Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

  • Opinion
  • Published:

The dawn of evolutionary genome engineering

Nature Reviews Genetics volume 15, pages 504–512 (2014)Cite this article

Subjects

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.

This is a preview of subscription content, access via your institution

Access options

Buy this article

  • Purchase on Springer Link
  • Instant access to full article PDF
Buy now

Prices may be subject to local taxes which are calculated during checkout

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.

Similar content being viewed by others

References

  1. Barrick, J. E. & Lenski, R. E. Genome dynamics during experimental evolution. Nature Rev. Genet. 14, 827–839 (2013).

    Article  CAS  Google Scholar 

  2. Vieira-Silva, S. & Rocha, E. P. The systemic imprint of growth and its uses in ecological (meta)genomics. PLoS Genet. 6, e1000808 (2010).

    Article  Google Scholar 

  3. Elena, S. F. & Lenski, R. E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nature Rev. Genet. 4, 457–469 (2003).

    Article  CAS  Google Scholar 

  4. Dettman, J. R. et al. Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol. Ecol. 21, 2058–2077 (2012).

    Article  CAS  Google Scholar 

  5. Barrick, J. E. et al. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 461, 1243–1247 (2009).

    Article  CAS  Google Scholar 

  6. Blount, Z. D., Borland, C. Z. & Lenski, R. E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc. Natl Acad. Sci. USA 105, 7899–7906 (2008).

    Article  CAS  Google Scholar 

  7. Nilsson, A. I. et al. Bacterial genome size reduction by experimental evolution. Proc. Natl Acad. Sci. USA 102, 12112–12116 (2005).

    Article  CAS  Google Scholar 

  8. Romero, P. A. & Arnold, F. H. Exploring protein fitness landscapes by directed evolution. Nature Rev. Mol. Cell Biol. 10, 866–876 (2009).

    Article  CAS  Google Scholar 

  9. Peisajovich, S. G. & Tawfik, D. S. Protein engineers turned evolutionists. Nature Methods 4, 991–994 (2007).

    Article  CAS  Google Scholar 

  10. Esvelt, K. M. & Wang, H. H. Genome-scale engineering for systems and synthetic biology. Mol. Systems Biol. 9, 641 (2013).

    Article  Google Scholar 

  11. Carr, P. A. & Church, G. M. Genome engineering. Nature Biotech. 27, 1151–1162 (2009).

    Article  CAS  Google Scholar 

  12. Woodruff, L. B. & Gill, R. T. Engineering genomes in multiplex. Curr. Opin. Biotechnol. 22, 576–583 (2011).

    Article  CAS  Google Scholar 

  13. Wang, H. H. et al. Programming cells by multiplex genome engineering and accelerated evolution. Nature 460, 894–898 (2009).

    Article  CAS  Google Scholar 

  14. Lajoie, M. J. et al. Genomically recoded organisms expand biological functions. Science 342, 357–360 (2013).

    Article  CAS  Google Scholar 

  15. Isaacs, F. J. et al. Precise manipulation of chromosomes in vivo enables genome-wide codon replacement. Science 333, 348–353 (2011).

    Article  CAS  Google Scholar 

  16. Pósfai, G. et al. Emergent properties of reduced-genome Escherichia coli. Science 312, 1044–1046 (2006).

    Article  Google Scholar 

  17. Patnaik, R. et al. Genome shuffling of Lactobacillus for improved acid tolerance. Nature Biotech. 20, 707–712 (2002).

    Article  CAS  Google Scholar 

  18. Zhang, Y. X. et al. Genome shuffling leads to rapid phenotypic improvement in bacteria. Nature 415, 644–646 (2002).

    Article  CAS  Google Scholar 

  19. Lartigue, C. et al. Genome transplantation in bacteria: changing one species to another. Science 317, 632–638 (2007).

    Article  CAS  Google Scholar 

  20. Rocha, E. P. The organization of the bacterial genome. Annu. Rev. Genet. 42, 211–233 (2008).

    Article  CAS  Google Scholar 

  21. Knight, R. D., Freeland, S. J. & Landweber, L. F. Rewiring the keyboard: evolvability of the genetic code. Nature Rev. Genet. 2, 49–58 (2001).

    Article  CAS  Google Scholar 

  22. Ambrogelly, A., Palioura, S. & Söll, D. Natural expansion of the genetic code. Nature Chem. Biol. 3, 29–35 (2007).

    Article  CAS  Google Scholar 

  23. Lajoie, M. J. et al. Probing the limits of genetic recoding in essential genes. Science 342, 361–363 (2013).

    Article  CAS  Google Scholar 

  24. Bezerra, A. R. et al. Reversion of a fungal genetic code alteration links proteome instability with genomic and phenotypic diversification. Proc. Natl Acad. Sci. USA 110, 11079–11084 (2013).

