ArticleRNA biology2016
Novel small RNA (sRNA) landscape of the starvation-stress response transcriptome of Salmonella enterica serovar typhimurium.
Article in RNA biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 31 citations in OpenAlex.
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- Understanding the Effect of Different Glucose Concentrations in the Oligotrophic BacteriumMicroorganisms · 2023Article
- Characterization of a novel sRNA contributing to biofilm formation inmicroPublication biology · 2023Article
- Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus.Functional & integrative genomics · 2022Article
- Characterization of 475 Novel, Putative Small RNAs (sRNAs) in Carbon-StarvedAntibiotics (Basel, Switzerland) · 2021Article
- Genome-wide identification of Azospirillum brasilense Sp245 small RNAs responsive to nitrogen starvation and likely involvement in plant-microbe interactions.BMC genomics · 2020Article
- The RNA-binding protein Hfq assembles into foci-like structures in nitrogen starvedThe Journal of biological chemistry · 2020Article
- Phenotypes, transcriptome, and novel biofilm formation associated with the ydcI gene.Antonie van Leeuwenhoek · 2020Article
- The Novel ncRNA OsiR Positively Regulates Expression ofInternational journal of molecular sciences · 2020Article
- Characterization of novel small RNAs (sRNAs) contributing to the desiccation response ofRNA biology · 2019Article
- APERO: a genome-wide approach for identifying bacterial small RNAs from RNA-Seq data.Nucleic acids research · 2019Article
- Small RNA AvrA Regulates IscR to Increase the Stress Tolerances in SmpB Deficiency ofFrontiers in cellular and infection microbiology · 2019Article
- The unusual glycine-rich C terminus of theThe Journal of biological chemistry · 2018Article
- The Stringent Response-Regulated sRNA Transcriptome ofFrontiers in cellular and infection microbiology · 2018Article
- Small regulatory bacterial RNAs regulating the envelope stress response.Biochemical Society transactions · 2017Review
- Review
- Preliminary Transcriptome Analysis of Mature Biofilm and Planktonic Cells ofFrontiers in microbiology · 2017Article
- SaaS sRNA promotesGut microbesArticle
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Authors and funding
24 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNAs (sRNAs) are short (∼50-200 nucleotides) noncoding RNAs that regulate cellular activities across bacteria. Salmonella enterica starved of a carbon-energy (C) source experience a host of genetic and physiological changes broadly referred to as the starvation-stress response (SSR). In an attempt to identify novel sRNAs contributing to SSR control, we grew log-phase, 5-h C-starved and 24-h C-starved cultures of the virulent Salmonella enterica subspecies enterica serovar Typhimurium strain SL1344 and comprehensively sequenced their small RNA transcriptomes. Strikingly, after employing a novel strategy for sRNA discovery based on identifying dynamic transcripts arising from "gene-empty" regions, we identify 58 wholly undescribed Salmonella sRNA genes potentially regulating SSR averaging an ∼1,000-fold change in expression between log-phase and C-starved cells. Importantly, the expressions of individual sRNA loci were confirmed by both comprehensive transcriptome analyses and northern blotting of select candidates. Of note, we find 43 candidate sRNAs share significant sequence identity to characterized sRNAs in other bacteria, and ∼70% of our sRNAs likely assume characteristic sRNA structural conformations. In addition, we find 53 of our 58 candidate sRNAs either overlap neighboring mRNA loci or share significant sequence complementarity to mRNAs transcribed elsewhere in the SL1344 genome strongly suggesting they regulate the expression of transcripts via antisense base-pairing. Finally, in addition to this work resulting in the identification of 58 entirely novel Salmonella enterica genes likely participating in the SSR, we also find evidence suggesting that sRNAs are significantly more prevalent than currently appreciated and that Salmonella sRNAs may actually number in the thousands.
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