Global transcriptome analysis of the heat shock response of Shewanella oneidensis

Abstract

Shewanella oneidensis is an important model organism for bioremediation studies because of its diverse respiratory capabilities. However, the genetic basis and regulatory mechanisms underlying the ability of S. oneidensis to survive and adapt to various environmentally relevant stresses is poorly understood. To define this organism's molecular response to elevated growth temperatures, temporal gene expression profiles were examined in cells subjected to heat stress by using whole-genome DNA microarrays for S. oneidensis. Approximately 15% (n = 711) of the total predicted S. oneidensis genes (n = 4,648) represented on the microarray were significantly up- or downregulated (P < 0.05) over a 25-min period after shift to the heat shock temperature. As expected, the majority of the genes that showed homology to known chaperones and heat shock proteins in other organisms were highly induced. In addition, a number of predicted genes, including those encoding enzymes in glycolysis and the pentose cycle, serine proteases, transcriptional regulators (MerR, LysR, and TetR families), histidine kinases, and hypothetical proteins were induced. Genes encoding membrane proteins were differentially expressed, suggesting that cells possibly alter their membrane composition or structure in response to variations in growth temperature. A substantial number of the genes encoding ribosomal proteins displayed downregulated coexpression patterns in response to heat stress, as did genes encoding prophage and flagellar proteins. Finally, a putative regulatory site with high conservation to the Escherichia coli sigma32-binding consensus sequence was identified upstream of a number of heat-inducible genes.

FIG. 1.

Histogram of log ratio expression difference of gene pairs within the same operon versus gene pairs selected at random. The normalized frequency was plotted against the ratio expression difference between the treatments and control. Genes within the same operon responded more similarly than genes randomly selected from the genome under heat shock.

FIG. 2.

Differentially expressed genes grouped by functional classification according to the TIGR S. oneidensis genome database (www.tigr.org). Columns: 1, amino acid biosynthesis; 2, biosynthesis of cofactors, prosthetic groups, and carriers; 3, cell envelope; 4, cellular processes; 5, central intermediary metabolism; 6, DNA metabolism; 7, energy metabolism; 8, fatty acid and phospholipid metabolism; 9, other categories; 10, protein fate; 11, protein synthesis; 12, purines, pyrimidines, nucleosides, and nucleotides; 13, regulatory functions; 14, signal transduction; 15, transcription; 16, transport and binding proteins; 17, unknown function; 18, hypothetical proteins.

FIG. 3.

Hierarchical clustering of selected genes that varied significantly (P < 0.05 and a fold change of >2 at least at one time point) in their expression profiles in response to a temperature change from 30 to 42°C. The red color indicates the levels of induction, while the green color represents repression. Each row represents the expression of a single gene, and each column represents an individual time point after the temperature increase.

FIG. 4.

Consensus sequence for σ³² promoters. Upstream sequences of heat-induced genes in both S. oneidensis and E. coli were analyzed with AlignACE to find potential regulatory motifs. (A) A motif conserved in the upstream regions of upregulated S. oneidensis genes is nearly identical to the E. coli σ³² binding site. The sequence logo was prepared by using public software at http://ep.ebi.ac.uk/EP/SEQLOGO (31). (B) Listed are promoters that display at least 7 of 12 matches in highlighted base pairs and 13- to 15-bp spacing. Asterisks indicate the positions with at least 50% matches.