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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Molecular Plant Pathology Laboratory » Research » Publications at this Location » Publication #410226
Research Project: Development of Novel Disease Control Strategies Based on Virus and Viroid Biology

Location: Molecular Plant Pathology Laboratory

Title: Dissecting the role of bHLH transcription factors in the potato spindle tuber viroid (PSTVd)-tomato pathosystem using network approaches

Author
item AVINA-PADILLA, KATIA - National Laboratory Of Genomics And Biodiversity
item ZAMBADA-MORENO, OCTAVIO - National Laboratory Of Genomics And Biodiversity
item JUMENEZ-LIMAS, MARCO - Centro De Investigacion Cientifica Y De Educacion Superior De Ensenada
item Hammond, Rosemarie
item HERNANDEZ-ROSALES, MARIBEL - National Laboratory Of Genomics And Biodiversity

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/19/2025
Publication Date: 5/7/2025
Citation: Avina-Padilla, K., Zambada-Moreno, O., Jumenez-Limas, M.A., Hammond, R., Hernandez-Rosales, M. 2025. Dissecting the role of bHLH transcription factors in the potato spindle tuber viroid (PSTVd)-tomato pathosystem using network approaches. PLOS ONE. 20(5). Article e0318573. https://doi.org/10.1371/journal.pone.0318573.
DOI: https://doi.org/10.1371/journal.pone.0318573

Interpretive Summary: Viroids are small infectious RNAs that cause economically important diseases in many crop plants. Viroid infection disrupts host development and interferes with crucial physiological processes. In tomato, infection by potato spindle tuber viroid and several pospiviroid species results in reprogramming of gene expression profiles leading to symptoms of plant disease. In our study, co-expression modules of plant gene families were identified and their regulatory patterns in leaf and root tissues unveiled tissue-specific responses associated with specific transcriptional regulatory proteins. The improved understanding of the host response to viroid infection offers insights into strategies to enhance plant resistance to these pathogens and will of interest to plant pathologists and breeders.

Technical Abstract: Viroids, minimalist plant pathogens, present significant threats to crops by causing severe diseases. The use of high-throughput sequencing technologies for analyzing the transcriptomes of viroid-infected host plants has yielded informative information on gene regulation by these pathogens, however a complete understanding of the transcriptome data suffers from the inclusion of numerous genes of unknown function. Co-expression analysis addresses this by clustering genes into modules based onglobal gene expression levels. Our previous study emphasized basic helix-loop-helix protein (bHLH) transcriptional reprogramming in tomato in response to different potato spindle tuber viroid (PSTVd) strains. In the current research, we delve into tissue-specific gene modules, particularly in root and leaf tissues, governed by bHLH transcription factors during PSTVd infections. Utilizing public datasets that span Control (C; mock-inoculated), PSTVd-mild (M), and PSTVd-severe (S23) strains in time-course infections, we uncovered differentially expressed gene modules. These modules were functionally characterized, identifying essential hub genes. We identified the roles of bHLH transcription factors (TFs) in managing processes like photosynthesis and rapid membrane repair in infected roots. In leaves, external layer alterations influenced photosynthesis, linking bHLH TFs to distinct metabolic functions. Expanding on these findings, we explored bipartite networks, discerning both common and unique bHLH TF regulatory roles, notably highlighting the bifan motif's significance in these interactions. Through this holistic approach, we deepen our understanding of viroid-host interactions and the intricate regulatory mechanisms underpinning them.