ArticleNature communications2021
Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis.
Article in Nature communications, 2021. 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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18 citing papers in PubMed.
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- Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.Bioinformatics (Oxford, England) · 2025Article
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- Hotspots of genetic change in Yersinia pestis.Nature communications · 2025Article
- Insight into the drug-resistant characteristics and genetic diversity of multidrug-resistantMicrobiology spectrum · 2023Article
- Phase variation as a major mechanism of adaptation inProceedings of the National Academy of Sciences of the United States of America · 2023Article
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- Features ofMicroorganisms · 2023Article
- Large genomic deletions delineate Mycobacterium tuberculosis L4 sublineages in South American countries.PloS one · 2023Article
- Comparative Genome Analysis of 19Antibiotics (Basel, Switzerland) · 2022Article
- The rate and role of pseudogenes of theMicrobial genomics · 2022Article
- Distinctive roles of translesion polymerases DinB1 and DnaE2 in diversification of the mycobacterial genome through substitution and frameshift mutagenesis.Nature communications · 2022Article
- Small Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis.Microbiology spectrum · 2022Review
- A critical evaluation ofMicrobial genomics · 2022Article
- Detection of minor variants in Mycobacterium tuberculosis whole genome sequencing data.Briefings in bioinformatics · 2022Article
- Reversible gene silencing through frameshift indels and frameshift scars provide adaptive plasticity for Mycobacterium tuberculosis.Nature communications · 2021Article
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Abstract
Mycobacterium tuberculosis can adapt to changing environments by non-heritable mechanisms. Frame-shifting insertions and deletions (indels) may also participate in adaptation through gene disruption, which could be reversed by secondary introduction of a frame-restoring indel. We present ScarTrek, a program that scans genomic data for indels, including those that together disrupt and restore a gene's reading frame, producing "frame-shift scars" suggestive of reversible gene inactivation. We use ScarTrek to analyze 5977 clinical M. tuberculosis isolates. We show that indel frequency inversely correlates with genomic linguistic complexity and varies with gene-position and gene-essentiality. Using ScarTrek, we detect 74 unique frame-shift scars in 48 genes, with a 3.74% population-level incidence of unique scar events. We find multiple scars in the ESX-1 gene cluster. Six scars show evidence of convergent evolution while the rest shared a common ancestor. Our results suggest that sequential indels are a mechanism for reversible gene silencing and adaptation in M. tuberculosis.
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