Promiscuously hitchhiking on a pathway

Saturday, 6 February 2016

Promiscuously hitchhiking on a pathway

In the seminal 1976 paper on enzyme evolution Roy Jensen first pointed out that the TCA cycle, the ketoadipate route to lysine, pantothenate, isoleucine, valine and leucine biosynthesis all operated via the same mechanistic steps (condensation with an acyl-CoA, rearrangement, oxidation and elimination of a carbon) and conjectured that they descent from a common primordial pathway.
Promiscuity is generally studied with a single enzyme as a model. A few paper tip-toe around it, but I am not sure that there are any that deal specifically with a pathway where the each enzyme along a pathway shows substrate ambiguity towards the promiscuous product of the previous reaction. I mentioned in another post that the branched chain amino acid pathway can produce norvaline, norleucine and homonorleucine when certain enzymes are overexpressed. Each enzyme in the pathway shows substrate ambiguity, so the whole pathway possess substrate ambiguity.
It is not a feature of the oxaloacetate-to-ketoglutarate–like pathways, but can be found in other pathways.

serCB and hisCB

During my PhD I did a series of experiments that did not go far, but found two consecutive promiscuous enzymes. It was not straightforward and had a biochemical twist. My PhD supervisor, Wayne Patrick, had found that E. coli hisB could rescue the KEIO ΔserB, while I found that untagged E. coli hisC could  rescue ΔserC if supplemented with pyridoxine. The reason for this is that E. coli SerC is bifunctional, acting as SerC (serine) and PdxC (PLP) and HisC can catalyse the serine pathway step and not the PLP pathway step. Unfortunately the reverse could not be tested easily as E. coli HisB is actually a fusion protein of a dehydratase and a phosphatase. So a homologue of a dehydratase would need to be inserted before testing. Furthermore, we were interesting in Pelagibacter ubique, which lacks serC and serB, but none of the native-encoding genes could not be expressed even with pRARE. A further twist was from Thermotoga maritima (another organism of interest) where serC and serA are in the loci TM1400 and TM1401 (old names), while the histidine cluster is from TM1035 to TM1043 and hisC was TM1040, which is rather dyslexically spooky —even if it did have dedicate amino transferases, hisB-N and serB might be encoded by a bifunctional hisB/serB phosphatase (TM0804).
This similarity between serine and histidine was not novel and in fact Roy Jensen had observed it in his paper —without having to test it.
The main point is that if one enzyme is able to promiscuously accept one substrate, it stands to reason it is likely that the chemistry of next enzyme along might be able with similar easy to promiscuous accept the promiscous product of the first unless the mechanism involve a part of the molecule that differs between the physiological substrate and the promiscuous one. As a consequence, a non-physiological substrate would hitchhike along a pathway.

Paralogous metabolism

In a nice fairly recent paper, the concept of shadow metabolism, called there paralogous metabolism, was discussed. Namely, seleno (and telluro) organocompounds are sometimes created, as are glutaramate, succinamate and oxamate, while some modifications, like 3-methyladenine, lack an annotated pathway for their degradation (dead end metabolites). These compounds require a shadow metabolic network to remove them, either via paralogues or via the substrate ambiguity* of the main enzymes themselves.

In summary, the ability of a side metabolite to hitchhike a ride along a pathway is likely to be a common phenomenon and may play a part in shaping shadow metabolism.


footnote


*) The semantics becomes problematic as the selective pressure on the shadow metabolic network would be near neutral, but not fully neutral. The reverse is probably more clear cut in many cases. A concept that I find fascinating is the suppression of certain reactions at the cost of the primary one —star activities of restriction endonucleases are the quintessential example of this. There likely are a large amount of reactions that are suppressed to prevent shadow metabolites (acetyl-CoA is more common than the other CoA adducts, yet many enzymes that act on the latter discern away the former). For many case it is simply speculation, for example Ketobutyrate is a curious case: there are no studies on transaminases that convert it to homoalanine nor any studies to detect the latter, yet transaminases have a broad specificity so either homoalanine is formed neutrally or the transaminases  are under negative selection to avoid that reaction while accommodating others.


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