Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice

Hardian Susilo Addy; Wulan Arum Hardiyani; Harits Ramadhan Fajrianto

doi:10.38042/biotechstudies.1826184

Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice

Abstract

Bacterial leaf blight (BLB) is caused by the phytopathogen Xanthomonas oryzae pv. oryzae (Xoo), a destructive disease that significantly threatens rice production. Controlling bacterial leaf blight on rice (Oryzae sativa) is important through the plant resistance approach, including pathogen-derived ligands such as flagella to induce plant resistance mechanisms, in addition to using lytic bacteriophage. This study investigated the interaction between the bacteriophage XooG01 and flagellar proteins from Xoo H02 on the expression of resistance genes in rice. Leaves were pre-treated with a mixture of the phage and bacterial cell surface appendages before pathogen inoculation, and gene expression was measured using semi-quantitative RT-PCR. The results revealed a paradoxical transcriptional response. While the expression of genes Xa10 and xa13 was significantly upregulated in treated leaves after pathogen challenge, the expression of the primary immune receptor Xa21 was, contrary to expectations, significantly decreased. The expression of Xa4 showed a slight, non-significant increase. This unexpected suppression of Xa21 suggests a phage-mediated interference in the host-pathogen recognition process, likely by the phage physically masking the flagellin elicitor from plant receptors. These findings reveal a complex tripartite interaction with critical implications for the design of future biocontrol strategies.

Keywords

Supporting Institution

This work was financially supported by Institute of Research and Community Services (LPPM) University of Jember.

Thanks

The authors thank the Institute of Research and Community Services (LPPM) University of Jember for financial support and thank the Center for Development of Advanced Sciences and Technology for facilitating and providing the research equipment.

References

Addy, H.S., Askora, A., Kawasaki, T., Fujie, M., Yamada, T. 2012. Utilization of filamentous phage ϕRSM3 to control bacterial wilt caused by Ralstonia solanacearum. Plant Dis. 96(8): 1204-1209. https://doi.org/10.1094/PDIS-12-11-1023-RE
Addy, H.S, Ahmad, A.A., Huang, Q. 2019. Molecular and biological characterization of Ralstonia phage RsoM1USA, a new species of P2virus, isolated in the United States. Front Microbiol. 10:267. https://doi.org/10.3389/fmicb.2019.00267
Addy, H.S., Habibullah, N., Hardiyani, W.A., Wafa, A. 2024. The effect of Tapak Liman (Elephantopus scaber L.) extract on Xa4 gene expression in rice IR64 infected by bacterial leaf blight (Xanthomonas oryzae). International Journal of Secondary Metabolite 11(1):15-22. https://doi.org/10.21448/ijsm.1224397
Antony, G., Zhou, J., Huang, S., Li, T. Liu, B., White, F., Yang, B. 2010. Rice xa13 recessive resistance to bacterial blight is defeated by induction of the disease susceptibility gene Os-11N3. Plant Cell 22(11): 3864–3876. https://doi.org/10.1105/tpc.110.078964
Antiabong, J.F., Ngoepe, M.G., Abechi, A.S. 2016. Semi-quantitative digital analysis of polymerase chain reaction-electrophoresis gel: Potential applications in low-income veterinary laboratories. Veterinary World 9(9): 935-939. https://doi.org/10.14202/vetworld.2016.935-939
Apel, D., Surette, M.G. 2008. Bringing order to a complex molecular machine: the assembly of the bacterial flagella. Biochimica et Biophysica Acta 1778(9): 1851-1858. https://doi.org/10.1016/j.bbamem.2007.07.005
Banerjee, S., Mitra, S., Velhal, M., Desmukh, V., Ghosh, B. 2021. Impact of agrochemicals on the environment and human health: The concerns and remedies. International Journal of Experimental Research and Review 26: 125–140. https://doi.org/10.52756/ijerr.2021.v26.010
Chen, L. Q, Qu, X. Q., Hou, B. H., Sosso, D., Osorio, S., Fernie, A. R., & Frommer, W. B. (2012). Sucrose efflux mediated by SWEET proteins as a key step for phloem transport. Science, 335(6065): 207-211. https://doi.org/10.1126/science.1213351

