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Commentary
The Nobel Prize for understanding autophagy,
a cellular mechanism of waste disposal that keeps us healthy
The Nobel Prize in Physiology or Medicine, 2016, was awarded to Prof Yoshinori Ohsumi from Tokyo
Institute of Technology, Yokohoma, Japan, for his work that helped in understanding the molecular
mechanisms of autophagy, a process used by most eukaryotic cells to degrade a portion of cytoplasm
including damaged organelles, large protein complexes and aggregated proteins in lysosomes. This process
of autophagy (self-eating) maintains cellular homeostasis and helps the cell and the organism to survive
during periods of stress, such as starvation, by recycling the cellular components to generate amino acids
and nutrients needed for producing energy. Autophagy and ubiquitin-proteasome system are the two major
protein degradation systems in the cell.
The lysosome was identified by Christian de Duve in the 1950s as a membrane bound organelle in the
cell that contains degradative enzymes such as proteases, lipases, acid phosphatases, etc. (de Duve, 2005).
The term autophagy was coined by Christian de Duve in 1963. Autophagy generally occurs at low level, but
it increases under conditions such as stress and differentiation/remodelling of tissues. Autophagy was
primarily studied by electron microscopy for decades because no molecular markers were available for its
molecular analysis.
1.
Formation of autophagosome, the hallmark of autophagy
The hallmark and major component of autophagy is the autophagosome, which is a double membrane
bound structure that carries the material to lysosome for degradation. The autophagosome fuses with the
lysosome to give rise to autolysosome where actual degradation and recycling takes place. The formation of
autophagosome has been studied extensively and initially a cup-shaped vesicle is formed known as
phagophore or isolation membrane (Yang and Klionsky, 2009). The machinery of autophagy extends this
phagophore leading to closure of this structure (figure 1). The formation of autophagosome from phagophore is a complex process that requires the function of two ubiquitin-like conjugation systems
(Mizushima et al. 1998; Ichimura et al. 2000). ATG12 and ATG8 (LC3) behave like ubiquitin and are
conjugated ultimately to ATG5 and PE (phosphatidylethanolamine), respectively (Mizushima et al. 1998;
Ichimura et al. 2000). The first of these two ubiquitin-like systems conjugates ATG5 with ATG12 to
produce ATG12-5 conjugate which in turn forms a non-covalent complex with ATG16L1. The ATG12-516L1 complex is recruited to the phagophore where it functions as an E3-like ligase in the second ubiquitinlike system to conjugate LC3I with PE to produce LC3II which localizes to membrane of autophagosome
(Ichimura et al. 2000). LC3I is produced from the newly synthesized LC3 by the action of a protease that
removes a C-terminal amino acid leaving glycine at the C-terminus. LC3II is often used as a marker of
autophagosome and the level of LC3II provides a measure of autophagy (Kabeya et al. 2000). LC3II is
involved in expansion and closure of phagophore to help in the formation of mature autophagosome. It also
helps in the recruitment of cargo in the autophagosome by binding to adaptor proteins that in turn directly
Keywords.
Atg proteins; Atg8/LC3; autophagosomes; phagophore; ubiquitin-like conjugation system
Abbreviations used: ALS, amyotrophic lateral sclerosis; Atg, Autophagy-related; PE, phosphatidylethanolamine
http://www.ias.ac.in/jbiosci
Published online: 04 November 2016
J. Biosci. 41(4), December 2016, 563–567 * Indian Academy of Sciences
DOI: 10.1007/s12038-016-9651-8
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interact with the cargo. Cargo selective autophagy is mediated by autophagy receptors that interact with the
autophagosomal protein LC3 and also with the ubiquitinated cargo. Ubiquitin molecule in the cargo very
often serves to anchor it with the autophagy receptors. Membrane needed during formation of autophagosome from phagophore is sourced from several different organelles including ER, mitochondria, plasma
membrane and recycling endosomes (Shibutani and Yoshimori 2014) .
2.
