Alkane production by the marine cyanobacterium Synechococcus sp. NKBG15041c possessing the α-olefin biosynthesis pathway

Biosynthesis pathways of expanding carbon chains for producing advanced biofuels

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

Insights into cyanobacterial alkane biosynthesis

Alkanes are high-energy molecules that are compatible with enduring liquid fuel infrastructures, which make them highly suitable for being next-generation biofuels. Though biological production of alkanes has been reported in various microorganisms, the reports citing photosynthetic cyanobacteria as natural producers have been the most consistent for the long-chain alkanes and alkenes (C15-C19). However, the production of alkane in cyanobacteria is low, leading to its extraction being uneconomical for commercial purposes. In order to make alkane production economically feasible from cyanobacteria, the titre and yield need to be increased by several orders of magnitude. In the recent past, efforts have been made to enhance alkane production, although with a little gain in yield, leaving space for much improvement. Genetic manipulation in cyanobacteria is considered challenging, but recent advancements in genetic engineering tools may assist in manipulating the genome in order to enhance alkane production. Further, advancement in a basic understanding of metabolic pathways and gene functioning will guide future research for harvesting the potential of these tiny photosynthetically efficient factories. In this review, our focus would be to highlight the current knowledge available on cyanobacterial alkane production, and the potential aspects of developing cyanobacterium as an economical source of biofuel. Further insights into different metabolic pathways and hosts explored so far, and possible challenges in scaling up the production of alkanes will also be discussed.

Composition and biotransformational changes in soluble microbial products (SMPs) along an anaerobic baffled reactor (ABR)

This work examined the production and catabolism/biotransformation dynamics of SMPs down the length of an eight-compartment-anaerobic baffled reactor (ABR) which physically separates the biological processes, in contrast to completely mixed reactors which do not enable these dynamics to measured, and this is totally novel. SMPs were extracted and characterised by gas and liquid chromatography coupled mass spectrometry to determine their composition and production/catabolism. 60%-70% of the feed compounds decreased from the first to fourth compartment; the increase in SMPs after the fourth compartment suggested a mixture of degraded and biotransformed compounds, and microbial products. High concentrations of low MW alkanes and alkenes, and higher MW (up to 2000 Da) lipids and amino acid derivatives accumulate in the last compartment at pseudo-steady state, and past work identifying polysaccharides/peptides as major membrane biofoulants have excluded these lipids. In addition, lipids and changes detected during feed transients have not been noted before in previous work. Finally, feed step-increases also increased some amino acid derivatives used in cell-signalling. Interestingly, some natural products from plant and fungal extracts were also found in the fourth compartment, where methanogenesis was the dominant process.

Engineering salt tolerance of photosynthetic cyanobacteria for seawater utilization

Photosynthetic cyanobacteria are capable of utilizing sunlight and CO₂ as sole energy and carbon sources, respectively. With genetically modified cyanobacteria being used as a promising chassis to produce various biofuels and chemicals in recent years, future large-scale cultivation of cyanobacteria would have to be performed in seawater, since freshwater supplies of the earth are very limiting. However, high concentration of salt is known to inhibit the growth of cyanobacteria. This review aims at comparing the mechanisms that different cyanobacteria respond to salt stress, and then summarizing various strategies of developing salt-tolerant cyanobacteria for seawater cultivation, including the utilization of halotolerant cyanobacteria and the engineering of salt-tolerant freshwater cyanobacteria. In addition, the challenges and potential strategies related to further improving salt tolerance in cyanobacteria are also discussed.

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.

