Deletion formation mutations in plasmid expression vectors are unfavored by runaway amplification conditions and differentially selected under kanamycin stress

Journal of Biotechnology

Volumn 143, Issue 4, 2009, Pages 231-238

  Oliveira, Pedro H ^a   Prazeres, Duarte M F ^a   Monteiro, Gabriel A ^a  

^a INSTITUTO SUPERIOR TÉCNICO   (Portugal)

Author keywords

Direct repeats; Escherichia coli; Expression vectors; Plasmid; Recombination; Stress

Indexed keywords

COPY NUMBER; DELETION FORMATION; DIRECT REPEATS; DISSOLVED OXYGEN TENSION; DNA VACCINE; ENVIRONMENTAL STRESS; EXPRESSION VECTORS; HETERODIMERS; KANAMYCINS; LOW FREQUENCY; MONOMERIC FORMS; NEOMYCIN RESISTANCE; PLASMID; RECOMBINANT MOLECULES; RECOMBINATION; RECOMBINATION FREQUENCIES; SIGNIFICANT IMPACTS;

AMPLIFICATION; ANTIBIOTICS; CONCENTRATION (PROCESS); DISSOLUTION; DISSOLVED OXYGEN; ESCHERICHIA COLI; MAMMALS; NUCLEIC ACIDS; VACCINES;

VECTORS;

KANAMYCIN;

ANTIBIOTIC RESISTANCE; ARTICLE; BACTERIAL GENE; BACTERIUM CULTURE; CONTROLLED STUDY; ESCHERICHIA COLI; EXPRESSION VECTOR; GENE AMPLIFICATION; GENE DELETION; GENE MUTATION; GENETIC RECOMBINATION; GENETIC TRANSCRIPTION; NONHUMAN; PLASMID; PRIORITY JOURNAL; RECOMBINANT PLASMID;

BASE SEQUENCE; CULTURE MEDIA; ESCHERICHIA COLI; GENE AMPLIFICATION; GENE DELETION; GENE DOSAGE; GENETIC VECTORS; KANAMYCIN; MOLECULAR SEQUENCE DATA; OXYGEN; PLASMIDS; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; STRESS, PHYSIOLOGICAL; TEMPERATURE; TIME FACTORS;

ESCHERICHIA COLI; MAMMALIA;

EID: 70249151468     PISSN: 01681656     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2009.08.002     Document Type: Article

References (63)

