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Global Metabolic Rewiring for Improved CO2 Fixation And ARTICLE Received 19 Nov 2016 | Accepted 25 Jan 2017 | Published 13 Mar 2017 DOI: 10.1038/ncomms14724 OPEN Global metabolic rewiring for improved CO2 fixation and chemical production in cyanobacteria Masahiro Kanno1,2, Austin L. Carroll1 & Shota Atsumi1 Cyanobacteria have attracted much attention as hosts to recycle CO2 into valuable chemicals. Although cyanobacteria have been engineered to produce various compounds, production efficiencies are too low for commercialization. Here we engineer the carbon metabolism of Synechococcus elongatus PCC 7942 to improve glucose utilization, enhance CO2 fixation and increase chemical production. We introduce modifications in glycolytic pathways and the Calvin Benson cycle to increase carbon flux and redirect it towards carbon fixation. The À 1 engineered strain efficiently uses both CO2 and glucose, and produces 12.6 g l of 2,3-butanediol with a rate of 1.1 g l À 1 d À 1 under continuous light conditions. Removal of native regulation enables carbon fixation and 2,3-butanediol production in the absence of light. This represents a significant step towards industrial viability and an excellent example of carbon metabolism plasticity. 1 Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, USA. 2 Asahi Kasei Corporation, 2767-11 Niihama, Shionasu, Kojima, Kurashiki, Okayama 711-8510, Japan. Correspondence and requests for materials should be addressed to S.A. (email: [email protected]). NATURE COMMUNICATIONS | 8:14724 | DOI: 10.1038/ncomms14724 | www.nature.com/naturecommunications 1 ARTICLE NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14724 etabolic engineering of photosynthetic organisms allows increase availability of the substrate for carbon fixation, solar energy to power carbon capture and the D-ribulose-1,5-bisphosphate (R15P), and enhance efficiency of Mproduction of food, fuels and valuable chemicals1,2. the reaction catalysed by RuBisCO. Cyanobacteria have attracted much interest as hosts for Here we propose a strategy to increase carbon fixation and photosynthetic chemical production due to the simplicity of chemical production in cyanobacterial grown under light and culture conditions, ease of genetic manipulation and relatively fast dark conditions. First, glucose metabolism is rewired through the cell growth compared to higher plants3–6. Several cyanobacterial oxidative pentose phosphate (OPP) pathway to overproduce strains have been engineered for photosynthetic chemical ribulose-5-phosphate (Ru5P), a precursor of the CO2 fixation production. However, despite progress in metabolic pathway. Next, because carbon metabolism in cyanobacteria manipulation and analysis, titres and productivities from is precisely controlled in response to environmental changes cyanobacteria are still far below industrial feasibility7,8. such as light and carbon availability22–24, cp12, a regulatory Dependency on continuous lighting and the slow process of gene of the CB cycle, is deleted to amplify conversion of Ru5P to carbon fixation are particularly limiting9,10. R15P (Fig. 1a,b). This integrated approach of essential gene We have previously engineered the model cyanobacterium overexpression and deletion of cp12 allows for enhanced CO2 Synechococcus elongatus PCC 7942 to produce 2,3-butanediol fixation, a remarkable increase of 23BD production in both light 11–13 (23BD) from CO2 and glucose . Under natural light, chemical and dark conditions through light-independent supply of glucose production from an engineered photosynthetic organism would carbons (Fig. 1a,b), and could be applied as a general strategy for be confined to a limited window of optimal sunlight exposure13. improving the efficiency of other photosynthetic organisms. However, in order to achieve industrial feasibility, chemical production under both light and dark conditions is essential. As demonstrated in our previous work, concurrent expression of Results heterologous sugar importers and the 23BD biosynthetic pathway Characterization of glucose catabolism in engineered strains. genes allows for chemical production and growth from both CO2 To achieve efficient 23BD production from glucose and CO2,we and glucose13. The oxidation of sugars provides an increased first optimized the genetic construct for the 23BD biosynthesis supply of metabolites and energy independent of photosynthesis, pathway (Fig. 1c), then paired this optimization with expression allowing for faster cell growth and continuous chemical of galP, which encodes a galactose-proton symporter from production throughout diurnal conditions (12 h light/12 h dark). Escherichia coli (Strain 3, Table 1). Details of optimization Carbon yield is one of the most important factors for economic and a summary of our previous work on 23BD production in feasibility and is calculated based on the theoretical maximum S. elongatus PCC 7942 can be found in the Supplementary Figs 1, À 1 yield (TMY). In this study, two substrates, CO2 and glucose, are and 2 and Supplementary Note 1. Strain 3 produced 2.5 g l of utilized simultaneously. Owing