Enhancing recombinant protein production with an Escherichia coli host strain lacking insertion sequences

Applied Microbiology and Biotechnology

Volumn 98, Issue 15, 2014, Pages 6701-6713

  Park, Myung Keun ^a   Lee, Sang Hee ^a   Yang, Kyung Seok ^a   Jung, Suk Chae ^a   Lee, Jun Hyoung ^a   Kim, Sun Chang ^a  

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

Author keywords

E. coli; Genomic stability; Insertion sequence; IS hopping

Indexed keywords

CELL DEATH; ESCHERICHIA COLI; FERMENTATION; GENE EXPRESSION; POPULATION STATISTICS; RECOMBINANT PROTEINS;

BONE MORPHOGENETIC PROTEIN-2; E. COLI; GENOMIC STABILITY; INDUSTRIAL PRODUCTION; INSERTION SEQUENCES; IS HOPPING; RECOMBINANT PROTEIN PRODUCTIONS; TUMOR NECROSIS FACTOR-RELATED APOPTOSIS-INDUCING LIGANDS;

GENE ENCODING;

BONE MORPHOGENETIC PROTEIN 2; TUMOR NECROSIS FACTOR RELATED APOPTOSIS INDUCING LIGAND; RECOMBINANT PROTEIN;

ARTICLE; BACTERIAL CELL; BACTERIAL GENE; BACTERIAL GROWTH; BACTERIAL STRAIN; BATCH FERMENTATION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE INSERTION SEQUENCE; HOST; NONHUMAN; PLASMID; PROTEIN EXPRESSION; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; UPREGULATION;

ESCHERICHIA COLI; MUTAGENESIS, INSERTIONAL; PLASMIDS; RECOMBINANT PROTEINS; UP-REGULATION;

EID: 84905054602     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-014-5739-y     Document Type: Article

References (58)