1. Abraham A.L., Rocha E.P.C., and Pothier J. Swelfe: a detector of internal repeats in sequences and structures. Bioinformatics 24 (2008) 1536-1537
2. Achaz G., Boyer F., Rocha E.P.C., Viari A., and Coissac E. Repseek, a tool to retrieve approximate repeats from large DNA sequences. Bioinformatics 23 (2007) 119-121
3. Atlas R.M. Handbook of Microbiological Media (1993), CRC Press, Boca Raton, FL
4. Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27 (1999) 573-580
5. Bi X., and Liu L.F. recA-independent and recA-dependent intramolecular plasmid recombination. Differential homology requirement and distance effect. J. Mol. Biol. 235 (1994) 414-423
6. Bi X., and Liu L.F. A replicational model for DNA recombination between direct repeats. J. Mol. Biol. 256 (1996) 849-858
7. Bierne H., Ehrlich S.D., and Michel B. Competition between parental and recombinant plasmids affects the measure of recombination frequencies. Plasmid 33 (1995) 101-112
8. Borgi I., and Gargouri A. A spontaneous direct repeat deletion in the pGEX fusion vector decreases the expression level of recombinant proteins in Escherichia coli. Protein Expr. Purif. 60 (2008) 15-19
9. Carnes A.E. Fermentation design for the manufacture of therapeutic plasmid DNA. BioProcess Int. 3 (2005) 36-44
10. Chowdhury R., Sahu G.K., and Das J. Stress response in pathogenic bacteria. J. Biosci. 21 (1996) 149-160
11. Chédin F., Dervyn E., Dervyn R., Ehrlich S.D., and Noirot P. Frequency of deletion formation decreases exponentially with distance between short direct repeats. Mol. Microbiol. 12 (1994) 561-569
12. Dianov G.L., Kuzminov A.V., Mazin A.V., and Salganik R.I. Molecular mechanisms of deletion formation in Escherichia coli plasmids I. Deletion formation mediated by long direct repeats. Mol. Gen. Genet. 228 (1991) 153-159
13. Duetz W.A., and Witholt B. Effectiveness of orbital shaking for the aeration of suspended bacterial cultures in square-deepwell microtiter plates. Biochem. Eng. J. 7 (2001) 113-115
14. Duetz W.A., and Witholt B. Oxygen transfer by orbital shaking of square vessels and deepwell microtiter plates of various dimensions. Biochem. Eng. J. 17 (2004) 181-185
15. Feschenko V.V., and Lovett S.T. Slipped misalignment mechanisms of deletion formation: analysis of deletion endpoints. J. Mol. Biol. 276 (1998) 559-569
16. Fitzwater T., Zhang X.Y., Elble R., and Polisky B. Conditional high copy number ColE1 mutants: resistance to RNA1 inhibition in vivo and in vitro. EMBO J. 7 (1988) 3289-3297
17. Fujitani Y., and Kobayashi I. Asymmetric random walk in a reaction intermediate of homologous recombination. J. Theor. Biol. 220 (2003) 359-370
18. Hoffmann F., and Rinas U. Plasmid amplification in Escherichia coli after temperature upshift is impaired by induction of recombinant protein synthesis. Biotechnol. Lett. 23 (2001) 1819-1825
19. Hopkins D.J., Betenbaugh M.J., and Dhurjati P. Effects of dissolved oxygen shock on the stability of recombinant Escherichia coli containing plasmid pKN401. Biotechnol. Bioeng. 29 (1987) 85-91
20. Kang J.M., Iovine N.M., and Blaser M.J. A paradigm for direct stress-induced mutation in prokaryotes. FASEB J. 20 (2006) 2476-2485
21. Kawe M., Horn U., and Pluckthun A. Facile promoter deletion in Escherichia coli in response to leaky expression of very robust and benign proteins from common expression vectors. Microb. Cell Fact 8 (2009) 8
22. Kupsch J., Alonso J.C., and Trautner T.A. Analysis of structural and biological parameters affecting plasmid deletion formation in Bacillus subtilis. Mol. Gen. Genet. 218 (1989) 402-408
23. Kurtz S., and Schleiermacher C. REPuter: fast computation of maximal repeats in complete genomes. Bioinformatics 15 (1999) 426-427
24. Labib K., and Hodgson B. Replication fork barriers: pausing for a break or stalling for time?. EMBO Rep. 8 (2007) 346-353
25. Lin-Chao S., Chen W.T., and Wong T.T. High copy number of the pUC plasmid results from a Rom/Rop-supressible point mutation in RNA II. Mol. Microbiol. 6 (1992) 3385-3393
26. Lovett S.T., Drapkin P.T., Sutera Jr. V.A., and Gluckman-Peskind T.J. A sister-strand exchange mechanism for recA-independent deletion of repeated DNA sequences in Escherichia coli. Genetics 135 (1993) 631-642
27. Lovett S.T., Gluckman T.J., Simon P.J., Sutera Jr. V.A., and Drapkin P.T. Recombination between repeats in Escherichia coli by a recA-independent, proximity-sensitive mechanism. Mol. Gen. Genet. 245 (1994) 294-300
28. Lupski J.R., Projan S.J., Ozaki L.S., and Godson G.N. A temperature-dependent pBR322 copy number mutant resulting from a Tn5 position effect. Proc. Natl. Acad. Sci. USA 83 (1986) 7381-7385
29. Lusetti S.L., and Cox M.M. The bacterial RecA protein and the recombinational DNA repair of stalled replication forks. Annu. Rev. Biochem. 71 (2002) 71-100
30. Mahillon J., and Chandler M. Insertion sequences. Microbiol. Mol. Biol. Rev. 62 (1998) 725-774
31. Martinez J.L., and Baquero F. Mutation frequencies and antibiotic resistance. Antimicrob. Agents Chemother. 44 (2000) 1771-1777
32. Mazin A.V., Kuzminov A.V., Dianov G.L., and Salganik R.I. Mechanisms of deletion formation in Escherichia coli plasmids II: deletions mediated by short direct repeats. Mol. Gen. Genet. 228 (1991) 209-214
