TargetRNA2: identifying targets of small regulatory RNAs in bacteria

Kery, Mary Beth; Feldman, Mónica; Livny, Jonathan; Tjaden, Brian

doi:10.1093/nar/gku317

Cited by 177 publications

(177 citation statements)

References 23 publications

(43 reference statements)

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“…As it has been proposed before (Gruber and Sperandio 2015;Kim et al 2015;Peng et al 2015), computational analysis of the sRNAs' targets is an excellent starting point toward understanding their physiological roles in the cell. Here, we used TargetRNA2 as a target predictor for being the algorithm with the best correlation of targets predicted and actually confirmed, among the programs widely used for this purpose (Kery et al 2014). Because many of the mRNAs predicted are potential targets of more than one sRNA, these regulators may share some of their targets, placing them in a characteristic entangled network of gene regulation (Modi et al 2011).…”

Section: Discussionmentioning

confidence: 71%

“…To investigate the possible targets and roles of the aforementioned validated trans-acting sRNAs (Arrc01,02,04,05,07,08,11,14,17,20, and 21), we performed a computational target prediction with TargetRNA2 (Kery et al 2014), considering all the annotated ORFs in the A. pleuropneumoniae L20 genome. The interactions within the vicinity of the mRNA translational start site with the lowest energies and P-value below 0.05 were considered to indicate the best mRNA candidates.…”

Section: Rna Sequencingmentioning

confidence: 99%

“…Searches were performed with the software TargetRNA2 (Kery et al 2014), considering the conservation (compared to every sequenced replicon available in GenBank) and accessibility of each sRNA given as input, structural accessibility of the mRNA and potential interactions preceded by a hybridization seed around the translation start site, from 80 nt upstream to 20 nt downstream from it. Only target interactions with a P-value less than or equal to 0.05 were reported.…”

Section: Investigation Of Putative Mrna Targetsmentioning

confidence: 99%

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A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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Bacterial regulatory small RNAs (sRNAs) play important roles in gene regulation and are frequently connected to the expression of virulence factors in diverse bacteria. Only a few sRNAs have been described for Pasteurellaceae pathogens and no in-depth analysis of sRNAs has been described for Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, responsible for considerable losses in the swine industry. To search for sRNAs in A. pleuropneumoniae, we developed a strategy for the computational analysis of the bacterial genome by using four algorithms with different approaches, followed by experimental validation. The coding strand and expression of 17 out of 23 RNA candidates were confirmed by Northern blotting, RT-PCR, and RNA sequencing. Among them, two are likely riboswitches, three are housekeeping regulatory RNAs, two are the widely studied GcvB and 6S sRNAs, and 10 are putative novel trans-acting sRNAs, never before described for any bacteria. The latter group has several potential mRNA targets, many of which are involved with virulence, stress resistance, or metabolism, and connect the sRNAs in a complex gene regulatory network. The sRNAs identified are well conserved among the Pasteurellaceae that are evolutionarily closer to A. pleuropneumoniae and/or share the same host. Our results show that the combination of newly developed computational programs can be successfully utilized for the discovery of novel sRNAs and indicate an intricate system of gene regulation through sRNAs in A. pleuropneumoniae and in other Pasteurellaceae, thus providing clues for novel aspects of virulence that will be explored in further studies.

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Section: Discussionmentioning

confidence: 71%

Section: Rna Sequencingmentioning

confidence: 99%

Section: Investigation Of Putative Mrna Targetsmentioning

confidence: 99%

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A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

Rossi

Bossé

et al. 2016

RNA

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“…Heme regulation via the PrrF and/or PrrH sRNAs may also To explore this hypothesis, we used the updated TargetRNA2 algorithm (48) to search for potential PrrH-specific targets with links to virulence. This analysis identified an extensive region of complementarity between the PrrH unique sequence and the translational start site and coding sequence of the vreR mRNA (Fig.…”

Section: Figmentioning

confidence: 99%

The prrF -Encoded Small Regulatory RNAs Are Required for Iron Homeostasis and Virulence of Pseudomonas aeruginosa

