the bacteria Marinobacter aquaeolei VT8 and the fatty acyl-ACP reductase DPW from the rice Oryza sativa. These platform strains became models for testing multiplex CRISPR-interference (CRISPRi) metabolic engineering strategies to both improve fatty alcohol production and to study membrane homeostasis. CRISPRi allowed partial repression of up to six genes simultaneously, each encoding enzymes of acyl-ACP-consuming pathways. We identified the essential phosphate acyltransferase enzyme PlsX (slr1510) as a key node in C18 fatty acyl-ACP consumption, repression of slr1510 increased octadecanol productivity threefold over the base strain and gave the highest specific titers reported for this host, 10.3mgg^-1 DCW. PlsX catalyzes the first committed step of phosphatidic acid synthesis, and has not been characterized in Synechocystis previously. We found that accumulation of fatty alcohols impaired growth, altered the membrane composition, and caused a build-up of reactive oxygen species.

Five Fatty Aldehyde Dehydrogenase Enzymes from Marinobacter and Acinetobacter spp. and Structural Insights into the Aldehyde Binding Pocket

Enzymes involved in lipid biosynthesis and metabolism play an important role in energy conversion and storage and in the function of structural components such as cell membranes. The fatty aldehyde dehydrogenase (FAldDH) plays a central function in the metabolism of lipid intermediates, oxidizing fatty aldehydes to the corresponding fatty acid and competing with pathways that would further reduce the fatty aldehydes to fatty alcohols or require the fatty aldehydes to produce alkanes. In this report, the genes for four putative FAldDH enzymes from Marinobacter aquaeolei VT8 and an additional enzyme from Acinetobacter baylyi were heterologously expressed in Escherichia coli and shown to display FAldDH activity. Five enzymes (Maqu_0438, Maqu_3316, Maqu_3410, Maqu_3572, and the enzyme reported under RefSeq accession no. WP_004927398) were found to act on aldehydes ranging from acetaldehyde to hexadecanal and also acted on the unsaturated long-chain palmitoleyl and oleyl aldehydes. A comparison of the specificities of these enzymes with various aldehydes is presented. Crystallization trials yielded diffraction-quality crystals of one particular FAldDH (Maqu_3316) from M. aquaeolei VT8. Crystals were independently treated with both the NAD⁺ cofactor and the aldehyde substrate decanal, revealing specific details of the likely substrate binding pocket for this class of enzymes. A likely model for how catalysis by the enzyme is accomplished is also provided.IMPORTANCE This study provides a comparison of multiple enzymes with the ability to oxidize fatty aldehydes to fatty acids and provides a likely picture of how the fatty aldehyde and NAD⁺ are bound to the enzyme to facilitate catalysis. Based on the information obtained from this structural analysis and comparisons of specificities for the five enzymes that were characterized, correlations to the potential roles played by specific residues within the structure may be drawn.

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.

Metabolic engineering of fatty alcohol production in transgenic hairy roots of Crambe abyssinica

Biotechnological production of fatty alcohols, important raw materials in the chemical industry, has been receiving considerable attention in recent years. Fatty alcohols are formed by the reduction of fatty acyl-CoAs or fatty acyl-ACPs catalyzed by a fatty acyl reductase (FAR). In this study, we introduced genes encoding FARs from Arabidopsis thaliana (AtFAR5) and Simmondsia chinensis (ScFAR) into Crambe abyssinica hairy roots via Agrobacterium rhizogenes-mediated transformation. The efficiency of the transformation ranged between 30 and 45%. The fatty alcohols were only detected in the transgenic hairy root lines expressing ScFAR gene. In all tested lines stearyl alcohol (18:0-OH), arachidyl alcohol (20:0-OH), and behenyl alcohol (22:0-OH) were produced. The content of 18:0-OH varied from 1 to 3% of total fatty acids and fatty alcohols, while the amount of either 20:0-OH and 22:0-OH did not exceed 2%. The transgenic hairy root lines produced from 0.98 to 2.59 nmol of fatty alcohols per mg of dry weight. Very low activity of ScFAR was detected in the microsomal fractions isolated from the selected hairy root lines. To our knowledge, this is the first report on the fatty alcohol production in the hairy root cultures. Biotechnol. Bioeng. 2017;114: 1275-1282. © 2016 Wiley Periodicals, Inc.

