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Autophagy: It’s a Cell-Eat-Self World

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If the thought of self-cannibalization is not appealing to you, you may not want to read the next sentence... Your cells are literally eating themselves right now! In the 1960s, Christian de Duve named this process “autophagy” from the Greek auto (self) and phagein (to eat). He was later awarded the Nobel Prize for Physiology or Medicine for his contribution to the cell biology field. Little did de Duve know what an issue this word would cause: do you pronounce it “aw-tof-a-gee” or, “auto-fay-gee”? Well, actually—it’s a bit like tom-ay-tow/tom-ah-tow—both are right! As de Duve himself said, “I coined the word, but not the pronunciation.”

In this post, we explore the mechanism of autophagy and the role of the ULK complex—and specifically, ULK1—in starvation-induced autophagy signaling.

Autophagy: It’s a Cell Eat Self World

However you say it, autophagy allows bulk cytoplasmic contents, abnormal proteins, and old or damaged organelles to be broken down and the resulting metabolites to be recycled. It occurs at a basal rate in “normal” cells to maintain homeostasis, but is also a survival mechanism employed during stressful conditions like nutrient starvation, oxygen depletion, and endoplasmic reticulum (ER) stress. We now know that autophagy is involved in many physiological and pathological events, and we are making great strides toward understanding the complex, highly regulated signaling involved in autophagy.

Mechanism of Autophagy

Historically, a lot of what we have learned about mammalian autophagy signaling came from studying yeast. It turns out that mammalian autophagy is highly conserved from yeast. Fifteen autophagy-related genes, ATGs, were first identified in a genetic screen performed on yeast, and mutations in these genes caused defects in autophagy1. Now, more than 36 ATG core genes have been reported for yeast. Many of the autophagy-related proteins in mammals are named for their yeast counterparts, which is why a lot of proteins in the mammalian autophagy pathway bear the name “AtgX”.

 

Signaling in Nutrient Starvation Autophagy

In response to stress like nutrient starvation, i.e., amino acid or glucose depletion, a double membrane structure called a phagophore forms within the cell, which elongates and starts to encompass the cytoplasmic components (cargo). Eventually, the membrane seals around the cargo, forming a structure called the autophagosome. The autophagosome then fuses with a lysosome, a membrane-bound organelle that contains a mixture of enzymes that work best in acidic conditions, to form an autolysosome. The cargo undergoes degradation by lysosomal enzymes and the resulting nutrients become available for the cell to reuse.

 

ULK1: A Bridge Between Nutrient Sensing and Autophagosome Formation

Prior to autophagosome assembly, the autophagy signaling pathway is initiated by activation of the ULK complex (in mammals, or the ATG1 complex in yeast), which comprises ULK1 or ULK2, FIP200, Atg101, and ATG132. The ULK1 complex acts as a bridge between the nutrient and energy sensors mTOR and AMPK upstream, and formation of autophagosomes downstream. ULK1 and ULK2 are highly phosphorylated; over 40 ULK1 phosphorylation sites have been reported3. When activated, the ULK1 complex associates with phagophores forming ULK1 puncta on the phagophore membrane where several other complexes are then recruited in a process that is still poorly understood4.

 

Regulation of Autophagy by ULK1

It has been known for a long time that phosphorylation of ULK1 is a key mechanism for autophagy regulation and that AMPK and mTOR are two of the kinases that phosphorylate ULK1. In fact, specific phosphorylation events catalyzed by both of these proteins play an important role in autophagy. Under nutrient starvation conditions, AMPK is active and mTOR is inactive. AMPK phosphorylates ULK1 at Ser 317, Ser 467, Ser 555, Ser 574, Ser 637, and Ser 777, which promotes autophagy. In times of plentiful nutrients, AMPK is inactive and mTOR associates with and phosphorylates ULK1 at Ser 757 preventing ULK1 activation by AMPK and disrupting the ULK1-AMPK interaction. In this situation, autophagy is “turned off”5, 6.

