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Control of the Galactose-To-Glucose Consumption Ratio in Co www.nature.com/scientificreports OPEN Control of the galactose‑to‑glucose consumption ratio in co‑fermentation using engineered Escherichia coli strains Hyeon Jeong Seong, Ji Eun Woo & Yu‑Sin Jang* Marine biomasses capable of fxing carbon dioxide have attracted attention as an alternative to fossil resources for fuel and chemical production. Although a simple co‑fermentation of fermentable sugars, such as glucose and galactose, has been reported from marine biomass, no previous report has discussed the fne-control of the galactose-to-glucose consumption ratio in this context. Here, we sought to fnely control the galactose-to-glucose consumption ratio in the co-fermentation of these sugars using engineered Escherichia coli strains. Toward this end, we constructed E. coli strains GR2, GR2P, and GR2PZ by knocking out galRS, galRS-pfA, and galRS-pfA-zwf, respectively, in parent strain W3110. We found that strains W3110, GR2, GR2P, and GR2PZ achieved 0.03, 0.09, 0.12, and 0.17 galactose-to-glucose consumption ratio (specifc galactose consumption rate per specifc glucose consumption rate), respectively, during co-fermentation. The ratio was further extended to 0.67 by integration of a brief process optimization for initial sugar ratio using GR2P strain. The strategy reported in this study will be helpful to expand our knowledge on the galactose utilization under glucose conditions. Excessive use of fossil fuel has caused global warming, which is one of the biggest problems currently facing humanity. Recently, biobased fuels and chemicals have gained attention as potential alternatives to fossil fuels 1–6. Some biobased fuels and chemicals can be produced via microbial fermentation from sustainable biomasses, such as wood and seaweed7–11. In addition to such cellulosic biomasses, marine biomasses have been suggested as promising renewable resources12, as they have the advantages of high biomass yield per unit area, high rates of carbon dioxide fxation, and natural abundance13. Marine macroalgae contain fermentable sugars, such as glucose and galactose whose contents are known about 20% and 23%, respectively14–18. Te proper utilization of galactose is important for the production of biobased fuels and chemicals from a marine macroalgal biomass. Also, given that galactose is 10 times more expensive than glucose, proper regulation of the galactose consumption rate is very important in the co-fermentation of glucose and galactose. On the other hand, in our recent study, it is reported that the production of some metabolite, such as hyaluronic acid could also be afected by the modulation of galactose and glucose consumption19. However, the exact determination of galactose and glucose consumption rates remains, in cultures using the metabolically engineered cells, yet. Most microorganisms use glucose as a primary feedstock in the co-fermentation of glucose and galactose. Tis preferential consumption of glucose, which occurs through carbon catabolite repression (CCR), makes it difcult for organisms to use glucose and galactose simultaneously. In a recent study, the CCR pathway was found to be completely deregulated when glucose and galactose were co-fermented using an engineered Escherichia coli with knockout of the galactose repressor (galR) and overexpression of the galactose operon (galP, galE, galT, galK and galM) and phosphoglucomutase (pgm)20. Te engineered strain simultaneously assimilated galactose and glucose in the co-fermentation of these sugars. However, no previous report has described a strategy for fnely controlling the galactose consumption rate during the co-fermentation of glucose and galactose. Division of Applied Life Science (BK21 Plus Program), Department of Agricultural Chemistry and Food Science Technology, Institute of Agriculture & Life Science (IALS), Gyeongsang National University, Jinju 52828, Republic of Korea. *email: [email protected] SCIENTIFIC REPORTS | (2020) 10:12132 | https://doi.org/10.1038/s41598-020-69143-3 1 Vol.:(0123456789) www.nature.com/scientificreports/ Figure 1. Control of the galactose-to-glucose consumption ratio in the co-fermentation of both sugars using the engineered E. coli. ‘X’ indicates gene knockout. Te relevant genes and their encoded enzymes are as follows: galR, DNA-binding transcriptional repressor; galS, DNA-binding transcriptional isorepressor; galK, galactokinase; galT, galactose-1-phosphate uridylyltransferase; pfA, 6-phosphofructokinase I; pfB, 6-phosphofructokinase II; zwf, glucose-6-phosphate dehydrogenase. Abbreviations: Gal1P, galactose-1- phosphate; G1P, glucose-1-phosphate; G6P, glucose-6-phosphate; F6P, fructose-6-phosphate; FBP, fructose- 1,6-phosphate; PYR, pyruvate; 6PG, 6-phosphate-gluconate; Ru5P, ribulose-5-phosphate; X5P, xylulose-5- phosphate; E4P, erythorse-4-phosphate; KDPG, 2-keto-3-deoxy-phosphogluconate. Name Genotype Reference