Engineers have shown that a protein vital to the ability of certain bacteria to break down cellulose, one of the most widespread biochemical processes on earth, speeds up the process by corralling enzymes together and ushering them into action. The evidence gathered by biochemical engineers at the University of Rochester, working with scientists from the Massachusetts Institute of Technology and from Taiwan, is verification of a model previously proposed by the team and is described in the September 26 issue of the Proceedings of the National Academy of Sciences.
"No one has imagined that bacteria have such sophisticated molecular machinery," says lead author David Wu. "As far as I know, this is the first protein discovered that organizes enzymes in this way." The discovery clarifies a previously murky step in biomass conversion; while the findings don't promise to immediately improve conversion rates, the results give a better understanding of the basics underlying a process widely studied by biotechnology companies and research laboratories around the world.
The decay of cellulose stands behind everything from the transformation of the compost heap to fertilizer, to cows' ability to digest grass and mushrooms' ability to grow in the forest. Now scientists are eyeing the process as one way to satiate our future energy demands: The breakdown of cellulose into simpler, useful materials such as cellobiose and glucose is one step in the conversion of biomass materials like trees, waste paper and crops into renewable energy products such as ethanol. Ethanol produced from corn already is used in many urban areas to run our automobiles.
Though biomass offers an abundant source of energy, and is much cleaner than conventional fossil fuels, it remains largely untapped because of the cost of producing useful energy. One bottleneck is the slow rate of the biochemical process where cellulose is broken down; while it's fast enough for nature, it's often too slow to be economically feasible.
Sometimes the process in nature works faster than at other times, and engineers are trying to learn why. Both fungi and bacteria use a concoction of several cellulase enzymes to break down cellulose, long chains of glucose bound tightly together by hydrogen bonds, like a group of pencils bound tightly with rubber bands. Some enzymes cut the long cellulose fibers, and then others begin devouring the ends. Fungal organisms are considered to be major players in cellulose degradation, but that's because they produce so much more protein. Pound for pound, certain bacteria are the real giants of the cellulose-degradation world: They can be 50 times as effective at breaking down cellulose per protein base, says Wu, associate professor of chemical engineering and microbiology and immunology at the University of Rochester. This bacterial advantage has long been a mystery.
Now engineers think they've solved at least part of the puzzle. Wu's team and an MIT group headed by renowned industrial microbiologist Arnold Demain discovered that a protein called CipA in the bacterium Clostridium thermocellum organizes several cellulase enzymes into a cohesive unit which it leads to the cellulose material, like a platoon of soldiers following its commander. The protein then anchors itself to the cellulose, and the well organized enzymes begin their work. The orderliness is a contrast to the slower process in fungi, where enzymes randomly attach and attack a cellulose surface.
"Bacteria are normally considered more primitive than fungi," says Wu, who began this work while a graduate student in Demain's laboratory. "However, we've known that bacteria are much more efficient even with their much smaller genome size. This elaborate system may explain why.
"Perhaps we can learn from these efficient bacteria and use genetic engineering to endow fungi with the same advantage, so that we'd have both a high volume and a high efficiency of cellulose degradation in one organism."
The discovery was made in an organism that comes equipped with many qualities that lend themselves to biotechnology processes, says Demain, a member of the National Academy of Sciences. It's able to grow directly on cellulose and to convert cellulose straight to ethanol, a rare combination. It's also an anaerobic bacterium that grows at high temperatures and thrives without oxygen; maintaining an adequate supply of oxygen for oxygen-dependent bacteria is often the most costly step in the fermentation process.
"Clostridium thermocellum is a bacterium with a remarkable combination of desirable qualities," says Demain.
Also working on the project were Wu's graduate student, Kristiina Kruus, and Ahai Lua of the Tzu Chi College of Medicine in Taiwan. The group's work was funded by the National Science Foundation, the Department of Energy, the National Renewable Energy Laboratory, and the U.S. Department of Agriculture. tr