Autophagy -
July 2009
Interview Date: September 2009
Yoshinori Ohsumi
From the Special Topic of
Autophagy
According to our Special Topics analysis of autophagy
research over the past decade, the work of Professor
Yoshinori Ohsumi ranks at #1 by total number of papers and
#2 by total cites, based on 93 papers cited a total of
7,061 times. Five of these papers are among the most-cited
over the past decade for the topic. In
Essential Science IndicatorsSMfromThomson
Reuters, Prof. Ohsumi's record includes 115
papers cited a total of 7,436 times between January 1, 1999
and April 30, 2009.
Prof. Ohsumi started his autophagy work at the Tokyo University, then
moved to the National Institute of Biology, Okazaki, and now belongs to the
Tokyo Institute of Technology's Integrated Research Institute.
Below,
ScienceWatch.com talks with Prof. Ohsumi about his
highly cited research.
Would you tell us a bit about your
educational background and research experiences?
I started graduate school at Tokyo University under the guidance of
Professor Kazutomo Imahori. Since the first subject I started to work with
was in vitro protein biosynthesis of E. coli,
intracellular dynamics of proteins has always been in my mind. From the
third grade I changed my research subject to the mode of action of Colicin
E3, which turned out to inactivate ribosomes after binding to the cell
surface receptor. Gradually I became interested in membrane phenomena.
Then I became a postdoc at Dr. G.M. Edelman's lab at Rockefeller University
for three years. I failed to get any satisfactory results, but learned
something in cell biology, and strangely enough I started yeast work in his
lab.
3 hrs nitrogen-starved cells
View/download five
accompanying slides and
descriptions. PDF
Then I came back to Japan and worked with Prof. Yasuhiro Anraku. His whole
lab had been working on amino acid transport in E. coli, while I
started biochemical studies on vacuolar membranes. By establishing a method
of vacuolar membrane vesicle preparation, I could show the vacuolar
membrane possesses active transport systems of amino acids and ions. We
also succeeded in showing that the vacuolar type H+-ATPase was a primary
pump for proton gradient across the vacuolar membrane. I realized that the
vacuole is a much more active organelle then ever thought and plays
important roles in maintaining intracellular homeostasis.
What first interested you in autophagy?
In 1988 I moved to College of Arts and Sciences at the University of Tokyo
as an associate professor. It was a small lab—just me and several
instruments. At that time I decided to study a lytic function of vacuoles
as my main research theme. Nothing was known about what and how cellular
proteins are degraded in this acidic compartment. It was hard to get a
clear strategy from where I should start. In the life cycle of yeast,
sporulation is a dramatic cell differentiation process, which is triggered
by depletion of the nitrogen source from the environment. So I thought bulk
protein degradation must occur to this cell remodeling.
At that time not many people had observed inside the yeast cell by light
microscope, though now fluorescence microscopic observation is quite
popular for yeast researchers. The vacuole in yeast is the only organelle
easily detectable under light microscope, so I had always observed them
this way. One simple idea stuck me. If vacuolar proteinase-deficient mutant
cells are shifted by the condition of nitrogen starvation, I might see some
structures inside the vacuole which had escaped from degradation. In fact,
this proved to be the case. I found such clear and impressive morphological
changes of the vacuole. Many vesicles, named autophagic bodies, were
vigorously moving around in the vacuole. This was the just the starting
point of my work on autophagy in yeast. It was quite natural that I started
to introduce genetic screening to get autophagy-defective mutants by
microscopy again.
Much of your highly cited work appears to focus on
various Apg proteins. Would you talk about this aspect of your
research, and tell us why Apg seems to be a key player in
autophagy?
Our first screen was quite efficient and we could get 14 APG genes
essential for autophagy. Our Apg (now renamed as Atg) proteins appeared to
consist of molecular machinery of autophagosome formation, which was the
most critical event of autophagy. I personally believe that nutrient
deficiency is the most frequent and serious stress for wildlife. In nature,
an organism needs to maintain viability against nutrient deficiency,
therefore a recycling system of its own constituents must be a fundamental
requirement of life. Therefore, starvation-induced autophagy is the origin
of autophagy in the evolution of eukaryotes. In the future we will have
much more factors required for autophagy in various physiological
circumstances, but the core machinery consisting of these Atg proteins must
play important roles for membrane dynamics.
We know now that these Atg proteins consist of five functional units
including two ubiqutin-like conjugation systems. Autophagy became quite a
popular field in biology, but still not so many people are working on the
molecular mechanism of membrane dynamics during autophagy. I believe
several basic questions about membrane dynamics still remain. Therefore my
group is challenging these mysteries by concentrating on the simplest
system, yeast, S. cerevisiae.
Earlier this year, you published a paper in
Biochemical and Biophysical Research Communications, "Lap3 is
a selective target of autophagy in yeast, Saccharomyces
cerevisiae." Could you tell our readers something about this
paper?
"I personally believe that nutrient
deficiency is the most frequent and serious
stress for wildlife."
We thought that starvation-induced autophagy is a non-selective process of
degradation. Standard medium of yeast, YEPD, is extremely rich in nitrogen
compounds and other nutrients. The cells growing in this medium are
adjusted to rapid growth and lack completely autophagy, which may be a
rather unusual situation in nature. So far we found Ald6 is preferentially
delivered into the vacuole to be degraded. It is the obvious question for
us whether yeast cells also have a selective and constitutive mode of
autophagy, which is crucial for such systems as neuronal cells in mammals.
We found Lap4 behaves quite similarly with Ape1(Lap3), main target of the
Cvt pathway, but it is not a vacuolar resident but rather degraded in the
vacuole.
We are interested in what kind of growth conditions induce selective mode
of autophagic degradation of cytoplasmic soluble enzymes, ribosomes, and
organelles. These studies will give clues to understand the various modes
of autophagy in mammals and plants.
How has our knowledge of autophagy changed over the past
decade?
Autophagy was discovered quite a long time ago by excellent electron
microscope work, but quite little was known about the physiological roles
of autophagy. Identification of ATG genes tremendously changed the studies
of autophagy. The effect of ATG gene disruption revealed vast involvements
of autophagy in various aspects of life. Now there is increasing consensus
that cellular proteins are in dynamic states between synthesis and
degradation.
Where would you like to take your research on autophagy in the next
decade?
With the field getting more crowded, I doubt that I myself will be able to
settle so much broad aspects of problems related to autophagy in the next
few years. As mentioned above, there are so many problems that remain to be
solved in membrane dynamics of autophagy, especially formation of
autophagosome and various modes of autophagy, which are at present called
collectively autophagy, but I think it is necessary to dissect them
according to molecular mechanism.
Yoshinori Ohsumi, Ph.D., Professor
Tokyo Institute of Technology
Integral Research Institute (IRI)
Nagatsuda, Midori-ku, Yokohama, Japan
Kabeya Y, et al., "LC3, a mammalian
homologue of yeast Apg8p, is localized in autophagosome
membranes after processing," EMBO J. 19(21):
5720-8, 1 November 2000. Source:
Essential Science Indicators from
Thomson
Reuters.
KEYWORDS: AUTOPHAGY, PROTEIN INTRACELLULAR DYNAMICS,
MEMBRANE PHENOMENA, YEAST, S. CEREVISIAE, E. COLI, VACUOLAR MEMBRANE
VESICLES, ACTIVE TRANSPORT SYSTEMS, PROTON GRADIENT, VACUOLE, BULK
PROTEIN DEGRADATION, NITROGEN STARVATION, GENETIC SCREEN, APG, ATG,
LAP3, LAP4.