Transcriptomics reveal several gene expression patterns in the piezophile Desulfovibrio hydrothermalis in response to hydrostatic pressure

Abstract

RNA-seq was used to study the response of Desulfovibrio hydrothermalis, isolated from a deep-sea hydrothermal chimney on the East-Pacific Rise at a depth of 2,600 m, to various hydrostatic pressure growth conditions. The transcriptomic datasets obtained after growth at 26, 10 and 0.1 MPa identified only 65 differentially expressed genes that were distributed among four main categories: aromatic amino acid and glutamate metabolisms, energy metabolism, signal transduction, and unknown function. The gene expression patterns suggest that D. hydrothermalis uses at least three different adaptation mechanisms, according to a hydrostatic pressure threshold (HPt) that was estimated to be above 10 MPa. Both glutamate and energy metabolism were found to play crucial roles in these mechanisms. Quantitation of the glutamate levels in cells revealed its accumulation at high hydrostatic pressure, suggesting its role as a piezolyte. ATP measurements showed that the energy metabolism of this bacterium is optimized for deep-sea life conditions. This study provides new insights into the molecular mechanisms linked to hydrostatic pressure adaptation in sulfate-reducing bacteria.

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).

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.