Advances in acetyl coenzyme A metabolic engineering with Escherichia coli

doi:10.16085/j.issn.1000-6613.2019-0081

Abstract

Abstract:

Biosynthesis of chemicals has the advantages of high efficiency, green and sustainable development. Acetyl coenzyme A, as an important intermediate of cellular metabolism in cells, is an important precursor for the synthesis of many biochemicals, and has played a vital role in the process of microbial carbon metabolism. Here we reviewed the synthesis and strategies of metabolic regulation of acetyl coenzyme A in Escherichia coli and its important applications. We also summarized the synthesis pathway of acetyl coenzyme A and the recent development of metabolic regulation strategies to increase the intracellular metabolic flux of acetyl coenzyme A production, these including metabolic regulation of the acetyl coenzyme A synthesized by acetic acid and pyruvate, metabolic regulation of the central carbon metabolic pathway and acetyl coenzyme A synthesized by beta oxidation pathway, and discovery of new pathways for acetyl coenzyme A synthesis. Finally, we prospected the feasible strategies of increasing acetyl coenzyme A supply and discussed methods of constructing cell factories for synthesizing acetyl coenzyme A as precursor chemicals by genome editing technology.

Key words: acetyl coenzyme A, Escherichia coli, metabolic engineering, flux

摘要：

利用生物法合成生物基化学品具有高效、绿色、可持续发展等优势。乙酰辅酶A作为细胞内物质代谢的重要中间产物，是利用生物转化法合成许多生物基化学品的重要前体，在微生物碳代谢过程中发挥着枢纽作用。本文综述了大肠杆菌乙酰辅酶A的合成、代谢调控策略及其重要应用，重点总结了乙酰辅酶A的合成途径及近期发展的提高乙酰辅酶A胞内通量的代谢调控策略，包括乙酸途径的代谢调控、丙酮酸合成乙酰辅酶A途径的代谢调控、中心碳代谢途径的代谢调控、β氧化合成乙酰辅酶A途径的代谢调控和乙酰辅酶A合成新途径的发掘，进一步展望了提高乙酰辅酶A供给的策略，利用基因组编辑技术构建合成乙酰辅酶A为前体化学品细胞工厂的方法。

关键词: 乙酰辅酶A, 大肠杆菌, 代谢工程, 通量

CLC Number:

Q756

Lu CHEN,Dingyu LIU,Baowei WANG,Yu jiao ZHAO,Guangtao JIA,Tao CHEN,Zhiwen WANG. Advances in acetyl coenzyme A metabolic engineering with Escherichia coli[J]. Chemical Industry and Engineering Progress, 2019, 38(9): 4218-4226.

陈露,刘丁玉,汪保卫,赵玉姣,贾广韬,陈涛,王智文. 大肠杆菌乙酰辅酶A代谢调控及其应用研究进展[J]. 化工进展, 2019, 38(9): 4218-4226.

