Essential genes: Difference between revisions

Latest revision as of 07:10, 28 May 2013

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)

<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 lysQ:Gene lysV:Gene lysW:Gene lysY:Gene lysZ:Gene lyx:Gene mazE:Gene mazF:Gene mdtQ:Gene metT:Gene metU:Gene metV:Gene metW:Gene metY:Gene metZ:Gene micA:Gene micC:Gene micF:Gene minD:Gene minE:Gene mnmG:Gene mokB:Gene mokC:Gene mraY:Gene mreD:Gene molR_3:Gene mug:Gene murA:Gene murB:Gene murF:Gene nadD:Gene nepI:Gene omrA:Gene omrB:Gene oriC:Gene orn:Gene oxyS:Gene pagP:Gene pgmB:Gene pheU:Gene pheV:Gene pinE:Gene pptA:Gene proK:Gene proL:Gene psrD:Gene psrN:Gene psrO:Gene ptrA:Gene purB:Gene qmcA:Gene queC:Gene queF:Gene racR:Gene raiA:Gene ravA:Gene rcnA:Gene rdlA:Gene rdlB:Gene rdlC:Gene rdlD:Gene rhaA:Gene rhaB:Gene rhaD:Gene rhaM:Gene rimN:Gene rlmG:Gene rlmL:Gene rluE:Gene rluF:Gene rnc:Gene rnlA:Gene rpoE:Gene rplP:Gene rplV:Gene rprA:Gene rpsF:Gene rpsG: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 rseX:Gene rsmE:Gene rsmF:Gene rttR:Gene rutA:Gene rutD:Gene rutF:Gene rutR:Gene rybA:Gene rydB:Gene rydC:Gene ryeA:Gene ryeB:Gene ryeE:Gene rybB:Gene ryeC:Gene ryeD:Gene ryfA:Gene ryfB:Gene ryfC:Gene ryfD:Gene rygC:Gene rygD:Gene rygE:Gene ryhA:Gene ryhB:Gene ryiA:Gene glmZ:Gene ryjA:Gene ryjB:Gene ryjC:Gene selC:Gene serU:Gene serV:Gene serW:Gene serX:Gene sgrS:Gene skp:Gene sokA:Gene sokB:Gene sokC:Gene spf:Gene sraA:Gene sroA:Gene sroB:Gene sroC:Gene sroD:Gene sroF:Gene sroG:Gene sroH:Gene ssrA:Gene ssrS:Gene suhB:Gene tadA:Gene tdcF:Gene tff:Gene thrT:Gene thrV:Gene thrW:Gene tisA:Gene tisB:Gene tp2:Gene tpke70:Gene trpH:Gene tusB:Gene tusC:Gene tusD:Gene tusE:Gene tyrT:Gene tyrU:Gene tyrV:Gene ubiB:Gene ubiD:Gene uof:Gene uspB:Gene valT:Gene valU:Gene valV:Gene valW:Gene valX:Gene valY:Gene valZ:Gene ves:Gene waaU:Gene wbbL_1:Gene wzyE:Gene xni:Gene yabQ:Gene yadR:Gene yafF:Gene yagG:Gene ybhU:Gene ybfK:Gene yccB:Gene yceM:Gene ycgH_2:Gene ychE_2:Gene ychG_1:Gene ychO:Gene ychS:Gene yciY:Gene yciZ:Gene ydbA_2:Gene ydfB:Gene ydfN:Gene ydgU:Gene ydiL:Gene yedN_1:Gene yedS_3:Gene yeeL_1:Gene yefM:Gene yegZ:Gene yejM:Gene yfaS_1:Gene yfdT:Gene yffL:Gene yffN:Gene yffP:Gene yffQ:Gene yffM:Gene yffO:Gene yffR:Gene yffS:Gene ygdT:Gene ygiA:Gene ygiD:Gene ygiT:Gene yhbV:Gene yhhQ:Gene yi82_1:Gene ylbE_2:Gene yibJ:Gene yibV:Gene yigP:Gene yjgX_1:Gene yjbS:Gene yjbT:Gene yjdP:Gene yjhW:Gene yjjL:Gene ykfM:Gene ykgO:Gene ylbG:Gene ylcH:Gene ylcI:Gene yliL:Gene ymfK:Gene ymgI:Gene ymgJ:Gene yncK_2:Gene yncL:Gene yneM:Gene ynhF:Gene yoaI:Gene yojO:Gene ypaB:Gene ypfM:Gene ypjK:Gene yqgD:Gene yraL:Gene yrbB:Gene yrfF:Gene yrhD:Gene ytcA:Gene ytjA:Gene ysaA:Gene </essentialGenes>