1. Arbabi-Ghahroudi M, Tanha J,MacKenzie R (2005) Prokaryotic expression of antibodies. Cancer Metastasis Rev 24(4):501-519. doi:10.1007/s10555-005-6193-1 (Pubitemid 43096998)
2. Baneyx F, Mujacic M (2004) Recombinant protein folding and misfolding in Escherichia coli. Nat Biotechnol 22(11):1399-1408. doi:10.1038/nbt1029
3. Barbotin JN (1994) Immobilization of recombinant bacteria. A strategy to improve plasmid stability. Ann N YAcad Sci 721:303-309
4. Bell CE (2005) Structure and mechanism of Escherichia coli RecA ATPase. Mol Microbiol 58(2):358-366. doi:10.1111/j.1365-2958.2005.04876.x
5. Bentley WE, Mirjalili N, Andersen DC, Davis RH, Kompala DS (1990) Plasmid-encoded protein: the principal factor in the "metabolic burden" associated with recombinant bacteria. Biotechnol Bioeng 35(7):668-681. doi:10.1002/bit.260350704 (Pubitemid 20150007)
6. Blattner FR, Plunkett G 3rd, Bloch CA, Perna NT, Burland V, Riley M, Collado-Vides J, Glasner JD, Rode CK, Mayhew GF, Gregor J, Davis NW, Kirkpatrick HA, Goeden MA, Rose DJ, Mau B, Shao Y (1997) The complete genome sequence of Escherichia coli K-12. Science 277(5331):1453-1462 (Pubitemid 27449228)
7. Bower DM, Prather KL (2009) Engineering of bacterial strains and vectors for the production of plasmid DNA. Appl Microbiol Biotechnol 82(5):805-813. doi:10.1007/s00253-009-1889-8
8. Charlesworth B, Sniegowski P, Stephan W (1994) The evolutionary dynamics of repetitive DNA in eukaryotes. Nature 371(6494):215-220 (Pubitemid 24293018)
9. Csorgo B, Feher T, Timar E, Blattner FR, Posfai G (2012) Low-mutationrate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs.Microb Cell Factories 11:11. doi:10.1186/1475-2859-11-11
10. Durfee T, Nelson R, Baldwin S, Plunkett G 3rd, Burland V, Mau B, Petrosino JF, Qin X, Muzny DM, Ayele M, Gibbs RA, Csorgo B, Posfai G,Weinstock GM, Blattner FR (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J Bacteriol 190(7):2597-2606. doi:10.1128/JB.01695-07 (Pubitemid 351466356)
11. Friehs K (2004) Plasmid copy number and plasmid stability. Adv Biochem Eng Biotechnol 86:47-82
12. Gibson DG, Benders GA, Andrews-Pfannkoch C, Denisova EA, Baden-Tillson H, Zaveri J, Stockwell TB, Brownley A, Thomas DW, Algire MA, Merryman C, Young L, Noskov VN, Glass JI, Venter JC, Hutchison CA 3rd, Smith HO (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319(5867):1215-1220. doi:10.1126/science.1151721 (Pubitemid 351323011)
13. Gillet R, Felden B (2001) Emerging views on tmRNA-mediated protein tagging and ribosome rescue. Mol Microbiol 42(4):879-885 (Pubitemid 33078373)
14. Glick BR (1995) Metabolic load and heterologous gene expression. Biotechnol Adv 13(2):247-261
15. Ikeda M (2003) Amino acid production processes. Adv Biochem Eng Biotechnol 79:1-35
16. Jain C (2002) Degradation of mRNA in Escherichia coli. IUBMB Life 54(6):315-321. doi:10.1080/15216540216036
17. Jana S, Deb JK (2005) Strategies for efficient production of heterologous proteins in Escherichia coli. ApplMicrobiol Biotechnol 67(3):289-298. doi:10.1007/s00253-004-1814-0 (Pubitemid 40684730)
18. Jang SA, Sung BH, Cho JH, Kim SC (2009) Direct expression of antimicrobial peptides in an intact form by a translationally coupled two-cistron expression system. Appl Environ Microbiol 75(12):3980-3986. doi:10.1128/AEM.02753-08
19. Keasling JD (1999) Gene-expression tools for the metabolic engineering of bacteria. Trends Biotechnol 17(11):452-460
20. Keseler IM, Mackie A, Peralta-Gil M, Santos-Zavaleta A, Gama-Castro S, Bonavides-Martinez C, Fulcher C, Huerta AM, Kothari A, Krummenacker M, Latendresse M, Muniz-Rascado L, Ong Q, Paley S, Schroder I, Shearer AG, Subhraveti P, Travers M, Weerasinghe D, Weiss V, Collado-Vides J, Gunsalus RP, Paulsen I, Karp PD (2013) EcoCyc: fusing model organism databases with systems biology. Nucleic Acids Res 41(Database issue):D605-D612. doi:10.1093/nar/gks1027
