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Gene amplification as a form of population-level gene expression regulation

Nature Ecology & Evolution volume 4, pages 612–625 (2020)Cite this article

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Abstract

Organisms cope with change by taking advantage of transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. Here, we investigate whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. Using real-time monitoring of gene-copy-number mutations in Escherichia coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy-number and, therefore, expression-level polymorphisms. This amplification-mediated gene expression tuning (AMGET) occurs on timescales that are similar to canonical gene regulation and can respond to rapid environmental changes. Mathematical modelling shows that amplifications also tune gene expression in stochastic environments in which transcription-factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune the expression of any gene, without leaving any genomic signature.

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Fig. 1: An experimental system for monitoring gene copy number under fluctuating selection in real time.
Fig. 2: AMGET occurs in fluctuating environments.
Fig. 3: High-frequency deletion and duplication events in the amplified locus create gene-copy-number polymorphisms in populations.
Fig. 4: AMGET requires continual generation of gene-copy-number polymorphisms.
Fig. 5: AMGET is a robust strategy for tuning population-level gene expression across a range of environments.

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Data availability

Experimental data that support the findings of this study have been deposited in IST DataRep and are publicly available at https://doi.org/10.15479/AT:ISTA:7016.

Code availability

The scripts for our mathematical model and for the analysis of microfluidics time traces have been deposited in IST DataRep and are publicly available at https://research-explorer.app.ist.ac.at/record/7383.

References

  1. Moxon, E. R., Rainey, P. B., Nowak, M. A. & Lenski, R. E. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 4, 24–33 (1994).

    Article  CAS  PubMed  Google Scholar 

  2. Savageau, M. A. Genetic regulatory mechanisms and the ecological niche of Escherichia coli. Proc. Natl Acad. Sci. USA. 71, 2453–2455 (1974).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Gerland, U. & Hwa, T. Evolutionary selection between alternative modes of gene regulation. Proc. Natl Acad. Sci. USA 106, 8841–8846 (2009).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Tuğrul, M., Paixão, T., Barton, N. H. & Tkačik, G. Dynamics of transcription factor binding site evolution. PLoS Genet. 11, e1005639 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Berg, J., Willmann, S. & Lässig, M. Adaptive evolution of transcription factor binding sites. BMC Evol. Biol. 4, 42 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Anderson, P. & Roth, J. Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons. Proc. Natl Acad. Sci. USA 78, 3113–3117 (1981).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Reams, A. B., Kofoid, E., Savageau, M. & Roth, J. R. Duplication frequency in a population of Salmonella enterica rapidly approaches steady state with or without recombination. Genetics 184, 1077–1094 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Pettersson, M. E., Sun, S., Andersson, D. I. & Berg, O. G. Evolution of new gene functions: simulation and analysis of the amplification model. Genetica 135, 309–324 (2009).

    Article  CAS  PubMed  Google Scholar 

  9. Sun, S., Ke, R., Hughes, D., Nilsson, M. & Andersson, D. I. Genome-wide detection of spontaneous chromosomal rearrangements in bacteria. PLoS ONE 7, e42639 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Roth, J. R. et al. in Escherichia coli and Salmonella: Cellular and Molecular Biology (ed. Neidhardt, F. C.) 2256–2276 (American Society for Microbiology, 1996).

  11. Nicoloff, H., Hjort, K., Levin, B. R. & Andersson, D. I. The high prevalence of antibiotic heteroresistance in pathogenic bacteria is mainly caused by gene amplification. Nat. Microbiol. 4, 504–514 (2019).

    Article  CAS  PubMed  Google Scholar 

  12. Bass, C. & Field, L. M. Gene amplification and insecticide resistance. Pest Manag. Sci. 67, 886–890 (2011).

    Article  CAS  PubMed  Google Scholar 

  13. Albertson, D. G. Gene amplification in cancer. Trends Genet. 22, 447–455 (2006).

    Article  CAS  PubMed  Google Scholar 

  14. Andersson, D. I. & Hughes, D. Gene amplification and adaptive evolution in bacteria. Annu. Rev. Genet. 43, 167–195 (2009).