Evolutionary Engineering of Cyanobacteria to Enhance the Production of α-Farnesene from CO2

Photosynthetic cyanobacteria can fix CO₂ and utilize it as the sole carbon source for cell growth and production of biochemicals. Here, we metabolically engineered Synechococcus elongatus PCC 7942 for an enhanced production of α-farnesene by optimizing the ribosome-binding site (RBS) of the codon-optimized farnesene synthase gene. The production of α-farnesene was found to be enhanced in strains with a low translation initiation rate, resulting in α-farnesene production (0.57 mg/(L day)). Using the RBS variants and random mutations, we performed fluorescence-based analysis of cells grown in 96-well culture plates to screen the α-farnesene-producing strains but could not improve the titers of the RBS-optimized strains. However, evolutionary engineering of the RBS-optimized strains resulted in a twofold increase in α-farnesene production (1.2 mg/(L day)) compared to the previous study. Therefore, combining metabolic and evolutionary engineering might be helpful for enhancing the cellular fitness of cyanobacteria for the production of target chemicals.

State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio-Economy Challenges

In recent years, metabolic engineering of microorganisms has attained much research interest to produce biofuels and industrially pertinent chemicals. Owing to the relatively fast growth rate, genetic malleability, and carbon neutral production process, cyanobacteria has been recognized as a specialized microorganism with a significant biotechnological perspective. Metabolically engineering cyanobacterial strains have shown great potential for the photosynthetic production of an array of valuable native or non-native chemicals and metabolites with profound agricultural and pharmaceutical significance using CO₂ as a building block. In recent years, substantial improvements in developing and introducing novel and efficient genetic tools such as genome-scale modeling, high throughput omics analyses, synthetic/system biology tools, metabolic flux analysis and clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease (CRISPR/cas) systems have been made for engineering cyanobacterial strains. Use of these tools and technologies has led to a greater understanding of the host metabolism, as well as endogenous and heterologous carbon regulation mechanisms which consequently results in the expansion of maximum productive ability and biochemical diversity. This review summarizes recent advances in engineering cyanobacteria to produce biofuel and industrially relevant fine chemicals of high interest. Moreover, the development and applications of cutting-edge toolboxes such as the CRISPR-cas9 system, synthetic biology, high-throughput "omics", and metabolic flux analysis to engineer cyanobacteria for large-scale cultivation are also discussed.

Identification of non-conserved residues essential for improving the hydrocarbon-producing activity of cyanobacterial aldehyde-deformylating oxygenase

BACKGROUND

Cyanobacteria produce hydrocarbons corresponding to diesel fuels by means of aldehyde-deformylating oxygenase (ADO). ADO catalyzes a difficult and unusual reaction in the conversion of aldehydes to hydrocarbons and has been widely used for biofuel production in metabolic engineering; however, its activity is low. A comparison of the amino acid sequences of highly active and less active ADOs will elucidate non-conserved residues that are essential for improving the hydrocarbon-producing activity of ADOs.

RESULTS

Here, we measured the activities of ADOs from 10 representative cyanobacterial strains by expressing each of them in Escherichia coli and quantifying the hydrocarbon yield and amount of soluble ADO. We demonstrated that the activity was highest for the ADO from Synechococcus elongatus PCC 7942 (7942ADO). In contrast, the ADO from Gloeobacter violaceus PCC 7421 (7421ADO) had low activity but yielded high amounts of soluble protein, resulting in a high production level of hydrocarbons. By introducing 37 single amino acid substitutions at the non-conserved residues of the less active ADO (7421ADO) to make its sequence more similar to that of the highly active ADO (7942ADO), we found 20 mutations that improved the activity of 7421ADO. In addition, 13 other mutations increased the amount of soluble ADO while maintaining more than 80% of wild-type activity. Correlation analysis showed a solubility-activity trade-off in ADO, in which activity was negatively correlated with solubility.

CONCLUSIONS

We succeeded in identifying non-conserved residues that are essential for improving ADO activity. Our results may be useful for generating combinatorial mutants of ADO that have both higher activity and higher amounts of the soluble protein in vivo, thereby producing higher yields of biohydrocarbons.

