Global transcriptional profiling of Shewanella oneidensis MR-1 during Cr(VI) and U(VI) reduction

Abstract

Whole-genome DNA microarrays were used to examine the gene expression profile of Shewanella oneidensis MR-1 during U(VI) and Cr(VI) reduction. The same control, cells pregrown with nitrate and incubated with no electron acceptor, was used for the two time points considered and for both metals. U(VI)-reducing conditions resulted in the upregulation (> or = 3-fold) of 121 genes, while 83 genes were upregulated under Cr(VI)-reducing conditions. A large fraction of the genes upregulated [34% for U(VI) and 29% for Cr(VI)] encode hypothetical proteins of unknown function. Genes encoding proteins known to reduce alternative electron acceptors [fumarate, dimethyl sulfoxide, Mn(IV), or soluble Fe(III)] were upregulated under both U(VI)- and Cr(VI)-reducing conditions. The involvement of these upregulated genes in the reduction of U(VI) and Cr(VI) was tested using mutants lacking one or several of the gene products. Mutant testing confirmed the involvement of several genes in the reduction of both metals: mtrA, mtrB, mtrC, and menC, all of which are involved in Fe(III) citrate reduction by MR-1. Genes encoding efflux pumps were upregulated under Cr(VI)- but not under U(VI)-reducing conditions. Genes encoding proteins associated with general (e.g., groL and dnaJ) and membrane (e.g., pspBC) stress were also upregulated, particularly under U(VI)-reducing conditions, pointing to membrane damage by the solid-phase reduced U(IV) and Cr(III) and/or the direct effect of the oxidized forms of the metals. This study sheds light on the multifaceted response of MR-1 to U(VI) and Cr(VI) under anaerobic conditions and suggests that the same electron transport pathway can be used for more than one electron acceptor.

FIG. 1.

U(VI) reduction by WT (MR-1) and MR-1 mutants deficient in various proteins. (A) MtrB (AQ38), MtrC (SR-522), MtrA (SR-524), MtrCAB (SR-8), and CymA (MR1-CYMA). (B) Fumarate reductase FccA (SR515), CymA (MR1-CYMA), the menaquinone precursor MenC (H2), and MtrA (SR-524). Error bars represent the data range for duplicate cultures.

FIG. 2.

Cr(VI) reduction by WT (MR-1) and MR-1 mutants deficient in MtrB (AQ38), MenC (H2), MtrA (SR-524), MtrC (SR-522), or MtrCAB (SR-8). Error bars represent the data range for duplicate cultures.

FIG. 3.

Cr(VI) reduction by WT (MR-1), spontaneous rifampin mutant MR-1R, and MR-1 mutants deficient in various proteins. (A) Fumarate reductase (SR-515), CymA (MR1-CYMA), the menaquinone precursor MenC (H2), and MtrA (SR-524). (B) CymA (MR1-CYMA). Error bars represent the data range for duplicate cultures.