Evidence

Add evidence for nonessentiality here:

Gene	Reference(s)	Comments
folA	PMID:8423162^[4]
micF	PMID:15466019^[5]
rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT	PMID:17277072^[6]	precise gene knockout by recombineering
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^[1]	accD listed as N*
ryeC, ryeD, rygC, rygD	PMID:18710431^[7]
dsrA	PMID:8670904^[8]
csrA	PMID:8366066^[9]
csrB	PMID:11567002^[10]
csrC	PMID:12694612^[11]
csrD	PMID:16980588^[12]
C0067, C0293, C0299, C0343, C0362, C0465, C0664, C0719, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA		Covered by deletions (see PEC)
suhB	PMID:17652087^[13]	precise gene knockout by recombineering
edit table

Add evidence for essentiality here:

Gene	Reference(s)	Comments
nusA	PMID:17277072^[6]
rpoD		Ts mutants and depletion studies
nusE	PMID:17277072^[6]
nusG	PMID:17277072^[6]
ffh	PMID:7559342^[14]
rpsU	PMID:17277072^[6]
accD	PMID:1886618^[15]
degS	PMID:11442831^[16]
fldA	PMID:15978585^[17]
ftsN	PMID:8509333^[18]
hflB	PMID:1104589^[19]
lolA	PMID:9849875^[20]
mraY	PMID:9829961^[21]
mreD	PMID:15612918^[22]
murA	PMID:7608103^[23]
murB	PMID:4563986^[24]
murF	PMID:4552998^[25]
nadD	PMID:16153292^[26]
rplV	no Keio or PEC deletion
rpsG	PMID:21219455^[27]
edit table

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
↑ ^6.0 ^6.1 ^6.2 ^6.3 ^6.4 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
↑ 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
↑ Wang, Y et al. (2007) The structure of the R184A mutant of the inositol monophosphatase encoded by suhB and implications for its functional interactions in Escherichia coli. J. Biol. Chem. 282 26989-96 PubMed
↑ 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
↑ Nagano, Y et al. (1991) An essential gene of Escherichia coli that has sequence similarity to a chloroplast gene of unknown function. Mol. Gen. Genet. 228 62-4 PubMed
↑ Alba, BM et al. (2001) degS (hhoB) is an essential Escherichia coli gene whose indispensable function is to provide sigma (E) activity. Mol. Microbiol. 40 1323-33 PubMed
↑ Puan, KJ et al. (2005) fldA is an essential gene required in the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis. FEBS Lett. 579 3802-6 PubMed
↑ Dai, K et al. (1993) Cloning and characterization of ftsN, an essential cell division gene in Escherichia coli isolated as a multicopy suppressor of ftsA12(Ts). J. Bacteriol. 175 3790-7 PubMed
↑ Santos, D & De Almeida, DF (1975) Isolation and characterization of a new temperature-sensitive cell division mutant of Escherichia coli K-12. J. Bacteriol. 124 1502-7 PubMed
↑ Tajima, T et al. (1998) Genetic analyses of the in vivo function of LolA, a periplasmic chaperone involved in the outer membrane localization of Escherichia coli lipoproteins. FEBS Lett. 439 51-4 PubMed
↑ Boyle, DS & Donachie, WD (1998) mraY is an essential gene for cell growth in Escherichia coli. J. Bacteriol. 180 6429-32 PubMed
↑ Kruse, T et al. (2005) The morphogenetic MreBCD proteins of Escherichia coli form an essential membrane-bound complex. Mol. Microbiol. 55 78-89 PubMed
↑ Brown, ED et al. (1995) MurA (MurZ), the enzyme that catalyzes the first committed step in peptidoglycan biosynthesis, is essential in Escherichia coli. J. Bacteriol. 177 4194-7 PubMed
↑ Miyakawa, T et al. (1972) Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112 950-8 PubMed
↑ Lugtenberg, EJ & v Schijndel-van Dam, A (1972) Temperature-sensitive mutants of Escherichia coli K-12 with low activities of the L-alanine adding enzyme and the D-alanyl-D-alanine adding enzyme. J. Bacteriol. 110 35-40 PubMed
↑ Stancek, M et al. (2005) Analysis of Escherichia coli nicotinate mononucleotide adenylyltransferase mutants in vivo and in vitro. BMC Biochem. 6 16 PubMed
↑ Schaub, RE & Hayes, CS (2011) Deletion of the RluD pseudouridine synthase promotes SsrA peptide tagging of ribosomal protein S7. Mol. Microbiol. 79 331-41 PubMed

