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

Turning food waste to microbial lipid towards a superb economic and environmental sustainability: An innovative integrated biological route

With the drastic growth of the economic and population, the global energy requirement is on the rise, and massive human and material resources have been put into the development of alternative and renewable energy sources. Biodiesel has been recognized as a green and sustainable alternative energy, but the raw materials-associated source and cost makes it difficult to achieve large-scale commercial production. Microbial lipids (ML) produced by oleaginous microbes have attracted more and more topics as feedstocks for biodiesel production because of their unique advantages (fast growth cycle, small footprint and so on). However, there are still many problems and challenges ahead towards commercialization of ML-based biodiesel, especially the cost of feedstock for ML production. Food waste (FW) rich in organic matters and nutrients is an excellent and almost zero-cost feedstock for ML production. However, current biological routes of FW-based ML production have some defects, which make it impossible to achieve full industrialization at present. Therefore, this review intends to provide a critical and comprehensive analysis of current biological routes of FW-based ML production with the focus on the challenges and solutions forward. The biological routes towards future FW-based ML production must be able to concurrently achieve economic feasibility and environmental sustainability. On this condition, an innovative integrated biological route for FW-based ML production has thus been put forward, which is also elucidated on its economic and environmental sustainability. Moreover, the prospective advantages, limitations and challenges for future scale-up of FW-based ML production have also been outlined, together with the perspectives and directions forward.

The adc1 knockout with proC overexpression in Synechocystis sp. PCC 6803 induces a diversion of acetyl-CoA to produce more polyhydroxybutyrate

BACKGROUND

Lack of nutrients, in particular nitrogen and phosphorus, has been known in the field to sense glutamate production via 2-oxoglutarate and subsequently accelerate carbon storage, including glycogen and polyhydroxybutyrate (PHB), in cyanobacteria, but a few studies have focused on arginine catabolism. In this study, we first time demonstrated that gene manipulation on proC and adc1, related to proline and polyamine syntheses in arginine catabolism, had a significant impact on enhanced PHB production during late growth phase and nutrient-modified conditions. We constructed Synechocystis sp. PCC 6803 with an overexpressing proC gene, encoding Δ1pyrroline-5-carboxylate reductase in proline production, and adc1 disruption resulted in lower polyamine synthesis.

RESULTS

Three engineered Synechocystis sp. PCC 6803 strains, including a ProC-overexpressing strain (OXP), adc1 mutant, and an OXP strain lacking the adc1 gene (OXP/Δadc1), certainly increased the PHB accumulation under nitrogen and phosphorus deficiency. The possible advantages of single proC overexpression include improved PHB and glycogen storage in late phase of growth and long-term stress situations. However, on day 7 of treatment, the synergistic impact created by OXP/Δadc1 increased PHB synthesis by approximately 48.9% of dry cell weight, resulting in a shorter response to nutrient stress than the OXP strain. Notably, changes in proline and glutamate contents in engineered strains, in particular OXP and OXP/Δadc1, not only partially balanced the intracellular C/N metabolism but also helped cells acclimate under nitrogen (N) and phosphorus (P) stress with higher chlorophyll a content in comparison with wild-type control.

CONCLUSIONS

In Synechocystis sp. PCC 6803, overexpression of proC resulted in a striking signal to PHB and glycogen accumulation after prolonged nutrient deprivation. When combined with the adc1 disruption, there was a notable increase in PHB production, particularly in situations where there was a strong C supply and a lack of N and P.

Improved lipid production and component of mycosporine-like amino acids by co-overexpression of amt1 and aroB genes in Synechocystis sp. PCC6803

Implementing homologous overexpression of the amt1 (A) and aroB (B) genes involved in ammonium transporter and the synthesis of mycosporine-like amino acids (MAAs) and aromatic amino acids, respectively, we created three engineered Synechocystis sp. PCC6803 strains, including Ox-A, Ox-B, and Ox-AB, to study the utilization of carbon and nitrogen in cyanobacteria for the production of valuable products. With respect to amt1 overexpression, the Ox-A and Ox-AB strains had a greater growth rate under (NH4)2SO4 supplemented condition. Both the higher level of intracellular accumulation of lipids in Ox-A and Ox-AB as well as the increased secretion of free fatty acids from the Ox-A strain were impacted by the late-log phase of cell growth. It is noteworthy that among all strains, the Ox-B strain undoubtedly spotted a substantial accumulation of glycogen as a consequence of aroB overexpression. Additionally, the ammonium condition drove the potent antioxidant activity in Ox strains with a late-log phase, particularly in the Ox-B and Ox-AB strains. This was probably related to the altered MAA component inside the cells. The higher proportion of P4-fraction was induced by the ammonium condition in both Ox-B and Ox-AB, while the noted increase of the P1 component was found in the Ox-A strain.

