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The dawn of evolutionary genome engineering

Abstract

Genome engineering strategies — such as genome editing, reduction and shuffling, and de novo genome synthesis — enable the modification of specific genomic locations in a directed and combinatorial manner. These approaches offer an unprecedented opportunity to study central evolutionary issues in which natural genetic variation is limited or biased, which sheds light on the evolutionary forces driving complex and extremely slowly evolving traits; the selective constraints on genome architecture; and the reconstruction of ancestral states of cellular structures and networks.

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Figure 1: Genome editing approaches for altering the genetic code on a genome-wide scale in E. coli.
Figure 2: Examples of large-scale genome architecture restructuring.
Figure 3: Optimization of complex phenotypic traits by identifying relevant genes and by searching for optimal combinations of mutations within these genes.

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Acknowledgements

The authors thank the anonymous reviewers for suggestions on the manuscript. C.P. and B.P. thank the Wellcome Trust and the Lendulet Programme of the Hungarian Academy of Sciences for supporting this work; G.P. thanks the Hungarian Research Council (OTKA) for supporting this work. B. Kintses, A. Nyerges and B. Csorgo gave comments on an earlier version of the manuscript.

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Correspondence to Csaba Pál.

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FURTHER INFORMATION

MAGE

Synthetic Yeast 2.0

PowerPoint slides

Glossary

Amino acid 'alphabet'

The set of amino acids used to build genetically encoded proteins.

Antagonistic pleiotropy

Pleiotropy occurs when a single gene influences multiple phenotypic traits that are seemingly unrelated. In the case of antagonistic pleiotropy, expression of the pleiotropic gene has mixed, competing effects; some of these are beneficial but others are detrimental to the organism.

Codon ambiguity

An extreme form of mistranslation in which a codon can be translated as two different amino acids.

Combinatorial explosion

A fundamental problem in evolutionary optimization and computing. As the size of the investigated system and the number of corresponding parameters increase, the number of combinations that one has to examine grows exponentially, which requires an intolerable amount of time to examine them.

Convergent evolution

Evolution of similar phenotypes in different populations or species as a result of adaptation to similar environments or ecological niches.

Directed protein evolution

A protein engineering method to evolve proteins with desirable properties. It mimics and accelerates natural evolutionary processes by applying in vitro diversification–selection–amplification cycles.

Epistatic interactions

Interactions between two mutations whereby the phenotypic effect of one mutation depends on the presence of another mutation.

Genome editing

Modification of the genetic information encoded by the genome using in vivo, directed modification (such as replacement, removal or insertion of DNA bases) of a single locus or multiple loci. It uses synthetic oligonucleotides and a range of accessory tools, including engineered nucleases, and DNA repair and recombination enzymes.

Leading DNA strand

The strand of nascent DNA that is being 'read' by the DNA polymerase in the same direction as the replication fork proceeds. It is being synthesized continuously, as opposed to the lagging strand.

Minimal genomes

Genomes that carry only the minimal genetic information necessary for life in a given environmental condition. Reduction towards a minimal essential gene set can occur either naturally (for example, in symbionts) or by genetic engineering.

Multiplex automated genome engineering

(MAGE). A highly efficient genome editing method that can generate a large and heterogeneous population of mutant bacterial genomes within days. Using oligonucleotide-mediated allelic replacement technology in a cyclic and automated manner, MAGE can simultaneously target and modify multiple genomic locations across a large population of cells.

Site-specific recombineering

A recombination engineering system that allows efficient manipulation of genomic DNA at predetermined locations. It does not require extensive sequence similarity and relies on site-specific recombinases that catalyse reciprocal recombination of DNA at short sequences.

Synthetic chromosome

An artificial chromosome synthesized from simple chemical building blocks. Owing to limitations in the length of DNA that is amenable to direct chemical synthesis, construction of synthetic chromosomes is a hierarchical process, in which synthetic oligonucleotides are assembled into larger DNA segments in a step-wise manner using in vitro and in vivo assembly methods.

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Pál, C., Papp, B. & Pósfai, G. The dawn of evolutionary genome engineering. Nat Rev Genet 15, 504–512 (2014). https://doi.org/10.1038/nrg3746

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