User:Dmeyer314

Plan for revising Degron page:

What first drew me to this page for revisions is the abundance of claims throughout the text that were unsupported by literature. Additionally, I found most of the current headings/sections were oddly specific and didn't tell the full story about degrons. My current plan for revising this page is to give a more thorough overview of what degrons are, what their functions are in protein turnover and how they can be useful in experimental/biotech environments. If I am able to find more literature that can support/elaborate on what is currently written, then I will incorporate those sections into my revision. Currently, I am searching for that literature as well as reading the other articles I've found in preperation for my update. I anticipate my article's structure being something along the lines of:

section 1: what is a degron (sequence or structure which targets protein for degredation)

section 2: Ubiquitin dependence

-here I'll reference the degron-proteasome connection briefly since proteasome page exists

section 3: Ubiquitin Independence

-IkBa degron example

section 4: utility in experimental biology

-this is where most of the previously written material may appear

https://wiki.riteme.site/wiki/Degron (shown below is my edited form in progress)

A degron is a specific sequence of amino acids in a protein that directs the starting place of degradation. A degron sequence can occur at either the N or C-terminal region: these are called N-degrons or C-degrons respectively. Degradation may be initiated in a ubiquitin-dependent or ubiquitin-independent manor.

A temperature sensitive degron takes advantage of the N-end rule pathway, in which a destabilizing N-terminal residue dramatically decreases the in vivo half-life of a protein. The degron appears a fusion protein of ubiquitin, arginine, and DHFR<cite paper that used this>. DHFR is dihydrofolate reductase, a mouse-derived enzyme that functions in the synthesis of thymine<citation>. It is also heat-labile - at a higher temperature of 37°C, becomes slightly unfolded<citation> and exposes an internal lysine, the site of poly-ubiquitination<citation on lysine being site of poly-ubiquitination>. Proteolysis is highly processive, and the protein is degraded by the proteasome. [][The degron can be fused to a gene]=>rephrase because fusing protein sequences to genes isn't what is happening here]]] to produce the corresponding temperature-sensitive protein. It is portable, and can be transferred on a plasmid<cite paper showing transferrability>.

A ligand controllable degron takes advantage of a mutant form of FKBP12 protein that can be controlled using a synthetic ligand. Small molecule Shield1 binds specifically to the degron making it inactive. An inactive degron is no longer recognized by the proteasome, and this [[[limits/stalls/inhibits]]] protein degradation. The degron is reactivated when the small molecule is removed by washing the cells and active protein degradation occurs through proteasome mediated proteolysis.

some other things to include:

->Mouse ornithine decarboxylase (MODC) has been fused to fluorophores to reduce half-life

->IkBa degron

See also

• N-end rule

Category:Peptide sequences

Reviews:

Ravid T, Hochstrasser M. Degradation signal diversity in the ubiquitin-proteasome system. Nat Rev Mol Cell Biol [Internet]. 2008 Sep [cited 2015 Nov 24];9(9):679–90. Available from:http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2606094

Jariel-Encontre I, Bossis G, Piechaczyk M. Ubiquitin-independent degradation of proteins by the proteasome. Biochimica et Biophysica Acta (BBA) - Reviews on Cancer [Internet]. 2008 Dec [cited 2015 Dec 1];1786(2):153–77. Available from: http://www.sciencedirect.com/science/article/pii/S0304419X0800027

Erales J, Coffino P. Ubiquitin-independent proteasomal degradation. Biochimica et Biophysica Acta (BBA) - Molecular Cell Research [Internet]. 2014 Jan [cited 2015 Dec 1];1843(1):216–21. Available from:http://www.sciencedirect.com/science/article/pii/S0167488913001882

• protein degredation can be Ub-dependent or -independent and so these are reviews of the system involved in each

Primary Lit:

Fortmann KT, Lewis RD, Ngo KA, Fagerlund R, Hoffmann A. A Regulated, Ubiquitin-Independent Degron in IκBα. Journal of Molecular Biology [Internet]. 2015 Aug 28 [cited 2015 Dec 1];427(17):2748–56. Available from:http://www.sciencedirect.com/science/article/pii/S0022283615003897

• degron on inhibitor of NFkB shown to be sufficient to destabilize GFP

Li X, Zhao X, Fang Y, Jiang X, Duong T, Fan C, et al. Generation of Destabilized Green Fluorescent Protein as a Transcription Reporter. J Biol Chem [Internet]. 1998 12–25 [cited 2015 Nov 29];273(52):34970–5. Available from:http://www.jbc.org/content/273/52/34970

Gonda DK, Bachmair A, Wünning I, Tobias JW, Lane WS, Varshavsky A. Universality and structure of the N-end rule. J Biol Chem. 1989 Oct 5;264(28):16700–12.

• basically, the amino acid occupying the N-terminus of a protein will determine its stability (primarily a yeast thing, but shows it also happens in mammalian cells)

Dantuma NP, Lindsten K, Glas R, Jellne M, Masucci MG. Short-lived green fluorescent proteins for quantifying ubiquitin/proteasome-dependent proteolysis in living cells. Nat Biotechnol. 2000 May;18(5):538–43.

• applied N-end rule to successfully create destabilized GFP in mammalian cells

Hackett EA, Esch RK, Maleri S, Errede B. A family of destabilized cyan fluorescent proteins as transcriptional reporters in S. cerevisiae. Yeast. 2006 Apr 15;23(5):333–49.

• applied N-end rule to successfully create a suite of destabilized CFPs in yeast

<find ODC articles>

Training for Students complete!