Dodds, P.N., Rathjen, J.P. 2010. Plant immunity: towards an integrated view of plant-pathogen interactions. Natural Review of Genetics 11(8): 539-48. https://doi.org/10.1038/nrg2812
Dunne, M., Prokhorov, N.S., Loessner, M.J., Leiman, P.G. 2021. Reprogramming bacteriophage host range: Design principles and strategies for engineering receptor binding proteins. Current Opinion in Biotechnology 68: 272-281. https://doi.org/10.1016/j.copbio.2021.02.006
Hajam, I.A., Dar, P.A., Shahnawaz, I., Jaume, J.C., Lee, J.H. 2017. Bacterial flagellin-a potent immunomodulatory agent. Experimental and Molecular Medicine 49(9): e373. https://doi.org/10.1038/emm.2017.172
Ilsan, N.A., Nawangsih, A.A., Wahyudi, A.T. 2016. Rice phyllosphere actinomycetes as biocontrol agent of bacterial leaf blight disease on rice. Asian Journal of Plant Pathology 10: 1-8. https://doi.org/10.3923/ajppaj.2016.1.8
Irpawa, D.M.I., Arwiyanto, T., Sulandari, S. 2024. The characterization, pathotype distribution and genetic diversity of Xanthomonas oryzae pv. oryzae in rice production centers of the special Region of Yogyakarta, Indonesia. Journal of Tropical Plant Pests and Diseases 24: 262-273. https://doi.org/10.23960/jhptt.224262-273
Jarrell, K.F., McBride, M.J. 2008. The surprisingly diverse ways that prokaryotes move. Natural Review Microbiology 6(6): 466-76. https://doi.org/10.1038/nrmicro1900
Jiang, N., Yan, J., Liang, Y., Shi, Y., He, Z., Wu, Y., Zeng, Q., Liu, X., Peng, J. 2020. Resistance genes and their interactions with bacterial blight/leaf streak pathogens (Xanthomonas oryzae) in rice (Oryza sativa L.)-an Updated Review. Rice 13(1): 3. https://doi.org/10.1186/s12284-019-0358-y
Lang, J.M., Pérez-Quintero, A.L., Koebnik, R., DuCharme, E., Sarra, S., Doucoure, H., Keita, I., Ziegle, J., Jacobs, J.M., Oliva, R., Koita, O., Szurek, B., Verdier, V., Leach, J. E. 2019. A Pathovar of Xanthomonas oryzae infecting wild grasses provides insight into the evolution of pathogenicity in rice agroecosystems. Frontiers in Plant Science 10: 507. https://doi.org/10.3389/fpls.2019.00507
Li, C., Li, W., Zhou, Z., Chen, H., Xie, C., Lin, Y. 2019. A new rice breeding method: CRISPR/Cas9 system editing of the Xa13 promoter to cultivate transgene-free bacterial blight-resistant rice. Plant Biotechnology Journal 18(2): 313-315. https://doi.org/10.1111/pbi.13217
Liang, B., Wang, H., Yang, C., Wang, L., Qi, L., Guo, Z., Chen, X. 2022. Salicylic Acid Is required for broad-spectrum disease resistance in rice. International Journal of Molecular Sciences 23(3): 1354. https://doi.org/10.3390/ijms23031354
Lippolis, J.D., Brunelle, B.W., Reinhardt, T.A., Sacco, R.E., Nonnecke, B.J., Dogan, B., Simpson, K., Schukken, Y. H. 2014. Proteomic analysis reveals protein expression differences in Escherichia coli strains associated with persistent versus transient mastitis. Journal of Proteomics 108: 373-381. https://doi.org/10.1016/j.jprot.2014.06.008
Liu, M., Tian, Y., Zaki, H. E. M., Ahmed, T., Yao, R., Yan, C., Leptihn, S., Loh, B., Shahid, M. S., Wang, F., Chen, J., Li, B. 2022. Phage resistance reduced the pathogenicity of Xanthomonas oryzae pv. oryzae on rice. Viruses 14(8):1770. https://doi.org/10.3390/v14081770
Malik, A.N.A., Kumar, I.S., Nadarajah, K. 2020. Elicitor and receptor molecules: Orchestrators of plant defense and immunity. International Journal of Molecular Sciences 21(3): 963. https://doi.org/10.3390/ijms21030963
