Identification of responsive genes and analysis of genes with bacterial-inducible cis-regulatory elements in the promoter regions in Oryza sativa L.



Bacterial blight of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most critical diseases in rice.  In order to study rice responsive genes to bacterial stress, microarray data were retrieved from GEO dataset. To identify the responsive genes to biotic stress (bacteria) bioinformatic tools were employed and the data presented in the forms of heatmap, gene ontology, gene network, and cis-element prediction were used. Almost all responsive genes were down-regulated at around 3 h time point and up-regulated 24 h time point in response to bacterial stress in rice varieties (Oryza sativa subs. japonica ‘IR64’, ‘IRBB5’, ‘IRBB7’ and ‘Y73’). Gene ontology showed that genes are involved in different biological processes including translation and cellular protein metabolic processes. Network analysis showed that genes expressed in response to pathogen infection (Xoo) included protein translation, eukaryotic initiation factors (eIFs), ribosomal proteins, protein ubiquitin, and MAPK genes. The genes expressed in response to bacterial stress can enable plant balance between synthesis and degradation of proteins which in turn allows plants for further growth and development. TATA-box and CAAT box had the highest number of cis elements involved in bacterial stress. These genes can provide novel insights into regulatory mechanisms in biotic stress responses in rice. Identification of bacterial stress response/tolerance genes of rice can assist the molecular breeding of new rice varieties tolerant to bacterial stress.


rice; differentially-expressed genes (DEGs); bacterial stress; gene ontology; gene network

Full Text:



Agrawal, G.K., Rakwal, R. and Iwahashi, H. (2002). Isolation of novel rice (Oryza sativa L.) multiple stress responsive MAP kinase gene, OsMSRMK2, whose mRNA accumulates rapidly in response to environmental cues. Biochemical and Biophysical Research Communications, 294(5), 1009-1016.

Boycheva, I., Vassileva, V., Revalska, M., Zehirov, G. and Iantcheva, A. (2015). Cyclin-like F-box protein plays a role in growth and development of the three model species Medicago truncatula, Lotus japonicus, and Arabidopsis thaliana. Research and Reports in Biology, 6, 117-130.

Bolstad, B.M., Irizarry, R.A., Åstrand, M. and Speed, T.P. (2003). A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics, 19(2), 185-193.

Chen, X., Dong, Y., Yu, C., Fang, X., Deng, Z., Yan, C., & Chen, J. (2016). Analysis of the proteins secreted from the Oryza meyeriana suspension-cultured cells induced by Xanthomonas oryzae pv. oryzae. PloS One, 11(5).

Dowd, C., Wilson, I.W. and McFadden, H. (2004). Gene expression profile changes in cotton root and hypocotyl tissues in response to infection with Fusarium oxysporum f. sp. vasinfectum. Molecular Plant-Microbe Interactions, 17(6), 654-667.

Du, Z., Zhou, X., Ling, Y., Zhang, Z. and Su, Z. (2010). agriGO: a GO analysis toolkit for the agricultural community. Nucleic acids research, 38(suppl_2), W64-W70.

Eisinger, D.P., Dick, F.A. and Trumpower, B.L. (1997). Qsr1p, a 60S ribosomal subunit protein, is required for joining of 40S and 60S subunits. Molecular and Cellular Biology, 17(9), 5136-5145.

Eulgem, T. and Somssich, I.E. (2007). Networks of WRKY transcription factors in defense signaling. Current Opinion in Plant Biology, 10(4), 366-371.

Fujimoto, S.Y., Ohta, M., Usui, A., Shinshi, H. and Ohme-Takagi, M. (2000). Arabidopsis ethylene-responsive element binding factors act as transcriptional activators or repressors of GCC box–mediated gene expression. The Plant Cell, 12(3), 393-404.

Ghanashyam, C. and Jain, M. (2009). Role of auxin-responsive genes in biotic stress responses. Plant Signaling & Behavior, 4(9), 846-848.

Gilmartin, P.M., Sarokin, L., Memelink, J. and Chua, N.H. (1990). Molecular light switches for plant genes. The Plant Cell, 2(5), 369.

Grewal, R.K., Gupta, S. and Das, S. (2012). Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice. BMC Genomics, 13(1), 49.

Hummel, M., Cordewener, J.H., de Groot, J.C., Smeekens, S., America, A.H. and Hanson, J. (2012). Dynamic protein composition of Arabidopsis thaliana cytosolic ribosomes in response to sucrose feeding as revealed by label free MS E proteomics. Proteomics, 12(7), 1024-1038.

Jain, M. and Khurana, J.P. (2009). Transcript profiling reveals diverse roles of auxin‐responsive genes during reproductive development and abiotic stress in rice. The FEBS Journal, 276(11), 3148-3162.

