Ubiquitin

Ubiquitin proteasome system involved in the process called ubiquitination, which also referred as ubiquitylation or molecular “kiss of death”. Ubiquitination is post-translational modification that has a major role in protein degradation. The two main protein degrading systems are found in eukaryotic cells, they are lysosome proteolytic system and proteasomes proteolytic system. Every protein present in the cell is under surveillance of cellular degradative machinery, if any unfavorable changes occurred in the protein structure then the protein will be undertaken by this machinery to protect cells from their malfunction.

 

1. Ubiquitination key points 
  1. Ubiquitin proteins covalently attaches to substrate proteins (damaged protein) to initiate the degradation; hence, this process is called ubiquitination.
  2. Prokaryotes have no molecules that are functionally equivalent to ubiquitin. However, structurally ubiquitin-related proteins such as Ubiquitin Bacterial (UBact) has been found in bioinformatic studies.
  3. Monomer of ubiquitin contains 76 amino acids that are folded into a compact, globular, tightly hydrogen-bonded structure with a terminal signature diglycine sequence. However, in some cases, diglycine-modified lysine uses as a signature of ubiquitination and also recognizes the specific site of modification.
  4. Ubiquitin protein initially synthesized in a precursor form, hence, to generate the signature Gly–Gly sequence, that must be processed by de‐ubiquitylating enzymes.
  5. Ubiquitination is a active enzymatic process that requires energy provided in the form of ATP hydrolasis.
  6. The process is highly specific and degrades only those proteins are marked by ubiquitination.
  7. In ubiquitination, the lysin residue in damaged protein will be conjugated with ubiquitin protein.
  8. Since the cytosolic degradation process recognizes only ubiquitinated proteins, the process is highly specific and cannot randomly degrade other proteins.
  9. The cytosolic protein degradation is carried out by 26S proteasomal complex that contains core 21S proteasomes.
  10. Ubiquitin is a low molecular weight heat shock protein that finds and marks substrate protein for proteasomal degradation.
  11. This process requires three more proteins called E1, E2, and E3.
  12. E1 protein is ubiquitin activase that activates ubiquitin.
  13. E2 protein is ubiquitin conjugase that binds to activated ubiquitin and facilitate the binding of ubiquitin to the substrate protein.
  14. E3 is ubiquitin ligase that recognize the protein to be degraded or to be ubiquitinated.
  15. The eukaryotic cell contains different types of E3 proteins, they can recognize different parameters of proteins for degradation. For instance, some E3 proteins recognizes N-terminal, some E3 identifies PEST sequence, some recognizes the oxidizes side chains where as other identifies misfolding.
  16. During ubiquitination, the activated ubiquitin combines with the Lys residue present in substrate protein, which is catalyzed by E3.
  17. The ubiquitinated protein is transferred to the 26S proteasomal complex, where the ubiquitin proteins are separated from substrate proteins and recycled to further substrate protein activation. Now ubiquitin protein is entered to the proteasomal core and degraded into octapeptides (small fragments).

 

2. Ubiquitin function in the cell

  1. Involved in the MHC class I-restricted antigen processing of ER-targeted proteins and also plays a major role in the processing of cytosolic proteins.
  2. Ubiquitination also involved in the Apoptosis.
  3. Plays a major role in biosynthesis of cellular organelles
  4. Ubiquitin regulates cell cycle and  and cell division and also responsible for several major cell cycle transitions via selective degradation of cyclin-dependent kinase inhibitors, cyclins, and anaphase inhibitors.
  5. Regulates DNA transcription and DNA repair.
  6. Involved in the cell differentiation and development.
  7. Participates in neural and muscular degeneration.
  8.  Regulates dynamic cellular mechanisms such as endocytosis, proteolysis, and immune signaling.
  9. Involved morphogenesis of neural networks.
  10.  Involved in inflammation and Immune responses.
  11. This protein plays a major role in modulation of cell surface receptors, ion channels, and the secretory pathways.
  12. Respond to stress and extracellular modulators.
  13.  Involved in ribosome biogenesis.
  14. Regulates viral infection, however, some viruses like influenza A virus (IAV) seize ubiquitination and ubiquitin-like modifications to establish viral infection.

A. Ubiquitination and other proteolytic meachanisms

Ubiquitination is proteasomal complex-mediated proteolytic process that contains various ubiquitin proteins to recruit the substrate protein for degradation. The protein degradation is a required process in all eukaryotic cells.  Hence, the cells own two types of proteolytic systems such as lysosomal degradation and cytosolic degradation (proteasomal-mediated degradation). These two mechanisms mainly involved in the degradation of aged or damaged proteins in order to keep the cells clean and healthy. Within these two mechanisms, lysosomes (membrane bound organelles)-mediated protein degradation play a pivotal role in recycling of cellular waste materials.  Lysosomes contain an assortment of acid hydrolases and many essential enzymes.

 

B. Mechanism of Ubiquitination (ubiquitylation of substrate protein)

Ubiquitin-mediated protein degradation is well-established mechanism to send the damage proteins to proteasomes by their modification with chains of protein called ubiquitin. In eukaryotes, this is highly conserved protein, contains 76 amino acids, is usually bind with substrate by an isopeptide bond, which forms between a lysin residue of substrate and C-terminal glycine of ubiquitin.

 

*Substrate protein will be activated in three steps before going to proteasomal degradation.

Proteosome complex

STEP: 1 In most organisms, a single E1 (ubiquitin activating enzyme) binds covalently with free ubiquitin protein via C-terminal residue of ubiquitin using energy from ATP.

STEP: 2 The activated ubiquitin is subsequently transferred to a cysteine on an ubiquitin conjugating enzyme 2 (E2).

STEP: 3 Finally, ubiquitin protein ligases (E3) transfer the activated ubiquitin from E2 to lysin residue of final target protein (substrate), forming an isopeptide bond.

Now, this ubiquitinated substrate protein is proteolytically degraded into small peptide fragments by proteasome, which is ATP-dependent process. Then, the released fragments subsequently engulfed by lysosomes for further degradation (complete lysis).

 

Read the subsequent process that occurred in proteasomes.

References

  1. Alina Rudnicka and Yohei Yamauchi. Ubiquitin in Influenza Virus Entry and Innate Immunity. Viruses. 2016 Oct; 8(10): 293. Published online 2016 Oct 24. doi: [10.3390/v8100293]
  2. Pickart CM, Eddins MJ. Ubiquitin: structures, functions, mechanisms. Biochim Biophys Acta. 2004 Nov 29;1695(1-3):55-72.
  3. The ubiquitin-proteasome pathway. Annual Reviews Collection [Internet].
  4. de Virgilio M, Weninger H, Ivessa NE. Ubiquitination is required for the retro-translocation of a short-lived luminal endoplasmic reticulum glycoprotein to the cytosol for degradation by the proteasome.J Biol Chem. 1998 Apr 17;273(16):9734-43.
  5. Ubiquitin B [ Mus musculus (house mouse).
  6. Kravtsova-Ivantsiv Y, Ciechanover A. Ubiquitination and degradation of proteins. Methods Mol Biol. 2011;753:335-57. doi: 10.1007/978-1-61779-148-2_23.

 

 

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