By bringing long-dead proteins back to life, researchers have worked out the process by which evolution added a component to a cellular machine. 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.
Joe Thornton at the University of Oregon in Eugene and his team 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. They 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.