Conversion of Sub-megasized DNA to Desired Structures Using a Novel Bacillus Subtilis Genome Vector

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2003 Sep 5

PMID 12954788

Citations 6

Authors

Shinya Kaneko

Kenji Tsuge

Takashi Takeuchi

Mitsuhiro Itaya

Affiliations

Soon will be listed here.

Abstract

A novel genome vector using the 4215 kb Bacillus subtilis genome provides for precise target cloning and processing of the cloned DNA to the desired structure. Each process highly dependent on homologous recombination in the host B.subtilis is distinguished from the other cloning systems. A 120 kb mouse jumonji (jmj) genomic gene was processed in the genome vector to give a series of truncated sub-megasized DNA. One of these truncated segments containing the first intron was copied in a plasmid by a recombinational transfer method developed for B.subtilis. DNA manipulation previously considered difficult is argued with respect to DNA size and accuracy.

Citing Articles

Development of the autonomous lab system to support biotechnology research.

Fushimi K, Nakai Y, Nishi A, Suzuki R, Ikegami M, Nimura R Sci Rep. 2025; 15(1):6648.

PMID: 39994271 PMC: 11850614. DOI: 10.1038/s41598-025-89069-y.

Optimizing Yeast Homologous Recombination for Splicing Large Coronavirus Genome Fragments.

Xiong G, Huang X, Hu A, Meng Z, Cui J, Feng Y Int J Mol Sci. 2025; 25(24.

PMID: 39769503 PMC: 11677428. DOI: 10.3390/ijms252413742.

Method of preparing an equimolar DNA mixture for one-step DNA assembly of over 50 fragments.

Tsuge K, Sato Y, Kobayashi Y, Gondo M, Hasebe M, Togashi T Sci Rep. 2015; 5:10655.

PMID: 25990947 PMC: 4438487. DOI: 10.1038/srep10655.

An inducible recA expression Bacillus subtilis genome vector for stable manipulation of large DNA fragments.

Ogawa T, Iwata T, Kaneko S, Itaya M, Hirota J BMC Genomics. 2015; 16:209.

PMID: 25879542 PMC: 4374399. DOI: 10.1186/s12864-015-1425-4.

Current development in genetic engineering strategies of Bacillus species.

Dong H, Zhang D Microb Cell Fact. 2014; 13:63.

PMID: 24885003 PMC: 4030025. DOI: 10.1186/1475-2859-13-63.

References

Narayanan K, Williamson R, Zhang Y, Stewart A, Ioannou P . 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. 1999; 6(3):442-7. DOI: 10.1038/sj.gt.3300901. View

Takeuchi T, Kojima M, Nakajima K, Kondo S . jumonji gene is essential for the neurulation and cardiac development of mouse embryos with a C3H/He background. Mech Dev. 1999; 86(1-2):29-38. DOI: 10.1016/s0925-4773(99)00100-8. View

Dubnau D . DNA uptake in bacteria. Annu Rev Microbiol. 1999; 53:217-44. DOI: 10.1146/annurev.micro.53.1.217. View

Nefedov M, Williamson R, Ioannou P . Insertion of disease-causing mutations in BACs by homologous recombination in Escherichia coli. Nucleic Acids Res. 2000; 28(17):E79. PMC: 110716. DOI: 10.1093/nar/28.17.e79. View

Orford M, Nefedov M, Vadolas J, Zaibak F, Williamson R, Ioannou P . Engineering EGFP reporter constructs into a 200 kb human beta-globin BAC clone using GET Recombination. Nucleic Acids Res. 2000; 28(18):E84. PMC: 110756. DOI: 10.1093/nar/28.18.e84. View

Itaya M, Nagata T, Shiroishi T, Fujita K, Tsuge K . Efficient cloning and engineering of giant DNAs in a novel Bacillus subtilis genome vector. J Biochem. 2000; 128(5):869-75. DOI: 10.1093/oxfordjournals.jbchem.a022825. View

Venter J, Adams M, Myers E, Li P, Mural R, Sutton G . The sequence of the human genome. Science. 2001; 291(5507):1304-51. DOI: 10.1126/science.1058040. View

Lander E, Linton L, Birren B, Nusbaum C, Zody M, Baldwin J . Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860-921. DOI: 10.1038/35057062. View

Tsuge K, Itaya M . Recombinational transfer of 100-kilobase genomic DNA to plasmid in Bacillus subtilis 168. J Bacteriol. 2001; 183(18):5453-8. PMC: 95433. DOI: 10.1128/JB.183.18.5453-5458.2001. View

10.

Nguyen T, Sherratt P, Pickett C . Regulatory mechanisms controlling gene expression mediated by the antioxidant response element. Annu Rev Pharmacol Toxicol. 2002; 43:233-60. DOI: 10.1146/annurev.pharmtox.43.100901.140229. View

11.

Pierce J, Sternberg N . Using bacteriophage P1 system to clone high molecular weight genomic DNA. Methods Enzymol. 1992; 216:549-74. DOI: 10.1016/0076-6879(92)16049-p. View

12.

Shizuya H, Birren B, Kim U, Mancino V, Slepak T, Tachiiri Y . 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 U S A. 1992; 89(18):8794-7. PMC: 50007. DOI: 10.1073/pnas.89.18.8794. View

13.

Itaya M . Isolation and characterization of a second RNase H (RNase HII) of Escherichia coli K-12 encoded by the rnhB gene. Proc Natl Acad Sci U S A. 1990; 87(21):8587-91. PMC: 55002. DOI: 10.1073/pnas.87.21.8587. View

14.

Itaya M . Effective Cloning of Unmarked DNA Fragments in the Bacillus subtilis 168 Genome. Biosci Biotechnol Biochem. 2016; 63(3):602-4. DOI: 10.1271/bbb.63.602. View

15.

Atchison M . Enhancers: mechanisms of action and cell specificity. Annu Rev Cell Biol. 1988; 4:127-53. DOI: 10.1146/annurev.cb.04.110188.001015. View

16.

Burke D, Carle G, Olson M . Cloning of large segments of exogenous DNA into yeast by means of artificial chromosome vectors. Science. 1987; 236(4803):806-12. DOI: 10.1126/science.3033825. View

17.

Hoess R, Ziese M, Sternberg N . P1 site-specific recombination: nucleotide sequence of the recombining sites. Proc Natl Acad Sci U S A. 1982; 79(11):3398-402. PMC: 346427. DOI: 10.1073/pnas.79.11.3398. View

18.

Itaya M . Toward a bacterial genome technology: integration of the Escherichia coli prophage lambda genome into the Bacillus subtilis 168 chromosome. Mol Gen Genet. 1995; 248(1):9-16. DOI: 10.1007/BF02456608. View

19.

Takeuchi T, Yamazaki Y, Tsuchiya R, Kondo S, MOTOYAMA J, Higashinakagawa T . Gene trap capture of a novel mouse gene, jumonji, required for neural tube formation. Genes Dev. 1995; 9(10):1211-22. DOI: 10.1101/gad.9.10.1211. View

20.

Cherepanov P, Wackernagel W . Gene disruption in Escherichia coli: TcR and KmR cassettes with the option of Flp-catalyzed excision of the antibiotic-resistance determinant. Gene. 1995; 158(1):9-14. DOI: 10.1016/0378-1119(95)00193-a. View