Production of shikimic acid from Escherichia coli through chemically inducible chromosomal evolution and cofactor metabolic engineering

Microbial Cell Factories

Volumn 13, Issue 1, 2014, Pages

  Cui, Yan Yan ^a   Ling, Chen ^b   Zhang, Yuan Yuan ^a   Huang, Jian ^a   Liu, Jian Zhong ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b SOUTH CHINA UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

Chemically induced chromosomal evolution; Escherichia coli; NAD kinase; NADPH; Shikimic acid; Transhydrogenase

Indexed keywords

CHROMOSOMES; DNA COPY NUMBER VARIATIONS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EVOLUTION, MOLECULAR; GENE KNOCKOUT TECHNIQUES; ILLICIUM; METABOLIC ENGINEERING; MULTIGENE FAMILY; NADP; NADP TRANSHYDROGENASES; PHOSPHOTRANSFERASES (ALCOHOL GROUP ACCEPTOR); PLASMIDS; PROMOTER REGIONS, GENETIC; SHIKIMIC ACID;

EID: 84893649889     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-13-21     Document Type: Article

References (35)

1. Kim CU, Lew W, Williams MA, Liu H, Zhang L, Swaminathan S, Bischofberger N, Chen MS, Mendel DB, Tai CY, Laver WG, Stevens RC. Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: design, synthesis, and structural analysis of carbocyclic sialic acid analogs with potent anti-influenza activity. J Am Chem Soc 1997, 119:681-690. 10.1021/ja963036t, 16526129.
2. Krämer M, Bongaerts J, Bovenberg R, Kremer S, Müller U, Orf S, Wubbolts M, Raeven L. Metabolic engineering for microbial production of shikimic acid. Metab Eng 2003, 5:277-283. 10.1016/j.ymben.2003.09.001, 14642355.
3. Ghosh S, Chisti Y, Banerjee Uttam C. Production of shikimic acid. Biotechnol Adv 2012, 30:1425-1431. 10.1016/j.biotechadv.2012.03.001, 22445787.
4. Escalante A, Calderon R, Valdivia A, de Anda R, Hernández G, Hernández OT, Gosset G, Bolivar F. Metabolic engineering for the production of shikimic acid in an evolved Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system. Microb Cell Fact 2010, 9:21. 10.1186/1475-2859-9-21, 2873404, 20385022.
5. Draths KM, Knop DR, Frost JW. Shikimic acid and quinic acid: replacing isolation from plant sources with recombinant microbial biocatalysis. J Am Chem Soc 1999, 121:1603-1604.
6. Knop DR, Draths KM, Chandran SS, Barker JL, Frost JW. Hydroaromatic equilibrium during biosynthesis of shikimic acid. J Am Chem Soc 2001, 123:10173-10182. 10.1021/ja0109444, 11603966.
7. Chandran SS, Yi J, Draths KM, Von Daeniken R, Weber W, Frost JW. Phosphoenolpyruvate availability and the biosynthesis of shikimic acid. Biotechnol Prog 2003, 19:808-814. 10.1021/bp025769p, 12790643.
8. Yi J, Draths KM, Li K, Frost JW. Altered glucose transport and shikimate pathway product yields in E. coli. Biotechnol Prog 2003, 19:1450-1459. 10.1021/bp0340584, 14524706.
9. Rodriguez A, Martínez JA, Báez-Viveros JL, Flores N, Hernández-Chávez G, Ramírez OT, Gosset G, Bolivar F. Constitutive expression of selected genes from the pentose phosphate and aromatic pathways increases the shikimic acid yield in high-glucose batch cultures of an Escherichia coli strain lacking PTS and pykF. Microb Cell Fact 2013, 12:86. 10.1186/1475-2859-12-86, 3852013, 24079972.
10. Bentley WE, Mirjalili N, Andersen DC, Davis RH, Kompala DS. Plasmid-encoded protein: the principal factor in the metabolic burden associated with recombinant bacteria. Biotechnol Bioeng 1990, 35:668-681. 10.1002/bit.260350704, 18592563.
11. Noack D, Roth M, Geuther R, Muller G, Undisz K, Hoffmeier C, Gaspar S. Maintenance and genetic stability of vector plasmids pBR322 and pBR325 in Escherichia coli K12 strains grown in a chemostat. Mol Gen Genet 1981, 184:121-124. 10.1007/BF00271207, 6278246.
12. O'Connor M, Peifer M, Bender W. Construction of large DNA segments in Escherichia coli. Science 1989, 244:1307-1312. 10.1126/science.2660262, 2660262.
13. Tyo KEJ, Ajikumar PK, Stephanopoulos G. Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat Biotechnol 2009, 27:760-765. 10.1038/nbt.1555, 19633654.
14. Chiang C-J, Chen PT, Chao YP. Replicon-free and markerless methods for genomic insertion of DNAs in phage attachment sites and controlled expression of chromosomal genes in Escherichia coli. Biotechnol Bioeng 2008, 101:985-995. 10.1002/bit.21976, 18553504.
