Manipulation of biological clocks teaches an important lesson

Synechococcus Elongatus in Petri dish

Evolution is a powerful force that optimises organisms to fit in their environment. But, in our attempts to understand life, biologists often stumble upon natural phenomena that leave them puzzled. According to a new study, solving one such puzzle has helped scientists understand why nature prefers to do things differently than humans would predict.

Proteins, the gears of a cell’s machinery work, are made from combinations of the same 20 building blocks called amino acids. These amino acids get stitched together by enzymes based on instructions from the organism’s DNA. A combination of three letters of the DNA sequence, called codons, instruct enzymes to use one amino acid. But because there are four types of letters (A, T, G and C) in DNA, there are 64 (4^3) ways of making up the three-letter combination of a codon. Because of this an organism has some room for error, because it can now make the same amino acid from three different codons. Consider an organism, for instance, in which the combination CCA codes for the amino acid proline. The same organism will also make proline from three more combinations, namely CCG, CCU and CCC.

It turns out, though not surprisingly, that each organism has a preference for which codon to use for a particular amino acid. Thus if an organism’s DNA carries these preferred codons, then its enzymes can read the code faster and make the protein more quickly. As organisms evolve, biologists assumed, its DNA would be altered to choose preferred codons over others by natural selection.

But that is not what nature does. In reports just published in Nature, two groups of researchers, one led by Carl Johnson at Vanderbilt University and the other by Yi Liu at the University of Texas Southwestern Medical Centre, have found two organisms that do not choose their preferred codons for making specific proteins. If the researchers forced these organism, through genetic manipulation, to use the preferred codons, they found that the mutants did far worse than their wild-types.

Dr Liu chose to work on Neurospora crassa, a fungus. Dr Johnson’s subject was Synechococcus elongatus, a photosynthetic bacteria. In both these organisms, proteins that make up the biological clock were made from codons that the organism did not prefer. “We wondered why evolution hadn’t hit upon that choice,” says Dr Johnson.

Dr Liu and Dr Johnson then rearranged the relevant bits of DNA to create a mutant versions of the two species. Surprisingly, Dr Liu and Dr Johnson got opposing results.

In Neurospora the rearranged letters led to more rapid production of the clock-running proteins, but, instead of making the biological clock more robust, it fell apart. Dr Liu noticed that this was because the faster-produced protein had the correct sequence of amino acids but its folding was not proper.

Proteins, as series of amino acids put together, are long-chain molecules. This gives them the freedom to fold in a number of ways, much like long piece of string can be folded in many ways. These folding patterns are as important for the function of the proteins as is their amino acid sequence. What Dr Liu found was not unusual. If the protein is not given enough time to get its folding tight then it does not function properly, leading to a broken biological clock.

With Synechococcus the result was the opposite. At first Dr Johnson’s experiment seemed to have worked. The mutant bacteria was producing more of the clock-running proteins and its biological cycle had become more robust (sticking closer to 24 hours than its wild variety). But strangely at at temperature of around 20° C the population of the mutant was growing much more slowly than the wild-type. At this temperature the wild-type Synechococcus had a 30-hour biological clock, whereas the mutant was being forced to a 24-hour cycle which Dr Johnson thought would help a photosynthesising bacteria.

Synechococcus’s optimal temperature for growth is about 30° C, which is perhaps what it experiences in its freshwater environment in the summer months. At that temperature the photosynthetic bacteria’s genes are expressed well enough to make its biological clock run closer to the 24-hour cycle where it works for 12 hours when the sun shines and sleeps for 12 hours when there is no sun. But at a lower temperature, which is perhaps what it experiences in the winter months, the gene expression is hampered which results in a 30-hour cycle.

“This 30-hour cycle seemed like an evolutionary adaptation at lower temperature,” says Dr Johnson. Although the reasons are not clear for the adaptation, it may be because of the reduced number of hours of sunlight that are available in winter months. Thus the mutant population with an apparently better biological clock of 24 hours was not doing as well as the wild population with its 30-hour clock. “Better understanding of this bacteria’s cycle is critical to be able to improve its efficiency in biofuels production,” says Dr Johnson.

The bigger lesson, though, is that what humans assumed would be an optimal way of doing things, turns out to be not optimal in evolutionary terms. Codon usage, it seems, is a fundamental part of gene regulation. Both Neurospora and Synechococcus chose to not use the preferred codons because that helped them adapt to their surroundings better. Natural selection works by choosing to make an organism better able to pass on its genes. If it has to do that through an inefficient way of making proteins, then so be it.

UPDATE (18 Feb; 8.53 am): It was incorrectly implied that proline has three codons. In fact, proline has four codons.


  1. Liu et al., Non-optimal codon usage affects expression, structure and function of clock protein FRQ, Nature, 2013.
  2. Johnson et al., Non-optimal codon usage is a mechanismto achieve circadian clock conditionality, Nature, 2013.