ArticleGenome biology2007
Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 33 citations in OpenAlex.
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- REPARATION: ribosome profiling assisted (re-)annotation of bacterial genomes.Nucleic acids research · 2017Article
- Determining the mode of action of anti-mycobacterial C17 diyne natural products using expression profiling: evidence for fatty acid biosynthesis inhibition.BMC genomics · 2016Article
- Proteogenomic Analysis of Mycobacterium smegmatis Using High Resolution Mass Spectrometry.Frontiers in microbiology · 2016Article
- GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences.Nucleic acids research · 2013Article
- Regulation of homocysteine metabolism by Mycobacterium tuberculosis S-adenosylhomocysteine hydrolase.Scientific reports · 2013Article
- Retrobiosynthetic approach delineates the biosynthetic pathway and the structure of the acyl chain of mycobacterial glycopeptidolipids.The Journal of biological chemistry · 2012Article
- High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade.BMC genomics · 2012Article
- A pilot study of bacterial genes with disrupted ORFs reveals a surprising profusion of protein sequence recoding mediated by ribosomal frameshifting and transcriptional realignment.Molecular biology and evolution · 2011Article
- Identification of the monooxygenase gene clusters responsible for the regioselective oxidation of phenol to hydroquinone in mycobacteria.Applied and environmental microbiology · 2011Article
- Proteomics-based confirmation of protein expression and correction of annotation errors in the Brucella abortus genome.BMC genomics · 2010Article
- Proteomics-based refinement of Deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons.Molecular & cellular proteomics : MCP · 2010Article
- Article
- Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.Genome research · 2009Article
- High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example.BMC genomics · 2008Article
- Comparative genomics-based investigation of resequencing targets in Vibrio fischeri: focus on point miscalls and artefactual expansions.BMC genomics · 2008Article
- Detecting the molecular scars of evolution in the Mycobacterium tuberculosis complex by analyzing interrupted coding sequences.BMC evolutionary biology · 2008Article
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Authors and funding
9 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundIn silico analysis has shown that all bacterial genomes contain a low percentage of ORFs with undetected frameshifts and in-frame stop codons. These interrupted coding sequences (ICDSs) may really be present in the organism or may result from misannotation based on sequencing errors. The reality or otherwise of these sequences has major implications for all subsequent functional characterization steps, including module prediction, comparative genomics and high-throughput proteomic projects.
resultsWe show here, using Mycobacterium smegmatis as a model species, that a significant proportion of these ICDSs result from sequencing errors. We used a resequencing procedure and mass spectrometry analysis to determine the nature of a number of ICDSs in this organism. We found that 28 of the 73 ICDSs investigated correspond to sequencing errors.
conclusionThe correction of these errors results in modification of the predicted amino acid sequences of the corresponding proteins and changes in annotation. We suggest that each bacterial ICDS should be investigated individually, to determine its true status and to ensure that the genome sequence is appropriate for comparative genomics analyses.
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