Increased Biomass and Polyhydroxybutyrate Production by Synechocystis sp. PCC 6803 Overexpressing RuBisCO Genes

The overexpression of the RuBisCO (rbc) gene has recently become an achievable strategy for increasing cyanobacterial biomass and overcoming the biocompound production restriction. We successfully constructed two rbc-overexpressing Synechocystis sp. PCC 6803 strains (OX), including a strain overexpressing a large subunit of RuBisCO (OXrbcL) and another strain overexpressing all large, chaperone, and small subunits of RuBisCO (OXrbcLXS), resulting in higher and faster growth than wild type under sodium bicarbonate supplementation. This increased biomass of OX strains significantly contributed to the higher polyhydroxybutyrate (PHB) production induced by nutrient-deprived conditions, in particular nitrogen (N) and phosphorus (P). As a result of higher PHB contents in OX strains occurring at days 7 and 9 of nutrient deprivation, this enhancement was apparently made possible by cells preferentially maintaining their internal lipids while accumulating less glycogen. The OXrbcLXS strain, with the highest level of PHB at about 39 %w/dry cell weight (DCW) during 7 days of BG11-NP treatment, contained a lower glycogen level (31.9 %w/DCW) than wild type control (40 %w/DCW). In contrast, the wild type control strain exposed to N- and NP-stresses tended to retain lipid levels and store more glycogen than PHB. In this model, we, for the first time, implemented a RuBisCO-overexpressing cyanobacterial factory for overproducing PHB, destined for biofuel and biomaterial biotechnology.

Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling

Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.

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.

Enhanced productivity of extracellular free fatty acids by gene disruptions of acyl-ACP synthetase and S-layer protein in Synechocystis sp. PCC 6803

Background

Based on known metabolic response to excess free fatty acid (FFA) products, cyanobacterium Synechocystis sp. PCC 6803 preferentially both recycles via FFA recycling process and secrets them into medium. Engineered cyanobacteria with well growth and highly secreted FFA capability are considered best resources for biofuel production and sustainable biotechnology. In this study, to achieve the higher FFA secretion goal, we successfully constructs Synechocystis sp. PCC 6803 mutants disrupting genes related to FFA recycling reaction (aas gene encoding acyl–acyl carrier protein synthetase), and surface layer protein (encoded by sll1951).

Results

Three Synechocystis sp. PCC 6803 engineered strains, including two single mutants lacking aas (KA) and sll1951 (KS), and one double mutant lacking both aas and sll1951 (KAS), significantly secreted FFAs higher than that of wild type (WT). Certain increase of secreted FFAs was noted when cells were exposed to nitrogen-deficient conditions, BG₁₁-half N and BG₁₁-N conditions, with the exception of strain KS. Under BG₁₁-N condition at day 10, strain KAS strikingly secreted FFAs products up to 40%w/DCW or 238.1 mg/L, with trace amounts of PHB. Unexpectedly, strain KS, with S-layer disruption, appeared to have endured longer in BG₁₁-N growth medium. This strain KS significantly acclimated to the BG₁₁-N environment by accumulating a greater glycogen pool with lower FFA production, whereas strain KA favored higher PHB and intracellular lipid accumulations with moderate FFA secretion.

Conclusions

Mutations of both aas and sll1951 genes in Synechocystis sp. PCC 6803 significantly improved the productivity of secreted FFAs, especially under nitrogen deprivation.

Native SodB Overexpression of Synechocystis sp. PCC 6803 Improves Cell Growth Under Alcohol Stresses Whereas Its Gpx2 Overexpression Impacts on Growth Recovery from Alcohol Stressors

To overcome the limited resistance to alcohol stress, genetically engineered Synechocystis sp. PCC 6803 strains with overexpressions of genes related with the ROS detoxification system (sodB and gpx2, which encode superoxide dismutase and glutathione peroxidase, respectively) were developed. Three engineered strains including a sodB-overexpressing strain (OE + S), a gpx2-overexpressing strain (OE + G), and a sodB/gpx2-overexpressing strain (OE + SG) grew similarly as wild-type control under normal condition. When compared to wild-type control, OE + S and OE + SG strains grew faster for 4 days under 2.0% (v/v) ethanol and 0.3% (v/v) n-butanol conditions, as well as having higher chlorophyll a levels. On the other hand, the prominent growth recovery of OE + G and OE + SG was noted within 4 days in normal BG₁₁ medium after treating cells with high alcohol stresses for 1 h, in particular 15% ethanol and 2.5% n-butanol. Under 4 days of recovery from butanol stress, specific levels of intracellular pigments including chlorophyll a and carotenoids were dramatically increased in all modified strains. The overexpression of antioxidant genes then revealed a significant improvement of alcohol tolerance in Synechocystis sp. PCC 6803.

