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Plants and humans are more similar than you think

You probably wouldn’t conclude that plants and humans are related just from looking at them. After all, we’re not green and we can’t use light to produce sugars. But if you look beyond the leaf and go deep into a plant’s genome, you’ll see some striking similarities.
Believe it or not, plants and animals share many of the same genes—but we use some of them in different ways. For a good example of this, you need only look to the Eyes Absent (EYA) genes. These genes help flies build eyes, aid in human development, and contribute to plant embryogenesis.
Like many genes, EYA was first described in fruit flies. Geneticists found that loss of the gene caused flies to develop without any eyes, hence the “Eyes Absent” name. Since that time, there have been numerous versions of EYA described. Humans have four different versions, flies have just one, and plants have their own distinct version as well. Though the DNA coding for each of these versions is different, they’re similar enough that they’ve been collectively labeled as the EYA genes1.

Gene families

If the DNA sequence differs between species, why do we call them all EYA genes? The answer has to do more with their similarities than their differences.
The DNA sequence is similar enough that scientists can trace them all back to a single ancient gene. Because each of these genes are derived from a single ancestor, they’re all considered members of the same family.1,2

The EYA genes produce proteins by the same name (a common convention in biology). Typically when we think of proteins, we think of them as serving one function—like how a hammer is used to hammer nails, but not to tighten bolts. EYA proteins are not like this. Instead, they’re like the Swiss Army Knife of proteins because they’re capable of doing some dramatically different processes within a cell. Their most well-known activity is to help regulate gene expression—the reading of a gene. In fact, EYA proteins help direct the formation of eyes in flies by regulating when and where important eye-forming genes are used. This is why variants in the DNA that prevent formation of EYA proteins results in loss of a fly’s eyes. Because of their ability to regulate gene expression, EYA proteins are considered transcriptional cofactors (similar to transcription factors). The “co-” points to the fact that the EYA proteins have to get help from other proteins in order to regulate gene expression1.
The function of EYA genes in regulating gene expression appears to be a relatively new ability. In plants, EYA is missing an important part of the protein which prevents it from acting as a transcriptional cofactor. Instead, its main function is to regulate the action of other proteins1.

To understand this concept, it helps to view proteins as small robots whose activity is controlled by an on-off switch. By flipping that switch, cells can control when a protein is functioning and when it’s not. In reality, it’s far more complex than this because there are many different kinds of switches and dials that control a protein’s function (and some proteins don’t have a switch at all). By altering these switches and dials, cells can control the processes that are happening inside them. Specialized proteins are built by a cell whose sole purpose is to regulate the function of other proteins. It appears that EYA proteins may have first evolved to serve this purpose.
By comparing and contrasting the EYA genes in different organisms, scientists believe that an ancient ancestor of both plants and animals first developed EYA genes to help it regulate other proteins. Over time, as plants and animals evolved separately, EYA proteins gained the added ability to regulate genes as well1.

An ancient ancestor of both plants and animals first developed EYA genes

So, what about in humans? Research has shown us that EYA proteins in humans are able to regulate both genes and other proteins. Studies in mice suggest that EYA genes influence development of the lungs, kidneys, and brain and have an active role to play in DNA damage repair. People with variants in the EYA1 gene (one of the human versions of EYA) offer evidence that EYA proteins may also influence development of our ear and auditory senses. These variants are believed to underlie Branchio-Oto-Renal syndrome—a developmental disease which affects about 1 in every 40,000 people. These variants affect development of the ears, neck, and kidneys. Curiously, despite the gene’s name, EYA genes actually seem to not have a critical role in mammalian eye development1.
Plants are different from humans in many ways, but perhaps not as many as you think. At the DNA level, genes can give us clues about how related we are to other organisms, even flies and plants. So the next time you look at a blade of grass, remember that you’re looking at a distant relative.

1Tadjuidje, Emmanuel, and Rashmi S. Hegde. “The Eyes Absent Proteins in Development and Disease.” Cellular and molecular life sciences : CMLS 70.11 (2013): 1897–1913. PMC. Web. 4 Apr. 2018.
2Koonin, Eugene V. “Orthologs, Paralogs, and Evolutionary Genomics.” Annual Review of Genetics, vol. 39, no. 1, 2005, pp. 309–338., doi:10.1146/annurev.genet.39.073003.114725. Web. 4 Apr. 2018.