Omegasome

Omegasome is a cell compartment consisting of lipid bilayer membranes enriched for phosphatidylinositol 3-phosphate (abbreviated PI(3)P or PtdIns3P) and related to a process of autophagy.[1] It is a subdomain of the endoplasmic reticulum (ER) membrane[2] and has a morphology resembling Greek capital letter omega (Ω). Omegasomes are the sites from which phagophores form.[1][2] Phagophores (also called "isolation membranes") are sack-like structures that mature into autophagosomes that fuse with lysosomes in order to degrade the contents of the autophagosomes.[3] The formation of omegasomes is increased as a response to starvation.[1]

Figure from original paper, showing line diagrams of phagosomes arising from omegasomes (part D).

Macroautophagy
Illustration showing steps from omegasome to autolysosome.[4]

Autophagy (from Greek words for “self” and “eating”) is a process of digesting or degrading cytoplasmic molecules (proteins, lipids, sugars and organelles). Macroautophagy is the main autophagic pathway, used primarily to eradicate damaged cell organelles such as mitochondria,[5] ribosomes, etc. The omegasome is present at the opening of the sack-like phagophore while items destined for degradation by macroautophagy are loaded into the phagophore. There are specific receptor proteins that recruit items to the phagophore.[6] The phagophore expands to accommodate the items, until the omegasome is closed to produce the roughly spherical autophagosome. How autophagosomes are "detached" or "exit" from the omegasome is not clear, but autophagocytosis associated protein Atg3 and other proteins are required, and collections of thin tubules at the junction between omegasome and phagophore appear to be involved.[7] Actin is also believed to be important.[8][4]

gollark: Why not simply not use perl?
gollark: Done, `/matt-api` goes to `localhost:18605`, just host on that.
gollark: .
gollark: Doing so···
gollark: ???

References
  1. Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, Griffiths G, Ktistakis NT, et al. (2008). "Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum". J Cell Biol. 182 (4): 685–701. doi:10.1083/jcb.200803137. PMC 2518708. PMID 18725538.
  2. Biazik J, Ylä-Anttila P, Vihinen H, Jokitalo E, Eskelinen EL (2015). "Ultrastructural relationship of the phagophore with surrounding organelles". Autophagy. 11 (3): 439–51. doi:10.1080/15548627.2015.1017178. PMC 4502653. PMID 25714487.
  3. Kern A, Dikic I, Behl C (2015). "The integration of autophagy and cellular trafficking pathways via RAB GAPs". Autophagy. 11 (12): 2393–7. doi:10.1080/15548627.2015.1110668. PMC 4835203. PMID 26565612.
  4. Kruppa AJ, Kendrick-Jones J, Buss F (2016). "Myosins, Actin and Autophagy". Traffic (Copenhagen, Denmark). 17 (8): 878–90. doi:10.1111/tra.12410. PMC 4957615. PMID 27146966.
  5. Yang JY, Yang WY (2013). "Bit-by-bit autophagic removal of parkin-labelled mitochondria". Nature Communications. 4: 2428. Bibcode:2013NatCo...4.2428Y. doi:10.1038/ncomms3428. PMID 24013556.
  6. Kim BW, Kwon DH, Song HK (2016). "Structure biology of selective autophagy receptors". BMB Reports. 49 (2): 73–80. doi:10.5483/bmbrep.2016.49.2.265. PMC 4915120. PMID 26698872.
  7. Uemura T, Yamamoto M, Kametaka A, Sou YS, Yabashi A, Yamada A, Annoh H, Kametaka S, Komatsu M, Waguri S (2014). "A cluster of thin tubular structures mediates transformation of the endoplasmic reticulum to autophagic isolation membrane". Molecular and Cellular Biology. 34 (9): 1695–706. doi:10.1128/MCB.01327-13. PMC 3993601. PMID 24591649.
  8. Aguilera MO, Berón W, Colombo MI (2012). "The actin cytoskeleton participates in the early events of autophagosome formation upon starvation induced autophagy". Autophagy. 8 (11): 1590–603. doi:10.4161/auto.21459. PMC 3494589. PMID 22863730.


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