A small RNA, RyhB, was found as part of a genomewide search for novel RNAs in Escherichia coli . The RyhB 90-nt RNA down-regulates set iron-storage and iron-using proteins when iron is limiting; it itself negatively regulated by the ferric uptake repressor protein, Fur ( F erric u ptake r egulator). levels are inversely correlated with mRNA sdhCDAB operon, encoding succinate dehydrogenase, well five other genes previously shown to be positively an unknown mechanism. These include two enzymes...

Susan Gottesman, Eric Roche, YanNing Zhou, and Robert T. Sauer Laboratory of Molecular Biology, National Cancer Institute, Bethesda, Maryland 20892 USA; Department Massachusetts Institute Technology, Cambridge, Masaschusetts 02139 USA

A burgeoning list of small RNAs with a variety regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify by sequence inspection. We used the high conservation among closely related bacterial species, as well analysis transcripts detected high-density oligonucleotide probe arrays, predict presence novel RNA genes intergenic regions Escherichia coli genome. The existence 23 distinct new species was confirmed Northern analysis....

RyhB is a small antisense regulatory RNA that repressed by the Fur repressor and negatively regulates at least six mRNAs encoding Fe-binding or Fe-storage proteins in Escherichia coli . When Fe limiting, levels rise, target are rapidly degraded. very stable when measured after treatment of cells with transcription inhibitor rifampicin, but unstable overall mRNA continues. We propose turnover coupled to dependent on pairing mRNAs. Degradation both targets RNase E slowed degradosome mutants....

Hfq, a bacterial member of the Sm family RNA-binding proteins, is required for action many small regulatory RNAs that act by basepairing with target mRNAs. Hfq binds this efficiently. We have used co-immunoprecipitation and direct detection bound on genomic microarrays to identify members RNA family. This approach was extremely sensitive; even Hfq-binding expressed at low levels were readily detected. At least 15 46 known in E. coli interact Hfq. In addition, high signals other intergenic...

DsrA RNA regulates both transcription, by overcoming transcriptional silencing the nucleoid-associated H-NS protein, and translation, promoting efficient translation of stress σ factor, RpoS. These two activities can be separated mutation: first three stem-loops 85 nucleotide is necessary for RpoS but not anti-H-NS action, while second stem-loop essential antisilencing less critical translation. The third stem-loop, which behaves as a transcription terminator, substituted trp terminator...

RyhB is a noncoding RNA regulated by the Fur repressor. It has previously been shown to cause rapid degradation of number mRNAs that encode proteins utilize iron. Here we examine effect ectopic production on global gene expression microarray analysis. Many identified targets were found, as well other encoding iron-binding proteins, bringing total operons at least 18, 56 genes. The two major involved in Fe-S cluster assembly showed different behavior; isc operon appears be direct target...

In many bacteria, iron homeostasis is controlled primarily by the ferric uptake regulator (Fur), a transcriptional repressor. However, some genes, including those involved in storage, are positively regulated Fur. A Fur-repressed regulatory small RNA (sRNA), RyhB, has been identified Escherichia coli , and it demonstrated that negative regulation of genes this sRNA responsible for positive No RyhB sequence homologs were found Pseudomonas aeruginosa despite identification its Fur homolog....

Escherichia coli lon mutants are defective in the ATP-dependent proteolysis of abnormal proteins. The also sensitive to ultraviolet light (UV) that septation is inhibited after exposure UV. sulA mutations, isolated as suppressors UV sensitivity unlinked lon, do not affect but allow occur DNA damage. We have confirmed hypothesis product gene degraded by proteolysis. If (the sulA) a UV-inducible division inhibitor, suggested variety experiments, lon) may regulate cell regulating half-life...

Blocks in DNA replication cause a rapid arrest of cell division Escherichia coli. We have previously established that the function SfiA (SulA), induced under these conditions as part SOS response, is involved this inhibition division. To separate effects from those other functions, we constructed plac-sfiA operon fusion, permitting specific induction protein by addition lac inducer isopropyl beta-D-thiogalactopyranoside (IPTG). In lon mutants, which unstable has longer half-life, IPTG caused...

Bacterial small noncoding RNAs carry out both positive and negative regulation of gene expression by pairing with mRNAs; in Escherichia coli , this often requires the RNA chaperone Hfq. Three regulatory (sRNAs), DsrA, RprA, ArcZ, positively regulate translation sigma factor RpoS, each 5′ leader to open up an inhibitory hairpin. In vitro, rpoS interaction sRNAs depends upon (AAN) 4 Hfq-binding site upstream region. Here we show that Hfq binding are required for RprA or ArcZ act vivo form a...