Directed evolution and identification of control regions of ColE1 plasmid replication origins using only nucleotide deletions

Journal of Molecular Biology

Volumn 351, Issue 4, 2005, Pages 763-775

  Kim, Dewey ^a   Rhee, Yoon ^b   Rhodes, Denise ^b   Sharma, Vikram ^a   Sorenson, Olav ^c   Greener, Alan ^b   Smider, Vaughn ^a  

^a IntegriGen Inc   (United States)

^b Stratagene   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Molecular evolution; Mutagenesis; Origin of replication; Plasmid replication

Indexed keywords

BETA GALACTOSIDASE; NUCLEOTIDE; PRIMER RNA;

ARTICLE; CONTROLLED STUDY; ENZYME ACTIVITY; ESCHERICHIA COLI; GENE DELETION; MOLECULAR EVOLUTION; MUTAGENESIS; MUTATION; NONHUMAN; PLASMID; PRIORITY JOURNAL; QUALITATIVE ANALYSIS; QUANTITATIVE ANALYSIS;

ESCHERICHIA COLI;

EID: 23444458590     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.06.051     Document Type: Article

References (33)

1. W.P. Stemmer The evolution of molecular computation Science 270 1995 1510
2. S. Hiraga, T. Sugiyama, and T. Itoh Comparative analysis of the replicon regions of eleven ColE2-related plasmids J. Bacteriol. 176 1994 7233 7243
3. V. Smider, and G. Chu The end-joining reaction in V(D)J recombination Sem. Immun. 9 1997 189 197
4. K. Furukawa, A. Akasako-Furukawa, H. Shirai, H. Nakamura, and T. Azuma Junctional amino acids determine the maturation pathway of an antibody Immunity 11 1999 329 338
5. W.P. Stemmer DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution Proc. Natl Acad. Sci. USA 91 1994 10747 10751
6. W.P. Stemmer Rapid evolution of a protein in vitro by DNA shuffling Nature 370 1994 389 391
7. V. Smider, W.K. Rathmell, G. Brown, S. Lewis, and G. Chu Failure of hairpin-ended and nicked DNA to activate DNA-dependent protein kinase: implications for V(D)J-recombination Mol. Cell. Biol. 18 1998 6853 6858
8. H. Murakami, T. Hohsaka, and M. Sisido Random insertion and deletion of arbitrary number of bases for codon-based random mutation of DNAs Nature Biotechnol. 20 2002 76 81
9. T.E. Shenk, C. Rhodes, P.W. Rigby, and P. Berg Biochemical method for mapping mutational alterations in DNA with S1 nuclease: the location of deletions and temperature-sensitive mutations in simian virus 40 Proc. Natl Acad. Sci USA 72 1975 989 993
10. D. Kowalski, and J.P. Sanford Action of mung bean nuclease on supercoiled PM2 DNA J. Biol. Chem. 257 1982 7820 7825
11. R.C. Wiegand, G.N. Godson, and C.M. Radding Specificity of the S1 nuclease from Aspergillus oryzae J. Biol. Chem. 250 1975 8848 8855
12. J. Sambrook, E.F. Fritsch, and T. Maniatis Molecular Cloning: A Laboratory Manual 2nd edit. 1989 Cold Spring Harbor Laboratory Press Cold Spring Harbor, New York
13. J.-I. Tomezawa Control of ColE1 plasmid replication: binding of RNAI to RNAII and inhibition of primer formation Cell 47 1986 89 97
14. J.P. Marino, R.S. Gregorian Jr, G. Csankovszki, and D.M. Crothers Bent helix formation between RNA hairpins with complementary loops Science 268 1995 1448 1454
15. Y. Eguchi, and J. Tomizawa Complex formed by complementary RNA stem-loops and its stabilization by a protein: function of CoIE1 Rom protein Cell 60 1990 199 209
16. Y. Eguchi, and J. Tomizawa Complexes formed by complementary RNA stem-loops. Their formations, structures and interaction with ColE1 Rom protein J. Mol. Biol. 220 1991 831 842
17. M. Muesing, J. Tamm, H.M. Shepard, and B. Polisky A single base-pair alteration is responsible for the DNA overproduction phenotype of a plasmid copy-number mutant Cell 24 1981 235 242
18. I. Boros, G. Posfai, and P. Venetianer High-copy-number derivatives of the plasmid cloning vector pBR322 Gene 30 1984 257 260
19. M. Zucker, and P. Stiegler Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information Nucl. Acids Res. 9 1981 133 148
20. T. Som, and J. Tomizawa Origin of replication of Escherichia coli plasmid RSF 1030 Mol. Gen. Genet. 187 1982 375 383
21. G. Selzer, T. Som, T. Itoh, and J. Tomizawa The origin of replication of plasmid p15A and comparative studies on the nucleotide sequences around the origin of related plasmids Cell 32 1983 119 129
22. T. Hashimoto-Gotoh, and J. Inselburg ColE1 plasmid incompatibility: localization and analysis of mutations affecting incompatibility J. Bacteriol. 139 1979 608 619
23. J.R. Bedbrook, H. Lehrach, and F.M. Ausubel Directive segregation in the basis of ColE1 plasmid incompatibility Nature 281 1979 447 452
24. A.C.Y. Chang, and S.N. Cohen Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid J. Bacteriol. 134 1978 1141 1156
25. M. Ostermeier, and S.J. Benkovic Evolution of protein function by domain swapping Advan. Protein Chem. 55 2000 29 77
26. T. Gallagher, P. Bryan, and G.L. Gilliland Calcium-independent subtilisin by design Proteins: Struct. Funct. Genet. 16 1993 205 213
27. S.D. Gillies, K.-M. Lo, C. Burger, Y. Lan, T. Dahl, and W.-K. Wong Improved circulating half-life and efficacy of an antibody-interleukin 2 immunocytokine based on reduced intracellular proteolysis Clin. Cancer Res. 8 2002 210 216
28. H. Tsen, and S.D. Levene Analysis of chemical and enzymatic cleavage frequencies in supercoiled DNA J. Mol. Biol. 336 2004 1087 1102
29. S.S. Ner, T.C. Atkinson, and M. Smith A method for introducing random single point deletions in specific DNA target sequences using oligonucleotides Nucl. Acids Res. 17 1989 4015 4023
30. V.R. Kaberdin, Y.H. Chao, and S. Lin-Chao RNase E cleaves at multiple sites in bubble regions of RNA I stem loops yielding products that dissociate differentially from the enzyme J. Biol. Chem. 271 1996 13103 13109
31. F.F. Xu, C. Gaggero, and S.N. Cohen Polyadenylation can regulate ColE1 type plasmid copy number independently of any effect on RNAI decay by decreasing the interaction of antisense RNAI with its RNAII target Plasmid 48 2002 49 58
32. V. Schramke, and R. Allshire Hairpin RNAs and retrotransposon LTRs effect RNAi and chromatin-based gene silencing Science 301 2003 1069 1074
33. S. Lin-Chao, and H. Bremer Effect of the bacterial growth rate on replication control of plasmid pBR322 in Escherichia coli Mol. Gen. Genet. 203 1986 143 149