Fearless about Folding

Susan Lindquist has never shied away from letting her curiosity guide her research career.

By | January 1, 2016

Professor, Department of Biology
   Massachusetts Institute of Technology
  Member and former director,
  Whitehead Institute for Biomedical Research  
  Cambridge, Massachusetts
Howard Hughes Medical Institute investigator
As a junior faculty member at the University of Chicago in the late 1970s, Susan Lindquist heard about a new system for knocking out yeast genes, developed by Terry Orr-Weaver, Jack Szostak, and Rodney Rothstein. “I thought, ‘Wow, you could knock out genes; that is really powerful.’ So I decided I would work on yeast,” says Lindquist, a professor in the biology department at MIT and a member (and former director) of the Whitehead Institute for Biomedical Research in Cambridge, Massachusetts.

At the time, Lindquist was studying the heat-shock response in Drosophila melanogaster using fly-cell tissue cultures. A more senior colleague, yeast geneticist Rochelle Esposito, took Lindquist aside and gave her some advice. “She said that she didn’t normally interfere, but wanted to tell me that it was really risky to switch organisms before getting tenure,” recalls Lindquist, who appreciated the advice, particularly at a time when female professors received little mentoring. But, that risk didn’t scare Lindquist—because she had never dreamed of being able to become a tenured professor. “I thought it was a miracle that I got this faculty appointment and was so happy to be there for a few years that I just wanted to follow what was exciting for me. I didn’t have expectations of getting tenure. So this was an aspect of gender inequality that was extremely positive. It allowed me to be fearless.”

“I like to do high-risk and high-payoff kind of research. And I had a gut feeling that MIT was a cool place to be with people who are fearless.”

Lindquist took the Cold Spring Harbor yeast course, received experimental help from Esposito, and published her first yeast study in 1981, establishing that the heat-shock response was driven by translational regulation and worked differently in yeast than it did in fruit flies.
Since discovering the fun of dreaming up experiments and then trying them in the lab as an undergraduate, Lindquist has let this spirit guide her career choices. Her initial decision to study the heat-shock response in fruit flies led her to examine wide-ranging topics in diverse fields including neurodegenerative disease, drug resistance, cancer, evolution, and prion biology as she tried to understand translational regulation and protein folding.

Here, Lindquist talks about an elementary school teacher who made her students think about big questions; how she benefited from the failure of her original graduate thesis project; and the brash resubmission of an almost identical grant application after it had been initially rejected.

Lindquist Learns

Aspirational thinking. Lindquist grew up in a middle-class neighborhood of Chicago. Her parents, first-generation Americans from Sweden and Italy, had not gone to college but revered education. Instead of playing with dolls, Lindquist tried to talk her friends into dissecting tree berries. She read books like the biography of Elizabeth Blackwell, the first woman to receive a medical degree in the U.S. “I remember being with my grandmother and mother and my uncle came in and asked what I wanted to be when grew up. I said ‘A doctor,’ which took him aback. He was expecting me to say ‘nurse’ or ‘actress.’ And my mother and grandmother laughed like, ‘Kids say the darndest things.’ I grew up in a time when women were not expected to do anything interesting.”

The ultimate question. “My fifth-grade teacher, Ms. Davis, made science really interesting. One day she told us to close our books and that we were going to talk about something for an hour. She wrote a question on the blackboard, ‘What is life?’ and we tried to come up with ideas like ‘It moves’ or ‘It consumes oxygen.’ That was such an electrifying moment for me.”

Seized opportunity. Lindquist did well in high school and received a scholarship to the University of Illinois at Urbana–Champaign in 1967. “This was fundamentally important to me, to be able to afford going to school, and I still believe so strongly in the value of public education and state-funded universities.” Her first biology class, microbiology, was taught by Samuel Kaplan, who “made it this exciting science of how you discover new knowledge. He would describe the experiments scientists had done and it was a different way of teaching. So I decided to major in microbiology.”

