The interaction between ribosomes and antibiotics

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FullSizeRenderDr. Venkatraman “Venki” Ramakrishnan is an Indian-born American and British structural biologist, who shared the 2009 Nobel Prize in Chemistry with Thomas A. Steitz and Ada E. Yonath, for studies of “the structure and function of the ribosome”. He obtained his PhD in physics from Ohio University and carried out his research at Yale University, Brookhaven National Laboratory and University of Utah. For the last 15years he has been working at the MRC Laboratory of Molecular Biology in Cambridge, England. He is also a fellow of the Royal Society, a member of EMBO and the U.S National Academy of Sciences and a Fellow of Trinity College, Cambridge.

He was in Singapore recently to give a lecture in Nanyang Technological University. The topic was “Seeing is believing: Revealing the workings of the large molecule that reads our genes and how antibiotics block it”. I, Laxmi Iyer, attended the talk and had a casual chat with him in the networking session. Here, is a brief report of his interesting and informative talk and our conversation.

We live in a world where modern health advancements have improved the overall quality of our life. However, several eminent personalities such as Srinivasa Ramanujan, John Keats amongst others, have succumbed to infectious diseases such as tuberculosis mainly due to lack of antibiotics and other anti-microbials during that era.

Despite the advent of modern day antibiotics, millions of people still suffer from tuberculosis and it results in about 2 million deaths worldwide every year. The main reason for this is emergence of antibiotic resistant strains, as in the case of Methicillin-resistant Staphylococcus aureus (MRSA) where S.aureus became resistant to penicillin and a large number of antibiotics causing almost 25,000 deaths in a year in Europe alone. It’s interesting to note that Alexander Fleming, who discovered Penicillin serendipitously in 1928, when accepting his Nobel Prize, warned that these bacteria could evolve to eat antibiotics.

The modern ideas of antibiotics stemmed from the German scientist, Dr. Paul Ehrlich who noticed that if you stain cells and looked at them under the microscope, there would be preferential staining of the rod like bacteria but not inside the cells. Hence he came to the conclusion that if he could have something that preferentially bound to the bacteria and if it was toxic, it could kill the bacteria. He tried an arsenic-based drug for syphilis but it wasn’t very successful. The first breakthrough came from Dr. Gerhard Domagk who discovered a compound called prontosil or the red dye, while screening thousands of dyes. It was the first highly effective drug against fatal diseases and was used to treat bacterial infections such as Streptococcus but once the active component was discovered as sulfanilamide the following year, it was essentially rendered useless.

However, it was the discovery of the first true antibiotic, Penicillin in 1929 that took the world by storm. Sir Alexander Fleming was known for his astute observation, so when he saw a plate which was left out and contaminated by mold spores; instead of throwing it away, he noticed that next to the spores, the bacterial colonies kept diminishing in size due to some compound secreted by the spore, which was inhibiting the bacterial growth- which was identified as Penicillin. He was awarded a Nobel Prize in 1945 for this discovery and it was not until 1940s that penicillin was actually manufactured in large amounts. Around the same time, a soil microbiologist Selman Waksman realized that soil bacteria could contain several such important compounds which led to the discovery of Streptomycin from the soil bacteria Streptomyces griseus by his student Albert Schatz, after years of painstaking work. It was the first antibiotic that was known to be effective against TB and his work was awarded the Nobel Prize in 1952. So, the discovery of streptomycin led to a huge search of antibiotics from soil bacteria which lead to large repertoire of compounds such as tetracycline, erythromycin, gentamycin, neomycin etc.

The commonality amongst all these antibiotics is that they work by blocking the protein production in bacteria. Thus, it’s important to learn how proteins are made before we understand how the antibiotics block protein production.

ribosomesThe central dogma of molecular biology which explains the flow of genetic information says that ‘DNA makes RNA and RNA makes protein’ with the help of tRNAs. Ribosomes are a highly complex cellular machine and are present in all living organisms. They play a vital role in formation of a full-length protein. They consist of two subunits namely the 50s and 30s subunit, and three sites- E, P and A sites to which the tRNA binds, and adds new amino acids in succession, creating a newly synthesized protein which assumes its functional 3d format once it is produced.

If we need a detailed picture of how antibiotics bind to ribosomes and prohibit their action, we need to know the atomic structure. And this is where crystallography has helped immensely. It has helped the entire structure of ribosome to be solved to a high resolution.

