Neuromuscular

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PROTEIN DEGRADATION 1,2

General principles
Protease classes

Autophagy
Chaperones
Cysteine
Lysosomal
Metalloproteinases
Mitochondrial
Muscle
Serine
Ubiquitin-Proteasome

Also see
  Apoptosis
  Caspases

PROTEIN DEGRADATION: GENERAL PRINCIPLES


SERINE PROTEASES
CYSTEINE PROTEASES
LYSOSOMAL PROTEASES
METALLOPROTEINASE

UBIQUITIN-PROTEASOME PROTEIN DEGRADATION 3-5,7

Classes of proteases
Degradation pathway
Diagrams
Diseases
Related cellular processes
Ubiquitination

26S Proteasome


Degradation Pathway

End products
Large 26S proteasome
Overall process
Ubiquitin
Ubiquitin binding process
Ubiquitination regulated cellular processes

MITOCHONDRIAL PROTEASES

Protein Folding & Chaperones 8

Chaperones
  Disorders
Protein Folding

Autophagy 11

General
Chaperone-mediated
Macroautophagy
Disorders

Autophagy: General Chaperone-mediated autophagy Macroautophagy (Autophagy)
  • Hallmarks
  • Stages
    • Membrane sequestration of cytoplasm & organelles
      • Organelle: Double-membrane Autophagosome
    • Autophagosome formation & maturation
    • Fusion of membrane bound vesicles with lytic component (Lysosomes)
    • Cargo Degradation
    • End products: Release of degradation products or Cell death
  • Action: Bulk lysosomal degradation
  • Targets
    • Larger cytoplasmic proteins: Folded or unfolded
    • Organelles: Mitochondria; Fractured endoplasmic reticulum; Peroxisomes
  • Mechanisms: Formation of double-membrane, non-Lysosomal vesicle (Autophagosome)
    • Several phases: All ATP dependent
    • Initiation
      • Phagophore (Crescent-shaped isolation membrane) generation
        • Membrane is formed de novo, not by budding
        • Sequestering membrane
          • Double layer
          • Separate from Lysosome
          • Contains: LC3-II (or another ATG8 ortholog)
            • Phosphatidylethanolamine-conjugated
            • Bound to inner & outer membranes
        • Phagophore transport
          • From: Perinuclear area
            • Where Nucleation occurs
          • To: Cell periphery
            • Cargo is sequestered
            • Autophagosomes formed
          • Kinesin- & FYCO1-mediated centrifugal transport
      • Phagophore Sequestration
        • Sequestered Contents: Cytoplasm & Organelles
        • Mechanism: Binding to LC3-II or Autophagy receptor (p62)
    • Expansion & Closing of Phagophore
      • Gives rise to Autophagosome
    • Autophagosome
      • Double-walled vesicle
      • Maturation
        • External proteins
          • LC3: Released & Reused
          • Binding of proteins mediating Autophagosome–Lysosome fusion
        • Transport
          • Binding to dynein–dynactin molecular motor
          • Transports autophagosome centripetally: Toward
            • Center of cell
            • Lysosomes at minus end of microtubules
        • Amphisome-formation
          • May fuse with Late endosome: Prior to fusion with lysosome
      • Actions
    • Induction
      • Upregulation of HDAC6
      • Rapamycin
      • Starvation (Low amino acids)
    • Autophagy: Proteins required
      • General
        • Function: Most at step of vesicle formation
        • Localization: At phagophore assembly site/preautophagosomal structure
      • Autophagy-related proteins
        • Ubiquitin-like
          • General
            • Activated by ATG7
          • ATG12
            • Conjugated to ATG5 during active autophagy
          • Microtubule-associated protein 1, light chain 3, alpha (MAP1LC3A)
            • Conjugated to phosphatidylethanolamine
            • Cleaved by ATG4
            • Associated with completed autophagosome
            • Function: Unknown
        • ATG7
          • Ubiquitin-activating enzyme E1-like protein
          • Essential for ATG12 conjugation system
          • Associated with membrane fusion in autophagy
          • Disease: SCAR31
        • ATG5
          • Essential for autophagy
          • Conjugated to ATG12
          • Binds Atg16: Part of tetrameric complex of unknown function
          • Conditional knock-out in brain
            • Develops: Aggregates & Ubiquitinated inclusions
          • Disease: SCAR25
        • ATG3
          • E2-like protein-conjugating enzyme
          • Covalently attaches ATG/LC3 to phosphatidylethanolamine
        • ATG4
          • Cysteine protease
          • Cleaves C-terminus of Atg8/LC3
            • Exposes glycine residue for subsequent conjugation
        • Beclin 1 (BECN1; ATG6)
          • Component of complex
            • Other component
              • Phosphatidylinositol 3-Kinase, Class 3 (PIK3C3; Vps34)
            • Produces PtdIns(3)-phosphate
            • Stimulatory for autophagy
          • Haploinsufficient & Mutated in some cancer lines
            • Especially breast tumours
        • Transmembrane proteins
          • ATG9
            • Involved in: Autophagosome formation
            • ? Marks site(s) of donor membrane used for phagophore expansion
              • Initial nucleating membrane: Develops into autophagosome
            • May be involved in: Membrane delivery to forming autophagosome
          • ATG27
          • Complex with ATG23
        • ATG10
          • Function: Ubiquitin-conjugating-like enzyme
          • Covalently attaches ATG12 to ATG5
        • ATG16L1
          • Binds ATG5
          • Homo-oligomerizes to form a tetrameric complex
          • Mutations: Missense; Related to Crohn's disease susceptibility
        • ATG32 : May play role in mitophagy
          • Recruits autophagic machinery to mitochondria
          • Regulates selective degradation of mitochondria
        • ULK1 (ATG1 homologue)
          • Serine/threonine protein kinase
          • May be involved in regulation & vesicle formation
          • Involved in axon growth
        • LAMP2: Danon disease
        • Phosphatidylinositol 3-kinase, Class I
          • Controls activation of
            • Kinases: Akt1 & Mammalian target of rapamycin (mTOR)
          • Composed of
            • Catalytic p110 subunits
            • p85 adaptor
          • Main product: PtdIns(3,4,5)P3
          • Inhibitory for autophagy
  • Autophagy: End pathway results
    • Autophagosome vesicles: Fuse with Lysosomes
      • Requirement: Microtubular system
      • Structure Formed: Autophagolysosome
      • Degradation
        • Contents exposed to acid hydrolases
        • Contents Degraded
          • Sequesterd Cargo molecules
          • Inner membrane with LC3-II
          • Autophagy receptors
    • Pathways after degradation
      • Macromolecules released back into the cytosol
        • Through permeases
        • For reuse in metabolic processes (during starvation)
      • Cargo inactivated or killed
        • When macroautophagy acts in immune response to eliminate microbial pathogens
      • Removal of cytoplasm may result in cell death
    • Major catabolic pathway for
      • Energy generation
      • Breakdown of macromolecules & damaged organelles into their essential constituents
      • Most prominent: During periods of stress or nutrient deprivation
Autophagy: Steps & Molecules

