– In this interview Venki Ramakrishnan reviews part of his work on the structural resolution of the ribosome, for which he was jointly awarded the Nobel Prize for Chemistry in 2009.
– He discusses the role that synchrotron facilities have played in unravelling the structure of the ribosome and how cryogenic electron microscopy (cryo-EM) has become an essential tool for structural biologists.
– He concludes with an overview on his current research activities at the MRC Laboratory of Molecular Biology.
The full original article is available at: https://scivpro.com/manuscript/10_32386_scivpro_000014/
Venki Ramakrishnan. If you ask the average non molecular biologist what a ribosome is, almost nobody would know. This always struck me as very surprising because everybody thinks they know what a gene is. Each gene contains information for how to make a particular protein or how to regulate the making of a protein. These instructions are encoded in our genetic material, which is a long molecule called DNA. In the DNA molecule there are hundreds of genes, which are represented as different sections within the DNA itself. Each section that contains a gene, contains information on how to make a particular protein or how to regulate it. Although the genetic information is stored in DNA, each gene is copied into a molecule called messenger RNA (mRNA) because it carries the genetic message. The mRNA goes from the nucleus to the cytoplasm of the cell. There, a large molecular machine – the ribosome – reads this genetic message and then, based on the instructions, stitches together a protein. This process is called translation because you are going from the language of DNA to the language of polymer. What the ribosome does is right at the crossroads of biology, it is the bridge between genes and the information they contain to making the products that are specified by the gene.
Ribosomes were discovered in the 1950s, but they are enormously complex molecules. To understand how it works, just as with any other molecule, you want to know what it looks like, how it interacts with the genetic message, how it stitches together amino acids to make a protein, how it moves, etc. To do that you need to understand its structure, you need to be able to visualize what the ribosome actually looks like, and not just in one state, but what does it look like as it is carrying out its function. That was a long complicated effort, which required several groups to determine its high resolution structure. From there it was then possible to understand some of the key functional mechanisms, such as how it reads the genetic code accurately and how it makes the peptide bond, which is the bond between amino acids. Because of that the Nobel Prize in 2009 was awarded to three groups.
After the structures of the ribosome were resolved, it was then straightforward to determine the structure of the ribosome with various antibiotics bound. That part became just a straightforward extension of the original structure. So for the first time we could visualize in atomic detail how these antibiotics bound to the ribosome. That not only allowed us to understand how these antibiotics worked but it also to understand why resistance would occur. For example, with a certain mutation, why these antibiotics would not work, or if the antibiotics were modified by some resistance mechanism.
At the moment we are looking at how ribosomes know where to begin reading the message. The way that is done is very different in bacteria and in human ribosomes or in yeast ribosomes. Yeast and us have more similarity because we are what are called eukaryotes, where cells contain a nucleus. Our ribosomes are more similar than those of bacteria. We are understanding this process called initiation, which involves a number of proteins that come and bind to the messenger RNA and to the small ribosomal subunit to bring it to the right beginning point, where it can begin translating the gene and making the protein. It is a highly regulated process and when it is deregulated it can lead to things like cancer. Moreover, there are viruses that can hijack this initiation process by having their own kind of machinery that does not require all these protein factors from the cell. The result is that all of the translation is diverted to translating the virus’s own genes. So, it is a way for the virus to stop the ribosome from making the host proteins and begin making the viruses proteins instead. This is a very interesting problem and some of our effort is focused on that.
We also have organelles in us called mitochondria, which are remnants of bacteria that were swallowed up by another cell about two billion years ago. Although they have been in us for two billion years they still retain a small genome and for that they have their own ribosomes (mitoribosomes), which translate their genes. These ribosomes have differentiated quite a lot from both bacterial ribosomes and from our own ribosomes. So, they are interesting biologically. They are also important medically. In fact many antibiotics are toxic as they bind to our mitochondrial ribosomes because they are sort of descendants of bacteria; they are bacteria-like in some respects. Antibiotics that normally might not be so toxic end up being toxic because they bind to our mitochondrial ribosomes. So, it is important to understand their structure for that reason and many genetic diseases map to mitochondrial ribosomes. We solved the structure of mitochondrial ribosomes along with Nenad Ban’s lab in Zürich. We were to some extent competitors, not collaborators, but friendly competitors. These structures are now paving the way for understanding how mitochondrial ribosomes work and possibly how mutations in them might cause various diseases. That is another area.
Finally, we are trying to understand how cells are regulating translation. If ribosomes get stuck, how does a cell rescue ribosome and regulate the whole process of translation and maintain quality control? How does it know when things are have gone awry, when you need to stop translation and begin again? These are sort of some of the areas we are working on.
Copyright notice. This blog article is a derivative of https://doi.org/10.32386/scivpro.000014 by V. Ramakrishnan et al., used under CC BY 4.0. The present blog article is licensed under CC BY 4.0.