Reassembly of functionally intact environmental DNA-derived biosynthetic gene clusters

Methods in Enzymology

Volumn 517, Issue , 2012, Pages 225-239

  Kallifidas, Dimitris ^a   Brady, Sean F ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

Heterologous expression; Metagenomics; Natural products; Streptomyces; Yeast recombination

Indexed keywords

CHLORAMPHENICOL; DNA; DNA FRAGMENT; GENOMIC DNA;

AGAR GEL ELECTROPHORESIS; ARTICLE; BIOSYNTHESIS; CELL CULTURE; CENTRIFUGATION; CHEMICAL REACTION; DNA ISOLATION; DNA LIBRARY; DNA RECOMBINATION; DNA VECTOR; DOWNSTREAM PROCESSING; GEL ELECTROPHORESIS; GENE CLUSTER; GENE EXPRESSION; GENETIC TRANSFORMATION; HIGH THROUGHPUT SCREENING; INCUBATION TEMPERATURE; LIQUID CHROMATOGRAPHY; MASS SPECTROMETRY; MICROARRAY ANALYSIS; MICROBIAL DIVERSITY; MOLECULAR LIBRARY; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; ROOM TEMPERATURE; SACCHAROMYCES CEREVISIAE; SCREENING; SPHEROPLAST; SPHEROPLAST FORMATION; SUPERNATANT;

EID: 84867638405     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-404634-4.00011-5     Document Type: Chapter

References (28)

1. J.J. Banik, and S.F. Brady Cloning and characterization of new glycopeptide gene clusters found in an environmental DNA megalibrary Proceedings of the National Academy of Sciences of the United States of America 105 2008 17273 17277
2. S.D. Bentley, K.F. Chater, A.M. Cerdeno-Tarraga, G.L. Challis, N.R. Thomson, and K.D. James Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2) Nature 417 2002 141 147 (Pubitemid 34506788)
3. M. Bierman, R. Logan, K. O'Brien, E.T. Seno, R.N. Rao, and B.E. Schoner Plasmid cloning vectors for the conjugal transfer of DNA from Escherichia coli to Streptomyces spp Gene 116 1992 43 49
4. T.M. Binz, S.C. Wenzel, H.J. Schnell, A. Bechthold, and R. Muller Heterologous expression and genetic engineering of the phenalinolactone biosynthetic gene cluster by using red/ET recombineering ChemBioChem 9 2008 447 454
5. S.F. Brady Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules Nature Protocols 2 2007 1297 1305 (Pubitemid 46901307)
6. S.F. Brady, L. Simmons, J.H. Kim, and E.W. Schmidt Metagenomic approaches to natural products from free-living and symbiotic organisms Natural Product Reports 26 2009 1488 1503
7. R. Daniel The metagenomics of soil Nature Reviews Microbiology 3 2005 470 478 (Pubitemid 40716173)
8. Z. Feng, J.H. Kim, and S.F. Brady Fluostatins produced by the heterologous expression of a TAR reassembled environmental DNA derived type II PKS gene cluster Journal of the American Chemical Society 132 2010 11902 11903
9. D.G. Gibson, G.A. Benders, C. Andrews-Pfannkoch, E.A. Denisova, H. Baden-Tillson, and J. Zaveri Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome Science 319 2008 1215 1220 (Pubitemid 351323011)
10. D.G. Gibson, G.A. Benders, K.C. Axelrod, J. Zaveri, M.A. Algire, and M. Moodie One-step assembly in yeast of 25 overlapping DNA fragments to form a complete synthetic Mycoplasma genitalium genome Proceedings of the National Academy of Sciences of the United States of America 105 2008 20404 20409
11. J. Handelsman, M.R. Rondon, S.F. Brady, J. Clardy, and R.M. Goodman Molecular biological access to the chemistry of unknown soil microbes: A new frontier for natural products Chemical Biology 5 1998 R245 R249
12. T. Kieser, M.J. Bibb, M.J. Buttner, K.F. Chater, and D.A. Hopwood Practical streptomyces genetics 2000 The John Innes Foundation Norwich, UK
13. J.H. Kim, Z. Feng, J.D. Bauer, D. Kallifidas, P.Y. Calle, and S.F. Brady Cloning large natural product gene clusters from the environment: Piecing environmental DNA gene clusters back together with TAR Biopolymers 93 2010 833 844
14. N. Kouprina, and V. Larionov Selective isolation of genomic loci from complex genomes by transformation-associated recombination cloning in the yeast Saccharomyces cerevisiae Nature Protocols 3 2008 371 377 (Pubitemid 351372227)
15. N. Kouprina, V.N. Noskov, and V. Larionov Selective isolation of large chromosomal regions by transformation-associated recombination cloning for structural and functional analysis of mammalian genomes Methods in Molecular Biology 349 2006 85 101
16. V. Larionov, N. Kouprina, M. Eldarov, E. Perkins, G. Porter, and M.A. Resnick Transformation-associated recombination between diverged and homologous DNA repeats is induced by strand breaks Yeast 10 1994 93 104 (Pubitemid 24052952)
17. V. Larionov, N. Kouprina, J. Graves, X.N. Chen, J.R. Korenberg, and M.A. Resnick Specific cloning of human DNA as yeast artificial chromosomes by transformation-associated recombination Proceedings of the National Academy of Sciences of the United States of America 93 1996 491 496 (Pubitemid 26038183)
18. K. Mathee, G. Narasimhan, C. Valdes, X. Qiu, J.M. Matewish, and M. Koehrsen Dynamics of Pseudomonas aeruginosa genome evolution Proceedings of the National Academy of Sciences of the United States of America 105 2008 3100 3105 (Pubitemid 351723674)
19. Y. Nagano, S. Takao, T. Kudo, E. Iizasa, and T. Anai Yeast-based recombineering of DNA fragments into plant transformation vectors by one-step transformation Plant Cell Reports 26 2007 2111 2117 (Pubitemid 350165574)
20. V.D. Pham, T. Palden, and E.F. DeLong Large-scale screens of metagenomic libraries Journal of visualized experiments 2007 201
21. M.S. Rappe, and S.J. Giovannoni The uncultured microbial majority Annual Review of Microbiology 57 2003 369 394 (Pubitemid 37392948)
22. M.R. Rondon, P.R. August, A.D. Bettermann, S.F. Brady, T.H. Grossman, and M.R. Liles Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms Applied and Environmental Microbiology 66 2000 2541 2547 (Pubitemid 30353963)
23. Z. Shao, H. Zhao, and H. Zhao DNA assembler, an in vivo genetic method for rapid construction of biochemical pathways Nucleic Acids Research 37 2009 e16
24. C. Simon, and R. Daniel Achievements and new knowledge unraveled by metagenomic approaches Applied Microbiology and Biotechnology 85 2009 265 276
25. C. Simon, and R. Daniel Construction of small-insert and large-insert metagenomic libraries Methods in Molecular Biology 668 2010 39 50
26. V. Torsvik, L. Ovreas, and T.F. Thingstad Prokaryotic diversity - magnitude, dynamics, and controlling factors Science 296 2002 1064 1066 (Pubitemid 34517113)
27. V. Torsvik, K. Salte, R. Sorheim, and J. Goksoyr Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria Applied and Environmental Microbiology 56 1990 776 781 (Pubitemid 20088453)
28. J. Zhou, M.A. Bruns, and J.M. Tiedje DNA recovery from soils of diverse composition Applied and Environmental Microbiology 62 1996 316 322 (Pubitemid 26047397)