The NADPH Oxidases (NOX) Gene Family Expression and Genome-Wide Characterization in Common Beans (Phaseolus vulgaris L.)

Year 2025, Volume: 12 Issue: 1, 9 - 17, 28.03.2025

Abdil Hakan Eren

https://doi.org/10.19159/tutad.1591075

Abstract

This study aimed to identify and characterize the NADPH oxidases (NOX) gene family in the common bean (Phaseolus vulgaris L.) to understand its role in plant growth, development, and stress responses. Using bioinformatic tools, the NOX gene family members were identified and analyzed for their molecular weights, isoelectric points, amino acid numbers, and evolutionary relationships. Segmental duplication analysis and phylogenetic studies were conducted using NOX genes from Arabidopsis thaliana, Cicer arietinum, Oryza sativa, and Glycine max. The results revealed nine Phvul-NOX proteins in the common bean genome, with molecular weights ranging from 92940.09 to 105660.24 kDa, isoelectric points from 7.86 to 9.36, and amino acid numbers from 823 to 946. Segmental duplication was observed in Phvul-NOX-1/Phvul-NOX-3, Phvul-NOX-2/Phvul-NOX-8, and Phvul-NOX-5/Phvul-NOX-6 gene pairs, and purifying selection was identified throughout the evolutionary process. Phylogenetic analysis grouped the NOX genes into three main clades, and a synteny map between A. thaliana and P. vulgaris was constructed. This study provides the first comprehensive characterization of the NOX gene family in the common bean, offering valuable insights for future functional genomics research and potential applications in enhancing stress tolerance and crop productivity.

Keywords

Abiotic stress, bioinformatic, common bean, functional genomics, phylogenetic, reactive oxygen species

