Transcriptome analysis of Sinorhizobium meliloti during symbiosis

Abstract

Background: Rhizobia induce the formation on specific legumes of new organs, the root nodules, as a result of an elaborated developmental program involving the two partners. In order to contribute to a more global view of the genetics underlying this plant-microbe symbiosis, we have mined the recently determined Sinorhizobium meliloti genome sequence for genes potentially relevant to symbiosis. We describe here the construction and use of dedicated nylon macroarrays to study simultaneously the expression of 200 of these genes in a variety of environmental conditions, pertinent to symbiosis.

Results: The expression of 214 S. meliloti genes was monitored under ten environmental conditions, including free-living aerobic and microaerobic conditions, addition of the plant symbiotic elicitor luteolin, and a variety of symbiotic conditions. Five new genes induced by luteolin have been identified as well as nine new genes induced in mature nitrogen-fixing bacteroids. A bacterial and a plant symbiotic mutant affected in nodule development have been found of particular interest to decipher gene expression at the intermediate stage of the symbiotic interaction. S. meliloti gene expression in the cultivated legume Medicago sativa (alfalfa) and the model plant M. truncatula were compared and a small number of differences was found.

Conclusions: In addition to exploring conditions for a genome-wide transcriptome analysis of the model rhizobium S. meliloti, the present work has highlighted the differential expression of several classes of genes during symbiosis. These genes are related to invasion, oxidative stress protection, iron mobilization, and signaling, thus emphasizing possible common mechanisms between symbiosis and pathogenesis.

Figure 1

Global analysis of gene expression profiles in liquid cultures and symbiotic conditions. (a) Principal component analysis. Projection on the two main axes of principal gene analysis. A-E (blue) are profiles derived from cultured bacteria. A, minimal medium (Vmini) + 10 μM luteolin; B, rich medium; C, aerated Vmini; D, microoxic Vmini (strong oxygen limitation); E, microoxic Vmini. F-J (orange) are profiles derived from symbiotic bacteria. F, 1021-TE7; G, 1021-M. sativa; H, 1021-J6 mature nodules; I, 1021-J6 young nodules; J, bacA-J6. (b) Hierarchical clustering of gene-expression data. Each row represents a separate gene target (PCR product) on the macroarrays and each column (A-J) a specific bacterial growth condition as indicated above. The results presented represent the normalized expression level and are depicted according to the color scale shown at the bottom.