6S / SsrS RNA

6S RNA was the first noncoding RNA to be sequenced, but its function was unknown until recently. It consists of 184 nucleotides that fold into an extended hairpin structure with a large single-stranded internal bulge. 6S RNA specifically associates with RNA polymerase holoenzyme containing the sigma70 specificity factor. This interaction represses expression from a sigma70-dependent promoter during stationary phase. [cite journal | last = Wassarman | first = KM | coauthors = Storz G | year = 2000 | title = 6S RNA regulates E. coli RNA polymerase activity | journal = Cell. | volume = 101 | pages = 613–623 | pmid = 10892648 | doi = 10.1016/S0092-8674(00)80873-9] 6S RNA homologs have recently been identified in most bacterial genomes. [cite journal | last = Trotochaud | first = AE | coauthors = Wassarman KM | year = 2005 | title = A highly conserved 6S RNA structure is required for regulation of transcription | journal = Nat Struct Mol Biol | volume = 12 | pages = 313–319 | pmid = 15793584 | doi = 10.1038/nsmb917] [cite journal | last = Barrick | first = JE | coauthors = Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR | year = 2005 | title = 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter | journal = RNA. | volume = 11 | pages = 774–784 | pmid = 15811922 | doi = 10.1261/rna.7286705] Many Gram-positive species have two copies of 6S RNA. In "Bacillus subtilis", both copies appear to interact with RNA polymerase holoenzyme containing the housekeeping sigma factor and be expressed during different stages of growth. In many proteobacteria, 6S RNA may be processed from a transcript encoding homologs of the "E. coli" YgfA protein which is a putative methenyltetrahydrofolate synthetase.

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