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. 2010 Dec 1;5(12):1543–1546. doi: 10.4161/psb.5.12.13494

Genome-wide analysis of thioredoxin fold superfamily peroxiredoxins in Arabidopsis and rice

Pavan Umate 1,✉
PMCID: PMC3115098  PMID: 21242720

Abstract

A broad range of peroxides generated in subcellular compartments, including chloroplasts, are detoxified with peroxidases called peroxiredoxins (Prx). The Prx are ubiquitously distributed in all organisms including bacteria, fungi, animals and also in cyanobacteria and plants. Recently, the Prx have emerged as new molecules in antioxidant defense in plants. Here, the members which belong to Prx gene family in Arabidopsis and rice are been identified. Overall, the Prx members constitute a small family with 10 and 11 genes in Arabidopsis and rice respectively. The prx genes from rice are assigned to their functional groups based on homology search against Arabidopsis protein database. Deciphering the Prx functions in rice will add novel information to the mechanism of antioxidant defense in plants. Further, the Prx also forms the part of redox signaling cascade. Here, the Prx gene family has been described for rice.

Key words: antioxidant defense, chloroplast, gene family, oxidative stress, reactive oxygen species

The formation of free radicals and reactive oxygen species (ROS) occur in several enzymatic and non-enzymatic reactions during cellular metabolism. The accumulation of these reactive and deleterious intermediates is suppressed by antioxidant defense mechanism comprised of low molecular weight antioxidants and enzymes. In photosynthetic organisms, the defense against the damage from free radicals and oxidative stress is crucial. For instance, the ROS production occurs in photosystem II with generation of singlet oxygen (1O2) and hydrogen peroxide (H2O2),1,2 photosystem I from superoxide anion radicals (O2−),3 and during photorespiration with generation of H2O2.4 ROS production may exceed under environmental stress conditions like excess light, low temperature and drought.5

The antioxidant defense mechanism is activated by antioxidant metabolities and enzymes which detoxify ROS and lipid peroxides. The detoxification of ROS can occur in various cellular compartments such as chloroplasts, mitochondria, peroxisomes and cytosol.6 The enzymes like ascorbate peroxidase, catalase, glutathione peroxidase and superoxide dismutase are prominent antioxidant enzymes.6 The peroxiredoxins (Prx) emerged as new components in the antioxidant defense network of barley.7,8 Later, Prx were studied in other plants.9–14

Prx can be classified into four different functional groups, PrxQ, 1-Cys Prx, 2-Cys Prx and Type-2 Prx.15,16 They are members of the thioredoxin fold superfamily.17,18 In this study, the prx genes found in Arabidopsis and rice genomes are been identified. The Arabidopsis genome encodes 10 prx genes classified into four functional categories, 1-Cys Prx, 2-Cys Prx, PrxQ and Type-2 Prx.13 Of these, one each of 1-Cys Prx and PrxQ, two of 2-Cys Prx (2-Cys PrxA and 2-Cys PrxB) and six Type-2 Prx (PrxA–F) are identified13 (Table 1). The members of Type-2 Prx category are more in number in Arabidopsis (Table 1).

Table 1.

A list of genes encoding peroxiredoxins in Arabidopsis thaliana L.

Locus Annotation Synonym A* B* C*
AT1G48130 1-Cysteine peroxiredoxin 1 (ATPER1) 1-Cys Prx 216 24081.3 6.603
AT1G60740 Peroxiredoxin type 2 Type-2 PrxD 162 17471.9 5.2297
AT1G65970 Thioredoxin-dependent peroxidase 2 (TPX2) Type-2 PrxC 162 17413.9 5.2297
AT1G65980 Thioredoxin-dependent peroxidase 1 (TPX1) Type-2 PrxB 162 17427.8 4.9977
AT1G65990 Type 2 peroxiredoxin-related Type-2 PrxA 553 62653.6 6.4368
AT3G06050 Peroxiredoxin IIF (PRXIIF) Type-2 PrxF 201 21445.2 9.3905
AT3G11630 2-Cys Peroxiredoxin A (2CPA, 2-Cys PrxA) 2-Cys PrxA 266 29091.7 7.5686
AT3G26060 ATPRX Q, periredoxin Q PrxQ 216 23677.8 10.0565
AT3G52960 Peroxiredoxin type 2 Type-2 PrxE 234 24684.0 9.572
AT5G06290 2-Cysteine Peroxiredoxin B (2CPB, 2-Cys PrxB) 2-Cys PrxB 273 29779.5 5.414
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*

A, amino acids; B, molecular weight; C, isoelectric point.

