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

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].

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].

von Meyenburg et al.[107] demonstrate growth of strains lacking intact ATP synthase on

glucose and other fermentable carbon source minimal media, at reduced growth rates.

Growth of atp null mutants is further discussed in [73, 108].

Green and Gennis [109] demonstrate aerobic growth of cyd mutants on glucose minimal

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].

Steinsiek and Bettenbrock [120] and Escalante et al.[121] review glucose uptake in E. coli

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 ^- 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].

Cox et al.[127] constructed ubiquinone-free mutants of K–12 capable of growth on

fermentable substrates including glucose. Wu et al.[128] constructed ubiA null mutants

capable of growing on minimal media containing fermentable carbon sources.

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].