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New Insights Into the Molecular Evolution of Metazoan Peroxiredoxins

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New Insights Into the Molecular Evolution of Metazoan Peroxiredoxins View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Archivio istituzionale della ricerca - Università di Padova Invited Review ACTA ZOOLOGICA BULGARICA Acta zool. bulg., 67 (2), 2015: 305-317 New Insights into the Molecular Evolution of Metazoan Peroxiredoxins RIGE R S BAKIU 1*, GIANF R ANCO SANTOVITO 2 1 Department of Aquaculture and Fisheries, Agricultural University of Tirana, Koder Kamez, 1029 Tirana, Albania; E-mail: [email protected] 2 Department of Biology, University of Padova, 35121 Padova, Italy Abstract: Peroxiredoxins (Prx) are enzymes present in all biological kingdoms, from bacteria to animals. The oxi- dised active site cysteine of Prx can be reduced by a cellular thiol, thus enabling Prx to function as a peroxidase. Peroxiredoxins have been object of an increasing interest for its pivotal role in cell defence and as conserved markers for circadian rhythms in metabolism across all three phylogenetic domains (Eukarya, Bacteria and Archaea). Metazoan cells express six Prx isoforms that are localised in various cellular compartments. Using bioinformatics tools, based on Bayesian approach, we analysed the phylo- genetic relationships among metazoan Prxs, with the aim to acquire new data on the molecular evolution of these proteins. Peroxiredoxin molecular evolution analyses were performed by the application of Mr. Bayes and HyPhy software to the coding and protein sequences of deuterostomes and protostomes. The obtained results confirmed that the molecular evolution of metazoan Prx was peculiar and suggested that the positive selection may had operated for the evolution of these proteins and a purifying selection was present during this process. Keywords: peroxiredoxin; metazoans; molecular evolution. Introduction An unusual antioxidant protein, now called perox- is specifically oxidised by H2O2 to cysteine sulfenic iredoxin (Prx, EC 1.11.1.15), was initially identified acid (Cys–SOH), which is resolved by reaction with on the basis of its capacity to protect proteins from Cys170–SH of the adjacent monomer. Theseis results oxidative damage caused by reactive oxygen species in the formation of a disulfide link, Cys47–S-S–Cys170 (ROS), catalysing the reduction of H2O2, to water (CHAE et al. 1994). The conserved Cys residue cor- and alcohol in the presence of dithiotreitol (DTT). responding to Cys47 of yeast Prx was later referred Analysis of Prx purified from yeast revealed that to as the peroxidatic Cys (CP) to reflect its sensitiv- it did not contain conventional redox centres such ity to oxidation by peroxides, and the conserved Cys as metals, heme, flavin, or selenocysteine, being residue corresponding to Cys170 was designated the OOD very different with respect to other known antioxi- resolving Cys (CR) (W et al. 2003). dant (KIM et al. 1988; CHAE et al. 1994). Later, it On the basis of the presence or absence of the has been found that (i) Prxs are present in all bio- CR residue, Prxs are classified into typical 2-Cys, logical kingdoms, from bacteria to animals; (ii) two atypical 2-Cys, and 1-Cys Prx subfamilies (RHEE cysteine residues, corresponding to Cys47 and Cys170 & WOO , 2011). Animal cells express six isoforms of yeast Prx, are highly conserved among Prx fam- of Prxs: isoforms from 1 to 4 belong to the typical ily members; (iii) Prxs are homodimers arranged in 2-Cys Prx group; Prx5 belongs to the class of 2-Cys a head-to-tail orientation; and (iv) Cys47–SH of Prx enzymes. Isoform 6 is the only one belonging to *Corresponding author 305 Bakiu R., G. Santovito 1-Cys Prxs (Fisher, 2011). Prx1 is mainly localised Metazoa is one of great eukaryote kingdoms. in the cytosol, nucleus and peroxisomes, but it has An increasingly well resolved Proterozoic fossil been found also in serum (IMMENS C HUH et al. 2003). record documents the presence of most of the major Prx2 is present in cytosol and nucleus and it has been taxa of eukaryotes, including the rhodophytes, stra- shown to bond the cell membrane (CHA et al. 2000). menopiles, alveolates and green plants during the late Prx3 is located exclusively in the mitochondria (CAO Mesoproterozoic to early Neoproterozoic (about one et al. 2007). Prx4 has been found in both cytosol and billion years ago). A coincident rise in acritarch diver- endoplasmic reticulum and contains a leader peptide sity, combined with molecular phylogeny evidence that is believed to be essential for protein secretion for rapid cladogenesis, points to a major radiation of (OK ADO -MATSUMOTO et al. 2000). Prx5 is localised in eukaryote groups at this time, sometimes referred to cytosol, mitochondria and peroxisomes (CAO et al. as the “big bang” of eukaryotic evolution (CON W AY 2007). Prx6 is located in cytosol, vesicles and lyso- MO rr IS et al. 1987). The most fundamental division somes (SO R O K INA et al. 2011). Prx localisation is mul- within the bilateral