To kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131

Tantoso, Erwin; Eisenhaber, Birgit; Kirsch, Miles; Shitov, Vladimir; Zhao, Zhiqin; Eisenhaber, Frank

doi:10.1186/s12915-022-01347-7

Cited by 20 publications

(29 citation statements)

References 186 publications

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“…Separately, we investigated the literature coverage of the 3056 GFs belonging to the 95%-threshold E. coli softcore genome [ 15 , 20 ]. We mapped literature data about genes belonging to six strains (Additional file 1 : Table S3) to the softcore GFs.…”

Section: Resultsmentioning

confidence: 99%

“…Comprehensive resources on E. coli genes, proteins, pathways, molecular interactions, and chemical reactions have been provided by EcoCyc [ 10 , 11 ] through manual curation and integration of literature and experimental evidence. Yet, pangenome analyses revealed many insufficiently uncharacterized gene groups [ 12 – 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…Besides analyzing genomes of specific E. coli strains such as that of K-12 MG1655, we need a list of genes for this research effort that characterizes E. coli as a species. Comparisons of available complete genomes shows that the pool of homologous gene families (GFs) shared by all strains of E. coli is very small (a few hundred) [ 15 ]. At the same time, the E. coli pangenome is open and grows with the sophistication of ever cheaper sequencing technology and the entry of genomes especially from strains in new habitats [ 8 , 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…Comparisons of available complete genomes shows that the pool of homologous gene families (GFs) shared by all strains of E. coli is very small (a few hundred) [ 15 ]. At the same time, the E. coli pangenome is open and grows with the sophistication of ever cheaper sequencing technology and the entry of genomes especially from strains in new habitats [ 8 , 15 ]. Undoubtedly, the accessory gene pool will keep increasing as more E. coli genomes are accumulated.…”

Section: Introductionmentioning

confidence: 99%

“…Where are the genome regions that would deserve enhanced scientific attention and promise new discovery? Subsequently, we search for functional hints for some of the so-called enigmatic genes—using co-occurrence analysis of genes of the accessory genome [ 15 , 19 ] among the lineages of E. coli , genomic co-localization as well as traditional gene/protein sequence analysis.…”

Section: Introductionmentioning

confidence: 99%

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About the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature

et al. 2023

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Background Although Escherichia coli (E. coli) is the most studied prokaryote organism in the history of life sciences, many molecular mechanisms and gene functions encoded in its genome remain to be discovered. This work aims at quantifying the illumination of the E. coli gene function space by the scientific literature and how close we are towards the goal of a complete list of E. coli gene functions. Results The scientific literature about E. coli protein-coding genes has been mapped onto the genome via the mentioning of names for genomic regions in scientific articles both for the case of the strain K-12 MG1655 as well as for the 95%-threshold softcore genome of 1324 E. coli strains with known complete genome. The article match was quantified with the ratio of a given gene name’s occurrence to the mentioning of any gene names in the paper. The various genome regions have an extremely uneven literature coverage. A group of elite genes with ≥ 100 full publication equivalents (FPEs, FPE = 1 is an idealized publication devoted to just a single gene) attracts the lion share of the papers. For K-12, ~ 65% of the literature covers just 342 elite genes; for the softcore genome, ~ 68% of the FPEs is about only 342 elite gene families (GFs). We also find that most genes/GFs have at least one mentioning in a dedicated scientific article (with the exception of at least 137 protein-coding transcripts for K-12 and 26 GFs from the softcore genome). Whereas the literature growth rates were highest for uncharacterized or understudied genes until 2005–2010 compared with other groups of genes, they became negative thereafter. At the same time, literature for anyhow well-studied genes started to grow explosively with threshold T10 (≥ 10 FPEs). Typically, a body of ~ 20 actual articles generated over ~ 15 years of research effort was necessary to reach T10. Lineage-specific co-occurrence analysis of genes belonging to the accessory genome of E. coli together with genomic co-localization and sequence-analytic exploration hints previously completely uncharacterized genes yahV and yddL being associated with osmotic stress response/motility mechanisms. Conclusion If the numbers of scientific articles about uncharacterized and understudied genes remain at least at present levels, full gene function lists for the strain K-12 MG1655 and the E. coli softcore genome are in reach within the next 25–30 years. Once the literature body for a gene crosses 10 FPEs, most of the critical fundamental research risk appears overcome and steady incremental research becomes possible.

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Section: Resultsmentioning

confidence: 99%