Takashi Yura: pioneer, visionary scientist, friend

Takashi Yura was a pioneer, a visionary scientist, and an amazing human being, who left an indelible mark on all who knew him. He was an enduring scientific collaborator and colleague, as well as my longstanding friend. Takashi changed the course of my life, in ways big and small, and I know I’m not alone in having that experience.

I first met Takashi Yura in the late 1970s, when I was a Research Scientist in Dick Burgess’ laboratory. Takashi had given a seminar and had a scheduled meeting with Dick to talk about the sigma (σ) subunit of RNA polymerase. I was invited to that meeting, and we immediately realized that we were on the same scientific wavelength—I think we talked for hours. At that time, Takashi and I were both trying to understand the in vivo role of σ and as a prelude, we both were mapping the location of its gene on the E. coli chromosome. Indeed, we each published papers in PNAS reporting the gene location within a few months of each other, with Takashi’s paper appearing first (Nakamura et al. 1977, Gross et al. 1978). Each of us combined extensive knowledge of cutting edge (at the time) E. coli genetics, with an appreciation of the biology of the organism to achieve this result, although our route to discovery was very different.

It was during these next few years that I first got an inkling of who Takashi was, as a person and a scientist. I was not even a faculty member when we had our first meeting, yet he came back again and again to talk with me about science, and continued doing so even after I started my own laboratory in 1981. Surely, I thought, Takashi must have considered the fact that this risked antagonizing Dick Burgess, a well-established member of the scientific community. As I got to know Takashi, I realized that, to the best of my understanding, he didn’t think about such trivialities—he was driven solely by the desire to do the best science that he could, and by supporting his chosen colleagues in their own vision of science.

I learned that Takashi had come to the USA to pursue science right after WWII, starting at the Carnegie Institute (now Cold Spring Harbor) and then moving with Vogel to Yale. Indeed, Takashi was the first Japanese national to obtain a Ph.D. in the USA after the war. Takashi had many stories to tell about his time at both places—all filled with fond recollections of the people he met and worked with. Not once did he mention any negative interactions, even though he must have experienced them—that was not his way. Takashi even briefly considered staying in the USA, intrigued by the scientific vibrancy and egalitarianism he experienced, particularly at Cold Spring Harbor, which really shaped his scientific career. Cold Spring Harbor was the epicenter of the nascent molecular biology revolution that began in the study of bacteria and their viruses (phage). The phage meeting brought together scientific leaders from all over the world. Takashi became part of this community and thereafter would feel at home doing science in many places and later on nurtured this universalism as part of his mission. Encouraged by his wife, Masako, Takashi returned to Japan and took a position at Kyoto University where he was incredibly successful. By the time I knew him, he was a world-renowned researcher, whose lab had already made many fundamental discoveries about how bacteria regulate and control central cellular processes, but I did not learn this from him—I had to figure it out myself.

Interestingly, after our parallel studies identifying the sigma subunit of RNA polymerase, Takashi and I independently turned our attention to the E. coli heat shock response (HSR), converging on the same questions but getting there by somewhat different paths. As a beginning scientist, I became aware of the HSR in the process of characterizing a σ mutant, and then followed this lead, only dimly aware of the field I was entering (Gross et al. 1984). In the process of characterizing his own σ mutant, Takashi discovered that the non-mutant strain increased expression of a number of proteins upon heat shock (heat shock proteins, HSPs) and demonstrated that their transcription increased coordinately. Takashi, world traveled and cognizant of major trends in science, was aware of the Drosophila heat shock literature, had seen the evidence that many eukaryotic organisms carried out a HSR, and immediately connected his results to the wider heat shock literature, thus providing the first evidence for a bacterial HSR (Yamamori and Yura 1980). Then, in a landmark paper (Yamamori and Yura 1982), Takashi realized that a previously described ts mutant was likely defective in production of one of these HSPs, based on MW analysis. His hunch proved correct—he found that this mutation prevented expression of all the HSPs he had observed, leading him to suspect that this enigmatic locus likely encoded a HSP transcription factor, and he followed this up by obtaining nonsense mutations in this gene, showing they had the expected phenotype, and determining the gene sequence (Yura et al. 1984).

