ArticleBMC genomics2014
Expression of antisense small RNAs in response to stress in Pseudomonas aeruginosa.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed, 32 citations in OpenAlex.
- Direct RNA Nanopore Sequencing of Pseudomonas aeruginosa Clone C Transcriptomes.Journal of bacteriology · 2022Article
- Global identification of RsmA/N binding sites inRNA biology · 2021Article
- Oxidative Stress Response inPathogens (Basel, Switzerland) · 2021Review
- Article
- A Novel Regulation of K-antigen Capsule Synthesis inFrontiers in oral health · 2021Article
- Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions.BMC genomics · 2020Article
- Full Transcriptomic Response ofFrontiers in microbiology · 2020Article
- AmBio · 2019Article
- Within-Host Adaptation Mediated by Intergenic Evolution in Pseudomonas aeruginosa.Genome biology and evolution · 2019Article
- Coherent Feedforward Regulation of Gene Expression by Caulobacter σJournal of bacteriology · 2018Article
- cAMP and Vfr Control Exolysin Expression and Cytotoxicity of Pseudomonas aeruginosa Taxonomic Outliers.Journal of bacteriology · 2018Article
- Antisense transcription in Pseudomonas aeruginosa.Microbiology (Reading, England) · 2018Article
- Identification of sRNA mediated responses to nutrient depletion in Burkholderia pseudomallei.Scientific reports · 2017Article
- Global Transcriptional Responses to Osmotic, Oxidative, and Imipenem Stress Conditions in Pseudomonas putida.Applied and environmental microbiology · 2017Article
- Systems-level understanding of ethanol-induced stresses and adaptation in E. coli.Scientific reports · 2017Article
- Comparative evaluation of rRNA depletion procedures for the improved analysis of bacterial biofilm and mixed pathogen culture transcriptomes.Scientific reports · 2017Article
- A computational strategy for the search of regulatory small RNAs in Actinobacillus pleuropneumoniae.RNA (New York, N.Y.) · 2016Article
- Identification and functional analysis of a bacteriocin, pyocin S6, with ribonuclease activity from a Pseudomonas aeruginosa cystic fibrosis clinical isolate.MicrobiologyOpen · 2016Article
- Bacterial antisense RNAs are mainly the product of transcriptional noise.Science advances · 2016Article
- A Transcriptome Map of Actinobacillus pleuropneumoniae at Single-Nucleotide Resolution Using Deep RNA-Seq.PloS one · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundRNA sequencing technologies reveal that bacteria express RNA molecules other than mRNA, rRNA or tRNA. During the last years genome-wide bacterial transcriptomes have been shown to comprise intergenic RNA, antisense RNA, and untranslated regions, all capable of performing diverse regulatory functions.
resultsIn this study we used RNA-seq to identify 232 antisense RNAs (asRNAs) in the opportunistic pathogen Pseudomonas aeruginosa grown under 13 different conditions. The conditions studied include exponential and stationary growth as well as osmotic, oxidative and antibiotic stress. We found a significant overrepresentation of asRNAs that are transcribed opposite to genes involved in cell division and in cell wall, lipopolysaccharide (LPS), and capsule biosynthesis, most likely reflecting the conditions used in this study. A substantial number of asRNAs significantly changed their expression under osmotic, oxidative and antibiotic stress, suggesting that asRNAs may play regulatory roles during these conditions. We also made a comparison between the asRNAs detected in this study in P. aeruginosa PAO1 with the asRNAs detected in two previous studies in P. aeruginosa PA14, and found that the extent of overlap between the studies is very limited.
conclusionsRNA-seq experiments are revealing hundreds of novel transcripts in all bacterial genomes investigated. The comparison between independent studies that used RNA-seq to detect novel asRNAs in P. aeruginosa shows that the overlap between the results reported is very narrow. It is necessary to address how reproducibility of these kind of studies should be reported in order to avoid misleading conclusions when comparing data generated by non-identical methods.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.