Table 1.
Comparison of transcriptome profiles used in the study.
Figure 1.
Expression profile of Rm1021 genes under low vs. high nitrogen.
The expression ratio of the 609 genes identified in the study as either nitrogen stress responsive (Cluster I and II) and/or affected by mutations in the GlnD/GlnBK regulatory cascade (Cluster III). 1– wgeA, wgdB, wgdA, wggR, and wgcA; 2– aap operon; 3a – rhs, rhb, and rhr region; 3b – SMb21429, SMb21430, SMb21431, SMb21432– Putative iron ABC transporter; 3c – hmu region; 3d – SMc01657, SMc01658, SMc01659; 4– nosR/Z, nnrU – denitrification regulator protein; 5– pho region; 6– fixN region; 7– carbon fixation.
Figure 2.
Comparison of log2-transformed microarray and qRT-PCR data of 7 representative genes differentially expressed in Rm1021 cells under high vs. low nitrogen.
Figure 3.
Distribution of differentially expressed genes in miroarray profiles.
Cluster I, genes upregulated under nitrogen limitation; GlnD-GlnB/K dependent; Cluster I (circle), genes upregulated under nitrogen limitation, GlnD-GlnB/K independent; Cluster II, genes downregulated under nitrogen limitation; Cluster III, genes with expression affected by GlnD/GlnBK regulatory cascade but not differentially expressed under high vs. low nitrogen.
Figure 4.
Distribution of differentially expressed genes in S. meliloti Rm1021 replicons.
Cluster I. Genes upregulated under nitrogen limitation (97); Cluster II. Genes downregulated under nitrogen limitation (78); Cluster III. genes with expression affected by GlnD/GlnBK regulatory cascade but not differentially expressed under high vs. low nitrogen (442). Total in MA (microarray). The distribution of the 609 genes found to have differential regulation in response to nitrogen stress or mutations in glnD or glnBglnK, as described in the text. Total in Genome. Distribution of annotated genes on pSymA, pSymB or the chromosome.
Table 2.
Functional classification of differentially expressed genes with >2.0 fold changes.
Figure 5.
Model of GlnD and GlnBK regulation in S. meliloti Rm1021.
A – GlnD acts strictly through PII proteins to regulate gene expression. General Stress Response affects the expression of several clusters of these genes. B, C – GlnD acts through the PII proteins as well as through PII independent regulation to alter gene expression.
Figure 6.
HMW EPS I production by S. meliloti strains.
Strains were grown in MM media with glutamate or NH4 as nitrogen source. The EPS I were harvested after 3, 5, 7 and 13 days and dried.
Figure 7.
Overlap between nitrogen and phosphate stress responses.
Left circle –609 genes were identified in our study that were regulated in response to nitrogen stress or had significantly different expression in Rm1021ΔglnD-sm2 or Rm1021ΔglnBΔglnK. Right circle –435 genes found to be differentially expressed under phosphate starvation in Rm1021 or/and Rm2011 [57]; Overlap –156 genes were found to be regulated by the conditions in both studies. Ellipse –96 putative Pho regulon members were identified [58], 34 Pho regulon members were differentially expressed under phosphate starvation [57]. Of these 34 genes, 20 were identified as differentially expressed in our microarrays by both sets of conditions.