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How I became a biochemist

2009; Wiley; Volume: 61; Issue: 7 Linguagem: Inglês

10.1002/iub.178

1521-6551

Jae‐Joon Yim,

Various Chemistry Research Topics

I was born in Seoul, two years before the outbreak of the Korean War. My first memories were of living in Busan, a southern port city to which we fled during the war; our family returned to Seoul when the war ended in 1953. Both my parents are graduates of Seoul National University (SNU), which is rare because it was difficult for Koreans to get a college education during Korea's years of Japanese occupation. My parents were devoted to providing their children with a good education and enrolled me in a special elementary school, SNU Elementary School. Entry into this school was very competitive; the school usually received 20–30 times the number of applications it could accept and gave entrance exams to selected students. I still remember questions asked by the examiners: “You have 8 apples and if you and your brother eat one apple per day, for how many days can you eat?” They also asked me to memorize the order of a sequence of about 10 animals. Thanks to a good memory inherited from my father, I did quite well, scoring first place in the exam and receiving flowers from the school principal at the entrance ceremony on behalf of my classmates. I went on to receive a secondary education at Kyung-gi Middle/High School. Having grown up in a strong Catholic family, I joined Regio Mariae as an extracurricular activity. I made various friends in the group, including one of my best friends, Jung Hun Kim, who sadly died during a mountain climbing accident while studying theology at Collegium Canisianum, a seminary in Innsbruck, Austria. Because of our family environment, many of my cousins chose to attend the Catholic University Medical School and become doctors, but I was not so interested in medical training. During my high school years, I wanted the answers to more fundamental questions and was interested in life phenomena: What is life, how did it originate? What is a soul? What makes a human soul different from that of animals? Is a human soul evolved from animals or given by God as described in the Bible? For me, the Bible explanations or those symbolically expressed in the Sistine Chapel by Michelangelo seemed too simple. In pursuit of answers, I discussed my questions with Rev. Tobias Kim, a Jesuit Father and long-time family friend. It was he who suggested that I study biology at Sogang University. Sogang is a small private university run by Jesuits from the United States. They had adapted United States university systems and curricula, and the level of education was comparable to that of average United States universities at the time. I received a good education from dedicated professors and am proud that Sogang is my alma mater. My most respected professor was Joseph Chang, a neurophysiologist who received his undergraduate and graduate degrees from Princeton, spent many years at Brown University, MBL (Woods Hole), and the Max-Planck Institute. Professor Chang emphasized the importance of neighboring disciplines, encouraging me to take many chemistry and physics courses. He not only taught me biology, but also modeled for me how a future teacher-scholar should be; he was my strongest influence during my career. In my senior year, the natural choice was to apply to graduate schools in the United States. I had good college records and test scores (GREs) and a few schools, including MIT, granted me admission. I accepted a place at MIT. The first year at MIT was challenging. A few weeks into the semester, there was a “mixer” for new graduate students in the biology department. I did not know what to expect at a mixer, but went prepared to sing, because at such parties in Korea, each new student is asked to sing a song. The Beatles were popular at that time and I planned to sing the newly released song “Let It Be.” The party did not go as I expected; only about 15 people showed up, they chatted, had snacks and soft drinks, and that was it. Nobody paid attention to me, asked me to sing, or even to introduce myself. The party ended in disappointment, but also some relief because I had not completely memorized the lyrics of the new song. My first year included many courses: Biochemistry with Gene Brown and Tom RajBhandary, Microbiology with Salvador Luria and Boris Magasanik, and Cell Biology with Penman and Gross. Brown and Magasanik were lecturing perfectionists. Brown never omitted a single H atom when drawing pathways on the board and Magasanik never repeated the same sentences in his loud voice that always kept students awake. Molecular Biology of Bacteria and Bacterial Viruses taught by Harvey Lodish was especially demanding. I had to read copious original papers to keep abreast of the rapidly developing new area. The professors of these courses poured knowledge into students like water from a fire hose. I spent most of my time at the Science Library (Wiesner Library) reading papers and at closing time, moved to another library at the Student Center (Kresge Library). Ashdown House, the dormitory for unmarried graduate students, was only my occasional sleeping place, and I complained that the Kresge Library was open all night. At the end of my second semester, I met Luria, the course advisor for first-year students, who suggested I see Gene Brown. Brown asked whether I had an interest in joining his lab. Although my field of interest was developmental biology, I was pleased with his offer because it gave me somewhere to go other than the library. Having my own desk in the lab also gave me a sense of belonging to the department. I learned how to run columns for protein purification while taking advanced biochemistry courses from Alex Rich, Phil Robbins, Paul Schimmel, and others. Enzyme Reaction Mechanisms, taught by Chris Walsh, was my favorite. These courses fulfilled the first part of my preliminary exam requirements. The second requirement consisted of written exams, followed by oral tests