Identification of genes involved in autophagy
When Ohsumi started his work on autophagy, it was not known whether or not autophagy occurs in yeast
(Saccharomyces cerevisiae). He created a mutant of yeast defective in three proteases present in the vacuole
(lysosome of yeast) and showed that these mutants accumulate undigested material (autophagic bodies) in the
vacuole when grown in nutrient-deficient media (Takeshige et al. 1992). This could be seen under a light
microscope. By then it was already known that autophagy is induced by deficiency of nutrients (carbon source,
amino acids). In the normal growth medium, this protease-deficient mutant did not accumulate autophagic bodies
due to very low level of autophagy. Wild-type yeast, when treated with a protease inhibitor, also accumulated
autophagic bodies. This protease-deficient mutant was mutagenized, and secondary mutants that did not show
accumulation of autophagic bodies when grown in nutrient-deficient medium were isolated. This selection strategy
for isolation of autophagy-defective mutants was crucial for identifying genes involved and understanding the
molecular mechanisms of autophagy. These mutants were first described in a landmark paper published in 1993
(Tsukada and Ohsumi 1993). Over 75 mutants isolated by him fell into 15 complementation groups (genes). These
mutants were defective in protein degradation in vacuole, and quickly lost viability upon nitrogen starvation,
showing clearly the role of autophagy-mediated degradation in cell survival under starvation conditions. These 15
mutants were named as Apg1-15 (renamed later as Atg1-15). Currently 33 Atg genes are known in yeast.
Over the years Ohsumi and his group cloned and characterized several of the genes involved in autophagy, and
determined their function. They also determined the order of the genes in mediating autophagy. One of the first
genes isolated was Atg1, which is a protein kinase that controls initiation of autophagy. The current picture of
autophagy that emerges from their work and the work of several other groups is depicted in figure 1. There are
several types of autophagy based on the way cargo is delivered to lysosomes. The most common is macroautophagy, often referred to as autophagy, where the cargo to be degraded is first enclosed in autophagosome and
the autophagosome fuses with the lysosome. Another type of autophagy is microautophagy, where the cytoplasmic
material is directly engulfed into the lysosome. The third type of autophagy is chaperone-mediated autophagy,
which involves recognition of cargo to be degraded by heat shock cognate protein HSC-70, which then delivers the
cargo into the lysosome. Autophagy is also classified based on the type of cargo which is degraded. Autophagy of
mitochondria is called mitophagy, whereas autophagy of bacteria is called xenophagy.
3.
Functions of autophagy and its relevance to human diseases
Most of the yeast autophagy genes have counterparts in mammals, sometimes having several homologues in
higher organisms. Mutational analysis of Atg genes in mice have revealed their functions. Mice deficient in Atg5
gene are born almost normally. However, all the newborn Atg5-deficient mice die within a day. Soon after birth,
mice need to be fed with milk and during this interval they depend on autophagy for survival (Kuma et al. 2004).
Autophagy is increased in many tissues of the new born wild type mice. The Atg5 protein is essential for
autophagosome formation. Therefore, for essential genes conditional and/or tissue specific gene knockout mice
have been created to study their function.
Tissue-specific inactivation of Atg genes have revealed that autophagy is required for survival and
normal function of neuronal cells. Brain-specific deficiency of Atg5 or Atg7 genes leads to neurodegeneration and accumulation of ubiquitinated protein aggregates in the neuronal cells (Hara et al. 2006;
Komatsu et al. 2006). Defects in autophagy are associated with various neurodegenerative disorders
including Parkinson’s disease, Alzheimer’s disease and Huntington’s disease. Further evidence for the role
of autophagy in neurodegenerative diseases is provided by the finding that certain mutations in an
autophagy receptor, optineurin, are causatively associated with ALS (Amyotrophic Lateral Sclerosis) and
J. Biosci. 41(4), December 2016
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The Nobel Prize 2016 for understanding autophagy
Figure 1. The steps involved in autophagy: Autophagic process can be divided into following steps. Initiation: It is mediated by complex
comprising of ULK1, FIP200 and ATG13. Activity of ULK1 is regulated by phosphorylation at specific residues by AMPK and mTOR.
