Degron

A degron is a portion of a protein that is important in regulation of protein degradation rates. Known degrons include short amino acid sequences,[1] structural motifs[2] and exposed amino acids (often Lysine[3] or Arginine[4]) located anywhere in the protein. In fact, some proteins can even contain multiple degrons.[2][5] Degrons are present in a variety of organisms, from the N-degrons (see N-end Rule) first characterized in yeast[6] to the PEST sequence of mouse ornithine decarboxylase.[7] Degrons have been identified in prokaryotes[8] as well as eukaryotes. While there are many types of different degrons, and a high degree of variability even within these groups, degrons are all similar for their involvement in regulating the rate of a protein's degradation.[9][10][11] Much like protein degradation (see proteolysis) mechanisms are categorized by their dependence or lack thereof on Ubiquitin, a small protein involved in proteasomal protein degradation,[12][13][14] Degrons may also be referred to as “Ubiquitin-dependent"[9] or “Ubiquitin-independent".[10][11]

Shown here in green is IkBa, the Inhibitor of NF-κB and regulator of the immune system. The red region highlights a Ubiquitin-Independent degron

Types

Ubiquitin-dependent degrons are so named because they are implicated in the polyubiquitination process for targeting a protein to the proteasome.[15][16] In some cases, the degron itself serves as the site for polyubiquitination as is seen in TAZ and β-catenin proteins.[17] Because the exact mechanism by which a degron is involved in a protein's polyubiqutination is not always known, degrons are classified as Ubiquitin-dependent if their removal from the protein leads to less ubiquitination or if their addition to another protein leads to more ubiquitination.[18][19]

In contrast, Ubiquitin-independent degrons are not necessary for the polyubiquitination of their protein. For example, the degron on IkBa, a protein involved in the regulation of the immune system, was not shown to be involved in ubiquitination since its addition to Green Fluorescent Protein (GFP) did not increase ubiquitination.[2] However, a degron can only hint at the mechanism by which a protein is degraded[20] and so identifying and classifying a degron is only the first step in understanding the degradation process for its protein.

Identification
Shown is a diagram representing two degron-identifying procedures outlined in the text. In the first (green) procedure, the unaltered form of the protein remains abundant over time while the mutant form containing a degron candidate decreases rapidly. In the second (red) procedure the unaltered form of a protein containing the degron candidate decreases rapidly over time while the mutant form stripped of its degron remains abundant. A' versus A are used to notate protein forms containing the degron vs not containing the degron.

In order to identify a portion of a protein as a degron, there are often three steps performed.[2][19][20] First, the degron candidate is fused to a stable protein, such as GFP, and protein abundances over time are compared between the unaltered protein and the fusion (as shown in green).[21] If the candidate is in fact a degron, then the abundance of the fusion protein will decrease much faster than that of the unaltered protein.[9][10][11] Second, a mutant form of the degron's protein is designed such that it lacks the degron candidate. Similar to before, the abundance of the mutant protein over time is compared to that of the unaltered protein (as shown in red). If the deleted degron candidate is in fact a degron, then the mutant protein abundance will decrease much slower than that of the unaltered protein.[9][10][11] Recall that degrons are often referred to as “Ubiquitin-dependent” or “Ubiquitin-independent” The third step performed is often done after one or both of the previous two steps, because it serves to identify the Ubiquitin dependence or lack thereof of a previously identified degron. In this step, protein A and A’ (identical in every way except the presence of degron in A’) will be examined. Note that mutation or fusion procedures could be performed here, so either A is a protein like GFP and A’ is a fusion of GFP with the degron (as shown in green) or A’ is the degron's protein and A is a mutant form without the degron (as shown in Red.) The amount of Ubiquitin bound to A and to A’ will be measured.[2][7][20] A significant increase in the amount of Ubiquitin in A’ as compared to A will suggest that the degron is Ubiquitin-dependent.[2][9]

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gollark: A true student of Pro.
gollark: Because their description ***LIES***.
gollark: I've only ever frozen one hatchling, to get a slot.
gollark: Recovery from what?

