A small RNA regulates the expression of genes involved in iron metabolism in <i>Escherichia</i> <i>coli</i>

TLDR

Fur positively regulates genes involved in iron metabolism, including TCA cycle enzymes acnA and fumA, ferritin genes ftnA and bfr, and superoxide dismutase sodB. RyhB is an antisense RNA that binds complementary sequences in target mRNAs, requiring the RNA‑binding protein Hfq for activity. When iron is limiting, RyhB is induced, down‑regulates iron‑storage and iron‑using proteins such as sdhCDAB, acnA, fumA, ftnA, bfr, and sodB, reverses Fur activation, and explains why fur mutants cannot grow on succinate.

Abstract

A small RNA, RyhB, was found as part of a genomewide search for novel small RNAs in Escherichia coli . The RyhB 90-nt RNA down-regulates a set of iron-storage and iron-using proteins when iron is limiting; it is itself negatively regulated by the ferric uptake repressor protein, Fur ( F erric u ptake r egulator). RyhB RNA levels are inversely correlated with mRNA levels for the sdhCDAB operon, encoding succinate dehydrogenase, as well as five other genes previously shown to be positively regulated by Fur by an unknown mechanism. These include two other genes encoding enzymes in the tricarboxylic acid cycle, acnA and fumA , two ferritin genes, ftnA and bfr , and a gene for superoxide dismutase, sodB . Fur positive regulation of all these genes is fully reversed in an ryhB mutant. Our results explain the previously observed inability of fur mutants to grow on succinate. RyhB requires the RNA-binding protein, Hfq, for activity. Sequences within RyhB are complementary to regions within each of the target genes, suggesting that RyhB acts as an antisense RNA. In sdhCDAB , the complementary region is at the end of the first gene of the sdhCDAB operon; full-length sdhCDAB message disappears and a truncated message, equivalent in size to the region upstream of the complementarity, is detected when RyhB is expressed. RyhB provides a mechanism for the cell to down-regulate iron-storage proteins and nonessential ironcontaining proteins when iron is limiting, thus modulating intracellular iron usage to supplement mechanisms for iron uptake directly regulated by Fur.