Identification of a large noncoding RNA in extremophilic eubacteria

Puerta-Fernández, Elena; Barrick, Jeffrey E.; Roth, Adam; Breaker, Ronald R.

doi:10.1073/pnas.0607493103

Cited by 37 publications

(95 citation statements)

References 54 publications

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“…In particular, Barrick et al [4] used a pairwise, BLAST-based approach to discover novel riboswitch candidates in bacterial genomes, many of which now have been experimentally verified. Similar studies have been conducted in various bacterial groups [5–8]. More recent work has extended these searches to eukaryotes [9–13], discovering a large number of known microRNAs while producing thousands of novel ncRNA candidates.…”

Section: Introductionmentioning

confidence: 73%

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

et al. 2007

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Noncoding RNAs (ncRNAs) are important functional RNAs that do not code for proteins. We present a highly efficient computational pipeline for discovering cis-regulatory ncRNA motifs de novo. The pipeline differs from previous methods in that it is structure-oriented, does not require a multiple-sequence alignment as input, and is capable of detecting RNA motifs with low sequence conservation. We also integrate RNA motif prediction with RNA homolog search, which improves the quality of the RNA motifs significantly. Here, we report the results of applying this pipeline to Firmicute bacteria. Our top-ranking motifs include most known Firmicute elements found in the RNA family database (Rfam). Comparing our motif models with Rfam's hand-curated motif models, we achieve high accuracy in both membership prediction and base-pair–level secondary structure prediction (at least 75% average sensitivity and specificity on both tasks). Of the ncRNA candidates not in Rfam, we find compelling evidence that some of them are functional, and analyze several potential ribosomal protein leaders in depth.

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Section: Introductionmentioning

confidence: 73%

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

et al. 2007

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“…The resulting DNA construct was cloned into a TOPO-TA vector (Invitrogen), transformed into Top10 E. coli cells (Invitrogen), and the resulting plasmid was isolated from cells using the Qiaprep Spin Miniprep Kit (QIAGEN) following protocols supplied by the manufacturers. DNA sequencing (The Keck Foundation Biotechnology Resource Center, Yale University) confirmed successful cloning, and all constructs used in this work were generated from this plasmid by PCR with appropriate synthetic DNA primers using methods similar to those described elsewhere (Puerta-Fernandez et al 2006). …”

Section: Chemicals and Oligonucleotidesmentioning

confidence: 99%

Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis

Welz

Breaker²

2007

RNA

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Most riboswitches are composed of a single metabolite-binding aptamer and a single expression platform that function together to regulate genes in response to changing metabolite concentrations. In rare instances, two aptamers or sometimes two complete riboswitches reside adjacent to each other in untranslated regions (UTRs) of mRNAs. We have examined an example of a tandem riboswitch in the Gram-positive bacterium Bacillus anthracis that includes two complete riboswitches for thiamine pyrophosphate (TPP). Unlike other complex riboswitch systems described recently, tandem TPP riboswitches do not exhibit cooperative ligand binding and do not detect two different types of metabolites. In contrast, both riboswitches respond independently to TPP and are predicted to function in concert to mimic the more ''digital'' gene control outcome observed when two aptamers bind ligands cooperatively. Our findings further demonstrate that simple gene control elements made only of RNA can be assembled in different architectures to yield more complex gene control outcomes.

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“…The size of OLE RNA is much bigger than those of riboswitches, and the metabolite responding to OLE RNA has not been identified. Therefore, OLE RNA was suggested as a novel gene regulation element (1). In relation to this, the gene product of which is located downstream of OLE RNA, BH2780 in B. halodurans, is known to make a complex with OLE RNA in vitro, and the complex is found in a cellular membrane fraction (R. Breaker, personal communication).…”

Section: Discussionmentioning

confidence: 99%

OLE RNA, an RNA motif that is highly conserved in several extremophilic bacteria, is a substrate for and can be regulated by RNase P RNA

Altman

2007

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

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OLE (ornate, large, and extremophilic) RNA is a noncoding RNA that is found in several extremophilic bacteria, including Bacillus halodurans. The function of OLE RNA has not been clarified. In this study, we found that RNase P cleaves OLE RNA and that the cleavage leads to a small reduction of expression of a downstream gene determined by analyses in vitro and in vivo. Under RNase P-deficient conditions, the amount of OLE RNA increased. Our results imply that RNase P could play a role in the regulation of gene expression in relation to conserved RNA motifs like OLE RNA as well as in riboswitches and operons. Bacillus haloduransO LE (ornate, large, and extremophilic) RNA is a highly conserved RNA motif that is found in several extremophilic Gram-positive eubacteria (1). It was identified with bioinformatic approaches for finding additional riboswitches. However, OLE RNA has different biological characteristics from those of riboswitches and is believed to be a different type of RNA element that is involved in gene regulation (1). In Bacillus halodurans, an extremophilic bacterium widely used for industrial purposes, OLE RNA is located between the BH2780 and BH2781 genes (Fig. 1). Although the functions of OLE and BH2780 RNAs have yet to be understood, OLE RNA can form a complex in vitro with the BH2780 protein, which is a possible transmembrane protein, suggesting that OLE RNA might play a role in a fundamental cellular process as a ribonucleoprotein complex (R. Breaker, personal communication). It is also unknown whether OLE RNA regulates the expression of downstream genes, and it is not apparent that the transcript of OLE RNA extends through the beginning of the BH2780 gene.RNase P is a well known endoribonuclease that is responsible for the 5Ј maturation of tRNA and several RNA molecules, including 4.5S RNA and operons in eubacteria (2). Besides these substrates, RNase P cleaves transient structures of some riboswitches, such as coenzyme B12 riboswitch in Escherichia coli (3,4). Here, we show that RNase P cleaves OLE RNA and that this cleavage can affect the expression of a downstream gene in vivo. This kind of RNase P function might be more general than is anticipated in bacterial species. ResultsRiboswitches are RNA elements regulating gene expression downstream of these elements by responding to metabolites, which are produced by the downstream gene product (4). In a previous report, we showed that cleavages by RNase P lead to the reduction of downstream genes in an operon by using lacZ as a reporter gene (3).␤-Galactosidase Activity in Wild-Type and Mutant Strains of RNase P in E. coli. The effects of the cleavages by RNase P on OLE RNA in vivo were investigated by using a model system with a lacZ reporter gene (Fig. 2). The plasmids pOLE-lacZ and pBADlacZ, a control plasmid, were introduced into NHY312 (wildtype) and NHY322 (RNase P ts ) strains. A wild-type strain, MG1693, and the mutant strain of RNase E, SK5665, also were transformed to identify the effects of one of the major endoribonucleases in E. c...

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Identification of a large noncoding RNA in extremophilic eubacteria

Cited by 37 publications

References 54 publications

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

A Computational Pipeline for High- Throughput Discovery of cis-Regulatory Noncoding RNA in Prokaryotes

Ligand binding and gene control characteristics of tandem riboswitches in Bacillus anthracis

OLE RNA, an RNA motif that is highly conserved in several extremophilic bacteria, is a substrate for and can be regulated by RNase P RNA

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