Essential genes
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. 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.
- 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)
<essentialGenes> List nonessential gene pages here C0067:Gene C0293:Gene C0299:Gene C0343:Gene C0362:Gene C0465:Gene C0664:Gene C0719:Gene accD:Gene acpH:Gene adrA:Gene araA:Gene araB:Gene araD:Gene csrA:Gene csrB:Gene csrC:Gene csrD:Gene arpB_2:Gene degS:Gene dpiA:Gene dpiB:Gene dsbD:Gene dsrA:Gene efeU_2:Gene entD:Gene etk:Gene eutD:Gene eutK:Gene eutM:Gene eutR:Gene eutS:Gene fldA:Gene folA:Gene folD:Gene ftnA:Gene ftnB:Gene ftsN:Gene ftsX:Gene gapC_1:Gene gatA:Gene gatR_2:Gene glcA:Gene glnU:Gene glnV:Gene glnX:Gene gpsA:Gene gsp:Gene hflB:Gene ilvG_2:Gene istR-1:Gene istR-2:Gene intZ:Gene kup:Gene lacZ:Gene leuX:Gene lolA:Gene lomR_2:Gene lysT:Gene lyx:Gene mazE:Gene mazF:Gene micF:Gene mraY:Gene mreD:Gene molR_3:Gene mug:Gene murA:Gene murB:Gene murF:Gene nadD:Gene oriC:Gene orn:Gene pgmB:Gene pinE:Gene pptA:Gene ptrA:Gene purB:Gene qmcA:Gene queC:Gene queF:Gene raiA:Gene ravA:Gene rcnA:Gene rimN:Gene rlmG:Gene rlmL:Gene rluE:Gene rluF:Gene rnlA:Gene rpsG:Gene rplP:Gene rplV:Gene rpsF:Gene rpsI:Gene rpsM:Gene rpsO:Gene rpsQ:Gene rpsT:Gene rrfA:Gene rrfB:Gene rrfC:Gene rrfD:Gene rrfE:Gene rrfF:Gene rrfG:Gene rrfH:Gene rrsA:Gene rrsB:Gene rrsC:Gene rrsD:Gene rrsE:Gene rrsF:Gene rrsG:Gene rrsH:Gene rrlA:Gene rrlB:Gene rrlC:Gene rrlD:Gene rrlE:Gene rrlF:Gene rrlG:Gene rrlH:Gene rsmE:Gene rsmF:Gene rutA:Gene ryeC:Gene ryeD:Gene rygC:Gene rygD:Gene rygE:Gene serU:Gene serV:Gene ssrA:Gene tp2:Gene tpke70:Gene trpH:Gene tusB:Gene tusC:Gene tusD:Gene tusE:Gene tyrT:Gene ubiD:Gene uspB:Gene wbbL_1:Gene xni:Gene yabQ:Gene yadR:Gene ybfK:Gene ycgH_2:Gene ychE_2:Gene ychG_1:Gene ychO:Gene ydbA_2:Gene ydiL:Gene yedN_1:Gene yedS_3:Gene yeeL_1:Gene yejM:Gene yfaS_1:Gene yffL:Gene yffN:Gene yffP:Gene yffQ:Gene ygiA:Gene ygiD:Gene yhbV:Gene yi82_1:Gene ylbE_2:Gene yibJ:Gene yigP:Gene yjgX_1:Gene yjjL:Gene yncK_2:Gene ypjK:Gene yraL:Gene yrbB:Gene yrfF:Gene ysaA:Gene </essentialGenes>
Evidence
Add evidence for nonessentiality here:
| Gene | Reference(s) | Comments |
|---|---|---|
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micF |
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rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT |
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accD, degS, dpiA, dpiB, entD, etk,eutD, eutK, eutM, eutR, eutS, fldA, folD, ftnA, ftnB, ftsN, ftsX, gatA, glcA, gpsA, gsp, hflB, intZ, kup, lolA, lyx, mraY, mreD, mug, murA, murB, murF, nadD, pgmB, pptA, ptrA, purB, qmcA, queC, queF, raiA, ravA, rimN, rlmG, rluE, rluF, rplP, rplV, rpsG, rsmE, rsmF, rutA, trpH, ubiD, uspB, xni, yabQ, yadR, ybfK, ychO, ydiL, yejM, yffL yffN, yffP, yffQ, ygiA, ygiD, yhbV, yibJ, yigP, yjjL, ypjK, yraL, yrbB, yrfF, ysaA |
accD listed as N* | |
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ryeC, ryeD, rygC, rygD |
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dsrA |
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csrA |
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csrB |
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csrC |
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csrD |
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C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, tpke70, tp2 |
Covered by deletions (see PEC) | |
| edit table |
Add evidence for essentiality here:
| Gene | Reference(s) | Comments |
|---|---|---|
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nusA |
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nusE |
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nusG |
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rpoD |
Ts mutants and depletion studies | |
| edit table |
See also
- Baba et al supplemental data
- Gerdes et al supplemental data
- PEC (EcoliWiki page)
- Kato (2007)[3] identified 303 essential genes
References
See Help:References for how to manage references in EcoliWiki.
- ↑ 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
- ↑ 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
- ↑ 3.0 3.1 Kato, J & Hashimoto, M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol. 3 132 PubMed
- ↑ Krishnan, BR & Berg, DE (1993) Viability of folA-null derivatives of wild-type (thyA+) Escherichia coli K-12. J. Bacteriol. 175 909-11 PubMed
- ↑ Chen, S et al. (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J. Bacteriol. 186 6689-97 PubMed
- ↑ 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
- ↑ Fozo, EM et al. (2008) Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol. Microbiol. 70 1076-93 PubMed
- ↑ 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
- ↑ 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
- ↑ 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
- ↑ Weilbacher, T et al. (2003) A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol. Microbiol. 48 657-70 PubMed
- ↑ 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
- ↑ 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