New & Noteworthy

A Simpler Way to Evolve

February 6, 2012

As life evolves there is a tendency for increased complexity.  Up until now, scientists have mostly focused on gain of function mutations as the motor for this change.  This has proven fertile ground for evolution deniers who have claimed that life’s complexity could not have arisen from these rare, gain of function mutations alone.

A new study by Finnigan and coworkers provides an important counterpunch to this argument.  These authors resurrected ancient proteins and showed that an increase in complexity can come from much more common, loss of function mutations.  Time for the deniers to find a new argument…

Making Molecular Machines

Proton pumps like this one may be easier to evolve than scientists first thought.

Finnigan and coworkers focused on the evolution of a protein called vacuolar H+ -ATPase or V-ATPase for short.  Like other molecular machines, this proton pump consists of many different proteins all working together in a coordinated fashion.  One key part of this machine is a rotary ring called V0.  (This would be the ring of C proteins in the image to the right.)

In most eukaryotes, V0 is made up of five identical subunits (called Vma3) and one subunit called Vma16.  In fungi, a third protein, Vma11, has replaced one of the Vma3 subunits.  In other words, the fungal version is a bit more complex than other eukaryotic versions.

Current theories are that these three proteins all arose through gene duplication.  Duplication of the Vma3 gene first led to the Vma16 gene and then later in fungi, Vma3 duplicated again this time becoming Vma11.  Yeast V-ATPase absolutely requires Vma11 to function and other eukaryotic Vma3 family members cannot replace Vma11.

Using the 139 family members of the Vma family available in GenBank, members of the Thornton and Stevens lab recreated the ancestral proteins that existed before and after the Vma11 gene duplication event.  Before the arrival of Vma11, there were only two proteins which the authors have named Anc.3-11 and Anc.16.  Anc.3-11 presumably has functions of both Vma3 and Vma11.  After the gene duplication event, there were three ancient proteins: Anc.3, Anc.11, and Anc.16.

Using these ancient proteins, the authors first showed that Anc.3-11 could substitute for either Vma3 or Vma11 in yeast. It could even partially rescue a yeast strain that lacked both of the other genes.  They then showed Anc.16 could replace Vma16 and most importantly, that the two ancient proteins could replace the three modern ones.  They reconstructed an ancient molecular machine that works.

The next step was to figure out what happened after Anc.3-11 duplicated again and the two genes began to evolve into the separate proteins, Anc.3 and Anc.11.  Again using the GenBank sequences, the authors predicted that two single mutations were an initial step on the way to the separation of Anc.3-11 activities into the Anc3 and the Anc11 proteins. 

The authors engineered each mutation independently into the Anc.3-11 protein and found that one mutation made Anc.3-11 more like Anc.3 and the other made Anc.3-11 more like Anc.11.  The complex now required all three Anc proteins instead of just the two for maximal activity.  The authors had recapitulated the first evolutionary steps that led to the formation of the three subunit V0 rotary ring.

Finally the authors showed that each of these mutations were loss of function mutations.  The Anc.3-11 protein has two different interfaces that interact with Anc.16.  The first mutation weakened one interface on Anc.3 and the second mutation weakened the other interface on Anc.11 causing both proteins to now be required to reconstitute the ring.  The added complexity arose from a combination of gene duplication and relatively common loss of function mutations.

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics