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Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals - PubMed

  • ️Sun Jan 01 2023

Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals

Olivia H Hewitt et al. Sci Rep. 2023.

Abstract

Oxygen is the sustenance of aerobic life and yet is highly toxic. In early life, antioxidants functioned solely to defend against toxic effects of reactive oxygen species (ROS). Later, as aerobic metabolisms evolved, ROS became essential for signalling. Thus, antioxidants are multifunctional and must detoxify, but also permit ROS signalling for vital cellular processes. Here we conduct metazoan-wide genomic assessments of three enzymatic antioxidant families that target the predominant ROS signaller, hydrogen peroxide: namely, monofunctional catalases (CAT), peroxiredoxins (PRX), and glutathione peroxidases (GPX). We reveal that the two most evolutionary ancient families, CAT and PRX, exhibit metazoan-wide conservation. In the basal animal lineage, sponges (phylum Porifera), we find all three antioxidant families, but with GPX least abundant. Poriferan CATs are distinct from bilaterian CATs, but the evolutionary divergence is small. Amongst PRXs, subfamily PRX6 is the most conserved, whilst subfamily AhpC-PRX1 is the largest; PRX4 is the only core member conserved from sponges to mammals and may represent the ancestral animal AhpC-PRX1. Conversely, for GPX, the most recent family to arise, only the cysteine-dependent subfamily GPX7 is conserved across metazoans, and common across Porifera. Our analyses illustrate that the fundamental functions of antioxidants have resulted in gene conservation throughout the animal kingdom.

© 2023. The Author(s).

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1

Summary of reaction mechanisms for (A): CAT, (B): PRX, and (C): GPX. In the first step of the reaction mechanism of all PRXs and CysGPXs, and GPX7, H2O2 reacts with the peroxidatic cysteine (CP) to form a sulfenic acid (SOH) intermediate. Whilst in SecGPXs, a catalytic selenocysteine first reacts to form a selenic acid (SeOH). If a second, resolving cysteine (CR) is present (i.e., in AhpC-PRX1, PRX5 & CysGPX), this quickly reacts with the SOH to form either an inter- or intramolecular disulfide bond that is then most commonly reduced by thioredoxin (TRX), reactivating the enzyme. PRX6 instead forms a disulfide with another molecule, commonly GST, and is then recycled by glutathione (GSH), generating oxidised glutathione (GSSG). In SecGPXs the SeOH is similarly reduced by two GSH generating GSSG, whilst GPX7 is described to be reactivated via the ER protein disulfide isomerase (PDI). For PRXs under high concentrations of H2O2, SOH reacts with another molecule of H2O2 to form a sulfenic acid (SO2H), resulting in hyperoxidation. Enzymes within the subfamily, AhpC-PRX1 only may then be slowly re-activated via the enzyme sulfiredoxin (SRX) via the inactivation loop. (D): Generalised domain structure for CAT, PRX, and GPX enzyme families. CAT enzymes comprise a catalase domain and catalase-related immune -responsive (catalase_rel). Stars denote presence of active site, His and Asn respectively. All PRX enzymes comprise the domain, Alkyl hydroperoxide reductase-Thiol specific antioxidant (AphC-TSA). The subfamilies AhpC-PRX1 and PRX6 additionally commonly encode the Peroxiredoxin, C-terminal domain (1-cysPrx_C). CP (red) and CR (blue) conserved active site are displayed, residues in bold denote absolutely conserved, and underlined residues denotes amino acids that deviated from that displayed within more than one metazoan sequence. GPX enzymes comprise a single GSHPx domain. GPX enzymes may encode either CP or a catalytic Sec (S) within the active site.

Figure 2
Figure 2

Maximum likelihood phylogenetic tree of monofunctional CAT enzyme family. (A): Unrooted tree displaying three main CAT clades indicated by branch colour: clade 1 (dark grey), clade 2 (light grey), clade 3 (black). Within clade 3 coloured shapes indicate identified evolutionary groups; Nematoda (orange), Demospongiae (blue), Invertebrate (yellow), inner dashed line indicates bilaterian-invertebrate species only, and Vertebrata (green). (B): Rooted phylogenetic tree using metazoan CAT protein sequences and the choanoflagellate M. brevicollis CAT as an outgroup. (M) denotes mitochondrial localised CAT sequences. Asterisk (*) next to A. queenslandica and T. wilhelma denotes full length CAT gene sequences for these two species. Labels coloured blue denote sequences encoded by phylum Porifera. Black numbers on branches indicate bootstrap support. Circles denote collapse tree nodes. Coloured shapes in B correspond to those displayed in (A). Branch lengths represent evolutionary distances, indicated by tree scale. Constructed based on edited alignment, 1000 bb and the evolutionary models, A: LG + I + G4 and B: LG + G4.