Meindl, T., Boller, T., Felix, G. 2000. The bacterial elicitor flagellin activates its receptor in tomato cells according to the address-message concept. The Plant Cell 12(9): 1783–1794. https://doi.org/10.1105/tpc.12.9.1783
Mohidem, N.A., Hashim, N., Shamsudin, R., Che Man, H. 2022. Rice for food security: Revisiting its production, diversity, rice milling process and nutrient content. Agriculture 12: 741. https://doi.org/10.3390/agriculture12060741
Nadhira, N.E, Wahyuni, I.D., Addy, H.S. 2021. The potency of plant resistance inducers (PRIs) against bacterial wilt disease on tobacco caused by Ralstonia solanacearum. IOP Conference Series. Earth and Environmental Science 759(1): 012067. https://doi.org/10.1088/1755-1315/759/1/012067
Nadhira, N.E., Wafa, A., Fanata, W.I.D., Addy, H.S. 2022. Resistance gene expression in selected Indonesian rice varieties against the infection by Xanthomonas oryzae pv. oryzae. Indonesian Journal of Biotechnology 27(4): 51-57. https://doi.org/10.22146/ijbiotech.70445
Narulita, E., Addy, H.S., Kawasaki, T., Fujie, M., Yamada, T. 2016. The involvement of the PilQ secretin of type IV pili in phage infection in Ralstonia solanacearum. Biochemical and Biophysical Research Communications 469(4): 868–872. https://doi.org/10.1016/j.bbrc.2015.12.071
Niño-Liu, D.O., Ronald, P.C., Bogdanove, A.J. 2006. Xanthomonas oryzae pathovars: model pathogens of a model crop. Mol. Plant Pathol. 7(5): 303-324. https://doi.org/10.1111/j.1364-3703.2006.00344.x
Palma, V., Gutiérrez, M.S., Vargas, O., Parthasarathy, R., Navarrete, P. 2022. Methods to evaluate bacterial motility and its role in bacterial-host interactions. Microorganisms 10(3): 563. https://doi.org/10.3390/microorganisms10030563
Peng, H., Chen, Z., Fang, Z., Zhou, J., Xia, Z., Gao, L., Chen, L., Li, L., Li, T., Zhai, W., Zhang, W. 2015. Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection. Scientific Reports 5: 12165. https://doi.org/10.1038/srep12165
Rashid, M.M., Nihad, S.A.I., Khan, M.A.I., Haque, A., Ara, A., Ferdous, T., Hasan, A. I., Latif M.A. 2021. Pathotype profiling, distribution, and virulence analysis of Xanthomonas oryzae pv. oryzae causing bacterial blight disease of rice in Bangladesh. J. Phytopathol. 169: 438– 446. https://doi.org/10.1111/jph.13000
Rejeki, D., Addy, H.S., Narulita, E. 2021. Partial characterization of bacteriophages from Indonesia and its potency as biocontrol of Xanthomonas oryzae pv. oryzae. International Journal of Agriculture and Biology 25: 75‒78. https://doi.org/10.17957/IJAB/15.1640
Roberts, R., Liu, A.E., Wan, L., Geiger, A.M., Hind, S.R., Rosli, H.G., & Martin, G.B. 2020. Molecular characterization of differences between the tomato immune receptors flagellin sensing 3 and flagellin sensing 2. Plant Physiology 183(4): 1825-1837. https://doi.org/10.1104/pp.20.00184
Roy, A., Khan, A., Ahmad, I., Alghamdi, S., Rajab, B.S., Babalghith, A.O., Alshahrani, M.Y., Islam, S., Islam, M.R. 2022. Flavonoids a bioactive compound from medicinal plants and its therapeutic applications. Biomed Research International 2022: 5445291. https://doi.org/10.1155/2022/5445291
Sanguankiattichai, N., Buscaill, P., Preston, G.M. 2022. How bacteria overcome flagellin pattern recognition in plants. Current Opinion in Plant Biology, 67, 102224. https://doi.org/10.1016/j.pbi.2022.102224
