While studies on the membrane origin of autophagosomes have started to provide some answers about the molecular mechanism and machinery, they have also created some confusion regarding the source of the lipids forming the membrane carriers mediating autophagy.
This apparent discrepancy between the conclusions reached by the different laboratories could be in part due to different experimental approaches and techniques used in the various laboratories. More importantly, the different contributions could vary depending on the tissues and conditions used to trigger autophagy (), with cells able to derive the membranes from the most suitable or expendable reservoirs.
This hypothesis could explain the reported contradictory results as different studies used different cell types, organisms and diverse conditions to induce starvation (). Thus, in a tissue with a defined function, in response to a specific stress stimulus, autophagy would be supplied with membranes from the most optimal reservoir: an organelle that could guarantee the delivery of a large amount of lipids, but ideally would not adversely affect the specific functions of the tissue. From a cursory look at the current available data, one might conclude that fasting animals utilize endoplasmic reticulum while nitrogen-starved yeast use Golgi (). However, accurate comparative studies are needed to determine whether, for example, NRK cells starved of amino acids indeed use the endoplasmic reticulum as the source for autophagosomal membranes [28
] and if they turn to mitochondria when autophagy is induced by either serum, or serum and amino acid, deprivation [39
]. Along the same lines, it would be important to study the various marker proteins used to implicate the different organelles in autophagy [26
] in parallel in the same experimental setup.
Another possibility that should not be discarded a priori
is that autophagosomes could be mosaics of membranes derived from more than one organelle. For example, the phagophore could originate from one compartment and the additional lipid bilayers required for its expansion could be acquired from another source (). For example, the plasma membrane and Atg9-positive membranes could contribute to the formation of the phagophore while the endoplasmic reticulum, mitochondria and/or Golgi might be necessary for its expansion. In this regard, it is important to note that the endosomal system provides the membranes required for the last steps of autophagy, i.e. amphisome and autolysosome formation () [51
]. The advantage to the cell of having a spectrum of membrane sources to choose from is the availability of a large supply of lipids to sustain the progression of autophagy; autophagosomes are huge carriers and a multitude of them are produced upon induction of this degradative pathway. One could imagine that a single intracellular organelle could not provide enough membranes, especially during prolonged period of starvation or stress.
Finally, it still remains to be determined whether the different organelles implicated so far in autophagosome biogenesis, contribute to non-selective bulk autophagy or to selective forms of autophagy such as mitophagy (selective degradation of mitochondria), or pexophagy (selective degradation of peroxisomes). In this regard, the observation that the endoplasmic reticulum is found connected to both the inside and the outside membrane of the phagophore [26
] could suggest that the endoplasmic reticulum found in the interior of the closing phagophore is not undergoing the general process of bulk autophagy but rather is specifically degraded through a seleletive type of autophagy known as endoplasmic reticulumphagy or reticulophagy [52
]. A similar explanation could be applicable to the other organelles acting in the phagophore and autophagosome biogenesis.
Is this hypothesis, implicating multiple membrane sources for autophagosomes, something reconcilable at the molecular mechanistc level? Potentially yes. Apart from the transmembrane protein Atg9, the core Atg machinery is composed of soluble proteins that transiently associate with membranes. Consequently, the cell could select the membrane source by targeting the signal and/or the molecule initiating the assembly of the Atg machinery to the organelle of choice.