6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

Barrick, Jeffrey E.; Sudarsan, Narasimhan; Weinberg, Zasha; Ruzzo, Walter L.; Breaker, Ronald R.

doi:10.1261/rna.7286705

Cited by 212 publications

(326 citation statements)

References 42 publications

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“…3C because the only difference between the two structures was a 3′ tail comprising the Rhoindependent terminator for the 182-nt transcript. The predicted structure was highly similar to the published consensus structure of the widely distributed 6S RNA that binds to RNAP (23,24) (see SI Text for details). To confirm that this sRNA is 6S RNA, coimmunoprecipitation experiments were then performed, as previously described (25).…”

Section: Resultssupporting

confidence: 65%

“…Together, the structure prediction and coimmunoprecipitation studies strongly suggest that this sRNA is the L. pneumophila 6S RNA. Therefore, its coding sequence was named ssrS in compliance with published nomenclature recommendations (23). The microarray data suggested that L. pneumophila 6S RNA is induced by H 2 O 2 and NaCl stresses in E phase, but this was not confirmed by northern blot (Table S1 and Fig.…”

Section: Resultsmentioning

confidence: 99%

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Legionella pneumophila 6S RNA optimizes intracellular multiplication

Faucher

Friedlander²,

Livny³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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Legionella pneumophila is a Gram-negative opportunistic human pathogen that infects and multiplies in a broad range of phagocytic protozoan and mammalian phagocytes. Based on the observation that small regulatory RNAs (sRNAs) play an important role in controlling virulence-related genes in several pathogenic bacteria, we attempted to identify sRNAs expressed by L. pneumophila. We used computational prediction followed by experimental verification to identify and characterize sRNAs encoded in the L. pneumophila genome. A 50-mer probe microarray was constructed to test the expression of predicted sRNAs in bacteria grown under a variety of conditions. This strategy successfully identified 22 expressed RNAs, out of which 6 were confirmed by northern blot and RACE. One of the identified sRNAs is highly expressed in postexponential phase, and computational prediction of its secondary structure reveals a striking similarity to the structure of 6S RNA, a widely distributed prokaryotic sRNA, known to regulate the activity of σ 70 -containing RNA polymerase. A 70-mer probe microarray was used to identify genes affected by L. pneumophila 6S RNA in stationary phase. The 6S RNA positively regulates expression of genes encoding type IVB secretion system effectors, stress response genes such as groES and recA, as well as many genes involved in acquisition of nutrients and genes with unknown or hypothetical functions. Deletion of 6S RNA significantly reduced L. pneumophila intracellular multiplication in both protist and mammalian host cells, but had no detectable effect on growth in rich media.Legionella pneumophila genome | microarray | sRNA | sRNA prediction | competition assay

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Section: Resultssupporting

confidence: 65%

Section: Resultsmentioning

confidence: 99%

Legionella pneumophila 6S RNA optimizes intracellular multiplication

Faucher

Friedlander²,

Livny³

et al. 2010

Proc. Natl. Acad. Sci. U.S.A.

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“…21). Many of these predicted RNA motifs carry only a few conserved nucleotides and have relatively simple secondary structure architectures compared with riboswitches (data not shown).…”

Section: Resultsmentioning

confidence: 99%

“…[17][18][19]. Additional examples of widespread noncoding RNAs in bacteria, such as 6S RNA (20)(21)(22), the dual-function tmRNA (23), and noncoding portions of messenger RNAs such as T-Box elements (24) and riboswitches (25)(26)(27) perform important gene control and molecular sensing tasks that are critical for cells to function normally. The existence of so many RNAs with atypical functions implies that some newly discovered noncoding RNAs might perform surprising and important roles in fundamental cellular processes.…”

