rpoS mRNA encodes for the rpoS stress factor, sigma

Sigma factor

A sigma factor is a bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promoters. Different sigma factors are activated in response to different environmental conditions...

 E (σ^E), where DsrA

DsrA RNA

DsrA RNA is a non-coding RNA that regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation, by promoting efficient translation of the stress sigma factor, RpoS...

 in conjunction with the Sm

LSm

In biology, LSm proteins are a family of RNA-binding proteins found in virtually every cellular organism. LSm is a contraction of 'like Sm', because the first identified members of the LSm protein family were the Sm proteins...

 like RNA binding protein, Hfq promote the translation

Translation

Translation is the communication of the meaning of a source-language text by means of an equivalent target-language text. Whereas interpreting undoubtedly antedates writing, translation began only after the appearance of written literature; there exist partial translations of the Sumerian Epic of...

 of this rpoS mRNA. The 5' UTR of the rpoS mRNA forms a self inhibitory stem loop that shields the shine-dalgarno sequence

Shine-Dalgarno sequence

The Shine-Dalgarno sequence , proposed by Australian scientists John Shine and Lynn Dalgarno , is a ribosomal binding site in the mRNA, generally located 8 basepairs upstream of the start codon AUG. The Shine-Dalgarno sequence exists only in prokaryotes. The six-base consensus sequence is AGGAGG;...

 and therefore inhibits translation. The secondary structure

Secondary structure

In biochemistry and structural biology, secondary structure is the general three-dimensional form of local segments of biopolymers such as proteins and nucleic acids...

 of the 5'UTR was predicted by acetylation

Acetylation

Acetylation describes a reaction that introduces an acetyl functional group into a chemical compound...

 of ribose 2'-hydroxyls with NMIA and by using a secondary structure prediction program, RNAstructure. DsrA stimulates rpoS translation by binding in the 5'UTR and causes the stem loop to open, exposing the ribosome binding site. Site-directed mutagenesis

Site-directed mutagenesis

Site-directed mutagenesis, also called site-specific mutagenesis or oligonucleotide-directed mutagenesis, is a molecular biology technique in which a mutation is created at a defined site in a DNA molecule. In general, this form of mutagenesis requires that the wild type gene sequence be known...

 and deletion analysis located an AAYAA motif identified upstream of the stem loop structure which is required for Hfq binding. Comparative genomics

Genomics

Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...

 has shown that this regulatory secondary structure is conserved across several gram negative bacteria species.