to their concurrent use and 23BD when glucose was supplied, whereas only 0.4 g l À 1 was culturing conditions that allow for gas exchange with the produced without glucose (Fig. 2a,b). environment, it is impossible to directly measure TMY from To investigate how glucose affects the carbon metabolism of both substrates. Therefore, we evaluate photomixotrophic Strain 3, we applied metabolomics analysis. Quantification of production by calculating TMY possible from glucose alone metabolites from Strain 3 may explain how the flow of carbon (0.5 g23BD/gglucose). TMY values above 100% indicate 23BD changes in S. elongatus because of glucose, which may in turn production beyond what is possible from glucose alone, and we allow optimization of carbon metabolism and 23BD production assume that these yields reflect the incorporation of CO2 in of the engineered strains. Cells were grown with or without addition to glucose. It is important to note that glucose utilization glucose for 72 h under continuous light. Among the several is not 100% efficient. The value of the TMY minus the maximum hundred metabolite signals detected, 136 metabolites were contribution from glucose (100%) represents only the minimum identified and quantified25,26 (Fig. 1c and Supplementary Data 1) value for CO2 incorporation, and the true contribution is likely and some key changes to central carbon pathway metabolites were higher. observed. Levels of gluconate and fructose-6-phosphate (F6P) The carbon yield achieved in our previous study was 40% of increased by 7.3- and 4.1-fold, respectively, in the presence of TMY12, with great potential for improvement. Thus, the goal of glucose (Fig. 1c). In contrast, metabolites of the lower part of the this study is to optimize glucose and CO2 utilization and to Embden–Meyerhof–Parnas (EMP) pathway, 3-phosphoglycerate improve 23BD production and yield. To accomplish this, we (3PGA) and phosphoenolpyruvate (PEP) were lowered by 66% and identify and relieve bottlenecks in glucose catabolism, deregulate 88%, respectively, upon the addition of glucose (Fig. 1c). This has and enhance CO2 fixation, combine successful modifications and also been observed in Synechocystis sp. PCC 6803 under similar characterize the resulting strain in a variety of production conditions27. Moreover, a decrease of TCA cycle metabolites, conditions. including malate, fumarate, succinate and citrate, was observed in Carbon flux in cyanobacteria is often limited by the carbon glucose-fed cells (Fig. 1c). fixation step in the Calvin Benson (CB) cycle14. To overcome this, In order to understand these data further, we constructed much work has been done to improve the catalytic activity of the several deletion mutants from Strain 3 (Table 1) that would key carbon fixation enzyme, ribulose-1,5-bisphosphate separately inactivate one of the branches of carbon metabolism. carboxylase/oxygenase (RuBisCO), but with very limited Three main pathways for glucose catabolism in cyanobacteria success15,16. Several studies have shown that the catalytic were investigated: the OPP pathway, the EMP pathway and the efficiency of RuBisCO is already naturally optimized17,18. Entner-Doudoroff (ED) pathway (Fig. 1c). Genes encoding the Rather than focusing on improving RuBisCO, we examine following enzymes were chosen as deletion targets in order to carbon metabolism as a whole. Enzyme and metabolite pools of assess the metabolic contribution of each pathway: glucose-6- the regenerative phase of the CB cycle are proposed to play a role phosphate dehydrogenase (encoded by zwf, Strain 4) and in determining the overall carbon fixation rate19,20. Modifications 6-phosphogluconate (6PG) dehydrogenase (gnd, Strain 5)of of other steps in the CB cycle, such as those catalysed by the OPP pathway, phosphoglucose isomerase (pgi, Strain 6) and sedoheptulose 1,7-bisphosphatase and transketolase, have phosphofructokinase (pfk, Strain 7) of the EMP pathway, and been utilized to improve carbon fixation19–21. Therefore, we 2-keto-3-deoxygluconate 6-phosphate aldolase (eda, Strain 8)of hypothesize that the supplementary carbon source glucose would the ED pathway (Table 1). Gene replacement with an antibiotic 2 NATURE COMMUNICATIONS | 8:14724 | DOI: 10.1038/ncomms14724 | www.nature.com/naturecommunications NATURE COMMUNICATIONS | DOI: 10.1038/ncomms14724 ARTICLE a c Glucose CO2 3PGA GaIP Gluconate GDH 10 ED pathway Glucose 5 EDD EDA PYR KDPG CB 0 GAP G1P G6P R15P Cycle 1.5 2 NADPH NADPH 1 OPP 1 0.5 6PG 0 0 ZWF GND pathway PGI 4 3 F6P 2 8 Xu5P 1 Ru5P EMP 6 0 4 2 R5P pathway E4P 2.5 23BD 0 2 PFK 1.5 1 Phe biomass S7P 0.5 ATP 0 1.5 FBP PRK 1 Ser Gly ADD 0.5 1.5 2 DHAP 0 1 1 Tyr b 0.5 1.5 0 0 GAP R15P 1 CO2 3PGA 0.5 GAPDH 0 NADPH RuBisCO CO2 3PGA Asp Lys 1.5 CB 3 8 1 2 6 0.5 4 R15P Cycle 1 2 0 0 0 Ala Val Leu Ile PEP 2 2 2 2 Met Thr 1.5 3 2 1 1 1 1 2 1 0.5 000 0 1 0 0 0 ALS ALDC ADH PYR Acetolactate Acetoin 23BD Glucose 23BD biomass AcCoA NADPH MAL CIT 1.5 OAA 1.5 1 1 0.5 0.5 0 0 FUM 1.5 2OG ICIT Glu Pro 2 20 1 SUC 5 0.5 1.5 1 10 2.5 0 1 0 0 0 0.5 0 Figure 1 | Rewiring of carbon metabolism in cyanobacteria.
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