Genome-wide Identification and Bioinformatics Analysis of the Rice DnaJ Gene Family
DOI:
https://doi.org/10.54097/34thdq93Keywords:
Rice, DnaJ gene, genome-wide identification, bioinformatics analysisAbstract
This study aims to analyze the structural characteristics of the DnaJ gene family in rice (Oryza sativa L.) and provide support for its molecular regulatory mechanism research. Using whole-genome data from the RAP-DB database, we identified 104 DnaJ family members, which are divided into three subfamilies (OsDjA, OsDjB, and OsDjC) based on phylogenetic relationships and conserved structural features. Most members contain a typical J domain, while some also have specific domains such as zinc finger, TPR, and PDI-related domains. Different subfamilies have highly conserved motif compositions but significant differences in arrangement, and their exon-intron structures also vary notably. The promoter regions of these DnaJ genes are rich in light-responsive, hormone-responsive, and stress-responsive elements, and extensive homologous collinearity between the rice DnaJ gene family and that of Arabidopsis reflects its high evolutionary conservation. This study provides an important theoretical basis and data support for further elucidating the functions of the rice DnaJ family in rice growth, development, and stress responses.
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[1] Berka, M., Kopecká, R., Berková, V., et al. (2022). Regulation of heat shock proteins 70 and their role in plant immunity. Journal of Experimental Botany, 73(7), 1894–1909. https://doi.org/10.1093/jxb/erac025
[2] Yurina, N. P. (2023). Heat shock proteins in plant protection from oxidative stress. Molecular Biology, 57(6), 951–964. https://doi.org/10.1134/S0026893323060148
[3] Quan, Y., Wang, Z., Wei, H., et al. (2022). Transcription dynamics of heat shock proteins in response to thermal acclimation in Ostrinia furnacalis. Frontiers in Physiology, 13, 992293. https://doi.org/10.3389/fphys.2022.992293
[4] Daniell, H., Jin, S., Zhu, X. G., et al. (2021). Green giant—a tiny chloroplast genome with mighty power to produce high-value proteins: History and phylogeny. Plant Biotechnology Journal, 19(3), 430–447. https://doi.org/10.1111/pbi.13526
[5] Stan, G., Lorimer, G. H., & Thirumalai, D. (2022). Friends in need: How chaperonins recognize and remodel proteins that require folding assistance. Frontiers in Molecular Biosciences, 9, 1071168. https://doi.org/10.3389/fmolb.2022.1071168
[6] Verma, A. K., Tamadaddi, C., Tak, Y., et al. (2019). The expanding world of plant J-domain proteins. Critical Reviews in Plant Sciences, 38(5–6), 382–400. https://doi.org/10.1080/07352689.2019.1658587
[7] Kampinga, H. H., Andreasson, C., Barducci, A., et al. (2019). Function, evolution, and structure of J-domain proteins. Cell Stress & Chaperones, 24(1), 7–15. https://doi.org/10.1007/s12192-018-00936-4
[8] Chen, T., Xu, T., Zhang, T., et al. (2021). Genome-wide identification and characterization of dnaJ gene family in grape (Vitis vinifera L.). Horticulturae, 7(12), 589. https://doi.org/10.3390/horticulturae7120589
[9] Liu, Y., Li, M., Yu, J., et al. (2023). Plasma membrane-localized Hsp40/DNAJ chaperone protein facilitates OsSUVH7-OsBAG4-OsMYB106 transcriptional complex formation for OsHKT1;5 activation. Journal of Integrative Plant Biology, 65(1), 265–279. https://doi.org/10.1111/jipb.13382
[10] Walsh, P., Bursać, D., Law, Y. C., et al. (2004). The J-protein family: Modulating protein assembly, disassembly and translocation. EMBO Reports, 5(6), 567–571. https://doi.org/10.1038/sj.embor.7400172
[11] Tamadaddi, C., Verma, A. K., Zambare, V., et al. (2022). J-like protein family of Arabidopsis thaliana: The enigmatic cousins of J-domain proteins. Plant Cell Reports, 41(6), 1343–1355. https://doi.org/10.1007/s00299-022-02856-2
[12] Wang, Y., Tang, H., DeBarry, J. D., et al. (2012). MCScanX: A toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research, 40(7), e49. https://doi.org/10.1093/nar/gkr1293
[13] Kampinga, H. H., & Craig, E. A. (2010). The HSP70 chaperone machinery: J proteins as drivers of functional specificity. Nature Reviews Molecular Cell Biology, 11(8), 579–592. https://doi.org/10.1038/nrm2941
[14] Maris, C., Dominguez, C., & Allain, F. H. T. (2005). The RNA recognition motif, a plastic RNA-binding platform to regulate post-transcriptional gene expression. The FEBS Journal, 272(9), 2118–2131. https://doi.org/10.1111/j.1742-4658.2005.04653.x
[15] Fristedt, R., Williams-Carrier, R., Merchant, S. S., et al. (2014). A thylakoid membrane protein harboring a DnaJ-type zinc finger domain is required for photosystem I accumulation in plants. Journal of Biological Chemistry, 289(44), 30657–30667. https://doi.org/10.1074/jbc.M114.578149
[16] Liu, J. Z., & Whitham, S. A. (2013). Overexpression of a soybean nuclear localized type–III DnaJ domain-containing HSP40 reveals its roles in cell death and disease resistance. The Plant Journal, 74(1), 110–121. https://doi.org/10.1111/tpj.12108
[17] Yang, J., Duan, G., Li, C., et al. (2019). The crosstalks between jasmonic acid and other plant hormone signaling highlight the involvement of jasmonic acid as a core component in plant response to biotic and abiotic stresses. Frontiers in Plant Science, 10, 1349. https://doi.org/10.3389/fpls.2019.01349
[18] Kong, F., Deng, Y., Zhou, B., et al. (2013). A chloroplast-targeted DnaJ protein contributes to maintenance of photosystem II under chilling stress. Journal of Experimental Botany, 65(1), 143–158. https://doi.org/10.1093/jxb/ert353
[19] Heidari, P., Faraji, S., Ahmadizadeh, M., et al. (2021). New insights into structure and function of TIFY genes in Zea mays and Solanum lycopersicum: A genome-wide comprehensive analysis. Frontiers in Genetics, 12, 657970. https://doi.org/10.3389/fgene.2021.657970
[20] Qian, W., & Zhang, J. (2014). Genomic evidence for adaptation by gene duplication. Genome Research, 24(8), 1356–1362. https://doi.org/10.1101/gr.173743.114
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