By bringing long-dead proteins back to life, researchers have worked out the process by which evolution added a component to a cellular machine. The result, they say, is a challenge to proponents of intelligent design who maintain that complex biological systems can only have been created by a divine force.
Cells rely on ‘machines’ made of multiple different protein components to carry out many vital functions in the cell, and molecular and evolutionary biologists have puzzled about how they evolved. In an effort to find out, Joe Thornton at the University of Oregon in Eugene chose to study a particular machine called the V-ATPase proton pump, which channels protons across membranes and is vital for keeping cell compartments at the right acidity. Part of this machine is a ring of six proteins that threads through the membrane.
In animals and most other eukaryotes, this ring is composed of two types of protein; fungi are alone in having a ring with three. Thornton wanted to know how the machine evolved from the simple to the more complex form. And, because he has built a lab that specializes in resurrecting ancient proteins, he had just the tools to find out at hand.
The team first scoured databases and pulled out 139 genetic sequences that encode the ring’s component proteins in a range of eukaryotic organisms. They then used computational methods to work backwards and find the most likely sequences of these proteins hundreds of millions of years ago, at key branching points on the evolutionary tree: just before and just after the ring increased in complexity. The team synthesized DNA that encoded these ‘ancestral’ proteins and put it into yeast, which had had parts of its own proton pump deleted. The technique allowed Thornton’s team to test in yeast whether various combinations of ancestral proteins produced a working, proton-pumping, machine.
The work, published online in Nature, reveals the pathway by which the two-component ancestral protein (let’s call the components A and B) became a three-component one (A, B and C). The gene encoding protein A duplicated, and two identical copies of the gene started making proteins A1 and A2. Then, A1 and A2 started to accumulate mutations so that they could no longer substitute for each other in the ring. To work out the exact sequence of events, the team identified the likely historical mutations and engineered them, one by one, into their version of ancestral A.
They found that just one key mutation in each of A1 and A2 created proteins that could no longer bind promiscuously with neighbouring proteins in the ring, and instead had to occupy specific spots. The proteins “went from being a generalist to a specialist,” Thornton says. And A2 eventually became C, the third part of the three-component ring now made up of A1, B and C.
The result challenges the assumption in biology that increased biological complexity evolves because it offers some kind of selective advantage. In this case, the more complex version doesn’t seem to work better or have any other obvious advantage compared with the simpler one; it is more likely that A1 and A2 proteins were just corrupted by random mutation. (The yeast didn’t seem worse off when they were stripped of their own three-protein ring and instead used one built of two ancestral proteins.) “What’s surprising to me is the idea that greater complexity doesn’t require acquisition of new functions. It can come from partial degeneration of the ancestor,” Thornton says.
To those studying evolutionary theory, the result “is an expectation rather than a surprise”, says Michael Lynch, who carries out such studies at Indiana University in Bloomington. “But science does not advance with theoretical work alone,” he says. The new results “bring the theory to life”.
And to intelligent-design proponents, Thornton adds, the results say that “complexity can appear through a very simple stepwise process — there is no supernatural process required to create them.” Still, evolution of a three-protein machine is unlikely to silence those proponents — there are many far more complicated biological machines with far more protein parts and intricate internal mechanisms. Thornton says that his and other groups will now probably use the same tools to dissect the evolution of more complex molecular machines.