ArticleBMC microbiology2016
Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality.
Article in BMC microbiology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
16 citing papers in PubMed, 28 citations in OpenAlex.
- Article
- Defining thebioRxiv : the preprint server for biology · 2026Article
- Genome-wide analysis exploring mechanisms used bymSystems · 2026Article
- HilE mediates motility thermoregulation in typhoidal Salmonella serovars at elevated physiological temperatures.PLoS pathogens · 2025Article
- A scalable gut epithelial organoid model reveals the genome-wide colonization landscape of a human-adapted pathogen.Nature genetics · 2025Article
- Tolerance mechanisms in polysaccharide biosynthesis: Implications for undecaprenol phosphate recycling in Escherichia coli and Shigella flexneri.PLoS genetics · 2025Article
- Gradients in gene essentiality reshape antibacterial research.FEMS microbiology reviews · 2022Review
- How sequence populations persist inside bacterial genomes.Genetics · 2021Article
- The impact of genetic diversity on gene essentiality within the Escherichia coli species.Nature microbiology · 2021Article
- Essential Genes ofFrontiers in microbiology · 2021Article
- Ecology, Structure, and Evolution ofAnnual review of virology · 2020Review
- A Mini-ISY100 Transposon Delivery System Effective in γ Proteobacteria.Frontiers in microbiology · 2019Article
- Robustness encoded across essential and accessory replicons of the ecologically versatile bacterium Sinorhizobium meliloti.PLoS genetics · 2018Article
- The Essential Genome ofmBio · 2018Article
- Creation of a Dense Transposon Insertion Library Using Bacterial Conjugation in Enterobacterial Strains Such As Escherichia Coli or Shigella flexneri.Journal of visualized experiments : JoVE · 2017Article
- A Comprehensive Overview of Online Resources to Identify and Predict Bacterial Essential Genes.Frontiers in microbiology · 2017Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGene essentiality - whether or not a gene is necessary for cell growth - is a fundamental component of gene function. It is not well established how quickly gene essentiality can change, as few studies have compared empirical measures of essentiality between closely related organisms.
resultsHere we present the results of a Tn-seq experiment designed to detect essential protein coding genes in the bacterial pathogen Shigella flexneri 2a 2457T on a genome-wide scale. Superficial analysis of this data suggested that 481 protein-coding genes in this Shigella strain are critical for robust cellular growth on rich media. Comparison of this set of genes with a gold-standard data set of essential genes in the closely related Escherichia coli K12 BW25113 revealed that an excessive number of genes appeared essential in Shigella but non-essential in E. coli. Importantly, and in converse to this comparison, we found no genes that were essential in E. coli and non-essential in Shigella, implying that many genes were artefactually inferred as essential in Shigella. Controlling for such artefacts resulted in a much smaller set of discrepant genes. Among these, we identified three sets of functionally related genes, two of which have previously been implicated as critical for Shigella growth, but which are dispensable for E. coli growth.
conclusionsThe data presented here highlight the small number of protein coding genes for which we have strong evidence that their essentiality status differs between the closely related bacterial taxa E. coli and Shigella. A set of genes involved in acetate utilization provides a canonical example. These results leave open the possibility of developing strain-specific antibiotic treatments targeting such differentially essential genes, but suggest that such opportunities may be rare in closely related bacteria.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.