A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

  • 1.

    Weber, S., Ramirez, C. & Doerfler, W. Sign hotspot mutations in SARS-CoV-2 genomes evolve because the virus spreads and actively replicates in numerous elements of the world. Virus Res. 289, 198170 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 2.

    Sekowska, A., Wendel, S., Fischer, E. C. & Nørholm, M. H. H. Technology of mutation hotspots in ageing bacterial colonies. Sci. Rep. 6, 4–10 (2016).

    Article 
    CAS 

    Google Scholar
     

  • 3.

    Galen, S. C. et al. Contribution of a mutational scorching spot to hemoglobin adaptation in high-Altitude Andean home wrens. Proc. Natl Acad. Sci. U. S. A. 112, 13958–13963 (2015).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 4.

    Trevino, V. HotSpotAnnotations — a database for hotspot mutations and annotations in most cancers. Database 1–8 (2020) https://doi.org/10.1093/database/baaa025.

  • 5.

    Fong, S. S., Joyce, A. R. & Palsson, B. Ø. Parallel adaptive evolution cultures of Escherichia coli result in convergent progress phenotypes with totally different gene expression states. Genome Res. 1365–1372 (2005) https://doi.org/10.1101/gr.3832305.15.

  • 6.

    Ostrowski, E. A., Woods, R. J. & Lenski, R. E. The genetic foundation of parallel and divergent phenotypic responses in evolving populations of Escherichia coli. Proc. R. Soc. B Biol. Sci. 275, 277–284 (2008).

    CAS 
    Article 

    Google Scholar
     

  • 7.

    Riehle, M. M., Bennett, A. F. & Lengthy, A. D. Genetic structure of thermal adaptation in Escherichia coli. Proc. Natl Acad. Sci. USA. 98, 525–530 (2001).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 8.

    Fraebel, D. T. et al. Atmosphere determines evolutionary trajectory in a constrained phenotypic house. Elife 6, e24669 (2017).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 9.

    Bull, J. J. et al. Distinctive Convergent Evolution in a Virus. Genetics 147, 1497–1507 (1997).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 10.

    Wichman, H. A., Badgett, M. R., Scott, L. A., Boulianne, C. M. & Bull, J. J. Completely different trajectories of parallel evolution throughout viral adaptation. Science 285, 422–424 (1999).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 11.

    Herron, M. D. & Doebeli, M. Parallel Evolutionary Dynamics of Adaptive Diversification in Escherichia coli. PLoS Biol. 11, e1001490 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 12.

    Kram, Ok. E. et al. Adaptation of Escherichia coli to Lengthy-Time period Serial Passage in Complicated Medium: Proof of Parallel Evolution. mSystems 2, 1–12 (2017).

    Article 

    Google Scholar
     

  • 13.

    Notley-McRobb, L. & Ferenci, T. Adaptive mgl-regulatory mutations and genetic range evolving in glucose-limited Escherichia coli populations. Environ. Microbiol. 1, 33–43 (1999).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 14.

    Miller, C. et al. Adaptation of Enterococcus faecalis to daptomycin reveals an ordered development to resistance. Antimicrob. Brokers Chemother. 57, 5373–5383 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 15.

    Avrani, S., Bolotin, E., Katz, S. & Hershberg, R. Fast Genetic Adaptation throughout the First 4 Months of Survival below Useful resource Exhaustion. Mol. Biol. Evol. 34, 1758–1769 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 16.

    Meyer, J. R. et al. Repeatability and contingency within the evolution of a key innovation in phage lambda. Science 335, 428–432 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 17.

    Van Ditmarsch, D. et al. Convergent Evolution of Hyperswarming Results in Impaired Biofilm Formation in Pathogenic Micro organism. Cell Rep. 4, 697–708 (2013).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 18.

    Bailey, S. F., Rodrigue, N. & Kassen, R. The impact of choice setting on the likelihood of parallel evolution. Mol. Biol. Evol. 32, 1436–1448 (2015).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 19.

    Tenaillon, O. et al. The molecular range of adaptive convergence. Science 335, 457–461 (2012).

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 20.

    Eyre-Walker, A. & Hurst, L. D. The evolution of isochores. Nat. Rev. Genet. 2, 549–555 (2001).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 21.

    Wooden, T. E., Burke, J. M. & Rieseberg, L. H. Parallel genotypic adaptation: When evolution repeats itself. Genetica 123, 157–170 (2005).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 22.

    Woods, R., Schneider, D., Winkworth, C. L., Riley, M. A. & Lenski, R. E. Exams of parallel molecular evolution in a long-term experiment with Escherichia coli. Proc. Natl Acad. Sci. U. S. A. 103, 9107–9112 (2006).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 23.

    Weinreich, D. M., Delaney, N. F., De Pristo, M. A. & Hartl, D. L. Darwinian Evolution Can Comply with Solely Very Few Mutational Paths to Fitter Proteins. Science. 312, (2006).

