Rives, N., Lamba, V., Cheng, C. C., & Zhuang, X. (2024). Diverse origins of near-identical antifreeze proteins in unrelated fish lineages provide insights into evolutionary mechanisms of new gene birth and protein sequence convergence. Molecular Biology and Evolution, 41(9), msae182.
Freezing fish
Temperatures in the frigid polar oceans can reach below zero because the salt in seawater lowers the freezing point (to about -2 °C or 28 °F). This raises a major question: how come fish don’t freeze? The answer lies with special molecular adaptation: antifreeze proteins.
Antifreeze proteins work by attaching to microscopic ice crystals in the body, preventing the crystals from growing. Many different groups of fish have evolved antifreeze proteins independently, making them an example of “convergent evolution.” Convergent evolution means that the same trait evolves more than once in different, unrelated groups of organisms—for example, the wings of birds, insects, and bats. Convergent traits are useful to evolutionary biologists because we can see, repeatedly, how evolution makes new traits.
Fish antifreeze proteins are a great system to study the origins of new genes because they have evolved convergently many times and have a clearly-defined molecular function. In this study, scientists investigate an antifreeze protein, AFP1, in three lineages of polar fish; flounder, sculpin, and cunner. By looking closely at the fishes’ genomes, they determine the origins of the AFP1 gene in each species, and describe how different genomes evolved to produce similar protein sequences.
Where do new genes come from?
In order for an organism to adapt to its environment, it needs genetic material that can acquire new, adaptive functions. Organisms can acquire new genes in many different ways, including modifications and duplications of existing genes. The duplicated gene is free to evolve new functions, while the old gene can keep performing its original function. Genes can also sometimes arise completely “de novo”, or anew, from other parts of the genome. However, we still don’t fully understand the mechanisms because the evolution of new genes.
A primer on evolution
Gene evolution is a little bit complicated, and there are a few concepts that we need to discuss in order to understand how it works. First, DNA can either be “coding” or “non-coding.” Coding DNA is the part of the genome that makes proteins-–the sequence of DNA encodes the structure of the protein, and the proteins go on to perform biological functions. Non-coding DNA, on the other hand, can do all sorts of other things, including regulating where, when, and how protein-coding genes are expressed. Non-coding DNA is kind of like the spaces and punctuation marks that help us read paragraphs, while the coding DNA is just the letters themselves.
A gene is a chunk of DNA that makes one protein, and it needs two parts in order to work: the protein-coding part, and the regulatory, non-coding part.
The other concepts we need to understand are natural selection and mutation. Mutations arise all the time, randomly, whenever an organism reproduces. Very rarely, mutations can be advantageous, but most of the time they are harmful or simply neutral. Natural selection removes harmful mutations, which is why genes maintain their sequences over long periods of time. If you had no selection, random mutations would accumulate and the gene would eventually decay. In other words, genes are maintained over time by natural selection as long as they provide an advantage for the organism to survive and reproduce.
Now, back to the fish!
The three fish have AFP1 genes are nearly identical in sequence, because they perform the same function. However, they arose independently. How did three genes independently acquire almost the same protein sequence?
To learn more about the origins of AFP1 genes, the researchers examined the parts of the genome that gave rise to each gene and reconstructed their evolutionary histories. They found that the genes arose from different precursor genes that each performed different functions in the three species. These genes had all duplicated and decayed, and were then re-purposed into the new antifreeze proteins. Importantly, the protein-coding parts of the genes were totally changed, but the non-coding regulatory parts of the genes were intact.
Putting this all together, the scientists outline the following steps to producing a new antifreeze protein.
You start with an original gene performing some other function. First, that gene duplicates due to a mutation. After a gene duplicates, the second copy is redundant—the organism doesn’t need two copies of the gene, so the second copy is free to accumulate random mutations and begins to degenerate. Critically, because the non-coding regulatory DNA is still around, the degenerating gene is still active. Then, the degenerated gene copy, by chance, gives the fish a survival advantage in cold temperatures because its structure has ice-binding abilities. Finally, selection acts to improve and maintain that new function.
Animals have many exquisite adaptations to their environment, and this research shows how studying those adaptations can help us learn about fundamental biological questions! In this case, we gained a clearer picture of how new genes arise out of the fragments of old genes.
I am a PhD student at MIT and the Woods Hole Oceanographic Institution, where I study the evolution and physiology of marine invertebrates. I usually work with zooplankton and sea anemones, and I am especially interested in circadian rhythms of these animals. Outside work, I love to play trumpet, listen to music, and watch hockey.
