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. 2025 Apr 22:16:1562718.
doi: 10.3389/fpls.2025.1562718. eCollection 2025.

Genome-wide identification of the nuclear redox protein gene family revealed its potential role in drought stress tolerance in rice

Zijie Liu  1 , Xingfei Zheng  2 , Dabing Yang  2 , Lanzhi Li  1 , Hexing Yin  3
Affiliations

Genome-wide identification of the nuclear redox protein gene family revealed its potential role in drought stress tolerance in rice

Zijie Liu et al. Front Plant Sci. .

Abstract

Introduction: Thioredoxins (TRX) are redox-active proteins critical for plant stress adaptation. As a TRX family member, nucleoredoxin (NRX) maintains drought-induced redox homeostasis, yet its genome-wide characterization in rice remains uninvestigated.

Methods: Using HMMER3.0 (E-value <1e-5) and TBtools, we identified OsNRX genes across three rice varieties (Minghui63, Nipponbare, 9311). Conserved domains were verified by SMART/CDD, while promoter cis-elements were systematically predicted with PlantCARE. Tissue-specific expression patterns were analyzed using RiceXPro data, and drought responses were quantified via qRT-PCR in drought-tolerant (Jiangnong Zao 1B) versus sensitive (TAISEN GLUTINOUS YU 1157) varieties under PEG6000 stress.

Results: Ten OsNRX genes were classified into three subfamilies (NRX1/NRX2/NRX3) exhibiting conserved domain architectures. Promoter analysis identified abundant stress-responsive elements (ABRE, MBS) and phytohormone signals (ABA/JA/SA). Tissue-specific expression profiles revealed NRX1a dominance in roots/hulls, versus NRX1b/NRX2 enrichment in endosperm. Drought stress triggered rapid OsNRX upregulation (20-53-fold within 3-6h), with tolerant varieties showing earlier NRX2 activation than sensitive counterparts.

Discussion: OsNRX genes exhibit dynamic drought-responsive regulation, while their spatiotemporal expression in glumes, embryos, and endosperm suggests potential dual roles in stress adaptation and grain development. These results provide molecular targets for improving drought resilience in rice breeding.

Keywords: drought stress; expression pattern; genome-wide identification; nucleoredoxin gene family; rice.

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Conflict of interest statement

Author HY was employed by Huazhi Biotechnology Co. Ltd. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic relationship, conserved motif structure and gene structure of OsNRX protein. (a) The phylogenetic tree of OsNRX. MH63 represented Minghui63(indica), Nip represented Nipponbare(japonica), 9311 represented 9311(indica). (b) The distribution of conserved motifs. Boxes with different colors represented different conserved motifs (Motif 1-10). (c) The gene structure of OsNRX. Green boxes represented the UTRs, yellow boxes represented exons.
Figure 2
Figure 2
Secondary structure analysis of OsNRX proteins. MH63 represented Minghui63(indica), Nip represented Nipponbare(japonica), 9311 represented 9311(indica). The blue color represents alpha helix (AH), the purple color represents random coil (RC), the green color represents beta turn (BT) and the red color represents extended strand (ES).
Figure 3
Figure 3
Protein 3D structure prediction model of OsNRX gene families. MH63 represented Minghui63(indica), Nip represented Nipponbare(japonica), 9311 represented 9311(indica).
Figure 4
Figure 4
Phylogenetic tree of NRX gene family proteins in rice and five species. Phylogenetic trees were constructed using the Neighbor-Joining (NJ) method of the MEGAX software with the bootstrap value set to 1000.
Figure 5
Figure 5
Distribution of cis-acting elements in promoter regions of OsNRX genes. MH63 represented Minghui63 (indica), Nip represented Nipponbare (japonica), 9311 represented 9311 (indica). Boxes with different colors represent cis-regulatory elements, with bold fonts indicating cis-regulatory elements related to drought induction, and the scale at the bottom represents the length of the promoter sequence.
Figure 6
Figure 6
Expression patterns of the OsNRX gene family in rice. The color scale represents the relative expression levels, ranging from low (blue) to high (red). “mm” represents millimeters, and “DAF” represents days after flowering.
Figure 7
Figure 7
Expression changes of OsNRX gene family under PEG6000 treatment in Drought-tolerant and Drought-sensitive varieties. Response of drought-tolerant (DT, green) and drought-sensitive (DS, blue) varieties to PEG6000 treatment over time (0, 3, 6, 12, and 24 hours). Asterisks (*) indicate significant differences between DT and DS at each time point, as determined by Student’s t-test: *p < 0.1, **p < 0.05, and ***p < 0.01. The results were the mean of three independent biological replicates using quantitative real-time PCR (qRT-PCR) technology.
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