DNA shuttling between plasmid vectors and a genome vector: Systematic conversion and preservation of DNA libraries using the Bacillus subtilis genome (BGM) vector

Journal of Molecular Biology

Volumn 349, Issue 5, 2005, Pages 1036-1044

  Kaneko, Shinya ^a   Akioka, Manami ^a   Tsuge, Kenji ^a   Itaya, Mitsuhiro ^a  

^a MITSUBISHI KAGAKU INSTITUTE OF LIFE SCIENCES   (Japan)

Author keywords

Genome vector; Recombination; Recombinational transfer; Spore formation; Transformation

Indexed keywords

COMPLEMENTARY DNA; MITOCHONDRIAL DNA; PLASMID VECTOR;

ARABIDOPSIS; ARTICLE; BACILLUS SUBTILIS; BACTERIAL ARTIFICIAL CHROMOSOME; BACTERIAL GENOME; CONTROLLED STUDY; DNA LIBRARY; DNA VECTOR; GENE VECTOR; GENETIC CONSERVATION; MOLECULAR CLONING; NONHUMAN; PRIORITY JOURNAL; ROOM TEMPERATURE; SPOROGENESIS;

ARABIDOPSIS THALIANA; BACILLUS SUBTILIS; ESCHERICHIA COLI;

EID: 20344385510     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.04.041     Document Type: Article

References (46)

