Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species
Abstract Background Toona sinensis and Toona ciliata both belong to the same genus in the Meliaceae family; however, the nitrate and nitrite contents in T. sinensis are significantly higher than those in T. ciliata. Given the growing emphasis on dietary health, it has become imperative to implement...
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SpringerOpen
2025-01-01
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| Series: | Chemical and Biological Technologies in Agriculture |
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| Online Access: | https://doi.org/10.1186/s40538-025-00728-8 |
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| author | Yi Wei Jianhua Dai Yanru Fan Hengfu Yin Jun Liu Xiaojiao Han |
| author_facet | Yi Wei Jianhua Dai Yanru Fan Hengfu Yin Jun Liu Xiaojiao Han |
| author_sort | Yi Wei |
| collection | DOAJ |
| description | Abstract Background Toona sinensis and Toona ciliata both belong to the same genus in the Meliaceae family; however, the nitrate and nitrite contents in T. sinensis are significantly higher than those in T. ciliata. Given the growing emphasis on dietary health, it has become imperative to implement breeding strategies to reduce the excessive nitrite levels in T. sinensis. Nitrate reductase (NR) and nitrite reductase (NiR) are crucial enzymes in plant nitrogen metabolism. In this study, we employed a comparative analysis of the NR and NiR gene families in T. sinensis and T. ciliata. By integrating bioinformatics and expression pattern assessments, we aimed to elucidate the underlying factors contributing to the variance in nitrate and nitrite levels between these two species. Results T. sinensis exhibited higher nitrate and nitrite contents than T. ciliata. Through comprehensive genome-wide analysis, we identified two TsNRs and two TsNiRs in T. sinensis, compared to one TcNiR and two TcNiRs in T. ciliata, suggesting an expansion of NR members in T. sinensis relative to T. ciliata. The NR and NiR proteins in T. sinensis and T. ciliata share high sequence similarity and exhibit close genetic relationships with their counterparts in Populus trichocarpa and Salix purpurea. The exon–intron structures and conserved motifs of these genes were stringently conserved throughout evolutionary history. All the seven NR and NiR genes in both T. sinensis and T. ciliata harbor various cis-regulatory elements within their promoter sequences, which are associated with development, stress response, and hormonal regulation. Furthermore, the expression of TsNiR and TcNiR genes was also found to be tissue-specific. Among them, TcNR1 and TsNR2 exhibited the highest expression observed in mature leaves. Especially, the expression level of TsNR2 in mature leaves was 400-fold higher than in other tissues. In addition, transient overexpression of TsNiR1 and TsNiR2 in T. sinensis significantly reduced nitrite content. Conclusions The higher nitrite accumulation in T. sinensis compared to T. ciliata is attributed to its lower nitrite reductase activity, the expansion of the NR gene family, and the elevated expression of TsNR2 in the leaves. Graphic Abstract |
| format | Article |
| id | doaj-art-5542f53f961b41a483c1b532db314937 |
| institution | Kabale University |
| issn | 2196-5641 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | SpringerOpen |
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| series | Chemical and Biological Technologies in Agriculture |
| spelling | doaj-art-5542f53f961b41a483c1b532db3149372025-01-26T12:19:00ZengSpringerOpenChemical and Biological Technologies in Agriculture2196-56412025-01-0112111310.1186/s40538-025-00728-8Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona speciesYi Wei0Jianhua Dai1Yanru Fan2Hengfu Yin3Jun Liu4Xiaojiao Han5Research Institute of Subtropical Forestry, Chinese Academy of ForestryResearch Institute of Subtropical Forestry, Chinese Academy of ForestryResearch Institute of Subtropical Forestry, Chinese Academy of ForestryResearch Institute of Subtropical Forestry, Chinese Academy of ForestryResearch Institute of Subtropical Forestry, Chinese Academy of ForestryResearch Institute of Subtropical Forestry, Chinese Academy of ForestryAbstract Background Toona sinensis and Toona ciliata both belong to the same genus in the Meliaceae family; however, the nitrate and nitrite contents in T. sinensis are significantly higher than those in T. ciliata. Given the growing emphasis on dietary health, it has become imperative to implement breeding strategies to reduce the excessive nitrite levels in T. sinensis. Nitrate reductase (NR) and nitrite reductase (NiR) are crucial enzymes in plant nitrogen metabolism. In this study, we employed a comparative analysis of the NR and NiR gene families in T. sinensis and T. ciliata. By integrating bioinformatics and expression pattern assessments, we aimed to elucidate the underlying factors contributing to the variance in nitrate and nitrite levels between these two species. Results T. sinensis exhibited higher nitrate and nitrite contents than T. ciliata. Through comprehensive genome-wide analysis, we identified two TsNRs and two TsNiRs in T. sinensis, compared to one TcNiR and two TcNiRs in T. ciliata, suggesting an expansion of NR members in T. sinensis relative to T. ciliata. The NR and NiR proteins in T. sinensis and T. ciliata share high sequence similarity and exhibit close genetic relationships with their counterparts in Populus trichocarpa and Salix purpurea. The exon–intron structures and conserved motifs of these genes were stringently conserved throughout evolutionary history. All the seven NR and NiR genes in both T. sinensis and T. ciliata harbor various cis-regulatory elements within their promoter sequences, which are associated with development, stress response, and hormonal regulation. Furthermore, the expression of TsNiR and TcNiR genes was also found to be tissue-specific. Among them, TcNR1 and TsNR2 exhibited the highest expression observed in mature leaves. Especially, the expression level of TsNR2 in mature leaves was 400-fold higher than in other tissues. In addition, transient overexpression of TsNiR1 and TsNiR2 in T. sinensis significantly reduced nitrite content. Conclusions The higher nitrite accumulation in T. sinensis compared to T. ciliata is attributed to its lower nitrite reductase activity, the expansion of the NR gene family, and the elevated expression of TsNR2 in the leaves. Graphic Abstracthttps://doi.org/10.1186/s40538-025-00728-8Toona sinensisToona ciliataNitrate reductase gene (NR)Nitrite reductase gene (NiR)Gene expressionTransient expression |
| spellingShingle | Yi Wei Jianhua Dai Yanru Fan Hengfu Yin Jun Liu Xiaojiao Han Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species Chemical and Biological Technologies in Agriculture Toona sinensis Toona ciliata Nitrate reductase gene (NR) Nitrite reductase gene (NiR) Gene expression Transient expression |
| title | Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species |
| title_full | Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species |
| title_fullStr | Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species |
| title_full_unstemmed | Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species |
| title_short | Comparative analysis of NR and NiR gene families reveals nitrite formation mechanisms in two Toona species |
| title_sort | comparative analysis of nr and nir gene families reveals nitrite formation mechanisms in two toona species |
| topic | Toona sinensis Toona ciliata Nitrate reductase gene (NR) Nitrite reductase gene (NiR) Gene expression Transient expression |
| url | https://doi.org/10.1186/s40538-025-00728-8 |
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