18 February 2020

Genes from "garbage"

The emergence of genes from scratch turned out to be a common phenomenon


Where do genes in the genome of a living being come from that no other species has? A new study shows that they most often arise almost "out of nothing", more precisely from junk DNA.

All living organisms are closely related to each other. 30% of human genes are shared with E. coli, and 50% with banana. By the way, this is one of the numerous proofs of the fact that all living things came from a common ancestor.

However, each species has a small percentage of genes unique only to it or its closest relatives. In the genomes of other organisms, there are not only exact copies of such DNA sections, but also their obvious analogues. Experts call them orphan genes.

Where do such new genes in evolutionary history come from? There are at least two possible ways. Firstly, the gradual accumulation of differences between related genes (divergence) can go so far that biologists simply do not recognize "cousins". It is believed that this scenario is the most common for the emergence of orphan genes.

There is another way. Recall that a gene is an instruction for the synthesis of RNA. RNA can serve as a prototype for protein synthesis (the main "workhorse" in the cell) or perform other functions.

But in every genome there is a mass of junk, or non-coding, DNA. These are "former genes" that once completely failed. The instructions for RNA synthesis contained in them have lost their functionality due to errors introduced by mutations.

However, junk DNA continues to mutate. Moreover, these mutations are not "washed out" by natural selection, since non-coding DNA does not affect the life of the cell and the organism as a whole (however, the latter thesis has recently been criticized). And sooner or later, as a result of such random changes, a new workable gene may arise from this "garbage". In this case, experts say that the gene originated de novo.

It is believed that this is an exotic scenario that is rarely implemented. But the results of two new studies published in the journals Nature Communications (Vakirlis et al., De novo emergence of adaptive membrane proteins from thymine-rich genomic sequences) and eLife (Vakirlis et al., Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes), indicate otherwise.

The authors have developed a new technique to determine whether an orphan gene has workable analogues in the genomes of other species, even if the "cousins" are completely different from each other. Relying on this method, the scientists searched for "lost relatives" for the genes of yeast, flies and humans.

The results were discouraging.

"To our surprise, at most about a third of orphan genes are the result of divergence. This, in turn, suggests that most of the unique genes in the species that we have studied are the result of other processes, including the appearance of de novo. Consequently, this happens much more often than scientists initially thought," says co-author of the article Ife McLysaght (Aoife McLysaght) from Trinity College in Dublin.

Biologists did not stop there and asked the following question: is the influence of new genes on the life of the organism great?

Scientists chose yeast as experimental organisms. They have short genomes, multiply rapidly and at the same time belong to eukaryotes, unlike, say, bacteria.

At first, the researchers disabled orphan genes that once arose in yeast de novo. Usually, this did not reduce the viability of these organisms either "in vitro" or in natural populations. In other words, most of the de novo genes that have appeared are not vital (at least in yeast). And there is an explanation for this: after all, there was a direct ancestor of yeast without them.

At the second stage, biologists went the other way. On the contrary, they artificially increased the work (expression) "newcomers". And yeast immediately activated growth. At the same time, experts have checked that this reaction is not caused by the expression of any other genes that are not de novo.

In other words, genes that have arisen "from garbage" can be very useful and give their carriers important evolutionary advantages.

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