Efficient retroelement-mediated DNA writing in bacteria

Cell Systems - Tập 12 - Trang 860-872.e5 - 2021
Fahim Farzadfard1,2,3, Nava Gharaei4, Robert J. Citorik1,2,3, Timothy K. Lu1,2,3
1Synthetic Biology Group, Research Laboratory of Electronics, Department of Electrical Engineering & Computer Science and Department of Biological Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
2MIT Synthetic Biology Center, 500 Technology Square, Cambridge, MA 02139, USA
3MIT Microbiology Graduate Program, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
4MCO Graduate Program, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA

Tài liệu tham khảo

Anzalone, 2019, Search-and-replace genome editing without double-strand breaks or donor DNA, Nature, 576, 149, 10.1038/s41586-019-1711-4 Caliando, 2015, Targeted DNA degradation using a CRISPR device stably carried in the host genome, Nat. Commun., 6, 6989, 10.1038/ncomms7989 Chan, 2007, A recombineering based approach for high-throughput conditional knockout targeting vector construction, Nucleic Acids Res, 35, e64, 10.1093/nar/gkm163 Chase, 1974, Exonuclease VII of Escherichia coli. Mechanism of action, J. Biol. Chem., 249, 4553, 10.1016/S0021-9258(19)42454-X Chasteen, 2006, Eliminating helper phage from phage display, Nucleic Acids Res, 34, e145, 10.1093/nar/gkl772 Citorik, 2014, Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases, Nat. Biotechnol., 32, 1141, 10.1038/nbt.3011 Corts, 2019, A new recombineering system for precise genome-editing in Shewanella oneidensis strain MR-1 using single-stranded oligonucleotides, Sci. Rep., 9, 39, 10.1038/s41598-018-37025-4 Costantino, 2003, Enhanced levels of lambda Red-mediated recombinants in mismatch repair mutants, Proc. Natl. Acad. Sci. USA, 100, 15748, 10.1073/pnas.2434959100 Cui, 2016, Consequences of Cas9 cleavage in the chromosome of Escherichia coli, Nucleic Acids Res., 44, 4243, 10.1093/nar/gkw223 Datsenko, 2000, One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products, Proc. Natl. Acad. Sci. USA, 97, 6640, 10.1073/pnas.120163297 Dutra, 2007, RecA-independent recombination is efficient but limited by exonucleases, Proc. Natl. Acad. Sci. USA, 104, 216, 10.1073/pnas.0608293104 Engler, 2014, Golden Gate cloning, Methods Mol. Biol., 1116, 119, 10.1007/978-1-62703-764-8_9 Farzadfard, 2019, Single-nucleotide-resolution computing and memory in living cells, Mol. Cell, 75, 769, 10.1016/j.molcel.2019.07.011 Farzadfard, 2014, Synthetic biology. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations, Science, 346, 1256272, 10.1126/science.1256272 Farzadfard, 2018, Emerging applications for DNA writers and molecular recorders, Science, 361, 870, 10.1126/science.aat9249 Ferrières, 2010, Silent mischief: bacteriophage Mu insertions contaminate products of Escherichia coli random mutagenesis performed using suicidal transposon delivery plasmids mobilized by broad-host-range RP4 conjugative machinery, J. Bacteriol., 192, 6418, 10.1128/JB.00621-10 Gao, 2014, Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing, J. Integr. Plant Biol., 56, 343, 10.1111/jipb.12152 Gaudelli, 2017, Programmable base editing of A⋅T to G⋅C in genomic DNA without DNA cleavage, Nature., 551, 464, 10.1038/nature24644 Gibson, 2011, Enzymatic assembly of overlapping DNA fragments, Methods Enzymol, 498, 349, 10.1016/B978-0-12-385120-8.00015-2 Glaser, 2015, Puzzle imaging: using large-scale dimensionality reduction algorithms for localization, PLoS One, 10, 10.1371/journal.pone.0131593 Hall, 2014, Growth rates made easy, Mol. Biol. Evol., 31, 232, 10.1093/molbev/mst187 Huen, 2006, The involvement of replication in single stranded oligonucleotide-mediated gene repair, Nucleic Acids Res, 34, 6183, 10.1093/nar/gkl852 Jermann, 1995, Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily, Nature, 374, 57, 10.1038/374057a0 Jiang, 2013, RNA-guided editing of bacterial