Unraveling the changes in important molecular mechanisms of Arabidopsis thaliana infected by Botrytis cinerea: insights from in silico analysis

Volume 13, Issue 3
September 2024
Pages 255-268

Document Type : Original Research

Authors

1 Department of Biology, Faculty of Basic Sciences, Azarbaijan Shahid Madani University, Tabriz, Iran.

2 Emam Hossein Hospital, Tabriz University of Medical Sciences, Hashtrood, Iran.

Abstract
Botrytis cinerea is one of the most important harmful fungi affecting agricultural products. This study focused on the expression changes of Arabidopsis thaliana infected with this fungus. The expression dataset of a microarray and two RNA-sequencing were integrated using the respective software. The list of differentially expressed genes was extracted, and the key genes with altered expression were identified through Cytoscape software. These key genes co-expression patterns and functional enrichment were analyzed. Subsequently, microRNAs and transcription factors associated with these genes were predicted. Ten genes, including GAPA-2, SBPASE, CRB, HCEF1, CaS, ATPD, LIL3:1, PSAH2, PRK, and PMDH2, were identified as crucial down-regulated genes. Additionally, ten genes, namely WRKY33, CZF1, SZF1, STZ, ERF11, RHL41, BAP1, AT1G07135, CMPG2, and TET8, were highlighted as key up-regulated genes. The key roles of the hub genes with a decreased expression included processes and pathways associated with the reductive pentose phosphate cycle, photosynthesis, cold response, fructose and sucrose metabolism, defense response against bacteria, and gluconeogenesis. The key over-expressed genes played important roles in responding to chitin, oxygen deprivation, temperature fluctuations, injuries, fungal attacks, and gene transcription functions. Key genes were associated with ath-miR850, ath-miR393a-5p, and ath-miR393b-5p. Transcription factor SPL7 was linked to the transcription of down-regulated key genes, while transcription factors SARD1, PIF5, CAMTA1, HY5, WRKY33, TOC1, CAMTA3, CAMTA2, BZR1, FAR1, and CAMTA5 were also predicted to be associated with up-regulated genes. Some of these results have not previously been reported. Therefore, they could be used to design practical experiments exploring the interaction between plants and pathogenic fungi.

