Parimi et al. Microb Cell Fact (2017) 16:114 DOI 10.1186/s12934-017-0729-2 Microbial Cell Factories RESEARCH Open Access Eliminating acetate formation improves citramalate production by metabolically engineered Escherichia coli Naga Sirisha Parimi, Ian A. Durie, Xianghao Wu, Afaq M. M. Niyas and Mark A. Eiteman* Abstract Background: Citramalate, a chemical precursor to the industrially important methacrylic acid (MAA), can be syn- thesized using Escherichia coli overexpressing citramalate synthase (cimA gene). Deletion of gltA encoding citrate synthase and leuC encoding 3-isopropylmalate dehydratase were critical to achieving high citramalate yields. Acetate is an undesirable by-product potentially formed from pyruvate and acetyl-CoA, the precursors of citramalate during aerobic growth of E. coli. This study investigated strategies to minimize acetate and maximize citramalate production in E. coli mutants expressing the cimA gene. Results: Key knockouts that minimized acetate formation included acetate kinase (ackA), phosphotransacetylase (pta), and in particular pyruvate oxidase (poxB). Deletion of glucose 6-phosphate dehydrogenase (zwf) and ATP synthase (atpFH) aimed at improving glycolytic fux negatively impacted cell growth and citramalate accumulation in shake fasks. In a repetitive fed-batch process, E. coli gltA leuC ackA-pta poxB overexpressing cimA generated 54.1 g/L citramalate with a yield of 0.64 g/g glucose (78% of theoretical maximum yield), and only 1.4 g/L acetate in 87 h. Conclusions: This study identifed the gene deletions critical to reducing acetate accumulation during aerobic growth and citramalate production in metabolically engineered E. coli strains. The citramalate yield and fnal titer relative to acetate at the end of the fed-batch process are the highest reported to date (a mass ratio of citramalate to acetate of nearly 40) without being detrimental to citramalate productivity, signifcantly improving a potential process for the production of this fve-carbon chemical. Keywords: Acetyl-CoA, Pyruvate, Citramalate, Escherichia coli, Acetate, Glucose, Fed-batch Background used in automobile, construction, medical device, light- Synthetic biology and metabolic engineering have ena- ing and the home appliance industries. Acrylates in gen- bled sustainable and eco-friendly manufacturing of com- eral are very toxic [3], and their direct microbial synthesis mercially important food products, pharmaceuticals, at relevant concentrations seems unlikely. MAA can for- commodity chemicals, and other high value products tunately be synthesized via a hybrid route: biochemical using microorganisms. Some chemicals which cannot be production of citramalate from glucose [40], and subse- synthesized exclusively by a biosynthetic route might be quently transforming this compound chemically using generated using hybrid approaches involving both bio- base-catalyzed decarboxylation and dehydration [22]. logical and chemical synthesis. For example, methacrylic Citramalate (or citramalic acid) is naturally found in the acid (MAA), a commodity chemical with an estimated metabolic pathways of some anaerobic bacteria [8, 18, annual global market of 2.2 million tons [42] is a mono- 32]. mer of poly(methyl methacrylate) or PMMA, which is Escherichia coli is a well-established microbial cell fac- tory for the biotechnology industry. Citramalate pro- *Correspondence: [email protected] duction in metabolically engineered E. coli expressing School of Chemical, Materials and Biomedical Engineering, Driftmier citramalate synthase coding the cimA gene (Fig. 1) has Engineering Center, University of Georgia, Athens, GA 30602, USA © The Author(s) 2017. This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Parimi et al. Microb Cell Fact (2017) 16:114 Page 2 of 10 Fig. 1 Metabolic pathways for citramalate synthesis in Escherichia coli expressing cimA coding citramalate synthase (blue). Key enzymes (and cor- responding genes) are: citrate synthase (gltA), 3-isopropylmalate dehydratase (leuC), acetate kinase (ackA), phosphotransacetylase (pta), acetyl-CoA synthetase (acs), pyruvate oxidase (poxB), phosphoenolpyruvate synthase (ppsA). All strains examined in this study had deletions in the gltA, leuC and ackA genes as indicated in red previously been demonstrated [4, 40]. In a recent study, acetate kinase and phosphotransacetylase (ackA and pta E. coli MG1655 gltA leuC ackA/pZE12-cimA containing genes), and from pyruvate via pyruvate oxidase (poxB). three key knockouts (citrate synthase, 3-isopropylmalate While the ackA-pta pathway is typically the route dur- dehydratase and acetate kinase) accumulated 46 g/L cit- ing exponential growth, pyruvate oxidase becomes active ramalate from glucose at a yield of 0.63 g/g (75% of the during late exponential and early stationary phases [15]. theoretical maximum). However, 10 g/L acetate also Deletion of ackA and/or pta genes has previously resulted accumulated despite the deletion of acetate kinase. At the in lower growth rates and lower but still signifcant ace- end of the fermentation, this by-product accumulated to tate accumulation in several E. coli mutants [9, 11, 14, an ultimate mass ratio citramalate-to-acetate (i.e., desir- 15]. Strains with poxB deleted but not the ackA-pta path- able product:undesirable product) of less than 5. Acetate way accumulated either similar or slightly lower acetate is a typical “overfow” metabolite when wild-type E. coli compared to wild type strains [15, 25]. Growth of strains cells are grown at a high growth rate, and the carbon fux in which both acetate producing pathways were deleted into central metabolic pathways exceeds the cells’ biosyn- showed very low acetate accumulation and growth rates thetic demands and the capacity for energy generation [2, similar to wild type strains [9, 15]. 17]. Acetate formation is undesirable because this acid: Te two precursors for citramalate, pyruvate and (i) negatively impacts cell growth even at concentrations acetyl-CoA, are generated through the glycolytic path- as low as 0.5 g/L [28]; (ii) is a sink which diverts carbon way, and increasing the fux through glycolysis might that could otherwise be used to synthesize the desired improve citramalate productivity and yield. Since the product [17]; (iii) necessitates additional downstream ATP/ADP ratio controls glycolysis [24], previous research separation step(s) that add to process costs. Acetate is has shown that decreasing ATP generation increased the generated by two pathways in E. coli: from acetyl-CoA via rate of glycolysis [30], and product formation [34, 45]. Parimi et al. Microb Cell Fact (2017) 16:114 Page 3 of 10 Glycolytic fux may also be improved by preventing fux achieving high citramalate yield [40]. Despite the deletion through the pentose phosphate pathway (PP pathway), of acetate kinase, over 10 g/L acetate accumulated in a for example, by a deletion in glucose 6-phosphate dehy- repetitive fed-batch process [40]. We therefore compared drogenase (zwf) [43]. citramalate formation after 24 h in shake fasks by sev- Te goal of this study was to improve the formation of eral E. coli strains having additional gene knockouts and citramalate in E. coli expressing citramalate synthase by expressing the pZE12-cimA plasmid (Fig. 2). MEC499/ blocking acetate formation. We also investigated whether pZE12-cimA (gltA leuC ackA) serves as the control strain strategies to increase glycolytic fux would increase citra- [40]. Specifcally, we examined the enzymes involved in malate yield and productivity. acetate formation from acetyl-CoA and pyruvate, the precursors of citramalate. We anticipated that screening Results at the 50 mL shake fask scale in shake fasks would pro- Citramalate and acetate formation in shake fasks vide guidance on strains to study in greater detail at the Citramalate synthase (coded by the cimA gene) medi- 1 L scale in a bioreactor. ates the conversion of pyruvate and acetyl-CoA to cit- In E. coli phosphotransacetylase (pta gene) and acetate ramalate. Knockouts in the gltA, leuC and ackA genes kinase (ackA) normally produce acetate during the expo- coding for citrate synthase, 3-isopropylmalate dehy- nential growth phase through the high energy acetyl dratase, and acetate kinase, respectively, were critical to phosphate (acetyl-P) intermediate [33]. Previous research Fig. 2 Comparison of citramalate and acetate yields at 24 h in shake fasks using various E. coli strains each expressing cimA gene on the pZE12- cimA plasmid. The defned medium contained 5 g/L glucose, 1 g/L L-glutamate and 0.2 g/L L-leucine. All studies were carried out in triplicate. Results with MEC499/pZE12-cimA are from [40] Parimi et al. Microb Cell Fact (2017) 16:114 Page 4 of 10 demonstrated that acetyl-P can form acetate even in the but no acetate, and grew to an OD of 1.92, nearly 30% absence of ackA [39]. Since an ackA deletion alone in lower than MEC562/pZE12-cimA. MEC568/pZE12- MEC499 was previously shown to be insufcient to pre- cimA showed a signifcantly increased