33. Mazin A.V., Timchenko T.V., Saparbaev M.K., and Mazina O.M. Dimerization of plasmid DNA accelerates selection for antibiotic resistance. Mol. Microbiol. 20 (1996) 101-108
34. Minton N.P., Chambers S.P., Prior S.E., Cole S.T., and Garnier T. Copy number and mobilization properties of pUC plasmid. Focus 10 (1988) 56
35. Mirkin E.V., and Mirkin S.M. Replication fork stalling at natural impediments. Microbiol. Mol. Biol. Rev. 71 (2007) 13-35
36. Morag A.S., Saveson C.J., and Lovett S.T. Expansion of DNA repeats in Escherichia coli: effects of recombination and replication functions. J. Mol. Biol. 289 (1999) 21-27
37. Moser D.R., and Campbell J.L. Characterization and complementation of pMB1 copy number mutant: effect of RNA I gene dosage on plasmid copy number and incompatibility. J. Bacteriol. 154 (1983) 809-818
38. Muesing M., Tamm J., Shepard H.M., and Polisky B. A single base-pair alteration is responsible for the DNA overproduction phenotype of a plasmid copy-number mutant. Cell 24 (1981) 235-242
39. Namdev P.K., Irwin N., Thompson B.G., and Gray M.R. Effect of oxygen fluctuations on recombinant Escherichia coli fermentation. Biotechnol. Bioeng. 41 (1993) 666-670
40. Nash K.A. Effect of drug concentration on emergence of macrolide resistance in Mycobacterium avium. Antimicrob. Agents Chemother. 45 (2001) 1607-1614
41. O'Kennedy R.D., Baldwin C., and Keshavarz-Moore E. Effects of growth medium selection on plasmid DNA production and initial processing steps. J. Biotechnol. 76 (2000) 175-183
42. Oliveira P.H., Lemos F., Monteiro G.A., and Prazeres D.M.F. Recombination frequency in plasmid DNA containing direct repeats-predictive correlation with repeat and intervening sequence length. Plasmid 60 (2008) 159-165
43. Oliveira P.H., Prather K.J., Prazeres D.M.F., and Monteiro G.A. Structural instabilities of plasmid biopharmaceuticals-challenges and implications. Trends Biotechnol. 27 (2009) 503-511
44. Peeters B.P.H., de Boer J.H., Bron S., and Venema G. Structural plasmid instability in Bacillus subtilis: effect of direct and inverted repeats. Mol. Gen. Genet. 212 (1988) 450-458
45. Prather K.J., Sagar S., Murphy J., and Chartrain M. Industrial scale production of plasmid DNA for vaccine and gene therapy: plasmid design, production, and purification. Enzyme Microb. Technol. 33 (2003) 865-883
46. Prazeres D.M.F., Ferreira G.N.M., Monteiro G.A., Cooney C.L., and Cabral J.M.S. Large-scale production of pharmaceutical-grade plasmid DNA for gene therapy: problems and bottlenecks. Trends Biotechnol. 17 (1999) 169-174
47. Reif H.J., and Saedler H. IS1 is involved in deletion formation in the gal region of E. coli K12. Mol. Gen. Genet. 137 (1975) 17-28
48. Ribeiro S.C., Oliveira P.H., Prazeres D.M.F., and Monteiro G.A. High frequency plasmid recombination mediated by 28 bp direct repeats. Mol. Biotechnol. 40 (2008) 252-260
49. Ribeiro, S.C., Prazeres, D.M.F., Monteiro, G.A. Evidence for the in vivo expression of a distant downstream gene under the control of ColE1 replication origin. (submitted)
50. Schroeter A., Riethdorf S., and Hecker M. Amplification of different ColE1 plasmids in an Escherichia coli relA strain. J. Basic Microbiol. 28 (1988) 553-555
51. Siguier P., Perochon J., Lestrade L., Mahillon J., and Chandler M. ISfinder: the reference centre for bacterial insertion sequences. Nucleic Acids Res. 34 (2006) D32-D36
52. Summers D.K., Beton C.W., and Withers H.L. Multicopy plasmid instability: the dimer catastrophe hypothesis. Mol. Microbiol. 8 (1993) 1031-1038
53. Szeverényi I., Hodel A., Arber W., and Olasz F. Vector for IS element entrapment and functional characterization based on turning on expression of distal promoterless genes. Gene 174 (1996) 103-110
54. 2 intermediate. Mol. Gen. Genet. 251 (1996) 281-289
55. Tartof K.D., and Hobbs C.A. Improved media for growing plasmid and cosmid clones. Bethesda Res. Lab. Focus 9 (1987) 12
56. Tatusova T.A., and Madden T.L. Blast 2 sequences, a new tool for comparing protein and nucleotide sequences. FEMS Microbiol. Lett. 174 (1999) 247-250
57. Twiss E., Coros A.M., Tavakoli N.P., and Derbyshire K.M. Transposition is modulated by a diverse set of host factors in Escherichia coli and is stimulated by nutritional stress. Mol. Microbiol. 57 (2005) 1593-1607
58. Wang Z., Le G., Shi Y., Wegrzyn G., and Wróbel B. A model for regulation of ColE1-like plasmid replication by uncharged tRNA's in amino acid-starved Escherichia coli cells. Plasmid 47 (2002) 69-78
59. Wegrzyn G. Replication of plasmids during bacterial response to amino acid starvation. Plasmid 41 (1999) 1-16
60. Wegrzyn G., and Wegrzyn A. Stress responses and replication of plasmids in bacterial cells. Microb. Cell Fact 1 (2002) 2
61. Wong E.M., Muesing M.A., and Polisky B. Temperature-sensitive copy number mutants of ColE1 are located in an untranslated region of the plasmid genome. Proc. Natl. Acad. Sci. USA 79 (1982) 3570-3574
62. Wróbel B., and Wegrzyn G. Differential amplification efficiency of pMB1 and p15A (ColE1-type) replicons in Escherichia coli stringent and relaxed strains starved for particular amino acids. Microbiol. Res. 152 (1997) 251-255
63. Yau S.Y., Keshavarz-Moore E., and Ward J. Host strain influences on supercoiled plasmid DNA production in Escherichia coli: implications for efficient design of large-scale processes. Biotechnol. Bioeng. 101 (2008) 529-544