administered by five professors in the biochemistry division. Committee member Gobind Khorana posed a question about membrane reconstitution. I knew little about Dr. Khorana and was nervous, but when I arrived to take his exam, he kindly offered me coffee and didn't ask any questions; the “exam” entailed only an explanation of his research. He later invited me to his summer house in Rockport and visited Seoul as our university guest. My research project was to investigate GTP cyclohydrolase I (CHase I) from Escherichia coli, the first enzyme in the pathway leading to the biosynthesis of the pteridine portion of folic acid and biopterin. A Sephadex column was used to purify the large enzyme but often caused clogging problems. I found the addition of salt in the buffer helped to increase the flow rate, and in the presence of 0.3 M KCl the enzyme disaggregated into smaller subunits of 51,000 Da. In the same lab, Forrest Foor was working on GTP cyclohydrolase II, the enzyme in riboflavin biosynthesis, which he discovered from E. coli. Because its molecular weight was similar to that of the CHase I subunit form, my finding raised the interesting possibility that CHase II was actually a component of the large CHase I complex. The best way determine this was to purify the complex in a native form. I prepared a GTP-coupled gel starting from Sepharose 4B (affinity medium was not available commercially) and successfully obtained the pure protein. With the pure enzyme in hand, the rest of the work went quickly. CHase I is a single protein consisting of four subunits of 51,000 Da, each of which contains two identical polypeptide chains. The subunit has no catalytic activity and, in the presence of the substrate GTP (3 μM), it reaggregates into the native form. The number of GTP binding sites was estimated and it was proposed that the active site is at the inter-phase of the subunits; immuno-diffusion tests then revealed that the two CHases are unrelated. Years later, the crystal structure, determined by Robert Huber, supported all the findings described in my first JBC paper (1). Gene was a wonderful mentor. Although heavily occupied with administrative work as the Head of the Biochemistry Division (later Chairman of the Biology Department and Dean of the School of Science at MIT), he was readily available in the lab. His house in Concord was some distance from Cambridge, so he always came to the office early: 8:00 on weekdays and 9:00 on Saturdays. Once I learned his habit, I tried to arrive 10 min before him on Saturdays because this was the best time for me to show him any new results. He never pressured his students, but gave only encouragement: “Don't waste your pure thinking with dirty enzymes!” was a typical phrase. Laboratory work was exciting, but so was the performance of Boston's professional sports teams. Other social events included parties organized by Korean students at MIT and our sister college, Wellesley, but I usually refused such invitations based on the absurd experience of my first department mixer. When I returned from the lab around 10 pm, I watched ball games in the dormitory TV room. Some students preferred “Startrek,” but most wanted the sports channel. The unbelievable maneuvering and slap shots of Bobby Orr and Dave Cowens' slam dunks gave me great satisfaction and renewed energy after a long day of work. I am thankful to the Red Sox and firmly believe the 1975 World Series was the best in the history of major league baseball. My thesis defense occurred in December 1975. Jon King asked a question regarding heat-stable versus cold-labile proteins (my enzyme surprisingly was very heat stable) and John Buchanan noted it would have been preferable had I determined the second and third amino acids to show the enzyme consisted of one polypeptide chain (I determined only the N-terminal amino acid). A small surprise party took place after the defense, at which Gene informed us the average time to finish a Ph.D. in the biology department was over 6 years. I had finished in 4.5 and was 27 years old. In the summer of 1975, Gene suggested two positions for my postdoctoral work, one at the University of Rochester and the other at Oak Ridge National Laboratory in Tennessee. I preferred ORNL because I could work on Drosophila there and have the opportunity to work on gene regulation in a higher organism. After a one-month break in Seoul, I returned to Ashdown House, packed my few books and my souvenirs from Fenway Park and Boston Garden, and drove to Oak Ridge with a new bride, whom I had married in Seoul in the Myung-dong Cathedral where I was an altar boy. Bruce Jacobson, a biochemist from Johns Hopkins who worked with Linus Pauling at Caltech before joining ORNL, had an interest in the fly eye color mutant known as purple. Purple is deficient in pteridine pigments such as drosopterin (red pigment) and sepiapterin (yellow pigment). We began to examine the level of enzymes in pteridine biosynthesis, for which we needed pure GTP cyclohydrolase. We had a clear advantage over other laboratories in pursuing the project. Separation of pteridine compounds was performed on thin-layer cellulose plates in the dark and we later developed new assay methods using reverse-phase HPLC. Ed Grell, the author of the Drosophila mutant catalog known as the “red book,” provided us with flies carrying different doses of purple. The collaboration was fruitful and we proposed that purple is the structural locus for sepiapterin synthase, more precisely PTP (6-pyruvoyl tetrahydropterin) synthase, one of two enzyme components required for the synthesis of sepiapterin (2). We continued our work on the biosynthesis of drosopterin, the major red eye pigment in wild type flies. In this project, we worked closely with Dale Dorsett, now at St. Louis University. After two years, I was appointed research associate and began to enjoy the idyllic atmosphere of the Tennessee countryside. I could have built up my career in Oak Ridge, but Helen, my wife, having spent her whole life in the big city of Seoul, felt differently. Around that time, Seoul