Posters - Schedules

Viroids are minimal plant pathogens that cause severe diseases in agronomic crops. Recently, the emergence of high-throughput technologies for viroid-infected hosts has become noticeable. However, plant genomes are known to have many genes with unknown functions, making interpretation challenging. Co-expression analysis overcomes this challenge since it uses global gene expression levels to cluster genes into modules. Previously, we have highlighted bHLH transcriptional reprogramming of gene regulatory networks specific to Potato spindle tuber viroid (PSTVd) variant infection in its tomato host. In this follow-up study, we employed publicly available datasets describing transcriptome-wide effects of PSTVd-tomato infection in root and leaf tissues. These datasets contain time-course experiments in three stages using Control (C), PSTVd-mild (M), and PSTVd-severe (S23) samples. Our results revealed tissue-specific gene modules differentially expressed and regulated by BHLH TFs during infection. We identified the hub genes in each module and characterized them functionally. For instance, in one module, genes are differentially expressed at 17 and 24 dpi in PSTVd-S23, and five hub genes are co-expressed and enriched in photosynthesis and plant defense functions. In addition, the gene modules identified were used to correlate with the disease conditions to reveal potential associations. Moreover, bipartite networks were constructed to identify the shared and unique regulation of BHLH-TFs in the above-mentioned experimental conditions. Finally, we identified bifan as the most enriched regulatory motif conserved and distributed along the analyzed biological networks.

Introduction: Bioactive compounds are a set of molecules with the synergistic action in cells, either as a source of cofactors, substrates for biosynthesis, or metabolic regulators. These compounds are commonly found in the human diet because they are secondary metabolites present in animals and plants, and the current importance of its study is mainly directed to the characterization of sources, the recognition of their molecular or cellular action (at a healthy level), or by its potential as drugs against different pathologies. Interestingly, molecular response to bioactive compounds is defined by the sensitivity of the related pathways to the synergic, allosteric, and interspecific regulation, that means key molecules like regulatory enzymes or transcription factors are modulated by inner or outer allosteric regulators. In consequences, it is possible to propose a possible molecular rearrangement at several molecular levels, which include gene expression as the basic state and whose validation requires a massive and intuitive integration of data in bioinformatics. Method: In consequence, to support this statement, we explore the genetic level by defining the most significant bioactives-response genes (BRG) by the processing of several datasets related to gene expression levels for bioactive compounds deposit in arrayexpress database, and then was exploring the configuration of genomics elements in the promoter region of those genes. Patterns of genomics elements were defined by hierarchical clustering, and the significant patterns were defined by unsupervised algorithms. Results: Herein, we found patterns based Simple_repeat and Transposable elements as significant structural elements in the promoter region of the most sensitive genes to bioactive compounds, besides the functional enrichment shows key nodes of sensitivity that could boost pathways in common metabolisms and cellular processes. Interestingly, standard metabolic pathways (like pentose phosphate pathway) or cellular adaptations (like cytoskeleton remodelling) show some bioactive-response genes as critical nodes of sensitivity, that could relate to common actions described to bioactive compounds as antioxidant or positive regulators of apoptosis.

Introduction: Bioactive compounds are a set of molecules with the synergistic action in cells, either as a source of cofactors, substrates for biosynthesis, or metabolic regulators. These compounds are commonly found in the human diet because they are secondary metabolites present in animals and plants, and the current importance of its study is mainly directed to the characterization of sources, the recognition of their molecular or cellular action (at a healthy level), or by its potential as drugs against different pathologies. Interestingly, molecular response to bioactive compounds is defined by the sensitivity of the related pathways to the synergic, allosteric, and interspecific regulation, that means key molecules like regulatory enzymes or transcription factors are modulated by inner or outer allosteric regulators. In consequences, it is possible to propose a possible molecular rearrangement at several molecular levels, which include gene expression as the basic state and whose validation requires a massive and intuitive integration of data in bioinformatics. Method: In consequence, to support this statement, we explore the genetic level by defining the most significant bioactives-response genes (BRG) by the processing of several datasets related to gene expression levels for bioactive compounds deposit in arrayexpress database, and then was exploring the configuration of genomics elements in the promoter region of those genes. Patterns of genomics elements were defined by hierarchical clustering, and the significant patterns were defined by unsupervised algorithms. Results: Herein, we found patterns based Simple_repeat and Transposable elements as significant structural elements in the promoter region of the most sensitive genes to bioactive compounds, besides the functional enrichment shows key nodes of sensitivity that could boost pathways in common metabolisms and cellular processes. Interestingly, standard metabolic pathways (like pentose phosphate pathway) or cellular adaptations (like cytoskeleton remodelling) show some bioactive-response genes as critical nodes of sensitivity, that could relate to common actions described to bioactive compounds as antioxidant or positive regulators of apoptosis.