Mutations that are considered harmless are found to cause problems

Enlarge / The genetic code. Note that many of the amino acids (the outer layer in gray) are encoded by several sets of three-base codes that divide the first two letters.

Mutations are the raw ingredient in evolution, and provide variation that sometimes makes an organism more successful in the environment. However, most mutations are expected to be neutral and have no effect on the condition of an organism. These can be incredibly useful since these random changes help us track evolutionary conditions without worrying about selection for or against the mutation that affects the frequency. All of the genetic lineage tests, for example, are highly dependent on detecting the presence of these neutral mutations.

But this week, a paper provided evidence that a significant category of mutations are not as neutral as we thought they were. The big caveat is that the study was done in yeast, which is a strange organism in a couple of ways, so we have to see if the results hold in others.

Really neutral?

One of the reasons why most mutations are neutral is that most of our DNA does not seem to do any good. Only a few percent of the human genome is composed of the part of genes that encode proteins, and only some of the nearby DNA is involved in controlling the activity of these genes. Outside these areas, mutations do not do much, either because the DNA there has no function or because the function is not very sensitive to having a precise sequence of bases in the DNA.

But even within the parts of genes that encode proteins, the exact sequence should not be so important. Each protein’s amino acid is encoded by a combination of three bases in DNA. This means that there are 64 possible codes for amino acids – but we only use 20 different amino acids. As a result, there is plenty of redundancy in the genetic code. For example, the base series ACG encodes the amino acid threonine. So does the ACA series. And ACC. All in all, four different codes will give you threonine.

The most important thing to note is that all four codes start with AC. If you have a mutation in one of these two bases, you will no longer receive threonine. But if you get a mutation in the third position, it does not matter – no matter what you change the base to, you still get threonine. It should be a completely neutral mutation. And researchers have used the assumption that it is neutral to help them track protein development.

This is the assumption that the new paper put to the test.

Do all the mutations

To test neutral mutations, the researchers started with a panel of 21 yeast genes, selected in part because they are involved in a wide range of cellular activities. The other part behind their choice is that eliminating these genes does not kill the yeast, but makes it less healthy. This should make it easier to detect partial effects, where the mutation makes the yeast less healthy.

Within this stretch, the researchers selected a stretch of 150 bases in the DNA and made every possible mutation using DNA editing to create a yeast strain that carries the mutation. There are a total of over 9000 individual yeast strains, with some bearing mutations that will change the amino acid sequence and others bearing mutations we expect to be neutral. But of course this involved laboratory work, where things do not work for random, unknown reasons, so the researchers had to content themselves with testing around 8,300 mutant yeast strains.

The test was quite simple. Throw as many normal and mutant yeasts in a flask and let them grow a little. Then test the population and check the relative levels of normal and mutant yeast. If the mutation lowered the condition, you would see more normal yeast when you sampled the flask.

This was true for mutations that altered an amino acid. These saw that their relative condition decreased slightly, but not much (their condition was 0.988 as for normal yeast). However, the neutral mutations were not very different – they also reduced the condition of the yeast by a small amount compared to a normal load. In fact, the mutations that did not alter any amino acids were, on average, indistinguishable from those that did. Beyond this average, you may notice a slight difference. There were several amino acid-altering mutations that had a stronger detrimental effect on fitness, and more neutral ones that had minimal effect. But it is clear that the class as a whole expected to be neutral was not.