Kaur, A., Pati, P.K., Pati, A.M. and Nagpal, A.K. (2017). In-silico analysis of cis-acting regulatory elements of pathogenesis-related proteins of Arabidopsis thaliana and Oryza sativa. PloS One, 12(9), e0184523.

Kawasaki, S., Borchert, C., Deyholos, M., Wang, H., Brazille, S., Kawai, K., Galbraith, D. and Bohnert, H.J. (2001). Gene expression profiles during the initial phase of salt stress in rice. The Plant Cell, 13(4), 889-905.

Kolupaeva, V.G., Unbehaun, A., Lomakin, I.B., Hellen, C.U. and Pestova, T.V. (2005). Binding of eukaryotic initiation factor 3 to ribosomal 40S subunits and its role in ribosomal dissociation and anti-association. Rna, 11(4), 470-486.

Lescot, M., Déhais, P., Thijs, G., Marchal, K., Moreau, Y., Van de Peer, Y., ... & 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.

Li, Q., Chen, F., Sun, L., Zhang, Z., Yang, Y. and He, Z. (2006). Expression profiling of rice genes in early defense responses to blast and bacterial blight pathogens using cDNA microarray. Physiological and Molecular Plant Pathology, 68(1-3), 51-60.

Lippok, B., Birkenbihl, R.P., Rivory, G., Brümmer, J., Schmelzer, E., Logemann, E. and Somssich, I.E. (2007). Expression of AtWRKY33 encoding a pathogen-or PAMP-responsive WRKY transcription factor is regulated by a composite DNA motif containing W box elements. Molecular Plant-Microbe Interactions, 20(4), 420-429.

Moin, M., Bakshi, A., Saha, A., Dutta, M., Madhav, S.M. and Kirti, P.B. (2016). Rice ribosomal protein large subunit genes and their spatio-temporal and stress regulation. Frontiers in Plant Science, 7, 1284.

Meena, K.K., Sorty, A.M., Bitla, U.M., Choudhary, K., Gupta, P., Pareek, A., Singh, D.P., Prabha, R., Sahu, P.K., Gupta, V.K. and Singh, H.B. (2017). Abiotic stress responses and microbe-mediated mitigation in plants: the omics strategies. Frontiers in Plant Science, 8, p.172.

O’Brien, J.A. and Benková, E. (2013). Cytokinin cross-talking during biotic and abiotic stress responses. Frontiers in Plant Science, 4, 451.

Saidi, A., & Hajibarat, Z. (2018). In silico analysis of floral mads-box gene in Brachypodium distachyon. BIONATURE, 366-375.

Saidi, A., & Hajibarat, Z. (2019). Characterization of cis-elements in hormonal stress-responsive genes in Oryza sativa.

Saidi, A., & Hajibarat, Z. (2020). In-silico analysis of eukaryotic translation initiation factors (eIFs) in response to environmental stresses in rice (Oryza sativa). Biologia, 1-8.

Sharma, T.R., Rai, A.K., Gupta, S.K., Vijayan, J., Devanna, B.N. and Ray, S. (2012). Rice blast management through host-plant resistance: retrospect and prospects. Agricultural Research, 1(1), 37-52.

Song, R., Li, J., Xie, C., Jian, W., & Yang, X. (2020). An Overview of the Molecular Genetics of Plant Resistance to the Verticillium Wilt Pathogen Verticillium dahliae. International Journal of Molecular Sciences, 21(3), 1120.

Sormani, R., Masclaux-Daubresse, C., Daniele-Vedele, F. and Chardon, F. (2011). Transcriptional regulation of ribosome components are determined by stress according to cellular compartments in Arabidopsis thaliana. PLoS One, 6(12), p.e28070.

Toufighi, K., Brady, S. M., Austin, R., Ly, E., & Provart, N. J. (2005). The Botany Array Resource: e‐Northerns, expression angling, and promoter analyses. The Plant Journal, 43(1), 153-163.

Ülker, B. and Somssich, I.E., 2004. WRKY transcription factors: from DNA binding towards biological function. Current Opinion in Plant Biology, 7(5), 491-498.

Yang, L., Mu, X., Liu, C., Cai, J., Shi, K., Zhu, W., and Yang, Q. (2015). Overexpression of potato miR482e enhanced plant sensitivity to Verticillium dahliae infection. Journal of Integrative Plant Biology, 57(12), 1078-1088.

Wang, W., Vinocur, B. and Altman, A. (2003). Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance. Planta, 218(1), 1-14.

Wang, P., Du, Y., Zhao, X., Miao, Y. and Song, C.P. (2013). The MPK6-ERF6-ROSE7/GCC-box complex modulates oxidative gene transcription and the oxidative response in Arabidopsis thaliana. Plant Physiology, 112.



  • There are currently no refbacks.

Copyright (c) 2020 Abbas Saidi

Creative Commons License
This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.


Acta agriculturae Slovenica is an Open Access journal published under the terms of the Creative Commons CC BY License.


eISSN 1854-1941