    Article  CAS  Google Scholar 

  25. Liu, C. C. & Schultz, P. G. Adding new chemistries to the genetic code. Annu. Rev. Biochem. 79, 413–444 (2010).

    Article  CAS  Google Scholar 

  26. Philip, G. K. & Freeland, S. J. Did evolution select a nonrandom “alphabet” of amino acids? Astrobiology 11, 235–240 (2011).

    Article  CAS  Google Scholar 

  27. Liu, C. C. et al. Protein evolution with an expanded genetic code. Proc. Natl Acad. Sci. 105, 17688–17693 (2008).

    Article  CAS  Google Scholar 

  28. Walter, K. U., Vamvaca, K. & Hilvert, D. An active enzyme constructed from a 9-amino acid alphabet. J. Biol. Chem. 280, 37742–37746 (2005).

    Article  CAS  Google Scholar 

  29. Hammerling, M. J. et al. Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Nature Chem. Biol. 10, 178 (2014).

    Article  CAS  Google Scholar 

  30. Wernegreen, J. J. Genome evolution in bacterial endosymbionts of insects. Nature Rev. Genet. 3, 850–861 (2002).

    Article  CAS  Google Scholar 

  31. Fehér, T., Papp, B., Pál, C. & Pósfai, G. Systematic genome reductions: theoretical and experimental approaches. Chem. Rev. 107, 3498–3513 (2007).

    Article  Google Scholar 

  32. Pál, C., Papp, B. & Lercher, M. J. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nature Genet. 37, 1372–1375 (2005).

    Article  Google Scholar 

  33. Umenhoffer, K. et al. Reduced evolvability of Escherichia coli MDS42, an IS-less cellular chassis for molecular and synthetic biology applications. Microb. Cell Fact 9, 38 (2010).

    Article  Google Scholar 

  34. Fehér, T. et al. Competition between transposable elements and mutator genes in bacteria. Mol. Biol. Evol. 29, 3153–3159 (2012).

    Article  Google Scholar 

  35. Pál, C. et al. Chance and necessity in the evolution of minimal metabolic networks. Nature 440, 667–670 (2006).

    Article  Google Scholar 

  36. Hurst, L. D., Pál, C. & Lercher, M. J. The evolutionary dynamics of eukaryotic gene order. Nature Rev. Genet. 5, 299–310 (2004).

    Article  CAS  Google Scholar 

  37. Dymond, J. S. et al. Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477, 471–476 (2011).

    Article  CAS  Google Scholar 

  38. Teresa Avelar, A., Perfeito, L., Gordo, I. & Godinho Ferreira, M. Genome architecture is a selectable trait that can be maintained by antagonistic pleiotropy. Nature Commun. 4, 2235 (2013).

    Article  Google Scholar 

  39. Annaluru, N. et al. Total synthesis of a functional designer eukaryotic chromosome. Science 344, 55–58 (2014).

    Article  CAS  Google Scholar 

  40. Lynch, M. & Abegg, A. The rate of establishment of complex adaptations. Mol. Biol. Evol. 27, 1404–1414 (2010).

    Article  CAS  Google Scholar 

  41. Nyerges, A. et al. Conditional DNA repair mutants enable highly precise genome engineering. Nucleic Acids Res. 42, e62 (2014).

    Article  CAS  Google Scholar 

  42. Warner, J. R., Reeder, P. J., Karimpour-Fard, A., Woodruff, L. B. & Gill, R. T. Rapid profiling of a microbial genome using mixtures of barcoded oligonucleotides. Nature Biotech. 28, 856–862 (2010).

    Article  CAS  Google Scholar 

  43. Papp, B., Notebaart, R. A. & Pál, C. Systems-biology approaches for predicting genomic evolution. Nature Rev. Genet. 12, 591–602 (2011).

    Article  CAS  Google Scholar 

  44. Wang, Z., Liao, B. Y. & Zhang, J. Genomic patterns of pleiotropy and the evolution of complexity. 107, 18034–18039 (2010).

  45. Benner, S. A., Sassi, S. O. & Gaucher, E. A. Molecular paleoscience: systems biology from the past. Adv. Enzymol. Relat. Areas Mol. Biol. 75, 1–132 (2007).

    CAS  PubMed  Google Scholar 

  46. Voordeckers, K. et al. Reconstruction of ancestral metabolic enzymes reveals molecular mechanisms underlying evolutionary innovation through gene duplication. PLoS Biol. 10, e1001446 (2012).

