Hunting 6S RNAs in Bacteria

@Article{Trotochaud:2005:Nat-Struct-Mol-Biol:15793584,
author = "Trotochaud, A E and Wassarman, K M",
title = {A highly conserved {6S RNA} structure is required for regulation of transcription},
abstract = {6S RNA, a highly abundant noncoding RNA, regulates transcription through interaction with RNA polymerase in Escherichia coli. Computer searches identified 6S RNAs widely among gamma-proteobacteria. Biochemical approaches were required to identify more divergent 6S RNAs. Two Bacillus subtilis RNAs were found to interact with the housekeeping form of RNA polymerase, thereby establishing them as 6S RNAs. A third B. subtilis RNA was discovered with distinct RNA polymerase-binding activity. Phylogenetic comparison and analysis of mutant RNAs revealed that a conserved secondary structure containing a single-stranded central bulge within a highly double-stranded molecule was essential for 6S RNA function in vivo and in vitro. Reconstitution experiments established the marked specificity of 6S RNA interactions for sigma(70)-RNA polymerase, as well as the ability of 6S RNA to directly inhibit transcription. These data highlight the critical importance of structural characteristics for 6S RNA activity.},
journal = "Nat Struct Mol Biol",
year = "2005",
volume = "12",
number = "4",
pages = "313-319",
month = "Apr",
pmid = "15793584",
url = "http://www.hubmed.org/display.cgi?uids=15793584",
doi = "10.1038/nsmb917"
}

@Article{Barrick:2005:RNA:15811922,
author = "Barrick, J E and Sudarsan, N and Weinberg, Z and Ruzzo, W L and Breaker, R R",
title = {{6S RNA} is a widespread regulator of eubacterial {RNA} polymerase that resembles an open promoter},
abstract = {6S RNA is an abundant noncoding RNA in Escherichia coli that binds to sigma70 RNA polymerase holoenzyme to globally regulate gene expression in response to the shift from exponential growth to stationary phase. We have computationally identified >100 new 6S RNA homologs in diverse eubacterial lineages. Two abundant Bacillus subtilis RNAs of unknown function (BsrA and BsrB) and cyanobacterial 6Sa RNAs are now recognized as 6S homologs. Structural probing of E. coli 6S RNA and a B. subtilis homolog supports a common secondary structure derived from comparative sequence analysis. The conserved features of 6S RNA suggest that it binds RNA polymerase by mimicking the structure of DNA template in an open promoter complex. Interestingly, the two B. subtilis 6S RNAs are discoordinately expressed during growth, and many proteobacterial 6S RNAs could be cotranscribed with downstream homologs of the E. coli ygfA gene encoding a putative methenyltetrahydrofolate synthetase. The prevalence and robust expression of 6S RNAs emphasize their critical role in bacterial adaptation.},
journal = "RNA",
year = "2005",
volume = "11",
number = "5",
pages = "774-784",
month = "May",
pmid = "15811922",
url = "http://www.hubmed.org/display.cgi?uids=15811922",
doi = "10.1261/rna.7286705"
}

@unpublished{Lechner:11,
author = {Lechner, M and Findei{\ss}, S and Steiner, L and Marz, M and Stadler, PF and Prohaska, SJ},
title = {Proteinortho: {D}etection of ({Co}-){O}rthologs in {L}arge-{S}cale {A}nalysis},
year = {2011}
}

@article{Beckmann,
author= {Beckmann, BM and Hoch, PG and Marz, M and Salas, M and Hartmann RK},
title= {The release mechanism of {RNA} polymerase from {B}acillus subtilis {6S}-1 {RNA}},
journal= {in progress}
}

