Degron

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Shown here in green is a portion of IkBa, an inhibitor of NF-kB and regulator of the immune system. The red region highlights the sixth ankyrin repeat domain, which contains a ubiquitin-independent degron. Ikba degron.jpg
Shown here in green is a portion of IκBα, an inhibitor of NF-κB and regulator of the immune system. The red region highlights the sixth ankyrin repeat domain, which contains a ubiquitin-independent 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, [2] structural motifs [1] and exposed amino acids (often lysine [3] or arginine [4] ) located anywhere in the protein. In fact, some proteins can even contain multiple degrons. [1] [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]

Contents

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 IκBα, 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. [1] 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. Abundance over time.jpg
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. [1] [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. [1] [7] [20] A significant increase in the amount of ubiquitin in A’ as compared to A will suggest that the degron is ubiquitin-dependent. [1] [9]

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References

  1. 1 2 3 4 5 6 7 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.
  2. ↑ 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.
  3. ↑ Dohmen RJ, Wu P, Varshavsky A (1994). "Heat-inducible degron: a method for constructing temperature-sensitive mutants". Science. 263 (5151): 1273–1276. doi:10.1126/science.8122109. PMID   8122109.
  4. ↑ Varshavsky, A. (1996-10-29). "The N-end rule: functions, mysteries, uses". Proceedings of the National Academy of Sciences. 93 (22): 12142–12149. Bibcode:1996PNAS...9312142V. 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. Bibcode:1986Sci...234..179B. doi:10.1126/science.3018930. ISSN   0036-8075. PMID   3018930.
  7. 1 2 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. doi: 10.1016/S0021-9258(18)99150-7 . 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. 1 2 3 4 5 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. 1 2 3 4 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. 1 2 3 4 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. Bibcode:2013PLoSO...878082M. 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. 1 2 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. 1 2 3 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.

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