21. Kim MH, Billiar TR, Seol DW (2004) The secretable form of trimeric TRAIL, a potent inducer of apoptosis. Biochem Biophys Res Commun 321(4):930-935. doi:10.1016/j.bbrc.2004.07.046 (Pubitemid 39044398)
22. Kwok R (2010) Five hard truths for synthetic biology. Nature 463(7279):288-290. doi:10.1038/463288a
23. Laemmli UK (1970) Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227(5259):680-685
24. Lee SY (1996) High cell-density culture of Escherichia coli. Trends Biotechnol 14(3):98-105. doi:10.1016/0167-7799(96)80930-9
25. 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. doi:10.1016/j.jbiotec.2005.11.014 (Pubitemid 44294582)
26. Lee JH, Sung BH, Kim MS, Blattner FR, Yoon BH, Kim JH, Kim SC (2009) Metabolic engineering of a reduced-genome strain of Escherichia coli for L-threonine production. Microb Cell Factories 8:2. doi:10.1186/1475-2859-8-2
27. Lesic B, Zouine M, Ducos-Galand M, Huon C, Rosso ML, Prevost MC, Mazel D, Carniel E (2012) A natural systemof chromosome transfer in Yersinia pseudotuberculosis. PLoS Genet 8(3):e1002529. doi:10.1371/journal.pgen.1002529
28. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25(4):402-408. doi:10.1006/meth.2001.1262 (Pubitemid 34164012)
29. Luo Q, Shen YL,Wei DZ, Cao W (2006) Optimization of culture on the overproduction of TRAIL in high-cell-density culture by recombinant Escherichia coli. Appl Microbiol Biotechnol 71(2):184-191. doi:10.1007/s00253-005-0131-6 (Pubitemid 43873245)
30. Morales-Soto N, Forst SA (2011) The xnp1 P2-like tail synthesis gene cluster encodes xenorhabdicin and is required for interspecies competition. J Bacteriol 193(14):3624-3632. doi:10.1128/JB.00092-11
31. Nakamura K, Inouye M (1981) Inactivation of the Serratia marcescens gene for the lipoprotein in Escherichia coli by insertion sequences, IS1 and IS5; sequence analysis of junction points. Mol Gen Genet 183(1):107-114 (Pubitemid 11014674)
32. Nesbeth DN, Perez-Pardo MA, Ali S, Ward J, Keshavarz-Moore E (2012) Growth and productivity impacts of periplasmic nuclease expression in an Escherichia coli Fab' fragment production strain. Biotechnol Bioeng 109(2):517-527. doi:10.1002/bit.23316
33. O'Kennedy RD, Baldwin C, Keshavarz-Moore E (2000) Effects of growth medium selection on plasmid DNA production and initial processing steps. J Biotechnol 76(2-3):175-183
34. Parkhill J, Wren BW, Thomson NR, Titball RW, Holden MT, Prentice MB, Sebaihia M, James KD, Churcher C, Mungall KL, Baker S, Basham D, Bentley SD, Brooks K, Cerdeno-Tarraga AM, Chillingworth T, Cronin A, Davies RM, Davis P, Dougan G, Feltwell T, Hamlin N, Holroyd S, Jagels K, Karlyshev AV, Leather S, Moule S, Oyston PC, Quail M, Rutherford K, Simmonds M, Skelton J, Stevens K, Whitehead S, Barrell BG (2001) Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413(6855):523-527. doi:10.1038/35097083 (Pubitemid 32938750)
35. Peternel S, Komel R (2011) Active protein aggregates produced in Escherichia coli. Int J Mol Sci 12(11):8275-8287. doi:10.3390/ijms12118275
36. Pfleger BF, Pitera DJ, Smolke CD, Keasling JD (2006) Combinatorial engineering of intergenic regions in operons tunes expression of multiple genes. Nat Biotechnol 24(8):1027-1032. doi:10.1038/nbt1226 (Pubitemid 44215398)
37. Posfai G, Plunkett G 3rd, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, Burland V, Harcum SW, Blattner FR (2006) Emergent properties of reduced-genome Escherichia coli. Science 312(5776):1044-1046. doi:10.1126/science.1126439
38. Rawat P, Kumar S, Pental D, Burma PK (2009) Inactivation of a transgene due to transposition of insertion sequence (IS 136) of Agrobacterium tumefaciens. J Biosci 34(2):199-202. doi:10.1007/s12038-009-0023-5
