Figure 1.
Genomic organization of D. hydrothermalis overlaid with differentially expressed genes and expression levels obtained from RNA-seq experiments.
Moving from the outside inward, the circles represent 1, 2) CDS on the plus and minus strands of the genome; loci of differentially expressed genes in 3) 26 MPa vs. 0.1 MPa, 4) 10 MPa vs. 0.1 MPa, 5) 26 MPa vs. 10 MPa; coverage (from BAM format) for 6) 26 MPa, 7) 10 MPa, 8) 0.1 MPa; 9) GC skew.
Figure 2.
Heatmap of D. hydrothermalis gene expression changes with pressure.
Normalized counts obtained with DESeq, transformed into log2 (RPKM+1), were used to generate a heatmap showing over-expressed (red) and under-expressed (green) genes with 2 replicates for 3 pressure conditions (0.1, 10 and 26 MPa). Three clusters corresponding to DESeq pressure-regulated genes, with an adjusted P-value<0.1, are shown (A: 10 vs. 0.1 MPa; B: 26 vs. 10 MPa; C: 26 vs. 0.1 MPa). Functional annotation corresponding to pressure-regulated genes is displayed.
Figure 3.
Venn diagram showing numbers of differentially expressed genes in D. hydrothermalis between the hydrostatic pressures of 0.1 MPa, 10 MPa and 26 MPa (adjusted P-value<0.1).
Table 1.
Differentially expressed genes between the 0.1 MPa, 10 MPa, and 26 MPa growth conditions (adjusted P value<0.1).
Figure 4.
Distribution of the differentially expressed genes according to the clusters of orthologous groups of proteins (COG) classification (in percentage).
The numbers in parentheses indicate the numbers of differentially expressed genes for each COG.
Figure 5.
Quantitation of glutamate levels (A) and intracellular ATP (B) in D. hydrothermalis cells grown under different pressure conditions.