Keywords

Subjects
Abdel-Hameed, A. A., Liao, W., Prasad, K. V., and Reddy, A. S. 2024. CAMTAs, a family of calmodulin-binding transcription factors, are versatile regulators of biotic and abiotic stress responses in plants. Critical Reviews in Plant Sciences 43, 171-210.
AbuQamar, S., Chen, X., Dhawan, R., Bluhm, B., Salmeron, J., Lam, S., Dietrich, R. A., and Mengiste, T. 2006. Expression profiling and mutant analysis reveals complex regulatory networks involved in Arabidopsis response to Botrytis infection. The Plant Journal 48, 28-44.
Agudelo-Romero, P., Carbonell, P., De La Iglesia, F., Carrera, J., Rodrigo, G., Jaramillo, A., Pérez-Amador, M. A., and Elena, S. F. 2008. Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus. Virology journal 5, 1-11.
Araújo, R. G., Chavez-Santoscoy, R. A., Parra-Saldívar, R., Melchor-Martínez, E. M., and Iqbal, H. M. 2023. Agro-food systems and environment: Sustaining the unsustainable. Current Opinion in Environmental Science & Health 31, 100413.
Arjmand, M. P., Lahiji, H. S., Biglouei, M. H., and Golfazani, M. M. 2021. Identification of drought-responsive hub genes and their related miRNAs in Arabidopsis thaliana.
Ascencio-Ibánez, J. T., Sozzani, R., Lee, T.-J., Chu, T.-M., Wolfinger, R. D., Cella, R., and Hanley-Bowdoin, L. 2008. Global analysis of Arabidopsis gene expression uncovers a complex array of changes impacting pathogen response and cell cycle during geminivirus infection. Plant physiology 148, 436-454.
Berger, S., Papadopoulos, M., Schreiber, U., Kaiser, W., and Roitsch, T. 2004. Complex regulation of gene expression, photosynthesis and sugar levels by pathogen infection in tomato. Physiologia Plantarum 122, 419-428.
Bolger, A., and Giorgi, F. 2014. Trimmomatic: a flexible read trimming tool for illumina NGS data. Bioinformatics 30, 2114-2120.
Bolouri‐Moghaddam, M. R., Le Roy, K., Xiang, L., Rolland, F., and Van den Ende, W. 2010. Sugar signalling and antioxidant network connections in plant cells. The FEBS journal 277, 2022-2037.
Castillo, D., Gálvez, J. M., Herrera, L. J., Román, B. S., Rojas, F., and Rojas, I. 2017. Integration of RNA-Seq data with heterogeneous microarray data for breast cancer profiling. BMC bioinformatics 18, 1-15.
Chen, S., Ma, T., Song, S., Li, X., Fu, P., Wu, W., Liu, J., Gao, Y., Ye, W., and Dry, I. B. 2021. Arabidopsis downy mildew effector HaRxLL470 suppresses plant immunity by attenuating the DNA‐binding activity of bZIP transcription factor HY5. New Phytologist 230, 1562-1577.
Chen, X., Zhang, Z., Liu, D., Zhang, K., Li, A., and Mao, L. 2010. SQUAMOSA promoter‐binding protein‐like transcription factors: Star players for plant growth and development. Journal of integrative plant biology 52, 946-951.
Chin, C.-H., Chen, S.-H., Wu, H.-H., Ho, C.-W., Ko, M.-T., and Lin, C.-Y. 2014. cytoHubba: identifying hub objects and sub-networks from complex interactome. BMC systems biology 8, 1-7.
Chou, H. M., Bundock, N., Rolfe, S. A., and Scholes, J. D. 2000. Infection of Arabidopsis thaliana leaves with Albugo candida (white blister rust) causes a reprogramming of host metabolism. Molecular plant pathology 1, 99-113.
Corkley, I., Fraaije, B., and Hawkins, N. 2022. Fungicide resistance management: Maximizing the effective life of plant protection products. Plant Pathology 71, 150-169.
Dai, X., Zhuang, Z., and Zhao, P. X. (2019). psRNATarget V2: a high-performance plant small rna target analysis server. In "Plant and Animal Genome XXVII Conference (January 12-16, 2019)". PAG.
Davis, S., and Meltzer, P. S. 2007. GEOquery: a bridge between the Gene Expression Omnibus (GEO) and BioConductor. Bioinformatics 23, 1846-1847.
Diwan, D., Rashid, M. M., and Vaishnav, A. 2022. Current understanding of plant-microbe interaction through the lenses of multi-omics approaches and their benefits in sustainable agriculture. Microbiological Research 265, 127180.
Eulgem, T., Weigman, V. J., Chang, H.-S., McDowell, J. M., Holub, E. B., Glazebrook, J., Zhu, T., and Dangl, J. L. 2004. Gene expression signatures from three genetically separable resistance gene signaling pathways for downy mildew resistance. Plant Physiology 135, 1129-1144.
Ferjani, A., Tsukagoshi, H., and Vassileva, V. 2023. Model organisms in plant science: Arabidopsis thaliana. Frontiers in Plant Science 14, 1279230.
