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

Abstract

The soil-dwelling ␣-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 Ϸ10,000 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.expression ͉ Medicago ͉ microarray ͉ Sinorhizobium meliloti

Flavonoids and Auxin Transport Inhibitors Rescue Symbiotic Nodulation in the Medicago truncatula Cytokinin Perception Mutant cre1

“…To exclude the possibility that defects in flavonoids in the cre1 mutant prevented proper nod gene activation in the symbiont (Zhang et al, 2009), we used, instead of a wild-type strain, a genotype of S. meliloti that constitutively expresses nodD3, i.e., that produces Nod factors in the absence of nod gene-inducing flavonoids from the legume host (Barnett et al, 2004); hereafter, this strain is referred to as E65. This strain formed a significantly higher number of nodules on wild-type roots compared with the reference strain S. meliloti 1021 (Supplemental Figure 1).…”

“…The Sinorhizobium meliloti strain A2102, a triple nodD mutant for nodD1, nodD2, and nodD3 derived from Sm1021, containing the pE65 plasmid encoding a constitutively expressed copy of nodD3 (Barnett et al, 2004) was used for all inoculations. The E65 strain was maintained on Bergersen's Modified Medium (BMM) (Rolfe et al, 1980) supplemented with 10 µg/mL tetracycline and 100 µg/mL streptomycin (Sigma Chemicals).…”

“…As the cre1 mutant was partially defective in the induction of isoliquiritigenin, which can act as a nod gene inducer in S. meliloti (Zuanazzi et al, 1998), this may affect the ability of rhizobia to induce nodules in the cre1 mutant. However, in our study, we used the A2102 strain harboring the pE65 plasmid, which expresses the NodD3 gene from a constitutive promoter (Barnett et al, 2004). Therefore, it is unlikely that a deficiency in nod gene inducing flavonoids was the reason for the lack of nodulation in the cre1 mutant inoculated with this S. meliloti strain.…”

Dual transcriptional profiling of a bacterial/fungal confrontation: Collimonas fungivorans versus Aspergillus niger

“…We exploited the availability of genomic resources for both partners and took a transcriptomic approach to listen in on the dialog that goes on during their interaction on nutrientpoor plates. Typically, such approaches have been very valuable by offering new insight into the complexity of prokaryotic-host cross-talk (Barnett et al, 2004;Tailleux et al, 2008), including bacterial/fungal interactions (Schrey et al, 2005;van Rij et al, 2005;Deveau et al, 2007;Maligoy et al, 2008;Barret et al, 2009). However, in many of these studies only one partner was profiled, treating the other one as a black-box component of the biotic environment.…”

Genetic and biochemical characterization of arginine biosynthesis in Sinorhizobium meliloti 1021

“…The potential for genetic regulation of the S. meliloti arginine pathway thus remains an open question, although decreased expression of arg genes (and hipO1) in bacteroids versus cultured cells has been reported (Barnett et al, 2004). To address their importance in planta, we are determining the symbiotic phenotypes of the 1021 argE, argJ and argEJ mutants on alfalfa, along with the construction of hipO1 and hipO2 mutants for this purpose.…”