Microarray transcription profiling of a Shewanella oneidensis etrA mutant

Abstract

DNA microarrays were used to examine the effect of an insertional mutation in the Shewanella oneidensis etrA (electron transport regulator) locus on gene expression under anaerobic conditions. The mRNA levels of 69 genes with documented functions in energy and carbon metabolism, regulation, transport, and other cellular processes displayed significant alterations in transcript abundance in an etrA-mutant genetic background. This is the first microarray study indicating a possible involvement of EtrA in the regulation of gene expression in S. oneidensis MR-1.

FIG.1.

Pairwise average-linkage clustering analysis of the 69 S. oneidensis MR-1 genes exhibiting altered mRNA levels in the ETRA1 mutant. Hierarchical clustering, based on pairwise correlations across all experimental points, groups together genes of known similar function (A to E) and also provides a means of obtaining leads as to the function of unknown or poorly characterized genes (9). Each column indicates a separate biological replicate (F₁ and F₂ refer to fumarate-reducing conditions; N₁ and N₂ refer to nitrate-reducing conditions). Red and green colors indicate genes that are induced and repressed, respectively, in the presence of etrA. The Pearson correlation coefficients (r) are displayed to the left of the nodes. a, sequence information provided as a courtesy by The Institute for Genomic Research (unpublished results). The ORF numbers provided here are for the purpose of tracking gene locations and sequence information; they may change once the complete version of S. oneidensis MR-1 genome sequence is released. b, relative mRNA levels presented as the ratio of the dye intensity of the parental strain to that of the etrA mutant averaged across two biological replicate experiments. Values in parentheses indicate the standard deviation for each mean expression ratio. c, value not significantly different from 1 at a P of 0.05 based on a one-tailed t test. d, unable to determine expression ratio for this ORF due to the very low levels of hybridization intensities in both DSP-10 and ETRA1 strains (nd).