A roadmap for the synthesis of separation networks for the recovery of bio-based chemicals: Matching biological and process feasibility

Microbial conversion of renewable feedstocks to high-value chemicals is an attractive alternative to current petrochemical processes because it offers the potential to reduce net CO₂ emissions and integrate with bioremediation objectives. Microbes have been genetically engineered to produce a growing number of high-value chemicals in sufficient titer, rate, and yield from renewable feedstocks. However, high-yield bioconversion is only one aspect of an economically viable process. Separation of biologically synthesized chemicals from process streams is a major challenge that can contribute to >70% of the total production costs. Thus, process feasibility is dependent upon the efficient selection of separation technologies. This selection is dependent on upstream processing or biological parameters, such as microbial species, product titer and yield, and localization. Our goal is to present a roadmap for selection of appropriate technologies and generation of separation schemes for efficient recovery of bio-based chemicals by utilizing information from upstream processing, separation science and commercial requirements. To achieve this, we use a separation system comprising of three stages: (I) cell and product isolation, (II) product concentration, and (III) product purification and refinement. In each stage, we review the technology alternatives available for different tasks in terms of separation principles, important operating conditions, performance parameters, advantages and disadvantages. We generate separation schemes based on product localization and its solubility in water, the two most distinguishing properties. Subsequently, we present ideas for simplification of these schemes based on additional properties, such as physical state, density, volatility, and intended use. This simplification selectively narrows down the technology options and can be used for systematic process synthesis and optimal recovery of bio-based chemicals.

Microbial production of fatty alcohols

Fatty alcohols have numerous commercial applications, including their use as lubricants, surfactants, solvents, emulsifiers, plasticizers, emollients, thickeners, and even fuels. Fatty alcohols are currently produced by catalytic hydrogenation of fatty acids from plant oils or animal fats. Microbial production of fatty alcohols may be a more direct and environmentally-friendly strategy since production is carried out by heterologous enzymes, called fatty acyl-CoA reductases, able to reduce different acyl-CoA molecules to their corresponding primary alcohols. Successful examples of metabolic engineering have been reported in Saccharomyces cerevisiae and Escherichia coli in which the production of fatty alcohols ranged from 1.2 to 1.9 g/L, respectively. Due to their metabolic advantages, oleaginous yeasts are considered the best hosts for production of fatty acid-derived chemicals. Some of these species can naturally produce, under specific growth conditions, lipids at high titers (>50 g/L) and therefore provide large amounts of fatty acyl-CoAs or fatty acids as precursors. Very recently, taking advantage of such features, over 8 g/L of C16-C18 fatty alcohols have been produced in Rhodosporidium toruloides. In this review we summarize the different metabolic engineering strategies, hosts and cultivation conditions used to date. We also point out some future trends and challenges for the microbial production of fatty alcohols.

Extending the biosynthetic repertoires of cyanobacteria and chloroplasts

Chloroplasts in plants and algae and photosynthetic microorganisms such as cyanobacteria are emerging hosts for sustainable production of valuable biochemicals, using only inorganic nutrients, water, CO2 and light as inputs. In the past decade, many bioengineering efforts have focused on metabolic engineering and synthetic biology in the chloroplast or in cyanobacteria for the production of fuels, chemicals and complex, high-value bioactive molecules. Biosynthesis of all these compounds can be performed in photosynthetic organelles/organisms by heterologous expression of the appropriate pathways, but this requires optimization of carbon flux and reducing power, and a thorough understanding of regulatory pathways. Secretion or storage of the compounds produced can be exploited for the isolation or confinement of the desired compounds. In this review, we explore the use of chloroplasts and cyanobacteria as biosynthetic compartments and hosts, and we estimate the levels of production to be expected from photosynthetic hosts in light of the fraction of electrons and carbon that can potentially be diverted from photosynthesis. The supply of reducing power, in the form of electrons derived from the photosynthetic light reactions, appears to be non-limiting, but redirection of the fixed carbon via precursor molecules presents a challenge. We also discuss the available synthetic biology tools and the need to expand the molecular toolbox to facilitate cellular reprogramming for increased production yields in both cyanobacteria and chloroplasts.

CRISPR/Cas9 mediated targeted mutagenesis of the fast growing cyanobacterium Synechococcus elongatus UTEX 2973

Background

As autotrophic prokaryotes, cyanobacteria are ideal chassis organisms for sustainable production of various useful compounds. The newly characterized cyanobacterium Synechococcus elongatus UTEX 2973 is a promising candidate for serving as a microbial cell factory because of its unusually rapid growth rate. Here, we seek to develop a genetic toolkit that enables extensive genomic engineering of Synechococcus 2973 by implementing a CRISPR/Cas9 editing system. We targeted the nblA gene because of its important role in biological response to nitrogen deprivation conditions.