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.

Overexpression of fatty acid synthesis genes in Synechocystis sp. PCC 6803 with disrupted glycogen synthesis increases lipid production with further enhancement under copper induced oxidative stress

In the present study, fatty acid synthesis genes such as alpha and beta subunits of acetyl CoA carboxylase (accA and accD) were overexpressed in the glgC (Glucose-1-phosphate adenylyltransferase) knockout Synechocystis sp. PCC 6803. The biomass and lipid contents were evaluated in both the wild type and the engineered strains after copper treatment. The maximum lipid production of 0.981 g/L with the productivity of 81.75 mg/L/d was obtained from the copper treated ΔglgC + A-OX strain, which showed a 3.3-fold increase compared to the untreated wild type with satisfactory biodiesel properties. After copper treatment the knockout strain improved the unsaturated fatty acids level contributing to the increase of the saturated and mono-unsaturated ratio with improvement of the fuel quality. Copper induced oxidative stress also improved the photosynthetic pigments in engineered strains leading to increased tolerance against oxidative stress in the engineered strains. The copper treatment increased the antioxidant enzyme activities in the engineered strains especially in ΔglgC + A-OX strain. The carbon flux to lipid synthesis was enhanced by the engineered strains particularly with the knockout-overexpression strains. The Synechocystis sp. PCC 6803 engineered with ΔglgC + A-OX showed high potential for fuel production after the copper treatment.

Overexpression of lipA or glpD_RuBisCO in the Synechocystis sp. PCC 6803 Mutant Lacking the Aas Gene Enhances Free Fatty-Acid Secretion and Intracellular Lipid Accumulation

Although engineered cyanobacteria for the production of lipids and fatty acids (FAs) are intelligently used as sustainable biofuel resources, intracellularly overproduced FAs disturb cellular homeostasis and eventually generate lethal toxicity. In order to improve their production by enhancing FFAs secretion into a medium, we constructed three engineered Synechocystis 6803 strains including KA (a mutant lacking the aas gene), KAOL (KA overexpressing lipA, encoding lipase A in membrane lipid hydrolysis), and KAOGR (KA overexpressing quadruple glpD/rbcLXS, related to the CBB cycle). Certain contents of intracellular lipids and secreted FFAs of all engineered strains were higher than those of the wild type. Remarkably, the KAOL strain attained the highest level of secreted FFAs by about 21.9%w/DCW at day 5 of normal BG₁₁ cultivation, with a higher growth rate and shorter doubling time. TEM images provided crucial evidence on the morphological changes of the KAOL strain, which accumulated abundant droplets on regions of thylakoid membranes throughout the cell when compared with wild type. On the other hand, BG₁₁-N condition significantly induced contents of both intracellular lipids and secreted FFAs of the KAOL strain up to 37.2 and 24.5%w/DCW, respectively, within 5 days. Then, for the first time, we shone a spotlight onto the overexpression of lipA in the aas mutant of Synechocystis as another potential strategy to achieve higher FFAs secretion with sustainable growth.

Cyanobacterium Synechocystis sp. PCC 6803 lacking adc1 gene produces higher polyhydroxybutyrate accumulation under modified nutrients of acetate supplementation and nitrogen-phosphorus starvation

Increased polyhydroxybutyrate production in cyanobacterium Synechocystis sp. PCC 6803 lacking adc1 gene (Δadc1) is first-timely reported in this study. We constructed the mutant by disrupting adc1 gene encoding arginine decarboxylase, thereby exhibiting a partial blockade of polyamine synthesis. This Δadc1 mutant had a proliferative growth and certain contents of intracellular pigments including chlorophyll a and carotenoids as similar as those of wild type (WT). Highest PHB production was certainly induced by BG₁₁-N-P+A condition in both WT and Δadc1 mutant of about 24.9 %w/DCW at day 9 and 36.1 %w/DCW at day 7 of adaptation time, respectively. Abundant PHB granules were also visualized under both BG₁₁-N-P and BG₁₁-N-P+A conditions. All pha transcript amounts of Δadc1 mutant grown at 7 days-adaptation time were clearly upregulated corresponding to its PHB content under BG₁₁-N-P+A condition. Our finding indicated that this adc1 perturbation is alternatively achieved for PHB production in Synechocystis sp. PCC 6803.

