Figure 2. The impacts of ∆sigE and ∆cyabrb2 on the time-course transcriptome.

(A) MA plot showing fold change (y-axis) and average (x-axis) of gene expression between wildtype and mutant strains at each timepoint. Red dots indicate defined differentially expressed genes (DEGs) (|Log₂ FC|>1 with false discovery rate [FDR]<0.05). (B) Log2 scaled expression fold change in genes in the hox and nifJ operons upon ∆cyabrb2 and ∆sigE under aerobic conditions (0 hr), 1 hr after microoxic condition (1 hr), and 2 hr after microoxic condition (2 hr). DEGs are marked with sky blue (downregulated upon deletion) or red (upregulated upon deletion). (C and D) Fraction of upregulated and downregulated genes upon the (C) ∆cyabrb2 and (D) ∆sigE at the timepoints of aerobic conditions (0 hr), 1 hr after anoxic condition (1 hr), and 2 hr after anoxic condition (2 hr). Genes are classified according to Figure 1C. Asterisk (*) and dagger (†) denote statistically significant enrichment and anti-enrichment compared with all upregulated genes tested by multiple comparisons of Fisher’s exact test (FDR<0.05).

Figure 2—figure supplement 1. RT-qPCR validated the transiently upregulated genes classified by RNA-seq.

Transcripts extracted from wildtype (solid line), ∆sigE mutant (dotty line), ∆cyabrb2 mutant (dashed line), and ∆sigE ∆cyabrb2 double mutant (dot-dashed line) were assayed in the aerobic condition (0 hr) and 1, 2, 4 hr incubation of microoxic conditions. As the representative of the transiently upregulated genes, expression of hoxF, hoxY, nifJ, and sll0744 were quantified by RT-qPCR. The line represents the mean of n=3, and individual data points are shown as dot plots. Data of each gene is normalized by the mean score of wildtypes in the aerobic condition.

Figure 2—figure supplement 2. Primary component scatter plot showing the profiles of RNA-seq data.