Results

First, we determined that the Streptococcus pyogenes Cas9 enzyme is toxic in cyanobacteria, and conjugational transfer of stable, replicating constructs containing the cas9 gene resulted in lethality. However, after switching to a vector that permitted transient expression of the cas9 gene, we achieved markerless editing in 100 % of cyanobacterial exconjugants after the first patch. Moreover, we could readily cure the organisms of antibiotic resistance, resulting in a markerless deletion strain.

Conclusions

High expression levels of the Cas9 protein in Synechococcus 2973 appear to be toxic and result in cell death. However, introduction of a CRISPR/Cas9 genome editing system on a plasmid backbone that leads to transient cas9 expression allowed for efficient markerless genome editing in a wild type genetic background.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0514-7) contains supplementary material, which is available to authorized users.

The Effect of Functional Groups in Bio-Derived Fuel Candidates

Interest in developing renewable fuels is continuing to grow and biomass represents a viable source of renewable carbon with which to replace fossil-based components in transportation fuels. During our own work, we noticed that chemists think in terms of functional groups whereas fuel engineers think in terms of physical fuel properties. In this Concept article, we discuss the effect of carbon and oxygen functional groups on potential fuel properties. This serves as a way of informing our own thinking and provides us with a basis with which to design and synthesize molecules from biomass that could provide useful transportation fuels.

Arabidopsis acyl-acyl carrier protein synthetase AAE15 with medium chain fatty acid specificity is functional in cyanobacteria

Cyanobacteria are potential hosts for the biosynthesis of oleochemical compounds. The metabolic precursors for such compounds are fatty acids and their derivatives, which require chemical activation to become substrates in further conversion steps. We characterized the acyl activating enzyme AAE15 of Arabidopsis encoded by At4g14070, which is a homologue of a cyanobacterial acyl-ACP synthetase (AAS). We expressed AAE15 in insect cells and demonstrated its AAS activity with medium chain fatty acid (C10-C14) substrates in vitro. Furthermore, we used AAE15 to complement a Synechocystis aas deletion mutant and showed that the new strain preferentially incorporates supplied medium chain fatty acids into internal lipid molecules. Based on this data we propose that AAE15 can be utilized in metabolic engineering strategies for cyanobacteria that aim to produce compounds based on medium chain fatty acids.

Comparison of aldehyde-producing activities of cyanobacterial acyl-(acyl carrier protein) reductases

BACKGROUND

Biosynthesis of alkanes is an attractive way of producing substitutes for petroleum-based alkanes. Acyl-[acyl carrier protein (ACP)] reductase (AAR) is a key enzyme for alkane biosynthesis in cyanobacteria and catalyzes the reduction of fatty acyl-ACP to fatty aldehydes, which are then converted into alkanes/alkenes by aldehyde-deformylating oxygenase (ADO). The amino acid sequences of AARs vary among cyanobacteria. However, their differences in catalytic activity, substrate specificity, and solubility are poorly understood.

RESULTS

We compared the aldehyde-producing activity, substrate specificity, and solubility of AARs from 12 representative cyanobacteria. The activity is the highest for AAR from Synechococcus elongatus PCC 7942, followed by AAR from Prochlorococcus marinus MIT 9313. On the other hand, protein solubility is high for AARs from PCC 7942, Microcystis aeruginosa, Thermosynechococcus elongatus BP-1, Synechococcus sp. RS9917, and Synechococcus sp. CB0205. As a consequence, the amount of alkanes/alkenes produced in Escherichia coli coexpressing AAR and ADO is the highest for AAR from PCC 7942, followed by AARs from BP-1 and MIT 9313. Strikingly, AARs from marine and freshwater cyanobacteria tend to have higher specificity toward the substrates with 16 and 18 carbons in the fatty acyl chain, respectively, suggesting that the substrate specificity of AARs correlates with the type of habitat of host cyanobacteria. Furthermore, mutational analysis identified several residues responsible for the high activity of AAR.

CONCLUSIONS

We found that the activity, substrate specificity, and solubility are diverse among various AARs. Our results provide a basis for selecting an AAR sequence suitable for metabolic engineering of bioalkane production while regulating carbon chain length.

Exploring fatty alcohol-producing capability of Yarrowia lipolytica

BACKGROUND

Fatty alcohols are important oleochemicals widely used in detergents, surfactants and personal care products. Bio-synthesized fatty alcohol provides a promising alternative to traditional fatty alcohol industry. Harnessing oleaginous microorganisms for fatty alcohol production may offer a new strategy to achieve a commercially viable yield that currently still seems to be a remote target.

