Abstract
Shewanella oneidensis produces an extensive electron transfer network that results in metabolic flexibility. A large number of c-type cytochromes are expressed by S. oneidensis and these function as the fundamental electron transport chain proteins. Although several S. oneidensis cytochromes have been well-characterized, little is known about how their expression is regulated. In this study, we investigate the role of the ferric uptake regulator (Fur) and the sRNA RyhB in regulation. Our results demonstrate that loss of Fur leads to diminished growth and an apparent decrease in heme-containing proteins. Remarkably, deleting the Fur-repressed ryhB gene almost completely reverses these physiological changes, indicating that the phenotypes resulting from loss of Fur are (at least partially) dependent on RyhB. RNA sequencing identified a number of possible RyhB repressed genes. A large fraction of these encode c-type cytochromes, among them two of the most abundant periplasmic cytochromes CctA (also known as STC) and ScyA. We show that RyhB destabilizes the mRNA of four of its target genes, cctA, scyA, omp35, and nrfA and this requires the presence of the RNA chaperone Hfq. Iron limitation decreases the expression of the RyhB target genes cctA and scyA and this regulation relies on the presence of both Fur and RyhB. Overall, this study suggests that controlling cytochrome expression is of importance to maintain iron homeostasis and that sRNAs molecules are important players in the regulation of fundamental processes in S. oneidensis MR-1.
Highlights
The gammaproteobacterium Shewanella oneidensis is a facultative anaerobe that is remarkable for its metabolic versatility
Overproduction of RyhB from a plasmid had a negative effect on growth of the wild-type and ryhB strains (Supplementary Figure 1C), indicating that the increased expression of RyhB in the fur strain is responsible for this phenomenon
These results suggest that the ferric uptake regulator (Fur) protein, through the sRNA RyhB, controls expression of proteins with importance for growth and controls the production of heme-containing proteins
Summary
The gammaproteobacterium Shewanella oneidensis is a facultative anaerobe that is remarkable for its metabolic versatility. In the absence of dissolved oxygen, it can utilize a large number of soluble compounds as terminal electron acceptors, and is capable of transferring electrons to reduce insoluble metal oxides in the extracellular environment (for review, see Hau and Gralnick, 2007). This remarkable respiratory capacity has been attributed to the large number of c-type cytochromes encoded in the genome of S. oneidensis MR-1 and serving as fundamental electron transport chain proteins (Meyer et al, 2004). But not all, of the remaining 41 c-type cytochromes have been characterized and their function determined, with most scrutiny given to the proteins involved in electron transfer to ferric iron.
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