Six "fingers" of ribosomal electron density (labeled a-f) tightly grip mRNA (red) and tRNA (blue) components to facilitate protein synthesis.

Building a Better Antibiotic

Ribosomes play an essential role in all living organisms: they manufacture proteins. Interfere with the mechanism of protein synthesis, and you interfere with an organism's ability to survive. Many antibiotics operate on this principle. Bacterial infections are often treated by antibiotics that selectively target bacterial ribosomes, while leaving mammalian ribosomes unaffacted. Examples of such antibiotics include streptomycin, tetracycline, and erythromycin. These are used to treat infections ranging from bacterial skin disorders to tuberculosis and Legionnaire's disease. Armed with the details of ribosomal structure, researchers can better understand how ribosomes work and perhaps devise more effective strategies for inhibiting protein synthesis in disease-causing bacteria.

Aside from such practical considerations, the illumination of the ribosome's structure is relevant to our quest to understand how life works. Ribosomes are ancient biological molecules with an overall structure that is common to all forms of life. It is where genetic information gets translated into an individual's observable characteristics. Detailed knowledge of the structure of this key molecule would represent a significant advancement in our understanding of the origins and evolution of life.

Bacterial ribosomes, which have the same basic structure as those of all life forms, are smaller than others and are therefore the most studied. Noller's team successfully crystallized 70S ribosome complexes (ribosomes plus various mRNA and tRNA fragments) from the bacterium Thermus thermophilus. Taking advantage of the high photon flux and collimation of Beamline 5.0.2 at the ALS, the researchers used multiple-wavelength anomalous diffraction (MAD) techniques to obtain electron-density maps of the ribosome complexes with a resolution as good as 7.8 angstroms.

In addition to confirming features of ribosome structure already known through other types of studies, the electron-density maps reveal many interesting new details. For example, the images indicate how tRNAs are bound to various sites in the ribosome. At the site where codon-anticodon matches are recognized, only weak contacts between the ribosome and tRNA were observed, suggesting a degree of flexibility. In contrast, at the site where the amino acid chain begins to form, the ribosome rigidly grips the tRNA with six "fingers" of electron density, stabilizing and orienting both tRNA and mRNA components. Another striking feature seen in the images is an RNA helix that runs along the length of the 30S subunit. This single feature contributes about half of all the contacts between the two subunits and may function as a relay switch, linking events occurring in the two subunits by alternating between two different configurations.

These results reinforce the impression that the ribosome is a dynamic molecular machine with moving parts and a very complicated mechanism of action. Through these studies, Noller et al. are, in a sense, reverse-engineering the ribosome: attempting to understand its function by examining how it is constructed. Toward this end, Noller and his colleagues are already working on improving their resolution and obtaining images of ribosomes at different stages of protein synthesis.

Research Funding: National Institutes of Health; Agouron Institute. Operation of the ALS is supported by the Materials Science Division of the U. S. Department of Energy.

Publication about this research: Cate, J.H., M.M. Yusupov, G.Zh. Yusupova, T.N. Earnest, and H.F. Noller, "X-ray crystal structures of 70S ribosome functional complexes," Science 285(5436), 2095-2104 (1999).