References

• Alam, M.M., Nahar, K., Hasanuzzaman, M., Fujita, M., 2014. Exogenous jasmonic acid modulates the physiology, antioxidant defense and glyoxalase systems in imparting drought stress tolerance in different Brassica species. Plant Biotechnology Reports, 8(3): 279-293.
• Amicucci, E., Gaschler, K., Ward, J.M., 1999. NADPH oxidase genes from tomato (Lycopersicon esculentum) and curly-leaf pondweed (Potamogeton crispus). Plant Biology, 1(05): 524-528.
• Aygören, A.S., Aydınyurt, R., Uçar, S., Kasapoğlu, A.G., Yaprak, E., Öner, B.M., Turan, M., 2022. Genome-wide analysis and characterization of the PIF gene family under salt and drought stress in common beans (Phaseolus vulgaris L.). Turkish Journal of Agricultural Research, 9(3): 274-285.
• Bailey, T. L., Williams, N., Misleh, C., Li, W.W., 2006. MEME: Discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research, 34(Suppl_2): 369-373.
• Bedard, K., Krause, K.H., 2007. The NOX family of ROS-generating NADPH oxidases: physiology and pathophysiology. Physiological Reviews, 87(1): 245-313.
• Bedard, K., Lardy, B., Krause, K.H., 2007. NOX family NADPH oxidases: Not just in mammals. Biochimie, 89(9): 1107-1112. Buttanri, A., Kasapoğlu, A.G., Öner, B.M., Aygören, A.S., Muslu, S., İlhan, E., Aydin, M., 2024. Predicting the role of β-GAL genes in bean under abiotic stress and genome-wide characterization of β-GAL gene family members. Protoplasma, 262(2): 1-19.
• Chang, Y.L., Li, W.Y., Miao, H., Yang, S.Q., Li, R., Wang, X., Li, W.Q., Chen, K.M., 2016. Comprehensive genomic analysis and expression profiling of the NOX gene families under abiotic stresses and hormones in plants. Genome Biology and Evolution, 8(3): 791-810.
• Chen, C., Wu, Y., Li, J., Wang, X., Zeng, Z., Xu, J., Xia, R., 2023. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Molecular Plant, 16(11): 1733-1742.
• Cheng, T., Ren, C., Xu, J., Wang, H., Wen, B., Zhao, Q., Zhang, Y., 2024. Genome-wide analysis of the common bean (Phaseolus vulgaris) laccase gene family and its functions in response to abiotic stress. BMC Plant Biology, 24(1): 688.
• D’Autréaux, B., Toledano, M.B., 2007. ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis. Nature Reviews Molecular Cell Biology, 8(10): 813-824.
• Du, H., Yang, S.S., Liang, Z., Feng, B.R., Liu, L., Huang, Y.B., Tang, Y.X., 2012. Genome-wide analysis of the MYB transcription factor superfamily in soybean. BMC Plant Biology, 12(1): 1-22.
• Groom, Q.J., Torres, M.A., Fordham‐Skelton, A.P., Hammond‐Kosack, K.E., Robinson, N.J., Jones, J.D., 1996. rbohA, a rice homologue of the mammalian gp91phox respiratory burst oxidase gene. The Plant Journal, 10(3): 515-522.
• Guo, A.Y., Zhu, Q.H., Chen, X., Luo, J.C., 2007. GSDS: A gene structure display server. Hereditas, 29(8): 1023-1026.
• Hasanuzzaman, M., Nahar, K., Alam, M.M., Roychowdhury, R., Fujita, M., 2013. Physiological, biochemical, and molecular mechanisms of heat stress tolerance in plants. International Journal of Molecular Sciences, 14(5): 9643-9684.
• Hiz, M.C., Canher, B., Niron, H., Turet, M., 2014. Transcriptome analysis of salt tolerant common bean (Phaseolus vulgaris L.) under saline conditions. PloS One, 9(3): e92598.
• Horton, P., Park, K.J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., Nakai, K., 2007. WoLF PSORT: Protein localization predictor. Nucleic Acids Research, 35(Suppl_2): 585-587.
• Hu, C.H., Wang, P.Q., Zhang, P.P., Nie, X.M., Li, B.B., Tai, L., Chen, K.M., 2020. NADPH oxidases: The vital performers and center hubs during plant growth and signaling. Cells, 9(2): 437.
• Hu, C.H., Wei, X.Y., Yuan, B.O., Yao, L.B., Ma, T.T., Zhang, P.P., Chen, K.M., 2018. Genome-wide identification and functional analysis of NADPH oxidase family genes in wheat during development and environmental stress responses. Frontiers in Plant Science, 9: 906.
• Jaspers, P., Kangasjärvi, J., 2010. Reactive oxygen species in abiotic stress signaling. Physiologia plantarum, 138(4): 405-413.