Sausset, R., Petit, M.A., Gaboriau-Routhiau, V., De Paepe, M. 2020. New insights into intestinal phages. Mucosal Immunology 13(2): 205-215. https://doi.org/10.1038/s41385-019-0250-5
Schofield, D.A., Sharp, N.J., Westwater, C. 2012. Phage-based platforms for the clinical detection of human bacterial pathogens. Bacteriophage 2(2): 105-283. https://doi.org/10.4161/bact.19274
Shen, Y., Ronald, P. 2002. Molecular determinants of disease and resistance in interactions of Xanthomonas oryzae pv. oryzae and rice. Microbes Infection 4(13): 1361-1367. https://doi.org/10.1016/s1286-4579(02)00004-7
Tian, D., Wang, J., Zeng, X., Gu, K., Qiu, C., Yang, X., Zhou, Z., Goh, M., Luo, Y., Murata-Hori, M., White, F.F, Yin Z. 2014. The rice TAL effector-dependent resistance protein XA10 triggers cell death and calcium depletion in the endoplasmic reticulum. Plant Cell 26(1): 497-515. https://doi.org/10.1105/tpc.113.119255
Tian, F., Yu, C., Li, H., Wu, X., Li, B., Chen, H., Wu, M., He, C. 2015. Alternative sigma factor RpoN2 is required for flagellar motility and full virulence of Xanthomonas oryzae pv. oryzae. Microbiol Research 170: 177-183. https://doi.org/10.1016/j.micres.2014.07.002
Tonelli, M.L., Figueredo, M.S., Rodríguez, J., Fabra, A., Ibañez, F. 2020. Induced systemic resistance-like responses elicited by rhizobia. Plant Soil 448: 1–14. https://doi.org/10.1007/s11104-020-04423-5 Vu, N.T., Oh, C.S. 2020. Bacteriophage usage for bacterial disease management and diagnosis in plants. Plant Pathology Journal 36(3): 204–217. https://doi.org/10.5423/PPJ.RW.04.2020.0074
Wang, S., Sun, Z., Wang, H., Liu, L., Lu, F., Yang, J., Zhang, M., Zhang, S., Guo, Z., Bent, A.F., Sun, W. 2015. Rice OsFLS2-Mediated perception of bacterial flagellins is evaded by Xanthomonas oryzae pvs. oryzae and oryzicola. Molecular Plant 8(7): 1024-1037. https://doi.org/10.1016/j.molp.2015.01.012
Wang, Z., Luo, W., Cheng, S., Zhang, H., Zong, J., Zhang, Z. 2023. Ralstonia solanacearum - A soil borne hidden enemy of plants: Research development in management strategies, their action mechanism and challenges. Front Plant Sci. 14:1141902. https://doi.org/10.3389/fpls.2023.1141902
Xu, B., Wozniak, D.J. 2015. Development of a novel method for analyzing Pseudomonas aeruginosa twitching motility and its application to define the amrz regulon. PLoS One 10(8): e0136426. https://doi.org/10.1371/journal.pone.0136426
Yang, Y., Zhou, Y., Sun, J., Liang, W., Chen, X., Wang, X., Zhou, J., Yu, C., Wang, J., Wu, S., Yao, X., Zhou, Y., Zhu, J., Yan, C., Zheng, B., Chen, J. 2022. Research progress on cloning and function of Xa genes against rice bacterial blight. Frontiers in Plant Sciences 13: 847199. https://doi.org/10.3389/fpls.2022.847199
Yugander, A., Sundaram, R.M., Singh, K., Senguttuvel, P., Ladhalakshmi, D., Kemparaju, K.B., Madhav, M.S., Prasad, M.S., Hariprasad, A.S., Laha, G.S. 2018. Improved versions of rice maintainer line, APMS 6B, possessing two resistance genes, Xa21 and Xa38, exhibit high level of resistance to bacterial blight disease. Molecular Breeding 38: 100. https://doi.org/10.1007/s11032-018-0853-7
Zafar, K., Khan, M.Z., Amin, I., Mukhtar, Z., Yasmin, S., Arif, M., Ejaz, K., Mansoor, S. 2020. Precise CRISPR-Cas9 mediated genome editing in super basmati rice for resistance against bacterial blight by targeting the major susceptibility gene. Frontiers in Plant Sciences 11: 575. https://doi.org/10.3389/fpls.2020.00575

