Identifying Small Open Reading Frames in Prokaryotes with Ribosome Profiling

Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations o...

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Published inJournal of bacteriology Vol. 204; no. 1; p. e0029421
Main Authors Vazquez-Laslop, Nora, Sharma, Cynthia M, Mankin, Alexander, Buskirk, Allen R
Format Journal Article
LanguageEnglish
Published United States American Society for Microbiology 18.01.2022
Subjects
Annotations
Anti-Bacterial Agents - pharmacology
Antibiotics
Bacteria - genetics
Bacteria - metabolism
Bacteriology
Codon
Codons
Gene Expression Regulation, Bacterial - drug effects
Gene Expression Regulation, Bacterial - physiology
Genomes
Genomics and Proteomics
Meeting Review
Open Reading Frames
Peptide Chain Initiation, Translational
Peptide Chain Termination, Translational
Prokaryotes
Ribosomes
RNA, Bacterial
RNA, Ribosomal
Special Sections: Small Proteins, Big Questions 2021
ribosome profiling
genome annotation
sORF
small protein
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Summary:Small proteins encoded by open reading frames (ORFs) shorter than 50 codons (small ORFs [sORFs]) are often overlooked by annotation engines and are difficult to characterize using traditional biochemical techniques. Ribosome profiling has tremendous potential to empirically improve the annotations of prokaryotic genomes. Recent improvements in ribosome profiling methods for bacterial model organisms have revealed many new sORFs in well-characterized genomes. Antibiotics that trap ribosomes just after initiation have played a key role in these developments by allowing the unambiguous identification of the start codons (and, hence, the reading frame) for novel ORFs. Here, we describe these new methods and highlight critical controls and considerations for adapting ribosome profiling to different prokaryotic species.
Bibliography:Citation Vazquez-Laslop N, Sharma CM, Mankin A, Buskirk AR. 2022. Identifying small open reading frames in prokaryotes with ribosome profiling. J Bacteriol 204:e00294-21. https://doi.org/10.1128/JB.00294-21.
The authors declare no conflict of interest.
ISSN:0021-9193
1098-5530
DOI:10.1128/JB.00294-21