Diverse hydrocarbon biosynthetic enzymes can substitute for olefin synthase in the cyanobacterium Synechococcus sp. PCC 7002

Cyanobacteria are among only a few organisms that naturally synthesize long-chain alkane and alkene hydrocarbons. Cyanobacteria use one of two pathways to synthesize alka/enes, either acyl-ACP reductase (Aar) and aldehyde deformylating oxygenase (Ado) or olefin synthase (Ols). The genomes of cyanobacteria encode one of these pathways but never both, suggesting a mutual exclusivity. We studied hydrocarbon pathway compatibility using the model cyanobacterium Synechococcus sp. PCC 7002 (S7002) by co-expressing Ado/Aar and Ols and by entirely replacing Ols with three other types of hydrocarbon biosynthetic pathways. We find that Ado/Aar and Ols can co-exist and that slower growth occurs only when Ado/Aar are overexpressed at 38 °C. Furthermore, Ado/Aar and the non-cyanobacterial enzymes UndA and fatty acid photodecarboxylase are able to substitute for Ols in a knockout strain and conditionally rescue slow growth. Production of hydrocarbons by UndA in S7002 required a rational mutation to increase substrate range. Expression of the non-native enzymes in S7002 afforded unique hydrocarbon profiles and alka/enes not naturally produced by cyanobacteria. This suggests that the biosynthetic enzyme and the resulting types of hydrocarbons are not critical to supporting growth. Exchanging or mixing hydrocarbon pathways could enable production of novel types of CO2-derived hydrocarbons in cyanobacteria.

Improved lipid production via fatty acid biosynthesis and free fatty acid recycling in engineered Synechocystis sp. PCC 6803

BACKGROUND

Cyanobacteria are potential sources for third generation biofuels. Their capacity for biofuel production has been widely improved using metabolically engineered strains. In this study, we employed metabolic engineering design with target genes involved in selected processes including the fatty acid synthesis (a cassette of accD, accA, accC and accB encoding acetyl-CoA carboxylase, ACC), phospholipid hydrolysis (lipA encoding lipase A), alkane synthesis (aar encoding acyl-ACP reductase, AAR), and recycling of free fatty acid (FFA) (aas encoding acyl-acyl carrier protein synthetase, AAS) in the unicellular cyanobacterium Synechocystis sp. PCC 6803.

RESULTS

To enhance lipid production, engineered strains were successfully obtained including an aas-overexpressing strain (OXAas), an aas-overexpressing strain with aar knockout (OXAas/KOAar), and an accDACB-overexpressing strain with lipA knockout (OXAccDACB/KOLipA). All engineered strains grew slightly slower than wild-type (WT), as well as with reduced levels of intracellular pigment levels of chlorophyll a and carotenoids. A higher lipid content was noted in all the engineered strains compared to WT cells, especially in OXAas, with maximal content and production rate of 34.5% w/DCW and 41.4 mg/L/day, respectively, during growth phase at day 4. The OXAccDACB/KOLipA strain, with an impediment of phospholipid hydrolysis to FFA, also showed a similarly high content of total lipid of about 32.5% w/DCW but a lower production rate of 31.5 mg/L/day due to a reduced cell growth. The knockout interruptions generated, upon a downstream flow from intermediate fatty acyl-ACP, an induced unsaturated lipid production as observed in OXAas/KOAar and OXAccDACB/KOLipA strains with 5.4% and 3.1% w/DCW, respectively.

CONCLUSIONS

Among the three metabolically engineered Synechocystis strains, the OXAas with enhanced free fatty acid recycling had the highest efficiency to increase lipid production.

Identification of two genes required for heptadecane production in a N2-fixing cyanobacterium Anabaena sp. strain PCC 7120

Cyanobacteria photosynthetically produce long-chain hydrocarbons, which are considered as infrastructure-compatible biofuels. However, native cyanobacteria do not produce these hydrocarbons at sufficient rates or yields to warrant commercial deployment. This research sought to identify specific genes required for photosynthetic production of alkanes to enable future metabolic engineering for commercially viable production of alkanes. The two putative genes (alr5283 and alr5284) required for long-chain hydrocarbon production in Anabaena sp. PCC 7120 were knocked out through a double crossover approach. The knockout mutant abolished the production of heptadecane (C₁₇H₃₆). The mutant is able to be complemented by a plasmid bearing the two genes along with their native promoters only. The complemented mutant restored photosynthetic production of heptadecane. This combined genetic and metabolite (alkanes) profiling approach may be broadly applicable to characterization of knockout mutants, using N₂-fixing cyanobacteria as a cellular factory driven by solar energy to produce a wide range of commodity chemicals and drop-in-fuels from atmospheric gases (CO₂ and N₂ gas) and mineralized water.

