Identification of small RNAs in diverse bacterial species

Livny, Jonathan; Waldor, Matthew K.

doi:10.1016/j.mib.2007.03.005

Cited by 159 publications

(125 citation statements)

References 46 publications

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“…Initially, these involved systematic bioinformatic searches for conserved intergenic sequence elements with accompanying orphan promoters and terminators in Escherichia coli (10). This was followed by the development of microarrays specific to intergenic regions (2,11,12).…”

mentioning

confidence: 99%

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

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SUMMARY Bacteria can employ widely diverse RNA molecules to regulate their gene expression. Such molecules include trans -acting small regulatory RNAs, antisense RNAs, and a variety of transcriptional attenuation mechanisms in the 5′ untranslated region. Thus far, most regulatory RNA research has focused on Gram-negative bacteria, such as Escherichia coli and Salmonella . Hence, there is uncertainty about whether the resulting insights can be extrapolated directly to other bacteria, such as the Gram-positive soil bacterium Bacillus subtilis . A recent study identified 1,583 putative regulatory RNAs in B. subtilis , whose expression was assessed across 104 conditions. Here, we review the current understanding of RNA-based regulation in B. subtilis , and we categorize the newly identified putative regulatory RNAs on the basis of their conservation in other bacilli and the stability of their predicted secondary structures. Our present evaluation of the publicly available data indicates that RNA-mediated gene regulation in B. subtilis mostly involves elements at the 5′ ends of mRNA molecules. These can include 5′ secondary structure elements and metabolite-, tRNA-, or protein-binding sites. Importantly, sense-independent segments are identified as the most conserved and structured potential regulatory RNAs in B. subtilis . Altogether, the present survey provides many leads for the identification of new regulatory RNA functions in B. subtilis .

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mentioning

confidence: 99%

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Mars

Nicolas

Denham

et al. 2016

Microbiol Mol Biol Rev

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“…Bacterial sRNAs are small non-coding RNA species (50-500 nucleotides), which regulate gene expression via base pairing with mRNA transcripts in a similar mechanism to eukaryotic siRNA or miRNA (Storz et al, 2004;Majdalani et al, 2005;Livny & Waldor, 2007;Gottesman & Storz, 2010). Hfq controls gene expression either by rearranging the RNA secondary structure, or by increasing the concentration of RNA locally to promote RNA-RNA interactions (Moll et al, 2003;Lease & Woodson, 2004;Afonyushkin et al, 2005).…”

Section: Specific Functions Of Bacterial Hfqmentioning

confidence: 99%

The Lsm Proteins: Ring Architectures for RNA Capture

Moll¹,

Sobti²,

Mabbutt³

2011

RNA Processing

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“…Recently, the intergenic regions (IGRs) of selected bacteria and yeast genomes were systematically searched for non-coding RNA genes. These computational screenings involved a combination of criteria, including large gaps between protein-coding genes 7,17 even though in Sulfolobus solfataricus, 13 small RNAs (sRNAs) have been found encoded either within, or overlapping, annotated open reading frames. 9 Recently Vogel and co-workers presented a generic strategy for the systems-level analysis of the post-transcriptional regulons of RNA-binding proteins and for sRNA discovery in a wide range of bacteria by using high-throughput sequencing technology.…”

Section: Bacterial Srna and Gene Regulationmentioning

confidence: 99%

“…Several sRNAs have been identified in V. cholerae through genetic screens and computational methods. [16][17][18] Lenz et al 16 used the following parameters in their analysis: (1) a σ54 binding site at the upstream region of the sRNA locus; (2) Rho-independent terminators (3) in IGRs (4) the sRNA must be conserved in V. cholerae, V. parahaemolyticus and V. vulnificus. They discovered the four sRNA (Qrr1-4) in V. cholerae.…”

Section: Why Couldn't Genome-wide Bioinformatics Programs Predict Vrra?mentioning

confidence: 99%

A novel sRNA that modulates virulence and environmental fitness ofVibrio cholerae

Song

Wai²

2009

RNA Biology

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Identification of small RNAs in diverse bacterial species

Cited by 159 publications

References 46 publications

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression

The Lsm Proteins: Ring Architectures for RNA Capture

A novel sRNA that modulates virulence and environmental fitness ofVibrio cholerae

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