From: Chris Weihl
ULK complex
  • ULK1
  • ATG13
  • ATG101
  • FIP200
  • Association: Class III PI3K complex
      VPS34, VPS15, Beclin1, RUBCN
      ATG14, WIPI2, DFCP1
Membrane expansion
  • ATG9: Phospholipid delivery
Conjugation System Fusion Machinery Autolysosome-related Molecules
  • SNX4/5/17 complex
  • TEFB/TEF13
  • INPP5K
Disorders of Autophagy 10

MUSCLE PROTEIN DEGRADATION

INCREASED PROTEIN BREAKDOWN DECREASED PROTEIN BREAKDOWN
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References
1. NEJM 1996;335:1897-1905
2. Human Mutation 1999;13:87-98
3. Immunol Today 1997;18:189-198
4. FASEB J 1997;11;1067-1075
5. Cell Mol Life Sci 1998;54:253-262
6. J Neuroimmunol 1999;94:1-14, Sem Cancer Biol 2000;10:415-433
7. Annu. Rev. Immunol. 1999;17:739-779
8. Human Mutation 1999;14:199-215, Int J Mol Sci 2020;21(4)
9. Molec Genet Metab 2000:71:261-266
10. Brain 2015 Dec 29, Prog Mol Biol Transl Sci 2020;172:157-202
11. Annu Rev Pathol 2020;15:261-285, Front Cardiovasc Med 2022;9:1000067

11/2/2022