Essential genes

Introduction and caveats

A number of studies have attempted to determine the minimum number of essential genes in E. coli. 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. 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 alaT:Gene alaU:Gene alaV:Gene alaW:Gene alaX:Gene araA:Gene araB:Gene araD:Gene arpB_2:Gene argQ:Gene argV:Gene argW:Gene argY:Gene argZ:Gene asnT:Gene asnU:Gene asnV:Gene asnW:Gene aspT:Gene aspU:Gene aspV:Gene bcsB:Gene csrA:Gene csrB:Gene csrC:Gene csrD:Gene cydA:Gene cydC:Gene degS:Gene dicA:Gene dicF:Gene dinQ:Gene dpiA:Gene dpiB:Gene dsbD:Gene dsrA:Gene efeU_2:Gene entD:Gene entS:Gene etk:Gene eutD:Gene eutK:Gene eutM:Gene eutR:Gene eutS:Gene fadJ:Gene fadK:Gene feoC:Gene fldA:Gene folA:Gene folD:Gene fruL:Gene ftnA:Gene ftnB:Gene ftsN:Gene ftsX:Gene gadY:Gene gapC_1:Gene gatA:Gene gatR_2:Gene gcvB:Gene gfcB:Gene ghrA:Gene ghrB:Gene glcA:Gene glnU:Gene glnV:Gene glnW:Gene glnX:Gene gltT:Gene gltU:Gene gltV:Gene gltW:Gene glyU:Gene glyV:Gene glyW:Gene glyX:Gene glyY:Gene gmm:Gene gpsA:Gene gsp:Gene gspB:Gene gsiA:Gene gsiB:Gene gsiD:Gene hflB:Gene hofM:Gene hspQ:Gene ileT:Gene ileU:Gene ileV:Gene ileX:Gene ileY:Gene ilvG_2:Gene isrA:Gene isrB:Gene isrC:Gene istR-1:Gene istR-2:Gene intZ:Gene kilR:Gene kup:Gene lafU:Gene lacZ:Gene ldrA:Gene ldrB:Gene ldrC:Gene ldrD:Gene leuP:Gene leuQ:Gene leuT:Gene leuV:Gene leuX:Gene lfhA: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 rttR:Gene rutA:Gene rybB: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
folA	PMID:8423162
micF	PMID:15466019
rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT	PMID:7751274
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	PMID:13129938	accD listed as N*
ryeC, ryeD, rygC, rygD	PMID:18710431
dsrA	PMID:8670904
csrA	PMID:8366066
csrB	PMID:11567002
csrC	PMID:12694612
csrD	PMID:16980588
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
nusA	PMID:17277072
rpoD		Ts mutants and depletion studies
nusE	PMID:17277072
nusG	PMID:17277072
ffh	PMID:7559342
edit table

See also

• Baba et al supplemental data
• Gerdes et al supplemental data
• PEC (EcoliWiki page)
• Kato (2007) identified 303 essential genes

References

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