The Endo Cannibal of the Cell-Autophagosome and Autophagy


The Nobel Prize in Physiology and Medicine 2016 to Yoshinori Ohsumi “for his discoveries of mechanisms for autophagy” announced last week stimulated me to write this article on autophagosome and autophagy, the process mediated by the former cell organelle.

What are autophagosomes and autophagy?

Autophagosomes are double membrane vesicles or organelles of unknown origin within the cell. Their main function is to facilitate the autophagy, a lysosomal mediated destruction process (autoG= self, phageinG= to eat, coined by Christian de Duve who was awarded Nobel Prize for discovering lysosomes). Autophagy is a higher order process compared to the simple ubiquitin mediated protein degradation pathway. As the name implies autophagy is process of digesting self-components of the cell. For example, the uni-parental inheritance of mitochondria from mother is due to autophagy of the sperm mitochondria by the fertilized egg machinery (i.e. autophagosome). Thus the pathways that lead to autophagy can vary according to the cell state and fate.


Image Source:  The Nobel Assembly at Karolinska Institute

In one form of autophagy called non-selective autophagy, a bulk portion of cytosol is surrounded by the autophagosome and digested when nutrients are limited i.e. the cell is starved. In selective autophagy (another form of autophagy) the specific cargo or any other macromolecule or even a damaged organelle like mitochondria (called mitophagy) is packed in to the autophagosome with little cytosol and digested. This particular form of autophagy occurs during a stressful condition of the cell like improper protein folding or during development to adjust size or due to a microbial infection as well.

The Genes Involved in Autophagy

The genes that mediate this special process of the cell came to limelight only after 30 years of their discovery by pioneering experiments done by the Japanese scientist Yoshinori Ohsumi using a simple yet effective model organism the Saccharomyces cervisiae (the baker’s yeast). Yes, the process of autophagy occurs in all eukaryotic organisms including single celled yeast ! The process of autophagy involves the following steps

1) Autophagosome nucleation (or initiation)

2) Autophagosome growth and completion (or elongation)

3) Autophagosome target and fusion


Image Source: The Worm Book

Schematic diagram of steps in autophagy in C. elegans


The nucleation or initiation of autophagosome is not clear but some evidence points outs to budding of vesicle from Golgi. The lack of evidence is due to absence of any integral proteins in autophagosome (Integral proteins are usually tagged with fluorescent tags or gold particles to observe the movement of membranes with its proteins by single particle tracking technique).

Growth and Completion

Yoshinori’s pioneering work comes in to picture here. With his colleagues, he developed many yeast mutants randomly, each one lacking a particular protein or enzyme of the vacuole (vacuoles are analogous to lysosomes and mediate the same function and are present in bacteria, yeast, fungi and plants). As many as 15 proteins were initially reported (FEBS letters, 1993) and are named as per the screening as APG 1-15 (APG for autophagy). Later, in 2003 a unified system was proposed by yeast researchers  to avoid confusion and are named as ATG (ATG for Autophagy related protein). One key protein in this whole process is Atg-8, a ubiquitin like protein (mammalian homolog is light chain 3 (LC3)). Atg-8 is covalently linked to phopshotidylethanolamine on the cytoplasmic side after the autophagosome nucleation reaction. Binding of Atg-8 initiates fusion of further vesicles and growth of autophagosome. When an autophagosome engulfs a particle or cell organelle it grows and then completely seals around it.

Target and Fusion

Soon after sealing, the covalently linked Atg-8 is cleaved and this step enables fusion of autophagosome with lysosome. Two tethering proteins required for this fusion are identified but their complementary SNARE proteins are not known yet. Thus Atg-8 prevents premature fusion of autophagosome – lysosome or autolyosome and untoward consequences.

Autophagy Associated Diseases


It is of no surprise that dysregulation in autophagy underlies many pathological conditions especially cancers and neurodegenerative diseases. For example the mammalian homolog of yeast Atg-6, Beclin-1 dysregulation is reported in many types of cancers. Misfolding of proteins is one of the main pathological feature of many neurodegenerative diseases like Alzheimer;s, Parkinson’s, Huntington’s etc. Protein misfolding triggers unfolded protein response (UPR) in ER lumen and leads to a specialised form of autophagy called chaperone mediated autophagy (CMA).

Xenophagy: When the process of autophagy is activated to engulf and eliminate virus and bacteria, it is termed as xenophagy. One key protein of autophagic machinery required for this process is Atg-5. Studies found that Atg-5 defective cells are unable to clear group A streptococcus (GAS) and contribute to virulence.

Some Facts About Autophagy

  • Fundamental principle of membrane biosynthesis is that cells synthesize new membranes only by expansion, however the formation of autophagosome happens de novo i.e through the formation of autophagic crescent involving Atg-8.
  • The process of autophagy is under the control of mechanistic target of rapamycin (mTOR) pathway. When mTOR is active, autophagy is inhibited and vice versa.
  • The whole process of autophagy completes in quick time since the half life of autophagosome is ~20 mins.


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