  • 24.

    Bailey, S. F., Blanquart, F., Bataillon, T. & Kassen, R. What drives parallel evolution?: How inhabitants dimension and mutational variation contribute to repeated evolution. BioEssays 39, 1–9 (2017).

    PubMed 
    Article 

    Google Scholar
     

  • 25.

    Lengthy, H. et al. Mutation charge, spectrum, topology, and context-dependency within the DNA mismatch repair-deficient Pseudomonas fluorescens ATCC948. Genome Biol. Evol. 7, 262–271 (2014).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 26.

    Duan, C. et al. Diminished intrinsic DNA curvature results in elevated mutation charge. Genome Biol. 19, 1–12 (2018).

    Article 
    CAS 

    Google Scholar
     

  • 27.

    De Boer, J. G. & Ripley, L. S. Demonstration of the manufacturing of frameshift and base-substitution mutations by quasipalindromic DNA sequences. Proc. Nail. Acad. Sci. USA 81 (1984).

  • 28.

    Turner, C. B., Marshall, C. W. & Cooper, V. S. Parallel genetic adaptation throughout environments differing in mode of progress or useful resource availability. Evol. Lett. 2, 355–367 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 29.

    Lässig, M., Mustonen, V. & Walczak, A. M. Predicting evolution. Nat. Ecol. Evol. 1, 1–9 (2017).

    Article 

    Google Scholar
     

  • 30.

    Hermisson, J. & Pennings, P. S. Tender sweeps: Molecular inhabitants genetics of adaptation from standing genetic variation. Genetics 169, 2335–2352 (2005).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 31.

    Barrett, R. D. H., M’Gonigle, L. Ok. & Otto, S. P. The distribution of useful mutant results below robust choice. Genetics 174, 2071–2079 (2006).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 32.

    Jerison, E. R. & Desai, M. M. Genomic investigations of evolutionary dynamics and epistasis in microbial evolution experiments. Curr. Opin. Genet. Dev. 35, 33–39 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 33.

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

    ADS 
    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 34.

    Mcgee, L. W. et al. Synergistic pleiotropy overrides the prices of complexity in viral adaptation. Genetics 202, 285–295 (2016).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 35.

    McGrath, P. T. et al. Parallel evolution of domesticated Caenorhabditis species targets pheromone receptor genes. Nature 477, 321–325 (2011).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 36.

    Sackman, A. M. et al. Mutation-driven parallel evolution throughout viral adaptation. Mol. Biol. Evol. 34, 3243–3253 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 37.

    Alsohim, A. S. et al. The biosurfactant viscosin produced by Pseudomonas fluorescens SBW25 aids spreading motility and plant progress promotion. Environ. Microbiol. 16, 2267–2281 (2014).

    CAS 
    PubMed 
    Article 
    PubMed Central 

    Google Scholar
     

  • 38.

    Lind, P. A., Libby, E., Herzog, J. & Rainey, P. B. Predicting mutational routes to new adaptive phenotypes. Elife 8, e38822 (2019).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 39.

    Wright, B. E., Reschke, D. Ok., Schmidt, Ok. H., Reimers, J. M. & Knight, W. Predicting mutation frequencies in stem-loop constructions of derepressed genes: Implications for evolution. Mol. Microbiol. 48, 429–441 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 40.

    Kudla, G., Murray, A. W., Tollervey, D. & Plotkin, J. B. Coding-sequence determinants of gene expression in Escherichia coli. Science 324, 255–258 (2009).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 41.

    Kristofich, J. et al. Synonymous mutations make dramatic contributions to health when progress is restricted by a weak-link enzyme. PLOS Genet. 14, e1007615 (2018).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • 42.

    Lebeuf-Taylor, E., McCloskey, N., Bailey, S. F., Hinz, A. & Kassen, R. The distribution of health results amongst synonymous mutations in a gene below choice. Elife e45952 (2019) https://doi.org/10.1101/553610.

  • 43.

    Frumkin, I. et al. Codon utilization of extremely expressed genes impacts proteome-wide translation effectivity. Proc. Natl Acad. Sci. U. S. A. 115, E4940–E4949 (2018).

    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 44.

    Fieldhouse, D. & Golding, B. A supply of small repeats in genomic DNA. Genetics 129, 563–572 (1991).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 45.

    Dong, F., Allawi, H. T., Anderson, T., Neri, B. P. & Lyamichev, V. I. Secondary construction prediction and structure-specific sequence evaluation of single-stranded DNA. Nucleic Acids Res. 29, 3248–3257 (2001).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 46.

    Merrikh, C. N. & Merrikh, H. Gene inversion potentiates bacterial evolvability and virulence. Nat. Commun. 9, 10 (2018).

    Article 
    CAS 

    Google Scholar
     

  • 47.