I think it is remarkable that Takashi completely supported my own scientific efforts on this problem, even though he was a scientific leader and I was an unknown scientist who was directly competing with him. After finding that HSPs were overexpressed in our σ⁷⁰ mutant (Gross et al. 1984), we considered the possibility that the gene identified by Takashi was a sigma factor, and showed that this was true (Grossman et al. 1984). I should mention here something that I have been aware of for a long time but never really put into context, until my recent extensive work on Diversity, Equity, and Inclusion gave me a framework for thinking about it. Takashi, my brilliant and famous friend, was at a huge disadvantage, compared to me. He was a member of an “out” group and had difficulty publishing his work in “high profile” journals, making it easier for Americans to claim primacy in this field and many others. Indeed, most of his high-profile papers were published in PNAS, and they were communicated by famous Japanese scientists. This is something that we need to discuss as a community to make sure it is not true going forward.

Our scientific relationship continued to strengthen throughout the 1980s and into the 1990s. Both of us continued deciphering circuitry of the HSR, with each of us making key discoveries of its complexity, sometimes in parallel (e.g.Taura et al. 1989; Straus et al. 1989). Takashi often spent several weeks at a time visiting the lab, attending our group meetings and talking with the students and postdocs, giving them ideas and new perspectives.

Here’s what Alan Grossman, my first graduate student, said:

It was an honor and pleasure to have known Takashi. For many years, including my most formative ones, his research interests paralleled those of my thesis advisor. I was continually impressed by the parallels in approaches, rigor, and creativity, and more so by the admiration and collaborations that developed between Takashi and Carol. Two labs that appeared to be 'competing' worked in parallel supportively and respectfully. This is how science should be done. To this day, I use one of his early papers (Yamamori and Yura 1982) on the heat shock response in E. coli in my graduate course in microbial genetics. This paper is a tour de force, measuring the heat shock response, demonstrating that it is transcriptional, and characterizing a mutant (then called hin or htpR, which we now know encodes sigma-32, the heat shock sigma factor of E. coli) that was defective in the response. My personal interactions with Takashi were always engaging. In his quiet way, he was insightful with a hidden sense of humor and a wry smile. He had a huge impact in science, and I suspect an even larger impact on those who were fortunate enough to know him.

David Straus, who followed Alan Grossman to continue working on HSR circuitry, has this recollection:

I certainly enjoyed Takashi’s presence but had not interacted with him much - both of us being reticent types- until Carol suggested that I show him some sigma-32 immunoprecipitation experiments I had been doing. The precipitations had worked well, we were able to measure synthesis rates, but I was puzzled by the apparent presence of heat shock proteins (DnaK and GroEL) in the immunoprecipitates. I was skeptical that this association was meaningful, but Takashi was enthusiastic. He encouraged me to believe it, and of course he turned out to be right.

I also remember when two of my students, Ding-Jun Jin and Yan-Ning Zhou, both from Nanjing, invited Takashi and me to dinner. Ding was in the first wave of students to come to the USA from mainland China. Takashi was visibly perturbed at the invitation. I was surprised because he had bonded with them in the lab. He explained to me that before he could enjoy dinner at their house, he would have to apologize for the Japanese brutality in Nanjing, as he carried it heavily in his heart. He did have that conversation with them, and we both enjoyed a fantastic Chinese dinner at their house. Interestingly, their son, Kang Xing, who was a little over 1 year old, demanded that Takashi use chopsticks, but was perturbed when I did as well—he had clearly internalized that recognizable groups had distinct ways of eating food. These recollections reveal a lot about Takashi. As a person, Takashi was reticent and also humble, and carried within himself a strong sense of morality and justice. As a scientist, Takashi was inspirational and had a unique way of motivating young scientists to do great things.