    Article  CAS  PubMed  Google Scholar 

  15. Hjort, K., Nicoloff, H. & Andersson, D. I. Unstable tandem gene amplification generates heteroresistance (variation in resistance within a population) to colistin in Salmonella enterica. Mol. Microbiol. 102, 274–289 (2016).

    Article  CAS  PubMed  Google Scholar 

  16. Näsvall, J., Sun, L., Roth, J. R. & Andersson, D. I. Real-time evolution of new genes by innovation, amplification, and divergence. Science 338, 384–387 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Elde, N. C. et al. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 150, 831–841 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Kussell, E. & Laibler. Phenotypic diversity, population growth, and information in fluctuating environments. Science 309, 2075–2078 (2005).

    Article  CAS  PubMed  Google Scholar 

  19. Veening, J.-W., Smits, W. K. & Kuipers, O. P. Bistability, epigenetics, and bet-hedging in bacteria. Annu. Rev. Microbiol. 62, 193–210 (2008).

    Article  CAS  PubMed  Google Scholar 

  20. Barkan, D., Stallings, C. L. & Glickman, M. S. An improved counterselectable marker system for mycobacterial recombination using galK and 2-deoxy-galactose. Gene 470, 31–36 (2011).

    Article  CAS  PubMed  Google Scholar 

  21. Steinrueck, M. & Guet, C. C. Complex chromosomal neighborhood effects determine the adaptive potential of a gene under selection. eLife 6, e25100 (2017).

    Article  PubMed  PubMed Central  Google Scholar 

  22. Bergmiller, T. et al. Biased partitioning of the multidrug efflux pump AcrAB-TolC underlies long-lived phenotypic heterogeneity. Science 356, 311–315 (2017).

    Article  CAS  PubMed  Google Scholar 

  23. Wang, P. et al. Robust growth of Escherichia coli. Curr. Biol. 20, 1099–1103 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Reams, A. B. & Roth, J. R. Mechanisms of gene duplication and amplification. Cold Spring Harb. Perspect. Biol. 7, a016592 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Tawfik, D. S. Messy biology and the origins of evolutionary innovations. Nat. Chem. Biol. 6, 692–696 (2010).

    Article  CAS  PubMed  Google Scholar 

  26. Jacob, F. Evolution and tinkering. Science 196, 4295 (1977).

    Article  Google Scholar 

  27. Troein, C., Ahrén, D., Krogh, M. & Peterson, C. Is transcriptional regulation of metabolic pathways an optimal strategy for fitness? PLoS ONE 2, e855 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Wolf, L., Silander, O. K. & van Nimwegen, E. Expression noise facilitates the evolution of gene regulation. eLife 4, e05856 (2015).

    Article  PubMed Central  Google Scholar 

  29. Anderson, R. P. & Roth, J. R. Tandem genetic duplications in phage and bacteria. Annu. Rev. Microbiol. 31, 473–505 (1977).

    Article  CAS  PubMed  Google Scholar 

  30. Taylor, T. B. et al. Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system. Science 347, 1014–1017 (2015).

    Article  CAS  PubMed  Google Scholar 

  31. Rodriguez-Beltran, J. et al. Multicopy plasmids allow bacteria to escape from fitness trade-offs during evolutionary innovation. Nat. Ecol. Evol. 2, 873–881 (2018).

    Article  PubMed  PubMed Central  Google Scholar 

  32. Perry, G. H. et al. Diet and the evolution of human amylase gene copy number variation. Nat. Genet. 39, 1256–1260 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  33. Gil, R., Sabater-Muñoz, B., Perez-Brocal, V., Silva, F. J. & Latorre, A. Plasmids in the aphid endosymbiont Buchnera aphidicola with the smallest genomes. A puzzling evolutionary story. Gene 370, 17–25 (2006).

