Volume 4, Issue 27 April 2007
The Protein Machine
Building a protein, like assembling a car, is a complicated business. It requires reading blueprints, finding parts, and attaching each component in the right order. Automakers rely on a combination of sophisticated robots and trained human workers to get these jobs done. Cells, however, are more efficient. They use a single organelle called a ribosome to perform all of these functions simultaneously.
Ribosome researcher Jamie Cate is now enlisting the aid of microbes to produce biofuels as an energy alternative to petroleum. Photo credit: courtesy Jamie Cate
"The ribosome is in some respects the prototypical nanomachine," says Jamie Cate, a UC Berkeley professor of biochemistry, molecular biology, and chemistry and QB3 faculty affiliate.
Cate is among the leaders in the current effort to map the ribosome's structure. Since its discovery in the 1950s, the ribosome has largely rebuffed scientists' attempts to study its structure in detail. What it looked like—and therefore how its parts operated—remained in frustratingly soft focus. Cate's work has provided some of the clearest images of the ribosome to date. His results are not only unveiling new aspects of this critical cellular component, but could eventually lead to designs for an entirely new generation of antibiotics.
The ribosome is about as complex as cellular machinery gets. Its job is known as translation: deciphering a genetic transcript known as messenger RNA (mRNA) into the amino acid sequence of a protein. The ribosome plays many roles. It holds both the mRNA and the growing protein chain, regulating which amino acid should be added next. It serves as a platform where helper molecules can land. It forms a bond between the protein chain and each new amino acid. Finally, it ratchets the growing protein forward so that the process can repeat and the chain can lengthen, a step called translocation.
The Escherichia coli bacterium ribosome caught in the act of protein synthesis. This ribosome (shown in grey, blues, and purples) is complexed to a DNA transcript called messenger RNA (mRNA). Also bound to the ribosome is a portion of transfer RNA (labeled ASL); its job is to deliver an amino acid. The ribosome slides along the mRNA, "reading" each segment to determine which amino acid is needed next to assemble the protein. Image credit: Veysel Berk and Jamie Cate
"It's the universal translator; it converts the four-letter code of mRNA into the 20-letter code of proteins," Cate says.
Though large for an enzyme, the ribosome is far too tiny to produce clear images under a conventional microscope. Instead, Cate uses a technique called x-ray crystallography, which provides the most detailed information about protein and RNA structure. It requires arranging trillions of copies of a ribosome into the ordered lattice of a crystal. When hit by x-rays, this repeating unit scatters the radiation in a distinctive pattern. Cate can then use computers and the intuition that comes of long scientific experience to decipher its structure.
The need to freeze this active biomolecule in order to study it has long been the bottleneck in ribosome studies. "It functions as a moving machine, with moving parts. It makes proteins at a clip of about 20 amino acids per second. But growing crystals – that takes weeks. We're slowing it down to try to isolate snapshots of all the things going on as it adds each amino acid," Cate says.
Despite these obstacles, and Cate and colleagues have been able to grow crystals that diffract well enough to provide high quality images. Bombarding the crystals with powerful x-rays from the Advanced Light Source at Lawrence Berkeley National Laboratory enabled the researchers to produce images so detailed they pinpoint the position of virtually every atom.
"It's the difference between knowing the car has an engine and knowing how that engine actually works," Cate says.
This past fall, the group was able to characterize a ribosome gripping both an mRNA transcript and part of a tRNA helper molecule delivering the first amino acid of a protein. These crystals contain copies of the ribosome in different poses, or conformations.
Though the ribosome they analyzed comes from the gut bacterium Escherichia coli, it provides plenty of insight into the ribosomes of humans and other animals. Because ribosomes are so vital to cell survival, they are among the most conserved, or unchanged, organelles in the tree of life. "You can take ribosomes from just about any organism and at some level translate mRNAs from any other," Cate says.
Close-ups of mRNA (gold) and tRNA (green) molecules within the ribosome (light blue). The three nucleotides of this mRNA code for a specific amino acid. By forming hydrogen bonds with the mRNA, the tRNA can put its amino acid in position to be added to the protein. Image credit: Veysel Berk and Jamie Cate
A large percentage of known antibiotics target bacterial ribosomes, including tetracycline, erythromycin, and streptomycin. Many of these antibiotics have been isolated from microbes themselves. "It's a byproduct of the chemical warfare that's been going on among bacteria for hundreds of millions of years," Cate says. "We want to understand how these natural products inhibit translation. Then, based on what we understand about the ribosome mechanism, we should be able to come up with new ways to stop bacterial translation based on the old compounds."
Cate's latest project involves helping to make biofuel production a reality. The project will contribute to the Energy Biosciences Institute collaboration UC Berkeley has developed with petroleum producer BP and several other research institutions. Cate's plan is to engineer bacteria to produce proteins capable of breaking down plant cell walls into simple sugars. Those sugars can then be used to feed other organisms that would then produce ethanol or other fuels. Says Cate, "It's not a substitute for conservation or other measures, but it is one piece of the puzzle."