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.Metal ion reducing microbes play a central role in the biogeochemical cycling of key elements by coupling the reduction of insoluble metal oxides to the oxidation of the organic carbon. Microbial metal reduction has been identified as an effective means for immobilizing heavy metals and radionuclides in situ thus preventing their migration in the environment. Among metal ion reducing bacteria, Shewanella oneidensis MR-1 is notable due to its extensive respiratory versatility. In addition to O 2 , this bacterium can respire various organic and inorganic substrates, including fumarate, nitrate, nitrite, thiosulfate, elemental sulfur, trimethylamine N-oxide (TMAO), dimethyl sulfoxide (DMSO), anthraquinone-2,6-disulphonate (AQDS), as well as various soluble and solid metal electron acceptors such as chromium, cobalt, iron, manganese, technetium, uranium, and vanadium (12,27,34).Analysis of the S. oneidensis MR-1 genome sequence predicts a branched electron transport system that contains 42 putative c-type cytochromes and supports the proposed complexity of the energy-generating pathways in this organism (20, 30) Gene expression and environmental sen...

A dynamic periplasmic electron transfer network enables respiratory flexibility beyond a thermodynamic regulatory regime

“…These proteins have a central function in anoxic electron transfer to a multitude of different electron acceptors. Several researchers already showed a coexpression of several c-type cytochromes at the level of the transcriptome (Beliaev et al, 2005;Gralnick et al, 2005). Nevertheless, it is unknown what this coexpression really infers regarding the physiology of the organism and the biochemistry of electron transfer to the arsenal of electron acceptors that S. oneidensis is able to reduce.…”

“…Therefore, it has to be assumed that proteins like MtrA can diffuse through the periplasm or that additional redox proteins mediate electron transfer through the periplasm. The genome of S. oneidensis MR-1 contains the genetic information for 27 c-type cytochromes that are putatively localized to the periplasm, and a surprising number of them is expressed in high concentration immediately after conditions change from oxic to suboxic (Beliaev et al, 2005;Romine et al, 2008;Gao et al, 2010). Nevertheless, it is not known which of these cytochromes are necessary to bridge the periplasmic gap between CymA and the outer membrane.…”

Inference of interactions in cyanobacterial–heterotrophic co-cultures via transcriptome sequencing

“…for 5 min at 4 1C, flash frozen in liquid nitrogen and stored at À 80 1C. Total RNA extraction was carried out according to previously published protocols (Beliaev et al, 2005). The quality and integrity of the RNA was assessed on an Agilent 2100 Bioanalyzer and only samples with integrity numbers between 8 and 10 were selected for further analysis (Schroeder et al, 2006).…”

The mechanisms of extracellular electron transfer

“…The observed increase in ribosomal abundance at higher potentials for both S. oneidensis and G. sulfurreducens, is supported by a study that suggests a direct relationship between ribosomal gene expression and the potential of electron acceptors [99], after reanalysing data from a previous study [193]. However, later it was suggested that S. oneidensis ribosomal expression may rather be related to EET and not electrode potential [99].…”

“…In addition, a correlation study of previous research on S. oneidensis [193] looked at the ribosomal protein expression levels of three different electron acceptors: iron, cobalt and manganese [99]. There was found to be a direct relationship between ribosomal gene expression and the redox potential of each of the solid electron acceptors.…”