How much do small changes actually matter?

Many, many small things in the world add up to big things. I’m sure you’ve heard of some of these:

  • Acts of kindness
  • Pieces of plastic
  • Mutations in bacteria

Wait what?? One of these isn’t like the others…

A brief run-down on bacteria: single-celled organisms that are found everywhere (even on you!). They have a singular chromosome, and occasionally a plasmid – which holds genetic information. On the chromosome is genes – things that code for proteins, and small changes (mutations) in these genes can have drastic effects. Overall, things on this chromosome is termed the genome.

Long term evolution experiments (LTEE) are commonly used to study evolution. Researchers sample parallel populations across thousands of generations, hence bacteria such as Escherichia Coli are often used [2, 3]. Organisms need to adapt to their environment to survive, which allows for divergence of populations, even if they remain in an unchanging environment. These genetic differences then may lead to further adaption [2]. Changes in the genome are believed to cause evolution, but mutations are not always positive for the individual. It is also thought that neutral mutations (ones that are neither beneficial nor harmful) would accumulate at a constant rate [3].

These papers investigated the OVERALL impact of beneficial mutations in E. Coli. Many studies have been done on the how fitness improves over time, but less work has focused on specific genes and how the genetic background of mutations affects gene fitness. Comparatively, Peng et al. looked at a specific gene (pyfK) and the effect of moving the gene into different genetic backgrounds (i.e. other populations of the same bacteria!). Genetic background is simple – just looking at the mutations which came before the one that gave a fitness boost. These mutations may rely on previous sequence changes to work.

Focusing on a specific gene allowed these researchers to directly measure the impact of certain mutations. This was important because it meant we could see how mutation effects change in different backgrounds. It also proves that mutations are not isolated events that randomly improve fitness. Instead, although mutations can have major beneficial effects, this may differ when placed into a new genetic background. They found that the evolved mutations had variable effects in their own background (neutral to +25%) however it varied when placed into the ancestral background [1].

[1] – Peng et al. 2018. Placing two mutations into new strains has differing effects on fitness.

You can see in the picture above (Fig4) that mutation alleles have varying effects when placed into a variety of different genetic backgrounds. The authors chose to take the ‘A301S point mutation’ or ‘deletion mutation’ allele and place in into new strains. This meant that they could compare the evolved alleles, the indel allele and the A301S allele and their effect on fitness.

As a broad generalization, the deletion had the greatest effect on fitness, and the point mutation was less beneficial than the original allele. The A301S point mutation was chosen to be transferred into other strains as it evolved independently in three strains of E. Coli. The deletion mutation was used as a proxy for the insertion mutation which arose [1]. Fitness effects were shown to be affected mainly by the genetic background, rather than the specific mutations being hugely beneficial.

The authors preformed a similar experiment, where they took all the evolved alleles and put them into the ancestor strains, measuring the difference in fitness. This shows a rise in RELATIVE fitness over the first 10-15,000 generations, which begins to drop off after 20,000 generations [1]. From six different populations where mutations had arisen, the pykF allele was taken and reverted to the ancestral gene. Hence the effect of the mutation within pykF could be measured. The evolved allele was placed into the ancestor and fitness effects were measured (Fig5 – below). Whilst pyfK mutations occurred early in the LTEE, the genetic background was less well understood, and so it is hard to understand the relationship between mutations in pyfK and fitness effects of other mutations. However, an understanding of the trend between pyfK and fitness can be inferred [1].

[1] – Peng et al. 2018. How mutations within pyfK can change fitness over time.

Fitness was measured by undertaking competitive fitness assays for both figures. These head to head competitions had relative fitness calculated by growth rate within the environment [1]. Therefore, the fitness effect of the mutation was calculated by “relative fitness minus one”.

Small changes within the genome can influence genes, even if these changes are not in a gene. How well bacteria survive in an unchanging environment is affected by mutations. Evolution is a complex process, with many factors at play, and long-term evolution experiments in bacteria are simply one way to help unravel the mystery of how small changes can have large effects – just like you can. Be kind, be happy and always be open to change.

1.            Peng, F., et al., Effects of Beneficial Mutations in pykF Gene Vary over Time and across Replicate Populations in a Long-Term Experiment with Bacteria. Mol Biol Evol, 2018. 35(1): p. 202-210.

2.            Richard E. Lenski, et al., Long-Term Experimental Evolution in Escherichia coli. I. Adaptation and Divergence During 2,000 Generations. The American Naturalist, 1991. 138(6): p. 1315-1341.

3.            Barrick, J.E., et al., Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature, 2009. 461(7268): p. 1243-7.

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7 Responses to How much do small changes actually matter?

  1. jcturnbullnz says:

    Thank you, a nice summary of this paper and some cool ideas! With regard to putting the evolved alleles into ancestral strains, did the authors have any thoughts on why there was a drop in relative fitness after 20,000 generations?

    • aearnshaw9 says:

      Hi Jo,

      Not sure why it was only after 20,000 generations, but I got the impression that around that time, other genes had mutations which increased the overall fitness of the organism, therefore causing a drop in relative fitness of the pykF gene. Hope that helps!

      Alyssa

      • lshewson says:

        It would be interesting to see further experiments performed looking at that 20000 generation mark. It would make sense that at that point, the effects would plateau due to an increase in fitness through other means

  2. msbdavies says:

    Hi Alyssa

    I really love that you made sure to highlight “relative fitness”, a great point to clarify! I also thought the little note in the end tied back into your introduction nicely and was in general a very sweet addition.

  3. annabehlingnz says:

    Nice post, Alyssa!
    It would be neat to see a direct comparison of an analogous experimental evolution experiment in prokaryotes and eukaryotes.
    Suppose even though we are eukaryotes, our ancestor 4 billion years ago would have been single-celled so these E. coli experiments can give us insights to our past in that way too.

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