After spending seven years at the world-famous Max Plank Institute of Biochemistry (Munich Germany) researching Rubisco, the most abundant protein on earth and deconstructing its production in plants, protein biochemist, Dr Javaid Yousuf is probing the response to infections by plants so that his laboratory at CIRI-KU is able to generate a novel vaccine that can replace the ecologically-dangerous pesticides. Excerpts from his detailed interview with Masood Hussain
KASHMIR LIFE (KL): Could you please explain how proteins and carbohydrates as food, function at the molecular level?
DR JAVAID YOUSUF (DJY): A cell is a basic unit for any biological process, within which various metabolic pathways are functional. Some of them are involved in glucose biosynthesis and its degradation, whereas others are involved in the metabolism of proteins and lipids. Multiple biochemical pathways operate simultaneously within the cell and are attuned to the individual’s needs in response to outside cues.
Proteins are biomolecules, which are formed through a specific pathway, and in turn take part in all the cellular pathways, including their own formation just like the chicken-egg dilemma. Proteins are essential for all biological processes. The proteins that we consume in the form of food are broken down to their constituent amino acids, which in turn are again utilized for the formation of proteins within our bodies and this cycle continues.
KL: Do you mean to say that the proteins we consume help in improving the proteins within our bodies?
DJY: Yes, protein consumption helps in increasing the proteins within our bodies. We see that sometimes in cases of protein malnutrition, which may be due to insufficient food consumption, overwork or because of some illness, protein degradation occurs, for which doctors recommend protein consumption either through natural sources or in the form of supplements. These proteins are then hydrolysed to their constituent amino acids, which in turn make new proteins within our body. Thus the more amino acids our body gets, the more proteins will be produced, and hence more muscle and bone mass will be formed.
KL: Before we get into protein chemistry further, can you tell us about your journey from school to CIRI?
DJY: I have done my initial schooling till the tenth standard from Anantnag, followed by plus-2 from Government Higher Secondary School Dialgam. I did my bachelor’s in science from Government Degree College Anantnag. Later, I qualified national-level entrance examination in biotechnology for pursuing my master’s from the School of Biotechnology, University of Jammu.
During my master’s I qualified CSIR-JRF examination and got selected for the PhD programme at Jawaharlal Nehru Centre for Advanced Scientific Research (JNCASR), Bangalore. It was there, that I specifically started to get trained in protein chemistry. In the master’s programme in biotechnology, we get an overview of many broad areas such as biochemistry, microbiology, immunology, and chemistry, however, the focus of my PhD revolved particularly around protein structure and function.
My PhD work was related to Plasmodium falciparum, the causal organism of malaria, mostly prevalent in the warmer areas of the country. Since malaria is very common in the states outside Kashmir, the laboratory I joined for PhD (Prof Hemalatha Balarama’s lab), was focused on Plasmodium biochemistry only.
During my PhD, I studied a specific enzyme from Plasmodium falciparum, GMP synthetase, which helps in the formation of Guanosine monophosphate, a building block of DNA. I have studied GMP synthetase in detail, including its structural analysis. We basically aimed at characterizing this protein in order to elucidate how different it is from its human counterpart for using it as a drug target against Plasmodium.
Our ultimate goal was to control malaria. We used a well-known technique of mass spectrometry for this study, and the data that we obtained, showed clear differences between human GMPs and Plasmodium falciparum, indicating that it can be a potential target for anti-malarial drugs. My previous laboratory in Bangalore is still exploring this enzyme even after more than ten years.
My training around protein structure and function continued unto Max Plank Institute of Biochemistry, Munich Germany, a world-renowned institute for protein science. There, I worked in the Cellular Biochemistry department headed by Prof Ulrich Hartl, in a laboratory (Prof Manajit Hayer-Hartl’s lab), which was focused specifically on protein structure and function analysis. There I worked on Rubisco, nature’s most abundant enzyme. The main aim of my study was to understand how Rubisco attains its functional form for its use in biotechnology.