15. Goh S, Good L. Plasmid selection in Escherichia coli using an endogenous essential gene marker. BMC Biotechnol 2008, 8:61. 10.1186/1472-6750-8-61, 2527308, 18694482.
16. Chen Y-Y, Shen H-J, Cui Y-Y, Chen S-G, Weng Z-M, Zhao M, Liu J-Z. Chromosomal evolution of Escherichia coli for the efficient production of lycopene. BMC Biotechnol 2013, 13:6. 10.1186/1472-6750-13-6, 3626847, 23356604.
17. Ahn J, Chung BKS, Lee D-Y, Park M, Karimi IA, Jung J-K, Lee H. NADPH-dependent pgi-gene knockout Escherichia coli metabolism producing shikimate on different carbon sources. FEMS Microbiol Lett 2011, 324:10-16. 10.1111/j.1574-6968.2011.02378.x, 22092758.
18. Yakandawala N, Romeo T, Friesen AD, Madhyastha S. Metabolic engineering of Escherichia coli to enhance phenylalanine production. Appl Microbiol Biotechnol 2008, 78:283-291. 10.1007/s00253-007-1307-z, 18080813.
19. Suzuki K, Babitzke P, Kushner SR, Romeo T. Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev 2006, 20:2605-2617. 10.1101/gad.1461606, 1578682, 16980588.
20. Patnaik R, Liao JC. Engineering of Escherichia coli central metabolism for aromatic metabolite production with near theoretical yield. Appl Environ Microbiol 1994, 60:3903-3908. 201913, 7993080.
21. Nishizaki T, Tsuge K, Itaya M, Doi N, Yanagawa H. Metabolic engineering of carotenoid biosynthesis in Escherichia coli by ordered gene assembly in Bacillus subtilis. Appl Environ Microbiol 2007, 73:1355-1361. 10.1128/AEM.02268-06, 1828653, 17194842.
22. Sauer U, Canonaco F, Heri S, Perrenoud A, Fischer E. The soluble and membrane-bound transhydrogenases udhA and pntAB have divergent functions in NADPH metabolism of Escherichia coli. J Biol Chem 2004, 279:6613-6619.
23. Kabus A, Georgi T, Wendisch VF, Michael B. Expression of the Escherichia coli pntAB genes encoding a membrane-bound transhydrogenase in Corynebacterium glutamicum improves L-lysine formation. Appl Microbiol Biotechnol 2007, 75:47-53. 10.1007/s00253-006-0804-9, 17216441.
24. Jiang LY, Chen SG, Zhang YY, Liu JZ. Metabolic evolution of Corynebacterium glutamicum for increased production of L-ornithine. BMC Biotechnol 2013, 13:47. 10.1186/1472-6750-13-47, 3681597, 23725060.
25. Lee HC, Kim JS, Jang W, Kim SY. High NADPH/NADP ratio improves thymidine production by a metabolically engineered Escherichia coli strain. J Biotechnol 2010, 149:24-32. 10.1016/j.jbiotec.2010.06.011, 20600382.
26. Lindner SN, Niederholtmeyer H, Schmitz K, Schoberth SM, Wendisch VF. Polyphosphate/ATP-dependent NAD kinase of Corynebacterium glutamicum: biochemical properties and impact of ppnK overexpression on lysine production. Appl Microbiol Biotechnol 2010, 87:583-593. 10.1007/s00253-010-2481-y, 20180116.
27. Shi A, Zhu X, Lu J, Zhang X, Ma Y. Activating transhydrogenase and NAD kinase in combination for improving isobutanol production. Metab Eng 2013, 16:1-10.
28. Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 2000, 97:6640-6645. 10.1073/pnas.120163297, 18686, 10829079.
29. Sharan SK, Thomason LC, Kuznetsov SG, Court DL. Recombineering: a homologous recombination-based method of genetic engineering. Nat Protoc 2009, 4:206-223. 10.1038/nprot.2008.227, 2790811, 19180090.
30. Guzman LM, Belin D, Carson MJ, Beckwith J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J Bacteriol 1995, 177:4121-4130. 177145, 7608087.
31. Haldimann A, Wanner BL. Conditional-replication, integration, excision, and retrieval plasmid-host systems for gene structure-function studies of bacteria. J Bacteriol 2001, 183:6384-6393. 10.1128/JB.183.21.6384-6393.2001, 100134, 11591683.
32. Li M, Wang J, Geng Y, Li Y, Wang Q, Liang Q, Qi Q. A strategy of gene overexpression based on tandem repetitive promoters in Escherichia coli. Microb Cell Fact 2012, 11:19. 10.1186/1475-2859-11-19, 3293061, 22305426.
33. Liu JZ, Huang MT, Cui YY, Chen YY. A series of expression plasmids for chromosomal integration and evolution. China patent 2012, 201210060042.
34. Huang MT, Chen YY, Liu JZ. Chromosomal engineering of Escherichia coli for the efficient production of coenzyme Q10. Chin J Chem Eng In press.
35. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2-ΔΔCt Method. Methods 2001, 25:402-408. 10.1006/meth.2001.1262, 11846609.