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Table 1 Genes artefactually inferred as essential in Shigella

From: Combining Shigella Tn-seq data with gold-standard E. coli gene deletion data suggests rare transitions between essential and non-essential gene functionality

Gene(s) Evidence for Artefactual Inference of Shigella Essentiality
acrAB, tolC, ybaB, ksgA, yebC, smpB (0.73) a Affect kanamycin resistance [3537]
dnaQ, holD, recD, xseA, ruvA (0.58), ruvB (0.60), ruvC (0.61), recB (0.58), recC (0.65) Likely to affect the transposition process; dnaQ, holD, ruvA, and ruvB inferred as essential using Tn-seq in Salmonella [14]
priB Deficient in plasmid maintenance [63, 64]
fhuACD, tonB Involved in iron acquisition which is critical for growth in the iron limited media used in this study [33]
rpsT S20 ribosomal subunit; new data indicates mutants have poor growth [42] (in conflict with Keio data)
miaA tRNA dimethyl transferase; previous data indicates E. coli mutants have poor growth [43] (in conflict with Keio data)
ompA Outer membrane porin; clean knockouts appear viable [65]; mutant forms are frequently lethal [44]
pitA Metal phosphate transporter with ten transmembrane segments; transposon disruption of substrate transporters is three-fold more likely to be inferred as essential compared to clean deletion (see main text; Fig. 5)
potB Type I ABC transporter (Putrescine / spermidine transporter); see above
sapB Type I ABC transporter (unknown substrate); see above
ptsH, yeaC, ydhR Short reading frames (306 bp, 272 bp, and 258 bp, respectively)
  1. aGene deletions of orthologous E. coli genes with growth levels less than OD600 0.75 have these levels in parentheses