Adaptation dynamics between copy-number and point mutations

  1. Isabella Tomanek
  2. Călin C Guet

  • Curated by eLife

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    eLife assessment

    This is an important paper that proposes a novel evolutionary mechanism by which copy-number mutations can slow down the accumulation of point mutations in populations evolving in certain environments. The authors use an evolution experiment in bacteria equipped with a clever reporter system to provide solid evidence that this mechanism indeed operates. This paper will be of broad interest to readers in evolutionary biology and related fields.

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Abstract

Together, copy-number and point mutations form the basis for most evolutionary novelty, through the process of gene duplication and divergence. While a plethora of genomic data reveals the long-term fate of diverging coding sequences and their cis -regulatory elements, little is known about the early dynamics around the duplication event itself. In microorganisms, selection for increased gene expression often drives the expansion of gene copy-number mutations, which serves as a crude adaptation, prior to divergence through refining point mutations. Using a simple synthetic genetic reporter system that can distinguish between copy-number and point mutations, we study their early and transient adaptive dynamics in real time in Escherichia coli . We find two qualitatively different routes of adaptation, depending on the level of functional improvement needed. In conditions of high gene expression demand, the two mutation types occur as a combination. However, under low gene expression demand, copy-number and point mutations are mutually exclusive; here, owing to their higher frequency, adaptation is dominated by copy-number mutations, in a process we term amplification hindrance. Ultimately, due to high reversal rates and pleiotropic cost, copy-number mutations may not only serve as a crude and transient adaptation, but also constrain sequence divergence over evolutionary time scales.

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  1. Version published to 10.7554/elife.82240 on eLife
  2. eLife

    eLife assessment

    This is an important paper that proposes a novel evolutionary mechanism by which copy-number mutations can slow down the accumulation of point mutations in populations evolving in certain environments. The authors use an evolution experiment in bacteria equipped with a clever reporter system to provide solid evidence that this mechanism indeed operates. This paper will be of broad interest to readers in evolutionary biology and related fields.

  3. eLife

    Reviewer #1 (Public Review):

    Tomanek and Guet describe the results of an evolution experiment where they allowed the bacterium E. coli to adapt to various concentrations of galactose as an additional carbon source. These conditions impose different degrees of demand for the galK enzyme, whose expression level depends on the promoter sequence and on the number of copies of the galK locus. Given that the initial promoter is random and weak, both amplifications of the locus and mutations in the promoter are expected to be adaptive. The experimental strains of E. coli were equipped with a fluorescent reporter system designed to discriminate between these two types of mutations. Furthermore, two strains, IS+ and IS-, were engineered with high and low rates of duplication around the galK locus, respectively. The main result is that at higher concentrations of galactose, where the demand for galK is high, E. coli adapts by acquiring combinations of both types of adaptive mutations, amplifications, and promoter mutations. In contrast, at low concentrations of galactose, where the demand for galK is low but not zero, E. coli appear to adapt by acquiring either an amplification or a promoter mutation but not their combinations. The observation of apparent interference between the acquisition of these two types of mutations is interesting and novel. The authors provide an intuitive explanation for it: when one mutation is sufficient to achieve the optimal expression of the gene, the mutation that is acquired first makes the other mutation obsolete, i.e., there is negative epistasis (possibly even sign epistasis) between these mutations, in the sense that the second mutation is much less adaptive (or possibly even deleterious) in the presence of the first one, in the low-demand environment. The authors discuss the possible implications of this finding for our understanding of molecular evolution and propose a new Amplification Hindrance hypothesis. This hypothesis states that, since amplifications occur at much higher rates than individual point mutations, they can slow down or even prevent sequence divergence. The amplification hindrance hypothesis stands in contrast to the Innovation-Amplification-Divergence hypothesis which is currently the default paradigm and states that amplifications generally accelerate sequence divergence.

    STRENGTHS:

    The authors designed a powerful reporter system that allows them to monitor the evolutionary dynamics of amplifications and promoter mutations. They ask an important question: how do early evolutionary dynamics of adaptation to environments with different demands for gene expression look like? The phenotypic data they present looks very interesting and shows the existence of interference between amplifications and point mutations in low-demand but not in high-demand conditions. The Amplification Hindrance hypothesis is a novel and useful intellectual contribution to the field.

    WEAKNESSES:

    In my opinion, the main weakness of the paper is that, while the interference between amplifications and point mutations in the low-demand condition clearly happens (most convincingly shown in Figure 5), its causes remain unclear. In particular, the authors claim that this interference is caused by negative epistasis, but the possibility of clonal interference without epistasis has not been decisively ruled out. The authors mention clonal interference tangentially in the Discussion, but they do not seriously address this alternative explanation. Yet, understanding the cause of this phenomenon is important because clonal interference and negative epistasis have different implications for long-term evolution.

    The authors' main hypothesis is that, in the low-demand conditions, expression-increasing point mutations in the promoter provide much lower fitness benefits (or even incur fitness costs) in strains with galK amplifications compared to the ancestral strain without amplifications. The most direct way to test this hypothesis would be to measure the fitness effects of a point mutation in genetic backgrounds with and without amplifications in conditions with low and high demand for galK. This decisive experiment has unfortunately not been done. Instead, the authors construct an indirect argument, whose essence is as follows.