et al. 2015

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Pseudomonas aeruginosa is an opportunistic pathogen that requires iron to cause infection, but it also must regulate the uptake of iron to avoid iron toxicity. The iron-responsive PrrF1 and PrrF2 small regulatory RNAs (sRNAs) are part of P. aeruginosa's iron regulatory network and affect the expression of at least 50 genes encoding iron-containing proteins. The genes encoding the PrrF1 and PrrF2 sRNAs are encoded in tandem in P. aeruginosa, allowing for the expression of a distinct, heme-responsive sRNA named PrrH that appears to regulate genes involved in heme metabolism. Using a combination of growth, mass spectrometry, and gene expression analysis, we showed that the ⌬prrF1,2 mutant, which lacks expression of the PrrF and PrrH sRNAs, is defective for both iron and heme homeostasis. We also identified phuS, encoding a heme binding protein involved in heme acquisition, and vreR, encoding a previously identified regulator of P. aeruginosa virulence genes, as novel targets of prrF-mediated heme regulation. Finally, we showed that the prrF locus encoding the PrrF and PrrH sRNAs is required for P. aeruginosa virulence in a murine model of acute lung infection. Moreover, we showed that inoculation with a ⌬prrF1,2 deletion mutant protects against future challenge with wild-type P. aeruginosa. Combined, these data demonstrate that the prrF-encoded sRNAs are critical regulators of P. aeruginosa virulence. Pseudomonas aeruginosa is a ubiquitous Gram-negative bacterium and versatile opportunistic pathogen. Iron is required for P. aeruginosa virulence (1-6) and is obtained through several mechanisms. In anaerobic environments, iron in its ferrous form is freely diffusible through the outer membrane (OM) and transported into the cytoplasm by the Feo inner membrane transport system (7,8). However, the insolubility of ferric iron in aerobic environments limits accessibility to this nutrient. Moreover, the sequestration of iron by host proteins creates a substantial barrier to infection (9, 10). To overcome this barrier, P. aeruginosa synthesizes and secretes two siderophores, pyoverdine and pyochelin, which scavenge ferric iron (1-4). P. aeruginosa can also acquire heme, an abundant source of iron in the human host (11). Once internalized, heme is sequestered by the cytosolic PhuS heme chaperone (12). PhuS transfers heme to the iron-regulated HemO heme oxygenase, which degrades heme to biliverdin, releasing carbon monoxide and iron (13,14). Several studies have shown that iron acquisition is essential for P. aeruginosa virulence (1-5) and biofilm formation (15-17), demonstrating the central role of this element in P. aeruginosa pathogenesis.Despite its essentiality, iron and heme can be toxic due to their ability to catalyze the formation of reactive oxygen species. Thus, to maintain iron homeostasis, P. aeruginosa must be able to not only acquire iron but also regulate uptake of iron and heme from the environment, as well as iron use and storage. Expression of genes encoding iron and heme uptake systems in P. aeruginosa is ...

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“…BLAST and intaRNA (Altschul et al 1990;Busch et al 2008) were implemented in the database while external Staphylococcus sRNA database www.rnajournal.org 1011 links to RNAtarget2 (Kery et al 2014) and to RNA predator (Eggenhofer et al 2011) are easily accessible from the webpage describing each sRNA. For BLAST comparisons, our databank includes the four initial reference genomes, the lists of validated sRNAs, and all the srn curated in the four strains.…”

Section: Srd Specific Featuresmentioning

confidence: 99%

SRD: a Staphylococcus regulatory RNA database

Sassi

Augagneur

Mauro

et al. 2015

RNA

108

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An overflow of regulatory RNAs (sRNAs) was identified in a wide range of bacteria. We designed and implemented a new resource for the hundreds of sRNAs identified in Staphylococci, with primary focus on the human pathogen Staphylococcus aureus. The "Staphylococcal Regulatory RNA Database" (SRD, http://srd.genouest.org/) compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes novel and simplified identifiers for Staphylococcal regulatory RNAs (srn) based on the sRNA's genetic location in S. aureus strain N315 which served as a reference. From a set of 894 sequences and after an in-depth cleaning, SRD provides a list of 575 srn exempt of redundant sequences. For each sRNA, their experimental support(s) is provided, allowing the user to individually assess their validity and significance. RNAseq analysis performed on strains N315, NCTC8325, and Newman allowed us to provide further details, upgrade the initial annotation, and identified 159 RNA-seq independent transcribed sRNAs. The lists of 575 and 159 sRNAs sequences were used to predict the number and location of srns in 18 S. aureus strains and 10 other Staphylococci. A comparison of the srn contents within 32 Staphylococcal genomes revealed a poor conservation between species. In addition, sRNA structure predictions obtained with MFold are accessible. A BLAST server and the intaRNA program, which is dedicated to target prediction, were implemented. SRD is the first sRNA database centered on a genus; it is a user-friendly and scalable device with the possibility to submit new sequences that should spread in the literature.

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TargetRNA2: identifying targets of small regulatory RNAs in bacteria

Cited by 177 publications

References 23 publications

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae

The prrF -Encoded Small Regulatory RNAs Are Required for Iron Homeostasis and Virulence of Pseudomonas aeruginosa

SRD: a Staphylococcus regulatory RNA database

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