Both Takashi and I were part of the vibrant heat shock community, whose biennial Heat Shock meetings at Cold Spring Harbor alternated with the FASEB Protein Folding in the Cell meeting. These meetings spanned the prokaryotic/eukaryotic divide from the very beginning, allowing all of us to see how essential features of the response had been conserved from bacteria to human, while being extensively elaborated in eukaryotic organisms (see Yura 2019). They also recreated the intellectual ferment that Takashi experienced earlier during his time at Cold Spring Harbor, and now, Takashi was able to carry this further. He set up Heat Shock meetings in Japan on a regular basis, promoting the intermingling and integration of Japanese science and scientists in the world community. These meetings introduced me and many others to Japan, and its wonderful culture—I treasure those memories to this day. It also allowed me to form strong relationships with many fantastic Japanese scientists, in adjacent fields—all promoted by Takashi, who was really a citizen of the world.

Takashi also suggested that he and I apply for a binational grant—a funding mechanism I didn’t even know existed, which funded the exchange of students as well the heads of laboratories. We got this grant, and I visited Takashi’s lab for the first time, spending a week talking to people. Takashi was particularly interested in my talking to his female students, as he worried that there were not enough Japanese female scientists to be their role models, and he was very anxious to do what he could to right the situation. This grant enabled my student, Jim Erickson, to visit Takashi’s lab, and Noriko Kusukawa, a female student of Takashi’s to visit my lab and talk extensively with people. Here’s what Jim had to say:

My trip to Japan came in part because Takashi's student, Hiroki Nagai, and I had independently discovered a new promoter for the rpoH gene, which encodes σ³²--me because it was induced by ethanol, Nagai, he was just Nagai, because it was under CAP/cAMP control. Takashi greeted me at the airport and the next morning took me on a thrilling drive through the very narrow streets of Kyoto. At his lab, I was greeted with excitement and given the grand tour. Within a few hours my visit had become a merger. Over the week, we talked science, planned experiments, and the outline of a paper. Those details have faded but I remember how welcome he and his lab made me feel. I remember a wonderful lab dinner party with plenty of food and drink and broad smiles from Takashi. I remember too, my friendships with Nagai, and with Noriko Kusukawa, who later visited our lab in Madison. My most treasured memory is of the walking tour of some of Kyoto's most famous landmarks with Takashi. Our conversation mixed science, history, travelogue and philosophy. Takashi's wisdom, gentle humor, and fundamental decency will be with me always.

Our binational grant ended in 1993, when Takashi’s lab at Kyoto University was closing, but Takashi’s journey in science did not end when he was forced to retire. Takashi reinvented himself, obtaining private funding for the HSP (Heat Shock Protein) Research Institute for 7 years (1993–2000) and becoming its founding and only Director. He continued all of his previous activities, but on a larger scale, publishing some of his most important work on the HSR. This position and Institute also enabled him to nurture young scientists—and Takashi was great at picking out those with stellar intellects and great scientific instincts. I particularly highlight Kazutoshi Mori who had been a postdoctoral fellow at University of Texas Southwestern with Drs. Mary-Jane Gething and Joe Sambrook, where he had discovered the circuitry of the unfolded protein response, just before Peter Walter came out with similar findings. Unfortunately, his mentors left for Australia, but Takashi was able to offer him a position at the HSP Research Institute, and nurtured Kazu’s career. I specifically remember one incident. I was visiting Japan, staying as usual with Takashi and Masako, when Takashi asked me to go over Kazu’s manuscript that he planned to submit to PNAS. Kazu and I worked on it together for several hours at Takashi’s kitchen table, and it turned out exceedingly well (Mori et al. 2000). Kazu, of course, went on to win many prizes, including the Lasker Award, jointly with Peter Walter. I was honored to be invited to the ceremony as Kazu’s guest. Kazu was also a recipient of the CSSI Medallion, awarded in Huangshan, China in 2015.