National University adapted a new “open system” for recruiting faculty and offered me a position in the microbiology department. We returned to Seoul with our one-year old daughter, Jennifer. Thirty years ago, my department had only two centrifuges, one scintillation counter, one HPLC, and a spectrophotometer for research purposes. SNU, as the most prestigious university, attracted students from all over Korea, but with such laboratory conditions we could not do much research. It took 3 to 4 years to set up my own fly room and dark room and purchase basic materials, such as gel media for chromatography. In the mid 1980s, reflecting a rapidly growing Korean economy, the government founded the Korea Science and Engineering Foundation (KOSEF), modeled after the U.S. NSF, and began to invest in research. The research grants offered jointly by KOSEF/NSF and KOSEF/German DFG were especially useful and I took advantage of the programs to continue research in pteridine biochemistry. In 1988, I spent my sabbatical year in Konstanz, Germany, with Wolfgang Pfleiderer. Wolfgang is well known in heterocyclic chemistry and he determined the structure of the drosopterin pigment; I knew his name from my graduate days. The year in Konstanz as a Humboldt Fellow was rewarding, both scientifically and personally. While learning pteridine chemistry from Wolfgang, we traveled to neighboring countries with our inquisitive son, Jinwoo, and made wonderful memories. The association with Pfleiderer continued and years later resulted in a joint publication describing the structure of a minor red eye pigment called aurodrosopterin (3). Scientists in the pteridine research field gathered once every 4 years; the 9th International Symposium on Pteridines and Folates, held in 1989 in Zurich, was one of the most memorable. Key participants were Adrian Albert, one of the founding fathers in pteridinology; Seymour Kaufman, who discovered the coenzyme function of H4-biopterin; George Hitchings, who reflected on his work that led to a Nobel Prize; and Gene Brown, who gave a nice overview of the metabolism of pteridines in his Gowland Hopkins Lecture. During the week-long symposium, I spent a wonderful evening with Gene, Bruce, and Wolfgang in a small restaurant outside Zurich. The photo taken with my three teachers at that restaurant is always near me in my office. Drosophila research took off again with the advent of the postgenomic era. Drosophila is undoubtedly the best model organism for developmental biology research. Since my undergraduate years, I was fascinated by how a fertilized egg could develop into tissues with diverse functions and wanted to explore this field. An opportunity arose in the mid 1990's when the Korean government launched a program called the Creative Research Initiative. Under the new program (with support of ∼$1 million/year for 9 years), I set up the CRI Center for Genetic Reprogramming at SNU. We recruited several junior faculty members from leading institutes in the United States and together established many enhancer trap fly lines to secure novel genes and investigate their functions in early drosophila development. In the past 10 years, my lab switched from a classical enzymology lab to one of developmental biology, but my preference remained in pteridine biochemistry. Now, 20 years after the Zurich Symposium, the 14th International Symposium of this series will be organized in Jeju, Korea. Nenad Blau, with whom I have enjoyed collaborating since my sabbatical year at Konstanz, is the co-organizer. I look forward to seeing many old friends and collaborators in the subtropical resort island this coming June. This is my 30th year at SNU and the University presented me with a gold ring for my service. Professors of SNU have certain advantages. As government employees, once appointed, 90% of professors can retain their position until retirement with a stable income. Many SNU faculty members serve on government policy-making committees and play leading roles in academic societies. However, working in a conservative system like SNU often brought disappointment and stress. Multidisciplinary collaboration is essential to cope with rapidly changing research environments, but it was often difficult to overcome department barriers due to a bureaucratic system and the existing cronyism among faculty members. The Bio-MAX Institute was established at SNU with a vision to support young star scientists and a strong emphasis on multidisciplinary research with prominent foreign scientists. As the founding director of the new institute, I am glad that the Bio-MAX spirit is strong and that our efforts have significantly influenced the globalization of the campus and the Korean scientific community as a whole. During my tenure at SNU, I have spent a considerable amount of time developing the Asia-Pacific International Molecular Biology Network (A-IMBN) with colleagues in Asia. Established in 1997, after the European model of EMBO, our mission is to promote molecular biology and biotechnology through organizing conferences, workshops, training courses, and other innovative programs. These activities are described elsewhere (4). SNU has a very strict, mandatory retirement policy. I can continue teaching biochemistry courses as an emeritus professor, but the time is approaching to end my research activity. I am greatly indebted to my wonderful teachers who showed me how to be a scientist and enjoy doing research as a biochemist. In the latter part of my career, I was fortunate to be able to devote myself to developmental biology in quest of the secrets of life. How can a single cell develop into tissues and organs and eventually into an organism with a soul? Mind and soul may originate from sophisticated brain function, but I am doubtful of the extent to which modern brain research can reveal this secret. My longest-standing and most fundamental question remains unsolved and I am beginning to realize that science alone cannot provide the answer. In that sense, I was on the right track and do not regret my career as a biochemist.