Skip to main content

Table 7 False gene essentiality predictions resulting from open questions in E. coli biology and gene essentiality

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

Gene HT Sim Conv Citations Comments
argD + + [35, 36] EcoCyc lists argD as the only enzyme capable of carrying out the N-succinyldiaminopimelate aminotransferase reaction in lysine biosynthesis. Cox and Wang [35] demonstrate that a second, thus far unidentified enzyme besides ArgD can catalyze the DapC reaction. argD is discussed in [36].
cysC + [5, 32, 34, 37, 38] Gene essentiality in the sulfate utilization pathway is bypassed until cysIJ in the experiments of [32],
cysH +   which were conducted in a MOPS buffer capable of being used as a sulfur source via ssuEADCB
cysN + +   alkanesulfonate desulfonation to sulfite. Joyce et al.[34] use MOPS-free M9 buffer and consequently shows cysADQUW essentiality for sulfate uptake. The MOPS desulfonation explanation of the data of [32] is complicated by the fact that sulfite from MOPS should bypasscysNDCH within the assimilatory sulfate reduction pathway. Instead, these deletions fall within or near the broad essentiality criteria of [5]; cysN is barely within the broad essentiality criteria (OD600 0.088 at 24 hr) and cysD is just above (OD600 0.104 at 24 hr) while cysCH are deep within the cutoff. We propose an explanation based on inactivation of the ssu pathway transcriptional regulator Cbl via binding of adenosine 5’-phosphosulfate (APS), the product of the CysND sulfate adenylyltransferase [37, 38]. cysND mutants express the ssu pathway well and are able to better support growth via MOPS catabolism. cysCH mutants can produce APS from extracellular sulfate, leading to Cbl inactivation by APS binding, repression of ssu, and weaker growth.
dapF + + [36, 39, 40] EcoCyc lists dapF as the only enzyme capable of converting LL-diaminopimelate tomeso-diaminopimelate in lysine biosynthesis, but [39] demonstrates that dapF null mutants grow in unsupplemented glucose minimal media. dapF is described in [36].
dut + [41, 42] NudI and MazG substitute for Dut activity in EcoCyc–18.0–GEM. The NudI Km for the dUTP-consuming reaction shared with Dut is in the mM range. MazG activity is 70% inhibited by the MazEF toxin-antitoxin system; see [42]. el-Hajj et al.[41] discuss Dut at greater length.
folB + N/A [32, 34, 43] folB reported as nonessential by [32], but essential by [34], despite no obvious reason for differential essentiality on glucose and glycerol. Haussmann et al.[43] studied the enzyme but did not construct a deletion mutant or test it on glucose minimal media; whether an attempt was made is unknown. folB is found upstream of genes reported essential by [32] in the folate biosynthesis pathway, including folK, folC, folA, and possibly folP (see below).
folP N/A [32, 33, 44, 45] To our knowledge, there has not been a clear folP or hemE null mutant test on glucose minimal
hemE N/A   media. A folP deletion mutant grows poorly in rich media according to [45]. folP and hemE gene duplications preventing observation of the null phenotype in [32] were identified in [33, 36] and these genes are described as of uncertain essentiality by [33]. Genes of uncertain essentiality in [33] are those with partial duplication for both isolates that are considered nonessential in [44], which tested culture growth on rich Antibiotic Medium 3 medium containing beef extract as opposed to the LB agar of [33]. Under the broad essentiality criteria of [6], genes with uncertain essentiality in [33] were considered nonessential. EcoCyc–18.0–GEM supports the conclusion of essentiality for folP and hemE.
ftsW + [4650] It is not clear whether FtsW, MurJ, or both carry out the lipid II flippase activity in E. coli. See the
murJ +   listed references for additional information on this topic.
kdsC + + [5153] kdsC is upstream of the essential genes kdsB and waaA in the CMP-KDO biosynthesis pathway. Sperandeo et al.[51] suggeststhat isozymes for KdsC’s 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase activity may exist. Nonspecific phosphatase activity might also carry out this reaction. See [52, 53] on the subject of CMP-KDO requirements and E. coli temperature sensitivity.
pabC + [32, 34, 36, 54] Green et al.[54] report that PABA, the product of pabC, is required for growth on minimal media (although the carbon source used on this media is not described) and establishes that only one copy of the gene exists in E. coli. PabC is upstream of enzymes reported essential by [32] in its pathway. Kim and Copley [36] hypothesize nutrient carryover from rich culture for lack of essentiality in [32]. pabC is also nonessential in the M9 glycerol medium of [34].
  1. Cases where EcoCyc–18.0–GEM essentiality predictions differed from experimental gene-essentiality results for aerobic growth on MOPS medium with 0.4% glucose, and posed open biological questions or highlight metabolic network interactions of particular interest in EcoCyc–18.0–GEM. Certain of these genes deserve further investigation by the experimental community; others highlight interesting aspects of essentiality testing. Kim and Copley [36] have discussed several of these genes, which remain open issues in the literature. See text for additional details. Column headings are as follows: HT: High-throughput experiment (loose essentiality criteria of [6]). Sim: Simulation. Conv: Conventional experiment. Column entries are as follows: –: In the experiments, deletion mutant could not be recovered for testing, or was tested and did not grow to more than 0.091 OD600 after 24 hr, or both isolates were found to have duplications. In the simulations, FBA biomass flux was zero. +: In the high-throughput experiments, a deletion mutant was tested and showed growth greater than 0.091 OD600 after 24 hr. In the conventional experiments, growth was observed. In the simulations, FBA biomass flux positive. N/A: Information not available for deletion mutant on glucose minimal media. For example, argD is essential in the data of [32] according to the broad essentiality criteria of [6], but EcoCyc–18.0–GEM predicts that it is nonessential.