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.

Unique marine derived cyanobacterial biosynthetic genes for chemical diversity

Cyanobacteria are a prolific source of structurally unique and biologically active natural products that derive from intriguing biochemical pathways. Advancements in genome sequencing have accelerated the identification of unique modular biosynthetic gene clusters in cyanobacteria and reveal a wealth of unusual enzymatic reactions involved in their construction. This article examines several interesting mechanistic transformations involved in cyanobacterial secondary metabolite biosynthesis with a particular focus on marine derived modular polyketide synthases (PKS), nonribosomal peptide synthetases (NRPS) and combinations thereof to form hybrid natural products. Further, we focus on the cyanobacterial genus Moorea and the co-evolution of its enzyme cassettes that create metabolic diversity. Progress in the development of heterologous expression systems for cyanobacterial gene clusters along with chemoenzymatic synthesis makes it possible to create new analogs. Additionally, phylum-wide genome sequencing projects have enhanced the discovery rate of new natural products and their distinctive enzymatic reactions. Summarizing, cyanobacterial biosynthetic gene clusters encode for a large toolbox of novel enzymes that catalyze unique chemical reactions, some of which may be useful in synthetic biology.

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.

Hydrocarbons, the advanced biofuels produced by different organisms, the evidence that alkanes in petroleum can be renewable

It is generally regarded that the petroleum cannot be renewable. However, in recent years, it has been found that many marine cyanobacteria, some eubacteria, engineered Escherichia coli, some endophytic fungi, engineered yeasts, some marine yeasts, plants, and insects can synthesize hydrocarbons with different carbon lengths. If the organisms, especially some native microorganisms and engineered bacteria and yeasts, can synthesize and secret a large amount of hydrocarbons within a short period, alkanes in the petroleum can be renewable. It has been documented that there are eight pathways for hydrocarbon biosynthesis in different organisms. Unfortunately, most of native microorganisms, engineered E. coli and engineered yeasts, only synthesize a small amount of intracellular and extracellular hydrocarbons. Recently, Aureobasidium pullulans var. melanogenum isolated from a mangrove ecosystem has been found to be able to synthesize and secret over 21.5 g/l long-chain hydrocarbons with a yield of 0.275 g/g glucose and a productivity of 0.193 g/l/h within 5 days. The yeast may have highly potential applications in alkane production.

Cyanobacteria: Photoautotrophic Microbial Factories for the Sustainable Synthesis of Industrial Products

Cyanobacteria are widely distributed Gram-negative bacteria with a long evolutionary history and the only prokaryotes that perform plant-like oxygenic photosynthesis. Cyanobacteria possess several advantages as hosts for biotechnological applications, including simple growth requirements, ease of genetic manipulation, and attractive platforms for carbon neutral production process. The use of photosynthetic cyanobacteria to directly convert carbon dioxide to biofuels is an emerging area of interest. Equipped with the ability to degrade environmental pollutants and remove heavy metals, cyanobacteria are promising tools for bioremediation and wastewater treatment. Cyanobacteria are characterized by the ability to produce a spectrum of bioactive compounds with antibacterial, antifungal, antiviral, and antialgal properties that are of pharmaceutical and agricultural significance. Several strains of cyanobacteria are also sources of high-value chemicals, for example, pigments, vitamins, and enzymes. Recent advances in biotechnological approaches have facilitated researches directed towards maximizing the production of desired products in cyanobacteria and realizing the potential of these bacteria for various industrial applications. In this review, the potential of cyanobacteria as sources of energy, bioactive compounds, high-value chemicals, and tools for aquatic bioremediation and recent progress in engineering cyanobacteria for these bioindustrial applications are discussed.