ArticleMolecular & cellular proteomics : MCP2011
Proteogenomic analysis of Mycobacterium tuberculosis by high resolution mass spectrometry.
Article in Molecular & cellular proteomics : MCP, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers.
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82 citing papers in PubMed, 78 citations in OpenAlex.
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- Proteogenomic Gene Structure Validation in the Pineapple Genome.Journal of proteome research · 2024Article
- Deep Proteogenomics of a Photosynthetic Cyanobacterium.Journal of proteome research · 2023Article
- The Mycobacterium tuberculosis protein O-phosphorylation landscape.Nature microbiology · 2023Article
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- From Nucleus to Membrane: A Subcellular Map of the N-Acetylation Machinery in Plants.International journal of molecular sciences · 2022Review
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- Mirror proteases of Ac-Trypsin and Ac-LysargiNase precisely improve novel event identifications inFrontiers in microbiology · 2022Article
- Tuberculous Granuloma: Emerging Insights From Proteomics and Metabolomics.Frontiers in neurology · 2022Review
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- Proteogenomic Analysis Provides Novel Insight into Genome Annotation and Nitrogen Metabolism inMicrobiology spectrum · 2021Article
- An Overview of Genetic Information of Latent Mycobacterium tuberculosis.Tuberculosis and respiratory diseases · 2021Article
- Protein N-Terminal Acetylation: Structural Basis, Mechanism, Versatility, and Regulation.Trends in biochemical sciences · 2021Review
- The genetic proteome: Using genetics to inform the proteome of mycobacterial pathogens.PLoS pathogens · 2021Review
- Predicting antimicrobial resistance using conserved genes.PLoS computational biology · 2020Article
22 more citing papers are in PubMed but not listed here.
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22 authors at 3 institutions in 2 countries.
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No grant is acknowledged in the PubMed record.
Abstract
The genome sequencing of H37Rv strain of Mycobacterium tuberculosis was completed in 1998 followed by the whole genome sequencing of a clinical isolate, CDC1551 in 2002. Since then, the genomic sequences of a number of other strains have become available making it one of the better studied pathogenic bacterial species at the genomic level. However, annotation of its genome remains challenging because of high GC content and dissimilarity to other model prokaryotes. To this end, we carried out an in-depth proteogenomic analysis of the M. tuberculosis H37Rv strain using Fourier transform mass spectrometry with high resolution at both MS and tandem MS levels. In all, we identified 3176 proteins from Mycobacterium tuberculosis representing ~80% of its total predicted gene count. In addition to protein database search, we carried out a genome database search, which led to identification of ~250 novel peptides. Based on these novel genome search-specific peptides, we discovered 41 novel protein coding genes in the H37Rv genome. Using peptide evidence and alternative gene prediction tools, we also corrected 79 gene models. Finally, mass spectrometric data from N terminus-derived peptides confirmed 727 existing annotations for translational start sites while correcting those for 33 proteins. We report creation of a high confidence set of protein coding regions in Mycobacterium tuberculosis genome obtained by high resolution tandem mass-spectrometry at both precursor and fragment detection steps for the first time. This proteogenomic approach should be generally applicable to other organisms whose genomes have already been sequenced for obtaining a more accurate catalogue of protein-coding genes.
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