Protein Cycling Diet: 16

Incomplete Autophagy

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Chapter 16
When maturation and completion fail

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Incomplete Autophagy

Macroautophagy is a complex cell procedure involving many independent steps. Before it happens at all, the cell must recognize that a need to perform it exists. A cellular signaling system must therefore be activated. Such signaling systems have been extensively characterized and many of their component proteins and the genes for those proteins have been identified but many holes remain.

One well characterized signal to which the cell responds is a high level of insulin indicating that supplies of glucose from the bloodstream are currently adequate. The insulin binds to the outside of the cell on a special protein complex imbedded in the cell membrane. The binding of insulin on the outside causes the complex to then bind phosphate to a particular soluble protein on the inside. The phosphorylated protein then carries the signal to certain other proteins in the signaling network causing autophagy for the purpose of energy production to be suppressed. Conversely, the absence of phosphate on the protein causes autophagy for the purpose of energy production to be promoted.

This fits the general model for how information is transmitted throughout the cell. Immobile proteins enzymatically modify mobile proteins (or some other soluble substance). Often the immobile proteins are imbedded in membranes and modify soluble substances on one side in response to a soluble substance on the other. The modified mobile substance, be it protein or otherwise, diffuses or is actively transported to other locations in the cell where it modifies or otherwise influences other specific proteins.

More than one modified substance may be necessary to cause the responding protein to propagate the signal. And more than one responding protein may react to a single modified substance. Or a single responding protein may react to more than one modified substance. In this way, multiple conditions may be necessary to initiate an event, or a single condition may initiate multiple events, or a single event may be initiated by multiple conditions. In system dynamics terms, this provides the ‘and’ and ‘or’ logic functions used to define feedback systems.

In the case of the autophagy signal generated by low insulin, it alone may be insufficient to initiate autophagy if the cell currently has a surplus of energy substrates. The cell has another signaling system that reports on low levels of glucose within the cell and both signals together may be needed to actually initiate autophagy.

The cell also need supplies of essential amino acids and lipids to perform its vital functions. Signal systems must exist for them as well and must initiate autophagy even when the glucose-responding signal is absent.In fact, amino acid deficiency is signaled by the accumulation of uncharged transfer RNAs (tRNAs), that is tRNAs without their specific amino acids attached. Normally tRNAs are recharged by specific enzymes after they are discharged during protein synthesis by the ribosomes. If an amino acid species is unavailable then its tRNAs remain uncharged. Uncharged tRNAs bind to an enzyme that then signals the cell to initiate or complete autophagy to free up some of the needed amino acids.

Also autophagy is used by the cell for purposes other than supplying nutrients. In particular, autophagy is seen to be induced when reactive oxygen species (ROS) or mis-folded proteins accumulate. ROS usually appear when mitochondria break down and it makes sense that the cell would then initiate autophagy to clear up the debris. The same can be said for the accumulation of mis-folded proteins. The cell needs to isolate these noxious substances from the rest of the cell. Wrapping them up in an autophagosome does the trick nicely.

Macroautophagy is often selective. Mechanisms exist to drag degraded mitochondria or other organelles or even aggregates to the mouth of an enveloping autophagosome initiated for just that purpose.

As first mentioned, autophagy is a complex multi-step process whose details have been skipped-over in earlier discussion. Normally an autophagosome ’matures’ by first merging with special vesicles produced by the ER. Two types of such vesicles have been identified, early and late. At least two things result from this maturation: the pH of the autophagosome is lowered and the autophagosome is now recognized by the transport system of the cell which then carries it from the region of the cell nucleus to the periphery where the lysosomes abound. There it merges with the lysosomes whose enzymes digest the inner vesicle of the autophagosome and its contents. The end products of digestion including fatty acids and amino acids exit the autophagosome and are reused for new synthesis or burned for energy.

What happens when the cell autophages for clearing debris but has no current need for it end products? Perhaps it can return the excess to the bloodstream. More likely it blocks completion at one or more of the many steps in the autophagy process. The cell’s immediate need was to isolate the noxious debris. It can wait for when it needs the digestion products before finishing. But what if that need never comes? Then autophagy is incomplete and autophagosomes accumulate in the cell perhaps to the point of disruption of normal cell processes by their sheer bulk alone.

In fact, extensive accumulation of autophagosomes is often observed in biopsies of nerve tissues from Huntington’s, Alzheimer’s, ALS, and Parkinson’s patients. This is puzzling. Why would the cell have only half a mechanism to handle mis-folded proteins? Why would it not have simply evolved a mechanism to force a nutritional deficit to unblock the maturation process when autophagosomes accumulate?

Perhaps the reason is that there was never any selection pressure for it because there were always periods of nutritional restriction when the blockage would be lifted. That period was the overnight fast endured by all tropical mammals including humans. It may then be the effective extinguishing of the overnight fast by many cosmopolitan humans that causes the diseases associated with protein aggregates.

With this view, protein or calorie cycling is not just a trick to avoid diseases but rather a natural practice whose absence causes disease. Eating after sunset could then be said to cause (or at least to encourage) AD, HD, ALS, and PD. Likewise the eating of a high-protein breakfast.

Incomplete autophagy may account for studies where starvation is not seen to increase autophagy in the CNS. The explanation given is that the CNS is a privileged system that gets its nutrients regardless of outside events. Even though no new autophagosomes are seen in these studies, perhaps pre-existing ones created to handle mis-folded proteins, are then being matured30.

Or the apparent lack of autophagy may just be a problem of methodology. Using a novel approach to detect, enumerate and characterize autophagosomes in vivo, researchers found extensive autophagy initiation in mouse neuronal tissue after as little as 24 hours of starvation82.

A failure of autophagy to complete after successful initiation has recently been implicated in the pathology of Paget’s disease of the bone and frontotemporal dementia47.

In view of these considerations, we may now restate the purpose of protein cycling – to clear autophageosomes initiated by earlier cell stresses

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