High aspirations. In her junior year, another microbiology professor, Jan Drake, asked Lindquist if she wanted to do research in his lab. “That was another electrifying moment for me. He suggested I apply for a National Science Foundation fellowship, and I got it. This stipend was an incredibly important influence on me. I had worked as a waitress and at a fruit stand in the summer to pay for my dorm fees. And now I received a stipend for doing something I thought was fun.” Lindquist worked on the bacteriophage T4, providing evidence for the “headful-packaging” hypothesis, which posits that replicated T4 DNA fills the phage head to capacity then stops. Some redundancy of the DNA sequence is necessary for the viral genome to circularize after it is injected into the host cell at the start of an infection cycle. Lindquist found that by making the DNA more compact, more of it could be stuffed into the phage head. “It was so cool to me that you could make a prediction and show that it could happen.” Drake suggested that Lindquist apply to graduate schools, including Harvard and MIT. “My jaw dropped open,” says Lindquist. “I didn’t even tell my friends I applied to these schools because I thought it was so presumptuous.”

Expectation management. Lindquist began graduate school in Harvard’s department of biology in 1971. “I came from a family environment where I was not expected to go to college or graduate school. Still, the name Harvard was awe-inspiring. I had an appointment with my graduate advisor there, Fotis Kafatos; I remember seeing the great big doors of the biology lab building and putting my hand on the door and not having the nerve to open it and talk to this Harvard professor. I was a modest person from a modest family, and I was so astonished that I could presume to be there and do well. Doing well there was a very important aspect of my development as a scientist.”

Lindquist Launches

Imposter syndrome. “Harvard was not a very welcoming place for young women at that time. It was tough, partly because of my own shyness. I was easily intimidated and had a heavy dose of imposter syndrome. But I developed a certain amount of toughness and confidence, so I must have been a good imposter,” says Lindquist. She joined Matthew Meselson’s laboratory, and when her first project failed to yield any data, she looked for a new angle for studying eukaryotic chromosomes. Lindquist had heard about the heat-shock response in fruit flies from a junior faculty member whose lab was across the hall. “She told me about this cool phenomenon in fruit flies where you can see puffs on salivary gland chromosomes in response to heat. If you labeled the salivary glands, you could see new proteins being made. I wondered if tissue-culture cells would make similar proteins. If so, it would make molecular analysis possible.” Lindquist got the go-ahead from Meselson to give the experiment a try. It took her a while to work out the methods to visualize the protein bands that appear after heat treatment of the cells. “I remember thinking ‘Holy Moly, I can see the bands on this film’ when I came out of the darkroom. It was one of those visual moments you remember for the rest of your life.”

Free to be me. “Having to devise my own project was the best learning experience I could have had. If Matthew had directed me, I would have followed, because I was so in awe of him. But because he was involved in chemical and biological warfare research, I had to create my own learning environment. That was a different time, when we could do basic research and students had freedom to follow interesting questions not tied to translational research.”

A corner of her own. After finishing graduate school in 1976, Lindquist joined Hewson Swift’s laboratory at the University of Chicago as a postdoc. “He was remarkable man who also ran an eclectic lab. He didn’t really know any molecular biology and let me come in and do what I wanted, which was to continue to study heat-shock proteins,” says Lindquist. She had to set up a lab space for herself, including molecular biology equipment and an area for doing fly-cell tissue culture. After two years of rapid success, the department offered her a faculty position. “I don’t remember thinking I could run my own lab, although it must have occurred to me at some point. I just really loved science. My highest aspiration then, if I did really well, was to have a corner of a lab and write grants under the auspice of a male professor.” Lindquist’s lab soon demonstrated that, following their synthesis, heat-shock proteins are rapidly shuttled into the nucleus, where they associate with chromosomes.

Window into cell dynamics. Lindquist initially used the heat-shock response as a tool to study gene expression. She was among the first to establish a model system for how eukaryotes orchestrate gene expression changes beyond the level of transcription. “We had no insight into gene expression at that time, and here you just apply a little heat treatment and you could change the whole pattern of gene expression. It seemed to me the best system to study how a cell could be making one set of proteins and then change. And unlike development, it took only half an hour for the change to occur.” Her lab showed that the heat-shock response is self-regulating—that upon heat shock of Drosophila cells, the quantity of the major heat-induced protein Hsp70 correlates with the amount of stress and that the level of this protein is controlled by other heat-shock proteins. The lab also showed that the regulation of the protein occurs on the level of RNA translation and that RNA splicing is interrupted during heat shock.