    Vogwill, T., Kojadinovic, M., Furió, V. & Maclean, R. C. Testing the function of genetic background in parallel evolution utilizing the comparative experimental evolution of antibiotic resistance. Mol. Biol. Evol. 31, 3314–3323 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 48.

    Blount, Z. D., Barrick, J. E., Davidson, C. J. & Lenski, R. E. Genomic evaluation of a key innovation in an experimental Escherichia coli inhabitants. Nature 489, 513–518 (2012).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 49.

    Spor, A. et al. Phenotypic and genotypic convergences are influenced by historic contingency and setting in yeast. Evolution (N. Y). 68, 772–790 (2014).


    Google Scholar
     

  • 50.

    Orr, H. A. The likelihood of parallel evolution. Evolution (N. Y). 59, 216 (2005).

    CAS 

    Google Scholar
     

  • 51.

    Zagorski, M., Burda, Z. & Waclaw, B. Past the hypercube: evolutionary accessibility of health landscapes with lifelike mutational networks. PLoS Comput. Biol. 12, 1–18 (2016).

    Article 
    CAS 

    Google Scholar
     

  • 52.

    Gillespie, J. H. Molecular evolution over the mutational panorama. Evolution (N. Y). 38, 1116 (1984).

    CAS 

    Google Scholar
     

  • 53.

    Bailey, S. F., Guo, Q. & Bataillon, T. Figuring out drivers of parallel evolution: A regression mannequin method. Genome Biol. Evol. 10, 2801–2812 (2018).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 54.

    Kimura, M. Evolutionary charge on the molecular stage. Nature 217, 624–626 (1968).

    ADS 
    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • 55.

    Lind, P. A., Farr, A. D. & Rainey, P. B. Experimental evolution reveals hidden range in evolutionary pathways. Elife 4, e07074 (2015).

  • 56.

    McDonald, M. J., Gehrig, S. M., Meintjes, P. L., Zhang, X. X. & Rainey, P. B. Adaptive divergence in experimental populations of Pseudomonas fluorescens. IV. Genetic constraints information evolutionary trajectories in a parallel adaptive radiation. Genetics 183, 1041–1053 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 57.

    Lind, P. A. & Andersson, D. I. Entire-genome mutational biases in micro organism. Proc. Natl Acad. Sci. U. S. A. 105, 17878–17883 (2008).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 58.

    Stoltzfus, A. & McCandlish, D. M. Mutational biases affect parallel adaptation. Mol. Biol. Evol. 34, 2163–2172 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 59.

    Robleto, E. A., López-Hernández, I., Silby, M. W. & Levy, S. B. Genetic evaluation of the AdnA regulon in Pseudomonas fluorescens: nonessential function of flagella in adhesion to sand and biofilm formation. J. Bacteriol. 185, 453–460 (2003).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 60.

    Seaton, S. C., Silby, M. W. & Levy, S. B. Pleiotropic results of gaca on pseudomonas fluorescens pf0-1 in vitro and in soil. Appl. Environ. Microbiol. 79, 5405–5410 (2013).

    ADS 
    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 61.

    Seemann, T. Snippy: quick bacterial variant calling from NGS reads. (2015).

  • 62.

    Connor, T. R. et al. CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an internet useful resource for the medical microbiology group. Microb. Genomics 2, 6 (2016).

    Article 

    Google Scholar
     

  • 63.

    Bryksin, A. V. & Matsumura, I. Overlap extension PCR cloning: a easy and dependable technique to create recombinant plasmids. Biotechniques 48, 463–465 (2010).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 64.

    Hmelo, L. R. et al. Precision-engineering the Pseudomonas aeruginosa genome with two-step allelic change. Nat. Protoc. 10, 1820–1841 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • 65.

    R Core Crew. R: A language and setting for statistical computing. R Basis for Statistical Computing, Vienna, Austria http://www.r-project.org/. (2014).

  • 66.

    Wickham, H. ggplot2: Elegant graphics for knowledge evaluation. ISBN 978-3-319-24277-4 (2016).

  • 67.

    Ogle, D. H., Wheeler, P. & Dinno, A. FSA: Fisheries Inventory Evaluation. (2020).

  • 68.

    Horton, J. S., Flanagan, L. M., Jackson, R. W., Priest, N. Ok. & Taylor, T. B. A mutational hotspot that determines extremely repeatable evolution will be constructed and damaged by silent genetic adjustments. Syn-sequence-parallel-evolution. Open Sci. Framew. (2021) https://doi.org/10.17605/OSF.IO/VUYWP.

  • 69.

    Horton, J. S., Flanagan, L. M., Jackson, R. W., Priest, N. Ok. & Taylor, T. B. A mutational hotspot that determines extremely repeatable evolution will be constructed and damaged by silent genetic adjustments. GitHub (2021) https://doi.org/10.5281/zenodo.5109984.

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