Abstract
BackgroundLegumes form root nodules to house nitrogen fixing bacteria of the rhizobium family. The rhizobia are located intracellularly in the symbiotic nodule cells. In the legume Medicago truncatula these cells produce high amounts of Nodule-specific Cysteine-Rich (NCR) peptides which induce differentiation of the rhizobia into enlarged, polyploid and non-cultivable bacterial cells. NCRs are similar to innate immunity antimicrobial peptides. The NCR gene family is extremely large in Medicago with about 600 genes.ResultsHere we used the Medicago truncatula Gene Expression Atlas (MtGEA) and other published microarray data to analyze the expression of 334 NCR genes in 267 different experimental conditions. We find that all but five of these genes are expressed in nodules but in no other plant organ or in response to any other biotic interaction or abiotic stress tested. During symbiosis, none of the genes are induced by Nod factors. The NCR genes are activated in successive waves during nodule organogenesis, correlated with bacterial infection of the nodule cells and with a specific spatial localization of their transcripts from the apical to the proximal nodule zones. However, NCR expression is not associated with nodule senescence. According to their Shannon entropy, a measure expressing tissue specificity of gene expression, the NCR genes are among the most specifically expressed genes in M. truncatula. Moreover, when activated in nodules, their expression level is among the highest of all genes.ConclusionsTogether, these data show that the NCR gene expression is subject to an extreme tight regulation and is only activated during nodule organogenesis in the polyploid symbiotic cells.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-712) contains supplementary material, which is available to authorized users.
Highlights
Legumes form root nodules to house nitrogen fixing bacteria of the rhizobium family
The transcriptome compendium is mostly derived from the M. truncatula genotype ‘Jemalong’ and contains data sets obtained from the genotypes ‘R108’ and ‘F83005.5’ all specific experiments discussed below were obtained with the ‘Jemalong’ genotype
An obvious global pattern instantly revealed by the heat map is that the nearly complete 334 Nodule-specific Cysteine-Rich (NCR) gene set is only expressed in nodules except for one experiment marked with the red arrowhead, which is a sample annotated in the Medicago truncatula Gene Expression Atlas (MtGEA) compendium as mycorrhizal roots but is contaminated with nodules (Additional file 2: Figure S1)
Summary
Legumes form root nodules to house nitrogen fixing bacteria of the rhizobium family. For the purpose of this symbiosis, the plant host forms new, specific organs on its roots called nodules, inside which the symbiotic rhizobia are housed, fix nitrogen (i.e. the enzymatic reduction of nitrogen gas to ammonium) and transfer the ammonium to the plant. Nodules contain several thousand endoreduplicated giant symbiotic cells, which are each infected with thousands of intracellular rhizobia. These symbiotic cells are adapted to the symbiosis, to the metabolic exchange with the nitrogen fixing cells have about 80-fold larger cell volume and endoploidy levels up to 64C compared to the diploid (2C) progenitor cells. Polyploid host cells may be a well suited adaptation as an interaction site for nutrient exchange with symbiotic microorganisms and some parasites may have evolved to exploit this
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