ArticleBMC genomics2016
In-silico prediction and deep-DNA sequencing validation indicate phase variation in 115 Neisseria meningitidis genes.
Article in BMC genomics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed, 25 citations in OpenAlex.
- Review
- Whole-genome sequencing resolves biochemical misidentification ofJournal of clinical microbiology · 2024Article
- Microevolution and Its Impact on Hypervirulence, Antimicrobial Resistance, and Vaccine Escape inMicroorganisms · 2023Review
- Genomic Insights on Variation Underlying Capsule Expression in Meningococcal Carriage Isolates From University Students, United States, 2015-2016.Frontiers in microbiology · 2022Article
- High coverage of diverse invasive meningococcal serogroup B strains by the 4-component vaccine 4CMenB in Australia, 2007-2011: Concordant predictions between MATS and genetic MATS.Human vaccines & immunotherapeutics · 2021Article
- Insights on Population Structure and Within-Host Genetic Changes among Meningococcal Carriage Isolates from U.S. Universities.mSphere · 2020Article
- Neisseria meningitidis: using genomics to understand diversity, evolution and pathogenesis.Nature reviews. Microbiology · 2020Review
- ReVac: a reverse vaccinology computational pipeline for prioritization of prokaryotic protein vaccine candidates.BMC genomics · 2019Article
- A Computational Method to Quantify the Effects of Slipped Strand Mispairing on Bacterial Tetranucleotide Repeats.Scientific reports · 2019Article
- Mode and Tempo of Microsatellite Length Change in a Malaria Parasite Mutation Accumulation Experiment.Genome biology and evolution · 2019Article
- Whole-Genome Sequencing for Characterization of Capsule Locus and Prediction of Serogroup of Invasive Meningococcal Isolates.Journal of clinical microbiology · 2019Article
- Single-molecule sequencing detection of N6-methyladenine in microbial reference materials.Nature communications · 2019Article
- Phase-Variable Genotypes Sweetened by Glycosylation Phenotypes.Journal of bacteriology · 2018Article
- Article
- Article
- Interplay Between Virulence and Variability Factors as a Potential Driver of Invasive Meningococcal Disease.Computational and structural biotechnology journal · 2018Review
- Regulation ofFEBS open bio · 2017Article
- Whole genome sequencing reveals within-host genetic changes in paired meningococcal carriage isolates from Ethiopia.BMC genomics · 2017Article
- Comparative Genome Sequencing Reveals Within-Host Genetic Changes in Neisseria meningitidis during Invasive Disease.PloS one · 2017Article
- Article
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Authors and funding
8 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe Neisseria meningitidis (Nm) chromosome shows a high abundance of simple sequence DNA repeats (SSRs) that undergo stochastic, reversible mutations at high frequency. This mechanism is reflected in an extensive phenotypic diversity that facilitates Nm adaptation to dynamic environmental changes. To date, phase-variable phenotypes mediated by SSRs variation have been experimentally confirmed for 26 Nm genes.
resultsHere we present a population-scale comparative genomic analysis that identified 277 genes and classified them into 52 strong, 60 moderate and 165 weak candidates for phase variation. Deep-coverage DNA sequencing of single colonies grown overnight under non-selective conditions confirmed the presence of high-frequency, stochastic variation in 115 of them, providing circumstantial evidence for their phase variability. We confirmed previous observations of a predominance of variable SSRs within genes for components located on the cell surface or DNA metabolism. However, in addition we identified an unexpectedly broad spectrum of other metabolic functions, and most of the variable SSRs were predicted to induce phenotypic changes by modulating gene expression at a transcriptional level or by producing different protein isoforms rather than mediating on/off translational switching through frameshifts. Investigation of the evolutionary history of SSR contingency loci revealed that these loci were inherited from a Nm ancestor, evolved independently within Nm, or were acquired by Nm through lateral DNA exchange.
conclusionsOverall, our results have identified a broader and qualitatively different phenotypic diversification of SSRs-mediated stochastic variation than previously documented, including its impact on central Nm metabolism.
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