Time course transcriptome changes in Shewanella algae in response to salt stress

Abstract

Shewanella algae, which produces tetrodotoxin and exists in various seafoods, can cause human diseases, such as spondylodiscitis and bloody diarrhea. In the present study, we focused on the temporal, dynamic process in salt-stressed S. algae by monitoring the gene transcript levels at different time points after high salt exposure. Transcript changes in amino acid metabolism, carbohydrate metabolism, energy metabolism, membrane transport, regulatory functions, and cellular signaling were found to be important for the high salt response in S. algae. The most common strategies used by bacteria to survive and grow in high salt environments, such as Na+ efflux, K+ uptake, glutamate transport and biosynthesis, and the accumulation of compatible solutes, were also observed in S. algae. In particular, genes involved in peptidoglycan biosynthesis and DNA repair were highly and steadily up-regulated, accompanied by rapid and instantaneous enhancement of the transcription of large- and small-ribosome subunits, which suggested that the structural changes in the cell wall and some stressful responses occurred in S. algae. Furthermore, the transcription of genes involved in the tricarboxylic acid (TCA) cycle and the glycolytic pathway was decreased, whereas the transcription of genes involved in anaerobic respiration was increased. These results, demonstrating the multi-pathway reactions of S. algae in response to salt stress, increase our understanding of the microbial stress response mechanisms.

Figure 1. Growth curves for S. algae 2736 grown in LB broth.

S. algae 2736 cells were cultured in LB broth containing 0.5%, 3%, 6%, 8%, or 9% NaCl.

Figure 2. Statistical chart of S. algae 2736 DEGS in response to salt stress.

Compared to the transcriptional level at 0-regulated and down-regulated, respectively, at 1 h. At 4 h, 835 genes and 227 genes were up-regulated and down-regulated, respectively, whereas 883 genes were up-regulated and 180 genes were down-regulated at 14 h.

Figure 3. Classification of differentially expressed genes based on the dynamics of the transcript changes during the time course.

The number of genes included within each cluster is reported in blue between parentheses.

Figure 4. Alterations in high salt-related genes in S. algae 2736.

The clusters were created using TMEW. (A) Sigma factor. (B) Na+ efflux, K+ uptake, and glutamate accumulation. (C) Accumulation of compatible solutes. (D) Large- and small-ribosome subunits. (E) Energy metabolism. (F) DNA repair system. (G) Flagellar system. (H) Peptidoglycan biosynthesis. Specific colors represent the different regulation patterns. Gray, no change. Red, up-regulation. Green, down-regulation.

Figure 5. Conceptual model of S. algae responses to the exposure to high NaCl concentration.

The protein elements involved in the changed pathways were showed and marked with different colors: Red indicates the transcription increase at all three time points (1 h, 4 h, 14 h); Orange indicates the increase at 1 h or 4 h, or both 1 h and 4 h; Yellow indicates the increase at 14 h; Green indicates the decreased transcription at any one time point, no increase was observed in all three time points. The names of the pathways and the transported substrates were shown as black fonts.