metazoans is the protostome- tifarious, being dependent on the cell type but also on deuterostome branch. Protostomes include at least the environmental conditions (RHEE et al. 2012). annelids, arthropods, molluscs and platyhelminths. Many studies suggest that Prxs are more than They have spiral cleavage and usually mosaic de- just simple antioxidant enzymes. For example Prx6 velopment, are schizocelic, form the mouth at (or also acts as phospholipase A2 (CHEN et al. 2000). near) the site of the blastopore and mesoderm from Other evidences suggest that Prx oxidation also al- a mesentoblast that is usually 4d. Deuterostomes in- lows them to function as molecular chaperones (JANG clude at least echinoderms and chordates, the latter et al. 2004) and regulates the cell cycle (PHALEN et group including the back-boned animals. They have al. 2006). A very interesting proposed role is en- radial cleavage and usually regulative development, compassed by the floodgate hypothesis (WOOD et al. are enterocelic, form the mouth away from the blas- 2003; WOO et al. 2010), in which active Prxs normal- topore and mesoderm from endodermal cells along ALENTINE ly keep H2O2 low (i.e. a closed floodgate) but, under the archeneteron (V et al. 1997). signalling conditions that causes loss of function via Approximately 2.5 billion years ago, photo- overoxidation in a localised region of the cell, allow- synthetic bacteria acquired the capacity to photodis- ing H2O2 to build up locally (i.e, be released by an sociate water, leading to the geologically rapid ac- open floodgate) for signalling purposes (HALL et al. cumulation of molecular oxygen during the Great 2009, HANS C HMANN et al. 2013). Oxidation Event (GOE), when anaerobic life un- The abundance of Prx is high: it can account derwent a catastrophic decline (EDGA R et al. 2012). for up to 1% of all soluble cellular proteins (WOOD Organisms that survived the transition to an aerobic et al. 2003). Furthermore, typical 2-Cys Prxs are the environment were those that respired and/or evolved largest and most widely distributed subfamily (SOITO oxygen. All oxygen-utiliszing organisms acquired et al. 2011). These Prxs are moonlighting proteins: constitutive antioxidant defensesdefences (both at high H2O2 concentrations they act as holdases, small molecules and enzymes), detoxifying and whereas when the rate of ROS formation is low they scavenging the ROS that are continuously produced are thioredoxin-dependent peroxidases (JANG et al. as a by-product of aerobic metabolism (Acw O R TH et 2004). The dual functions of typical 2-Cys Prxs, al. 1997, HALLI W ELL & GUTTE R IDGE 1999). Among modulating ROS concentrations and preventing pro- them, Prx has been object of an increasing inter- tein aggregation, may play pivotal roles in cellular est for its pivotal role in cell defensedefence and as response to pathogens and external stress (JANG et conserved marker for circadian rhythms in metabo- al. 2004). The importance of Prxs is unarguable, as lism. EDGA R and colleagues (2012) studied the cy- transgenic/knockout mouse models overexpressing cles of Prx oxidation-reduction in Eukarya, Bacteria or deficient in most highly expressed Prxs has dem- and Archaea and proposed that all these organisms onstrated a decrease in genome stability and acceler- have cellular rhythms sharing a common molecular ated aging, and an overexpression of these proteins origin. In fact, it has been proposed that the ability is associated with various problems related to can- to survive cycles of oxidative stress may have con- cers treatment (HAMILTON et al. 2012). Recent stud- tributed a selective advantage from the beginnings ies show Prxs expressed in tumortumour cells play of aerobic life. Twenty-four hours cycles of Prx positive roles in their progression and/or metastasis oxidation–reduction in all domains were observed in transplanted animals. Different functions of Prxs in both Archaea, Bacteria and Eukaryota supporting are required for their progression/metastasis in vivo the hypothesis that cellular rhythms share a common depending on tumortumour types (ISHII et al. 2012). molecular origin (EDGA R et al. 2012). However, only 306 New Insights into the Molecular Evolution of Metazoan Peroxiredoxins a few studies have been dedicated to the evolution of tion criterion (Akaike Information Criterion-AIC Prxs (CO P LEY et al. 2004; KNOO P S et al. 2007; PÉ R EZ - and Corrected Akaike Information Criterion-cAIC). SÁN C HEZ et al. 2011). Our study aims and we decided Models of nucleotide substitution allow for the cal- to extend the research on Prx evolution performing culation of probabilities of change between nucle- phylogenetic analysis on the most studied group of otides along the branches of a phylogenetic tree. The eucariotic organisms (Eukarya), the animals, using use of a particular substitution model may change Bayesian approach. Fortunately, there is sufficient the outcome of the phylogenetic analysis (LEMMON information about many characterised nucleotide and MO R IA R TY , 2004).
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