@Article{Wurm:2010:Biol-Chem:20030589,
author = "Wurm, R and Neusser, T and Wagner, R",
title = {6{S RNA-}dependent inhibition of {RNA }polymerase is released by {RNA}-dependent synthesis of small de novo products},
abstract = {6S RNA from Escherichia coli is known to bind to RNA polymerase, preventing interaction with many promoters during stationary growth. The resulting repression is released under conditions of nutritional upshift, when the growth situation improves. 6S RNA, which binds to the active site of RNA polymerase, has the particularly interesting feature to act as a template, causing the transcription of defined de novo RNAs (dnRNA) that are complementary to a specific sequence region of the 6S RNA. We analyzed the conditions of dnRNA synthesis and determined their effect on the 6S RNA-mediated inhibition of RNA polymerase in vitro and in vivo. Upon nutritional upshift the RNA polymerase/6S RNA complex induces the rapid synthesis of dnRNAs, which form stable hybrids with the 6S RNA template. The resulting structural change destabilizes the inactivated RNA polymerase complex, causing sigma subunit release. Both dnRNA and 6S RNA are rapidly degraded after complex disintegration. Experiments using the transcriptional inhibitor rifampicin demonstrate that active transcription is required for the disintegration of the RNA polymerase/6S RNA complex. Our results support the conclusion that 6S RNA not only inhibits transcription during stationary growth but also enables cells to resume rapid growth after starvation and help to escape from stationary phase.},
journal = "Biol Chem",
year = "2010",
volume = "391",
number = "2-3",
pages = "187-196",
month = "Feb-Mar",
pmid = "20030589",
url = "http://www.hubmed.org/display.cgi?uids=20030589",
doi = "10.1515/BC.2010.018"
}


@Article{Wassarman:2000:Cell:10892648,
author = "Wassarman, K M and Storz, G",
title = {6{S RNA} regulates {E.} coli {RNA} polymerase activity},
abstract = {The E. coli 6S RNA was discovered more than three decades ago, yet its function has remained elusive. Here, we demonstrate that 6S RNA associates with RNA polymerase in a highly specific and efficient manner. UV crosslinking experiments revealed that 6S RNA directly contacts the sigma70 and beta/beta' subunits of RNA polymerase. 6S RNA accumulates as cells reach the stationary phase of growth and mediates growth phase-specific changes in RNA polymerase. Stable association between sigma70 and core RNA polymerase in extracts is only observed in the presence of 6S RNA. We show 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. Our results suggest that the interaction of 6S RNA with RNA polymerase modulates sigma70-holoenzyme activity.},
journal = "Cell",
year = "2000",
volume = "101",
number = "6",
pages = "613-623",
month = "Jun",
pmid = "10892648",
url = "http://www.hubmed.org/display.cgi?uids=10892648",
doi = ""
}

@Article{Shephard:2010:RNA:20354151,
author = "Shephard, L and Dobson, N and Unrau, P J",
title = {Binding and release of the 6{S} transcriptional control {RNA}},
abstract = {6S RNA is an important noncoding RNA that regulates eubacterial transcription. In Escherichia coli this RNA binds to the sigma(70) RNA polymerase holoenzyme and is released by the synthesis of a short product RNA. In order to determine how binding and release are controlled by the 6S RNA sequence, we used in vitro selection to screen a high diversity library containing approximately 4 x 10(12) sequences for functional 6S RNA variants. Residues critical for binding were found to be located in a "-35" region upstream of the 6S RNA transcription bubble mimic structure. Mutating these phylogenetically conserved residues invariably led to decreases in binding and removing them abolished binding, implicating these nucleotides in a biologically important interaction with the Esigma(70) complex. Interestingly, mutation of phylogenetically conserved "-10" residues that were also upstream of the site of pRNA synthesis was found to influence 6S RNA release rates in addition to modulating -35 binding. These results indicate how 6S RNA -35 binding to sigma(70) RNA polymerase holoenzyme can regulate expression from "strong" and "weak" -35 DNA promoters and suggest that 6S RNA release rates have been fine tuned over evolutionary time so as to correctly regulate cellular levels of transcription.},
journal = "RNA",
year = "2010",
volume = "16",
number = "5",
pages = "885-892",
month = "May",
pmid = "20354151",
url = "http://www.hubmed.org/display.cgi?uids=20354151",
doi = "10.1261/rna.2036210"
}