Cloning the acholeplasma laidlawii pg-8a genome in saccharomyces cerevisiae as a yeast centromeric plasmid

ACS Synthetic Biology

Volumn 1, Issue 1, 2012, Pages 22-28

  Karas, Bogumil J ^a   Tagwerker, Christian ^a   Yonemoto, Isaac T ^a   Hutchison, Clyde A ^a   Smith, Hamilton O ^a  

^a J CRAIG VENTER INSTITUTE   (United States)

Author keywords

Acholeplasma laidlawii; Saccharomyces cerevisiae; Transformation associated homologous recombination; Yeast centromeric plasmid

Indexed keywords

ACHOLEPLASMA LAIDLAWII; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; CENTROMERE; CLONING, MOLECULAR; DEOXYRIBONUCLEASES, TYPE II SITE-SPECIFIC; GENETIC ENGINEERING; GENOME, BACTERIAL; PLASMIDS; SACCHAROMYCES CEREVISIAE; SYNTHETIC BIOLOGY;

EID: 84868247020     PISSN: None     EISSN: 21615063     Source Type: Journal    
DOI: 10.1021/sb200013j     Document Type: Article

References (34)

1. Gibson, D. G., Glass, J. I., Lartigue, C., Noskov, V. N., Chuang, R. Y., Algire, M. A., Benders, G. A., Montague, M. G., Ma, L., Moodie, M. M., Merryman, C., Vashee, S., Krishnakumar, R., Assad-Garcia, N., Andrews-Pfannkoch, C., Denisova, E. A., Young, L., Qi, Z. Q., Segall-Shapiro, T. H., Calvey, C. H., Parmar, P. P., Hutchison, C. A. 3rd, Smith, H. O., and Venter, J. C. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52-56.
2. Lartigue, C., Vashee, S., Algire, M. A., Chuang, R. Y., Benders, G. A., Ma, L., Noskov, V. N., Denisova, E. A., Gibson, D. G., Assad-Garcia, N., Alperovich, N., Thomas, D. W., Merryman, C., Hutchison, C. A. 3rd, Smith, H. O., Venter, J. C., and Glass, J. I. (2009) Creating bacterial strains from genomes that have been cloned and engineered in yeast. Science 325, 1693-1696.
3. Lartigue, C., Glass, J. I., Alperovich, N., Pieper, R., Parmar, P. P., Hutchison, C. A. 3rd, Smith, H. O., and Venter, J. C. (2007) Genome transplantation in bacteria: changing one species to another. Science 317, 632-638. (Pubitemid 47229957)
4. Noskov, V. N., Segall-Shapiro, T. H., and Chuang, R. Y. (2010) Tandem repeat coupled with endonuclease cleavage (TREC): a seamless modification tool for genome engineering in yeast. Nucleic Acids Res. 38, 2570-2576.
5. Suzuki, Y., St Onge, R. P., Mani, R., King, O. D., Heilbut, A., Labunskyy, V. M., Chen, W., Pham, L., Zhang, L. V., Tong, A. H., Nislow, C., Giaever, G., Gladyshev, V. N., Vidal, M., Schow, P., Lehar, J., and Roth, F. P. (2011) Knocking out multigene redundancies via cycles of sexual assortment and fluorescence selection. Nat. Methods 8, 159-164.
6. Hinnen, A., Hicks, J. B., and Fink, G. R. (1978) Transformation of yeast. Proc. Natl. Acad. Sci. U.S.A. 75, 1929-1933. (Pubitemid 8337583)
7. Gietz, R. D., and Woods, R. A. (2002) Transformation of yeast by lithium acetate/single-stranded carrier DNA/polyethylene glycol method. Methods Enzymol. 350, 87-96. (Pubitemid 34619485)
8. Ito, H., Fukuda, Y., Murata, K., and Kimura, A. (1983) Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153, 163-168. (Pubitemid 13119852)
9. Kouprina, N., and Larionov, V. (2008) Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae. Nat. Protoc. 3, 371-377. (Pubitemid 351372227)
