I was just talking here about targeted protein degradation, not for the first time, and in almost every case when you’re talking TPD you’re talking ubiquitination. Ubiquitin, as the name indicates, is indeed all over the place. It’s a small protein (76 amino acids), but it doesn’t quite qualify for being one of those “microprotein” sequences that I was also talking about the other day, since its genes have it coded for as part of a larger protein sequence, not just by itself. But it is a good example of how proteins that length can be pretty flippin’ important – Ub itself is important enough that its human and yeast sequences are still 96% identical, for example. It has definitely earned Classic Protein status with numbers like that.
Ubiquitin is conjugated to lysine residues on a huge variety of proteins, and then it’s often stapled in there a few more times to make polyubiquitin chains. The single-ubiquitination versus polyubiquitination is naturally an important difference, so that complicates things. For example, monoubiquitination is generally some sort of membrane localization signal for the proteins involved, but four Ubs in a row off the same lysine is generally the “Haul this thing to the proteasome and break it up for scrap” signal. Depending on the circumstances, ubiquitination can also be a “Haul this thing to the lysosomes and break it up” or a “Haul this thing to the endoplasmic reticulum and break it up” signal, to be completist about it. You can ubiquitinate more than one exposed lysine residue, and more than one at a time, so that complicates things even more. What complicates things a great deal is that you can form those polyubiquitins though more than one type of linkage, because ubiquitin itself has seven lysines of its own (as well as its own amino terminus). K48 of ubiquitin is the most well-characterized of those ubiquitinated-ubiquitin residues, but all the others are known to join in, too, and these different linkage patterns also can have different effects downstream. Some of them actually stabilize proteins from degradation under some conditions rather than marking them for destruction, for example. And I haven’t even mentioned the whole list of deubiquitinating (DUB) enzymes that can reverse some of these steps! We’re still figuring all this out.
You’d think that would be enough to keep folks occupied, and it definitely is. But cell biology does not take our workloads into account, as is often mentioned here, and this paper will show you yet another example of that. Now we get to move beyond lysines entirely, since there are apparently enzymes that also ubiquitinate serine, threonine, and cysteine residues, often by making an ester group with the carboxylate end of the ubiquitin protein. Such things had been seen in the context of viral infection years ago, but were written off as some sort of virus-associated weirdness. But apparently not – they are real protein pathways, and we’re only starting to understand what their functions are. Some of the known DUBs seem to have esterase activity, so they might well be working for several kinds of deubiquitination, and you can’t rule out other esterases being involved, either. These non-lysine ubiquitination events seem to be important in tissue development and in immune system pathways, neither of which were exactly short of fractally dense complications already.
But wait! There’s more! (Yes, I was a teenager during the early years of cable TV ads, thanks for asking). If you call now – well, actually, even if you don’t, it turns out that ubiquitin doesn’t just modify proteins, either. Ubiquitinated polysaccharides and lipopolysaccharides have been found, with the latter being (among other things) a defense against invaring bacteria. Slapping Ub residues all over them exposes them to some of those degradation pathways mentioned above, and this might turn out to apply to more substrates than we currently realize. There’s evidence from genetically-associated disease that polysaccharide UB pathways are involved in more than just the immune response as well.
Perhaps as we continue to hack the ubiquitination system for our own purposes we will see that some of these things are responsible for unexpected activities (good and bad). And at any rate, all the work going into protein degradation pathways as a drug modality will surely help to uncover some new stuff in this line, if we’re aware that it’s out there to be seen in the first place. So the paper linked to above can serve as formal notice: there’s more to ubiquitin than you thought.