Figures/Tables 4

References 55

1	KRIVORUCHKOA, ZHANGY, SIEWERSV, et al. Microbial acetyl-CoA metabolism and metabolic engineering[J]. Metabolic Engineering, 2015, 28: 28-42.
2	CHENX, ZHOUL, TIANK, et al. Metabolic engineering of Escherichia coli: a sustainable industrial platform for bio-based chemical production[J]. Biotechnology Advances, 2013, 31(8): 1200-1223.
3	HOLMSW H. The central metabolic pathways of Escherichia coli: relationship between flux and control at a branch point, efficiency of conversion to biomass, and excretion of acetate[J]. Current Topics in Cellular Regulation, 1986, 28(4): 69-105.
4	HAHMD H, PANJ, RHEEJ S. Characterization and evaluation of a pta (phosphotransacetylase) negative mutant of Escherichia coli HB101 as production host of foreign lipase[J]. Appl. Microbiol. Biotechnol., 1994, 42(1): 100-107.
5	LINH, CASTRON M, BENNETTG N, et al. Acetyl-CoA synthetase overexpression in Escherichia coli demonstrates more efficient acetate assimilation and lower acetate accumulation: a potential tool in metabolic engineering[J]. Applied Microbiology and Biotechnology, 2006, 71(6): 870-874.
6	WANGR, SHIZ, CHENJ, et al. Enhanced co-production of hydrogen and poly-(R)-3-hydroxybutyrate by recombinant PHB producing E. coli over-expressing hydrogenase and acetyl-CoA synthetase[J]. Metabolic Engineering, 2012, 14(5): 496-503.
7	SOMAY, YAMAJIT, MATSUDAF, et al. Synthetic metabolic bypass for a metabolic toggle switch enhances acetyl-CoA supply for isopropanol production by Escherichia coli[J]. Journal of Bioscience and Bioengineering, 2017, 123(5): 625-633.
8	LEONARDE, LIM K H, SAW P N, et al. Engineering central metabolic pathways for high-level flavonoid production in Escherichia coli[J]. Applied and Environmental Microbiology, 2007, 73(12): 3877-3886.
9	WOLFEA J. The acetate switch[J]. Microbiology and Molecular Biology Reviews, 2005, 69(1): 12-50.
10	CHANGD E, SHINS, RHEEJ S, et al. Acetate metabolism in a pta mutant of Escherichia coli W3110: importance of maintaining acetyl coenzyme A flux for growth and survival[J]. Journal of Bacteriology, 1999, 181(21): 6656-6663.
11	MIYAKEM, MIYAMOTOC, SCHNACKENBERGJ, et al. Phosphotransacetylase as a key factor in biological production of polyhydroxybutyrate[J]. Applied Biochemistry Biotechnology, 2000, 84-86(1): 1039-1044.
12	VADALIR V, HORTONC E, RUDOLPHF B, et al. Production of isoamyl acetate in ackA-pta and/or ldh mutants of Escherichia coli with overexpression of yeast ATF2[J]. Applied Microbiology and Biotechnology, 2004, 63(6): 698-704.
13	ZHAW, RUBIN-PITELS B, SHAOZ, et al. Improving cellular malonyl-CoA level in Escherichia colivia metabolic engineering[J]. Metabolic Engineering, 2009, 11(3): 192-198.
14	FENGJ, ATKINSONM R, MCCLEARYW, et al. Role of phosphorylated metabolic intermediates in the regulation of glutamine synthetase synthesis in Escherichia coli[J]. Journal of Bacteriology, 1992, 174(19): 6061-6070.
15	OH M, ROHLINL, KAO K C, et al. Global expression profiling of acetate-grown Escherichia coli[J]. Journal of Biological Chemistry, 2002, 277(15): 13175-13183.
16	LIUY, WUH, LIQ, et al. Process development of succinic acid production by Escherichia coli NZN111 using acetate as an aerobic carbon source[J]. Enzyme and Microbial Technology, 2011, 49(5): 459-464.
17	MURARKAA, CLOMBURGJ M,MORANS,et al. Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose[J]. The Journal of Biological Chemistry, 2010, 285(41): 31548-31558.
18	JANTAMAK, HAUPTM J, SVORONOSS A, et al. Combining metabolic engineering and metabolic evolution to develop nonrecombinant strains of Escherichia coli C that produce succinate and malate[J]. Biotechnology and Bioengineering, 2008, 99(5): 1140-1153.
19	SKOROKHODOVAA Y. Anaerobic synthesis of succinic acid by recombinant Escherichia coli strains with activated NAD⁺-reducing pyruvate dehydrogenase complex[J]. Applied Biochemistry and Microbiology, 2011, 4(47): 373-380.
20	SKOROKHODOVAA Y, GULEVICHA Y, MORZHAKOVAA A, et al. Comparison of different approaches to activate the glyoxylate bypass in Escherichia coli K-12 for succinate biosynthesis during dual-phase fermentation in minimal glucose media[J]. Biotechnology Letters, 2013, 35(4): 577-583.
21	KIMY, INGRAML O, SHANMUGAMK T. Dihydrolipoamide dehydrogenase mutation alters the NADH sensitivity of pyruvate dehydrogenase complex of Escherichia coli K-12[J]. Journal of Bacteriology, 2008, 190(11): 3851-3858.
22	ATSUMIS, CANNA F, CONNORM R, et al. Metabolic engineering of Escherichia coli for 1-butanol production[J]. Metabolic Engineering, 2008, 10(6): 305-311.
23	ABDEL-HAMIDA M, ATTWOODM M, GUESTJ R. Pyruvate oxidase contributes to the aerobic growth efficiency of Escherichia coli[J]. Microbiology, 2001, 147(6): 1483-1498.
24	PARIMIN S, DURIEI A, WUX, et al. Eliminating acetate formation improves citramalate production by metabolically engineered Escherichia coli[J]. Microbial Cell Factories, 2017, 16(1): 114-124.
25	DITTRICHC R, VADALIR V, BENNETTG N, et al. Redistribution of metabolic fluxes in the central aerobic metabolic pathway of E. coli mutant strains with deletion of the ackA-pta and poxB pathways for the synthesis of isoamyl acetate[J]. Biotechnology Progress, 2005, 21(2): 627-631.
26	HANM J, YOONS S, LEE S Y. Proteome analysis of metabolically engineered Escherichia coli producing poly(3-hydroxybutyrate)[J]. Journal of Bacteriology, 2001, 183(1): 301-308.
27	LEE S H, KANGK, KIME Y, et al. Metabolic engineering of Escherichia coli for enhanced biosynthesis of poly(3-hydroxybutyrate) based on proteome analysis[J]. Biotechnology Letters, 2013, 35(10): 1631-1637.