10. Larionov, V., Kouprina, N., Graves, J., Chen, X. N., Korenberg, J. R., and Resnick, M. A. (1996) Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination. Proc. Natl. Acad. Sci. U.S.A. 93, 491-496. (Pubitemid 26038183)
11. Gibson, D. G., Benders, G. A., Axelrod, K. C., Zaveri, J., Algire, M. A., Moodie, M., Montague, M. G., Venter, J. C., Smith, H. O., and Hutchison, C. A. 3rd (2008) One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome. Proc. Natl. Acad. Sci. U.S.A. 105, 20404-20409.
12. Benders, G. A., Noskov, V. N., Denisova, E. A., Lartigue, C., Gibson, D. G., Assad-Garcia, N., Chuang, R. Y., Carrera, W., Moodie, M., Algire, M. A., Phan, Q., Alperovich, N., Vashee, S., Merryman, C., Venter, J. C., Smith, H. O., Glass, J. I., and Hutchison, C. A. 3rd (2010) Cloning whole bacterial genomes in yeast. Nucleic Acids Res. 38, 2558-2569.
13. Gibson, D. G., Benders, G. A., Andrews-Pfannkoch, C., Denisova, E. A., Baden-Tillson, H., Zaveri, J., Stockwell, T. B., Brownley, A., Thomas, D. W., Algire, M. A., Merryman, C., Young, L., Noskov, V. N., Glass, J. I., Venter, J. C., Hutchison, C. A. 3rd, and Smith, H. O. (2008) Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome. Science 319, 1215-1220. (Pubitemid 351323011)
14. Lazarev, V. N., Levitskii, S. A., Basovskii, Y. I., Chukin, M. M., Akopian, T. A., Vereshchagin, V. V., Kostrjukova, E. S., Kovaleva, G. Y., Kazanov, M. D., Malko, D. B., Vitreschak, A. G., Sernova, N. V., Gelfand, M. S., Demina, I. A., Serebryakova, M. V., Galyamina, M. A., Vtyurin, N. N., Rogov, S. I., Alexeev, D. G., Ladygina, V. G., and Govorun, V. M. (2011) Complete genome and proteome of Acholeplasma laidlawii. J. Bacteriol. 193, 4943-4953.
15. Leem, S. H., Noskov, V. N., Park, J. E., Kim, S. I., Larionov, V., and Kouprina, N. (2003) Optimum conditions for selective isolation of genes from complex genomes by transformation-associated recombination cloning. Nucleic Acids Res. 31, e29.
16. Storici, F., Durham, C. L., Gordenin, D. A., and Resnick, M. A. (2003) Chromosomal site-specific double-strand breaks are efficiently targeted for repair by oligonucleotides in yeast. Proc. Natl. Acad. Sci. U.S.A. 100, 14994-14999. (Pubitemid 37518005)
17. Lazarev, V. N., Levitskii, S. A., Basovskii, Y. I., Chukin, M. M., Akopian, T. A., Vereshchagin, V. V., Kostrjukova, E. S., Kovaleva, G. Y., Kazanov, M. D., Malko, D. B., Vitreschak, A. G., Sernova, N. V., Gelfand, M. S., Demina, I. A., Serebryakova, M. V., Galyamina, M. A., Vtyurin, N. N., Rogov, S. I., Alexeev, D. G., Ladygina, V. G., and Govorun, V. M. (2011) The complete genome and proteome of Acholeplasma laidlawii. J. Bacteriol. 193, 4943-4953.
18. Sorek, R., Zhu, Y., Creevey, C. J., Francino, M. P., Bork, P., and Rubin, E. M. (2007) Genome-wide experimental determination of barriers to horizontal gene transfer. Science 318, 1449-1452. (Pubitemid 350208955)
19. Smailus, D. E., Warren, R. L., and Holt, R. A. (2007) Constructing large DNA segments by iterative clone recombination. Syst. Synth. Biol. 1, 139-144. (Pubitemid 351448388)