    Article  CAS  PubMed  Google Scholar 

  34. Latorre, A., Gil, R., Silva, F. J. & Moya, A. Chromosomal stasis versus plasmid plasticity in aphid endosymbiont Buchnera aphidicola. Heredity 95, 339–347 (2005).

    Article  CAS  PubMed  Google Scholar 

  35. Lercher, M. J. & Pál, C. Integration of horizontally transferred genes into regulatory interaction networks takes many million years. Mol. Biol. Evol. 25, 559–567 (2008).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  37. Dobrindt, U., Hochhut, B., Hentschel, U. & Hacker, J. Genomic islands in pathogenic and environmental microorganisms. Nat. Rev. Microbiol. 2, 414–424 (2004).

    Article  CAS  PubMed  Google Scholar 

  38. Juhas, M. et al. Genomic islands: tools of bacterial horizontal gene transfer and evolution. FEMS Microbiol. Rev. 33, 376–393 (2009).

    Article  CAS  PubMed  Google Scholar 

  39. Pettersson, M. E., Andersson, D. I., Roth, J. R. & Berg, O. G. The amplification model for adaptive mutation. Genetics 169, 1105–1115 (2005).

    Article  PubMed  PubMed Central  Google Scholar 

  40. Gusev, O. et al. Comparative genome sequencing reveals genomic signature of extreme desiccation tolerance in the anhydrobiotic midge. Nat. Commun. 5, 4784 (2014).

    Article  CAS  PubMed  Google Scholar 

  41. Hooper, S. D. & Berg, O. G. Duplication is more common among laterally transferred genes than among indigenous genes. Genome Biol. 4, R48 (2003).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Eme, L., Gentekaki, E., Curtis, B., Archibald, J. M. & Roger, A. J. Lateral gene transfer in the adaptation of the anaerobic parasite blastocystis to the gut. Curr. Biol. 27, 807–820 (2017).

    Article  CAS  PubMed  Google Scholar 

  43. Nguyen, T. N., Phan, Q. G., Duong, L. P., Bertrand, K. P. & Lenski, R. E. Effects of carriage and expression of the Tn10 tetracycline-resistance operon on the fitness of Escherichia coli K12. Mol. Biol. Evol. 6, 213–225 (1989).

    CAS  PubMed  Google Scholar 

  44. Gladman, S. L. et al. Large tandem chromosome expansions facilitate niche adaptation during persistent infection with drug-resistant Staphylococcus aureus. Microb. Genomics 1, e000026 (2015).

    Google Scholar 

  45. Elliott, K. T., Cuff, L. E. & Neidle, E. L. Copy number change: evolving views on gene amplification. Future Microbiol. 8, 887–899 (2013).

    Article  CAS  PubMed  Google Scholar 

  46. Eydallin, G., Ryall, B., Maharjan, R. & Ferenci, T. The nature of laboratory domestication changes in freshly isolated Escherichia coli strains. Environ. Microbiol. 16, 813–828 (2014).

    Article  CAS  PubMed  Google Scholar 

  47. Greenblum, S., Carr, R. & Borenstein, E. Extensive strain-level copy-number variation across human gut microbiome species. Cell 160, 583–594 (2015).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Dhar, R., Bergmiller, T. & Wagner, A. Increased gene dosage plays a predominant role in the initial stages of evolution of duplicate TEM-1 beta lactamase genes. Evolution 68, 1775–1791 (2014).

    Article  CAS  PubMed  Google Scholar 

  49. Datta, S., Costantino, N. & Court, D. L. A set of recombineering plasmids for gram-negative bacteria. Gene 379, 109–115 (2006).

