Mitochondrial Ribosome Deciphered

January 24, 2014
Image Caption: Model of the large subunit of the mitochondrial ribosome. Credit: Group Prof. Nenad Ban / ETH Zurich

ETH Zurich

Researchers at the Swiss Federal Institute of Technology (ETH) in Zurich have deciphered the structure of part of the ribosome found in mitochondria, the power plants of the cell. The scientists were able to benefit from advancements in the field of electron microscopy and capture images of the mitochondrial ribosome at a level of resolution never achieved before.



Structure determination with obstacles

Until now, the molecular structure of the ribosomes found in mitochondria, the power plants of the cell, was still largely unknown. Mitochondrial ribosomes differ considerably from the ‘ordinary’ ribosomes found in the cytoplasm, which are composed of 60% ribonucleic acids (RNA) and 40% protein components. In the case of mitochondrial ribosomes, RNA accounts for just under a third of the entire complex. One reason for this is that the RNA molecules have shortened significantly over the course of evolutionary history. Mitochondrial ribosomes in the cell are primarily localized at the inner membrane of mitochondria and are present within the cell in a far smaller number than the cytoplasmic ribosomes. This makes them more difficult to isolate, hampering progress of research in the field.

A team of researchers from the ETH research groups of Nenad Ban and Ruedi Aebersold have now succeeded in elucidating the structure of the large subunit of the mitochondrial ribosomes from mammalian cells to a resolution of 4.9 angstroms (less than 0.5 nanometers). Such a level of resolution allows, for example, the visualization of individual phosphate groups of the ribosomal RNA. The researchers’ findings were published in the January 23rd issue of Nature as the cover story.

One of the difficulties encountered was that no usable crystals could be produced from mitochondrial ribosomes in order to determine their structure. Until now, X-ray crystallography, where the molecule is isolated, crystallized and analyzed by X-rays, has been the method of choice to examine the structure of large biological molecules at high resolution. The X-rays are deflected by the atoms in the crystal, thereby creating a specific pattern that can be used to calculate the atom positions. However, for such an experiment to succeed, the crystal must be sufficiently big and of high quality. The large subunit of the mitochondrial ribosome is not suitable for this procedure, as its structure is too heterogeneous, and insufficient amounts of material can be extracted for the crystallization process. “We would have needed hundreds of kilograms of pig liver in order to isolate sufficient quantities of ribosomal material for crystallographic structure analysis; it was logistically impossible to achieve,” says Basil Greber, the lead author of the study and a post-doctoral researcher in Nenad Ban’s group.

Success thanks to a clever combination


In order to interpret the calculated structure as precisely as possible and to determine the exact location of the RNA and protein molecules within the enzyme complex, the researchers used a method derived from Aebersold’s laboratory – a method called ‘chemical cross-linking combined with mass spectrometry.’ Here, the individual protein components of the ribosome are chemically cross-linked, fragmented into peptides for further analysis, and sequenced in the mass spectrometer. From this data, it is then possible to determine the structure of a protein complex, such as the ribosome and its large subunit. A great deal of computer power is required, however, and so the research team used Brutus, ETH’s high-performance cluster.


Key to the study of disease

Thanks to their new findings, the researchers can now explain why mitochondrial ribosomes are always located at the membrane of the mitochondrion. In the vicinity of the tunnel exit, through which freshly synthesized proteins leave the ribosome, the biologists were able to localize a protein with similarity to membrane anchor proteins. From this observation, they have been able to conclude that during the course of evolution an anchor protein of this kind was integrated in the ribosome in order to fix it to the mitochondrial membrane, thus allowing the freshly synthesized proteins to be targeted directly to their destination in the membrane.


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Source: ETH Zurich

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