ArticleBMC genomics2011
Identification and functional characterization of small non-coding RNAs in Xanthomonas oryzae pathovar oryzae.
Article in BMC genomics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 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
19 citing papers in PubMed, 38 citations in OpenAlex.
- Codon bias shapes bacterial small RNA binding sites within protein-coding sequences.RNA (New York, N.Y.) · 2026Article
- Strain ofPlants (Basel, Switzerland) · 2024Article
- Genome-Wide Computational Prediction and Analysis of Noncoding RNAs inMicroorganisms · 2024Article
- Suppression of host plant defense by bacterial small RNAs packaged in outer membrane vesicles.Plant communications · 2024Article
- The Role of Iron in Phytopathogenic Microbe-Plant Interactions: Insights into Virulence and Host Immune Response.Plants (Basel, Switzerland) · 2023Review
- Hfq Is a Critical Modulator of Pathogenicity ofMicroorganisms · 2022Article
- Do small RNAs unlock the below ground microbiome-plant interaction mystery?Frontiers in molecular biosciences · 2022Review
- A key antisense sRNA modulates the oxidative stress response and virulence in Xanthomonas oryzae pv. oryzicola.PLoS pathogens · 2021Article
- Genome-wide screen and functional analysis in Xanthomonas reveal a large number of mRNA-derived sRNAs, including the novel RsmA-sequester RsmU.Molecular plant pathology · 2020Article
- Local-to-global signal transduction at the core of a MnNature communications · 2019Article
- Biological and transcriptomic studies reveal hfq is required for swimming, biofilm formation and stress response in Xanthomonas axonpodis pv. citri.BMC microbiology · 2019Article
- Two virulent sRNAs identified by genomic sequencing target the type III secretion system in rice bacterial blight pathogen.BMC plant biology · 2018Article
- Small RNAs--the secret agents in the plant-pathogen interactions.Current opinion in plant biology · 2015Review
- Determination of essentiality and regulatory function of staphylococcal YeaZ in branched-chain amino acid biosynthesis.Virulence · 2015Article
- Small non-coding RNAs in plant-pathogenic Xanthomonas spp.RNA biology · 2014Review
- Small RNA sX13: a multifaceted regulator of virulence in the plant pathogen Xanthomonas.PLoS pathogens · 2013Article
- Computational small RNA prediction in bacteria.Bioinformatics and biology insights · 2013Article
- Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.Nucleic acids research · 2012Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSmall non-coding RNAs (sRNAs) are regarded as important regulators in prokaryotes and play essential roles in diverse cellular processes. Xanthomonas oryzae pathovar oryzae (Xoo) is an important plant pathogenic bacterium which causes serious bacterial blight of rice. However, little is known about the number, genomic distribution and biological functions of sRNAs in Xoo.
resultsHere, we performed a systematic screen to identify sRNAs in the Xoo strain PXO99. A total of 850 putative non-coding RNA sequences originated from intergenic and gene antisense regions were identified by cloning, of which 63 were also identified as sRNA candidates by computational prediction, thus were considered as Xoo sRNA candidates. Northern blot hybridization confirmed the size and expression of 6 sRNA candidates and other 2 cloned small RNA sequences, which were then added to the sRNA candidate list. We further examined the expression profiles of the eight sRNAs in an hfq deletion mutant and found that two of them showed drastically decreased expression levels, and another exhibited an Hfq-dependent transcript processing pattern. Deletion mutants were obtained for seven of the Northern confirmed sRNAs, but none of them exhibited obvious phenotypes. Comparison of the proteomic differences between three of the ΔsRNA mutants and the wild-type strain by two-dimensional gel electrophoresis (2-DE) analysis showed that these sRNAs are involved in multiple physiological and biochemical processes.
conclusionsWe experimentally verified eight sRNAs in a genome-wide screen and uncovered three Hfq-dependent sRNAs in Xoo. Proteomics analysis revealed Xoo sRNAs may take part in various metabolic processes. Taken together, this work represents the first comprehensive screen and functional analysis of sRNAs in rice pathogenic bacteria and facilitates future studies on sRNA-mediated regulatory networks in this important phytopathogen.
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.