    Article  CAS  PubMed  Google Scholar 

  50. Datsenko, K. A. & Wanner, B. L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc. Natl Acad. Sci. USA 97, 6640–6645 (2000).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  51. Khlebnikov, A., Datsenko, K. A., Skaug, T., Wanner, B. L. & Keasling, J. D. Homogeneous expression of the PBAD promoter in Escherichia coli by constitutive expression of the low-affinity high-capacity AraE transporter. Microbiology 147, 3241–3247 (2001).

    Article  CAS  PubMed  Google Scholar 

  52. Baba, T. et al. Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2, 2006.0008 (2006).

  53. Nagelkerke, F. & Postma, P. W. 2-Deoxygalactose, a specific substrate of the Salmonella typhimurium galactose permease: its use for the isolation of galP mutants. J. Bacteriol. 133, 607–613 (1978).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Zhou, L. et al. Chromosome engineering of Escherichia coli for constitutive production of salvianic acid A. Microb. Cell Fact. 16, 84 (2017).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  55. Lutz, R. & Bujard, H. Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I1-I2 regulatory elements. Nucleic Acids Res. 25, 1203–1210 (1997).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Guzman, L. M., Belin, D., Carson, M. J. & Beckwith, J. Tight regulation, modulation, and high-level expression by vectors containing the arabinose PBAD promoter. J. Bacteriol. 177, 4121–4130 (1995).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Chait, R., Shrestha, S., Shah, A. K., Michel, J. B. & Kishony, R. A differential drug screen for compounds that select against antibiotic resistance. PLoS ONE 5, e15179 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. Pfaffl, M. W. A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res. 29, 45e (2001).

    Article  Google Scholar 

  59. Drake, J. W. A constant rate of spontaneous mutation in DNA-based microbes. Proc. Natl Acad. Sci. USA 88, 7160–7164 (1991).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  60. Elez, M. et al. Seeing mutations in living cells. Curr. Biol. 20, 1432–1437 (2010).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  61. Bayliss, C. D. Determinants of phase variation rate and the fitness implications of differing rates for bacterial pathogens and commensals. FEMS Microbiol. Rev. 33, 504–520 (2009).

    Article  CAS  PubMed  Google Scholar 

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Acknowledgements

We thank L. Hurst, N. Barton, M. Pleska, M. Steinrück, B. Kavcic and A. Staron for input on the manuscript, and To. Bergmiller and R. Chait for help with microfluidics experiments. I.T. is a recipient the OMV fellowship. R.G. is a recipient of a DOC (Doctoral Fellowship Programme of the Austrian Academy of Sciences) Fellowship of the Austrian Academy of Sciences.

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Author notes

  1. These authors contributed equally: I. Tomanek, R. Grah.

Authors and Affiliations

  1. Institute of Science and Technology Austria, Klosterneuburg, Austria

    I. Tomanek, R. Grah, M. Lagator, A. M. C. Andersson, G. Tkačik & C. C. Guet

  2. School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK

    M. Lagator

  3. Institute of Integrative Biology, Functional and Comparative Genomics, University of Liverpool, Liverpool, UK

    J. P. Bollback

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Contributions

C.C.G., R.G., M.L., G.T. and I.T. conceived the study. I.T. performed experiments. A.M.C.A., R.G. and I.T. analysed data. R.G. and G.T. performed the formal analysis. R.G. and I.T. wrote the original draft and revised with A.M.C.A., J.P.B., C.C.G., M.L. and G.T.

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Correspondence to C. C. Guet.

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Supplementary Information

Supplementary note, Figs. 1–7, Tables 2, 4 and 5, and references.

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Supplementary Tables

Supplementary Table 1: verification of amplification events by detailed analysis of time-lapse microscopy images. Supplementary Table 3: a list of oligonucleotides.

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Tomanek, I., Grah, R., Lagator, M. et al. Gene amplification as a form of population-level gene expression regulation. Nat Ecol Evol 4, 612–625 (2020). https://doi.org/10.1038/s41559-020-1132-7

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