A dual-genome Symbiosis Chip for coordinate study of signal exchange and development in a prokaryote-host interaction

Abstract

The soil-dwelling alpha-proteobacterium Sinorhizobium meliloti engages in a symbiosis with legumes: S. meliloti elicits the formation of plant root nodules where it converts dinitrogen to ammonia for use by the plant in exchange for plant photosynthate. To study the coordinate differentiation of S. meliloti and its legume partner during nodule development, we designed a custom Affymetrix GeneChip with the complete S. meliloti genome and approximately 10,000 probe sets for the plant host, Medicago truncatula. Expression profiling of free-living S. meliloti grown with the plant signal molecule luteolin in defined minimal and rich media or of strains altered in the expression of key regulatory proteins (NodD1, NodD3, and RpoN) confirms previous data and identifies previously undescribed regulatory targets. Analyses of root nodules show that this Symbiosis Chip allows the study of gene expression in both partners simultaneously. Our studies detail nearly 5,000 transcriptome changes in symbiosis and document complex transcriptional profiles of S. meliloti in different environments.

Fig. 1.

Replicon distribution of coding probe sets increased in bacteroids or with nodD3 overexpression.

Fig. 2.

Relative proportion of plant and bacterial probe sets increased in WT vs. mutant nodules. The groups of plant (Left) and bacterial (Right) probe sets that increased expression only in WT nodules are shown in orange. Those that increased only in fixJ^– mutant nodules are shown in blue. Increases that occurred in both WT and mutant nodules are represented by the overlap.