Journal
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
Volume 23, Issue 11, Pages -Publisher
MDPI
DOI: 10.3390/ijms23115983
Keywords
regulation of gene expression; master transcription factors; microproteins; plant-pathogen bioinformatics; biological networks analysis; systems biology; non-coding RNAs; interactome
Funding
- internal USDA-ARS project [8042-22000-295-00D, CVU:227919, CVU:1147042, CVU:1035685]
- Fulbright Garcia-Robles foundation
- CONACyT
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This study used a network approach to analyze the transcription factors and differentially expressed target genes in tomato infected with mild and severe variants of PSTVd. The results identified specific transcription factors that regulate genes involved in critical signaling pathways. Functional enrichment analysis showed that these transcription factors are associated with metabolism, plant defense, signaling, and hormone-related processes. The study also found other transcription factors that are associated with symptom development.
Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.
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