Much
of what living cells do is carried out by “molecular machines”—physical
complexes of specialized proteins working together to carry out some
biological function. How the minute steps of evolution produced these
constructions has long puzzled scientists, and provided a favorite
target for creationists.
In a study published in Nature,
a team of scientists from the University of Chicago and the University
of Oregon demonstrate how just a few small, high-probability mutations
increased the complexity of a molecular machine more than 800 million
years ago. By biochemically resurrecting ancient genes and testing their
functions in modern organisms, the researchers showed that a new
component was incorporated into the machine due to selective losses of
function rather than the sudden appearance of new capabilities.
“Our
strategy was to use ‘molecular time travel’ to reconstruct and
experimentally characterize all the proteins in this molecular machine
just before and after it increased in complexity,” said the study’s
senior author Joe Thornton, PhD, professor of human genetics and
evolution and ecology at the University of Chicago, professor of
biology at the University of Oregon, and an Early Career Scientist of
the Howard Hughes Medical Institute.
“By
reconstructing the machine’s components as they existed in the deep
past,” Thornton said, “we were able to establish exactly how each
protein’s function changed over time and identify the specific genetic
mutations that caused the machine to become more elaborate.”
The
study—a collaboration of Thornton’s molecular evolution laboratory
with the biochemistry research group of the UO’s Tom Stevens, professor
of chemistry and member of the Institute of Molecular Biology—focused
on a molecular complex called the V-ATPase proton pump, which helps
maintain the proper acidity of compartments within the cell.
One
of the pump’s major components is a ring that transports hydrogen ions
across membranes. In most species, the ring is made up of a total of six
copies of two different proteins, but in fungi a third type of protein
has been incorporated into the complex.
To
understand how the ring increased in complexity, Thornton and his
colleagues “resurrected” the ancestral versions of the ring proteins
just before and just after the third subunit was incorporated. To do
this, the researchers used a large cluster of computers to analyze the
gene sequences of 139 modern-day ring proteins, tracing evolution
backwards through time along the Tree of Life to identify the most
likely ancestral sequences. They then used biochemical methods to
synthesize those ancient genes and express them in modern yeast cells.
Thornton’s
research group has helped to pioneer this molecular time-travel
approach for single genes; this is the first time it has been applied to
all the components in a molecular machine.
The
group found that the third component of the ring in Fungi originated
when a gene coding for one of the subunits of the older two-protein ring
was duplicated, and the daughter genes then diverged on their own
evolutionary paths.
The
pre-duplication ancestor turned out to be more versatile than either of
its descendants: expressing the ancestral gene rescued modern yeast
that otherwise failed to grow because either or both of the descendant
ring protein genes had been deleted. In contrast, each resurrected gene
from after the duplication could only compensate for the loss of a
single ring protein gene.
The
researchers concluded that the functions of the ancestral protein were
partitioned among the duplicate copies, and the increase in complexity
was due to complementary loss of ancestral functions rather than gaining
new ones. By cleverly engineering a set of ancestral proteins fused to
each other in specific orientations, the group showed that the
duplicated proteins lost their capacity to interact with some of the
other ring proteins. Whereas the pre-duplication ancestor could occupy
five of the six possible positions within the ring, each duplicate gene
lost the capacity to fill some of the slots occupied by the other, so
both became obligate components for the complex to assemble and
function.
“It’s
counterintuitive but simple: complexity increased because protein
functions were lost, not gained,” Thornton said. “Just as in society,
complexity increases when individuals and institutions forget how to be
generalists and come to depend on specialists with increasingly narrow
capacities.”
The
research team’s last goal was to identify the specific genetic
mutations that caused the post-duplication descendants to functionally
degenerate. By reintroducing historical mutations that occurred after
the duplication into the ancestral protein, they found that it took only
a single mutation from each of the two lineages to destroy the same
specific functions and trigger the requirement for a three-protein ring.
“The
mechanisms for this increase in complexity are incredibly simple,
common occurrences,” Thornton said. “Gene duplications happen frequently
in cells, and it’s easy for errors in copying to DNA to knock out a
protein’s ability to interact with certain partners. It’s not as if
evolution needed to happen upon some special combination of 100
mutations that created some complicated new function.”
Thornton
proposes that the accumulation of simple, degenerative changes over
long periods of times could have created many of the complex molecular
machines present in organisms today. Such a mechanism argues against the
intelligent design concept of “irreducible complexity,” the claim that
molecular machines are too complicated to have formed stepwise through
evolution.
“I
expect that when more studies like this are done, a similar dynamic
will be observed for the evolution of many molecular complexes,”
Thornton said.
“These
really aren’t like precision-engineered machines at all,” he added.
“They’re groups of molecules that happen to stick to each other, cobbled
together during evolution by tinkering, degradation, and good luck, and
preserved because they helped our ancestors to survive.”
The paper, “Evolution of increased complexity in a molecular machine,” will appear in the January 18, 2012, issue of Nature
[doi: 10.1038/nature10724]. The work was a collaboration of Thornton’s
molecular evolution lab with the research group of Tom Stevens, a yeast
geneticist at the University of Oregon. Other authors include Gregory C.
Finnigan and Victor Hanson-Smith, of the University of Oregon.
Funding
for this work was provided by the National Institutes of Health, the
National Science Foundation, and the Howard Hughes Medical Institute.