28	XUP, RANGANATHANS, FOWLERZ L, et al. Genome-scale metabolic network modeling results in minimal interventions that cooperatively force carbon flux towards malonyl-CoA[J]. Metabolic Engineering, 2011, 13(5): 578-587.
29	FOWLERZ L, GIKANDIW W, KOFFASM A G. Increased malonyl coenzyme A biosynthesis by tuning the Escherichia coli metabolic network and its application to flavanone production[J]. Applied and Environmental Microbiology, 2009, 75(18): 5831-5839.
30	LIUM, DINGY, CHENH, et al. Improving the production of acetyl-CoA-derived chemicals in Escherichia coli BL21(DE3) through iclR and arcA deletion[J]. BMC Microbiology, 2017, 17(1): 2-9.
31	LEE E. Directing vanillin production from ferulic acid by increased acetyl-CoA consumption in recombinant Escherichia coli[J]. Biotechnology, 2009, 1(102): 200-208.
32	JUNGY-M,J-NLEE,H-DSHIN, et al. Role of tktA gene in pentose phosphate pathway on odd-ball biosynthesis of poly-β-hydroxybutyrate in transformant Escherichia coli harboring phbCAB operon[J]. Journl of Bioscience and Bioengineering, 2004, 98(3): 224-227.
33	SONGB, KIMT, JUNGY, et al. Modulation of talA gene in pentose phosphate pathway for overproduction of poly-β-hydroxybutyrate in transformant Escherichia coli harboring phbCAB operon[J]. Journal of Bioscience and Bioengineering, 2006, 102(3): 237-240.
34	LIM S, JUNGY, SHINH, et al. Amplification of the NADPH-related genes zwf and gnd for the oddball biosynthesis of PHB in an E. coli transformant harboring a cloned phbCAB operon[J]. Journal of Bioscience and Bioengineering, 2002, 93(6): 543-549.
35	ZHANGY, LINZ, LIUQ, et al. Engineering of Serine-Deamination pathway, Entner-Doudoroff pathway and pyruvate dehydrogenase complex to improve poly(3-hydroxybutyrate) production in Escherichia coli[J]. Microbial Cell Factories, 2014, 13(1): 172.
36	CHANGA S, SHERAZIS T H, KANDHROA A, et al. Characterization of palm fatty acid distillate of different oil processing industries of pakistan[J]. Journal of Oleo Science, 2016, 65(11): 897-901.
37	LIUB, XIANGS, ZHAOG, et al. Efficient production of 3-hydroxypropionate from fatty acids feedstock in Escherichia coli[J]. Metabolic Engineering, 2019, 51: 121-130.
38	RAGSDALES W, PIERCEE. Acetogenesis and the wood–Ljungdahl pathway of CO₂ fixation[J]. Biochimica et Biophysica Acta (BBA): Proteins and Proteomics, 2008, 1784(12): 1873-1898.
39	BOGORADI W, LINT, LIAOJ C. Synthetic non-oxidative glycolysis enables complete carbon conservation[J]. Nature, 2013, 502(7473): 693-697.
40	ZHENGY, YUANQ, YANGX, et al. Engineering Escherichia coli for poly(3-hydroxybutyrate) production guided by genome-scale metabolic network analysis[J]. Enzyme and Microbial Technology, 2017, 106: 60-66.
41	YANGX, YUANQ, ZHENGY, et al. An engineered non-oxidative glycolysis pathway for acetone production in Escherichia coli[J]. Biotechnology Letters, 2016, 38(8): 1359-1365.
42	LINP P, JAEGERA J, WUT, et al. Construction and evolution of an Escherichia coli strain relying on nonoxidative glycolysis for sugar catabolism[J]. Proceedings of the National Academy of Sciences, 2018, 115(14): 3538-3546.
43	WANGQ, XUJ, SUNZ, et al. Engineering an in vivo EP-bifido pathway in Escherichia coli for high-yield acetyl-CoA generation with low CO₂ emission[J]. Metabolic Engineering, 2019, 51: 79-87.
44	PIETROCOLAF, GALLUZZIL, KROEMERG. Acetyl coenzyme A：a central matabolite and second messenger[J]. Cell Metabolism, 2015, 6(21): 805-821.
45	HADADIN, HAFNERJ, SHAJKOFCIA, et al. ATLAS of biochemistry: a repository of all possible biochemical reactions for synthetic biology and metabolic engineering studies[J]. ACS Synthetic Biology, 2016, 5(10): 1155-1166.
46	RENJ, ZHOUL, WANGC, et al. An unnatural pathway for efficient 5-aminolevulinic acid biosynthesis with glycine from glyoxylate based on retrobiosynthetic design[J]. ACS Synthetic Biology, 2018, 7(12): 2750-2757.
47	WILKESH, BUCKELW, GOLDINGB T, et al. Metabolism of hydrocarbons in n-alkane-utilizing anaerobic bacteria[J]. Journal of Molecular Microbiology and Biotechnology, 2016, 26(1-3): 138-151.
48	CHOONY W, MOHAMADM S, DERISS, et al. A hybrid of bees algorithm and flux balance analysis with OptKnock as a platform for in silico optimization of microbial strains[J]. Bioprocess and Biosystems Engineering, 2014, 37(3): 521-532.
49	TYO K E, KOCHARINK, NIELSENJ. Toward design-based engineering of industrial microbes[J]. Current Opinion in Microbiology, 2010, 13(3): 255-262.
50	WARNERJ R, REEDERP J, KARIMPOUR-FARDA, et al. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides[J]. Nature Biotechnology, 2010, 28(8): 856-862.
51	WANGH H, ISAACSF J, CARRP A, et al. Programming cells by multiplex genome engineering and accelerated evolution[J]. Nature, 2009, 460(7257): 894-898.
52	SANTOSC N S, REGITSKYD D, YOSHIKUNIY. Implementation of stable and complex biological systems through recombinase-assisted genome engineering[J]. Nature Communications, 2013, 4(1) : 1-10.
53	GARSTA D, BASSALOM C, PINESG, et al. Genome-wide mapping of mutations at single-nucleotide resolution for protein, metabolic and genome engineering[J]. Nature Biotechnology, 2016, 35(1): 48-55.
54	LIUR, LIANGL, CHOUDHURYA, et al. Iterative genome editing of Escherichia coli for 3-hydroxypropionic acid production[J]. Metabolic Engineering, 2018, 47: 303-313.
55	LIUR, LIANGL, GARSTA D, et al. Directed combinatorial mutagenesis of Escherichia coli for complex phenotype engineering[J]. Metabolic Engineering, 2018, 47: 10-20.

