Transcript Abundance Explains mRNA Mobility Data in Arabidopsis thaliana

Abstract

Recently, a large population of mRNA was shown to be able to travel between plant organs via sieve elements as a putative long-distance signaling molecule. However, a mechanistic basis by which transcripts are selected for transport has not yet been identified. Here, we show that experimental mRNA mobility data in Arabidopsis can be explained by transcript abundance and half-life. This suggests that the majority of identified mobile transcripts can be accounted for by non-sequence-specific movement of mRNA from companion cells into sieve elements.

Figure 1.

Workflow for the Simulation of mRNA Mobility. (A) mRNA abundance model. Green boxes represent cells, with the side facing inwards being adjacent to sieve elements. The rows of cells represent different simulation runs and different transcription rates. Blue diffusion paths indicate simulations in which the transcript was considered to be mobile, and red indicates those in which the transcript was nonmobile. (B) Output of the abundance model (left, mobility versus abundance plot) was combined with experimental mRNA abundance data to predict the distributions for mobile and nonmobile mRNA (see Methods).

Figure 2.

An Abundance Model of mRNA Mobility Captures the Experimental mRNA Distributions. (A) Fitted and experimentally derived P(mobile) curve; 95% experimental confidence intervals are shown. The experimental P(mobile) was estimated as the ratio of the number of mobile over nonmobile transcripts, binned by abundance. The confidence interval was calculated using the Clopper-Pearson Exact Binomial method. (B) Experimental (left) and modeled (right) abundance distributions of mobile and nonmobile mRNA using the fitted P(mobile) curve. (C) Experimental and predicted abundance distribution for mobile mRNA only; 95% confidence intervals are shown, calculated using the Clopper-Pearson Binomial method.

Figure 3.

Mobile Transcripts May Be Preferentially Expressed Proximal to Sieve Elements. The transcript expression ratio in cells proximal to the sieve element relative to the rest of the leaf: in the bundle sheath (B.S.; [A]) and in companion cells (C.C.; [B]). The statistical significance of the difference of the means, P value, was calculated using Welch’s t test. Abundance data were taken from Mustroph et al. (2009), Aubry et al. (2014), and Thieme et al. (2015); mobility classification was from Thieme et al. (2015).

Figure 4.

The Distribution of Half-Life for Experimentally Determined Mobile and Nonmobile mRNA Populations. Data are taken from Narsai et al. (2007) and Thieme et al. (2015); 95% Clopper-Pearson binomial confidence intervals are shown.

Figure 5.

Transcript Mobility as a Function of Transcript Length. This plot shows the mRNA abundance in the distal tissue as a function of transcript length. Data are taken from Thieme et al. (2015). P values were computed from Spearman’s rank correlation; the moving average (red) was calculated with a window size of 300.