Engineered bacterial orthogonal DNA replication system for … – Nature.com

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125131 (1998).

Article CAS Google Scholar

Davis, A. M., Plowright, A. T. & Valeur, E. Directing evolution. The next revolution in drug discovery? Nat. Rev. Drug Discov. 16, 681698 (2017).

Article CAS PubMed Google Scholar

Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379394 (2015).

Article CAS PubMed Google Scholar

Arnold, F. H. Directed evolution. Bringing new chemistry to life. Angew. Chem. 57, 41434148 (2018).

Article CAS Google Scholar

Rix, G. & Liu, C. C. Systems for in vivo hypermutation. A quest for scale and depth in directed evolution. Curr. Opin. Chem. Biol. 64, 2026 (2021).

Article CAS PubMed PubMed Central Google Scholar

Morrison, M. S., Podracky, C. J. & Liu, D. R. The developing toolkit of continuous directed evolution. Nat. Chem. Biol. 16, 610619 (2020).

Article CAS PubMed Google Scholar

Meyer, A. J. & Ellington, A. D. Molecular evolution picks up the PACE. Nat. Biotechnol. 29, 502503 (2011).

Article CAS PubMed Google Scholar

Simon, A. J., dOelsnitz, S. & Ellington, A. D. Synthetic evolution. Nat. Biotechnol. 37, 730743 (2019).

Article CAS PubMed Google Scholar

Komor, A. C., Kim, Y. B., Packer, M. S., Zuris, J. A. & Liu, D. R. Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533, 420424 (2016).

Article CAS PubMed PubMed Central Google Scholar

Chen, H. et al. Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nat. Biotechnol. 38, 165168 (2020).

Article CAS PubMed Google Scholar

Cravens, A., Jamil, O. K., Kong, D., Sockolosky, J. T. & Smolke, C. D. Polymerase-guided base editing enables in vivo mutagenesis and rapid protein engineering. Nat. Commun. 12, 1579 (2021).

Article CAS PubMed PubMed Central Google Scholar

Hao, W. et al. Development of a base editor for protein evolution via in situ mutation in vivo. Nucleic Acids Res. 49, 95949605 (2021).

Article CAS PubMed PubMed Central Google Scholar

Schubert, M. G. et al. High-throughput functional variant screens via in vivo production of single-stranded DNA. Proc. Natl Acad. Sci. USA 118, e2018181118 (2021).

Article CAS PubMed PubMed Central Google Scholar

Jensen, E. D. et al. A synthetic RNA-mediated evolution system in yeast. Nucleic Acids Res. 49, e88 (2021).

Article CAS PubMed PubMed Central Google Scholar

Crook, N. et al. In vivo continuous evolution of genes and pathways in yeast. Nat. Commun. 7, 13051 (2016).

Article CAS PubMed PubMed Central Google Scholar

Halperin, S. O. et al. CRISPR-guided DNA polymerases enable diversification of all nucleotides in a tunable window. Nature 560, 248252 (2018).

Article CAS PubMed Google Scholar

Yi, X., Khey, J., Kazlauskas, R. J. & Travisano, M. Plasmid hypermutation using a targeted artificial DNA replisome. Sci. Adv. 7, eabg8712 (2021).

Article CAS PubMed PubMed Central Google Scholar

Blum, T. R. et al. Phage-assisted evolution of botulinum neurotoxin proteases with reprogrammed specificity. Science 371, 803810 (2021).

Article CAS PubMed PubMed Central Google Scholar

Esvelt, K. M., Carlson, J. C. & Liu, D. R. A system for the continuous directed evolution of biomolecules. Nature 472, 499503 (2011).

Article CAS PubMed PubMed Central Google Scholar

Ravikumar, A., Arzumanyan, G. A., Obadi, M. K., Javanpour, A. A. & Liu, C. C. Scalable, continuous evolution of genes at mutation rates above genomic error thresholds. Cell 175, 19461957 (2018).

Article CAS PubMed PubMed Central Google Scholar

Zhong, Z. & Liu, C. C. Probing pathways of adaptation with continuous evolution. Curr. Opin. Syst. Biol. 14, 1824 (2019).

Article PubMed PubMed Central Google Scholar

Ravikumar, A., Arrieta, A. & Liu, C. C. An orthogonal DNA replication system in yeast. Nat. Chem. Biol. 10, 175177 (2014).

Article CAS PubMed Google Scholar

Wellner, A. et al. Rapid generation of potent antibodies by autonomous hypermutation in yeast. Nat. Chem. Biol. 17, 10571064 (2021).

Javanpour, A. A. & Liu, C. C. Evolving small-molecule biosensors with improved performance and reprogrammed ligand preference using OrthoRep. ACS Synth. Biol. 10, 27052714 (2021).

Article CAS PubMed PubMed Central Google Scholar

Rix, G. et al. Scalable continuous evolution for the generation of diverse enzyme variants encompassing promiscuous activities. Nat. Commun. 11, 5644 (2020).

Article CAS PubMed PubMed Central Google Scholar

Muoz-Espn, D., Holguera, I., Ballesteros-Plaza, D., Carballido-Lpez, R. & Salas, M. Viral terminal protein directs early organization of phage DNA replication at the bacterial nucleoid. Proc. Natl Acad. Sci. USA 107, 1654816553 (2010).

Article PubMed PubMed Central Google Scholar

van Nies, P. et al. Self-replication of DNA by its encoded proteins in liposome-based synthetic cells. Nat. Commun. 9, 1583 (2018).

Article PubMed PubMed Central Google Scholar

Gillis, A. & Mahillon, J. Phages preying on Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis. Past, present and future. Viruses 6, 26232672 (2014).