genomes using CRISPR-Cas systems, Nat. Biotechnol., 31, 233, 10.1038/nbt.2508 Komor, 2016, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature., 533, 420, 10.1038/nature17946 Lou, 2013, High-throughput DNA sequencing errors are reduced by orders of magnitude using circle sequencing, Proc. Natl. Acad. Sci. USA, 110, 19872, 10.1073/pnas.1319590110 Milo, 2010, BioNumbers--the database of key numbers in molecular and cell biology, Nucleic Acids Res, 38, D750, 10.1093/nar/gkp889 Nadell, 2016, Spatial structure, cooperation and competition in biofilms, Nat. Rev. Microbiol., 14, 589, 10.1038/nrmicro.2016.84 Pál, 2014, The dawn of evolutionary genome engineering, Nat. Rev. Genet., 15, 504, 10.1038/nrg3746 Peikon, 2017, Using high-throughput barcode sequencing to efficiently map connectomes, Nucleic Acids Res, 45, e115, 10.1093/nar/gkx292 Perli, 2016, Continuous genetic recording with self-targeting CRISPR-Cas in human cells, Science, 353, aag0511, 10.1126/science.aag0511 Pines, 2015, Bacterial recombineering: genome engineering via phage-based homologous recombination, ACS Synth. Biol., 4, 1176, 10.1021/acssynbio.5b00009 Qi, 2013, Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, 152, 1173, 10.1016/j.cell.2013.02.022 Risso, 2013, Hyperstability and substrate promiscuity in laboratory resurrections of Precambrian beta-lactamases, J. Am. Chem. Soc., 135, 2899, 10.1021/ja311630a Ronda, 2016, CRMAGE: CRISPR optimized MAGE Recombineering, Sci Rep., 6, 10.1038/srep19452 Roquet, 2016, Synthetic recombinase-based state machines in living cells, Science, 353, aad8559, 10.1126/science.aad8559 Ross, 2013, Characterizing and measuring bias in sequence data, Genome Biol, 14, R51, 10.1186/gb-2013-14-5-r51 Sawitzke, 2011, Probing cellular processes with oligo-mediated recombination and using the knowledge gained to optimize recombineering, J. Mol. Biol., 407, 45, 10.1016/j.jmb.2011.01.030 Schaaper, 1987, Spectra of spontaneous mutations in Escherichia coli strains defective in mismatch correction: the nature of in vivo DNA replication errors, Proc. Natl. Acad. Sci. USA, 84, 6220, 10.1073/pnas.84.17.6220 Schmitt, 2012, Detection of ultra-rare mutations by next-generation sequencing, Proc. Natl. Acad. Sci. USA, 109, 14508, 10.1073/pnas.1208715109 Sharon, 2018, Functional genetic variants revealed by massively parallel precise genome editing, Cell, 175, 544, 10.1016/j.cell.2018.08.057 Shipman, 2016, Molecular recordings by directed CRISPR spacer acquisition, Science, 353, aaf1175, 10.1126/science.aaf1175 Simon, 2018, Retroelement-based genome editing and evolution, ACS Synth. Biol., 7, 2600, 10.1021/acssynbio.8b00273 Swingle, 2010, Oligonucleotide recombination in Gram-negative bacteria, Mol. Microbiol., 75, 138, 10.1111/j.1365-2958.2009.06976.x Tang, 2018, Rewritable multi-event analog recording in bacterial and mammalian cells, Science, 360, 10.1126/science.aap8992 Thornton, 2004, Resurrecting ancient genes: experimental analysis of extinct molecules, Nat. Rev. Genet., 5, 366, 10.1038/nrg1324 Wang, 2009, Programming cells by multiplex genome engineering and accelerated evolution, Nature, 460, 894, 10.1038/nature08187 Wannier, 2020, Improved bacterial recombineering by parallelized protein discovery, bioRxiv Weinreich, 2006, Darwinian evolution can follow only very few mutational paths to fitter proteins, Science, 312, 111, 10.1126/science.1123539 Yamamoto, 1970, Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification, Virology, 40, 734, 10.1016/0042-6822(70)90218-7 Yu, 2000, An efficient recombination system for chromosome engineering in Escherichia coli, Proc. Natl. Acad. Sci. USA, 97, 5978, 10.1073/pnas.100127597 Zador, 2012, Sequencing the connectome, PLoS Biol, 10, 10.1371/journal.pbio.1001411 Zeitoun, 2015, Multiplexed tracking of combinatorial genomic mutations in engineered cell populations, Nat. Biotechnol., 33, 631, 10.1038/nbt.3177