39. Riesenberg D, Menzel K, Schulz V, Schumann K, Veith G, Zuber G, Knorre WA (1990) High cell density fermentation of recombinant Escherichia coli expressing human interferon alpha 1. Appl Microbiol Biotechnol 34(1):77-82 (Pubitemid 20375639)
40. Sambrook J, RussellDW(2001) Molecular cloning: a laboratorymanual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
41. Schneider D, Lenski RE (2004)Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol 155(5):319-327. doi:10.1016/j.resmic.2003.12.008
42. Schneider D, Duperchy E, Coursange E, Lenski RE, Blot M (2000) Long-term experimental evolution in Escherichia coli : IX. Characterization of insertion sequence-mediated mutations and rearrangements. Genetics 156(2):477-488
43. Serres MH, Goswami S, Riley M (2004) GenProtEC: an updated and improved analysis of functions of Escherichia coli K-12 proteins. Nucleic Acids Res 32(Database issue):D300-D302. doi:10.1093/nar/gkh087 (Pubitemid 38081662)
44. Siguier P, Varani A, Perochon J, Chandler M (2012) Exploring bacterial insertion sequences with ISfinder: objectives, uses, and future developments. Methods Mol Biol 859:91-103. doi:10.1007/978-1-61779-603-6-5
45. Solyga A, Bartosik D (2004) Entrapment vectors - how to capture a functional transposable element. Pol J Microbiol 53(3):139-144 (Pubitemid 39381934)
46. Sprenger M (2011) ECDC and the Escherichia coli outbreak in Germany. Lancet 377(9784):2180. doi:10.1016/S0140-6736(11)60963-X
47. Stroeher UH, Jedani KE, Dredge BK, Morona R, Brown MH, Karageorgos LE, AlbertMJ,Manning PA (1995) Genetic rearrangements in the rfb regions of Vibrio cholerae O1 and O139. Proc Natl Acad Sci U S A 92(22):10374-10378
48. Tobes R, Pareja E (2006) Bacterial repetitive extragenic palindromic sequences are DNA targets for Insertion Sequence elements. BMC Genomics 7:62. doi: 10.1186/1471-2164-7-62
49. Umenhoffer K, Feher T,Baliko G, Ayaydin F, Posfai J, Blattner FR, Posfai G (2010) Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications. Microb Cell Factories 9:38. doi:10.1186/1475-2859-9-38
50. Vallejo LF, Brokelmann M, Marten S, Trappe S, Cabrera-Crespo J, Hoffmann A, Gross G, Weich HA, Rinas U (2002) Renaturation and purification of bone morphogenetic protein-2 produced as inclusion bodies in high-cell-density cultures of recombinant Escherichia coli. J Biotechnol 94(2):185-194 (Pubitemid 34127660)
51. Wang ZJ, Le GW, Shi YH, Wegrzyn G (2001) Medium design for plasmid DNA production based on stoichiometric model. Process Biochem 36(11):1085-1093. doi:10.1016/S0032-9592(01)00149-2
52. Win MN, Smolke CD (2007) A modular and extensible RNA-based gene-regulatory platform for engineering cellular function. Proc Natl Acad Sci U S A 104(36):14283-14288. doi:10.1073/pnas.0703961104
53. Wozney JM, Rosen V, Celeste AJ, Mitsock LM, Whitters MJ, Kriz RW, Hewick RM, Wang EA (1988) Novel regulators of bone formation: molecular clones and activities. Science 242(4885):1528-1534 (Pubitemid 19023695)
54. Yamazaki Y, Niki H, Kato J (2008) Profiling of Escherichia coli Chromosome database. Methods Mol Biol 416:385-389. doi:10.1007/978-1-59745-321- 9-26
55. Yau SY, Keshavarz-Moore E, Ward J (2008) Host strain influences on supercoiled plasmid DNA production in Escherichia coli: implications for efficient design of large-scale processes. Biotechnol Bioeng 101(3):529-544. doi:10.1002/bit.21915
56. Yu Y, Lee C, Kim J, Hwang S (2005) Group-specific primer and probe sets to detect methanogenic communities using quantitative real-time polymerase chain reaction. Biotechnol Bioeng 89(6):670-679. doi:10.1002/bit.20347 (Pubitemid 40470355)
57. Yu BJ, Kang KH, Lee JH, Sung BH, Kim MS, Kim SC (2008) Rapid and efficient construction of markerless deletions in the Escherichia coli genome. Nucleic Acids Res 36(14):e84. doi:10.1093/nar/gkn359
58. Zhou J, Rudd KE (2013) EcoGene 3.0. Nucleic Acids Res 41(Database issue):D613-D624. doi:10.1093/nar/gks1235