Figure 3
Figure 3

Presence of antioxidant enzymes within 8 different subcellular compartments of 19 metazoan species. Shapes denote enzyme family, namely CAT (circle), PRX (triangle), or GPX (square). Subcellular compartments indicated are predictions based on amino acid sequence analysis by DeepLoc-2.0,

https://services.healthtech.dtu.dk/service.php?DeepLoc-2.0

,. Colours denote individual PRX and GPX enzyme subfamilies, based on phylogeny corresponding to Figs. 4 and 5. Total number of CAT, PRX, and GPX gene sequences encoded by each species in Table 1.

Figure 4
Figure 4

(A): Maximum likelihood phylogenetic tree of PRX enzyme family. Unrooted tree displaying PRX animal subfamilies; AhpC-PRX1 (green), PRX5 (blue), and PRX6 (pink) that correspond with the three broad classes, typical 2-Cys PRX, atypical 2-Cys PRX, and 1-Cys PRX, respectively. Within AhpC-PRX1 orange shape denotes strongly supported monophyletic clade named PRX4. (B): Depicts zoomed in region of AhpC-PRX1 clade. Monophyletic clades comprising isoforms, PRX1/2 (turquoise) and PRX3 (purple) of Vertebrata are indicated. These isoforms were previously used to classify PRXs across all metazoan species until a revision of PRX system of classification,. CNID-PRX denotes recently established subfamily found only within species belonging to phylum Cnidaria. Orange circle indicates collapsed nodes of PRX4 clade. Labels coloured blue denote sequences encoded by phylum Porifera. Black numbers on branches indicate bootstrap support. Branch lengths represent evolutionary distances, indicated by tree scale. Constructed based on edited alignment, 1000 bb and the WAG + I + G4 evolutionary model. FW: fresh water, SW: sea water.

Figure 5
Figure 5

Maximum likelihood phylogenetic tree of GPX enzyme family. Unrooted tree displaying GPX subfamilies, GPX1/2 (peach), GPX3/GPX5/GPX6 (orange), GPX7/GPX8 (turquoise), and PHGPX/GPX4 (grey). Labels in blue denote sequences encoded by phylum Porifera. Labels with a star indicate cysteine GPXs, where cysteine is the catalytic residue. Subfamily GPX7 is exclusively cysteine dependant for all species. Black numbers on branches indicate bootstrap support. Branch lengths represent evolutionary distances, indicated by tree scale. Constructed based on edited alignment, 1000 bb and the LG + G5 evolutionary model.

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References

    1. Ślesak I, Ślesak H, Kruk J. Evolution of life on earth: In silico comparative analysis of biochemical pathways. Astrobiology. 2012;12:775–784. doi: 10.1089/ast.2011.0704. - DOI - PMC - PubMed
    1. Gough, D. & Cotter, T. Hydrogen peroxide: a Jekyll and Hyde signalling molecule. Cell Death Dis 2, e213 (2011). 10.1038/cddis.2011.96 - PMC - PubMed
    1. Stadtman ER, Berlett BS. Reactive oxygen-mediated protein oxidation in aging and disease. Chem. Res. Toxicol. 1997;10(5):485–494. doi: 10.1021/tx960133r. - DOI - PubMed
    1. Halliwell, B. & Gutteridge, J.M.C. Free Radicals in Biology and Medicine. Oxford: Oxford Univ. Press. 5th ed. (2015)
    1. Sies H. Hydrogen peroxide as a central redox signaling molecule in physiological oxidative stress: Oxidative eustress. Redox Biol. 2017;11:613–619. doi: 10.1016/j.redox.2016.12.035. - DOI - PMC - PubMed

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