• Kasapoğlu, A.G., İlhan, E., Kızılkaya, D., Hossein-Pour, A., Halı̇loğlu, K., 2020. Genome-wide analysis of BES1 transcription factor family in sorghum [Sorghum bicolor (L.) Moench] genome. Turkish Journal of Agricultural Research, 7(1): 85-95. (In Turkish).
• Kasapoğlu, A.G., Muslu, S., Aygören, A.S., Öner, B.M., Güneş, E., İlhan, E., Aydin, M., 2024. Genome-wide characterization of the GPAT gene family in bean (Phaseolus vulgaris L.) and expression analysis under abiotic stress and melatonin. Genetic Resources and Crop Evolution, 71(8): 1-21.
• Kaya, H., Iwano, M., Takeda, S., Kanaoka, M.M., Kimura, S., Abe, M., Kuchitsu, K., 2015. Apoplastic ROS production upon pollination by RbohH and RbohJ in Arabidopsis. Plant Signaling Behavior, 10(2): e989050.
• Kaya, H., Nakajima, R., Iwano, M., Kanaoka, M.M., Kimura, S., Takeda, S., Kuchitsu, K., 2014. Ca2+-activated reactive oxygen species production by Arabidopsis RbohH and RbohJ is essential for proper pollen tube tip growth. The Plant Cell, 26(3): 1069-1080.
• Kelley, L.A., Mezulis, S., Yates, C.M., Wass, M.N., Sternberg, M.J.E., 2015. The Phyre2 web portal for protein modeling, prediction and analysis. Nature Protocols, 10(6): 845-858.
• Khan, N., You, F.M., Datla, R., Ravichandran, S., Jia, B., Cloutier, S., 2020. Genome-wide identification of ATP binding cassette (ABC) transporter and heavy metal associated (HMA) gene families in flax (Linum usitatissimum L.). BMC Genomics, 21(1): 722.
• Lamesch, P., Berardini, T.Z., Li, D., Swarbreck, D., Wilks, C., Sasidharan, R., Huala, E., 2011. The Arabidopsis information resource (TAIR): Improved gene annotation and new tools. Nucleic Acids Research, 40(D1): 1202-1210.
• Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., Rouzé, P., Rombauts, S., 2002. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research, 30(1): 325-327.
• Letunic, I., Bork, P., 2011. Interactive tree of life v2: Online annotation and display of phylogenetic trees made easy. Nucleic Acids Research, 39(2): 475-478.
• Li, W., Liu, B., Yu, L., Feng, D., Wang, H., Wang, J., 2009. Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants. BMC Evolutionary Biology, 9(1): 1-19.
• Marino, D., Andrio, E., Danchin, E.G., Oger, E., Gucciardo, S., Lambert, A., Pauly, N., 2011. A Medicago truncatula NADPH oxidase is involved in symbiotic nodule functioning. New Phytologist, 189(2): 580-592.
• Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L., Wold, B., 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5(7): 621-628.
• Nestler, J., Liu, S., Wen, T.J., Paschold, A., Marcon, C., Tang, H.M., Hochholdinger, F., 2014. Roothairless5, which functions in maize (Zea mays L.) root hair initiation and elongation encodes a monocot‐specific NADPH oxidase. The Plant Journal, 79(5): 729-740.
• Pettersen, E.F., Goddard, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E., 2004. UCSF Chimera-A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13): 1605-1612.
• Quevillon, E., Silventoinen, V., Pillai, S., Harte, N., Mulder, N., Apweiler, R., Lopez, R., 2005. InterProScan: Protein domains identifier. Nucleic Acids Research, 33(2): W116-W120.
• Rogozin, I.B., Wolf, Y.I., Sorokin, A.V., Mirkin, B.G., Koonin, E.V., 2003. Remarkable interkingdom conservation of intron positions and massive, lineage-specific intron loss and gain in eukaryotic evolution. Current Biology, 13(17): 1512-1517.
• Sagi, M., Fluhr, R., 2006. Production of reactive oxygen species by plant NADPH oxidases. Plant physiology, 141(2): 336-340.
• Shannon, P., Markiel, A., Ozier, O., Baliga, N.S., Wang, J.T., Ramage, D., Amin, N., Schwikowski, B., Ideker, T., 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Research, 13(11): 2498-2504.
• Shi, Y.C., Fu, Y.P., Liu, W.Q., 2012. NADPH oxidase in plasma membrane is involved in stomatal closure induced by dehydroascorbate. Plant Physiology and Biochemistry, 51: 26-30.
• Silva-Gigante, M., Hinojosa-Reyes, L., Rosas-Castor, J.M., Quero-Jiménez, P.C., Pino-Sandoval, D.A., Guzmán-Mar, J.L., 2023. Heavy metals and metalloids accumulation in common beans (Phaseolus vulgaris L.): A review. Chemosphere, 335: 139010.
