By tweaking the smallest units of life, scientists are making bigger gains in producing alternative and renewable energy, with recent efforts aimed at molecule-level controls and promoting fractal growth patterns to create different fuels and improve efficiencies.

Bacteria, which range from 0.5 to 5 microns in size, perform functions that can be exploited, enhanced and modified to produce fuels. As they move, breathe, eat and reproduce, bacteria produce byproducts like ethanol and hydrogen while feeding on simple sugars, starches and sunlight. The cells themselves can also be harvested for biodiesel precursors.

At the U.S. Department of Energy's Joint BioEnergy Institute (JBEI), researchers are developing ways to control these fuel pathways with designer RNA molecules. RNA, like DNA, encodes information for cell functions, but RNA can also fold up and perform tasks, like signaling, regulating or catalyzing reactions.

Changing how the RNA folds can serve as a control knob in cellular processes -- increasing, decreasing or altering activity in specific pathways -- but determining how to make RNA so it folds in a particular way has long been a tedious and arduous process.

Now, using computer simulations, James Carothers and his colleagues at JBEI have sped up the RNA design phase, creating computer tools that will help researchers design molecules to precisely control gene expression in bacteria to optimize fuel production.

"The idea was to apply these engineering principles to formalize the design process," said Carothers, who is also a research scientist at the California Institute for Quantitative Biosciences at the University of California, Berkeley.

Starting with a model organismThe team studied the bacterium Escherichia coli as a model organism, comparing how 28 RNA sequences behaved in their model and in the microbe. They found that their computer predictions accurately agreed with how the bacteria responded to the control system.

"In the long run, what we'd like to be able to do is start with a model of metabolism and then implement that genetic program," said Carothers. "Rather than trying to do lots of trial and error, instead if you have a model for how the pathway should work, then you should make the whole [engineering] process easier and more effective."

In other words, rather than combing through thousands of molecules seeded in thousands of bacterial cultures, a scientist may one day be able to design RNA with software akin to computer-aided drafting programs used by engineers and architects. This way, engineers can not only improve natural biofuel pathways, but create new ones.

"The next phase of biofuel production will be getting away from ethanol; it's less energy-dense than petroleum," said Carothers. Using these tools, Carothers expects that bacteria can renewably produce hydrocarbons already in use today, like diesel and jet fuel, creating "drop-in" replacements for fossil energy.

Last year, JBEI developed a method to produce a synthetic form of diesel fuel from E. coli called bisabolane (ClimateWire, Sept. 29, 2011). Researchers have now uncovered the protein that holds the key for producing this fuel by the gallon.

The bisobolane pathway actually comes from the grand fir tree, Abies grandis. The tree naturally produces a precursor to the fuel, bisabolene, as a way to fight insect infestation. Scientists transplanted the mechanism to E. coli, which is easier to control, eats only sugar, reproduces faster and can produce bisabolene in much larger quantities than A. grandis. Bisabolene can then be processed to make bisabolane.

Can we mimic Mother Nature?However, in current systems, bisabolene production reaches a bottleneck, since the molecular mechanisms can't keep up with the supply of raw materials. "We can produce high quantities of farnesyl pyrophosphate (the starting material for bisabolene), but the enzyme doesn't work fast enough," explained Ryan McAndrew, a postdoctoral researcher at JBEI.

Because of this, the researchers decided to investigate the enzyme that forms bisabolene, called AgBIS. Using X-ray diffraction, McAndrew and his colleagues established the enzyme's structure. They presented their findings this month in the journal Structure. By knowing what the enzyme looks like, the scientists can find ways to make it work better. "We can try to engineer out some of the inhibitions involved," said McAndrew.

It's not just what goes on inside a bacterium that's interesting for researchers; bacterial colony structures may have properties that are useful for biofuel production.

Sean Shaheen, an associate professor in the Department of Physics and Astronomy at the University of Denver, was part of a team that recently received a grant from the Research Corporation for Science Advancement to see how bacterial fractals can more efficiently produce hydrogen and biodiesel.

"We want to ask the fundamental question if fractal geometry is more useful than a colony growing in a big clump," said Shaheen. Fractals are patterns that repeat at multiple scales often in found in nature, like in tree branches or landscapes. Each subsection is similar or identical to the whole in terms of its geometry. In living systems, these patterns emerge as organisms reproduce, grow and develop.

Shaheen and his colleagues reasoned that there must be some benefit for bacteria to grow in fractal shapes, so they are investigating whether fractal geometries can offer benefits in biofuels. "The idea is to create an optimized morphology with the bacterial colony," Shaheen said.

The researchers are looking at bacteria like Paenibacillus dendritiformis, which forms circular, fan-shaped colonies, measuring how efficiently it soaks up nutrients and produces useful products. If their hypothesis proves correct, the team will then engineer fractal growth in bacteria that can more effectively make fuel, optimizing its growth patterns.

Reprinted from Climatewire with permission from Environment & Energy Publishing, LLC., 202-628-6500