Ferri, M., Righetti, L., and Tassoni, A. 2011. Increasing sucrose concentrations promote phenylpropanoid biosynthesis in grapevine cell cultures. Journal of Plant Physiology 168, 189-195.
Fujita, M., Fujita, Y., Noutoshi, Y., Takahashi, F., Narusaka, Y., Yamaguchi-Shinozaki, K., and Shinozaki, K. 2006. Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Current opinion in plant biology 9, 436-442.
Gendron, J. M., Pruneda-Paz, J. L., Doherty, C. J., Gross, A. M., Kang, S. E., and Kay, S. A. 2012. Arabidopsis circadian clock protein, TOC1, is a DNA-binding transcription factor. Proceedings of the National Academy of Sciences 109, 3167-3172.
Huang, D. W., Sherman, B. T., Tan, Q., Collins, J. R., Alvord, W. G., Roayaei, J., Stephens, R., Baseler, M. W., Lane, H. C., and Lempicki, R. A. 2007. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome biology 8, 1-16.
Koene, S., Shapulatov, U., van Dijk, A. D., and van der Krol, A. R. 2023. Transcriptional Feedback in Plant Growth and Defense by PIFs, BZR1, HY5, and MYC Transcription Factors. Plant Molecular Biology Reporter 41, 59-80.
Kulkarni, S. R., Vaneechoutte, D., Van de Velde, J., and Vandepoele, K. 2018. TF2Network: predicting transcription factor regulators and gene regulatory networks in Arabidopsis using publicly available binding site information. Nucleic acids research 46, e31-e31.
Libault, M., Wan, J., Czechowski, T., Udvardi, M., and Stacey, G. 2007. Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. Molecular plant-microbe interactions 20, 900-911.
Lodha, T., and Basak, J. 2012. Plant–pathogen interactions: what microarray tells about it? Molecular biotechnology 50, 87-97.
Lozano-Durán, R., Macho, A. P., Boutrot, F., Segonzac, C., Somssich, I. E., and Zipfel, C. 2013. The transcriptional regulator BZR1 mediates trade-off between plant innate immunity and growth. elife 2, e00983.
Ma, X., Yan, H., Yang, J., Liu, Y., Li, Z., Sheng, M., Cao, Y., Yu, X., Yi, X., and Xu, W. 2022. PlantGSAD: a comprehensive gene set annotation database for plant species. Nucleic acids research 50, D1456-D1467.
Mitsuya, Y., Takahashi, Y., Berberich, T., Miyazaki, A., Matsumura, H., Takahashi, H., Terauchi, R., and Kusano, T. 2009. Spermine signaling plays a significant role in the defense response of Arabidopsis thaliana to cucumber mosaic virus. Journal of plant physiology 166, 626-643.
Morkunas, I., and Ratajczak, L. 2014. The role of sugar signaling in plant defense responses against fungal pathogens. Acta Physiologiae Plantarum 36, 1607-1619.
Peyraud, R., Dubiella, U., Barbacci, A., Genin, S., Raffaele, S., and Roby, D. 2017. Advances on plant–pathogen interactions from molecular toward systems biology perspectives. The Plant Journal 90, 720-737.
Qin, J., Wang, K., Sun, L., Xing, H., Wang, S., Li, L., Chen, S., Guo, H.-S., and Zhang, J. 2018. The plant-specific transcription factors CBP60g and SARD1 are targeted by a Verticillium secretory protein VdSCP41 to modulate immunity. Elife 7, e34902.
Riseh, R. S., Fathi, F., Vatankhah, M., and Kennedy, J. F. 2024. Exploring the role of levan in plant immunity to pathogens: A review. International Journal of Biological Macromolecules, 135419.
Ritchie, M. E., Phipson, B., Wu, D., Hu, Y., Law, C. W., Shi, W., and Smyth, G. K. 2015. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic acids research 43, e47-e47.
Rojas, C. M., Senthil-Kumar, M., Tzin, V., and Mysore, K. S. 2014. Regulation of primary plant metabolism during plant-pathogen interactions and its contribution to plant defense. Frontiers in plant science 5, 17.
Ross, R. L., and Santiago-Tirado, F. H. 2024. Advanced genetic techniques in fungal pathogen research. Msphere, e00643-23.
Różewicz, M., Wyzińska, M., and Grabiński, J. 2021. The most important fungal diseases of cereals—Problems and possible solutions. Agronomy 11, 714.
Schmieder, R., and Edwards, R. 2011. Quality control and preprocessing of metagenomic datasets. Bioinformatics 27, 863-864.
Scholes, J. D., and Rolfe, S. A. 1996. Photosynthesis in localised regions of oat leaves infected with crown rust (Puccinia coronata): quantitative imaging of chlorophyll fluorescence. Planta 199, 573-582.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. 2003. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome research 13, 2498-2504.
