Synthetic Evolution

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2019 Jun 19

PMID 31209374

Citations 33

Authors

Anna J Simon

Simon dOelsnitz

Andrew D Ellington

Affiliations

Soon will be listed here.

Abstract

The combination of modern biotechnologies such as DNA synthesis, λ red recombineering, CRISPR-based editing and next-generation high-throughput sequencing increasingly enables precise manipulation of genes and genomes. Beyond rational design, these technologies also enable the targeted, and potentially continuous, introduction of multiple mutations. While this might seem to be merely a return to natural selection, the ability to target evolution greatly reduces fitness burdens and focuses mutation and selection on those genes and traits that best contribute to a desired phenotype, ultimately throwing evolution into fast forward.

Citing Articles

Synthetic evolution of for biomanufacturing: Approaches and applications.

Wang Z, Qi X, Ren X, Lin Y, Zeng F, Wang Q mLife. 2025; 4(1):1-16.

PMID: 40026576 PMC: 11868838. DOI: 10.1002/mlf2.12167.

Orthogonal RNA replication enables directed evolution and Darwinian adaptation in mammalian cells.

Ma L, Lin Y Nat Chem Biol. 2025; 21(3):451-463.

PMID: 39753704 DOI: 10.1038/s41589-024-01783-2.

Engineering Phages to Fight Multidrug-Resistant Bacteria.

Peng H, Chen I, Qimron U Chem Rev. 2024; 125(2):933-971.

PMID: 39680919 PMC: 11758799. DOI: 10.1021/acs.chemrev.4c00681.

Automating life science labs at the single-cell level through precise ultrasonic liquid sample ejection: PULSE.

Zhang P, Tian Z, Jin K, Yang K, Collyer W, Rufo J Microsyst Nanoeng. 2024; 10(1):172.

PMID: 39567484 PMC: 11579414. DOI: 10.1038/s41378-024-00798-y.

The design and engineering of synthetic genomes.

James J, Dai J, Chew W, Cai Y Nat Rev Genet. 2024; .

PMID: 39506144 DOI: 10.1038/s41576-024-00786-y.

References

Cong L, Ran F, Cox D, Lin S, Barretto R, Habib N . Multiplex genome engineering using CRISPR/Cas systems. Science. 2013; 339(6121):819-23. PMC: 3795411. DOI: 10.1126/science.1231143. View

Doudna J, Charpentier E . Genome editing. The new frontier of genome engineering with CRISPR-Cas9. Science. 2014; 346(6213):1258096. DOI: 10.1126/science.1258096. View

Jinek M, Chylinski K, Fonfara I, Hauer M, Doudna J, Charpentier E . A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science. 2012; 337(6096):816-21. PMC: 6286148. DOI: 10.1126/science.1225829. View

Kumar S, Jain S, Dilbaghi N, Ahluwalia A, Hassan A, Kim K . Advanced Selection Methodologies for DNAzymes in Sensing and Healthcare Applications. Trends Biochem Sci. 2018; 44(3):190-213. DOI: 10.1016/j.tibs.2018.11.001. View

Popovic M, Fliss P, Ditzler M . In vitro evolution of distinct self-cleaving ribozymes in diverse environments. Nucleic Acids Res. 2015; 43(14):7070-82. PMC: 4538833. DOI: 10.1093/nar/gkv648. View

Aquino-Jarquin G, Toscano-Garibay J . RNA aptamer evolution: two decades of SELEction. Int J Mol Sci. 2012; 12(12):9155-71. PMC: 3257122. DOI: 10.3390/ijms12129155. View

Kaur H . Recent developments in cell-SELEX technology for aptamer selection. Biochim Biophys Acta Gen Subj. 2018; 1862(10):2323-2329. DOI: 10.1016/j.bbagen.2018.07.029. View

Liu R, Li X, Lam K . Combinatorial chemistry in drug discovery. Curr Opin Chem Biol. 2017; 38:117-126. PMC: 5645069. DOI: 10.1016/j.cbpa.2017.03.017. View

Dietrich J, McKee A, Keasling J . High-throughput metabolic engineering: advances in small-molecule screening and selection. Annu Rev Biochem. 2010; 79:563-90. DOI: 10.1146/annurev-biochem-062608-095938. View

10.

Reidhaar-Olson J, Sauer R . Combinatorial cassette mutagenesis as a probe of the informational content of protein sequences. Science. 1988; 241(4861):53-7. DOI: 10.1126/science.3388019. View

11.

Oliphant A, Struhl K . An efficient method for generating proteins with altered enzymatic properties: application to beta-lactamase. Proc Natl Acad Sci U S A. 1989; 86(23):9094-8. PMC: 298440. DOI: 10.1073/pnas.86.23.9094. View

12.

Palzkill T, Botstein D . Identification of amino acid substitutions that alter the substrate specificity of TEM-1 beta-lactamase. J Bacteriol. 1992; 174(16):5237-43. PMC: 206357. DOI: 10.1128/jb.174.16.5237-5243.1992. View

13.

Evnin L, VASQUEZ J, Craik C . Substrate specificity of trypsin investigated by using a genetic selection. Proc Natl Acad Sci U S A. 1990; 87(17):6659-63. PMC: 54596. DOI: 10.1073/pnas.87.17.6659. View

14.

Graham L, Haggett K, Jennings P, Le Brocque D, Whittaker R, Schober P . Random mutagenesis of the substrate-binding site of a serine protease can generate enzymes with increased activities and altered primary specificities. Biochemistry. 1993; 32(24):6250-8. DOI: 10.1021/bi00075a019. View

15.

Beckman R, Mildvan A, Loeb L . On the fidelity of DNA replication: manganese mutagenesis in vitro. Biochemistry. 1985; 24(21):5810-7. DOI: 10.1021/bi00342a019. View

16.

Cadwell R, Joyce G . Randomization of genes by PCR mutagenesis. PCR Methods Appl. 1992; 2(1):28-33. DOI: 10.1101/gr.2.1.28. View

17.

Zaccolo M, Williams D, Brown D, Gherardi E . An approach to random mutagenesis of DNA using mixtures of triphosphate derivatives of nucleoside analogues. J Mol Biol. 1996; 255(4):589-603. DOI: 10.1006/jmbi.1996.0049. View

18.

Bloom J, Meyer M, Meinhold P, Otey C, Macmillan D, Arnold F . Evolving strategies for enzyme engineering. Curr Opin Struct Biol. 2005; 15(4):447-52. DOI: 10.1016/j.sbi.2005.06.004. View

19.

Chen W, Struhl K . Saturation mutagenesis of a yeast his3 "TATA element": genetic evidence for a specific TATA-binding protein. Proc Natl Acad Sci U S A. 1988; 85(8):2691-5. PMC: 280064. DOI: 10.1073/pnas.85.8.2691. View

20.

Beaudry A, Joyce G . Directed evolution of an RNA enzyme. Science. 1992; 257(5070):635-41. DOI: 10.1126/science.1496376. View