20. Boulton, S. J., and Jackson, S. P. (1996) Identification of a Saccharomyces cerevisiae Ku80 homologue: roles in DNA double strand break rejoining and in telomeric maintenance. Nucleic Acids Res. 24, 4639-4648. (Pubitemid 26413339)
21. Mezard, C., and Nicolas, A. (1994) Homologous, homeologous, and illegitimate repair of double-strand breaks during transformation of a wild-type strain and a rad52 mutant strain of Saccharomyces cerevisiae. Mol. Cell. Biol. 14, 1278-1292. (Pubitemid 24036578)
22. Raymond, C. K., Sims, E. H., Kas, A., Spencer, D. H., Kutyavin, T. V., Ivey, R. G., Zhou, Y., Kaul, R., Clendenning, J. B., and Olson, M. V. (2002) Genetic variation at the O-antigen biosynthetic locus in Pseudomonas aeruginosa. J. Bacteriol. 184, 3614-3622. (Pubitemid 34625670)
23. Raymond, C. K., Sims, E. H., and Olson, M. V. (2002) Linkermediated recombinational subcloning of large DNA fragments using yeast. Genome Res. 12, 190-197. (Pubitemid 34065601)
24. Umezu, K., Amaya, T., Yoshimoto, A., and Tomita, K. (1971) Purification and properties of orotidine-5′-phosphate pyrophosphorylase and orotidine-5′-phosphate decarboxylase from baker's yeast. J. Biochem. 70, 249-262.
25. Boeke, J. D., LaCroute, F., and Fink, G. R. (1984) A positive selection for mutants lacking orotidine-5′-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol. Gen. Genet. 197, 345-346.
26. Itaya, M., Tsuge, K., Koizumi, M., and Fujita, K. (2005) Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc. Natl. Acad. Sci. U.S.A. 102, 15971-15976. (Pubitemid 41552852)
27. Celniker, S. E., Sweder, K., Srienc, F., Bailey, J. E., and Campbell, J. L. (1984) Deletion mutations affecting autonomously replicating sequence ARS1 of Saccharomyces cerevisiae. Mol. Cell. Biol. 4, 2455-2466. (Pubitemid 15212261)
28. Nieduszynski, C. A., Knox, Y., and Donaldson, A. D. (2006) Genome-wide identification of replication origins in yeast by comparative genomics. Genes Dev. 20, 1874-1879. (Pubitemid 44079324)
29. Theis, J. F., and Newlon, C. S. (1997) The ARS309 chromosomal replicator of Saccharomyces cerevisiae depends on an exceptional ARS consensus sequence. Proc. Natl. Acad. Sci. U.S.A. 94, 10786-10791. (Pubitemid 27430812)
30. Stinchcomb, D. T., Thomas, M., Kelly, J., Selker, E., and Davis, R. W. (1980) Eukaryotic DNA segments capable of autonomous replication in yeast. Proc. Natl. Acad. Sci. U.S.A. 77, 4559-4563.
31. Newlon, C. S., and Theis, J. F. (1993) The structure and function of yeast ARS elements. Curr. Opin. Genet. Dev. 3, 752-758. (Pubitemid 23305048)
32. Larionov, V., Kouprina, N., Solomon, G., Barrett, J. C., and Resnick, M. A. (1997) Direct isolation of human BRCA2 gene by transformation-associated recombination in yeast. Proc. Natl. Acad. Sci. U.S.A. 94, 7384-7387. (Pubitemid 27345324)
33. Tully, J. G., Rose, D. L., Whitcomb, R. F., and Wenzel, R. P. (1979) Enhanced isolation of Mycoplasma pneumoniae from throat washings with a newly-modified culture medium. J Infect Dis 139, 478-482. (Pubitemid 9151120)
34. Alberti, S., Gitler, A. D., and Lindquist, S. (2007) A suite of Gateway cloning vectors for high-throughput genetic analysis in Saccharomyces cerevisiae. Yeast 24, 913-919. (Pubitemid 47611130)