Synthetic genomes with altered genetic codes

Current Opinion in Systems Biology - Tập 24 - Trang 32-40 - 2020
Nili Ostrov1, Akos Nyerges1, Anush Chiappino-Pepe1,2, Alexandra Rudolph1, Maximilien Baas-Thomas1, George M. Church1,2
1Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
2Wyss Institute for Biologically Inspired Engineering, Boston, MA 02115, USA

Tài liệu tham khảo

Nirenberg, 2004, Historical review: deciphering the genetic code--a personal account, Trends Biochem Sci, 29, 46, 10.1016/j.tibs.2003.11.009 Richmond, 1962, The effect of amino acid analogues on growth and protein synthesis in microorganisms, Bacteriol Rev, 26, 398, 10.1128/BR.26.4.398-420.1962 Brenner, 1965, Genetic code: the “nonsense” triplets for chain termination and their suppression, Nature, 206, 994, 10.1038/206994a0 Arranz-Gibert, 2018, Next-generation genetic code expansion, Curr Opin Chem Biol, 46, 203, 10.1016/j.cbpa.2018.07.020 Effraim, 2009, Natural amino acids do not require their native tRNAs for efficient selection by the ribosome, Nat Chem Biol, 5, 947, 10.1038/nchembio.255 Young, 2018, Playing with the molecules of life, ACS Chem Biol, 13, 854, 10.1021/acschembio.7b00974 Roy, 2020, Development of a high yielding expression platform for the introduction of non-natural amino acids in protein sequences, mAbs, 12, 1684749, 10.1080/19420862.2019.1684749 Fischer, 2020, New codons for efficient production of unnatural proteins in a semisynthetic organism, Nat Chem Biol, 10.1038/s41589-020-0507-z Dunkelmann, 2020, Engineered triply orthogonal pyrrolysyl–tRNA synthetase/tRNA pairs enable the genetic encoding of three distinct non-canonical amino acids, Nat Chem, 12, 535, 10.1038/s41557-020-0472-x Neumann, 2010, Encoding multiple unnatural amino acids via evolution of a quadruplet-decoding ribosome, Nature, 464, 441, 10.1038/nature08817 Marliere, 2009, The farther, the safer: a manifesto for securely navigating synthetic species away from the old living world, Syst Synth Biol, 3, 77, 10.1007/s11693-009-9040-9 Calles, 2019, Fail-safe genetic codes designed to intrinsically contain engineered organisms, Nucleic Acids Res, 47, 10439, 10.1093/nar/gkz745 Blazejewski, 2019, Synthetic sequence entanglement augments stability and containment of genetic information in cells, Science, 365, 595, 10.1126/science.aav5477 Ostrov, 2019, Technological challenges and milestones for writing genomes, Science, 366, 310, 10.1126/science.aay0339 Lajoie, 2013, Genomically recoded organisms expand biological functions, Science, 342, 357, 10.1126/science.1241459 Mandell, 2015, Biocontainment of genetically modified organisms by synthetic protein design, Nature, 518, 55, 10.1038/nature14121 Rovner, 2015, Recoded organisms engineered to depend on synthetic amino acids, Nature, 518, 89, 10.1038/nature14095 Chatterjee, 2014, A bacterial strain with a unique quadruplet codon specifying non-native amino acids, Chembiochem, 15, 1782, 10.1002/cbic.201402104 Ma, 2016, Genomic recoding broadly obstructs the propagation of horizontally transferred genetic elements, Cell Syst, 3, 199, 10.1016/j.cels.2016.06.009 Annaluru, 2014, Total synthesis of a functional designer eukaryotic chromosome, Science, 344, 55, 10.1126/science.1249252 Mitchell, 2017, Synthesis, debugging, and effects of synthetic chromosome consolidation: synVI and beyond, Science, 355, 10.1126/science.aaf4831 Pretorius, 2018, Yeast 2.0-connecting the dots in the construction of the world's first functional synthetic eukaryotic genome, FEMS Yeast Res, 18, 10.1093/femsyr/foy032 Lajoie, 2013, Probing the limits of genetic recoding in essential genes, Science, 342, 361, 10.1126/science.1241460 Napolitano, 2016, Emergent rules for codon choice elucidated by editing rare arginine codons in Escherichia coli, Proc Natl Acad Sci U S A, 113, E5588, 10.1073/pnas.1605856113 Lau, 2017, Large-scale recoding of a bacterial genome by iterative recombineering of synthetic DNA, Nucleic Acids Res, 10.1093/nar/gkx415 Wang, 2016, Defining synonymous codon compression schemes by genome recoding, Nature, 539, 59, 10.1038/nature20124 Venetz, 2019, Chemical synthesis rewriting of a bacterial genome to achieve design flexibility and biological functionality, Proc Natl Acad Sci U S A, 116, 8070, 10.1073/pnas.1818259116 Fredens, 2019, Total synthesis of Escherichia coli with a recoded genome, Nature, 569, 514, 10.1038/s41586-019-1192-5 Ostrov, 2016, Design, synthesis, and testing toward a 57-codon genome, Science, 353, 819, 10.1126/science.aaf3639 Pines, 2017, Refactoring the genetic code for increased evolvability, mBio, 8, 10.1128/mBio.01654-17 Anderson, 2004, An expanded genetic code with a functional quadruplet codon, Proc Natl Acad Sci U S A, 101, 7566, 10.1073/pnas.0401517101 Ohtsuki, 2005, Multiple incorporation of non-natural amino acids into