Variability of plant transcriptomic responses under stress acclimation: a review from high throughput studies

Abstract

Plant transcriptomes are complex entities shaped spatially and temporally by a multitude of stressors. The aim of this review was to summarize the most relevant transcriptomic responses to selected abiotic (UV radiation, chemical compounds, drought, suboptimal temperature) and biotic (bacteria, fungi, viruses, viroids) stress conditions in a variety of plant species, including model species, crops, and medicinal plants. Selected basic and applicative studies employing RNA-seq from various sequencing platforms and single-cell RNA-seq were involved. The transcriptomic responsiveness of various plant species and the diversity of affected gene families were discussed. Under stress acclimation, plant transcriptomes respond particularly dynamically. Stress response involved both distinct, but also similar gene families, depending on the species, tissue, and the quality and dosage of the stressor. We also noted the over-representation of transcriptomic data for some plant organs. Studies on plant transcriptomes allow for a better understanding of response strategies to environmental conditions. Functional analyses reveal the multitude of stress-affected genes as well as acclimatory mechanisms and suggest metabolome diversity, particularly among medicinal species. Extensive characterization of transcriptomic responses to stress would result in the development of new cultivars that would cope with stress more efficiently. These actions would include modern methodological tools, including advanced genetic engineering, as well as gene editing, especially for the expression of selected stress proteins in planta and for metabolic modifications that allow more efficient synthesis of secondary metabolites.

Keywords: RNA-seq; acclimation; differentially expressed genes; plant transcriptome; stress response.

FIGURE 1

Plant transcriptome as a central stress-responsive entity in the cell. The plant transcriptome is a highly dynamic structure in plant cells (bluish ovals at the top). It links genomic, proteomic, and metabolomic levels, responding on a multidimensional scale, across various tissues, and along time (the center). The response of plant nuclear and organellar transcriptomes is also shaped by a number of factors, including abiotic and biotic stressors (green and black arrows encompassing the light brown central rectangle), which affect the differential expression pattern of various gene sets (bottom). For proper organellar biogenesis under stress acclimation, inter-organellar signaling between actively transcribed nuclear, plastid, and mitochondrial genomes is indispensable (small arrows within marked organelles on the panel in the center and to the left). The diversity of transcriptomes from model, crop, and medicinal species (bottom) under selected stress conditions was discussed in this paper. More details in the text.

FIGURE 2

Comparison of the most relevant gene ontology (GO:) terms of plant genes and transcription factors active under abiotic stress conditions from various RNA-seq studies. The data were presented in Venn diagrams (drawn by Venny v. 2.1 from https://bioinfogp.cnb.csic.es/tools/venny/). The top enriched GO: terms (mostly relevant molecular functions and biological procesess) as well as transcription factors for regulated genes from the discussed studies were indicated. The data specific for the given stressor were denoted in italics and by different font colors (for the chemical treatment and UV radiation in blue, for drought in brown, for cold and freeze in green and for heat stress in red). GO: terms and transcription factors common for responses to all abiotic stressors were displayed within yellow text boxes. More details in the text.

FIGURE 3

Comparison of the most relevant gene ontology (GO:) terms of plant genes and transcription factors active under biotic stress conditions from various RNA-seq studies. The data were presented in Venn diagrams (drawn by Venny v. 2.1 from https://bioinfogp.cnb.csic.es/tools/venny/). The top enriched GO: terms (mostly relevant molecular functions and biological procesess) as well as transcription factors for regulated genes from the discussed studies were indicated. The data specific for the given stressor were denoted in italics and by different font colors (for bacterial infections in blue, for virus/viroid infections in brown and for fungal infections in green). GO: terms and transcription factors common for responses to all abiotic stressors were displayed within yellow text boxes. More details in the text.

FIGURE 4

The detailed number of publications per year related to RNA-seq and specified stressors (values indicated above each bar; subterms indicated by the various color and checking pattern in the histogram). The key words used in the NCBI PubMed search (https://pubmed.ncbi.nlm.nih.gov/) included: plant, RNA-seq, and the given subterm (indicated in the legend below the histogram). The data for “UV” (in dark magenta), “drought” (in gray), “heat” (in orange), “cold” (in blue) and “pathogen” (in green; the joint data for bacterial, fungal and viral/viroid infections) were presented from 2010 onwards. The analysis was performed in September 2024.