Autophagy (literally, self-eating) was first described in the 1950s, but the last decade has seen an explosion of interest in this degradative pathway. Cytoplasmic components are enclosed in a double-membraned vesicle—the autophagosome—and delivered to the lysosome to be broken down.
Daniel Klionsky didn't set out to study this process. In fact he was initially disappointed when, as a junior faculty member at UC Davis, he discovered that the unusual protein-targeting pathway he worked on in yeast was actually a specialized version of autophagy (1). The cytoplasm to vacuole targeting (Cvt) pathway delivers the enzyme aminopeptidase I directly to the yeast equivalent of lysosomes (2), diverging from the usual transport of vacuole enzymes through the secretory pathway that Klionsky studied as a postdoc with Scott Emr at Caltech (3). Before that, Klionsky, a California native, was a biology major at UCLA and a graduate student at Stanford, investigating the bacterial ATP synthase with Bob Simoni (4).
Klionsky eventually left his home state in 2000, moving to the University of Michigan's Life Sciences Institute where he has continued to study autophagy in yeast, recently uncovering proteins that target damaged mitochondria for degradation (5). In addition, Klionsky has developed new approaches to teaching science (6) that have earned him educational grants from the NSF and the Howard Hughes Medical Institute. Also the editor of the journal Autophagy, Klionsky was nevertheless happy to make time in his busy schedule to discuss his research and extracurricular activities.
Did you always want to be a scientist?
I actually started college as a history major. But I wondered what I'd do with that after I graduated, so I switched to science—I'd enjoyed biology in high school. My main interest was marine biology, and I even had an offer to go to grad school at the Scripps Institute of Oceanography. But my professors at UCLA told me to focus on basic science for my PhD. I should've known that marine biology wasn't the subject for me, because I'm prone to getting seasick. I spent an academic quarter at the research station on Santa Catalina Island, and we took these huge, slow boats out there. I was so ill by the time I got to the island that I remember seriously thinking, “What am I going to do here for the rest of my life? Because there's no way I'm getting on that boat again to go back.”
“I view my teaching the same way I do my research: it's an ongoing experiment.”
Of all the basic science you could've done in grad school, how did you end up working on the bacterial ATP synthase?
One of my courses at UCLA was taught by an electron microscopist who had done some of the early work on the mitochondrial ATP synthase. He was a good instructor, and I found the subject interesting. I interviewed at Stanford, and talked with Bob Simoni, and it just clicked in my mind: “That enzyme really is fascinating. This could be great.” And I also felt—correctly—that Bob would be a wonderful person to work with.
Why did you change fields and work with Scott Emr for your postdoc?
During graduate school, I developed an interest in protein targeting. Bacteria aren't a great system for that so I decided to switch to a eukaryote. I wasn't keen on working in mammalian cells—half of Bob's lab worked on mammalian tissue culture and I saw how I could start a bacterial culture at night to do an experiment the next day, whereas the people doing tissue culture would have to plan weeks ahead.
I went to interview with Scott and it was another really good connection. He was almost jumping out of his seat with excitement, telling me about his research. I felt that if I was ever run down by my project, I could just plug into this guy and he'd re-energize me. He worked on protein targeting in a fairly simple system—I didn't know much about yeast but I knew it was relatively easy to work with—and to top it all off, I could stay in California. It was a match made in heaven.
A JUNK PATHWAY
How did you end up on autophagy?
I mapped the vacuolar targeting signal in proteinase A in Scott's lab, and I suggested that I could do the same for aminopeptidase I (ApeI). Scott essentially said, “Who cares? It's another vacuolar hydrolase and it won't be that much more interesting.”
When I started my own lab, Scott forwarded me a letter from someone looking for a postdoc and said, “I can't take this person, but I thought you might be interested.” The postdoc was from one of the labs that had sequenced the APEI gene and I suggested that we take a look at the corresponding enzyme. That led us to the Cvt pathway, because we discovered it didn't traffic through the regular secretory pathway. I owe my career to Scott's lack of interest!