    They show that, over the course of the experiment in the low-demand environment, the IS+ populations have acquired fewer point mutations than IS- populations (Figure 5). In addition, the phenotypic data in Figures 2 and 4 demonstrate that IS+ mutations in the low-demand environment contain three phenotypic classes of cells: ancestral, YFP+ and YFP+CFP+. The YFP+ clones are shown to have only one or two promoter mutations. The YFP+CFP+ cells must have duplications, and it is likely (although not quite certain, see below) that they do not have any promoter mutations. These data demonstrate quite convincingly that, whenever adaptation by duplications is possible, the rate at which point mutations segregate and accumulate declines. These data are consistent with the authors' hypothesis based on negative epistasis. However, they also seem to be consistent with the idea that amplifications and point mutations exhibit clonal interference without negative epistasis.

    It may be possible to construct an argument against this alternative hypothesis based on the comparison between different environments, but such an argument would have to take into account the fact that clonal interference depends not only on the rates of mutations (which are presumably the same in all environments) but also on their fitness effects which vary across the environment. Another possibility to argue against clonal interference might be by carrying out simulations, although this approach also seems challenging without knowing some key population genetic parameters. The most direct way to resolve this ambiguity would be to demonstrate negative epistasis as discussed above.

    Another, less critical but still important, issue mentioned above concerns the authors' claim that the YFP+CFP+ cells have only duplications but no promoter mutations (e.g., LL. 276-277). This is certainly consistent with intuition since these cells have an increased level of both YFP and CFP relative to the ancestor. However, as far as I can tell, there is no evidence to support this claim directly. My understanding is that the authors base this claim on the fact that YFP+CFP+ cells form a cluster of points on the YFP vs CFP plots that is distinct from the cluster of "mixed" cells, which are shown to have both an amplification and a promoter point mutation (Figure 3). But it is still logically possible that the YFP+CFP+ cells have an amplification and a promoter mutation other than the one found in the "mixed" cells (e.g., weaker). The most direct way to show that YFP+CFP+ cells have no promoter mutations would be to sequence a few of them. Another possibility would be to calibrate the YFP/CFP fluorescence measurements against galK copy number.

  4. eLife

    Reviewer #2 (Public Review):

    This paper by Tomanek and Guet investigates the evolutionary dynamics of the very earliest steps in the process of evolution through gene duplication and divergence. They use a cleverly designed experimental system where they can tune the benefit of mutations that cause increased expression of a gene, and where they have reporter genes that can be used to distinguish between promoter up mutations and (most) gene duplications.

    The major conclusion is that the dynamics of adaptive gene duplications and adaptive point mutations can be very different in different conditions - In "low demand" conditions, where a single mutation (duplication or snp) is enough to achieve the maximum (for that environment) fitness improvement duplications and promoter mutations acts with negative epistasis and become mutually exclusive. Contrary to previous literature that discusses evolution by duplication - divergence, duplications can thus act to prevent or slow down divergence.

    The strengths of the paper: The genetic system is simple but cleverly designed. Using a gene (galK) that made it possible to tune the benefit of increased expression (by varying the amounts of galactose in the growth medium) made it possible to make observations that others have missed.

    Possible weakness, which this paper has in common with much of the literature on evolution by duplication-divergence: Duplications are very often very unstable and are lost at rates that exceed their rate of formation. This means that in the absence of selection duplications are usually lost very quickly unless selected for, and all experiments and conclusions are based on stable conditions with a continuous selection that may not reflect a natural situation.

    The aims of the paper were achieved and the presented data support the conclusions nicely.

    This paper provides evidence that evolution by gene duplication is more complex than how it is usually described. Even if two mutations (e.g. gene duplication and promoter mutations) have additive or positive epistasis on a measurable quantity (be it enzyme kinetics, gene expression levels, or some other observable trait) the mutations could show negative (or even sign?) epistasis on the fitness of an organism. Hopefully, this paper will serve as a reminder of this even outside of the duplication-divergence field.

  5. eLife

    Reviewer #3 (Public Review):

    The goal of this study was to determine the conditions in which adaptive copy-number mutations interfere with point mutations. One of the strengths of this study is its experimental design. The authors engineered a genetic reporter system to 'easily' distinguish between the two types of mutations: copy-number and point mutations. Thus, this system allows capturing mutations that appear 'de novo' during the evolution experiment and could be broadly used to study early duplication events. This system is also powerful given that gene expression demand can be tuned, allowing determining the conditions in which the Amplification Hindrance hypothesis holds. Finally, by combining measures of single-cell fluorescence and sequencing of the promoter region, the authors give more support to their conclusions (e.g., confirming the presence/absence of mutations).

    An additional strength of this study is the use of three additional random promoter sequences. Even if the evolutionary dynamics for one of the promoters differed from the original promoter, the authors propose that this is due to the promoter mimicking a low expression demand. Thus, the use of three additional random promoter sequences strengthens their conclusion that negative epistasis between copy-number and point mutations occurs in low gene expression demand environments.

    Overall, the methods and analyses are sound, and the conclusion that gene amplification hinders the fixation of adaptive mutations is correctly supported by the data. These findings have the potential to have broad implications for our understanding of the adaptive process in bacteria given that it provides a new mechanism for rapid adaptation that does not require de novo point mutations.

  6. Version published to 10.1101/2022.08.11.503575v1 on bioRxiv