Adaptive laboratory evolution of the fast-growing cyanobacterium Synechococcus elongatus PCC 11801 for improved solvent tolerance

Cyanobacteria hold promise as cell factories for the photoautotrophic conversion of carbon dioxide to useful chemicals. For the eventual commercial viability of such processes, cyanobacteria need to be engineered for (i) efficient channeling of carbon flux toward the product of interest and (ii) improved product tolerance, the latter being the focus of this study. We chose the recently reported, fast-growing, high light and CO₂ tolerant cyanobacterium Synechococcus elongatus PCC 11801 for adaptive laboratory evolution. In two parallel experiments that lasted over 8400 h of culturing and 100 serial passages, S. elongatus PCC 11801 was evolved to tolerate 5 g/L n-butanol or 30 g/L 2,3-butanediol representing a 100% improvement in concentrations tolerated. The evolved strains retained alcohol tolerance even after being passaged several times without the alcohol stress suggesting that the changes were permanent. Whole genome sequencing of the n-butanol evolved strains revealed mutations in a number of stress responsive genes encoding translation initiation factors, RpoB and an ABC transporter. In 2,3-butanediol evolved strains, genes for ClpC, a different ABC transporter, glyceraldehyde-3-phosphate dehydrogenase and phosphoribulokinase were found to be mutated. Furthermore, the evolved strains showed significant improvement in tolerance toward several other alcohols. Notably, the n-butanol evolved strain could tolerate up to 32 g/L ethanol, thereby making it a promising host for photosynthetic production of biofuels via metabolic engineering.

Adaptations in chloroplast membrane lipid synthesis from synthesis in ancestral cyanobacterial endosymbionts

Cyanobacteria and chloroplasts are believed to share a common ancestor, but synthetic pathways for membrane lipids are different. Lyso-phosphatidic acid (lyso-PA) is the precursor for the synthesis of all membrane lipids and synthesized by an acyl-ACP dependent glycerol-3-phosphate acyltransferase (GPAT) in chloroplasts. In cyanobacteria, GPAT genes are not found and, instead, genes coding for enzymes in the acyl-phosphate dependent lyso-PA synthetic pathway (plsX and plsY) are conserved. We report that the PlsX/Y dependent lyso-PA synthetic pathway is essential in cyanobacteria, but can be replaced by acyl-ACP dependent GPAT from Escherichia coli (plsB) and Arabidopsis thaliana (ATS1). Cyanobacteria thus display the capacity to accept enzymes from other organisms to synthesize essential components. This ability may have enabled them to evolve into current chloroplasts from their ancestral origins.

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.

Synechocystis sp. PCC 6803 overexpressing genes involved in CBB cycle and free fatty acid cycling enhances the significant levels of intracellular lipids and secreted free fatty acids

The integrative aspect on carbon fixation and lipid production is firstly implemented in cyanobacterium Synechocystis sp. PCC 6803 using metabolic engineering approach. Genes related to Calvin–Benson–Bassham (CBB) cycle including rbcLXS and glpD and free fatty acid recycling including aas encoding acyl-ACP synthetase were practically manipulated in single, double and triple overexpressions via single homologous recombination. The significantly increased growth rate and intracellular pigment contents were evident in glpD-overexpressing (OG) strain among all strains studied under normal growth condition. The triple aas_glpD_rbcLXS-overexpressing (OAGR) strain notably gave the highest contents of both intracellular lipids and extracellular free fatty acids (FFAs) of about 35.9 and 9.6% w/DCW, respectively, when compared to other strains at day 5 of cultivation. However, the highest intracellular lipid titer and production rate were observed in OA strain at day 5 (228.7 mg/L and 45.7 mg/L/day, respectively) and OG strain at day 10 (358.3 mg/L and 35.8 mg/L/day, respectively) due to their higher growth. For fatty acid (FA) compositions, the main saturated fatty acid of palmitic acid (C16:0) was dominantly found in both intracellular lipid and secreted FFAs fractions. Notably, intracellular FA proportion of myristic acid (C14:0) was induced in all engineered strains whereas the increase of stearic acid (C18:0) composition was found in extracellular FFAs fraction. Altogether, these overexpressing strains efficiently produced higher lipid production via homeostasis balance on both its lipid synthesis and FFAs secretion.

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.