A lot of what scientists do is curating nature. That is, describing the different bits of nature, at different scales, categorizing them, and listing their relationships, in which they look for patterns. Scientists did this when they undertook the Human Genome Project, a massive effort to describe the chemical composition and order of human DNA. Having a map of human DNA only spurred further mapping.
Some scientists, wanting to create a better map, chose to continue by introducing higher complexity into the map’s pieces. For example, the first map ignored the variation between individuals. A better map could incorporate that variation. Still, wanting a better map, some scientists chose to introduce a higher order of complexity into the map’s scope. For example, annotating the map so that it didn’t merely describe the pieces that make-up DNA, but furthermore labelled those same sequences to explain that they can encode different proteins.
In the second of these two directions, in the quest to annotate DNA to explain the significance of its chemical composition and order, progress paralleled surprise. It was – and remains – a case of dealing with the inherently unknown; the unknown unknown. Every discovery sets a new standard for expectation, and shatters the old one. For example, even prior to the initiation of the human genome project it was established that DNA (via messenger RNA) could encode for proteins, and also that some proteins can catalyse chemical reactions. Thus it was expected and no surprise to find that the DNA was littered with sequences that could code for proteins, including catalytic proteins, which had been labelled ‘enzymes‘. Given the additional information that proteins are the doers of cell biology (out of which enzymes are the cell’s chemistry sets), it seemed sufficient to expect that the task of DNA annotation could be largely completed with these just these two labels: protein, and its sub-category, enzyme.
Of course, it would have been a rare mind to honestly believe that those two labels might be enough. But if they were not enough, then what else?
One early surprise was the discovery that some sequences for a type of enzyme – a sub-category termed kinases, which catalyze the chemistry of a phosphate group transfer – look exactly like their kin kinases, except for the fact that at least one of three essential chemical groups are missing. The category of kinases had been established on the reasonable expectation that it encompasses a group of similar proteins, and that their similarity is dependent on a shared function. But what does the scientist do after discovering an array of kinases they discover a protein that looks exactly like one of the known kinases except for a single change would / could be considered minute if not for the fact that it occurs in the kinase-defining part of the protein?
Perhaps the scientist could call it a freak; an evolutionary oddity, an exception to the rule, or the sole member of a fluke category. Perhaps. But only until 2002, when a focused look at all the places in the human genome that at first glance look like they code for kinases (which, importantly, are only one sub-category of enzymes), discovered that about 10% lack at least one of the three chemicals necessary for phosphate transfer. So, to continue the question which till then could be subtly brushed aside: what’s a kinase that doesn’t transfer phosphates? Esoteric jargon aside, this is hardly different from asking, “What’s a phone that doesn’t call?” or “…a book without words?” or “…a buggy without a horse?” or “…a newspaper without news?” Hover your mouse over each for suggested answers; they’re all arguable, but the answers I suggest illustrate that there is meaning in the question, and that different perspectives may be necessary to derive each.
What’s an enzyme that doesn’t enzyme? A pseudoenzyme.
Names are useful. They collect properties and similarities, and short-cut them all into an abbreviation that also serves as a pointer. Now, with just a name, and a handful of background facts, it’s possible to state and hypothesize a little about pseudoenzymes. For instance, the fact that they are not incredibly rare, and the fact that their chemical structures are conserved through evolution means something very important: they are useful to their host organism; they are functional. Therefore they are the product of evolutionary force. What’s more, by looking at these chemical structures across evolutionary lineages it is possible to hypothesize how they originated.
One possibility, which is likely to be responsible more often for the creation of pseudoenzymes, is that a duplication of an enzyme’s code was eventually followed by a loss-of-enzyme-function mutation in one copy. (Incidentally, the duplication event is not necessary for this narrative; it is possible for a pseudoenzyme to be created from an original enzyme sequence).
A second less likely possibility is that duplication of a protein code was followed by one copy mutating to gain enzyme function. (Again, duplication is helpful but not necessary. It is helpful because it reduces pressure, since it is easier for evolution to play around with a sequence if its essential functionality has a back-up).
What’s the purpose of an enzyme that doesn’t enzyme? Everything else.