1. H. Shizuya, B. Birren, U.J. Kim, V. Mancino, T. Slepak, and Y. Tachiiri Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F- factor-based vector Proc. Natl Acad. Sci. USA 89 1992 8794 8797
2. U.J. Kim, B.W. Birren, T. Slepak, V. Mancino, C. Boysen, and H.L. Kang Construction and characterization of a human bacterial artificial chromosome library Genomics 34 1996 213 218
3. E. Frengen, D. Weichenhan, B. Zhao, K. Osoegawa, M.V. Geel, and P.J. Jong A modular, positive selection bacterial artificial chromosome vector with multiple cloning sites Genomics 58 1999 250 253
4. K. Nordström, and S.J. Austin Mechanisms that contribute to the stable segregation of plasmids A. Campbell Annual Review of Genetics vol. 23 1989 Annual Reviews Inc. Palo Alto, CA, USA 37 69
5. F. Hosoda, S. Nishimura, H. Uchida, and M. Ohku An F factor based cloning system for large DNA fragments Nucl. Acids Res. 18 1990 3863 3869
6. J.C. Venter, M.D. Adams, E.W. Myers, P.W. Li, R.J. Mural, and G.G. Sutton The sequence of the human genome Science 291 2001 1304 1351
7. International Human Genome Sequencing Consortium E.S. Lander, L.M. Linton, B. Birren, C. Nusbaum, M.C. Zody, and J. Baldwin Initial sequencing and analysis of the human genome Nature 409 2001 860 921
8. Mouse Genome Sequencing Consortium R.H. Waterston, K. Lindblad-Toh, E. Birney, J. Rogers, J.F. Abril, and P. Agarwal Initial sequencing and comparative analysis of the mouse genome Nature 420 2002 520 562
9. X.W. Yang, P. Model, and N. Heintz Homologous recombination based modification in Escherichia coli and germline transmission in transgenic mice of a bacterial artificial chromosome Nature Biotechnol. 15 1997 859 865
10. K. Narayanan, R. Williamson, Y. Zhang, A.F. Stewart, and P.A. Ioannou Efficient and precise engineering of a 200 kb beta-globin human/bacterial artificial chromosome in E. coli DH10B using an inducible homologous recombination system Gene Ther. 6 1999 442 447
11. N. Mikhail, W. Robert, and A.I. Panayiotis Insertion of disease-causing mutation in BACs by homologous recombination in Escherichia coli Nucl. Acids Res. 28 2000 e79
12. O. Michael, N. Mikhail, V. Jim, Z. Faten, W. Robert, and A.I. Panayiotis Engineering EGFP reporter constructs into a 200 kb human β-globin BAC clone using GET recombination Nucl. Acids Res. 28 2000 e84
13. J. Spizizen Transformation of biochemically deficient strains of Bacillus subtilis by deoxyribonuclease Proc. Natl Acad Sci. USA 44 1958 1072 1078
14. D. Dubnau DNA uptake in bacteria Ann. Rev. Microbiol. 53 1999 217 244
15. M. Itaya Genetic transfer of large DNA inserts to designated loci of the Bacillus subtilis 168 genome J. Bacteriol. 181 1999 1045 1048
16. S. Kaneko, K. Tsuge, and T. Takeuchi Conversion of sub-megasized DNA to desired structures using a novel Bacillus subtilis genome vector Nucl. Acids Res. 31 2003 e112
17. M. Itaya, K. Fujita, M. Ikeuchi, M. Koizumi, and K. Tsuge Stable positional cloning of long continuous DNA in the Bacillus subtilis genome vector J. Biochem. 134 2003 513 519
18. M. Itaya, T. Nagata, T. Shiroishi, K. Fujita, and K. Tsuge Efficient cloning and engineering of giant DNAs in a novel Bacillus subtilis genome vector J. Biochem. 128 2000 869 875
19. M. Itaya Effective cloning of unmarked DNA fragments in the Bacillus subtilis 168 genome Biosci. Biotechnol. Biochem. 63 1999 602 604
20. M. Itaya Toward a bacterial genome technology: integration of the Escherichia coli prophage lambda genome into the Bacillus subtilis 168 chromosome Mol. Gen. Genet. 248 1995 9 16
21. M. Itaya Integration of repeated sequences (pBR322) in the Bacillus subtilis 168 chromosome without affecting the genome structure Mol. Gen. Genet. 241 1993 287 297
22. K. Tsuge, and M. Itaya Recombinational transfer of 100-kilobase genomic DNA to plasmid in Bacillus subtilis 168 J. Bacteriol. 183 2001 5453 5458
23. W.L. Nicholson, N. Munakata, G. Horneck, H.J. Melosh, and P. Setlow Resistance of Bacillus endospores to extreme terrestrial and extraterrestrial environments Microbiol. Mol. Biol. Rev. 64 2000 548 572
24. T. Mozo, S. Fisher, S. Meier-Ewert, H. Lehrach, and T. Altmann Use of the IGF library for physical mapping of the Arabidopsis thaliana genome Plant J. 16 1998 377 384
25. T. Mozo, S. Fisher, H. Shizuya, and T. Altmann Construction and characterization of the IGF Arabidopsis BAC library Mol. Gen. Genet. 258 1998 562 570
26. The Arabidopsis Genome Initiative Analysis of the genome sequence of the flowering plant Arabidopsis thaliana Nature 408 2000 796 815
27. D.H. Howard The preservation of bacteria by freezing in glycerol broth J. Bacteriol. 71 1956 625
28. F.E. Kocka, and H.W. Bretz Survival of Escherichia coli after storage in various frozen menstrua Antonie van Leeuwenhoek 35 1969 65 76
29. T.M. Sidyakina, and V.E. Golimbet Viability and genetic stability of the bacterium Escherichia coli HB101 with the recombinant plasmid during preservation by various methods Cryobiology 28 1991 251 254
30. D.T. Salt, B. Arret, and J. Wilner Low temperature maintenance of test organism suspensions for antibiotic assays J. Pharm. Sci. 62 1973 2040 2043
31. A.R. Grivell, A.K. Ganesan, and P.C. Hanawalt Preservation of Escherichia coli on silica gel Microb. Genet. Bull. 34 1972 15
32. J.E. Devay, and W.C. Schnathorst Single-cell isolation and preservation of bacterial cultures Nature 199 1963 775 777
33. A. Dietz Nitrogen preservation of stock cultures of unicellular and filamentous microorganisms A.P. Rinfret B. LaSalle Round Table Conference on the Cryogenic Preservation of Cell Cultures 1975 National Academic of Science Washington, DC
34. J. Antheunisse Preservation of microorganisms Antonie van Leeuwenhoek J. Microbiol. Serol. 38 1972 617 622
35. J. Antheunisse Viability of lyophilized microorganisms after storage Antonie van Leeuwenhoek J. Microbiol. Serol. 39 1973 243 248
36. S.P. Lapage, J.E. Shelton, T.G. Mitchell, and A.R. Mackenzie Culture collections and the preservation of bacteria J.R. Norris D.W. Ribbons Methods in Microbiology vol. 3a 1970 Academic Press New York 135 228
37. A.M. Kropinski Stability of bacterial mutants in saline Appl. Microbiol. 29 1975 448 450
38. Y. Miyamoto-Shinohara, T. Imaizumi, J. Sukenobe, S. Murakami, S. Kawamura, and Y. Komatsu Survival rate of microbes after freeze-drying and long-term storage Cryobiology 41 2000 251 255
39. M. Klein, U. Eckert-Ossenkopp, I. Schmiedeberg, P. Brandt, M. Unseld, and A. Brennicke Physical mapping of the mitochondrial genome of Arabidopsis thaliana by cosmid and YAC clones Plant J. 6 1994 447 455
40. M. Unseld, J.R. Marienfeld, P. Brandt, and A. Brennicke The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides Nature Genet. 15 1997 57 61
41. M. Itaya, and T. Tanaka Predicted and unsuspected alterations of the genome structure of genetically defined Bacillus subtilis 168 strains Biosci. Biotechnol. Biochem. 61 1997 56 64
42. M. Itaya, and T. Tanaka Complete physical map of the Bacillus subtilis 168 chromosome constructed by a gene-directed mutagenesis method J. Mol. Biol. 220 1991 631 648
43. P. Schaeffer, J. Millet, and J.P. Aubert Catabolic repression of bacterial sporulation Proc. Natl Acad. Sci. USA 54 1965 704 711
44. W. Nicholson, and P. Setlow C.R. Harwood S.M. Cutting Molecular Biological Methods for Bacillus. Sporulation, Germination and Outgrowth 1990 John Wiley and Sons Chichester, England
45. S. Tomita, K. Tsuge, Y. Kikuchi, and M. Itaya Targeted isolation of a designated region of the Bacillus subtilis genome by recombinational transfer Appl. Environ. Microbiol. 70 2004 2508 2513
46. M. Itaya Isolation and characterization of a second RNase H (RNase HII) of Escherichia coli K-12 encoded by the rnhB gene Proc. Natl Acad. Sci. USA 87 1990 8587 8591