a single protein using tRNAs with non-standard structures, FEBS Lett, 579, 6769, 10.1016/j.febslet.2005.11.010 Sanger, 1977, DNA sequencing with chain-terminating inhibitors, Proc Natl Acad Sci U S A, 74, 5463, 10.1073/pnas.74.12.5463 Ledbetter, 2018, Reprograming the replisome of a semisynthetic organism for the expansion of the genetic alphabet, J Am Chem Soc, 140, 758, 10.1021/jacs.7b11488 Malyshev, 2014, A semi-synthetic organism with an expanded genetic alphabet, Nature, 509, 385, 10.1038/nature13314 Zhang, 2017, A semi-synthetic organism that stores and retrieves increased genetic information, Nature, 551, 644, 10.1038/nature24659 Zhang, 2017, A semisynthetic organism engineered for the stable expansion of the genetic alphabet, Proc Natl Acad Sci U S A, 114, 1317, 10.1073/pnas.1616443114 Hoshika, 2019, Hachimoji DNA and RNA: a genetic system with eight building blocks, Science, 363, 884, 10.1126/science.aat0971 Sauna, 2011, Understanding the contribution of synonymous mutations to human disease, Nat Rev Genet, 12, 683, 10.1038/nrg3051 Cetnar, 2020, Systematic quantification of sequence and structural determinants controlling mRNA stability in bacterial operons, bioRxiv Hanson, 2018, Codon optimality, bias and usage in translation and mRNA decay, Nat Rev Mol Cell Biol, 19, 20, 10.1038/nrm.2017.91 Carey, 2015, RNA polymerase errors cause splicing defects and can be regulated by differential expression of RNA polymerase subunits, Elife, 4, 10.7554/eLife.09945 Tenaillon, 2018, Experimental evolution heals the scars of genome-scale recoding, Proc Natl Acad Sci U S A, 115, 2853, 10.1073/pnas.1801699115 Courel, 2019, GC content shapes mRNA storage and decay in human cells, Elife, 8, 10.7554/eLife.49708 Macklin, 2020, Simultaneous cross-evaluation of heterogeneous E. coli datasets via mechanistic simulation, Science, 369 Mitchell, 2018, De novo assembly, delivery and expression of a 101 kb human gene in mouse cells, bioRxiv Lloyd, 2020, The deep genome project, Genome Biol, 21, 18, 10.1186/s13059-020-1931-9 Mittal, 2018, Codon usage influences fitness through RNA toxicity, bioRxiv Cambray, 2018, Evaluation of 244,000 synthetic sequences reveals design principles to optimize translation in Escherichia coli, Nat Biotechnol, 36, 1005, 10.1038/nbt.4238 Wannier, 2018, Adaptive evolution of genomically recoded Escherichia coli, Proc Natl Acad Sci U S A, 115, 3090, 10.1073/pnas.1715530115 Chen, 2018, Controlling the replication of a genomically recoded HIV-1 with a functional quadruplet codon in mammalian cells, ACS Synth Biol, 10.1021/acssynbio.8b00096 Riba, 2019, Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates, Proc Natl Acad Sci U S A, 116, 15023, 10.1073/pnas.1817299116 Servick, 2018, Genome writing project aims to rally scientists around virus-proofing cells, Science Khan, 2018, Deciphering the rationale behind specific codon usage pattern in extremophiles, Sci Rep, 8, 15548, 10.1038/s41598-018-33476-x Sánchez-Romero, 2020, The bacterial epigenome, Nat Rev Microbiol, 18, 7, 10.1038/s41579-019-0286-2 Furi, 2019, Methylation warfare: interaction of pneumococcal bacteriophages with their host, J Bacteriol, 201, 10.1128/JB.00370-19 Bell, 2019, DNA methylation aging clocks: challenges and recommendations, Genome Biol, 20, 249, 10.1186/s13059-019-1824-y Verma, 2019, Architecture of the Escherichia coli nucleoid, PLoS Genet, 15, 10.1371/journal.pgen.1008456 Freddolino, 2020, Dynamic landscape of protein occupancy across the Escherichia coli chromosome, bioRxiv Shao, 2018, Creating a functional single-chromosome yeast, Nature, 560, 331, 10.1038/s41586-018-0382-x Luo, 2018, Karyotype engineering by chromosome fusion leads to reproductive isolation in yeast, Nature, 560, 392, 10.1038/s41586-018-0374-x Mercy, 2017, 3D organization of synthetic and scrambled chromosomes, Science, 355, 10.1126/science.aaf4597 Wang, 2009, Programming cells by multiplex genome engineering and accelerated evolution, Nature, 460, 894, 10.1038/nature08187 Leconte, 2008, Discovery, characterization, and optimization of an unnatural base pair for expansion of the genetic alphabet, J Am Chem Soc, 130, 2336, 10.1021/ja078223d Palluk, 2018, De novo DNA synthesis using polymerase-nucleotide conjugates, Nat Biotechnol, 10.1038/nbt.4173 Lee, 2019, Terminator-free template-independent enzymatic DNA synthesis for digital information storage, Nat Commun, 10, 2383, 10.1038/s41467-019-10258-1 Marlière, 2011, Chemical evolution of a bacterium's genome, Angew Chem Int Ed, 50, 7109, 10.1002/anie.201100535 Liu, 2018, Toward an orthogonal central dogma, Nat Chem Biol, 14, 103, 10.1038/nchembio.2554 Messerschmidt, 2015, Synthetic secondary chromosomes in Escherichia coli based on the replication origin of chromosome II in Vibrio cholerae, Biotechnol J, 10, 302, 10.1002/biot.201400031