Where Do Genes Come From? Part 2: De novo Genes

Author: Bryan Moyers

Editors: Theresa Mau, Alex Taylor, and Kevin Boehnke

“The probability that a functional protein would appear de novo by random association of amino acids is practically zero.” ~ Francois Jacob, 1977

If you’ve ever gotten into arguments about evolution, you may have heard the argument that goes something like this: A new gene randomly forming is as improbable as a tornado blowing through a junkyard and assembling a working 747. The above quote by Francois Jacob shows that scientists have been pretty skeptical about this idea, too.

But something seeming unlikely doesn’t mean that it doesn’t happen. As we learned last time, most mutations are harmful, and most gene duplications are lost—but the rare times when they are beneficial, a new gene can have a huge effect on species survival.

So, is it possible that a protein-coding gene might form randomly?

The Genome’s Junkyard

There are two main types of DNA in your genome: “coding” and “non-coding” DNA. The body’s cells use coding DNA to produce proteins, which perform many of the functions of the cell. Coding DNA turned out to be only 1.5% of the genome, while the other 98.5% was non-coding. This non-coding DNA had the unfortunate and inaccurate name “junk DNA” because if you took a chunk of this non-coding DNA and ran it through the protein-making machinery, the protein that comes out would be useless.

While a lot of this junk DNA does appear to be just junk (or maybe we just don’t know what it does yet), some non-coding DNA sequences do important jobs. These bits of DNA serve as signposts, instructions, and switches that tell the cell’s machinery when and where to turn coding DNA genes off and on so that they can do their jobs at the right time and place.

These functional bits of non-coding DNA can cause new genes to form. Sometimes, changes in the DNA will cause a new signpost to form, which can cause the cell’s machinery to read the nearby DNA (that might contain a bit of junk DNA) and transcribe it into RNA. Once the process has reached the RNA stage, the cell’s machinery can translate RNA into protein. But will this protein be functional, given that it came from junk DNA? This leaves us with that big question: can we get a working 747 airplane out of junkyard scraps?

Gene Birth: Tuning Up a Junkyard Bicycle

Transcribing and translating junk DNA happens all over the human genome, at different locations in different individuals. Imagine a bunch of curious gnomes wandering around in a junkyard, picking things up and asking: “Is this useful? What about this? Or this thing?” Most of the time, they just find junk. But every once in a while, something useful is found—a new gene that helps a species survive or reproduce better.

As an example, let’s say the army of gnomes finds a broken-down, beat-up bicycle in the junkyard. Maybe it doesn’t work very well, and it could probably use some tender loving care. It’s not a great bike…but if you don’t have a vehicle, or you can’t afford gas, it’s better than nothing! So, the gnomes use it anyway. And over time, they can fix the bike up until it’s actually worth riding.

Most of these junkyard genes start off not being very important. But even a small advantage can quickly spread through a population if it gives organisms some edge over the competition. Once that happens, the junkyard gene starts undergoing tune-ups through mutation and natural selection, getting minor improvements over time to make it more useful and better at its job. Eventually, it’s not really a junkyard gene anymore—it’s just a gene.

Finding the Genes

You might wonder how scientists know that junkyard genes actually become functional, protein-coding genes. After all, we can’t watch all the genomes of all organisms all the time and see when a piece of junk DNA starts making protein. Fortunately, there are ways we can infer the creation of a junkyard gene.

Closely related organisms have genomes with an extremely similar organization. We can look at a protein expressed in one species and find where in the genome it’s coming from. By examining that same spot in one or more closely-related species, we can see if that section of the genome is producing a protein—or if it even has the ability to do so. If one species produces a given protein and all of its closely related species don’t, this usually means that one species gained a new gene.

A gene like that was likely made from the junkyard of stuff lying around in the genome. As discussed above, this kind of gene is probably beneficial to the species in some way. But since these kinds of genes are so special, there’s a strong desire among scientists to know what exactly they’re doing. How do they help the organisms that carry them?

How Can Junkyard Genes Help Us?

There doesn’t seem to be one single answer to that question, though it’s one that scientists have wrestled with for many years. Through meticulous research, they’ve found that junkyard genes can do a variety of things. In yeast, a junkyard gene was found to be involved in DNA repair. In fruit flies, mice, and other species, it seems as though new genes are being expressed in the testes. In rice, one is involved in fighting off infectious disease.

If there is a pattern to what junkyard genes tend to do, it has yet to emerge. Identifying these genes and their function takes a lot of time and effort. And once you’ve found a gene, it’s not always easy to figure out exactly what it does—these kinds of experiments can take years.

But the hard work of studying junkyard genes is worth it. Findings of junkyard genes have generated a lot of scientific inquiry. For instance, since many junkyard genes are preferentially active in the human brain, could they give us new insights into brain disorders? Do junkyard genes perform similar functions in closely related species, or do they help to drive species apart by giving them diverse new features? Have junkyard genes always performed the same kind of roles, or were genes formed billions of years ago wildly different than the ones we see today? These kinds of questions show us how much of our own evolution, and how much of our own genome, have yet to be explored.

The analogy of the 747 created by throwing junk together has some merit. It’s ridiculous to think that a large, complicated set of machinery would just fall into place by chance. But Francois Jacob’s skepticism was based on an incomplete understanding of how genomes work (and the same goes for creationists that use the 747 argument). Instead of one vastly unlikely coincidence, it only takes a series of minor accidents, plus natural selection, to make a useful gene out of junk.


About the author

Our secobryannd co-founder, Bryan Moyers, is a recent alumnus of the Bioinformatics program at the University of Michigan. Bryan’s PhD research focused on methodological problems in molecular evolution, and correctly inferring information from data. In other words, his research sheds light on problems with the methods commonly used in the field of Evolutionary Biology so that improvements can be made. Bryan also holds degrees in Biology and Psychology from Purdue University. His interests are in science and education issues, philosophy of science, and the intersection of science and business. Outside of science, Bryan enjoys reading, running, hiking, and brewing/consuming beer.

Read more by Bryan here.




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