In protein biochemistry, we use a basic technique known as recombinant DNA technology, wherein we can express a gene from any organism in bacteria, from which the desired protein can be obtained in pure form for further downstream analysis. Through this study, we were able to understand that five different proteins assist Rubisco at various stages during its formation. Using these proteins that we found, we were successfully able to express the enzyme in its functional form in Escherichia coli. These proteins are now being used the world over for the successful expression of Rubisco in Escherichia coli. This was a very significant study, which got published in a prestigious journal – Science.
In some other projects that I undertook we aimed at understanding the functional regulation of Rubisco. Here we revealed the molecular mechanism of a chaperone required by Rubisco to attain its functional form. Chaperones are proteins which assist other proteins to fold properly and attain a functionally active form.
KL: What are your current researches?
DJY: My current research is the structure-function analysis of AAA chaperone proteins. Recently one of our projects that got approved from ICMR is about a protein involved in ribosome biogenesis. Interestingly, ribosomes although being the main players in protein biosynthesis themselves require the assistance of other proteins for their biogenesis reflecting again a chicken-egg like situation. If we mutate these chaperones it manifests in the form of various neurodegenerative diseases as well as cancers.
Another project in our laboratory revolves around plant immunity. For example, if a human body encounters any kind of foreign invasion, it generates an immune response against it. Similarly, an immune response is generated in plants, which are more susceptible to infections for being sessile. The immune response in plants is very advanced. Upon foreign invasion, two types of defence mechanisms are activated. Firstly, a response is activated when a foreign body lands on the plant surface generating a localised immune response from the plant. The other one is activated when infectious agents like bacteria, or fungi enter the plant body. The response envisages triggering a chain of reactions known as the hypersensitive response, which can be seen as blisters on the plant surface.
These proteins also belong to the AAA+ family of chaperones which we are studying in rice. Rice is the staple food of the quarter population of the world, especially in India, so it is a very important crop which sustains the economy and helps the basic society.
These things are yet unexplored in rice. So we are trying to study how it can cope with these infections. Once these pathways are understood in rice, we can expand this concept to other crops as well. This is a highly unexplored area. If we explore these defence mechanisms, we can generate novel vaccines against various diseases in plants, which can replace pesticides. As everybody knows pesticides envisage huge environmental risk factors. If we succeed, it can help humanity better.
KL: You have also worked as a scientist after your post-doctorate. How was that experience? And also tell us how much have we been able to understand these proteins.
DJY: After spending nearly seven years in Munich as a postdoctoral fellow, which was mostly based on the characterization of Rubisco, I became familiar with mass spectrometry, a very important technique used the world over for protein science. This is a highly evolved technique with applications in diverse fields such as chemistry, physics, astronomy and biology.
I learned this technique first in Bangalore and gained more expertise in Munich where this technique was highly advanced. We used it for analysing protein dynamics.
Proteins are not static. To be functional, a protein has to be dynamic, and this protein dynamics can be measured using mass spectrometry. After gaining expertise in this field, I moved to a Medical Research Institute in Riyadh where I was the in-charge of the proteomics facility.
As for as the number of proteins within a cell, only one to two per cent of the genome is expressing proteins and has the capacity to produce around 100,000 proteins. Because of the mass spectrometry revolution, 10,000 proteins can be routinely identified nowadays. In Riyadh, my focus was on diabetes, and we wanted to study the effect of fasting on diabetes. From Riyadh, before that study could conclude, I shifted to the University of Kashmir.
KL: Now that you are back home. What should we expect from your laboratory in a few years?
DJY: I am a basic biochemist, which means that I am trying to understand biology at the basic level. So, we anticipate that our findings will be taken up in the next ten or twenty years and utilized for drug design.
Earlier I spoke about the chaperone involved in ribosome biogenesis. If we can perform its structural and functional analysis, the next level will be to identify its inhibitors, which can finally be used as therapeutics. We anticipate that our basic findings will be translated into therapeutic strategies for related diseases.
KL: Are all the researchers in your lab working on the same protein?
DJY: No, they are working on different proteins although we have a similar strategy for their molecular analysis.