Baek et al. 2017 (PRJNA347980)

General Details

Title Identification of unannotated small genes in Salmonella
Organism
Number of Samples 4
Release Date 2016/10/12 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP091438
ENA SRP091438
GEO GSE87871
BioProject PRJNA347980

Publication

Title
Authors Baek J, Lee J, Yoon K, Lee H
Journal G3 (Bethesda, Md.)
Publication Date 2017 Mar 10
Abstract Increasing evidence indicates that many, if not all, small genes encoding proteins ≤100 aa are missing in annotations of bacterial genomes currently available. To uncover unannotated small genes in the model bacterium Salmonella enterica Typhimurium 14028s, we used the genomic technique ribosome profiling, which provides a snapshot of all mRNAs being translated (translatome) in a given growth condition. For comprehensive identification of unannotated small genes, we obtained Salmonella translatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg 2+ (10 µM) and low pH (5.8). To facilitate the identification of small genes, ribosome profiling data were analyzed in combination with in silico predicted putative open reading frames and transcriptome profiles. As a result, we uncovered 130 unannotated ORFs. Of them, 98% were small ORFs putatively encoding peptides/proteins ≤100 aa, and some of them were only expressed in the infection-relevant low Mg 2+ and/or low pH condition. We validated the expression of 25 of these ORFs by western blot, including the smallest, which encodes a peptide of 7 aa residues. Our results suggest that many sequenced bacterial genomes are underannotated with regard to small genes and their gene annotations need to be revised. Copyright © 2017 Baek et al.
PMC PMC5345727
PMID 28122954
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR4417735 PRJNA347980 Salmonella enterica 0.0 Ribo-Seq 0.0
SRR4417736 PRJNA347980 Salmonella enterica 0.0 Ribo-Seq 0.0
SRR4417737 PRJNA347980 Salmonella enterica 0.0 Ribo-Seq 0.0
SRR4417738 PRJNA347980 Salmonella enterica 0.0 Ribo-Seq 0.0
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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