    Article  CAS  Google Scholar 

  47. Finnigan, G. C., Hanson-Smith, V., Stevens, T. H. & Thornton, J. W. Evolution of increased complexity in a molecular machine. Nature 481, 360–364 (2012).

    Article  CAS  Google Scholar 

  48. Gaucher, E. A., Thomson, J. M., Burgan, M. F. & Benner, S. A. Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425, 285–288 (2003).

    Article  CAS  Google Scholar 

  49. Isalan, M. et al. Evolvability and hierarchy in rewired bacterial gene networks. Nature 452, 840–845 (2008).

    Article  CAS  Google Scholar 

  50. Cagatay, T., Turcotte, M., Elowitz, M. B., Garcia-Ojalvo, J. & Süel, G. M. Architecture-dependent noise discriminates functionally analogous differentiation circuits. Cell 139, 512–522 (2009).

    Article  CAS  Google Scholar 

  51. Haseltine, E. L. & Arnold, F. H. Synthetic gene circuits: design with directed evolution. Annu. Rev. Biophys. Biomol. Struct. 36, 1–19 (2007).

    Article  CAS  Google Scholar 

  52. Peisajovich, S. G., Garbarino, J. E., Wei, P. & Lim, W. A. Rapid diversification of cell signaling phenotypes by modular domain recombination. Science 328, 368–372 (2010).

    Article  CAS  Google Scholar 

  53. Yokobayashi, Y., Weiss, R. & Arnold, F. H. Directed evolution of a genetic circuit. Proc. Natl Acad. Sci. USA 99, 16587–16591 (2002).

    Article  CAS  Google Scholar 

  54. Renda, B. A., Hammerling, M. J. & Barrick, J. E. Engineering reduced evolutionary potential for synthetic biology. Mol. Biosyst. http://dx.doi.org/10.1039/C3MB70606K (2014).

  55. Fehér, T. et al. Scarless engineering of the Escherichia coli genome. Methods Mol. Biol. 416, 251–259 (2008).

    Article  Google Scholar 

  56. Csörgo, B., Fehér, T., Tímár, E., Blattner, F. R. & Pósfai, G. Low-mutation-rate, reduced-genome Escherichia coli: an improved host for faithful maintenance of engineered genetic constructs. Microb. Cell Fact 11, 11 (2012).

    Article  Google Scholar 

  57. Ellis, H. M., Yu, D., DiTizio, T. & Court, D. L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc. Natl Acad. Sci. USA 98, 6742–6746 (2001).

    Article  CAS  Google Scholar 

  58. Soskine, M. & Tawfik, D. S. Mutational effects and the evolution of new protein functions. Nature Rev. Genet. 11, 572–582 (2010).

    Article  CAS  Google Scholar 

  59. Bogdanove, A. J. & Voytas, D. F. TAL effectors: customizable proteins for DNA targeting. Science 333, 1843–1846 (2011).

    Article  CAS  Google Scholar 

  60. Jiang, W., Bikard, D., Cox, D., Zhang, F. & Marraffini, L. A. RNA-guided editing of bacterial genomes using CRISPR–Cas systems. Nature Biotech. 31, 233–239 (2013).

    Article  CAS  Google Scholar 

  61. Enyeart, P. J. et al. Generalized bacterial genome editing using mobile group II introns and Cre–lox. Mol. Syst. Biol. 9, 685 (2013).

    Article  CAS  Google Scholar 

  62. Gibson, D. G. et al. Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329, 52–56 (2010).

    Article  CAS  Google Scholar 

  63. Chan, L. Y., Kosuri, S. & Endy, D. Refactoring bacteriophage T7. Mol. Syst. Biol. 1, 2005.0018 (2005).

    Article  Google Scholar 

  64. Rhodius, V. A. et al. Design of orthogonal genetic switches based on a crosstalk map of σs, anti-σs, and promoters. Mol. Syst. Biol. 9, 702 (2013).

    Article  CAS  Google Scholar 

  65. Itaya, M., Tsuge, K., Koizumi, M. & Fujita, K. Combining two genomes in one cell: stable cloning of the Synechocystis PCC6803 genome in the Bacillus subtilis 168 genome. Proc. Natl Acad. Sci. USA 102, 15971–15976 (2005).

    Article  CAS  Google Scholar 

Download references

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.

Author information

Authors and Affiliations

  1. Synthetic and Systems Biology Unit, Institute of Biochemistry, Biological Research Centre of the Hungarian Academy of Sciences, Szeged, H-6726, Hungary

    Csaba Pál, Balázs Papp & György Pósfai

Authors
  1. Csaba Pál
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Balázs Papp
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. György Pósfai
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Csaba Pál.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Related links

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.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrg3746

This article is cited by

Search

Advanced search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing