By David N. Leff
Consider the common zipper, or slide fastener. This now-ubiquitous accessory made its debut just over a century ago, in 1893, at the World's Columbian Exposition in Chicago. An inventor named Whitman Judson exhibited his working model of hooks and eyes, with a sliding clasp to open and close that metallic seam.
Evolution beat Judson to his punch by several billion years. That was when life appeared on earth, depending on DNA and RNA to produce and reproduce itself. Those processes eventually employed ribosomes to operate the genetic code, by which double-helix DNA-assembled genes convert to single-stranded messenger RNA on their way to synthesizing proteins.
"You could compare that process," observed structural biologist Jamie Cate, "to messenger RNA moving along the zipper-like teeth. The ribosome's other teeth," he added, are in the next phase - the transfer RNA. There the ribosome comes and goes, using three teeth at a time - representing the three-base triplet codon on the genetic code. Then you have two or three of those at a time bound to the ribosome transfer DNA."
Cate is lead author of a paper in today's Science, dated Sept. 24, 1999, which describes, for the first time, mapping the crystal structure of the entire ribosome. Its title: "X-ray crystal structure of 70S ribosome functional complexes." Its senior author is molecular biologist Harry Noller at the University of California, Santa Cruz. ("70S" defines the sedimentation rate by which the ribosome molecule settles in a solvent.)
"Ribosomes," Cate told BioWorld Today, "are really central to any expression of a phenotype, because they convert the DNA blueprint to RNA, which is then encoded in the cell's mRNA function, in the form of proteins. That's a universal part of life that we really don't understand very well. What's really held back that understanding," he added, "is grasping the structure of the ribosome.
"What our group and other structural biology groups are doing," he pointed out, "is dissecting the basic architecture of the ribosome, and figuring out where its ligands bind, so we can comprehend the fundamental mechanism."
Forty Years In Ribosomal Wilderness
Those other groups pursuing the ribosome's structure and function are many. The Santa Cruz team's paper in Science today, analyzing the ribosome's two molecular subunits, represents a grail sought for four decades by researchers in many countries. Within the past four weeks, two other teams, at Yale and the University of Utah, have published in Science and Nature, respectively, the structures of the ribosome's large and small subunits.
To lay hands, as it were, on a single ribosome for X-ray crystallography, Cate explained, "involves a very intricate purification process. We started with about 200 liters of culture fermentation and ended up with enough usable ribosome material in solution to do the crystallization."
Their designated ribosome came from an extremophile bacterium, Thermus thermophilus. "Especially in crystallography," Cate pointed out, "thermophilic organisms tend to provide better material for doing structural studies. Their proteins or macromolecules or complexes tend to be more stable and more easily manipulated. They can withstand more physical perturbations than the same systems from other types of organisms.
"The core elements," he went on, "are very highly conserved through all of life. Where the eukaryotic [mammalian] ribosomes are going to be different is that they will have a lot more regulation of protein synthesis going on. And I think that initiation - the first step in RNA translation - is going to be one of the areas that's very highly regulated in eukaryotic ribosomes, including human."
Cate has just moved from University of California at Santa Cruz to an appointment as associate member at the Whitehead Institute for Biomedical Research in Cambridge, Mass.
"I'm going to continue working on the 70S ribosome," he said, "because it has so many different moving parts. It's a machine in motion, and we don't really understand how those motions work. So it's probably going to take many structural studies of the ribosome in order to piece together its different movements. These large-scale movements are choreographed by the ribosome in some way. So I'm working on that aspect.
"Actually," he continued, "there are two issues. One is that the ribosome is moving. And the other is it has to move transfer RNAs from one subunit site to the next.
"Working with human ribosomes," Cate observed, "is something that I'd certainly want to start doing, because I do think there will be a lot of interesting things there. For example, there are a number of pathogenic viruses that sort of take over, or can enhance expression of their particular proteins, by co-opting the initiation phase of translation in the ribosome."
How Antibiotics Cripple Infective Ribosomes
Antibiotics are another arena of potential ribosomal relevance. "In terms of biotechnology applications," Cate pointed out, "this is going to become interesting. And that aspect, I think, will happen when we understand how antibiotics interfere with ribosomal function. There are many classes of antibiotics that target the ribosome. In examining their structures, we now know roughly where two different classes of antibiotics, aminoglycosides and streptomycins, bind to the ribosome.
"There they interfere with how the tRNA anticodon binds to the mRNA, and decreases the specificity of that interaction. We're seeing how these tRNAs are positioned within the ribosome. That begins to give us a clue to their antibiotic effect. These drugs interfere with the decoding process of reading out the triplet genetic code from the RNA, which leads to error-prone phenotypes. At the other end of the tRNA, there are antibiotics that interfere with peptide-bond formation. And we now have a clue as to where those regions might be."
Cate conceives the application of these structural insights to design of new or better antibiotics "is a long-term project. As opposed to most other attempts at structure-based drug design, the structure of the ribosome is huge, and it's not clear what resolution we'll ultimately be able to get of it.
"Most structure-based drug design," he pointed out, "is at very high resolution - say 2 Angstroms or better. And the ribosome may be 3 to 3.5 Angstroms. So it could be a little bit tricky to do that. But because of the huge amount of biochemistry that's been done on the ribosome, coupled with this new structural information, it's something worth pursuing."