ArticleBMC genomics2017
Differentiation of ncRNAs from small mRNAs in Escherichia coli O157:H7 EDL933 (EHEC) by combined RNAseq and RIBOseq - ryhB encodes the regulatory RNA RyhB and a peptide, RyhP.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed, 33 citations in OpenAlex.
- Distribution of prophage-encoded Pas sRNAs across pathogenicbioRxiv : the preprint server for biology · 2026Article
- Abridged Ribosome Profiling for Accurate Bacterial Translation Measurements.Methods and protocols · 2026Article
- Uncovering the small proteome of Methanosarcina mazei using Ribo-seq and peptidomics under different nitrogen conditions.Nature communications · 2024Article
- Non-canonical transcriptional start sites in E. coli O157:H7 EDL933 are regulated and appear in surprisingly high numbers.BMC microbiology · 2023Article
- Revealing the small proteome ofmicroLife · 2023Article
- Small RNAs beyond Model Organisms: Have We Only Scratched the Surface?International journal of molecular sciences · 2022Article
- RiboReport - benchmarking tools for ribosome profiling-based identification of open reading frames in bacteria.Briefings in bioinformatics · 2022Article
- Overlapping genes in natural and engineered genomes.Nature reviews. Genetics · 2022Review
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- Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling.Journal of bacteriology · 2022Article
- Small Proteins in Archaea, a Mainly Unexplored World.Journal of bacteriology · 2022Review
- Hundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.Molecular biology and evolution · 2022Article
- Structured RNA Contaminants in Bacterial Ribo-Seq.mSphere · 2020Article
- Recommendations for bacterial ribosome profiling experiments based on bioinformatic evaluation of published data.The Journal of biological chemistry · 2020Article
- A Novel pH-Regulated, Unusual 603 bp Overlapping Protein Coding GeneFrontiers in microbiology · 2020Article
- Are Antisense Proteins in Prokaryotes Functional?Frontiers in molecular biosciences · 2020Article
- Article
- The novel EHEC gene asa overlaps the TEGT transporter gene in antisense and is regulated by NaCl and growth phase.Scientific reports · 2018Article
- After the Fact(or): Posttranscriptional Gene Regulation in Enterohemorrhagic Escherichia coli O157:H7.Journal of bacteriology · 2018Review
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic acids research · 2018Article
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Authors and funding
10 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundWhile NGS allows rapid global detection of transcripts, it remains difficult to distinguish ncRNAs from short mRNAs. To detect potentially translated RNAs, we developed an improved protocol for bacterial ribosomal footprinting (RIBOseq). This allowed distinguishing ncRNA from mRNA in EHEC. A high ratio of ribosomal footprints per transcript (ribosomal coverage value, RCV) is expected to indicate a translated RNA, while a low RCV should point to a non-translated RNA.
resultsBased on their low RCV, 150 novel non-translated EHEC transcripts were identified as putative ncRNAs, representing both antisense and intergenic transcripts, 74 of which had expressed homologs in E. coli MG1655. Bioinformatics analysis predicted statistically significant target regulons for 15 of the intergenic transcripts; experimental analysis revealed 4-fold or higher differential expression of 46 novel ncRNA in different growth media. Out of 329 annotated EHEC ncRNAs, 52 showed an RCV similar to protein-coding genes, of those, 16 had RIBOseq patterns matching annotated genes in other enterobacteriaceae, and 11 seem to possess a Shine-Dalgarno sequence, suggesting that such ncRNAs may encode small proteins instead of being solely non-coding. To support that the RIBOseq signals are reflecting translation, we tested the ribosomal-footprint covered ORF of ryhB and found a phenotype for the encoded peptide in iron-limiting condition.
conclusionDetermination of the RCV is a useful approach for a rapid first-step differentiation between bacterial ncRNAs and small mRNAs. Further, many known ncRNAs may encode proteins as well.
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