Metabolite Damage and Metabolite Damage Control

When we look at a metabolic pathway, we usually assume that the metabolites behave as diagrammed; that substance A will remain substance A unless acted upon by enzymes X or Y. It is becoming clear that this assumption is false, and that metabolite damage occurs alongside normal metabolic processes. Metabolite damage is described by Hanson et al in a new article in Annual Review of Plant Biology as “the conversion of a normal metabolite to an abnormal one as the result of a chemical or enzymatic side reaction.” With improvements in the ability to detect small quantities of metabolites and their side products comes the realization that these conversions can be considerable. Furthermore, processes that repair or remove damaged metabolites (metabolite damage control) have been identified, some of which are highly conserved. Damage control is needed because damaged metabolites can be toxic or can interfere with other metabolic reactions for example by serving as inappropriate substrates or as enzyme inhibitors.

As Hanson et al observe, although metabolite damage occurs in all organisms, plants are particularly susceptible to it as a consequence of the wide-ranging environments they are exposed to, which in turn affects metabolite stability, enzyme activity, and metabolite pool sizes. They further observe that enzyme-mediated metabolite damage is of two types: substrate promiscuity, when an enzyme carries out its normal reaction on an abnormal substrate, or the less common catalytic promiscuity, when the enzyme carries out the wrong reaction on the right substrate.

Reprinted from Hanson et al, 2016.
Reprinted from Hanson et al, 2016.

Damage control measures limit the harmful impacts of damaged metabolites by damage repair or damage pre-emption. Repair involves enzymatically converting the damaged metabolite back to its original form (and is analogous to DNA or protein repair). Pre-emption can involve enzymatic removal of toxic damage products or deflection of reactions towards other, less harmful outcomes; directed overflow is a type of pre-emption that modulates levels of metabolites susceptible to damage.


An interesting example of metabolite damage and repair involves the carbon-fixing enzyme Rubisco. Rubisco’s normal substrate is ribulose 1,5-bisphosphate (RuBP), but it occasionally “misfires” and converts this substrate to xylulose 1,5-bisphosphate (XuBP), which differs only in the stereochemistry at the C3 position (Pearce, 2006). XuBP is a harmful metabolite-damage product because it serves as a potent competitive inhibitor for Rubisco. When analysing an operon encoding the large and small subunits of Rubisco in the photosynthetic bacterium Rhodobacter sphaeroides, Bracher et al (2015) identified a gene encoding CbbY, a sugar phosphatase that selectively dephosphorylates XuBP. The high selectivity of CbbY, which shows a 6000-fold preference for XuBP over RuBP, enables it to remove small amounts of the competitive inhibitor in the presence of much larger amounts of RuBP.

The occurrence of CbbY within a Rubisco-encoding operon provided clues to its function in R. sphaeroides, and subsequent studies showed that homologues are present in all photosynthetic genomes including that of Arabidopsis. As Hanson et al observe, the conservation of some of the damage repair pathways from prokaryotes to eukaryotes can facilitate their identification and characterization.

An important take-home message from the Hanson et al review is the idea that known metabolic space is just a tiny portion of the available chemical space, or as they eloquently summarize, “Metabolic pathways are thus narrow, well-lit tunnels of known chemistry boring through a huge, dark matrix of unknown chemistry.” This message is reflected by the fact that there are more than 40 million structures in current chemical databases, but only 15,000 metabolic substrates and products in the KEGG (Kyoto Encyclopedia of Genes and Genomes) database. Clearly, the age of exploration is not over for cellular chemistry.

I encourage anyone interested in metabolism to read the excellent reviews by Linster et al (2013) and Hanson et al (2016), which provide several further examples of metabolite damage and repair and also discuss the implications of these processes for metabolomic analysis and evolution.


Bracher, A., Sharma, A., Starling-Windhof, A., Hartle, F.U., and Hayer-Hartl M. (2015). Degradation of potent Rubisco inhibitor by selective sugar phosphatase. Nat. Plants. 1: 14002.

Hanson, A.D., Henry, C.S. Fiehn, O., and de Crécy-Legard, V. (2016). Metabolite damage and metabolite damage control in plants. Annu. Rev. Plant Biol. 67: DOI: 10.1146/annurev-arplant-043015-111648.

Linster, C.L., Van Schaftingen, E., and Hanson, A.D. (2013). Metabolite damage and its repair or pre-emption. Nat. Chem. Biol. 9: 72 – 80.

Pearce, F.G. (2006). Catalytic by-product formation and ligand binding by ribulose bisphosphate carboxylases from different phylogenies. Biochem. J. 399: 525-534.



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