Genome-Wide Identification of OsZIPs in Rice and Gene Expression Analysis under Manganese and Selenium Stress

Abstract

Zinc (Zn)- and iron (Fe)-regulating transport-like proteins (ZIPs) are a class of proteins crucial for metal uptake and transport in plants, particularly for Zn and Fe absorption and distribution. These proteins ensure the balance of trace elements essential for plant growth, development, and metabolic activities. However, the role of the rice (Oryza sativa) OsZIP gene family in manganese (Mn) and selenium (Se) transport remains underexplored. This research conducted an all-sided analysis of the rice OsZIPs and identified 16 OsZIP sequences. Phylogenetic analysis categorized the OsZIPs predominantly within the three subfamilies. The expression levels of OsZIPs in rice root and leaf subjected to Mn and Se toxicity stress were examined through quantitative real-time PCR (qRT-PCR). The findings revealed significant differential expression of many OsZIPs under these conditions, indicating a potential regulating effect in the response of rice to Mn and Se toxicity. This work lays a foundation for further functional studies of OsZIPs, enhancing our understanding of the response mechanisms of rice to Mn and Se toxicity and their roles in growth, development, and environmental adaptation.

Keywords: OsZIPs; expression analysis; manganese toxicity stress; rice; selenium toxic stress.

Figure 1

Results of structure and domain analysis of OsZIPs: (A) Structure of genetics; (B) analysis of domain. The conserved protein domain families Zip, the Zip superfamily, and Zup T were classified as models that might span multiple domains.

Figure 2

The OsZIPs domain was searched by InterPro. All the OsZIPs contained the ZIP/Zip domain (number PF02535). F indicates the InterPro domain number.

Figure 3

A phylogenetic tree was constructed using ZIPs from G. max, O. sativa, Z. mays, and A. thaliana. O. sativa: OsZIP1 (LOC_Os01g74110.1), OsZIP2 (LOC_Os03g29850.1), OsZIP3 (loc_OS04G52310.11), OsZIP4 (LOC_Os08g10630.1), OsZIP5 (LOC_Os05g39560.1), OsZIP6 (loc_OS05G072101.1), OsZIP7 (loc_OS05G10940.01), OsZIP8 (LOC_Os02g10230.1), OsZIP9 (LOC_Os05g39540.1), OsZIP10 (LOC_Os06g37010.1), OsZIP11 (loc_OS05G25194-1), OsZIP12 (LOC_Os03g46470.1), OsZIP13 (LOC_Os07g12890.1), OsZIP14 (LOC_Os08g36420.1), OsZIP15 (LOC_Os03g46454.1), OsZIP16 (LOC_Os08g01030.1); A. thaliana: AtZIP1 (AT3G12750.1), AtZIP2 (AT5G59520.1), AtZIP3 (AT2G32270.1), AtZIP4 (AT1G10970.1), AtZIP5 (AT1G05300.1), AtZIP6 (AT2G30080.1), AtZIP7 (AT2G04032.1), AtZIP8 (AT5G45105.2), AtZIP9 (AT4G33020.1), AtZIP10 (AT1G31260.1), AtZIP11 (AT1G5590.1), AtZIP12 (AT5G62160.1), AtZIP13 (AT4G19690.2), AtZIP14 (AT4G19680.2), AtZIP15 (AT1G60960.1); G. max: GmZIP1 (Glyma.20g063100), GmZIP2 (Glyma.08g164400), GmZIP3 (Glyma.15g262800), GmZIP4 (Glyma.13g004400), GmZIP5 (Glyma.17g228600), GmZIP6 (Glyma.11g169300), GmZIP7 (Glyma.14g196200), GmZIP8 (Glyma.04g051100), GmZIP9 (Glyma.18g060300), GmZIP10 (Glyma.14g094900), GmZIP13 (Glyma.18g078600), GmZIP14 (Glyma.15g036200), GmZIP15 (Glyma.15g036300), GmZIP16 (Glyma.13g338300), GmZIP17 (Glyma.13g340900), GmZIP18 (Glyma.15g033500), GmZIP19 (Glyma.11g132500), GmZIP20 (Glyma.12g056900), GmZIP21 (Glyma.16g221000), GmZIP22 (Glyma.09g271900), GmZIP23 (Glyma.18g217100); Z. mays: ZmZIP1 (NM_001137726), ZmZIP2 (NM_001159169), ZmZIP3 (NM_001155536), ZmZIP4 (HM048832), ZmZIP5 (NM_001154257), ZmZIP6 (NM_001156151), ZmZIP7 (NM_001157018), ZmZIP8 (NM_001154769), ZmZIP9 (NM_001158638).

Figure 4

Conserved motifs of rice ZIPs. All genes except OsZIP15 contained motif 3.

Figure 5

Location of OsZIPs on rice chromosomes: OsZIP1, OsZIP2, OsZIP3, OsZIP5, OsZIP6, OsZIP7, OsZIP8, OsZIP9, OsZIP10, OsZIP11, OsZIP12, OsZIP13, OsZIP14, OsZIP15, and OsZIP16 were located in gene-dense areas (red and yellow); OsZIP4 was located in the gene dispersion region (blue).

Figure 6

Analysis of cis-acting elements in the OsZIP promoters. The 2000 bp region of the OsZIP promoters was used for analysis.

Figure 7

Results of qRT–PCR test of 16 OsZIPs in rice leaf and root with 10 and 500 μM Mn treatment. The relative expression levels of OsZIPs in the root (A) and leaf (B) of rice plants were calculated and are presented as the average value and standard deviation (SD) of three experimental replicates. A t-test was applied to determine the differences between the control group and Mn toxicity group, with * indicating p < 0.05 and ** indicating p < 0.01.

Figure 8

Results of qRT–PCR test of 16 OsZIPs in rice leaf and root with 0 and 64 μM Se treatment. The relative expression of OsZIPs in rice roots (A) and leaves (B) was calculated. The relative expression levels of OsZIPs in the root (A) and leaf (B) of rice plants were calculated and are presented as the average value and standard deviation (SD) of three experimental replicates. A t-test was applied to determine the differences between the control group and Mn toxicity group, with * indicating p < 0.05 and ** indicating p < 0.01.