We got some Cvt pathway mutants and, because nothing had been cloned, to see if they were unique I compared them with other mutants that had been isolated. Even though they were completely unconnected in my mind, I got autophagy mutants from Yoshinori Ohsumi's and Michael Thumm's labs. I was shocked and depressed to find almost a complete overlap. At that time, autophagy was thought of as a garbage disposal system. Who'd want to study that?
What changed your mind?
We started to collaborate with the Ohsumi lab and sent them some antisera to ApeI. I got a phone call from Yoshinori saying, “You must come and look at these results. It's very interesting—I can't explain it to you.” I said, “Are you sure you can't give me a hint? You're in Japan, I can't just hop over there!” But he arranged for me to visit and he showed me these EM images from Misuzu Baba where clusters of ApeI were inside double-membraned vesicles. They weren't being taken up as if they were junk, it was clearly a more specialized mechanism.
Suddenly it was a lot more exciting. It wasn't just a garbage pathway. Then, in 1999, Beth Levine's lab made the first connection between autophagy and disease, showing that it suppresses tumors. For me, that was the last little bit in terms of making it exciting, and almost yearly after that, the pathway has been linked to other diseases—neurodegeneration, removal of pathogens, aging—one thing after another. The field, particularly in higher eukaryotes, has exploded.
What are some of the big questions in the autophagy field at the moment?
We still have fundamental questions about how the autophagy machinery works. There are presently 33 autophagy-related genes in yeast and we know the absolute function of perhaps half a dozen. How does autophagy target different things, like damaged organelles? We recently screened for mutants defective in selective mitochondrial degradation and identified several new genes.
Where does the membrane that forms the autophagosome come from? And how is it commandeered for the pathway when autophagy is up-regulated? We're doing a lot of work on the pathway's regulation right now: we have an exciting project on a transcription factor that controls an important step.
The role of autophagy in various diseases isn't very clear. Autophagy occurs in some myopathies, but it's not known whether it's protective or the cause of the disease. And how autophagy acts in tumor suppression is largely unknown. The pathway can cause both cell survival and cell death, so we have to understand its regulation better if we're going to exploit it for therapeutic purposes.
You're the founding editor of the journal Autophagy. How did that come about?
When Landes Bioscience asked me to start this journal, my initial response was, “It's not the right time, the field's too young.” But the publisher, Ron Landes, replied, “If you wait until it's time, it'll be too late,” meaning that someone else will have started it and I wouldn't get to be in charge. So I thought why not give it a try? I didn't know what I was getting into though. Producing the first issue isn't a big deal because you can publish whenever you're ready to go. But you have a deadline for the second issue, so you're pleading for articles to come in.
Also, I foolishly envisioned all these papers coming in on yeast autophagy, but I've had to learn much more about autophagy in lots of other organisms too, which is great. The journal forces me to interact with lots of people. In 2008, we published a paper that set guidelines for monitoring autophagy in higher eukaryotes. It had over 200 authors and it was fun to write to all these people and say, “Hey, would you like to contribute to and endorse these guidelines?” I want to keep the autophagy community as friendly and interactive as possible. So, although the journal's been more work than I expected, it's also been very exciting.
You're also interested in teaching, and take a different approach to your classes.
I view my teaching the same way I do my research: it's an ongoing experiment to find what works best. I have pretty much eliminated lectures from my Introductory Biology course—it's clear from many studies that lecturing isn't an effective way for students to learn. It's a method that originated before the invention of the printing press as a way to give information verbally, but we don't need to do that now.
I give students my notes at the start of the term and require that they read them before class. I ensure they do it by giving them a reading quiz every session, which counts for half the course grade. With this approach I don't have to lecture on that material and can spend the majority of the class solving problems instead. I'll pose a problem, let them work on it in groups, and then we'll discuss not only what the answer is, but the thought process that got them to that answer. It teaches students to work with facts rather than just memorize them.
Between research, teaching, and editing, do you have any hobbies outside of work?
I do, thanks to my wife, who keeps me from spending my entire life in the office. I'm currently taking a drawing class and teaching myself to play the guitar. In warmer months we like to garden. But yes, the academic life takes a huge amount of time; it can be all consuming. Really, you just have to know when it's time to get on with the other parts of your life.
Text and Interview by Ben Short