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What is autophagy? How and under which circumstances is it used by the cell? I believe The reason for autophagy is some kind of recycling, am I right? But why does it occur in infections?

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Autophagy is a cellular process that is occurring all the time, but it can be elevated during times of need (see below).

In autophagy, cargo (can be anything - mostly macromolecules but also bacteria/viruses etc) is taken up by a lipid membrane which folds on itself to form an autophagosome, which is like a vesicle but have markers on it that makes it specialized in carrying out autophagy. These autophagosomes are then transported to, and merge with, lysosomes, releasing the cargo into the lysosome to be degraded. The broken down materials are then released back into the cytosol, where other processes can make use of them. That is the "some kind of recycling" you are referring to.

There are two types of autophagy - selective and general. In selective autophagy, receptors on the membrane of the autophagosome specifically selects for ligands (e.g. p62, ndp52 selects for ubiquinylated substrates, which usually marks molecules for degradation). In general autophagy, the uptake into the autophagosome is random.

So, you can think of general autophagy as maintaining a basic level of turnover - to ensure everything in the cell is not worn out; and selective autophagy as a response to specific ligands that needs to be degraded.

By this logic, autophagy activity increases during infection because those infectious agents, once gaining entry into the cell (either through phagocytosis or by forced entry), will need the autophagy machinery to transport it to the lysosome to be degraded. Interestingly, some bacteria actualy hi-jacks this process to ensure its survival in the cell. Here's a good review to get you started if you are interested.

Note that the proteasome also recycles macromolecules, although the things it can recycle is limited by size.

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I like your answer. But in most sources I read there is a distinction between normal phagosomes which have one membrane layer and autophagosomes which have 2 to 3 membrane layers. Which is the only distinction I found so far. Are there any other reasons to differentiate between these two processes? –  NeoDevlin Jun 10 '13 at 19:48
    
Like I said, autophagosomes can take up any cargo - this includes other vesicles and phagosomes. The autophagosome is double-membraned, so when it fuses with the lysosome, the inner membrane is 'released' into the lumen of the lysosome, whereas the outer membrane fuses with that of the lysosome. Thus, the outer membrane of the autophagosome would resemble more of the lysosomal membrane (and they do share similar markers and it's often hard to distinguish the two in microscopy). This is different from the the membrane of phagosomes, which originate from the plasma membrane. –  dayuloli Jun 10 '13 at 21:10
    
Having said this, no one is sure as to the origins of the autophagosome membrane - where the lipids are sourced from. –  dayuloli Jun 10 '13 at 21:10
    
To answer your question - you can distinguish the two processes as their place of origins, phagocytosis originates at the cell membrane and autophagy originates inside the cell. The phagocytotic process may feed into the autophagosomal process, although it may not be an requirement. If you read the review I suggested, you'll appreciate that some bacteria that is taken in using phagosomes, break out of their phagosomes and replicate in the cell. This is when autophagy can come in and restrict their replication. So I, a very crude distinction would be - phagocytosis outside, autophagy inside –  dayuloli Jun 10 '13 at 21:12
    
Thank you, I will definitely read the review. –  NeoDevlin Jun 11 '13 at 13:09

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