Transcriptional Reprogramming of Legume Genomes: Perspective and Challenges Associated With Single-Cell and Single Cell-Type Approaches During Nodule Development

Abstract

Transcriptomic approaches revealed thousands of genes differentially or specifically expressed during nodulation, a biological process resulting from the symbiosis between leguminous plant roots and rhizobia, atmospheric nitrogen-fixing symbiotic bacteria. Ultimately, nodulation will lead to the development of a new root organ, the nodule. Through functional genomic studies, plant transcriptomes have been used by scientists to reveal plant genes potentially controlling nodulation. However, it is important to acknowledge that the physiology, transcriptomic programs, and biochemical properties of the plant cells involved in nodulation are continuously regulated. They also differ between the different cell-types composing the nodules. To generate a more accurate picture of the transcriptome, epigenome, proteome, and metabolome of the cells infected by rhizobia and cells composing the nodule, there is a need to implement plant single-cell and single cell-types strategies and methods. Accessing such information would allow a better understanding of the infection of plant cells by rhizobia and will help understanding the complex interactions existing between rhizobia and the plant cells. In this mini-review, we are reporting the current knowledge on legume nodulation gained by plant scientists at the level of single cell-types, and provide perspectives on single cell/single cell-type approaches when applied to legume nodulation.

Single-Cell Metabolic Profiling: Metabolite Formulas from Isotopic Fine Structures in Heterogeneous Plant Cell Populations

“…At 21 days postinoculation, the root nodule is considered mature. However, as our SEM images have revealed, the individual infected plant cells can exist at different infection stages . These can be defined by the plant cellular volume, bound by the cell wall, fully or partially occupied by the bacteroids.…”

Gene Expression in Nitrogen-Fixing Symbiotic Nodule Cells in Medicago truncatula and Other Nodulating Plants

“…These new methods include single cell-type or single cell transcriptome analysis. Single cell types or single cells or the corresponding nuclei could be obtained through LCM, through isolating nuclei tagged in specific cell types (INTACT), or through flow cytometry and sorting of nuclei based on genome size (Figure 4; Libault, 2018). The latter technique could also be combined with fluorescent labeling of nuclei in specific cells in transgenic plant lines with cell type-specific promoters driving the expression of a fluorescent marker.…”

Metabolomic profiling of wild‐type and mutant soybean root nodules using laser‐ablation electrospray ionization mass spectrometry reveals altered metabolism

“…To determine the molecular mechanisms involved in nodulation, researchers have utilized transcriptomics and proteomics to identify and characterize genes and proteins critical for the symbiosis (Stacey et al, 2006;Libault, 2018). Relatively few studies have explored the nodule metabolome.…”