E. coli is indeed the coolest thing on the planet - Carl Zimmer

From EcoliWiki

Introduction and caveats

A number of studies have attempted to determine the minimum number of essential genes in E. coli^[1][2][3]. Although some essentiality has been rigorously tested for individual genes, much of the data comes from determining what is not essential. Any genes that were annotated after these studies were done will be missing from the supplemental data tables that list whether genes are essential or nonessential.

This page displays a list of E. coli genes that may be essential. A more accurate description of this list might be "Genes that have not been shown to be nonessential". The list is generated by a wiki extension that starts with the members of the Gene Lists for MG1655 and removes

• all genes where Keio deletions have been isolated,
• all ins genes that are from insertion elements.

Manually curating nonessential genes

The extension is displayed on this page between a pair of tags that allow addition of nonessential genes from manual curation. Placing a gene page name between the tags removes that gene from the list of candidates for essentiality.

<essentialGenes>
nonessential gene 1:Gene
nonessential gene 2:Gene
etc.
</essentialGenes>

Manual curation so far includes:

• Pseudogenes were recognized by the presence of a gene name with an underscore and a number.
• tRNA genes that can be mutated to nonsense suppressors are marked as nonessential. Note that in many cases these are redundant and not all copies of a tRNA isoacceptor can be simultaneously deleted.
• Similarly, although ribosomal RNA genes are not on this list, at least one of each rRNA is needed for viability.
• Genes where Tn insertions were found by Gerdes et al. ^[1] were added for to the list of nonessentials.
• Checking what PEC has to say about the genes
• Limited checking of the literature for specific genes

Community curation is still needed to improve the quality of this list.

Missing essential genes

In some cases, the Keio collection reports a deletion strain for an essential gene. These often reflect trapping of duplications that provide a second complementing copy of the gene. To add back an essential gene, go to its gene page and edit the alleles table to remove any alleles with the PMID:16738554 code (that's how the extension recognizes the presence of the deletion strain on the list. To update the list on this page, you will need to clear the cache by clicking edit and then saving. See rpoD:Gene for an example.

The list (Edit this)

261 candidates

Evidence

Add evidence for nonessentiality here:

Add evidence for essentiality here:

See also

• Baba et al supplemental data
• Gerdes et al supplemental data
• PEC (EcoliWiki page). PEC is a curated database that focuses on phenotypes of E. coli genes. To display essential genes, go to the PEC gene search and uncheck nonessential, unknown, and Kohara phage (See figure).
• Kato (2007)^[3] identified 303 essential genes

References

See Help:References for how to manage references in EcoliWiki.

1. ↑ ^{1.0 1.1 1.2} Gerdes SY et al. (2003) Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185: 5673-84 PubMed EcoliWiki page
2. ↑ Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
3. ↑ ^{3.0 3.1} Kato J & Hashimoto M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol Syst Biol 3: 132 PubMed EcoliWiki page
4. ↑ Krishnan BR & Berg DE (1993) Viability of folA-null derivatives of wild-type (thyA+) Escherichia coli K-12. J Bacteriol 175: 909-11 PubMed EcoliWiki page
5. ↑ Chen S et al. (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J Bacteriol 186: 6689-97 PubMed EcoliWiki page
6. ↑ Liu MY et al. (1995) The product of the pleiotropic Escherichia coli gene csrA modulates glycogen biosynthesis via effects on mRNA stability. J Bacteriol 177: 2663-72 PubMed EcoliWiki page
7. ↑ Fozo EM et al. (2008) Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol Microbiol PubMed EcoliWiki page
8. ↑ Sledjeski DD et al. (1996) The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coli. EMBO J 15: 3993-4000 PubMed EcoliWiki page
9. ↑ Romeo T & Gong M (1993) Genetic and physical mapping of the regulatory gene csrA on the Escherichia coli K-12 chromosome. J Bacteriol 175: 5740-1 PubMed EcoliWiki page
10. ↑ Gudapaty S et al. (2001) Regulatory interactions of Csr components: the RNA binding protein CsrA activates csrB transcription in Escherichia coli. J Bacteriol 183: 6017-27 PubMed EcoliWiki page
11. ↑ Weilbacher T et al. (2003) A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol Microbiol 48: 657-70 PubMed EcoliWiki page
12. ↑ Suzuki K et al. (2006) Identification of a novel regulatory protein (CsrD) that targets the global regulatory RNAs CsrB and CsrC for degradation by RNase E. Genes Dev 20: 2605-17 PubMed EcoliWiki page
13. ↑ ^{13.0 13.1 13.2} Bubunenko M et al. (2007) Essentiality of ribosomal and transcription antitermination proteins analyzed by systematic gene replacement in Escherichia coli. J Bacteriol 189: 2844-53 PubMed EcoliWiki page
14. ↑ Persson BC et al. (1995) Functional analysis of the ffh-trmD region of the Escherichia coli chromosome by using reverse genetics. J Bacteriol 177: 5554-60 PubMed EcoliWiki page