A living test tube. Lindquist then decided it was time to figure out what those new proteins were doing. The first major breakthrough involved Hsp90, an essential protein that was upregulated by heat. She observed that higher levels of the protein were required when cells were grown at higher temperatures. Hsp90 appeared to interact with completely unrelated proteins such as mutated, oncogenic kinase receptors and steroid receptors. Because these proteins were inactive when bound to Hsp90, the working hypothesis of other labs was that Hsp90 was a protein repressor. But when Lindquist’s lab expressed human oncogenic v-src in yeast—using yeast as a living test tube to study mammalian proteins—they found that Hsp90 was necessary for the activity of the v-src tyrosine kinase. “If you really want to investigate the biological function of proteins, doing it in a crowded cellular cytoplasm is really important. It proved pivotal for Hsp90 because we were able to use genetics to show that it was not a repressor but a chaperone that was helping these proteins to fold.” Because association of other oncogenic tyrosine kinases with Hsp90 is necessary for their maturation, but wild-type kinases required little Hsp90 to function, Lindquist reasoned that Hsp90 facilitates changes in protein function and could drive malignant transformation. The lab went on to show that the protein also assists in the evolution of drug resistance in different types of fungi.

“What is unique about Hsp90 is that it is made at high level and serves as a buffer, a reservoir for protein folding at normal temps. This is what allows it to play a very important role in evolution, allowing proper folding of a new mutation that would otherwise misfold. Hsp90 allows those proteins to acquire new functions with new mutations”

Daring work. In 2001, Lindquist moved her lab from the University of Chicago (where she had become a full professor in 1988) to the Whitehead Institute at MIT. “I like to do high-risk and high-payoff kind of research. And I had a gut feeling that MIT was a cool place to be with people who are fearless.” Lindquist’s ability to pursue such research began in 1998 when she became a Howard Hughes Medical Institute investigator. “It’s been tremendous for my lab because it allows you freedom to do high-risk research like the Hsp90 work. I would never have been able to continue that research under my normal NIH grant.”

Lindquist Leaps

Different expectations. “My parents both expected that I would quit science once I had kids. But they were very supportive and helpful when they realized I was not about to quit. My mother thought it was very cool that I was a professor; she was quite proud of me.”

Undeterred vision. After submission of her first NIH grant renewal was rejected, Lindquist resubmitted practically the same application to a different study section for review—and got the stamp of approval. “Someone told me that I needed to find the NIH study section with the smartest people because what I was proposing was novel and unique. It was scary advice, but turned out to be right. I only changed one section and wrote a cover letter saying these are important experiments and the right experiments to do. I think they were amazed that I had the nerve to do that.”  

Partnership. “I have the most wonderful husband who has been the biggest influence on my life and my professional success. We met on the dance floor at a ‘favorite professors’ party in a dorm at the University of Chicago. I deliberately wanted to find someone who was not working in my profession because I was interested in art and literature but had to drop a lot of that to focus on science.” 

Greatest Hits

  • Using heat-shock response as a tool, was among the first to show that certain mRNAs, including those that code for the heat-shock protein Hsp70, contain translational control elements that autoregulate the message’s transcription and translation
  • Using several different model systems (Drosophila melanogaster, Arabidopsis thaliana, yeast, and human cells), demonstrated that Hsp90, a protein-folding chaperone, favors evolution by allowing mutated proteins to fold into functional forms
  • Established that Hsp104 can disentangle heat-induced protein aggregates and return them to normal function
  • Provided the first biochemical and cell biological evidence that some genetic traits can be transmitted by self-perpetuating changes in protein folding without any modifications to DNA or RNA, supporting the prion hypothesis
  • Established that Hsp90 and prions provided two different but completely logical mechanisms for Lamarkian inheritance

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Avatar of: Roy Niles

Roy Niles

Posts: 106

January 16, 2016

"Established that Hsp90 and prions provided two different but completely logical mechanisms for Lamarkian inheritance."

Logical mechanisms.  In other words, intelligently constructed systems, and as noted above, parts of the hypothetical Lamarkian self adapting "mechanisms."

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