Under conditions of nutrient sufficiency mTOR inhibits autophagy while AMPK activates autophagy under energy insufficiency. ULK1
complex acts as a scaffold for recruitment of downstream ATG proteins. Nucleation: ULK1 complex targets class III phosphatidylinositol
3-kinase (PI(3)K) complex, which contains Beclin 1 and VPS34 (vacuolar protein sorting 34) among others. Phosphorylated Beclin1
induces local generation of PI3P (phosphatidylinositol3-phosphate) by VPS 34. PI3P then recruits PI3P effectors such as DFCP1 and
WIPI2. Elongation: Presence of WIPI proteins at the nucleation site leads to localization of ATG12-5-16L1 complex at this site. This
complex acts as an E3 ligase in converting LC3I to LC3II by conjugating it with PE, which in turn helps in localizing LC3 to phagophore
membrane. LC3 proteins promote phagophore elongation and closure. Membrane for elongation possibly comes from different sources.
Autophagosome formation: Phagophore elongates and finally forms a double membraned autophagosome. LC3II plays an important role in
phagophore closure and cargo recruitment. During autophagosome maturation, autophagosomes fuse with endosomes to form amphisomes.
Autolysosome: autophagosomes finally fuse with lysosomes to form autolysosomes. Cargo is degraded into common building blocks in
autolysosomes and transported back into the cytoplasm completing the process of autophagy.
glaucoma, both neurodegenerative diseases. Some of the glaucoma-associated mutants of optineurin cause
impaired autophagy that leads to death of retinal cells (Sirohi and Swarup 2016). Certain mutations in p62,
another autophagy receptor, are associated with ALS (Rea et al. 2014). Independent studies have revealed
that aggregation prone proteins with polyglutamine expansion are degraded by autophagy in model
organisms (Ravikumar et al. 2002).
Autophagy is also involved in the development of cancer. First compelling evidence for involvement
of autophagy in cancer was provided by the finding that the gene coding for Beclin1 (gene BECN)
functions as a tumour suppressor in breast and ovarian tumours in humans and is also required for
initiation of autophagy. About 40–70% of breast and ovarian tumours have deletion of one copy of the
gene coding for Beclin1 (Liang et al. 1999). Beclin1 functions at an early stage of autophagosome
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formation, where it regulates enzyme activity of VPS34 (figure 1). However, the connection between
autophagy and cancer is quite complex, and in some cases autophagy helps in the survival of tumour
cells (Choi 2012).
Autophagy plays an important role in immune response and in the fight against bacteria such as Mycobacterium
tuberculosis and certain streptococci (Nakagawa et al. 2004) (Gutierrez et al. 2004). Apart from directly eliminating
certain microorganisms through xenophagy, autophagy is also involved in the control of inflammation, activation of
adaptive immunity through antigen presentation, and secretion of immune mediators (Deretic et al. 2013).
Autophagy has also been shown to affect lifespan of many model organisms. Various studies done on
ageing in these model organisms have shown that longevity promoting interventions like caloric restriction,
inhibition of insulin signaling, or administration of rapamycin, at least partly, if not fully, mediate their
effects by enhancing autophagy. It is however not known that these interventions will have similar effect in
humans on account of lack of any suitable technique to measure autophagic flux in living humans
(Rubinsztein et al. 2011).
4.
Concluding remarks
Autophagy is basically a cell survival mechanism that is induced by stress. Amino acid starvation is one of
the most powerful inducers of autophagy. Deregulation of autophagy leads to several diseases including
metabolic disorders such as diabetes. Therefore, it is expected that small molecule modulators of autophagy
would be useful either alone or in combination with other drugs for therapeutic intervention (Levine et al.
2015). Ohsumi’s elegant studies in yeast have shown that basic research in model organisms can provide
crucial insights relevant for understanding pathological mechanisms in humans. Funding agencies should
take a note of it. This is not the first instance where genetic studies in yeast have provided fundamental
insights into basic cellular processes relevant for human health and disease. Earlier genetic studies in yeast
have led to the Nobel Prize–winning discoveries in the area of cell division cycle and membrane vesicle
trafficking.
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MEGHA BANSAL and GHANSHYAM SWARUP*
Centre for Cellular and Molecular Biology,
Council for Scientific and Industrial Research
Hyderabad 500 007, India
*Corresponding author (Email, [email protected])
J. Biosci. 41(4), December 2016