References
  1. Cho, Sungchan; Dreyfuss, Gideon (2010-03-01). "A degron created by SMN2 exon 7 skipping is a principal contributor to spinal muscular atrophy severity". Genes & Development. 24 (5): 438–442. doi:10.1101/gad.1884910. ISSN 1549-5477. PMC 2827839. PMID 20194437.
  2. Fortmann, Karen T.; Lewis, Russell D.; Ngo, Kim A.; Fagerlund, Riku; Hoffmann, Alexander (2015-08-28). "A Regulated, Ubiquitin-Independent Degron in IκBα". Journal of Molecular Biology. 427 (17): 2748–2756. doi:10.1016/j.jmb.2015.07.008. ISSN 1089-8638. PMC 4685248. PMID 26191773.
  3. Dohmen, R.J., P. Wu, and A. Varshavsky, Heat-inducible degron: a method for constructing temperature-sensitive mutants. Science, 1994. 263(5151): p. 1273-1276.
  4. Varshavsky, A. (1996-10-29). "The N-end rule: functions, mysteries, uses". Proceedings of the National Academy of Sciences. 93 (22): 12142–12149. doi:10.1073/pnas.93.22.12142. ISSN 0027-8424. PMC 37957. PMID 8901547.
  5. Kanarek, Naama; London, Nir; Schueler-Furman, Ora; Ben-Neriah, Yinon (2010-02-01). "Ubiquitination and degradation of the inhibitors of NF-kappaB". Cold Spring Harbor Perspectives in Biology. 2 (2): a000166. doi:10.1101/cshperspect.a000166. ISSN 1943-0264. PMC 2828279. PMID 20182612.
  6. Bachmair, A.; Finley, D.; Varshavsky, A. (1986-10-10). "In vivo half-life of a protein is a function of its amino-terminal residue". Science. 234 (4773): 179–186. doi:10.1126/science.3018930. ISSN 0036-8075. PMID 3018930.
  7. Loetscher, P.; Pratt, G.; Rechsteiner, M. (1991-06-15). "The C terminus of mouse ornithine decarboxylase confers rapid degradation on dihydrofolate reductase. Support for the pest hypothesis". The Journal of Biological Chemistry. 266 (17): 11213–11220. ISSN 0021-9258. PMID 2040628.
  8. Burns, Kristin E.; Liu, Wei-Ting; Boshoff, Helena I. M.; Dorrestein, Pieter C.; Barry, Clifton E. (2009-01-30). "Proteasomal Protein Degradation in Mycobacteria Is Dependent upon a Prokaryotic Ubiquitin-like Protein". Journal of Biological Chemistry. 284 (5): 3069–3075. doi:10.1074/jbc.M808032200. ISSN 0021-9258. PMC 2631945. PMID 19028679.
  9. Ravid, Tommer; Hochstrasser, Mark (2008-09-01). "Degradation signal diversity in the ubiquitin-proteasome system". Nature Reviews. Molecular Cell Biology. 9 (9): 679–690. doi:10.1038/nrm2468. ISSN 1471-0072. PMC 2606094. PMID 18698327.
  10. Erales, Jenny; Coffino, Philip (2014-01-01). "Ubiquitin-independent proteasomal degradation". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. Ubiquitin-Proteasome System. 1843 (1): 216–221. doi:10.1016/j.bbamcr.2013.05.008. PMC 3770795. PMID 23684952.
  11. Jariel-Encontre, Isabelle; Bossis, Guillaume; Piechaczyk, Marc (2008-12-01). "Ubiquitin-independent degradation of proteins by the proteasome". Biochimica et Biophysica Acta (BBA) - Reviews on Cancer. 1786 (2): 153–177. doi:10.1016/j.bbcan.2008.05.004. ISSN 0006-3002. PMID 18558098.
