Plant resistance from a systems biology perspective: the role of biological networks
DOI:
https://doi.org/10.52673/18570461.26.2-81.05Keywords:
network biology, plant resistance to stress, abiotic stress, biotic stressAbstract
Plants are sessile organisms, that are continuously exposed to biotic and abiotic stresses, which has driven the evolution of complex adaptation and resistance mechanisms. These mechanisms result from coordinated interactions among genes, proteins, metabolites, and hormonal signaling pathways. One-dimensional approaches focused on individual genes or proteins, are insufficient to capture this complexity. Network biology provides an integrative framework for studying plant responses to stress. This article highlights, from a comparative perspective, the role of biological networks in elucidating the regulatory interactions underlying processes involved in plant resistance to biotic stress (pathogens, pests) and abiotic stress (drought, salinity, extreme temperatures, nutrient deficiency), as well as the associated limitations and challenges, including the static nature of most networks, the heterogeneity and incompleteness of molecular data, the difficulty of establishing causal relationships, and the necessity of experimental validation of predictions.
References
1. Cui, H.; Tsuda, K.; Parker, J.E. Effector-triggered immunity: from pathogen perception to robust defense, în: Annual Review of Plant Biology, 2015, 66: 487-511. https://doi.org/10.1146/annurev-arplant-050213-040012
2. Wang, W.; Vinocur, B.; Altman, A. Plant responses to drought, salinity and extreme temperatures: towards genetic engineering for stress tolerance, în: Planta, 2003, 218(1): 1-14. https://doi.org/10.1007/s00425-003-1105-5
3. Kitano, H. Systems biology: a brief overview, în: Science, 2002, 295(5560): 1662-1664. https://doi.org/10.1126/science.1069492
4. Delplace, F.; Huard-Chauveau, C.; Berthomé,R.; Roby, D. Network organization of the plant immune system: from pathogen perception to robust defense induction, în: Plant J., 2022, 109(2):447-470. ttps://doi.org/10.1111/tpj.15462
5. Barabási, A.L.; Oltvai, Z.N. Network biology: understanding the cell's functional organization, în: Nature Reviews Genetics, 2004, 5:101-113. https://doi.org/10.1038/nrg1272
6. Albert, R. Scale-free networks in cell biology, în: Journal of Cell Science, 2005, 118: 4947-4957. https://doi.org/10.1242/jcs.02714
7. Barabási, A.L.; Gulbahce, N.; Loscalzo, J. Network medicine: a network-based approach to human disease, în: Nature Reviews Genetics, 2011, 12:56-68. https://doi.org/10.1038/nrg2918
8. Vidal, M.; Cusick, M.E.; Barabási, A.L. Interactome networks and human disease, în: Cell, 2011, 144(6):986-998. https://doi.org/10.1016/j.cell.2011.02.016
9. Dablander, F.; Hinne, M. Node centrality measures are a poor substitute for causal inference, în: Scientific Reports, 2019, 9:6846. https://doi.org/10.1038/s41598-019-43033-9
10. Wang, M.; Wang, H.; Zheng, H. A Mini Review of Node Centrality Metrics in Biological Networks, în: International Journal of Network Dynamics Intelligence, 2022, 1(1):99-110. https://doi.org/10.53941/ijndi0101009
11. Andersen, E.J.; Shaukat, A.; Byamukama, E.; Yang, Y.; Madhav, P.N. Disease resistance mechanisms in plants, în: Genes, 2018, 9(7):339. https://doi.org/10.3390/genes9070339
12. Zhang, J.; Coaker, G.; Zhou, J.M.; Dong, X. Plant immune mechanisms: from reductionistic to holistic points of view, în: Molecular Plant, 2020, 13(10):1358-1378. https://doi.org/10.1016/j.molp.2020.09.007
13. Janni, M.; Gullì, M.; Maestri, E.; Marmiroli, M.; Valliyodan, B.; Nguyen, H.T.; Marmiroli, N. Molecular and genetic bases of heat stress responses in crop plants, în: Journal of Experimental Botany, 2020, 71(13):3780-3802. https://doi.org/10.1093/jxb/eraa034
14. Rivas, S.; Thomas, C.M. Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum, în: Annual Review of Phytopathology, 2005, 43:395-436. https://doi.org/10.1146/annurev.phyto.43.040204.140224
15. Kumar, A., et all. Adapting Crops to Rising Temperatures: Understanding Heat Stress and Plant Resilience Mechanisms, în: J. Mol. Sci., 2025, 26(21) 10426. https://doi.org/10.3390/ijms262110426
16. Vandereyken, K.; Leene, J. van de; De Coninck, B.; Cammue, B.P.A. Hub protein controversy: taking a closer look at plant stress response hubs, în: Frontiers in Plant Science, 2018, 9:694. https://doi.org/10.3389/fpls.2018.00694
