Seamless site-directed mutagenesis in complex cloned DNA sequences using the RedEx method

Atanasov, A. G., Zotchev, S. B., Dirsch, V. M., the International Natural Product Sciences Taskforce & Supuran, C. T. Natural products in drug discovery: advances and opportunities. Nat. Rev. Drug Discov. 20, 200–216 (2021).

Smanski, M. J. et al. Synthetic biology to access and expand nature’s chemical diversity. Nat. Rev. Microbiol. 14, 135–149 (2016).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rutledge, P. J. & Challis, G. L. Discovery of microbial natural products by activation of silent biosynthetic gene clusters. Nat. Rev. Microbiol. 13, 509–523 (2015).

Article  CAS  PubMed  Google Scholar 

Dutta, S. et al. Structure of a modular polyketide synthase. Nature 510, 512–517 (2014).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Bagde, S. R., Mathews, I. I., Fromme, J. C. & Kim, C. Y. Modular polyketide synthase contains two reaction chambers that operate asynchronously. Science 374, 723–729 (2021).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Grininger, M. Enzymology of assembly line synthesis by modular polyketide synthases. Nat. Chem. Biol. 19, 401–415 (2023).

Article  CAS  PubMed  Google Scholar 

Winn, M., Fyans, J. K., Zhuo, Y. & Micklefield, J. Recent advances in engineering nonribosomal peptide assembly lines. Nat. Prod. Rep. 33, 317–347 (2016).

Article  CAS  PubMed  Google Scholar 

Tao, X. B. et al. ClusterCAD 2.0: an updated computational platform for chimeric type I polyketide synthase and nonribosomal peptide synthetase design. Nucleic Acids Res. 51, D532–D538 (2023).

Article  CAS  PubMed  Google Scholar 

Englund, E. et al. Expanding extender substrate selection for unnatural polyketide biosynthesis by acyltransferase domain exchange within a modular polyketide synthase. J. Am. Chem. Soc. 145, 8822–8832 (2023).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wlodek, A. et al. Diversity oriented biosynthesis via accelerated evolution of modular gene clusters. Nat. Commun. 8, 1206 (2017).

Article  PubMed  PubMed Central  Google Scholar 

Ji, C. H. et al. Top-down synthetic biology approach for titer improvement of clinically important antibiotic daptomycin in Streptomyces roseosporus. Metab. Eng. 69, 40–49 (2022).

Article  CAS  PubMed  Google Scholar 

Song, C. et al. RedEx: a method for seamless DNA insertion and deletion in large multimodular polyketide synthase gene clusters. Nucleic Acids Res. 48, e130 (2020).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Zhang, Y., Buchholz, F., Muyrers, J. P. P. & Stewart, A. F. A new logic for DNA engineering using recombination in Escherichia coli. Nat. Genet. 20, 123–128 (1998).

Article  CAS  PubMed  Google Scholar 

Zhang, Y., Muyrers, J. P. P., Testa, G. & Stewart, A. F. DNA cloning by homologous recombination in Escherichia coli. Nat. Biotechnol. 18, 1314–1317 (2000).

Article  CAS  PubMed  Google Scholar 

Sarov, M. et al. A recombineering pipeline for functional genomics applied to Caenorhabditis elegans. Nat. Methods 3, 839–844 (2006).

Article  CAS  PubMed  Google Scholar 

Bird, A. W. et al. High-efficiency counterselection recombineering for site-directed mutagenesis in bacterial artificial chromosomes. Nat. Methods 9, 103–109 (2012).

Article  CAS  Google Scholar 

Wang, H. et al. Improved seamless mutagenesis by recombineering using ccdB for counterselection. Nucleic Acids Res. 42, e37 (2014).

Article  CAS  PubMed  Google Scholar 

Wang, H. et al. RecET direct cloning and Redαβ recombineering of biosynthetic gene clusters, large operons or single genes for heterologous expression. Nat. Protoc. 11, 1175–1190 (2016).

Article  CAS  PubMed  Google Scholar 

Wang, H. H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894–898 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Isaacs, F. J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348–353 (2011).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gallagher, R. R., Li, Z., Lewis, A. O. & Isaacs, F. J. Rapid editing and evolution of bacterial genomes using libraries of synthetic DNA. Nat. Protoc. 9, 2301–2316 (2014).

Article  CAS  PubMed  Google Scholar 

Fredens, J. et al. Total synthesis of Escherichia coli with a recoded genome. Nature 569, 514–518 (2019).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sharan, S. K., Thomason, L. C., Kuznetsov, S. G. & Court, D. L. Recombineering: a homologous recombination-based method of genetic engineering. Nat. Protoc. 4, 206–223 (2009).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Li, R., Li, A., Zhang, Y. & Fu, J. The emerging role of recombineering in microbiology. Eng. Microbiol. 3, 100097 (2023).

Article  CAS  Google Scholar 

Zheng, L., Baumann, U. & Reymond, J. L. An efficient one-step site-directed and site-saturation mutagenesis protocol. Nucleic Acids Res. 32, e115 (2004).

Article  PubMed  PubMed Central  Google Scholar 

Muyrers, J. P. P. et al. Point mutation of bacterial artificial chromosomes by ET recombination. EMBO Rep. 1, 239–243 (2000).

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).

Article  CAS  PubMed  Google Scholar 

Wang, H. et al. ExoCET: exonuclease in vitro assembly combined with RecET recombination for highly efficient direct DNA cloning from complex genomes. Nucleic Acids Res. 46, e28 (2018).

Article  PubMed  Google Scholar 

Wong, Q. N. et al. Efficient and seamless DNA recombineering using a thymidylate synthase A selection system in Escherichia coli. Nucleic Acids Res. 33, e59 (2005).

Article  PubMed  PubMed Central  Google Scholar 

Warming, S., Costantino, N., Court, D. L., Jenkins, N. A. & Copeland, N. G. Simple and highly efficient BAC recombineering using galK selection. Nucleic Acids Res. 33, e36 (2005).

Article  PubMed  PubMed Central  Google Scholar 

DeVito, J. A. Recombineering with tolC as a selectable/counter-selectable marker: remodeling the rRNA operons of Escherichia coli. Nucleic Acids Res. 36, e4 (2008).

Article  PubMed  Google Scholar 

Kudo, K. et al. In vitro Cas9-assisted editing of modular polyketide synthase genes to produce desired natural product derivatives. Nat. Commun. 11, 4022 (2020).

Article  CAS 

留言 (0)

沒有登入
gif