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Posted by 15 Jun, 2012

Molecular machinery

Synthetic biology, nanostructures could boost biofuel production

Over the centuries humans have used microorganisms for activities from making wine and beer to baking bread. Common microorganisms like yeast and bacteria can carry out surprisingly complex chemical transformations in the space of a few nanometers. Today, scientists working in the field of synthetic biology are developing methods of modifying and controlling the molecular machinery within these organisms. Their goal is creating nanoscale chemical factories that are more efficient than aditional production methods and can be easily modified and eproduced.One of these eforts, aimed at boosting the efficiencyf biofuel production, is a collaboration between ORNL physicist Miguel Fuentes-Cabrera and Qing Lin, associate professor of chemistry at the University at Bufalo, The State University of New York.

Investigating microcompartments

The pair’s research, begun under a grant from the Keck Foundation, is focused on transplanting the chemical processing capability of nanoscale bacterial structures called microcompartments into a strain of yeast used in commercial biofuel production. “These microcompartments usually have a specialized function associated with cellular metabolism,” Lin says. “The structures act like completely isolated entities—small machines within a big factory,” Fuentes-Cabrera adds. “They take material from the host bacteria, perform various enzyme-catalyzed metabolic reactions, and then release the resulting products into the host organism.”

“For example,” Lin says, “we know that under certain conditions bacteria use microcompartments to convert ethanolamine to acetaldehyde and ammonia for nourishment. By performing this essential metabolic function in a segregated compartment, the bacteria are able to tolerate levels of acetaldehyde which would otherwise be toxic. Because the ethanol production pathway in yeast also involves acetaldehyde, we thought a good way to demonstrate the potential of these microcompartments would be to import them into yeast to boost ethanol production and improve ethanol tolerance. That’s the goal we’re working toward.”

Both researchers note that the ability to engineer these organisms to produce ethanol, propanol or other biofuels hinges on gaining access to the chemical processing capabilities of the nano-sized microcompartments—and that requires understanding how molecules move in and out of these structures.

Understand then modify

Computer simulations may hold the key to understanding the ins and outs of microcompartments. That’s where Fuentes-Cabrera’s primary contribution to the collaboration comes into play. The simulated microcompartments he creates not only improve the general understanding of these structures, but also help Lin’s team determine how to proceed in unlocking their function.

Microcompartments are made of collections of proteins, which include a number of pores. Some researchers suggest that these pores act like “gates” that allow molecules to move in and out; however, they’re not sure what causes the pores to open and close. The gates could be regulated by metabolites—materials produced by the bacterium during digestion and other chemical processes—in reaction to concentrations of these materials within the cell. “That’s what our simulation is helping to determine,” Fuentes-Cabrera says. “There is a lot of speculation as to how metabolites are transported through the microcompartments.” His post-doctoral assistant, Yungok Ihm, is investigating this process by creating a simulation of ions and metabolites passing through the pores in the microcompartments.

Once they understand how molecules are transported in and out of the compartments, Fuentes-Cabrera and Lin plan to turn their attention to understanding other aspects of the structures. Using simulations, Fuentes-Cabrera will investigate the proteins that spontaneously self-assemble into the microcompartments. For his part, Lin will attempt to introduce new enzymes into the interior of the microcompartments to enable the production of ethanol or propanol. “The critical fist step is to determine whether the native metabolic pathway present in these structures can be re-engineered to facilitate the bioethanol production,” Lin says. “First we understand, then we modify,” Fuentes-Cabrera says.

Bacteria to yeast

If the biofuels production capability of microcompartments can be achieved in bacteria, Lin’s goal is to reproduce the same process genetically in yeast used to produce biofuels. Providing yeast with the added metabolic capability of microcompartments could reduce the number of steps involved in the biofuels production process and, therefore, its cost.

However, genetically engineering new qualities into an organism can be problematic. “Often when researchers try to genetically modify an organism to do something that it doesn’t normally do, it dies,” Fuentes-Cabrera says. Despite that note of caution, he and Lin feel they have a good chance of having bacterial microcompartments work in yeast because of their self-contained nature. He explains this optimism by pointing to the fact that all of the engineered metabolic reactions occur within the confines of the microcompartments. “We are more confident of success because we are not interfering with the yeast’s normal metabolic processes,” he says.

So far, the two researchers have been able to express the five compartment-related proteins in yeast. Their assumption is that, once expressed, these proteins should spontaneously assemble themselves into microcompartments—which is what occurs in bacteria. The researchers are now in the process of isolating the potential microcompartments from the yeast in order to study them using transmission electron microscopy. To gain additional molecular-level insight into the protein self-assembly, they are also using simulations to model the interactions among the proteins. “When we have a better understanding of how the proteins interact,” says Fuentes-Cabrera, “we will be able to suggest genetic modifications to facilitate the self-assembly process.”

Biological advantage

Both Fuentes-Cabrera and Lin maintain that biofuel production is just one of many potential applications of this relatively new facet of synthetic biology. They emphasize that one of the goals of the field is to learn from nature and then apply what you have learned to your advantage. “In this case,” Fuentes-Cabrera says, “we are showing that we can harness natural biological processes to provide us with technologies we need. Much of the system we are working with occurs naturally. We didn’t have to invent it. It was already there.”

Lin notes that the biggest advantage of a purely biological approach to biofuel production over those using artificial or manufactured components is the ease with which changes to the system can be implemented. “Because microcompartments are naturally produced by certain microorganisms,” Lin says, “they are part of a genetically encoded system. If we want microcompartments to do other tasks, we can simply modify the genes that control the biological parts in the system and scale up the production by growing more microorganisms. Ramping up production for a new generation of nanomaterials, on the other hand, could be far more difficult.”— Jim Pearce

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