Details

Primary Language

English

Subjects

Plant Bacteriology in Agriculture, Plant Biotechnology in Agriculture, Agricultural Biotechnology Diagnostics

Journal Section

Research Article

Authors

Hardian Susilo Addy ^*
0000-0001-7823-0859
Indonesia

Wulan Arum Hardiyani
0009-0008-5354-6003
Indonesia

Harits Ramadhan Fajrianto This is me
0009-0008-4151-1233
Indonesia

Early Pub Date

November 18, 2025

Publication Date

March 5, 2026

Submission Date

January 16, 2025

Acceptance Date

September 22, 2025

Published in Issue

Year 2026 Number: 35

DOI

https://doi.org/10.38042/biotechstudies.1826184

IZ

https://izlik.org/JA86UM46EX

Cite

RIS / Bibtex

APA

Addy, H. S., Hardiyani, W. A., & Fajrianto, H. R. (2026). Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice. Biotech Studies, 35, 1826184. https://doi.org/10.38042/biotechstudies.1826184

AMA

1.Addy HS, Hardiyani WA, Fajrianto HR. Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice. Biotech Studies. 2026;(35):1826184. doi:10.38042/biotechstudies.1826184

Chicago

Addy, Hardian Susilo, Wulan Arum Hardiyani, and Harits Ramadhan Fajrianto. 2026. “Effect of Phage XooG01 and Flagella Protein of Xanthomonas Oryzae Pv. Oryzae on Xa Genes Expression in Rice”. Biotech Studies, nos. 35: 1826184. https://doi.org/10.38042/biotechstudies.1826184.

EndNote

Addy HS, Hardiyani WA, Fajrianto HR (March 1, 2026) Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice. Biotech Studies 35 1826184.

IEEE

[1]H. S. Addy, W. A. Hardiyani, and H. R. Fajrianto, “Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice”, Biotech Studies, no. 35, p. 1826184, Mar. 2026, doi: 10.38042/biotechstudies.1826184.

ISNAD

Addy, Hardian Susilo - Hardiyani, Wulan Arum - Fajrianto, Harits Ramadhan. “Effect of Phage XooG01 and Flagella Protein of Xanthomonas Oryzae Pv. Oryzae on Xa Genes Expression in Rice”. Biotech Studies. 35 (March 1, 2026): 1826184. https://doi.org/10.38042/biotechstudies.1826184.

JAMA

1.Addy HS, Hardiyani WA, Fajrianto HR. Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice. Biotech Studies. 2026;:1826184.

MLA

Addy, Hardian Susilo, et al. “Effect of Phage XooG01 and Flagella Protein of Xanthomonas Oryzae Pv. Oryzae on Xa Genes Expression in Rice”. Biotech Studies, no. 35, Mar. 2026, p. 1826184, doi:10.38042/biotechstudies.1826184.

Vancouver

1.Hardian Susilo Addy, Wulan Arum Hardiyani, Harits Ramadhan Fajrianto. Effect of phage XooG01 and flagella protein of Xanthomonas oryzae pv. oryzae on Xa genes expression in rice. Biotech Studies. 2026 Mar. 1;(35):1826184. doi:10.38042/biotechstudies.1826184