Abstract
The formal oxidation state of carbon atoms in organic molecules depends on the covalent structure. In proteins, the average oxidation state of carbon (Z(C)) can be calculated as an elemental ratio from the chemical formula. To investigate oxidation-reduction (redox) patterns, groups of proteins from different subcellular locations and phylogenetic groups were selected for comparison. Extracellular proteins of yeast have a relatively high oxidation state of carbon, corresponding with oxidizing conditions outside of the cell. However, an inverse relationship between Z(C) and redox potential occurs between the endoplasmic reticulum and cytoplasm. This trend provides support for the hypothesis that protein transport and turnover are ultimately coupled to the maintenance of different glutathione redox potentials in subcellular compartments. There are broad changes in Z(C) in whole-genome protein compositions in microbes from different environments, and in Rubisco homologues, lower Z(C) tends to occur in organisms with higher optimal growth temperature. Energetic costs calculated from thermodynamic models are consistent with the notion that thermophilic organisms exhibit molecular adaptation to not only high temperature but also the reducing nature of many hydrothermal fluids. Further characterization of the material requirements of protein metabolism in terms of the chemical conditions of cells and environments may help to reveal other linkages among biochemical processes with implications for changes on evolutionary time scales.
Highlights
Chemical reactions involving the transfer of electrons, known as oxidation– reduction or redox reactions, are ubiquitous in cellular and environmental systems [1,2]
The purpose of this study is to investigate a particular stoichiometric quantity, the average oxidation state of carbon (ZC, defined below), as a comparative tool for identifying compositional patterns at different levels of biological organization
Comparisons of the average oxidation state of carbon in proteins can be used to visualize the compositional diversity of proteins in relation to redox chemistry in subcellular compartments and external environments
Summary
Chemical reactions involving the transfer of electrons, known as oxidation– reduction or redox reactions, are ubiquitous in cellular and environmental systems [1,2]. The oxidation of thiol groups in proteins to form disulfides has the potential to regulate (activate or inhibit) enzymatic function [3]. Because these reactions are reversible on short time scales, a regulatory network known as redox signalling is made possible by reactions of small-molecule metabolites, including glutathione (GSH) and reactive oxygen species [4]. Forces outside of individual cells and organisms sustain the redox disequilibria between inorganic and/or organic species that provide the energy sources for metabolisms suited to a multitude of environments [7]. The actions of organisms can alter the redox conditions on the Earth; the oxygenation of the atmosphere and oceans over geological time is linked to biological activity and changed the course of later evolution [8]
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