By Bryn Nelson

By mimicking plant evolution, a team of researchers has improved upon nature?s
design to build a leafy energy-producing powerhouse ? or at least a virtual
one on a supercomputer.

Efforts to improve crop yields without resorting to more nitrogen-based
fertilizer and a growing interest in plant-based biofuels have combined to
make the energy-amassing process of photosynthesis a hot research topic. A
big challenge, according to University of Illinois at Urbana-Champaign crop
sciences professor Steve Long, is ensuring that enough energy can be
produced to yield both food and fuel.

In a study published within the journal Plant Physiology, Long and
colleagues have suggested a way forward for both aims by using a
supercomputer to design a photosynthetic pathway that is 76 percent more
efficient than anything found within natural greenery.

In photosynthesis, all green plants, algae and some microbes use sunlight to
convert water and carbon dioxide into oxygen and energy stored as
carbohydrates. Some scientists view the pathway as the most important
biological process on Earth because it supplies most building materials and
all food (either directly or through plant-eating animals). Photosynthesis
also counteracts the effect of burning fossil fuels by consuming carbon
dioxide.

The carbon-converting prowess of photosynthesis, in fact, is why planting
more trees is commonly cited as a way to help mitigate global warming.
Understanding the underlying mechanisms of the pathway could help increase
wheat and other crop yields, make better use of existing solar energy, and
augment the production of corn, switchgrass and other plant-derived biofuels
as oil alternatives.

Photosynthesis is inefficient

Over the past half-century, researchers have been able to describe the
dozens of enzymes and reactions involved in photosynthesis. ?And one of
things that?s known about this process is that it?s not very efficient,?
Long said. If green plants aren?t optimizing their investment, he thought,
might scientists be able to tweak the process to essentially build a better
plant?

On a supercomputer, at least, it?s no contest.

Robert Blankenship, a professor of biology and chemistry at Washington
University in St. Louis, said he was surprised by the ?dramatic? increase in
efficiency obtained by Long?s group. ?If you could increase carbon fixation
by 76 percent (in the real world), that would be a huge deal,? said
Blankenship, who wasn?t involved with the study.

At its core, the study consisted of a series of linked differential
equations that essentially mimicked each reaction within photosynthesis. The
computer-assisted linkup, Blankenship said, allowed the scientists to
reconstruct the complicated pathway on the computer and tinker with it in
way that would be very difficult to do with real plants. Long?s team
determined the starting amounts of each protein from prior studies, and
after linking up the equations, kept testing and tweaking the model until it
successfully predicted the outcome of experiments performed on living
leaves.

?For reactions strung together in a fairly complicated way, it?s very
difficult to go in there and say, ?Maybe we should change this one or that
one,? ? Long said.

An evolutionary algorithm

Instead, his team used an evolutionary algorithm that selected a reaction at
random and either increased or decreased the relevant protein by 10 percent.
Adjusting the amount of an enzyme effectively changes the rate of its
corresponding reaction. Because the reactions were all linked, a relatively
minor alteration could impact the entire pathway.

After every round of adjustments, the supercomputer determined whether the
virtual plant, given a steady level of nitrogen and overall protein, could
fix more or less carbon dioxide per unit of light (the standard measure for
photosynthesis efficiency).

?What we find is that 99 times out of 100, we?re actually making it worse,
rather than better,? Long said. But that rare improvement could be used to
seed the next generation in the plant?s simulated evolution. The computer
repeated the process for 1,500 generations, always hunting for the best
possible solution. By the time it was finished, the virtual plant?s
photosynthesis output had clobbered its real-world competition.

The big question, of course, is whether the tinkering could work within a
living plant.

Some independent findings have given Long reason for optimism. One protein
whose levels increased significantly within the simulation ? inscrutably
named sedoheptulose-1,7-bisphosphatase ? has been found to aid real plant
production when upped experimentally by researchers in England and Japan.
?That?s one clue we have. It was striking that the computer actually
selected this protein,? Long said.

Boosting virtual plant proteins

For a more efficient plant, in fact, the supercomputer suggested the protein
should be increased four-fold. The simulation gave another big boost to a
notoriously inefficient but abundant enzyme abbreviated RuBisCO, which
Blankenship called the ?800 pound gorilla of plant proteins? and a key
player in photosynthesis.

A handful of other proteins were significantly increased as well in the
virtual plant, whereas most others were increased or decreased by no more
than 20 percent to 30 percent. As a start, Long suggested, maybe the
half-dozen proteins whose levels were altered the most could be the focus of
future genetic engineering. ?We view this as a guide,? he said. ?These are
the best bets.?

If the evolutionary algorithm produced such a clear increase in efficiency,
why hasn?t evolution naturally done the same thing?

One reason, Long said, may have to do with a plant?s priorities. Evolution
selects for those individuals producing the most viable offspring, which isn?t
the same thing as selecting for a photosynthetic superstar. Getting the
biggest bang for the buck from photosynthesis may require cutbacks in other
plant processes.

Long believes the computer?s simulated shortchanging of some enzymes known
to hamper photosynthesis could prove lethal for real plants exposed to high
temperatures and drought conditions. Higher photosynthesis efficiency, it
seems, may come at the cost of reduced stress tolerance ? just one of the
many potential pitfalls of messing with Mother Nature that will have to be
addressed in the future.

In addition, most vegetation evolved under atmospheric conditions far
different from what exists today. Perhaps, Long and his co-authors reasoned
in their study, the plants? photosynthetic cycle simply hasn?t been able to
adequately adjust to the spike in atmospheric carbon dioxide levels over the
past 150 years.

Nor are green plants the photosynthetic champions of the natural world. That
distinction belongs to tiny cyanobacteria and some microalgae, which have
generated considerable interest from researchers seeking to harness their
long-term potential for producing bioenergy.

Nevertheless, Blankenship said exploring different avenues is likely to be
the best strategy, and he lauded Long?s efforts at trying to maximize what
nature didn?t necessarily intend. ?There?s really no reason to think that we
can?t do better,? he said. ?You shouldn?t assume that nature is just
perfect.?

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