The widespread role of non-enzymatic reactions in cellular metabolism

Abstract

Enzymes shape cellular metabolism, are regulated, fast, and for most cases specific. Enzymes do not however prevent the parallel occurrence of non-enzymatic reactions. Non-enzymatic reactions were important for the evolution of metabolic pathways, but are retained as part of the modern metabolic network. They divide into unspecific chemical reactivity and specific reactions that occur either exclusively non-enzymatically as part of the metabolic network, or in parallel to existing enzyme functions. Non-enzymatic reactions resemble catalytic mechanisms as found in all major enzyme classes and occur spontaneously, small molecule (e.g. metal-) catalyzed or light-induced. The frequent occurrence of non-enzymatic reactions impacts on stability and metabolic network structure, and has thus to be considered in the context of metabolic disease, network modeling, biotechnology and drug design.

Graphical abstract

Figure 1

Non-enzymatic reactions in cellular metabolism. (a)Evolution. Non-enzymatic reactions (R1, R3, R4, left panel) provide a template for the evolutionary selection of enzymes (E1, E3, E4). Enzymes can achieve higher substrate specificity and reaction rate, can be regulated and decrease the dependency on rare catalysts. (b)Three classes of non-enzymatic reactions dominate in modern metabolism. The presence of enzymes does not prevent or replace non-enzymatic metabolic reactions, which divide into three classes: Class I reactions are non-specific and act on a broad range of substrates, Class II reactions are specific and occur exclusively non-enzymatic as part of the metabolic network, while Class III reactions occur simultaneously in an enzymatic and non-enzymatic manner.

Figure 2

Class III non-enzymatic reactions occur in parallel to the six main classes of enzymes. Non-enzymatic counterparts of six enzymes representatives to the six general chemical reaction types/main classes of enzymatic reactions (top hierarchical level of enzyme commission number). Enzymes are exemplified by crystallographic structures illustrated in pymol; Protein Structure Databank (PDB, accession codes: 8CAT (catalase [19]), 1PKW (human glutathione transferase A1-1 [66]), 2J0E (6-phosphogluconolactonase [67]), 1N8P (PLP-dependent cystathionine gamma-lyase [68]), 4OWG (triosephosphate isomerase [53]) and 2G36 (iron–sulfur cluster containing tryptophanyl-tRNA synthetase [39]).

Figure 3

Examples for biologically important non-enzymatic chemical reactions. (a) The intermolecular redox reaction of two hydrogen peroxide molecules into water and oxygen is catalyzed non-enzymatically or by catalase (EC 1.11.1.6). (b) The thiol group of GSH is an acceptor of electrophiles allowing the formation of glutathione-S-conjugates, either non-enzymatically or through GSTs (EC 2.5.1.18). (c) 6-phosphogluconolactone is hydrolyzed to 6-phosphogluconate in the PPP spontaneously, or through 6-phosphogluconolactonase (EC 3.1.1.31), whose main function is to prevent unwanted side-reactions. (d) The final step in ergothioneine biosynthesis is the decomposition of hercynylcysteine sulfoxide either by a pyridoxal phosphate-dependent lyase, or non-enzymatically by pyridoxal phosphate alone. (e) The two final steps in cholecalciferol (vitamin D₃) biosynthesis are non-enzymatic isomerizations, one UV-light dependent and one spontaneous. For both reactions no enzymatic counterpart is known (Class II reactions). (f) Tryptophan-tRNA ligase or a non-enzymatic reaction conjugate tryptophan to its tRNA.

Figure 4

The success of enzymatic catalysis in cellular metabolism. The conversion of a substrate into its product can be mediated by non-enzymatic catalysts (organic/metal, left panel) or enzymatically (right panel). Non-enzymatic catalysts accelerate reactions but often display a broad substrate and product spectrum. While this variability is exploited during evolution, metabolism gains efficiency with enzymes that are specific and are less dependent on availability of rare catalysts. Moreover enzymes allow to more precisely regulate certain reactions and therewith to distribute flux through-out the metabolic network.