• Suzuki, N., Miller, G., Morales, J., Shulaev, V., Torres, M.A., Mittler, R., 2011. Respiratory burst oxidases: the engines of ROS signaling. Current Opinion in Plant Biology, 14(6): 691-699.
• Tamura, K., Stecher, G., Kumar, S., 2021. MEGA11: Molecular evolutionary genetics analysis version 11. Molecular Biology and Evolution, 38(7): 3022-3027.
• Tewari, R.K., Watanabe, D., Watanabe, M., 2012. Chloroplastic NADPH oxidase-like activity-mediated perpetual hydrogen peroxide generation in the chloroplast induces apoptotic-like death of Brassica napus leaf protoplasts. Planta, 235(1): 99-110.
• Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F., Higgins, D.G., 1997. The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Research, 25(24): 4876-4882.
• Torres, M.A., Dangl, J.L., 2005. Functions of the respiratory burst oxidase in biotic interactions, abiotic stress and development. Current opinion in plant biology, 8(4): 397-403.
• Valliyodan, B., Cannon, S.B., Bayer, P.E., Shu, S., Brown, A.V., Ren, L., Nguyen, H.T., 2019. Construction and comparison of three reference‐quality genome assemblies for soybean. The Plant Journal, 100(5): 1066-1082.
• Wang, G.F., Li, W.Q., Li, W.Y., Wu, G.L., Zhou, C.Y., Chen, K.M., 2013. Characterization of rice NADPH oxidase genes and their expression under various environmental conditions. International Journal of Molecular Sciences, 14(5): 9440-9458.
• Wang, J., Liu, Z., She, H., Xu, Z., Zhang, H., Fang, Z., Qian, W., 2024. Genome-wide identification and characterization of U-Box gene family members and analysis of their expression patterns in Phaseolus vulgaris L. under cold stress. International Journal of Molecular Sciences, 25(14): 7968.
• Wudick, M.M., Feijó, J.A., 2014. At the intersection: merging Ca2+ and ROS signaling pathways in pollen. Molecular Plant, 7(11): 1595-1597.
• Xie, H.T., Wan, Z.Y., Li, S., Zhang, Y., 2014. Spatiotemporal production of reactive oxygen species by NADPH oxidase is critical for tapetal programmed cell death and pollen development in Arabidopsis. The Plant Cell, 26(5): 2007-2023.
• Xu, G., Guo, C., Shan, H., Kong, H., 2012. Divergence of duplicate genes in exon–intron structure. Proceedings of the National Academy of Sciences, 109(4): 1187-1192.
• Ye, H., Liu, H., Han, M., Zhang, N., Feng, X., Gao, T., Wang, Y., 2024. The genome-wide identification, characterization, and expression profiles of the NADPH oxidase (NOX) gene family under drought and salt stress in Opisthopappus taihangensis (Asteraceae). Agronomy, 14(4): 653.
• Yoshioka, H., Mase, K., Yoshioka, M., Kobayashi, M., Asai, S., 2011. Regulatory mechanisms of nitric oxide and reactive oxygen species generation and their role in plant immunity. Nitric Oxide, 25(2): 216-221.
• Yoshioka, H., Numata, N., Nakajima, K., Katou, S., Kawakita, K., Rowland, O., Doke, N., 2003. Nicotiana benthamiana gp91 phox homologs NbrbohA and NbrbohB participate in H2O2 accumulation and resistance to Phytophthora infestans. The Plant Cell, 15(3): 706-718.
• Yoshioka, H., Sugie, K., Park, H.J., Maeda, H., Tsuda, N., Kawakita, K., Doke, N., 2001. Induction of plant gp91 phox homolog by fungal cell wall, arachidonic acid, and salicylic acid in potato. Molecular Plant-Microbe Interactions, 14(6): 725-736.
• Zhang, Y., Zhu, H., Zhang, Q., Li, M., Yan, M., Wang, R., Wang, X., 2009. Phospholipase Dα1 and phosphatidic acid regulate NADPH oxidase activity and production of reactive oxygen species in ABA-mediated stomatal closure in Arabidopsis. The Plant Cell, 21(8): 2357-2377.
• Zhang, Z., Zhao, Y., Feng, X., Luo, Z., Kong, S., Zhang, C., Wang, X., 2019. Genomic, molecular evolution, and expression analysis of NOX genes in soybean (Glycine max). Genomics, 111(4): 619-628.
• Zhou, J., Wang, J., Li, X., Xia, X.J., Zhou, Y.H., Shi, K., Yu, J.Q., 2014. H2O2 mediates the crosstalk of brassinosteroid and abscisic acid in tomato responses to heat and oxidative stresses. Journal of Experimental Botany, 65(15): 4371-4383.