Distribution and Features of the Six Classes of Peroxiredoxins

Abstract

Peroxiredoxins are cysteine-dependent peroxide reductases that group into 6 different, structurally discernable classes. In 2011, our research team reported the application of a bioinformatic approach called active site profiling to extract active site-proximal sequence segments from the 29 distinct, structurally-characterized peroxiredoxins available at the time. These extracted sequences were then used to create unique profiles for the six groups which were subsequently used to search GenBank(nr), allowing identification of ∼3500 peroxiredoxin sequences and their respective subgroups. Summarized in this minireview are the features and phylogenetic distributions of each of these peroxiredoxin subgroups; an example is also provided illustrating the use of the web accessible, searchable database known as PREX to identify subfamily-specific peroxiredoxin sequences for the organism Vitis vinifera (grape).

Keywords: active site profiling; bioinformatics; disulfide reductase; peroxide reductase; thiol peroxidase.

Fig. 1.

Identification of peroxiredoxin sequences using the Deacon Active Site Profiling (DASP) tool. (1) The active site of human Prx6 (PDB identifier 1prx) is shown with the four key residues highlighted in red. (2) Structural segments located within 10 Å of the center of geometry of the key catalytic residues are identified (each segment shown in a different color) and extracted from the global structure. (3) The sequence fragments are then combined to form a functional site signature (residue colors correspond to the color of structure segments in 2; key residues are highlighted in red). (4) Functional-site signatures for structurally characterized members of the Prx6 subfamily are aligned using ClustalW (Larkin et al., 2007; Thompson et al., 1994) to create a functional site profile. (5) Motifs are identified within any fragments that contain at least three residues and position specific scoring matrices (PSSM) (Bailey and Gribskov, 1998b) are created for each motif. (6) For each sequence in a user-selected sequence database, the PSSM for each motif is used to find and score the segment within a query sequence which best matches the motif. (7) Each time a motif is matched to a position in the protein sequence, a p-value is calculated that represents the probability of finding a match as good as the observed match within a random sequence. The p-values for all motifs in a single sequence are then combined using QFAST to obtain the final statistical significance score (final p-value) (Bailey and Gribskov, 1998a). (8) The protein information (including accession numbers, annotations, and species), final p-value, and sequence fragments matched to each queried motif are exported for all sequences with a final p-value more significant than a user-selected p-value. This figure was adapted from Soito et al. (2011).

Fig. 2.

Output from two web tools used to search for peroxiredoxins present in Vitis vinifera (grape). (A) shows the output from a search for “peroxiredoxin” and the organism name at http://uniprot.org. (B) shows the output from a parallel search conducted using the PREX database at http://csb.wfu.edu/PREX.

Fig. 3.

Sequence alignments of V. vinifera Prxs of interest generated by PREX (A) or by multiple sequence alignments of all six true Prxs (B). (A) shows two of the automatically-generated sequence alignments, accessed by clicking on an individual sequence signature in the output from a PREX search such as that depicted in Fig. 2B. Note that the PREX query sequence (the signature that was selected) is shown aligned with several other members of the same subgroup as well as one representative from each of the other 5 subgroups. (B) depicts a section around the conserved active site sequence of the multiple sequence alignment of all six bona fide Prxs from V. vinifera, listed by their uniprot designation and aligned using Clustal W (Larkin et al., 2007; Thompson et al., 1994).

Fig. 4.

Phylogenetic distribution of individual Prx groups across all species. The organism name for each Prx sequence was first extracted from the DASP output file and the complete lineage of each organism was obtained from the NCBI Taxonomy databases. This information was used to calculate the fraction of sequences within each subfamily that belong to the indicated biological subdivision. Each species was only counted once in each subfamily even if multiple protein sequences were identified. To prevent results being biased by oversampling of sequences from multiple bacterial strains, multiple strains of the same species were only counted once for each subfamily. The prevalence of cyan in the figure reflects the huge number of bacterial species compared to archaeal and eukaryotic species.

Fig. 5.

Variable locations of the resolving Cys (C_R). Shown are the various positions of the peroxiredoxin C_R (colored sidechains) in relation to the active site peroxidatic Cys (C_P, circled and in red). Intramolecular C_P-C_R disulfides are formed for the α2 (yellow), α3 (green), and α5 (blue) types, and intermolecular disulfides are formed for the N-terminal (Nt, orange C_R in the gold chain) and C-terminal (Ct, magenta C_R in the black chain) types. (C_R residues are mapped onto a composite structure based on S. typhimurium AhpC, Protein Databank Identifier 4MA9). Reproduced with permission from (Perkins et al., 2015).

Fig. 6.

Dimeric interfaces and quaternary structures of Prxs. Homodimeric complexes are formed using either an A-type interface, where the monomers interact near helix α3, or B-type dimers where the interaction is through the β-strands, generating an extended 10–14 strand β-sheet. Further interactions at the A-interfaces of some Prx1 and Prx6 members generate (α₂)₅ decamers [or in rare cases (α₂)₆ dodecamers]. The blue subunit is displayed at approximately the same orientation in each of the structures to illustrate these interaction interfaces that together build the decamer. For a number of Prx1 members, the structural change upon disulfide bond formation destabilizes the A-type dimer interface, and the decamer dissociates to B-type dimers. The structures depicted are: Aeropyrum pernix PrxQ (A-type dimer, Protein Data Bank Identifier 4GQF), and wild type S. typhimurium AhpC (B-type dimer and decamer, Protein Data Bank Identifier 4MA9). Adapted from (Perkins et al., 2015).