Sherry, S., Xiao, C., Durbrow, K., Kimelman, M., Rodarmer, K., Shumway, M., and Yaschenko, E. (2012). Ncbi sra toolkit technology for next generation sequence data. In "Plant and Animal Genome XX Conference (January 14-18, 2012). Plant and Animal Genome".
Shiade, S. R. G., Zand-Silakhoor, A., Fathi, A., Rahimi, R., Minkina, T., Rajput, V. D., Zulfiqar, U., and Chaudhary, T. 2024. Plant metabolites and signaling pathways in response to biotic and abiotic stresses: Exploring bio stimulant applications. Plant Stress, 100454.
Singh, J., and Thakur, J. K. (2018). Photosynthesis and abiotic stress in plants. In "Biotic and abiotic stress tolerance in plants", pp. 27-46. Springer.
Spada, M., Pugliesi, C., Fambrini, M., and Pecchia, S. 2024. Challenges and Opportunities Arising from Host–Botrytis cinerea Interactions to Outline Novel and Sustainable Control Strategies: The Key Role of RNA Interference. International Journal of Molecular Sciences 25, 6798.
Swarbrick, P. J., Schulez‐Lefert, P., and Scholes, J. D. 2006. Metabolic consequences of susceptibility and resistance (race‐specific and broad‐spectrum) in barley leaves challenged with powdery mildew. Plant, Cell & Environment 29, 1061-1076.
Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., and Bork, P. 2019. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic acids research 47, D607-D613.
Theissinger, K., Fernandes, C., Formenti, G., Bista, I., Berg, P. R., Bleidorn, C., Bombarely, A., Crottini, A., Gallo, G. R., and Godoy, J. A. 2023. How genomics can help biodiversity conservation. Trends in genetics 39, 545-559.
Thines, B., Parlan, E. V., and Fulton, E. C. 2019. Circadian network interactions with jasmonate signaling and defense. Plants 8, 252.
Wan, J., Zhang, X.-C., and Stacey, G. 2008. Chitin signaling and plant disease resistance. Plant signaling & behavior 3, 831-833.
Wang, W., Tang, W., Ma, T., Niu, D., Jin, J. B., Wang, H., and Lin, R. 2016. A pair of light signaling factors FHY3 and FAR1 regulates plant immunity by modulating chlorophyll biosynthesis. Journal of integrative plant biology 58, 91-103.
Wen, G. (2017). A simple process of RNA-sequence analyses by Hisat2, Htseq and DESeq2. In "Proceedings of the 2017 International Conference on Biomedical Engineering and Bioinformatics", pp. 11-15.
Wickham, H., Chang, W., Henry, L., Pedersen, T., Takahashi, K., Wilke, C., Woo, K., Yutani, H., and Dunnington, D. (2021). Package ‘ggplot2’: Create Elegant Data Visualisations Using the Grammar of Graphics. R package version 3.3. 2.
Wu, Y., Zheng, L., Bing, J., Liu, H., and Zhang, G. 2021. Deep sequencing of small RNA reveals the molecular regulatory network of AtENO2 regulating seed germination. International journal of molecular sciences 22, 5088.
Yang, C., and Wei, H. 2015. Designing microarray and RNA-Seq experiments for greater systems biology discovery in modern plant genomics. Molecular plant 8, 196-206.
Zhang, Y., Xu, S., Ding, P., Wang, D., Cheng, Y. T., He, J., Gao, M., Xu, F., Li, Y., and Zhu, Z. 2010. Control of salicylic acid synthesis and systemic acquired resistance by two members of a plant-specific family of transcription factors. Proceedings of the National Academy of Sciences 107, 18220-18225.
Zheng, P.-F., Wang, X., Yang, Y.-Y., You, C.-X., Zhang, Z.-L., and Hao, Y.-J. 2020. Identification of phytochrome-interacting factor family members and functional analysis of MdPIF4 in Malus domestica. International journal of molecular sciences 21, 7350.
Zheng, X., Xing, J., Zhang, K., Pang, X., Zhao, Y., Wang, G., Zang, J., Huang, R., and Dong, J. 2019. Ethylene response factor ERF11 activates BT4 transcription to regulate immunity to Pseudomonas syringae. Plant physiology 180, 1132-1151.
Zheng, Z., Qamar, S. A., Chen, Z., and Mengiste, T. 2006. Arabidopsis WRKY33 transcription factor is required for resistance to necrotrophic fungal pathogens. The Plant Journal 48, 592-605.
Zhu, T., Sun, Y., and Chen, X. 2022. Arabidopsis Tetraspanins Facilitate Virus Infection via Membrane-Recognition GCCK/RP Motif and Cysteine Residues. Frontiers in Plant Science 13.