17. Weckwerth, W. Green systems biology - from single genomes to ecosystems, în: Journal of Proteomics, 2011, 75(1):284-305. https://doi.org/10.1016/j.jprot.2011.07.010
18. Dusad, V.; Thiel, D.; Barahona, M.; Keun, H.C.; Oyarzún, D.A. Opportunities at the interface of network science and metabolic modeling, în: Frontiers in Bioengineering and Biotechnology, 2021, 8:591049:1-9. https://doi.org/10.3389/fbioe.2020.591049
19. Wang, R.; Li, J.; Yan, L. Role of ROS signaling in plant defense against vascular pathogens, în: Current Opinion in Plant Biology, 2024, V.81. https://doi.org/10.1016/j.pbi.2024.102617
20. Rajput, V.D.; Harish, Singh, R.K.; Verma, K.K.; Sharma, L.; Quiroz-Figueroa, F.R.; Meena, M.; Gour, V.S.; Minkina, T.; Sushkova, S. et al. Recent developments in enzymatic antioxidant defence mechanism in plants with special reference to abiotic stress, în: Biology, 2021, 10(4):267. https://doi.org/10.3390/biology10040267
21. Lupașcu, G.A.; Rudakova, A.; Rudakov, S.; Cherdivară, A.; Gavzer, S.; Kristya, N. Influence of temperature and fungal pathogens on the activity of peroxidases in common wheat, în: Buletinul Academiei de Ştiinţe a Moldovei. Ştiinţele vieţii, 2022, nr. 3(347): 54-61. https://doi.org/10.52388/1857-064X.2022.3.06
22. Lupașcu, G.; Andronic, L.; Smerea, S.; Mihnea, N. Rolul relațiilor gazdă-patogen în declanșarea bolilor la plante și identificarea genotipurilor rezistente, în: Akademos, 2019, nr. 3(54): 33-39. DOI: 10.5281/zenodo.3525081
23. Cauș, M.; Dascaliuc, A.; Borozan, P. Activitatea catalazei, peroxidazei și peroxidării lipidelor în rădăcinile porumbului sub influența șocului termic și a reglalgului, în: Protecţia plantelor - realizări şi perspective, 2023, nr. 57: 301-307. https://doi.org/10.53040/ppap2023.44
24. Cauș, M.; Ralea, T., Dascaliuc, A. Influența șocului termic asupra activității catalazei și eficienței fotosintetice a frunzelor de cimișir (Buxus sempervirens), în: Ştiinţa în Nordul Republicii Moldova: realizări, probleme, perspective, 2021: 37-41.
25. Duca, M. Aspecte privind mecanismele de rezistență ale florii-soarelui la lupoaie, în: Akademos, 2019, nr. 4(55): 34-43. DOI: 10.5281/zenodo.3631297
26. Bai, W.; Cheng, L.; Li, W., et al. Machine learning assists prediction of genes responsible for plant specialized metabolite biosynthesis by integrating multi-omics data, în: BMC Genomics, 2024, 25:418. https://doi.org/10.1186/s12864-024-10258-6
27. Tucci, A.; Flores-Vergara, M.A.; Franks, R.G. Machine learning inference of gene regulatory networks in developing Mimulus seeds, în: Plants, 2024, 13(23):3297: 2-13. https://doi.org/10.3390/plants13233297
28. Hegde, A.; Nguyen, T.; Cheng, J. Machine learning methods for gene regulatory network inference, în: Briefings in Bioinformatics, 2025, 26 (5). https://doi.org/10.1093/bib/bbaf470
29. Yao, J.; Marand, A.P.; Bai, Y.; Schmitz, R.J.; Fan, L. Advances in plant spatial multi-omics data analysis, în: Trends in Plant Science, 2026, vol. 31(3):337-352. https://doi.org/10.1016/j.tplants.2025.10.005
30. Cutler, S.R. et al. Abscisic acid: emergence of a core signaling network, în: Annual Review of Plant Biology, 2010, 61:651-679. https://doi.org/10.1146/annurev-arplant-042809-112122
31. Anee, T.I.; Sewelam, N.A.; Bautista, N.S., et al. Roles of ROS and NO in Plant Responses to Individual and Combined Salt Stress and Waterlogging, în: Antioxidants. 2025, 14, 1455: 2-35. https://doi.org/10.3390/antiox14121455
32. Jones, J.D.G.; Dangl, J.L. The plant immune system, în: Nature, 2006, 444:323-329. https://doi.org/10.1038/nature05286
33. Liu Yu.; He, Ch. A review of redox signaling and the control of MAP kinase pathway in plants, în: Redox Biology, 2017, vol. 11:192-204. https://doi.org/10.1016/j.redox.2016.12.009
34. Zhu, J.; Moreno-Pérez, A.; Coaker, G. Understanding plant pathogen interactions using spatial and single-cell technologies, în: Communications Biology, 2023, vol. 6, art. 814. https://doi.org/10.1038/s42003-023-05156-8
35. Liping, S.; Congcong, T.; Xinyi, R., et al. Spatial transcriptomics reveals the spatiotemporal response of garden asparagus stem cells to Phomopsis asparagi infection, în: Phytopathology Research, 2026, vol. 8(4): 2-19. https://doi.org/10.1186/s42483-025-00398-2
36. Wiesel, L.; Newton, A.C., Elliott, I., et al. Molecular effects of resistance elicitors from biological origin and their potential for crop protection, în: Frontiers in Plant Science, 2014, vol. 5. https://doi.org/10.3389/fpls.2014.00655
