Development of a high-copy-number plasmid via adaptive laboratory evolution of Corynebacterium glutamicum

Applied Microbiology and Biotechnology

Volumn 102, Issue 2, 2018, Pages 873-883

  Choi, Jae Woong ^a   Yim, Sung Sun ^a,b   Jeong, Ki Jun ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b NewYork Presbyterian Hospital   (United States)

Author keywords

Adaptive evolution; Corynebacterium glutamicum; ParB; Plasmid copy number

Indexed keywords

BATCH CELL CULTURE; FLUORESCENCE; RECOMBINANT PROTEINS;

ADAPTIVE EVOLUTION; CONTINUOUS CULTIVATION; COPY NUMBER; CORYNEBACTERIUM GLUTAMICUM; ENHANCED GREEN FLUORESCENT PROTEIN; FED-BATCH CULTIVATION; FLUORESCENCE INTENSITIES; PARB;

DNA;

AMINO ACID; ENHANCED GREEN FLUORESCENT PROTEIN; RECOMBINANT PROTEIN; XYLOSE; BACTERIAL PROTEIN; ENDO 1,4 BETA XYLANASE; GREEN FLUORESCENT PROTEIN;

ADAPTIVE RADIATION; AMINO ACID; BACTERIUM; BIOCHEMICAL COMPOSITION; CONCENTRATION (COMPOSITION); ENZYME; ENZYME ACTIVITY; EVOLUTION; FLOW CYTOMETRY; MUTATION; PLASMID; PROTEIN;

AGAR GEL ELECTROPHORESIS; ARTICLE; BACTERIAL CHROMOSOME; BACTERIUM ISOLATE; BIOTRANSFORMATION; CONTROLLED STUDY; COPY NUMBER VARIATION; CORYNEBACTERIUM GLUTAMICUM; FED BATCH CULTURE; FLOW CYTOMETRY; FLUORESCENCE ACTIVATED CELL SORTING; GENE LOCUS; MAXIMUM CONCENTRATION; MOLECULAR EVOLUTION; NONHUMAN; NONSENSE MUTATION; PLASMID; POLYACRYLAMIDE GEL ELECTROPHORESIS; SHUTTLE VECTOR; BATCH CELL CULTURE; CULTURE MEDIUM; DIRECTED MOLECULAR EVOLUTION; GENE DOSAGE; GENETICS; METABOLIC ENGINEERING; METABOLISM; STOP CODON;

CORYNEBACTERIUM GLUTAMICUM;

BACTERIAL PROTEINS; BATCH CELL CULTURE TECHNIQUES; CODON, NONSENSE; CORYNEBACTERIUM GLUTAMICUM; CULTURE MEDIA; DIRECTED MOLECULAR EVOLUTION; ENDO-1,4-BETA XYLANASES; GENE DOSAGE; GREEN FLUORESCENT PROTEINS; METABOLIC ENGINEERING; PLASMIDS; RECOMBINANT PROTEINS; XYLOSE;

EID: 85034839013     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-017-8653-2     Document Type: Article

References (40)

