14 Chapter 1 Autophagic degradation and its role in malnutrition Both mitochondria and peroxisomes are commonly degraded via selective autophagy61,62. Autophagy is a degradation process based on the delivery of cargo, encapsulated in autophagosomes, to the lysosome, where different biological polymers are broken down by a combination of enzymes63. The autophagic process starts by the formation of a structure known as the phagophore. Once the membrane of the phagophore closes around its cargo, it forms the autophagosome. This then fuses with the lysosome forming the autolysosome in which the lysosome secrets a set of enzymes able to degrade proteins, lipids and carbohydrates64,65. Traditional autophagy markers, mentioned throughout this thesis, are LC3-I, LC3-II and p62. LC3-I is conjugated with phosphatidylethanolamine to form LC3-II which is then targeted to the autophagosomal membrane. Once the autophagosome fuses with the lysosome, LC3-II is degraded. Therefore, the LC3-II/LC3-I is commonly used to track the autolysosome formation. P62 is an autophagy adaptor protein which delivers polyubiquitinated cargo to the phagophore66. This process is regulated in response to different nutritional states such as amino acid starvation, a well-known autophagy activator67–69. Since most proteins and organelles are degraded via autophagy, regulation of this process grants autophagy the ability to maintain the levels of amino acids, especially during scarcity of these nutrients70. The decrease in the number of peroxisomes in the liver of rats on a low protein diet has been linked to autophagic degradation56. These results were in line with the induction of autophagy in vitro using amino acid deprivation67. Moreover, peroxisomes have been described to be highly sensitive to amino acid levels and have been reported to rapidly degrade via pexophagy, selective peroxisomal autophagy, under low-amino acid concentration conditions71. Another example of peroxisomes responding to nutrient deprivation is the induction of pexophagy in yeast under nitrogen starvation conditions72. A low-protein-diet study in rats showed induction of autophagy after 1 week, illustrated by elevated levels of LC3-II and reduced levels of p62. Interestingly, after 4 weeks of LPD the levels of p62 were elevated while LC3-II remained high. These results were interpreted as a potential block in autophagy after prolonged starvation56. Some other studies in mice showed that already two weeks of LPD led to a decreased autophagy activation in mice57,58. All these studies focused on the assessment of autophagy based on snapshots of LC3 and P62 at given times. However, it is important to take into consideration that autophagy is a dynamic process. While LC3-II levels are known to relate to the
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