E. coli strains W3110 Coli genetic stock center strain no.4474 CGSCa GR E. coli K12 W3110, △galR Tis study GR2 E. coli K12 W3110, △galR, △galS Tis study GR2P E. coli K12 W3110, △galR, △galS, △pfA Tis study GR2PZ E. coli K12 W3110, △galR, △galS, △pfA, △zwf Tis study Plasmids ApR, λ‐Red recombinase under arabinose‐inducible BAD promoter, Cre‐recombinase under IPTG‐inducible pCW611 36 lacUV5 promoter, temperature sensitive origin pMtrc9 trc promoter downstream of lox66‐cat‐lox71 cassette 37 Table 1. Escherichia coli strains and plasmids used in this study. a CGSC, Coli Genetic Stock Center (New Haven, CT). In this study, as a proof-of-concept, we tried to fnely control the galactose-to-glucose consumption ratio during the co-fermentation of both sugars by engineering the sugar metabolism in E. coli on the basis of our recent study19, followed by a brief process optimization for sugar ratio and concentration. Results Galactose‑to‑glucose consumption ratio in E. coli GR2, which lacked the galactose operon repressors, during glucose consumption. In an efort to fnely control the galactose consumption rate in the co-fermentation of glucose and galactose using E. coli, we frst constructed the galRS mutant, E. coli strain GR2 (Fig. 1 and Table 1), which was not able to produce the galactose operon repressors encoded from the galRS genes21–27. We expected that the resulting strain would consume galactose at a higher rate than the parent strain in the co-fermentation of glucose and galactose, although we anticipated that this rate would still be fairly low. To determine the galactose consumption rate of the galRS mutant, we cultured GR2 cells in R/2 medium supple- mented with 4 g/L glucose and 4 g/L galactose. Parent strain W3110 was cultured under the same conditions as a control. In the co-fermentation of glucose and galactose, E. coli strain GR2 had completely consumed the glucose at 12 h of culture, yielding a specifc glucose consumption rate of 1.3629 g/gDCW/h (Fig. 2a and Table 2). During this period, GR2 consumed 0.36 g/L galactose, for a specifc consumption rate of 0.1262 g/gDCW/h. Under the same conditions, parent strain W3110 showed a similar level of glucose consumption (Fig. 2b) but had a lower specifc galactose consumption rate at 0.0373 g/gDCW/h (Table 2). Strain GR2 yielded Rgal/glu = 0.09, whereas parent strain W3110 yielded Rgal/glu = 0.03 (Table 2). SCIENTIFIC REPORTS | (2020) 10:12132 | https://doi.org/10.1038/s41598-020-69143-3 2 Vol:.(1234567890) www.nature.com/scientificreports/ Figure 2. Time profles of various parameters tested for E. coli strains (a) GR2 and (b) W3110 grown in R/2 medium containing 4 g/L glucose and 4 g/L galactose. Overall specifc sugar Overall specifc sugar consumption rate (g/ consumption rate (mM/ gDCW/h) gDCW/h) Strain Maximum specifc growth rate (μmax;/h) Glucose Galactose Glucose Galactose Rgal/glu W3110 0.5653 ± 0.01 1.3706 ± 0.04 0.0373 ± 0.00 7.614 ± 0.22 0.207 ± 0.00 0.03 GR2 0.4469 ± 0.02 1.3629 ± 0.12 0.1262 ± 0.08 7.572 ± 0.68 0.701 ± 0.44 0.09 GR2P 0.2993 ± 0.02 0.4714 ± 0.03 0.0552 ± 0.03 2.619 ± 0.16 0.307 ± 0.15 0.12 GR2PZ 0.2076 ± 0.01 0.4419 ± 0.01 0.0737 ± 0.02 2.455 ± 0.07 0.410 ± 0.13 0.17 Table 2. Fermentation parameters obtained from the cultures of E. coli strains W3110, GR2, GR2P, and GR2PZ in R/2 medium containing 4 g/L glucose and 4 g/L galactose. Galactose‑to‑glucose consumption ratio in E. coli GR2P, which lacked the galactose operon repressors and 6-phosphofructokinase, during glucose consumption. Embden–Meyerhof–Par- nas pathway (EMPP) was chosen as the next target to be engineered, because a metabolic intermediate glu- cose-6-phosphate is formed from both glucose and galactose. However, glucose-6-phosphate formation from both sugars are quietly difer from each other. To yield glucose-6-phosphate, glucose is catabolized by one-step reaction, while galactose is metabolized via Leior pathway 28. Tus, it was expected that glucose and galactose consumption could be individually afected by modulation of EMPP. To further modulate R gal/glu, rather than overexpressing the galactose operon, we next knocked out the pfA gene, which encodes ATP-dependent 6-phos- phofructokinase, in E. coli strain GR2. As 6-phosphofructokinase is a key enzyme in the EMPP, we expected that the specifc glucose consumption rate could be negatively afected by the lack of 6-phosphofructokinase in the resulting GR2P cells under the co-fermentation of glucose and galactose. In fask cultures, GR2P showed a maximum specifc growth rate (µmax) of 0.2993/h with a short lag time, which was rather lower than the 0.5653/h and 0.4469/h obtained from cultures of W3110 and GR2, respectively (Fig. 3 and Table 2). Tis indicates that the additional knockout of the pfA gene negatively afected cell growth. E. coli GR2P had completely consumed the glucose at 24 h of culture, yielding a specifc glucose consumption rate of 0.4714 g/gDCW/h (Fig.
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