In rice (rice.plantbiology.msu.edu/), there are 11 genomic loci which encode for Prx proteins (Table 2). These loci are distributed on chromosomes 1, 2, 4, 6 and 7 (Table 2). The two Prx, peroxiredoxin-2E-1 (LOC_Os01g24740) and 2-Cys peroxiredoxin BAS1 (LOC_Os04g33970) are annotated to contain a chloroplast precursor (Table 2). The rest of Prx genes are been annotated as “peroxiredoxin, putative, expressed” (Table 2). During the study, these genes are assigned to their functional groups based on BLAST searches against Arabidopsis protein database. The Table 3 summarizes these results wherein rice LOCs and their corresponding homologs in Arabidopsis are enlisted. A nomenclature for rice prx genes is been proposed based on protein homology %identity/similarity with their Arabidopsis counterparts (Tables 1 and 3). Interestingly, a new prx gene (LOC_Os07g15670) annotated as “peroxiredoxin, putative, expressed” is identified making the tally of prx genes to eleven in rice as compared to ten in Arabidopsis (Tables 1 and 2). The BLAST search has identified its counterpart in Arabidopsis which has been annotated as “antioxidant/oxidoreductase” (AT1G21350) in the TAIR database (www.arabidopsis.org). The rice LOC_Os07g15670 and Arabidopsis AT1G21350 share protein homology %68/78 for 236 amino acids (Table 3).

Table 2.

Genes encoding peroxiredoxins in rice

Chromosome Locus Id Putative function/Annotation A* B* C*
1 LOC_Os01g16152 peroxiredoxin, putative, expressed 199 20873.6 8.2209
1 LOC_Os01g24740 peroxiredoxin-2E-1, chloroplast precursor, putative 107 11591.5 6.7906
1 LOC_Os01g48420 peroxiredoxin, putative, expressed 163 17290.8 5.6828
2 LOC_Os02g09940 peroxiredoxin, putative, expressed 226 23179.5 6.535
2 LOC_Os02g33450 peroxiredoxin, putative, expressed 262 28096.9 5.7709
4 LOC_Os04g33970 2-Cys peroxiredoxin BAS1, chloroplast precursor, putative, expressed 122 13410.2 4.3705
6 LOC_Os06g09610 peroxiredoxin, putative, expressed 266 28926 10.5097
6 LOC_Os06g42000 peroxiredoxin, putative, expressed 233 23688.3 9.2059
7 LOC_Os07g15670 peroxiredoxin, putative, expressed 253 27684.6 9.8545
7 LOC_Os07g44440 peroxiredoxin, putative, expressed 221 24232.6 5.3618
7 LOC_Os07g44430 peroxiredoxin, putative 256 27785.3 6.8544
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*

A, amino acids; B, molecular weight; C, isoelectric point.

Table 3.

Identification of rice homologs of peroxiredoxins in A. thaliana

Locus Id (Os*) Homolog (At*) Nomenclature Identitity/Similarity (%) No. of aa* compared
LOC_Os01g16152 AT3G06050 Type-2 PrxF 73/84 201
LOC_Os01g24740 AT1G65980 Type-2 PrxB 42/59 77
LOC_Os01g48420 AT1G65970 Type-2 PrxC 74/86 162
LOC_Os02g09940 AT1G60740 Type-2 PrxD 56/72 166
LOC_Os02g33450 AT5G06290 2-Cys Prx B 74/82 272
LOC_Os04g33970 AT3G11630 2-Cys PrxA 92/96 88
LOC_Os06g09610 AT3G26060 PrxQ 78/89 159
LOC_Os06g42000 AT3G52960 Type-2 PrxE 61/74 240
LOC_Os07g15670 AT1G21350 Antioxidant 68/78 236
LOC_Os07g44440 AT1G65990 Type-2 PrxA 27/44 83
LOC_Os07g44430 AT1G48130 1-Cys Prx 69/83 221
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*

Os, Oryza sativa L.; At, Arabidopsis thaliana L.; aa, amino acids.

The protein alignment study of Prx members in rice with the canonical Prx2-B and Prx2-E of Arabidopsis is shown in Figure 1. The Type-2 Prx proteins are characterized by the presence of catalytic cysteine (Cys) residues (Fig. 1). The alignment of rice Prx proteins shows that the Cys residue is well conserved in members like LOC_Os02g09940 (Type-2 PrxD), LOC_Os06g42000 (Type-2 Prx E), LOC_Os01g48420 (Type-2 Prx C), LOC_Os01g16152 (Type-2 Prx F), LOC_Os02g33450 (2-Cys Prx B), LOC_Os07g44440 (Type-2 Prx A), LOC_Os07g44430 (1-Cys Prx) and LOC_Os06g09610 (PrxQ) (Fig. 1). However, LOC_Os01g24740 (Type-2 PrxB) and LOC_Os04g33970 (2-Cys PrxA) which contain a chloroplast precursor do not have the catalytic Cys residues (Fig. 1). The newly identified LOC_Os07g15670 and AT1G21350 with annotations “peroxiredoxin, putative, expressed” and “antioxidant/oxidoreductase” respectively do not have catalytic Cys residues as well (Fig. 1).

Figure 1.

Figure 1

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Amino acid alignment of peroxiredoxins (Prx) in rice. The rice proteins are aligned with the canonical Arabidopsis Prx2-B and Prx2-E. The conserved cysteine residues are indicated by arrows on top of the alignment. Note the sequence conservation between the newly identified LOC_Os07g15670 and AT1G21350. The rice locus Ids are identified on left and amino acid positions on right. The alignment was made with ClustalX.

Taken together, the results demonstrate that like Arabidopsis, the Prx constitute a small gene family in rice. However, the functional role of Prx in rice is not clearly understood.

Footnotes

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