mentioning

confidence: 99%

Identification of a large noncoding RNA in extremophilic eubacteria

Puerta-Fernández

Barrick

Roth

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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We have discovered a large and highly conserved RNA motif that typically resides in a noncoding section of a multigene messenger RNA in extremophilic Gram-positive eubacteria. RNAs of this class adopt an ornate secondary structure, are large compared with most other noncoding RNAs, and have been identified only in certain extremophilic bacteria. These ornate, large, extremophilic (OLE) RNAs have a length of Ϸ610 nucleotides, and the 35 representatives examined exhibit extraordinary conservation of nucleotide sequence and base pairing. Structural probing of the OLE RNA from Bacillus halodurans corroborates a complex secondary structure model predicted from comparative sequence analysis. The patterns of structural conservation, and its unique phylogenetic distribution, suggest that OLE RNA carries out a complex and critical function only in certain extremophilic bacteria.isoprenoid ͉ riboswitch ͉ ribozyme ͉ superoperon I n recent years, a large number of small noncoding RNAs (1-3) have been identified in eubacteria (4), archaea (5), and eukaryotes (6). In many instances, novel noncoding RNAs in bacteria have been discovered by using bioinformatics search strategies (e.g., refs. 7-13) that take advantage of the conserved nucleotide sequences and secondary structures of these functional RNAs. Another productive way to identify numerous noncoding RNAs from bacteria is by cloning and sequencing small RNAs isolated from cell extracts (e.g., refs. 13-16), and this approach is useful particularly for those examples that are not well conserved through evolution.RNAs such as tRNAs, rRNAs, and some ribozymes have noncoding functions that have long been known to be central to RNA processing and protein synthesis mechanisms. However, it seems possible that additional noncoding RNAs will be found that perform fundamental biochemical tasks that to date have been assumed to be the exclusive province of protein factors. A number of noncoding RNAs discovered recently have proven to participate as the key components of gene regulation systems (e.g., refs. 17-19). Additional examples of widespread noncoding RNAs in bacteria, such as 6S RNA (20-22), the dual-function tmRNA (23), and noncoding portions of messenger RNAs such as T-Box elements (24) and riboswitches (25-27) perform important gene control and molecular sensing tasks that are critical for cells to function normally. The existence of so many RNAs with atypical functions implies that some newly discovered noncoding RNAs might perform surprising and important roles in fundamental cellular processes. In this article, we describe features of a noncoding RNA element whose size, structural sophistication, and unique phylogenetic distribution are suggestive of a complex biological function. ResultsIdentifying Ornate, Large, Extremophilic (OLE) RNAs by Using Bioinformatics. We have previously used computer-aided search strategies that employ comparative sequence analysis (e.g., refs. 11 and 28-30) to identify noncoding RNAs whose nucleotide sequences and secondary structures are c...

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“…6S RNA presents a DNA promoter-like secondary structure consisting of two long irregular double-stranded stem regions, which are interrupted by small bulge loops and a largely single-stranded internal loop in the central region. Along the central bulge and through the continuous stem sequences there are mostly adenines (A) and guanines (G) (Barrick et al, 2005), which were described to interact preferably with histidine (Hoffman et al, 2004). Interestingly, in newly described aspects on the function of 6S RNA, A and G were also identified as specific nucleotides involved in close contact with RNA polymerase (Gildehaus et al, 2007).…”

Section: Chromatographic Separation Of Srna 6smentioning

confidence: 99%

A new affinity approach to isolate Escherichia coli 6S RNA with histidine‐chromatography

Martins

Queiroz

Sousa

2010

J of Molecular Recognition

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6S RNA is an abundant non-coding RNA in Escherichia coli (E. coli), but its function has not been discovered until recently. The first advance on 6S RNA function was the demonstration of its ability to bind the s 70 -holoenzyme form of RNA polymerase, inhibiting its activity and consequently the transcription process. The growing interest in the investigation of non-coding small RNAs (sRNA) calls for the development of new methods for isolation and purification of RNA. This work presents an optimized RNA extraction procedure and describes a new affinity chromatography method using a histidine support to specifically purify 6S RNA from other E. coli sRNA species. The RNA extraction procedure was optimized, and a high yield was obtained in the separation of sRNA and ribosomal RNA (rRNA) from total RNA (RNAt). This improved method takes advantage of its simplicity and significant cost reduction, since some complex operations have been eliminated. A purification strategy was also developed to separate 6S RNA from an sRNA mixture. Pure RNA can be advantageously obtained using the histidine-affinity chromatography method, aiming at its application to structural or functional studies.

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6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter

Cited by 212 publications

References 42 publications

Legionella pneumophila 6S RNA optimizes intracellular multiplication

Legionella pneumophila 6S RNA optimizes intracellular multiplication

Identification of a large noncoding RNA in extremophilic eubacteria

A new affinity approach to isolate Escherichia coli 6S RNA with histidine‐chromatography

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