慶應義塾大学先端生命科学研究所慶應義塾大学先端生命科学研究所

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Assistant Professor Martin Robert

Assistant Professor Martin Robert
Assistant Professor Martin Robert

─ Please tell us about your current research.

I am currently working on several basic research projects, all focusing on the greater objective to improve our understanding of how the cell works as a whole or as a complex system, by observing the function and changes of molecular components and their regulation. For this purpose, I am using the simple bacterium E. coli as a model organism.

The first of the those projects is about the characterization of parts of the cells of unknown function. Now that the genome sequence is available, we can assume that we already have a good working parts list of the E. coli cell. However, this is valid mainly for nucleic acids and proteins whose sequence are directly encoded in the genome. Other components, that we refer to as metabolites, such as amino acids, lipids, sugars and multiple other small molecules are not encoded in the genome and are the products of the multiple activities of metabolic enzymes which are themselves proteins encoded in the genome. This is the main reason I am particularly interested in metabolism and the discovery and understanding of how these other cellular building blocks are made. We still don't know well the function of nearly half of E. coli genes and a large proportion of these appear to be putative enzymes that must also be important for the cell. It can be frustrating to try to make sense of a cell for which we still don't know what about one half of all these proteins are doing. So here we hope to first fill some of these holes in metabolic knowledge. So we go about this mainly in two ways. One is to select enzyme candidates in the genome sequence, express and purify them, and then look for which compounds they are responsible for making or breaking down. The other way around is taking a biochemical transformation which we already know is or should be present in E. coli and to try to find the enzyme (protein) that is responsible for this function. We can select enzyme candidates simply by looking at the sequence information and its computational annotations or by using additional layers of available information such as gene expression patterns or the identity of proteins with which a candidate is known to interact with. At this stage, we may or may not know what the specific metabolite targets are, but we have designed a screening system to allow the identification of the function regardless of the knowledge about the chemistry of the targeted reaction. This is unlike traditional approaches that simply look for the predicted catalysis using specific assay using the predicted substrate and product pair.

We can do this by placing a purified enzyme into a "metabolite soup", a mixture of hundreds of metabolites, and by observing the changes caused by the protein using global measurements of the biochemical composition of the mixture (metabolomics or metabolome analysis). As a result of enzyme catalysis, one or more metabolites are expected to decrease in amount, and in parallel other metabolite(s) are expected to increase. When we can link the two, we can basically work out the reaction, that is identify the substrate(s) and product(s) of the reaction as catalyzed by the purified enzyme.

Recently because of the large amount of data accumulating from experiments performed all around the world, we often have better guesses about what the uncharacterized proteins may be doing. In this case we try to confirm the guess more directly by targeting a reaction and its expected substrate and products only. This is simpler and takes less time so we can try to solve more puzzles at once.

A related second project, is that we can come up with metabolic changes that were not suspected to exist within the E. coli. Sometimes some could turn out to be useful for specific purposes. Obviously, from the cell's perspective the reaction is important for its maintenance and survival but it could also have engineering applications for the industrial production of molecules that are difficult to obtain otherwise. I imagine here possible new drugs or industrially important biochemicals or biofuels. We hope to generate clues in this way from this originally purely discovery-oriented approach.

I've also has the opportunity to work with colleagues on more computational projects. Because our activity-based screening methods look for any molecular changes in the cell in order to find out the new activity, we need to look at multiple molecules at the same time and analyzing such metabolomics data is difficult. When I started working at IAB, there were very few good tools we could use to analyze the large and complex data we were collecting (a big problem at first!). But I had some idea about possible way a of doing it, and so we started this development of bioinformatics tools. These tools now allow us to probe into metabolomics data, try to find the very small changes in complex profiles of molecules and identify the molecules associated with them. These tools have been widely used both in our projects and in other metabolomics projects at IAB as well as other laboratories around the world. It's very gratifying when the solutions we come up for solving our problems eventually end up helping others too. And this is pretty much what science in about anyway. Building from the work of others and sharing of our findings/tools, is at the core of the process.

The third major project I had the chance to be involved in was a large multi-scale study of E. coli. This was a big partnership with a lot of people at IAB. Most research groups at IAB were involved at some level and my contribution was obviously just a part of a very large collaborative effort. In this project we analyzed the gene and protein expression levels, as well as measured the concentration of metabolites and metabolic fluxes in E. coli. This was a real quantitative biology project where the cell was examined following various deletions (about 25 gene knock-outs were analyzed) of important genes in central carbon metabolism. In addition to these genetic changes, we have also looked at the effects of changes in growth conditions, where the cell is fed limited but increasing amounts of glucose and so its rate of growth increases proportionally. We could observe what happens inside of the cell when its growth rate changes and seen how it reorients most of its resources for producing the machinery for making proteins, when the growth rate increases. We have also observed how resistant central metabolism is to the removal of a single enzyme. Our findings naturally reflect how important such pathways are for the cell and how it is well equipped to face problems by shifting gears or using alternative roads (pathways). It's been a fascinating learning experience for all of us and has been the source of inspiration for more projects for me and I believe for other scientists around the world as well. Therefore while this project is now completed (as if a research project was ever completed!) both the data and findings are still the source of continuous derivatives and sources of ideas for more work on E. coli biology.

Finally, I'm now also now working on some other projects related to how E. coli metabolism changes during adaptation to a different environment and also how metabolism varies with time to shape a complex network of well organized metabolic activities. It's fascinating to explore how a simple bacterium seems to find new ways to optimize its activities so as to overcome some growth handicaps induced by changes in its environment and how it therefore evolves and retain new characteristics in its genome information. This is obviously a complex issue but luckily at we have at IAB very good experimental facilities to address such problems, and most importantly I have excellent colleagues to facilitate and support such studies.