The enzymatic function of an enzyme is the defining function of an enzyme, but not its sole function. In order to be the best enzyme that it can, enzymes have a number of supporting functions, as well as functions that act in parallel to the central task of catalysis (i.e. assisting chemical reactions). Compared with its kin enzyme, a pseudoenzyme might retain the abilities to bind to the same molecules, which may be other copies of the enzyme, or binding-partners of the enzyme, or even the target-molecule which the enzyme processes by catalysing a chemical reaction in which it is involved. Thus the pseudoenzyme can be a supporter of its kin enzyme, and it might help its kin enzyme by creating protein platforms that regulate its activity. The possibilities of how the pseudoenzyme helps its kin enzyme via protein platforms are similarly many (and by no means necessarily limited to known categories). Protein platforms – which are basically any functional aggregate of proteins – might regulate the kin enzyme due to the other proteins it brings into association, which bring their own functions into play, or by changing conformations of any members of the platform in some important way, or by moving the platform to some other part of the cell, which may have different chemistry conditions, et cetera et cetera: The possibilities are limited by 3.5 billion years of evolutionary tinkering, not by my imagination.
The revelation of the unknown is one of science’s great delights; it can occur on any scale or resolution of scientific inquiry. In this case, an inquiry that began with the very basic building blocks of DNA, the four sugars that form DNA’s four-letter alphabet A-C-T-G, continued along one path that sought to bring meaning to the order of that composition. The DNA code was enlightened by demonstrating that it could encode for protein sequences, and that those protein sequences determined properties, including chemical properties. Once proteins could be seen as bound collections of properties, it became easier to talk about their function, how that particular array of properties reacted to its host environment, and even how those environment-determined reactions contributed-to, or partook-in the continued existence of the host organism. Which leads to the next question…
What motivation does an organism have in favour of pseudoenzymes? Many; depending.
I’ve already described some possible properties that a pseudoenzyme might hold. But just like the famously incessant questioning of young children, where each question requires a higher, incrementally more holistic, picture of reality, so too with regards the meaning and identity of nature. What’s DNA for? It’s the actuality of the genetic code. What’s that for? To serve as instructions, some for making proteins. What are proteins? Different types, some are pseudoenzymes. What are they for? Providing different property-sets, like protein binding. What are those properties for? Providing different functions, like… a mode of arms-race flexibility.
As with every level of scientific exploration, the unknown can only be summed by reference to the known. That’s far more helpful than its language makes it sound. Examples are useful, even with the admission that they’re minute and relatively insignificant in the face of the whole, most of which is hidden in darkness. They are useful in these severely limited cases because they provide an anchor that is not completely random.
In one species of parasite which attacks mice, pseudoenzymes offer cells a flexibility in an evolutionary arms race. Mice have (metaphorically speaking) learned to make IRG proteins to block the parasites’ entry. In turn, the parasite have learned to counter IRG by using proteins called ROP18 and a group of pseudoenzymes called ROP5. It’s not important here just precisely how those proteins challenge each other. What is important is that over evolutionary time-scales, the parasites’ and the mice’s lineages have been locked in an arms race. Each lineage has been evolving those enzymes to counter its opponents, and to overcome their “latest” developments. PS. These proteins’ names, IRG, ROP15, ROP18, don’t matter here.
Why does the parasite have ROP5 pseudoenzymes? Because that allows the parasite to compartmentalize different aspects of its arm race. It has isolated a department, the ROP5 family, which can be relatively liberal with mutations, since ROP5 are more resilient to mutations, since they don’t have to worry about invalidating some central, key enzyme function. The enzyme-aspect of the war effort is meanwhile held separately, by ROP18, and thus protected from-, and therefore allows- a generous mutation project over at ROP5.
So that’s a tiny tiny part of what pseudoenzymes do, which in turn are a small part of what enzymes are, which are a small part of proteins, which are a small part of the totality of the genome, which is only a part of the totality of biological information inherent to an organism, which is just one way of looking at life, which is a single category of the totality of reality..........
tl;dr: Pseudoenzymes are proteins that closely resemble enzymes but are missing the function of an enzymatic ability. They retain other functions that enzymes have, and that serves whatever role they play in the cell, often assisting the actual-enzyme they resemble.
Further reading and references:
- A “News Focus” published in the journal Science entitled “‘Dead’ Enzymes Show Signs of Life“. This is the most readable item on this list.
- The 2002 paper published in Science entitled “The Protein Kinase Complement of the Human Genome“, which was significant in appreciating the scope of pseudoenzymes.
- A set of 2012 papers published in Science entitled “Tumor Necrosis Factor Signaling Requires iRhom2 to Promote Trafficking and Activation of TACE” and “iRhom2 Regulation of TACE Controls TNF-Mediated Protection Against Listeria and Responses to LPS“, which describe functions the pseudoenzymes have.
- A 2011 paper published in PNAS entitled “Polymorphic family of injected pseudokinases is paramount in Toxoplasma virulence“, which demonstrated what it says in the title.
Update: New review: Day of the dead: pseudokinases and pseudophosphatases in physiology and disease (2014) Trends in Cell Biology