This is how a bacterial ribosome looks like. Most of it is RNA (yellow chain) folded into a complex conformation. The three dimensional structure is stabilized by a number of small proteins (orange + blue) bound to the outer surface of the RNA.  Pic courtesy: http://bit.ly/1AMbRW3
This is how a bacterial ribosome looks like. Most of it is RNA (yellow chain) folded into a complex conformation. The three dimensional structure is stabilized by a number of small proteins (orange + blue) bound to the outer surface of the RNA. Pic courtesy: http://bit.ly/1AMbRW3

From these structures, it is possible to determine the structure of the antibiotics bound to the ribosome. Molecular biologists thought it much easier to do diffraction experiment on crystals of the ribosome into which antibiotics have been soaked in and then subtract it from the image of the empty ribosome and that gave them the image of just the antibiotic.

Using these techniques, we have come a long way in understanding how antibiotics work in inhibiting protein production- like preventing the tRNA from entering the ribosome itself (Tetracycline), blocking the peptidyl transferase site (Macrolides) etc. Streptomycin inhibits the translocation step by binding to the small subunit ribosomal RNA and blocking the activity of EF-G.

Dr. Venki aired his concerns about the problem of antibiotic resistance which has become a major clinical and public health problem. According to him no matter what new compound we make, resistance will always emerge. Bacteria have a number of ways of acquiring resistance. So, Vancomycin which was thought to be beyond all this,  has established resistance over time. Similarly triple-antibiotic therapy for HIV has given way to a multi-drug resistance strain for HIV.

So, the need of the hour is strategies to combat this resistance problem. How can we help in this endeavor?

  • We need a good surveillance team that ensures that there is a rational use of antimicrobials. In developing countries, it is very easy to buy antibiotics without prescription for seemingly irrelevant things. Even today in the US, a million prescriptions for flu are being given annually which is just absurd, because antibiotics have NO effect against the flu which is a viral disease. All these practices need to be abolished if we want to preserve those few antibiotics which we have and not allow resistance to emerge.
  • Infection control is the key and is a matter of sanitation and public hygiene. When there was an outbreak of MRSA in hospitals in UK, they imposed a very strict hand washing regime in hospitals, so that every staff member or visitor had to disinfect their hands prior to even entering the wards during visits. That single-handedly brought down the levels of infection.
  • Finally, Scientists play a very crucial role as they need to help us understand about how bacteria cause disease. Rapid and easy diagnostics for detecting infections should be available. This is important, so that you could take tailor-made antibiotics which will specifically treat your infection, rather than taking broad spectrum antibiotics which are more likely to spread resistance. Vaccine development is incredibly important too, as is developing new drugs and having new compounds that bind to their target, for which Structural biology studies are very important.

He concluded his talk by extolling the versatility of ribosomes in one sentence, “Essentially every molecule in every cell in every living thing is either made by the ribosomes or made by enzymes, which themselves were made by the ribosomes”.

 In conversation with Dr. Venkatraman Ramakrishnan:

You have said that sooner or later, every antibiotic will become resistant. What do you have to say about the recently discovered antibiotic, Teixobactin, which they say prevents resistance?

Well, Teixobactin like Vancomycin and Penicillin act on the cell wall, but they have become resistant too. They say that Teixobactin will not become resistant, but I am a bit skeptical.

What does it take to become a good scientist?

You need a lot of perseverance. Most of the time nothing works well. And as soon as it works, you are moving on to the next problem. And then that’s not working. So you have to psychologically enjoy doing something like that and the reason to enjoy doing science is because you are curious about how things work, or about nature. So if you have that kind of a curiosity and you have a problem which you are interested in then you will be fine. That way every day you will be eager to go to work. Also, you won’t get rich being a scientist. 99.9% of scientists don’t get any kind of award. That’s the goal of science, to enjoy finding out things. You have to work on a problem you care about. If you find you are working on a problem you are not interested in, that’s a bad sign. You need to change your field.

In a talk in 2010 at the Indian Institute of Science, you mentioned that you did not get into IIT or other prestigious schools. Do you think it is important to be in a good school and pursue science or is hard work sufficient ? 

A good school does matter. If you go to an IIT or Harvard, you will be surrounded by bright minds and highly motivated individuals, which will raise your level when you graduate and you are more likely to get a good job or get into a good PhD program. I did not go to great schools initially, but I was an exception who survived it. It worked for me because of luck and a lot of persistence. If I had a chance to go to IITs it would have been better, not easier. Most of the time people don’t have the opportunity to go to a top tier school, and they are not exposed to the best science. It may slow down their career and can even derail it. But if you are in a good university, you are exposed to the best ideas, and really the best kind of science, and you get very good criticism from your colleagues, classmates and Professors. I always tell people to go to the best school they can.

Dr. Venki interacting with students during the networking session
Dr. Venki interacting with students during the networking session