Happily for me, Takashi continued visiting my lab even though his duties and responsibilities had increased significantly in his new role as Institute Director. And, happily for both of us, this led to Takashi’s next re-invention. When the HSP Research Institute closed its doors, Takashi was not ready to stop doing and thinking about science, even though he was 71 years old. In contrast to the vast bulk of scientists aged 70 + years, who have forgotten how to do bench work and are pursuing other interests, Takashi spent time in my laboratory over a span of the next 5–8 years. As an adjunct faculty member, Takashi either did the science himself or collaborated with my students/postdocs to complete projects that he felt were of pressing interest. Most important was our incomplete understanding of a group of σ³² mutants with aberrant regulatory properties, obtained from conceptually similar screens carried out in both my lab and Takashi’s lab (Horikoshi et al. 2004). The mutants mapped to a small 4-aa region of σ³², but neither lab understood the mechanistic basis of the phenotype. Collaborating with me, my students and postdocs, Takashi led the effort to figure this out. First, Takashi together with my student, Eric Guisbert, examined these mutants rigorously in vivo and in vitro. They made the surprising finding that in vivo the mutants were simultaneously resistant to degradation by the FtsH protease, and to inactivation—the negative regulatory loop in which excess chaperones bind to σ³² and inactivate it. Here’s what Eric had to say about interacting with Takashi about these mutants:

Upon his retirement from the HSP Institute, Takashi paved a unique scientific pathway as what he liked to call a “gypsy scientist”. He travelled the world and spent time working in several different laboratories. He found a second home in the laboratory of Carol Gross, where he entered a productive phase of research continuing his focus in σ³² and the heat shock response. He travelled to San Francisco several times a year and spent several months for each visit.

I always admired his fearlessness, both scientifically and personally, that would allow him to travel by himself to a different country and work in an unfamiliar environment. This is evidenced by the fact that he was one of the first Japanese scientists to travel to the US after the end of World War II. That he accomplished so much in post-war Japan and also after his retirement under difficult circumstances says a lot about his character.

While in Carol’s lab, Takashi made a remarkable discovery that a series of hyperactive σ³² mutants were defective in chaperone-mediated feedback regulation, thereby uncoupling their activity from cellular protein folding. This discovery sparked several lines of investigation into the relevant regulatory mechanisms and the utility of these mutants for recombinant protein expression (Zhang et al. 2014).

While Takashi referred to himself as a “gypsy scientist”, the students and postdocs in the Gross laboratory saw him as more of a “gentleman scientist”. Despite his impressive reputation and amazing accomplishments, Takashi was polite, humble, and easy to get along with. He also had a great sense of humor and his keen observations often led to humorous comments. Moreover, he had a “joie de vie” that manifested in dinners out, tide-pooling, and whale watching trips with members of the laboratory. No person that I ever met had a single bad word to say about Takashi, which is in and of itself quite a remarkable feat.

But behind his pleasant exterior, there was a passionate and dedicated scientist, who was driven by his curiosity to uncover the mysteries of the cell. These qualities contributed to his central role as a leader in the heat shock field, serving as a mentor, collaborator, and contributor to the lives of innumerable researchers from all over the world. In the Gross lab, Takashi took on a central role contributing to the research and serving as a second mentor for some of the graduate students, who benefitted immensely from his wisdom, insights, and passion.