1. An SJ, Yim SS, Jeong KJ (2013) Development of a secretion system for the production of heterologous proteins in Corynebacterium glutamicum using the Porin B signal peptide. Protein Expr Purif 89(2):251–257. https://doi.org/10.1016/j.pep.2013.04.003
2. Angov E (2011) Codon usage: nature’s roadmap to expression and folding of proteins. Biotechnol J 6(6):650–659. https://doi.org/10.1002/biot.201000332
3. Becker J, Wittmann C (2012) Bio-based production of chemicals, materials and fuels–Corynebacterium glutamicum as versatile cell factory. Curr Opin Biotechnol 23(4):631–640. https://doi.org/10.1016/j.copbio.2011.11.012
4. Bower DM, Prather KL (2009) Engineering of bacterial strains and vectors for the production of plasmid DNA. Appl Microbiol Biotechnol 82(5):805–813. https://doi.org/10.1007/s00253-009-1889-8
5. Choi JW, Yim SS, Lee SH, Kang TJ, Park SJ, Jeong KJ (2015) Enhanced production of gamma-aminobutyrate (GABA) in recombinant Corynebacterium glutamicum by expressing glutamate decarboxylase active in expanded pH range. Microb Cell Factories 14(1):1
6. Correa A, Oppezzo P (2011) Tuning different expression parameters to achieve soluble recombinant proteins in E. coli: advantages of high-throughput screening. Biotechnol J 6(6):715–730. https://doi.org/10.1002/biot.201100025
7. De Paepe B, Peters G, Coussement P, Maertens J, De Mey M (2016) Tailor-made transcriptional biosensors for optimizing microbial cell factories. J Ind Microbiol Biotechnol:1–23
8. Donovan C, Schwaiger A, Krämer R, Bramkamp M (2010) Subcellular localization and characterization of the ParAB system from Corynebacterium glutamicum. J Bacteriol 192(13):3441–3451. https://doi.org/10.1128/JB.00214-10
9. Dragosits M, Mattanovich D (2013) Adaptive laboratory evolution–principles and applications for biotechnology. Microb Cell Factories 12(1):64. https://doi.org/10.1186/1475-2859-12-64
10. Freudl R (2017) Beyond amino acids: Use of the Corynebacterium glutamicum cell factory for the secretion of heterologous proteins. J Biotechnol In press
11. Harper M, Lee CJ (2012) Genome-wide analysis of mutagenesis bias and context sensitivity of N-methyl-N′-nitro-N-nitrosoguanidine (NTG). Mutat Res 731(1):64–67. https://doi.org/10.1016/j.mrfmmm.2011.10.011
12. Heider SA, Wendisch VF (2015) Engineering microbial cell factories: metabolic engineering of Corynebacterium glutamicum with a focus on non-natural products. Biotechnol J 10(8):1170–1184. https://doi.org/10.1002/biot.201400590
13. Humphreys DP, Carrington B, Bowering LC, Ganesh R, Sehdev M, Smith BJ, King LM, Reeks DG, Lawson A, Popplewell AG (2002) A plasmid system for optimization of fab′ production in Escherichia coli: importance of balance of heavy chain and light chain synthesis. Protein Expr Purif 26(2):309–320. https://doi.org/10.1016/S1046-5928(02)00543-0
14. Jones KL, Kim S-W, Keasling J (2000) Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab Eng 2(4):328–338. https://doi.org/10.1006/mben.2000.0161
15. Ju SY, Kim JH, Lee PC (2016) Long-term adaptive evolution of Leuconostoc mesenteroides for enhancement of lactic acid tolerance and production. Biotechnol Biofuels 9(1):240. https://doi.org/10.1186/s13068-016-0662-3
16. Lee C, Kim J, Shin SG, Hwang S (2006) Absolute and relative QPCR quantification of plasmid copy number in Escherichia coli. J Biotechnol 123(3):273–280. https://doi.org/10.1016/j.jbiotec.2005.11.014
17. Liu X, Yang Y, Zhang W, Sun Y, Peng F, Jeffrey L, Harvey L, McNeil B, Bai Z (2016) Expression of recombinant protein using Corynebacterium glutamicum: progress, challenges and applications. Crit Rev Biotechnol 36(4):652–664. https://doi.org/10.3109/07388551.2015.1004519
18. Mahr R, Gätgens C, Gätgens J, Polen T, Kalinowski J, Frunzke J (2015) Biosensor-driven adaptive laboratory evolution of L-valine production in Corynebacterium glutamicum. Metab Eng 32:184–194. https://doi.org/10.1016/j.ymben.2015.09.017
19. Nešvera J, Pátek M (2011) Tools for genetic manipulations in Corynebacterium glutamicum and their applications. Appl Microbiol Biotechnol 90(5):1641–1654. https://doi.org/10.1007/s00253-011-3272-9
20. Okibe N, Suzuki N, Inui M, Yukawa H (2010) Antisense-RNA-mediated plasmid copy number control in pCG1-family plasmids, pCGR2 and pCG1, in Corynebacterium glutamicum. Microbiology 156(12):3609–3623. https://doi.org/10.1099/mic.0.043745-0