途径	基因操作	产物	产量		参考文献
途径	基因操作	产物	对照	工程菌株	参考文献
乙酸途径	过表达hyc和acs	聚-β-羟丁酸	0.55mg聚-β-羟丁酸/mg 葡萄糖	5.34mg聚-β-羟丁酸/mg葡萄糖	[6]
	敲除ackA-pta和nuo	乙酰辅酶A	产量提高31%		[12]
	敲除ackA-pta，过表达acs	丙二酰辅酶A	产量提高两倍		[13]
丙酮酸途径	过表达aceEF-lpdA	琥珀酸	7.0mmol/L	17.5mmol/L	[18]
	过表达aceEF-lpdA	琥珀酸	4.2mmol/L	12.2mmol/L	[19]
	敲除iclR，fadR	琥珀酸	0.5mol/mol	0.98mol/mol	[20]
	敲除fnr	1-丁醇	130mg/L	373mg/L	[22]
	过表达aceEF-IpdA，panK	乙酸异戊酯	0.1mmol/L	0.18mmol/L	[25]
糖酵解途径	过表达tpiA，fbaA	聚-β-羟丁酸	0.4g/L	1.6g/L	[27]
三羧酸循环途径	敲除fumB/C 或sucC	丙二酰辅酶A	2.55μmol/gDW	4.43μmol/gDW	[28]
	敲除sdhA和citE	丙二酰辅酶A	0.95nmol/mg	2.60nmol/mg	[29]
乙醛酸途径	敲除iclR	3-羟基丙酸	产量提高1.9倍		[30]
	敲除icdA	香草醛	0.79g/L	2.06g/L	[31]
磷酸戊糖途径	过表达tktA	聚-β-羟丁酸	产量提高1.7倍		[32]
	过表达zwf	聚-β-羟丁酸	产量提高41%		[33]
2-酮-3-脱氧-6-磷酸葡糖酸途径	过表达edd、eda 和aceEF	聚-β-羟丁酸	产量提高81.1%		[35]
β氧化途径	敲除fadR	3-羟基丙酸	产量达到52g/L		[37]
非氧化酵解途径	过表达xpk（Bifidobacterium adolescentis）和fba	聚-β-羟丁酸	2.36g/L	4.69g/L	[40]
	过表达xpk（Bifidobacterium adolescentis）	丙酮	0.38mol/mol	0.47mol/mol	[41]