  12. Asher, Gad; Tsvetkov, Peter; Kahana, Chaim; Shaul, Yosef (2005-02-01). "A mechanism of ubiquitin-independent proteasomal degradation of the tumor suppressors p53 and p73". Genes & Development. 19 (3): 316–321. doi:10.1101/gad.319905. ISSN 0890-9369. PMC 546509. PMID 15687255.
  13. Erales, Jenny; Coffino, Philip (2014-01-01). "Ubiquitin-independent proteasomal degradation". Biochimica et Biophysica Acta (BBA) - Molecular Cell Research. 1843 (1): 216–221. doi:10.1016/j.bbamcr.2013.05.008. ISSN 0006-3002. PMC 3770795. PMID 23684952.
  14. Hochstrasser, M. (1996-01-01). "Ubiquitin-dependent protein degradation". Annual Review of Genetics. 30: 405–439. doi:10.1146/annurev.genet.30.1.405. ISSN 0066-4197. PMID 8982460.
  15. Coux, O.; Tanaka, K.; Goldberg, A. L. (1996-01-01). "Structure and functions of the 20S and 26S proteasomes". Annual Review of Biochemistry. 65: 801–847. doi:10.1146/annurev.bi.65.070196.004101. ISSN 0066-4154. PMID 8811196.
  16. Lecker, Stewart H.; Goldberg, Alfred L.; Mitch, William E. (2006-07-01). "Protein Degradation by the Ubiquitin–Proteasome Pathway in Normal and Disease States". Journal of the American Society of Nephrology. 17 (7): 1807–1819. doi:10.1681/ASN.2006010083. ISSN 1046-6673. PMID 16738015.
  17. Melvin, Adam T.; Woss, Gregery S.; Park, Jessica H.; Dumberger, Lukas D.; Waters, Marcey L.; Allbritton, Nancy L. (2013). "A Comparative Analysis of the Ubiquitination Kinetics of Multiple Degrons to Identify an Ideal Targeting Sequence for a Proteasome Reporter". PLOS ONE. 8 (10): e78082. doi:10.1371/journal.pone.0078082. PMC 3812159. PMID 24205101.
  18. Wang, YongQiang; Guan, Shenheng; Acharya, Poulomi; Koop, Dennis R.; Liu, Yi; Liao, Mingxiang; Burlingame, Alma L.; Correia, Maria Almira (2011-03-18). "Ubiquitin-dependent proteasomal degradation of human liver cytochrome P450 2E1: identification of sites targeted for phosphorylation and ubiquitination". The Journal of Biological Chemistry. 286 (11): 9443–9456. doi:10.1074/jbc.M110.176685. ISSN 1083-351X. PMC 3058980. PMID 21209460.
  19. Ju, Donghong; Xie, Youming (2006-04-21). "Identification of the Preferential Ubiquitination Site and Ubiquitin-dependent Degradation Signal of Rpn4". Journal of Biological Chemistry. 281 (16): 10657–10662. doi:10.1074/jbc.M513790200. ISSN 0021-9258. PMID 16492666.
  20. Schrader, Erin K; Harstad, Kristine G; Matouschek, Andreas (2009-11-01). "Targeting proteins for degradation". Nature Chemical Biology. 5 (11): 815–822. doi:10.1038/nchembio.250. ISSN 1552-4450. PMC 4228941. PMID 19841631.
  21. Li, Xianqiang; Zhao, Xiaoning; Fang, Yu; Jiang, Xin; Duong, Tommy; Fan, Connie; Huang, Chiao-Chain; Kain, Steven R. (1998-12-25). "Generation of Destabilized Green Fluorescent Protein as a Transcription Reporter". Journal of Biological Chemistry. 273 (52): 34970–34975. doi:10.1074/jbc.273.52.34970. ISSN 0021-9258. PMID 9857028.

See also
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