{"id":1116312,"date":"2023-07-17T14:20:47","date_gmt":"2023-07-17T18:20:47","guid":{"rendered":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/uncategorized\/engineered-bacterial-orthogonal-dna-replication-system-for-nature-com\/"},"modified":"2023-07-17T14:20:47","modified_gmt":"2023-07-17T18:20:47","slug":"engineered-bacterial-orthogonal-dna-replication-system-for-nature-com","status":"publish","type":"post","link":"https:\/\/www.euvolution.com\/prometheism-transhumanism-posthumanism\/transhuman-news-blog\/dna\/engineered-bacterial-orthogonal-dna-replication-system-for-nature-com\/","title":{"rendered":"Engineered bacterial orthogonal DNA replication system for … – Nature.com"},"content":{"rendered":"

Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125131 (1998). <\/p>\n

Article CAS Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

Arnold, F. H. Directed evolution. Bringing new chemistry to life. Angew. Chem. 57, 41434148 (2018). <\/p>\n

Article CAS Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

Meyer, A. J. & Ellington, A. D. Molecular evolution picks up the PACE. Nat. Biotechnol. 29, 502503 (2011). <\/p>\n

Article CAS PubMed Google Scholar <\/p>\n

Simon, A. J., dOelsnitz, S. & Ellington, A. D. Synthetic evolution. Nat. Biotechnol. 37, 730743 (2019). <\/p>\n

Article CAS PubMed Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

Crook, N. et al. In vivo continuous evolution of genes and pathways in yeast. Nat. Commun. 7, 13051 (2016). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

Zhong, Z. & Liu, C. C. Probing pathways of adaptation with continuous evolution. Curr. Opin. Syst. Biol. 14, 1824 (2019). <\/p>\n

Article PubMed PubMed Central Google Scholar <\/p>\n

Ravikumar, A., Arrieta, A. & Liu, C. C. An orthogonal DNA replication system in yeast. Nat. Chem. Biol. 10, 175177 (2014). <\/p>\n

Article CAS PubMed Google Scholar <\/p>\n

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

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article PubMed PubMed Central Google Scholar <\/p>\n

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

Article PubMed PubMed Central Google Scholar <\/p>\n

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

Article PubMed PubMed Central Google Scholar <\/p>\n

Meijer, W. J., Horcajadas, J. A. & Salas, M. Phi29 family of phages. Microbiol. Mol. Biol. Rev. 65, 261287 (2001). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article PubMed PubMed Central Google Scholar <\/p>\n

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

Article PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

Doron, S. et al. Systematic discovery of antiphage defense systems in the microbial pangenome. Science 359, eaar4120 (2018). <\/p>\n

Article PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article PubMed Google Scholar <\/p>\n

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). <\/p>\n

Article PubMed Google Scholar <\/p>\n

Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583589 (2021). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

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

Article PubMed PubMed Central Google Scholar <\/p>\n

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

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

Cai et al. Cell-free chemoenzymatic starch synthesis from carbon dioxide. Science 373, 15231527 (2021). <\/p>\n

Article CAS PubMed Google Scholar <\/p>\n

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

Article CAS PubMed Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

Article CAS PubMed PubMed Central Google Scholar <\/p>\n

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). <\/p>\n

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Originally posted here:
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