ArticleTuberculosis (Edinburgh, Scotland)2013
Reannotation of translational start sites in the genome of Mycobacterium tuberculosis.
Article in Tuberculosis (Edinburgh, Scotland), 2013. 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.
- Within-host pathogen population diversity predicts treatment response in Tuberculosis.medRxiv : the preprint server for health sciences · 2026Article
- The public health utility of whole genome sequencing: Insights from a tuberculosis outbreak in Australia and perspectives of public health professionals.PLOS global public health · 2026Article
- Large-scale proteogenomics characterization of microproteins in Mycobacterium tuberculosis.Scientific reports · 2024Article
- A novel regulatory interplay between atypical B12 riboswitches and uORF translation in Mycobacterium tuberculosis.Nucleic acids research · 2024Article
- The rate and role of pseudogenes of theMicrobial genomics · 2022Article
- On the Occurrence and Multimerization of Two-Polypeptide Phage Endolysins Encoded in Single Genes.Microbiology spectrum · 2022Article
- Comparative genome characterization of Echinicola marina sp. nov., isolated from deep-sea sediment provide insight into carotenoid biosynthetic gene cluster evolution.Scientific reports · 2021Article
- Article
- AssessORF: combining evolutionary conservation and proteomics to assess prokaryotic gene predictions.Bioinformatics (Oxford, England) · 2020Article
- Development and Optimization of Chromosomally-Integrated FluorescentFrontiers in microbiology · 2020Article
- Structure and functional implications of WYL domain-containing bacterial DNA damage response regulator PafBC.Nature communications · 2019Article
- Structural and functional insight into the Mycobacterium tuberculosis protein PrpR reveals a novel type of transcription factor.Nucleic acids research · 2019Article
- Mycobacterium tuberculosis 6C sRNA binds multiple mRNA targets via C-rich loops independent of RNA chaperones.Nucleic acids research · 2019Article
- Cell-wall synthesis and ribosome maturation are co-regulated by an RNA switch in Mycobacterium tuberculosis.Nucleic acids research · 2018Article
- Construction of an overexpression library forBiology methods & protocols · 2018Article
- Article
- Structural Similarities and Differences between Two Functionally Distinct SecA Proteins, Mycobacterium tuberculosis SecA1 and SecA2.Journal of bacteriology · 2015Article
- Environmental Sensing in Actinobacteria: a Comprehensive Survey on the Signaling Capacity of This Phylum.Journal of bacteriology · 2015Article
- Article
- Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis.Cell reports · 2013Article
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3 authors.
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Abstract
Identification and correction of incorrect ORF start sites is important for a variety of experimental and analytical purposes, ranging from cloning to inference of operon structure. The genome of the H37Rv reference strain of Mycobacterium tuberculosis (Mtb) was originally annotated when it was first sequenced nearly 15 years ago. While this annotation has served the TB research community well as a standard of reference for over a decade, it has been demonstrated experimentally that the actual start sites for an estimated 5-10% of open reading frames differ from the annotation. In this paper, we present a comprehensive bioinformatic analysis of all 3989 ORFs (open reading frames) in the M. tuberculosis H37Rv genome. Our method combines information from comparative analysis (alignment to start sites of orthologs in other Actinobacteria), sequence conservation, "protein likeness", putative ribosome binding sites, and other data to identify translational start sites. The features are combined in a linear model that is trained on dataset of known start sites verified by mass spectrometry, with a cross-validated accuracy of 94%. The method can be viewed as an augmentation of Hidden Markov Model-based tools such as Glimmer and GeneMark by incorporating more information than just the raw genomic sequence to decide which position is the legitimate translational start site for each ORF. Using this analysis, we identify 269 genes that most likely need to be re-annotated, and identify the best alterative translational start site for each. These revised ORF definitions could be used in the reannotation of the H37Rv genome, as well as to prioritize genes for experimental start-site validation.
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