Proteins are the main machines that make life happen, so if you are interested in the function of cells and their machinery, like I am, then you are often looking at proteins. Now I still have much interest in proteins, and as mentioned earlier I now particularly enjoy the study of metabolism as it sits at the core of this link between genetically encoded proteins and purely biochemically-derived metabolites.

─ What was your first research experience?

I was studying biochemistry as an undergraduate student at McGill University in Montreal, Canada, so I had a good general background but not so much research laboratory experience. But near the end of my studies I had the chance to spend a whole summer in the urology laboratory in a large university hospital in my hometown. This experience gave me the chance to learn what experimental research was really like. It pulled the trigger for me and made me want to come back, half a year later to do related research work for my graduate studies.

For my Ph.D project, I worked on the biochemistry of seminal plasma, analyzing proteins that affect the movement of spermatozoa. The basic work involved tedious purification of a protein that affected the movement of spermatozoa, through standard biochemical approaches to purify the proteins and isolate the active component. Once I had done this, I found that this protein turned out to be a protein fragment, a small piece of a larger protein. I discovered that the fragments came from a larger precursor molecule, which was cleaved into smaller pieces. This provided a good opportunity to study the fragmentation process, so I also isolated this original precursor form of the protein encoded by the same gene. I then looked for and successfully found the enzyme that is cutting this protein into pieces. This was an unexpected finding, but this enzyme turned out to be a well-known protein, prostate-specific antigen (PSA), which was already widely used as a marker of prostate cancer. At least at that time, it was the best marker of prostate cancer progression, but physicians using it didn't really know what its biological function was. I thus discovered that the enzymatic activity of this protein was important to degrade this motility inhibitor. Its use in the clinic as a marker of cancer is mostly due to the fact that it is one of only few prostate-specific proteins that can be detected reliably in serum and whose level generally increases with cancer grade.

Sometimes life takes you onto unexpected paths and directions. So because I was in this particular urology laboratory for many years, I befriended some of the several Japanese physicians and scientists that came to train in our lab, and also sometimes worked on closely related research topics. Before the end of my Ph.D degree, one such former laboratory member invited me to his laboratory in Japan. I enthusiastically grabbed this opportunity and I came and spent about six months in Japan when I was still a student in Canada. To say that I really liked the experience would be an understatement. I was completely thrilled and fascinated by everything. It probably was the most exhilarating experience of my life. After that, I went back to my hometown in Canada to finish my degree, but this experience had a large impact on the career choices I would make subsequently. It gave me the idea of coming back to Japan after I finished my degree to pursue more research. As you can see, I am still here after over ten years! If I had not been in this particular lab in Canada at this particular time, this probably would have not happened. My life would likely be very different in many ways. This illustrates one of many occurrences that all of us experience, often by chance but that significantly change our life. It keeps fascinating me.

─ Tell us about your daily practice outside of research.

I try to get a few hours of sleep everyday, but I'm sure that's not exactly your point (laughs). Mainly keeping some time for family (to which I owe much) and myself when I go home is a practice I try to maintain. Some free time that could be used for anything, like reading, watching TV, listening music, or do some web surfing, anything really. Basically some quiet moments, usually in the late evening, to reset my mind and relax. So it's not really an active pursuit in the traditional sense, but rather different relatively common activities I try to keep some time for everyday.

─ What is your hobby?

I enjoy photography at a very casual level rather than as a technical pursuit. I try to have fun and to make the best of simply capturing moments. It's fascinating how much fixed instants in pictures can sometimes both represent well a scene while sometimes they don't. I guess it's the distorsion of reality introduced by having captured only an instant of a dynamic scene. To me photography is an interesting and accessible mixture of art and science and I can manage to have fun while doing it without much technical skills or fancy equipment. Recently I also started playing the ukulele, thanks to the support and patience of some of my IAB colleagues. It's been a very humbling experience because while I've always been a music lover, playing this relatively simple instrument has been quite a challenge. But it's been fun and relaxing!

─ What do you value in your life?

I am an easy-going person, and like to think that I'm also friendly and accessible. I like to interact with people and share experiences with them. Unless you live alone at the top of the high mountain as a hermit, if you live in a society,

whatever its size and location open-mindedness, respect and tolerance are important keys to a happy life. And among the many things this country (Japan) has taught me, these values are near the top of the list. There are many hurdles in life too and it comes without any guarantee, but these values can take you a long way, in your personal relationships, your work, or at any other level really. To me these values are crucial although I also know that they are not always easy for anyone to follow. I like to think I can still learn every day so there is much to always look forward to and I hope to remain open-minded even as aging sometimes naturally tends to erode this desire.

─ In your future, what do you want to achieve in your life?

I think my dreams involve progress and evolution throughout life. I was fortunate enough to realize some of my dreams already and for this I am very grateful. Of course, dreams and targets keep changing and what I think about now can likely be different a few years later. I hope to be able to continue to pursue basic research and keep being fortunate enough to do work that I also really enjoy. I know the research world is not an easy one but I want to keep going and growing. In the end the greater goal, of course, is to make a significant contribution to society through my work and other actions.

I want to continue following this path I've chosen. I think this is only possible through sustained and renewed efforts, not by waiting for things to happen. I also hope to pursue novel avenues in both my research and personal life and of course make great discoveries. But I will still be able to find satisfaction in solving smaller pieces of a very large puzzle. Because to me, life in all its aspects, both personal and at work, is really a collective effort.

(Nov. 8th, 2007. Interviewer: Yukino Ogawa Editor: Nobuhiro Kido and Kaoru Kikuta Photograph: Takeshi Masuda)

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