Transcription reprogramming during root nodule development in Medicago truncatula

Abstract

Many genes which are associated with root nodule development and activity in the model legume Medicago truncatula have been described. However information on precise stages of activation of these genes and their corresponding transcriptional regulators is often lacking. Whether these regulators are shared with other plant developmental programs also remains an open question. Here detailed microarray analyses have been used to study the transcriptome of root nodules induced by either wild type or mutant strains of Sinorhizobium meliloti. In this way we have defined eight major activation patterns in nodules and identified associated potential regulatory genes. We have shown that transcription reprogramming during consecutive stages of nodule differentiation occurs in four major phases, respectively associated with (i) early signalling events and/or bacterial infection; plant cell differentiation that is either (ii) independent or (iii) dependent on bacteroid differentiation; (iv) nitrogen fixation. Differential expression of several genes involved in cytokinin biosynthesis was observed in early symbiotic nodule zones, suggesting that cytokinin levels are actively controlled in this region. Taking advantage of databases recently developed for M. truncatula, we identified a small subset of gene expression regulators that were exclusively or predominantly expressed in nodules, whereas most other regulators were also activated under other conditions, and notably in response to abiotic or biotic stresses. We found evidence suggesting the activation of the jasmonate pathway in both wild type and mutant nodules, thus raising questions about the role of jasmonate during nodule development. Finally, quantitative RT-PCR was used to analyse the expression of a series of nodule regulator and marker genes at early symbiotic stages in roots and allowed us to distinguish several early stages of gene expression activation or repression.

Figure 1. Transcriptome analysis of root nodules induced by wild-type and mutant strains of Sinorhizobium meliloti.

A, B, C: 50 µm sections of representative 10-day-old nodules analysed in the experiment, respectively induced by wild-type (A), exoA (B) and bacA (C) S. meliloti strains containing a hemA:lacZ reporter; the blue color indicates the presence of bacteria revealed by beta-galactosidase activity. Bars = 100 µm. D: number of differentially regulated genes, in comparison to non-inoculated nitrogen-starved roots (adjusted Pval≤0.05 ratio ≥1.5), with white and grey columns representing and down- and up- regulated genes respectively. E: fraction of genes found to be up-regulated only in this nodule sample. WT4, 10, 14, NN correspond to nodules induced by wild-type S. meliloti 2011 at 4, 10, 14 and 16 days post-inoculation; NN nodules were treated for 2 days with 10 mM NH₄NO₃ before harvesting.

Figure 2. Hierarchical analysis of genes differentially regulated in Medicago truncatula nodules as compared to nitrogen-starved roots.

These genes were identified by a comparison of non-inoculated roots and isolated nodule samples using Mt16KPlus microarrays The hierarchical analysis was carried out with Pearson correlation and average linkage. The green and pink colors indicate down- and up-regulated genes respectively, following the color scale shown on the left (with fold ratios indicated as log2 values).

Figure 3. Expression of the leghemoglobin gene family in nodule samples (MapMan representation).

Gene expression was analysed with Mt16KPlus microarrays, by comparison to nitrogen-starved uninoculated roots. Each square represents a different gene probe. Up-regulated genes are represented as red squares, following the color scale shown on the right (with fold ratios indicated as log2 values). WT4, 10, 14, NN correspond to nodules induced by wild-type S. meliloti 2011 at 4, 10, 14 and 16 days post-inoculation; NN nodules were treated for 2 days with 10 mM NH₄NO₃ before harvesting. exoA, bacA and fixJ correspond to nodules induced by indicated mutant strains of S. meliloti at 10 days post-inoculation.

Figure 4. Graphical representation of the major expression classes identified in Medicago truncatula nodules.

The classes were defined from the genes scored as differentially regulated in Medicago truncatula nodules as compared to nitrogen-starved uninoculated roots. Color code: blue = down-regulated in nodules; black = weak induction; brown = maximal induction; grey = not considered for pattern definition.

Figure 5. Localisation by in situ hybridisation of MtCKX1 cytokinin oxidase transcripts in Medicago truncatula nodule.

Use of antisense (A) or sense (B) digoxygenin-labelled RNA probes: hybridization signals were detected only with the antisense probe, in the zone 2 and upper zone 3, and appeared brownish on these methyl green-stained nodule sections. (I), (II) and (III) indicate the nodule zone 1, 2 and 3 respectively. Bar = 50 µm.

Figure 6. Expression pattern of secondary metabolism genes in wild type and S. meliloti exoA-induced nodules.

Nodules were harvested at 4 (WT4) or 10 (WT10, exoA) days post inoculation and gene expression was analysed using Mt16KPlus microarrays, by comparison to nitrogen-starved uninoculated roots. Each square represents a different gene probe (MapMan representation).

Figure 7. Graphical representation of the different expression patterns identified in Medicago truncatula roots.

Classes were defined from the genes scored as differentially regulated in Medicago truncatula roots by Q-RT-PCR analyses, following 10⁻⁸ M NF addition (24 h incubation, in the sunn sickle double mutant background) or S. meliloti inoculation as compared to control roots. WT1 and WT3 respectively mean one or three day post-inoculation with wild type S. meliloti. Color code: blue = down-regulated; white = no differential expression; brownish = up-regulated (the darkest corresponding to maximal induction).