The Impact of Non-Enzymatic Reactions and Enzyme Promiscuity on Cellular Metabolism during (Oxidative) Stress Conditions

Abstract

Cellular metabolism assembles in a structurally highly conserved, but functionally dynamic system, known as the metabolic network. This network involves highly active, enzyme-catalyzed metabolic pathways that provide the building blocks for cell growth. In parallel, however, chemical reactivity of metabolites and unspecific enzyme function give rise to a number of side products that are not part of canonical metabolic pathways. It is increasingly acknowledged that these molecules are important for the evolution of metabolism, affect metabolic efficiency, and that they play a potential role in human disease-age-related disorders and cancer in particular. In this review we discuss the impact of oxidative and other cellular stressors on the formation of metabolic side products, which originate as a consequence of: (i) chemical reactivity or modification of regular metabolites; (ii) through modifications in substrate specificity of damaged enzymes; and (iii) through altered metabolic flux that protects cells in stress conditions. In particular, oxidative and heat stress conditions are causative of metabolite and enzymatic damage and thus promote the non-canonical metabolic activity of the cells through an increased repertoire of side products. On the basis of selected examples, we discuss the consequences of non-canonical metabolic reactivity on evolution, function and repair of the metabolic network.

Keywords: enzyme promiscuity; metabolic damage; metabolite repair; oxidative stress; reactive oxygen species; underground metabolism.

Figure 1

Formation of non-canonical metabolites and repair strategies. Chemical modification of metabolites leads to unwanted reactions, causing damage to both macromolecules and small molecules (i). Molecular scavengers cleanse and channel ROS toward less toxic products (ii). Stress sensors activate genes involved in specific protein-based repair responses (iii); or in unspecific transport processes (iv). As a general outcome, the metabolome reconfigures, affecting metabolite levels and fluxes; this in turn affects the specificity of enzymatic reactions. (v–vi) Selection of relevant examples from metabolism. Abbreviations: ROS, reactive oxygen species; Met, Methionine; GR, glutathione reductase; GSSG, oxidized glutathione or glutathione disulfide; GSH, reduced glutathione; MEP, multidrug efflux pump; LA, lipid; L•, lipid radical; LOO•, lipid peroxyl radical; R• complex radicals; GLDH, glutamate dehydrogenase; α-KG, α-ketoglutarate; Glu, glutamate; MDH, malate dehydrogenase; OA, oxaloacetate; L-2-HG, L-2-hydroxyglutarate; PK, protein kinase; PDC, pyruvate dehydrogenase complex; Pyr, pyruvate; Ac-CoA, acetyl-coenzyme A; SerC, phosphoserine transaminase; 3P-HPyr, 3-phosphohydroxypyruvate; Ser, serine; Ala, alanine.

Figure 2

Oxidative damage on methionine and its repair enzymes. Methionine is oxidized to methionine-S-sulfoxide and methionine-R-sulfoxide derivatives. Three families of methionine sulfoxide reductases (Msr, different colors), revert the process depending on thioredoxin, each being stereo-specific against the R- or the S-enantiomeric form. While MsrA and MsrB are highly conserved with preference for protein integrated methionine sulfoxides, MsrC (fRMsr) is limited to unicellular organisms and reduces free methionine-R-sulfoxide. MsrB has evolved by duplication and divergence (red dashed arrows), accounting for coverage of diverse subcellular localizations, and enabling in plants the appearance of a subtype active against the free methionine-R-sulfoxide. Color intensities illustrate different strength in catalytic efficiency.

Figure 3

Mechanistic classification of enzyme promiscuity. (A) Substrate promiscuity or multispecificity: A certain enzyme can perform the same catalytic reaction on a diverse set of substrates indistinctly; (B) Catalytic promiscuity: Different chemical transformations are allowed by the same enzyme, according to which this can be classified with various E.C. numbers. (C) Conditional promiscuity: Latent secondary activities of an enzyme might gain activity in response to environmental changes, e.g., due to an increase in the concentration of substrate analogs with lower affinity for the enzyme, or by post-translational signals related with induced conformational changes. The three examples shown are merely illustrative but inspired by transaminase TyrB, cytosine methyltransferase and thymidine kinase, respectively.

Figure 4

Impact of metabolic inaccuracy on the genotype-to-phenotype relationship. Biological processes, including transcription, translation and metabolism are not totally accurate. During the gene-protein-metabolite information flow, errors generated at each operational layer that are not compensated (depicted as angles α, β, γ) propagate, overall shaping the phenotypic space to be achieved from the same genotype (variation in the x-axis). Phenotypic variability arising due to error propagation can be enhanced by environmental stress conditions and enables a wide space of positions in the fitness landscape (red curve), all of which contribute to define the selection pressure over the given genotype (A). Promiscuity, noise, and unspecificity may thus facilitate the physiological adaptation to changing conditions, which would otherwise require the evolution to a different genotype (B).