Posted by: Kay at Suicyte | August 6, 2007

Ubiquitin Nation

Today another silly post (due to lack of time required for serious discussion). Over the weekend, I read three different texts, all dealing with the attachment of ubiquitin to proteins. As usual, the authors could not agree on a single name for this process. Some people call it “ubiquitination”, others call it “ubiquitylation” and yet others (including myself) use either one or the other, depending on daytime, temper, moon phase, or whatever. Some people actually combine the best of both worlds and say “ubiquitinylation”. So, one of the most pressing questions in the field of ubiquitinology remains: which one is correct?

First, let us consult the wisdom of the masses. A quick search by Google shows that at least in the discipline, ubiquitination wins hands-down. Here is the score: ubiquitination: 1.36 Mio hits, ubiquitylation: 0.22 Mio hits, ubiquitinylation 0.07 Mio hits. If we rather trust the scientists, the relation looks similar (but with much smaller numbers) . A pubmed search yielded ubiquitination : 4063 hits, ubiquitylation: 562 hits, ubiquitinylation 134 hits. Oh, and there is also ubiquination: 34 hits. The latter word reminds me of that confused ISMB07 speaker, who found in some text mining effort an enrichment of the term “ubiquinone” and told the audience that meant a link to regulated protein degradation. We can count ourselves lucky that ubiquinone and ubiquinol don’t get conjugated to proteins – this saves us from ubiquinolation, ubiquinonylation and the like. To my surprise, Pubmed doesn’t know of a single instance of ubiquinylation.

So, should we all use ubiquination? I don’t know. For people with a background in chemistry (like myself) ubiquitylation might be more attractive, likening ubiquitin to the functional groups that you can attach to a substance (methyl-, alkyl-, aryl-, hydroxyl-) The same reasoning would work for ubiquitinylation, although in most functional groups the original ending gets clipped off before the ‘yl’ suffix is applied. We don’t say “methanyl” for the “methyl” groups. A second argument in favor of ubiquitylation is a perceived consistence with other ubiquitin-like modifiers. Sumo does sumoylation, Nedd8 does neddylation, Urm1 does urmylation (or does it?), ISG15 does Isgylation, and so on. Not quite sure what Fat10 does. Fatylation? Fattenylation? Fatuation?

Nevertheless, most people (including myself, most of the time) use “ubiquitination”, and one good reason for that is a positive feedback loop. People are using it because this is what they read in most of the literature. A similar mechanism governs choice of desktop computer operating systems. I wonder if the folks who use ‘ubiquitylation’ are also using Macs?

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Responses

  1. For what it’s worth, I say “ubiquitination”.

    (And I usually drive a Mac.)

  2. I read it all wrong, I thought it was someone like Nostradamus saying “U’be quitting Nation”!

  3. I remember an old cartoon published in TiBS, where ubiquitin was interpreted as a signal, saying: U be quittin’ (this world). If I remember correctly, the proteasomes were depicted as a gang of Hell’s Angels type, uttering things like: let’s break some bonds!
    The cartoon was well made and quite funny, but I don’t find it online.

  4. Not quite sure what Fat10 does.

    Fattening, of course.

  5. I guess the photo you described is on the cover of the TiBS containing the article “Orchestrating nuclear functions: ubiquitin sets the rhythm” 🙂

  6. Animesh, I think the cartoon was much older than that. If I strain my memory hard, it could have been 1996 as an illustration of an article on PEST regions by Martin Rechsteiner and Scott Rogers.
    doi:10.1016/0968-0004(96)10031-1
    I am not sure if the cartoon is contained in the PDF, as I don’t have online access to TiBS, although I probably have a paper copy of that issue somewhere in my basement. Thanks to Elsevier’s close-access policy, there is no way of showing this cartoon on my blog (I guess)

  7. Does anyone know if suppressed levels of ubiquitin enable certain destructive proteins to increase, possibly leading to diseases such as ALS? If yes, then is there a way to increase ubiquitin levels to possibly fight the disease?

  8. Randy: I am not aware of any established connection between ubiquitin shortage and human disease. This is different for proteasomal impairment, which is intensively discussed to play a role in a number of diseases. It is probably true that a lack of free ubiquitin can be a problem for cells, so a possible connection to disease states is conceivable. However, I am not aware of any known examples.
    Even if such a connection were true, I doubt that this can be easily used for a therapeutic approach. After all, ubiquitin has to be present inside of the cells, and you cannot just administer ubiquitin and hope that it gets taken up. The only hope would be to lock for molecules that can alter cellular ubiquitin homeostasis.


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