Global transcriptome analysis of Shewanella oneidensis MR-1 exposed to different terminal electron acceptors

Abstract

To gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer Shewanella oneidensis MR-1, global mRNA patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. Gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. Several groups of genes exhibited elevated expression levels in the presence of metals, including those encoding putative multidrug efflux transporters, detoxification proteins, extracytoplasmic sigma factors and PAS-domain regulators. Only one of the 42 predicted c-type cytochromes in MR-1, SO3300, displayed significantly elevated transcript levels across all metal-reducing conditions. Genes encoding decaheme cytochromes MtrC and MtrA that were previously linked to the reduction of different forms of Fe(III) and Mn(IV), exhibited only slight decreases in relative mRNA abundances under metal-reducing conditions. In contrast, specific transcriptome responses were displayed to individual non-metal electron acceptors resulting in the identification of unique groups of nitrate-, thiosulfate- and TMAO-induced genes including previously uncharacterized multi-cytochrome gene clusters. Collectively, the gene expression results reflect the fundamental differences between metal and non-metal respiratory pathways of S. oneidensis MR-1, where the coordinate induction of detoxification and stress response genes play a key role in adaptation of this organism under metal-reducing conditions. Moreover, the relative paucity and/or the constitutive nature of genes involved in electron transfer to metals is likely due to the low-specificity and the opportunistic nature of the metal-reducing electron transport pathways.

FIG. 1.

Distribution of 2827 differentially expressed S. oneidensis MR-1 genes across different electron acceptor conditions (A). Distribution of S. oneidensis MR-1 genes involved in amino acid biosynthesis (B), protein synthesis (C), and energy metabolism (D) across different electron acceptor conditions. The functional classification corresponds to the main role categories assigned in the TIGR database (http://www.tigr.org/tigr-scripts/CMR2/gene_table.spl?db = gsp). Electron acceptor abbreviations: O₂, oxygen; CO, Co(III) EDTA; FC, ferric citrate; FO, hydrous ferric oxide; MC, colloidal manganese(IV); MO - manganese dioxide; S₂O₃, sodium thiosulfate; NO₃, sodium nitrate; TM, trimethylamine N-oxide; DMSO, dimethyl sulfoxide. Red bars indicate up-regulated genes, green bars represent down-regulated genes.

FIG. 2.

Correlation between the top 2 principal components representing the behavior of the S. oneidensis MR-1 transcriptome (A) and expression profiles of 6 S. oneidensis genes encoding putative sigma factors (B). Relative transcript abundances represent a ratio of mRNA levels in test cultures to these displayed by the fumarate-grown reference. Values of >1 indicate mRNA abundance increase under test conditions; values of <1 indicate decrease under test conditions. Electron acceptor abbreviations: O₂, oxygen; CO, Co(III) EDTA; FC, ferric citrate; FO, hydrous ferric oxide; MC, colloidal manganese(IV); MO, manganese dioxide; S₂O₃, sodium thiosulfate; NO₃, sodium nitrate; TM, trimethylamine N-oxide; DMSO, dimethyl sulfoxide.

FIG. 3.

Hierarchical clustering of 2827 S. oneidensis genes exhibiting differential expression in cultures exposed to metal and non-metal electron acceptors. Each column indicates individual electron acceptor. Relative transcript abundances represent a ratio of mRNA levels in test cultures to these displayed by the fumarate-grown reference. Electron acceptor abbreviations: O₂, oxygen; CO, Co(III) EDTA; FC, ferric citrate; FO, hydrous ferric oxide; MC, colloidal manganese(IV); MO, manganese dioxide; S₂O₃, sodium thiosulfate; NO₃, sodium nitrate; TM, trimethylamine N-oxide; DMSO, dimethyl sulfoxide.