title: Identification of Unannotated Small Genes inSalmonella.
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 bacteriumSalmonella entericaTyphimurium 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 obtainedSalmonellatranslatomes from four different growth conditions: LB, MOPS rich defined medium, and two infection-relevant conditions low Mg2+(10 µM) and low pH (5.8). To facilitate the identification of small genes, ribosome profiling data were analyzed in combination within silicopredicted 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 Mg2+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.
authors.affiliation: Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Illinois 60607.
authors.forename: Jonghwan
authors.initials: J
authors.lastname: Baek
authors.affiliation: Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Illinois 60607.
authors.forename: Jiyoung
authors.initials: J
authors.lastname: Lee
authors.affiliation: Next Sci Solutions, San Antonio, Texas 78256.
authors.forename: Kihoon
authors.initials: K
authors.lastname: Yoon
authors.affiliation: Department of Biopharmaceutical Sciences, University of Illinois at Chicago, Illinois 60607 hlee31@uic.edu.|Center for Biomolecular Sciences, College of Pharmacy, University of Illinois at Chicago, Illinois 60607.
authors.forename: Hyunwoo
authors.initials: H
authors.lastname: Lee
mesh_terms: D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D058977:Molecular Sequence Annotation; D016366:Open Reading Frames / Q000235:genetics; D015203:Reproducibility of Results; D012475:Salmonella / Q000235:genetics*
keywords: genome annotation; ribosome profiling; short ORF; small genes; small proteins