Potential Networks of Nitrogen-Phosphorus-Potassium Channels and Transporters in Arabidopsis Roots at a Single Cell Resolution

Abstract

Nitrogen (N), phosphorus (P), and potassium (K) are three major macronutrients essential for plant life. These nutrients are acquired and transported by several large families of transporters expressed in plant roots. However, it remains largely unknown how these transporters are distributed in different cell-types that work together to transfer the nutrients from the soil to different layers of root cells and eventually reach vasculature for massive flow. Using the single cell transcriptomics data from Arabidopsis roots, we profiled the transcriptional patterns of putative nutrient transporters in different root cell-types. Such analyses identified a number of uncharacterized NPK transporters expressed in the root epidermis to mediate NPK uptake and distribution to the adjacent cells. Some transport genes showed cortex- and endodermis-specific expression to direct the nutrient flow toward the vasculature. For long-distance transport, a variety of transporters were shown to express and potentially function in the xylem and phloem. In the context of subcellular distribution of mineral nutrients, the NPK transporters at subcellular compartments were often found to show ubiquitous expression patterns, which suggests function in house-keeping processes. Overall, these single cell transcriptomic analyses provide working models of nutrient transport from the epidermis across the cortex to the vasculature, which can be further tested experimentally in the future.

Keywords: NPK transport networks; expression analysis; nitrate transport; nutrient transporters; phosphate transport; potassium transport; root single cell transcriptomics.

FIGURE 1

Plant growth highly depends on the continual nutrient supplies. Without N, P, or K (0 mM, 1/6 MS), 5-days old Arabidopsis seedlings displayed stunted shoot growth (top rows) and modified root architectures including primary root and root hair growth (bottom rows) compared to the sufficient-nutrient (1/6 MS) conditions. MS for Murashige and Skoog media.

FIGURE 2

Expression of the low-affinity NPF transporters in Arabidopsis root single cells, (A,B) NPF1-2, (C) NPF3/4, and (D–G) NPF5-8. In dot plots, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 3

Expression of the high-affinity NRT transporters in Arabidopsis root single cells. In dot plot, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 4

Expression of the (A) CLC antiporters and (B) SLAC1 channels in Arabidopsis root single cells. In dot plots, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount). The expression of CLCg was not detected in any single cells.

FIGURE 5

Potential network of nitrate (NO₃^–) channels and transporters in the root system of 5–7 days old Arabidopsis seedlings grown under the normal growth conditions. Expressed NO₃^– transporters involved in longitudinal transport (left) at the meristematic zone and radial transport (right) at the elongation/maturation zones were shown. Nitrate transporter genes not expressed under the normal growth conditions were excluded.

FIGURE 6

Expression of the high-affinity PHT1 transporters in Arabidopsis root single cells. In dot plot, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 7

Expression of the (A) PHT2/4, (B) PHT3 and (C) VPT and G3Pp transporters in Arabidopsis root single cells. In dot plots, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 8

Expression of the PHO1 transporters in Arabidopsis root single cells. In dot plot, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 9

Potential network of phosphate (Pi) transporters in the root system of 5–7 days old Arabidopsis seedlings grown under the normal growth conditions. Expressed Pi transporters involved in longitudinal transport (left) at the meristematic zone and radial transport (right) at the elongation/maturation zones were shown. Pi transporter genes not expressed under the normal growth conditions were excluded.

FIGURE 10

Expression of the (A) Shaker-type channels (B) KUP transporters in Arabidopsis root single cells. In dot plots, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 11

Expression of the (A) CHX, (B) KEA and (C) NHX antiporters in Arabidopsis root single cells. In dot plots, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 12

Expression of the TPK channels in Arabidopsis root single cells. In dot plot, the circle size represents the proportion (%) of cells expressing a given gene, and the color of scale bar represents the mean expression (natural log +1 pseudocount).

FIGURE 13

Potential network of potassium (K⁺) channels and transporters in the root system of 5–7 days old Arabidopsis seedlings grown under the normal growth conditions. Expressed K⁺ transporters involved in longitudinal transport (left) at the meristematic zone and radial transport (right) at the elongation/maturation zones were shown. K⁺ transporter genes not expressed under the normal growth conditions were excluded.