21. Olson-Manning CF, Wagner MR, Mitchell-Olds T (2012) Adaptive evolution: evaluating empirical support for theoretical predictions. Nat Rev Genet 13(12):867–877. https://doi.org/10.1038/nrg3322
22. Ozaki A, Katsumata R, Oka T, Furuya A (1984) Functional expression of the genes of Escherichia coli in gram-positive Corynebacterium glutamicum. Mol Gen Genet 196(1):175–178. https://doi.org/10.1007/BF00334113
23. Pal C, Papp B, Posfai G (2014) The dawn of evolutionary genome engineering. Nat Rev Genet 15(7):504–512. https://doi.org/10.1038/nrg3746
24. Park J-U, Jo J-H, Kim Y-J, Chung S-S, Lee J-H, Lee HH (2008) Construction of heat-inducible expression vector of Corynebacterium glutamicum and C. ammoniagenes: fusion of lambda operator with promoters isolated from C. ammoniagenes. J Microbiol Biotechnol 18(4):639–647
25. Sarin S, Bertrand V, Bigelow H, Boyanov A, Doitsidou M, Poole RJ, Narula S, Hobert O (2010) Analysis of multiple ethyl methanesulfonate-mutagenized Caenorhabditis elegans strains by whole-genome sequencing. Genetics 185(2):417–430. https://doi.org/10.1534/genetics.110.116319
26. Silva F, Queiroz JA, Domingues FC (2012) Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli. Biotechnol Adv 30(3):691–708. https://doi.org/10.1016/j.biotechadv.2011.12.005
27. Škulj M, Okršlar V, Jalen Š, Jevševar S, Slanc P, Štrukelj B, Menart V (2008) Improved determination of plasmid copy number using quantitative real-time PCR for monitoring fermentation processes. Microb Cell Factories 7(1):1
28. Summers DK, Sherratt DJ (1984) Multimerization of high copy number plasmids causes instability: ColE 1 encodes a determinant essential for plasmid monomerization and stability. Cell 36(4):1097–1103. https://doi.org/10.1016/0092-8674(84)90060-6
29. Swartz JR (2001) Advances in Escherichia coli production of therapeutic proteins. Curr Opin Biotechnol 12(2):195–201. https://doi.org/10.1016/S0958-1669(00)00199-3
30. Tauch A, Pühler A, Kalinowski J, Thierbach G (2003) Plasmids in Corynebacterium glutamicum and their molecular classification by comparative genomics. J Biotechnol 104(1):27–40. https://doi.org/10.1016/S0168-1656(03)00157-3
31. Terpe K (2006) Overview of bacterial expression systems for heterologous protein production: from molecular and biochemical fundamentals to commercial systems. Appl Microbiol Biotechnol 72(2):211–222. https://doi.org/10.1007/s00253-006-0465-8
32. Wendisch VF, Jorge JM, Pérez-García F, Sgobba E (2016) Updates on industrial production of amino acids using Corynebacterium glutamicum. World J Microbiol Biotechnol 32(6):105. https://doi.org/10.1007/s11274-016-2060-1
33. Wieschalka S, Blombach B, Bott M, Eikmanns BJ (2013) Bio-based production of organic acids with Corynebacterium glutamicum. Microb Biotechnol 6(2):87–102. https://doi.org/10.1111/1751-7915.12013
34. Williams TC, Pretorius IS, Paulsen IT (2016) Synthetic evolution of metabolic productivity using biosensors. Trends Biotechnol 34(5):371–381. https://doi.org/10.1016/j.tibtech.2016.02.002
35. Williamson MA (2010) US biobased products market potential and projections through 2025. Nova Science Publishers
36. Yim SS, An SJ, Kang M, Lee J, Jeong KJ (2013) Isolation of fully synthetic promoters for high-level gene expression in Corynebacterium glutamicum. Biotechnol Bioeng 110(11):2959–2969. https://doi.org/10.1002/bit.24954
37. Yim SS, An SJ, Choi JW, Ryu AJ, Jeong KJ (2014) High-level secretory production of recombinant single-chain variable fragment (scFv) in Corynebacterium glutamicum. Appl Microbiol Biotechnol 98(1):273–284. https://doi.org/10.1007/s00253-013-5315-x
38. Yim SS, Choi JW, Lee RJ, Lee YJ, Lee SH, Kim SY, Jeong KJ (2016) Development of a new platform for secretory production of recombinant proteins in Corynebacterium glutamicum. Biotechnol Bioeng 113(1):163–172. https://doi.org/10.1002/bit.25692
39. Yim SS, Choi JW, Lee SH, Jeon EJ, Chung WJ, Jeong KJ (2017) Engineering of Corynebacterium glutamicum for consolidated conversion of hemicellulosic biomass into xylonic acid. Biotechnol J In press. doi:https://doi.org/10.1002/biot.201700040
40. Zahoor A, Lindner SN, Wendisch VF (2012) Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products. Comput Struct Biotechnol J 3(4):1–11