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Table 10 Genes for which EcoCyc–18.0–GEM predictions identified likely errors in high-throughput essentiality screening, and the EcoCyc–18.0–GEM predictions were confirmed by conventional essentiality experiments

From: A genome-scale metabolic flux model of Escherichia coli K–12 derived from the EcoCyc database

Gene HT Sim Conv Citations Comments
alsK + N/A [32, 103, 104] The circumstances leading to this gene’s essentiality in [32] are uncertain. Kim et al. 1997 [103] and Poulsen et al. 1999 [104] demonstrate that alsK is not required for growth on allose, and demonstrate growth on glycerol minimal media. Poulsen et al.[104] constructed alsK null mutants with transposon insertions, demonstrating that alsK was not required for allose catabolism, and renamed the gene yjcT. alsK/yjcT is listed as essential on rich media (LB) by [32].
aroD + [32, 36, 105, 106] Baba et al.[32] suggest that an aroD null mutant can grow on glucose minimal media, but [105] established that E. coli K–12 aroD mutants require all of the aromatic amino acids for growth. See also the discussion in [36] with reference to [106].
atpB + + [73, 107, 108] von Meyenburg et al.[107] demonstrate growth of strains lacking intact ATP synthase on
atpC + +   glucose and other fermentable carbon source minimal media, at reduced growth rates.
atpE + +   Growth of atp null mutants is further discussed in [73, 108].
cydA + + [73, 109114] Green and Gennis [109] demonstrate aerobic growth of cyd mutants on glucose minimal
cydC + +   media through use of cytochrome bo. See references for further discussion of redundancy in E. coli cytochromes and operation of cytochrome bd-I. Discussed in [73].
ptsH + + [77, 115121] Steinsiek and Bettenbrock [120] and Escalante et al.[121] review glucose uptake in E. coli
ptsI + +   mutant strains with glucose PTS defects. See references for additional details. Patrick et al.[77] identified overexpression of FucP fucose transporter, XylE xylose transporter, or GalE UDP-glucose 4-epimerase as capable of rescuing ptsI deletion mutants.
spoT + + [73, 122126] spoT - mutants grow slowly on glucose minimal media [122, 123]. Absence of SpoT ppGpp hydrolase activity leads to high levels of ppGpp, which are inversely correlated with growth rate [126]. See references for additional details. Discussed in [73].
ubiA + + [127, 128] Cox et al.[127] constructed ubiquinone-free mutants of K–12 capable of growth on
ubiD + +   fermentable substrates including glucose. Wu et al.[128] constructed ubiA null mutants
ubiE + +   capable of growing on minimal media containing fermentable carbon sources.
waaU + + [129, 130] Essentiality in glucose minimal media has not been clearly determined. Klena et al.[129] constructed waaU null mutants and demonstrated their viability in rich media, in contradiction to the determination of essentiality in rich media in [32].
  1. See Table 7 caption for a description of column headings.