RESULTS

In this study, we introduced functional fatty acyl-CoA reductase (FAR), TaFAR1 to direct the conversion from fatty acyl-CoA to fatty alcohol in Yarrowia lipolytica (Y. lipolytica), an oleaginous non-conventional yeast showing great lipid-producing capability. Tri-module optimizations including eliminating fatty alcohol degradation pathway, enhancing TaFAR1 expression, and increasing fatty acyl-CoA supply were furtherly conducted, resulting in 63-fold increase in intracellular fatty alcohol-producing capability compared to the starting strain. Thus, this work demonstrated successful construction of first generation of Y. lipolytica fatty alcohol-producing cell factory. Through the study of effect of environmental nutrition on fatty alcohol production, up to 636.89 mg/L intracellular hexadecanol (high fatty alcohol-retaining capability) and 53.32 mg/L extracellular hexadecanol were produced by this cell factory through batch fermentation, which was comparable to the highest production of Saccharomyces cerevisiae under the similar condition.

CONCLUSION

This work preliminarily explored fatty alcohol-producing capability through mobilization of FAR and fatty acid metabolism, maximizing the intracellular fatty alcohol-producing capability, suggesting that Y. lipolytica cell factory potentially offers a promising platform for fatty alcohol production.

Metabolic Engineering and Comparative Performance Studies of Synechocystis sp. PCC 6803 Strains for Effective Utilization of Xylose

Wood sugars such as xylose can be used as an inexpensive carbon source for biotechnological applications. The model cyanobacterium Synechocystis sp. PCC 6803 lacks the ability to catabolize wood sugars as an energy source. Here, we generated four Synechocystis strains that heterologously expressed XylAB enzymes, which mediate xylose catabolism, either in combination with or without one of three xylose transporters, namely XylE, GalP, or Glf. Except for glf, which is derived from the bacterium Zymomonas mobilis ZM4, the heterologous genes were sourced from Escherichia coli K-12. All of the recombinant strains were able to utilize xylose in the absence of catabolite repression. When xylose was the lone source of organic carbon, strains possessing the XylE and Glf transporters were most efficient in terms of dry biomass production and xylose consumption and the strain lacking a heterologous transporter was the least efficient. However, in the presence of a xylose-glucose mixed sugar source, the strains exhibited similar levels of growth and xylose consumption. This study demonstrates that various bacterial xylose transporters can boost xylose catabolism in transgenic Synechocystis strains, and paves the way for the sustainable production of bio-compounds and green fuels from lignocellulosic biomass.

The state of autotrophic ethanol production in Cyanobacteria

Ethanol production directly from CO2 , utilizing genetically engineered photosynthetic cyanobacteria as a biocatalyst, offers significant potential as a renewable and sustainable source of biofuel. Despite the current absence of a commercially successful production system, significant resources have been deployed to realize this goal. Utilizing the pyruvate decarboxylase from Zymomonas species, metabolically derived pyruvate can be converted to ethanol. This review of both peer-reviewed and patent literature focuses on the genetic modifications utilized for metabolic engineering and the resultant effect on ethanol yield. Gene dosage, induced expression and cassette optimizat-ion have been analyzed to optimize production, with production rates of 0·1-0·5 g L(-1) day(-1) being achieved. The current 'toolbox' of molecular manipulations and future directions focusing on applicability, addressing the primary challenges facing commercialization of cyanobacterial technologies are discussed.

Biosynthesis of odd-chain fatty alcohols in Escherichia coli

Engineered microbes offer the opportunity to design and implement artificial molecular pathways for renewable production of tailored chemical commodities. Targeted biosynthesis of odd-chain fatty alcohols is very challenging in microbe, due to the specificity of fatty acids synthase for two-carbon unit elongation. Here, we developed a novel strategy to directly tailor carbon number in fatty aldehydes formation step by incorporating α-dioxygenase (αDOX) from Oryza sativa (rice) into Escherichia coli αDOX oxidizes Cn fatty acids (even-chain) to form Cn-1 fatty aldehydes (odd-chain). Through combining αDOX with fatty acyl-acyl carrier protein (-ACP) thioesterase (TE) and aldehyde reductase (AHR), the medium odd-chain fatty alcohols profile (C11, C13, C15) was firstly established in E. coli. Also, medium even-chain alkanes (C12, C14) were obtained by substitution of AHR to aldehyde decarbonylase (AD). The titer of odd-chain fatty alcohols was improved from 7.4mg/L to 101.5mg/L in tube cultivation by means of fine-tuning endogenous fatty acyl-ACP TE (TesA'), αDOX, AHRs and the genes involved in fatty acids metabolism pathway. Through high cell density fed-batch fermentation, a titer of 1.95g/L odd-chain fatty alcohols was achieved, which was the highest reported titer in E. coli. Our system has greatly expanded the current microbial fatty alcohols profile that provides a new brand solution for producing complex and desired molecules in microbes.