途径	基因操作	产物	产量		参考文献
途径	基因操作	产物	对照	工程菌株	参考文献
乙酸途径	过表达hyc和acs	聚-β-羟丁酸	0.55mg聚-β-羟丁酸/mg 葡萄糖	5.34mg聚-β-羟丁酸/mg葡萄糖	[6]
	敲除ackA-pta和nuo	乙酰辅酶A	产量提高31%		[12]
	敲除ackA-pta，过表达acs	丙二酰辅酶A	产量提高两倍		[13]
丙酮酸途径	过表达aceEF-lpdA	琥珀酸	7.0mmol/L	17.5mmol/L	[18]
	过表达aceEF-lpdA	琥珀酸	4.2mmol/L	12.2mmol/L	[19]
	敲除iclR，fadR	琥珀酸	0.5mol/mol	0.98mol/mol	[20]
	敲除fnr	1-丁醇	130mg/L	373mg/L	[22]
	过表达aceEF-IpdA，panK	乙酸异戊酯	0.1mmol/L	0.18mmol/L	[25]
糖酵解途径	过表达tpiA，fbaA	聚-β-羟丁酸	0.4g/L	1.6g/L	[27]
三羧酸循环途径	敲除fumB/C 或sucC	丙二酰辅酶A	2.55μmol/gDW	4.43μmol/gDW	[28]
	敲除sdhA和citE	丙二酰辅酶A	0.95nmol/mg	2.60nmol/mg	[29]
乙醛酸途径	敲除iclR	3-羟基丙酸	产量提高1.9倍		[30]
	敲除icdA	香草醛	0.79g/L	2.06g/L	[31]
磷酸戊糖途径	过表达tktA	聚-β-羟丁酸	产量提高1.7倍		[32]
	过表达zwf	聚-β-羟丁酸	产量提高41%		[33]
2-酮-3-脱氧-6-磷酸葡糖酸途径	过表达edd、eda 和aceEF	聚-β-羟丁酸	产量提高81.1%		[35]
β氧化途径	敲除fadR	3-羟基丙酸	产量达到52g/L		[37]
非氧化酵解途径	过表达xpk（Bifidobacterium adolescentis）和fba	聚-β-羟丁酸	2.36g/L	4.69g/L	[40]
	过表达xpk（Bifidobacterium adolescentis）	丙酮	0.38mol/mol	0.47mol/mol	[41]

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