Unfortunately, in vitro, the mutants exhibited almost normal binding to both RNA polymerase and chaperones (Yura et al. 2007), indicating that there was a missing step. Faced with the conundrum of mutants without an explanation, Takashi took the path of any good bacterial geneticist—select more mutants! Specifically, he was looking for mutants located outside of σ³² that exhibited the same phenotype as our tight cluster of σ³² mutants, which could help us identify the transacting factor responsible for this phenotype. His transposon screen netted DnaK (Hsp70), and DnaJ as expected, but also identified a novel locus, which Takashi together with Dr. Deborah Siegele, a former graduate student, now a Professor at Texas A & M, who was doing a sabbatical in the lab mapped to the promoter region upstream of FtsY. Here’s how she remembers this interaction:

In 2007, I had the good fortune to work in the same lab as Takashi Yura for several months. I was an Associate Professor on sabbatical and Dr. Yura was a theoretically retired emeritus professor and we had both come to do experiments in Carol Gross’s lab at the University of California San Francisco. I had come to work with a new post-doc, Nassos Typas, on developing a genome-wide genetic interaction screen for E. coli. During my time in the Gross lab, I also worked with Dr. Yura. Helping him to find the elusive transposon insertion upstream of the E. coli ftsY gene that interfered with homeostatic regulation of the heat shock response is one of my proudest scientific accomplishments. A favorite memory from that time was Dr. Yura finishing some minipreps for me, so I could leave the lab and catch the train to visit friends in Davis. I am honored to have known and worked with Dr. Yura, someone I had looked up to both as a scientist and an exemplary human being, ever since meeting him when I was a graduate student.

FtsY is the Receptor (SR) for the Signal Recognition Particle (SRP), composed of Ffy and 4.5S RNA, which together mediate co-translational insertion of inner membrane proteins. Now Takashi and I had to figure out the relationship, if any, between the SRP/SR system and the σ³²-mediated HSR. Our thinking was guided by the fact that several lines of evidence indicated a close relationship between the two processes. Working with my graduate student, Bentley Lim, at University of California San Francisco, and many collaborators both in San Francisco, and later, when he returned home, in Japan, Takashi finally pieced together the story. Previously, σ³² was thought to reside in the cytoplasm. This work showed that the central regulatory feature of the response was to target σ³² to the inner membrane via its interaction with SRP/SR. It is from this location that degradation and activity control are carried out. Importantly, this allows the σ³² response to simultaneously monitor cytoplasmic and inner membrane protein folding, thus integrating proteostasis in both compartments of the cell (Lim et al. 2013). Here’s what Bentley had to say about the impact of working with Takashi:

I had the pleasure of working with Takashi during my Ph.D. in Carol Gross's Lab, where he and I identified and characterized the connection between the co-translational SRP/SRP receptor protein targeting machinery and □³² in regulating protein homeostasis. When Carol talked about the challenging project that Takashi was working on, I eagerly joined Takashi on this scientific journey knowing I would work with another scientific great during my Ph.D. It was apparent Takashi had immense dedication and passion for his work - developing extraordinary technical and intellectual expertise that I strive for with all my scientific pursuits. But my time working with him also showed me how to be an outstanding member of the scientific community. Through him, I learned to value the importance of collaborations well beyond borders and time zones. He taught me how to embrace differences in cultural, technological, and scientific environments, which has only led to my success as a scientist. Through him, I learned how to love science, manage it, and share that joy with others. Ultimately, I was honored and blessed to engage with Takashi for several years of his life. These few years significantly shaped who I am as a scientist today.

When he was almost 80, Takashi returned to Japan, and became a visiting researcher at Kyoto University, and subsequently at Kyoto Sangyo University, undertaking to advise students in return for having a lab bench to carry out his experiments. There, he continued to follow up the ramifications of SRP/SR targeting of σ³² to the inner membrane (Miyazaki et al. 2016; Yura et al. 2018).

Takashi spurned accolades and fame, preferring instead to spend his hours at the bench, wrestling with and unlocking the mysteries of life. He was the epitome of a true scientist, with an unusual ability to inspire others to find joy in this pursuit. Takashi was a true friend, and an amazing person. I miss him greatly.

From the left, Takashi Yura, Carol Gross and Eric Guisbert