As well as being at the hub of autophagy signaling, ULK is notable for being the only serine/threonine kinase among the core autophagy proteins. Despite these facts, little is known about which proteins are phosphorylated by ULK1. Recently, Egan et al reported a ULK1 consensus phosphorylation motif7. To identify ULK1 substrates they searched the human proteome for proteins containing this motif. Not surprisingly, many core autophagy proteins were found. These included Atg13, Vps34, and Beclin-17.

Vps34 (Class III PI3 Kinase) is another essential autophagy protein and is also an important regulator of the signaling pathway8. The Vps34 complex, which contains Vps34, Beclin-1, p150, and Atg14, is directly downstream from the ULK1 complex. In fact, Beclin-1 phosphorylation at Ser15 by ULK1 is required for autophagy9

Unraveling the autophagy signaling pathway will help us understand more clearly the role of autophagy in maintaining cell homeostasis and how it is misregulated in diseases like cancer, diabetes, and neurodegeneration. Could inhibiting autophagy by inactivating essential proteins like ULK1 be a therapeutic possibility for these diseases? It definitely provides some food for thought.

Additional Resources:

Interested in learning more about signaling in autophagy? Download our Cell Growth & Viability Signaling Pathways, including our Autophagy Pathway Handout:

 

Download Pathway

 

You can also watch an on-demand webinar featuring Dr. Reuben Shaw of the Salk Institute for Biological Studies, which focuses on autophagy and ULK1 as a potential therapeutic target.

 

Select References:

  1. Tsukada M, Ohsumi Y (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 333(1-2), 169–74.
  2. Ganley IG, Lam du H, Wang J, Ding X, Chen S, Jiang X (2009) ULK1.ATG13.FIP200 complex mediates mTOR signaling and is essential for autophagy. J. Biol. Chem. 284(18), 12297–305.
  3. Bach M, Larance M, James DE, Ramm G (2011) The serine/threonine kinase ULK1 is a target of multiple phosphorylation events. Biochem. J. 440(2), 283–91.
  4. Itakura E, Mizushima N (2010) Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins. Autophagy 6(6), 764–76.
  5. Kim J, Kundu M, Viollet B, Guan KL (2011) AMPK and mTOR regulate autophagy through direct phosphorylation of Ulk1. Nat. Cell Biol. 13(2), 132–41.
  6. Egan DF, Shackelford DB, Mihaylova MM, Gelino S, Kohnz RA, Mair W, Vasquez DS, Joshi A, Gwinn DM, Taylor R, Asara JM, Fitzpatrick J, Dillin A, Viollet B, Kundu M, Hansen M, Shaw RJ (2011) Phosphorylation of ULK1 (hATG1) by AMP-activated protein kinase connects energy sensing to mitophagy. Science 331(6016), 456–61.
  7. Egan DF, Chun MG, Vamos M, Zou H, Rong J, Miller CJ, Lou HJ, Raveendra-Panickar D, Yang CC, Sheffler DJ, Teriete P, Asara JM, Turk BE, Cosford ND, Shaw RJ (2015) Small Molecule Inhibition of the Autophagy Kinase ULK1 and Identification of ULK1 Substrates. Mol. Cell 59(2), 285–97.

  8. Jaber N, Dou Z, Chen JS, Catanzaro J, Jiang YP, Ballou LM, Selinger E, Ouyang X, Lin RZ, Zhang J, Zong WX (2012) Class III PI3K Vps34 plays an essential role in autophagy and in heart and liver function. Proc. Natl. Acad. Sci. U.S.A. 109(6), 2003–8.

  9. Russell RC, Tian Y, Yuan H, Park HW, Chang YY, Kim J, Kim H, Neufeld TP, Dillin A, Guan KL (2013) ULK1 induces autophagy by phosphorylating Beclin-1 and activating VPS34 lipid kinase. Nat. Cell Biol. 15(7), 741–50.
Claire S
Claire S
Claire is a Science Writer at CST

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