Article PubMed PubMed Central Google Scholar

Meijer, W. J., Horcajadas, J. A. & Salas, M. Phi29 family of phages. Microbiol. Mol. Biol. Rev. 65, 261287 (2001).

Article CAS PubMed PubMed Central Google Scholar

Gillis, A. & Mahillon, J. Influence of lysogeny of Tectiviruses GIL01 and GIL16 on Bacillus thuringiensis growth, biofilm formation, and swarming motility. Appl. Environ. Microbiol. 80, 76207630 (2014).

Article PubMed PubMed Central Google Scholar

Biggel, M. et al. Whole genome sequencing reveals biopesticidal origin of Bacillus thuringiensis in foods. Front. Microbiol. 12, 775669 (2022).

Article PubMed PubMed Central Google Scholar

Verheust, C., Fornelos, N. & Mahillon, J. GIL16, a new gram-positive tectiviral phage related to the Bacillus thuringiensis GIL01 and the Bacillus cereus pBClin15 elements. J. Bacteriol. 187, 19661973 (2005).

Article CAS PubMed PubMed Central Google Scholar

Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018).

Article PubMed PubMed Central Google Scholar

Wannier, T. M. et al. Improved bacterial recombineering by parallelized protein discovery. Proc. Natl Acad. Sci. USA 117, 1368913698 (2020).

Article CAS PubMed PubMed Central Google Scholar

Wu, Y. et al. Design of a programmable biosensor-CRISPRi genetic circuits for dynamic and autonomous dual-control of metabolic flux in Bacillus subtilis. Nucleic Acids Res. 48, 9961009 (2020).

Article CAS PubMed Google Scholar

Soengas, M. S. et al. Site-directed mutagenesis at the Exo III motif of phi 29 DNA polymerase; overlapping structural domains for the 35 exonuclease and strand-displacement activities. EMBO J. 11, 42274237 (1992).

Article CAS PubMed PubMed Central Google Scholar

Vega, M., de, Lazaro, J. M., Salas, M. & Blanco, L. Primer-terminus stabilization at the 35 exonuclease active site of phi29 DNA polymerase. Involvement of two amino acid residues highly conserved in proofreading DNA polymerases. EMBO J. 15, 11821192 (1996).

Article PubMed PubMed Central Google Scholar

Truniger, V., Lzaro, J. M., Salas, M. & Blanco, L. A DNA binding motif coordinating synthesis and degradation in proofreading DNA polymerases. EMBO J. 15, 34303441 (1996).

Article CAS PubMed PubMed Central Google Scholar

Vega, M., de, Lzaro, J. M. & Salas, M. Phage 29 DNA polymerase residues involved in the proper stabilisation of the primer-terminus at the 35 exonuclease active site. J. Mol. Biol. 304, 19 (2000).

Article PubMed Google Scholar

Prez-Arnaiz, P., Lzaro, J. M., Salas, M. & de Vega, M. Functional importance of bacteriophage 29 DNA polymerase residue tyr148 in primer-terminus stabilisation at the 3'-5' exonuclease active site. J. Mol. Biol. 391, 797807 (2009).

Article PubMed Google Scholar

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583589 (2021).

Article CAS PubMed PubMed Central Google Scholar

Liu, Y., Liu, L., Li, J., Du, G. & Chen, J. Synthetic biology toolbox and chassis development in Bacillus subtilis. Trends Biotechnol. 37, 548562 (2019).

Article CAS PubMed Google Scholar

Lu, Z. et al. CRISPR-assisted multi-dimensional regulation for fine-tuning gene expression in Bacillus subtilis. Nucleic Acids Res. 47, e40 (2019).

Article PubMed PubMed Central Google Scholar

Tian, R. et al. Titrating bacterial growth and chemical biosynthesis for efficient N-acetylglucosamine and N-acetylneuraminic acid bioproduction. Nat. Commun. 11, 5078 (2020).

Article CAS PubMed PubMed Central Google Scholar

Cai et al. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 373, 15231527 (2021).

Article CAS PubMed Google Scholar

Gao, B. et al. Constructing a methanol-dependent Bacillus subtilis by engineering the methanol metabolism. J. Biotechnol. 343, 128137 (2022).

Article CAS PubMed Google Scholar

Li, C., Zou, Y., Jiang, T., Zhang, J. & Yan, Y. Harnessing plasmid replication mechanism to enable dynamic control of gene copy in bacteria. Metab. Eng. 70, 6778 (2022).

Article CAS PubMed PubMed Central Google Scholar

Fornelos, N., Bamford, J. K. H. & Mahillon, J. Phage-borne factors and host LexA regulate the lytic switch in phage GIL01. J. Bacteriol. 193, 60086019 (2011).

Article CAS PubMed PubMed Central Google Scholar

Fornelos, N. et al. Lytic gene expression in the temperate bacteriophage GIL01 is activated by a phage-encoded LexA homologue. Nucleic Acids Res. 46, 94329443 (2018).

Article CAS PubMed PubMed Central Google Scholar

Fornelos, N. et al. Bacteriophage GIL01 gp7 interacts with host LexA repressor to enhance DNA binding and inhibit RecA-mediated auto-cleavage. Nucleic Acids Res. 43, 73157329 (2015).

Article CAS PubMed PubMed Central Google Scholar

del Solar, G., Giraldo, R., Ruiz-Echevarra, M. J., Espinosa, M. & Daz-Orejas, R. Replication and control of circular bacterial plasmids. Microbiol. Mol. Biol. Rev. 62, 434464 (1998).

Originally posted here:
Engineered bacterial orthogonal DNA replication system for ... - Nature.com