[PMID:13129938-1] 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

[PMID:16738554-2] 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

[PMID:17700540-3] 3.0 ^3.1 Kato, J & Hashimoto, M (2007) Construction of consecutive deletions of the Escherichia coli chromosome. Mol. Syst. Biol. 3 132 PubMed

[PMID:8423162-4] Krishnan, BR & Berg, DE (1993) Viability of folA-null derivatives of wild-type (thyA+) Escherichia coli K-12. J. Bacteriol. 175 909-11 PubMed

[PMID:15466019-5] Chen, S et al. (2004) MicC, a second small-RNA regulator of Omp protein expression in Escherichia coli. J. Bacteriol. 186 6689-97 PubMed

[PMID:17277072-6] 6.0 ^6.1 ^6.2 ^6.3 ^6.4 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

[PMID:18710431-7] Fozo, EM et al. (2008) Repression of small toxic protein synthesis by the Sib and OhsC small RNAs. Mol. Microbiol. 70 1076-93 PubMed

[PMID:8670904-8] 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

[PMID:8366066-9] 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

[PMID:11567002-10] 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

[PMID:12694612-11] Weilbacher, T et al. (2003) A novel sRNA component of the carbon storage regulatory system of Escherichia coli. Mol. Microbiol. 48 657-70 PubMed

[PMID:16980588-12] 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

[PMID:17652087-13] Wang, Y et al. (2007) The structure of the R184A mutant of the inositol monophosphatase encoded by suhB and implications for its functional interactions in Escherichia coli. J. Biol. Chem. 282 26989-96 PubMed

[PMID:7559342-14] 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

[PMID:1886618-15] Nagano, Y et al. (1991) An essential gene of Escherichia coli that has sequence similarity to a chloroplast gene of unknown function. Mol. Gen. Genet. 228 62-4 PubMed

[PMID:11442831-16] Alba, BM et al. (2001) degS (hhoB) is an essential Escherichia coli gene whose indispensable function is to provide sigma (E) activity. Mol. Microbiol. 40 1323-33 PubMed

[PMID:15978585-17] Puan, KJ et al. (2005) fldA is an essential gene required in the 2-C-methyl-D-erythritol 4-phosphate pathway for isoprenoid biosynthesis. FEBS Lett. 579 3802-6 PubMed

[PMID:8509333-18] Dai, K et al. (1993) Cloning and characterization of ftsN, an essential cell division gene in Escherichia coli isolated as a multicopy suppressor of ftsA12(Ts). J. Bacteriol. 175 3790-7 PubMed

[PMID:1104589-19] Santos, D & De Almeida, DF (1975) Isolation and characterization of a new temperature-sensitive cell division mutant of Escherichia coli K-12. J. Bacteriol. 124 1502-7 PubMed

[PMID:9849875-20] Tajima, T et al. (1998) Genetic analyses of the in vivo function of LolA, a periplasmic chaperone involved in the outer membrane localization of Escherichia coli lipoproteins. FEBS Lett. 439 51-4 PubMed

[PMID:9829961-21] Boyle, DS & Donachie, WD (1998) mraY is an essential gene for cell growth in Escherichia coli. J. Bacteriol. 180 6429-32 PubMed

[PMID:15612918-22] Kruse, T et al. (2005) The morphogenetic MreBCD proteins of Escherichia coli form an essential membrane-bound complex. Mol. Microbiol. 55 78-89 PubMed

[PMID:7608103-23] Brown, ED et al. (1995) MurA (MurZ), the enzyme that catalyzes the first committed step in peptidoglycan biosynthesis, is essential in Escherichia coli. J. Bacteriol. 177 4194-7 PubMed

[PMID:4563986-24] Miyakawa, T et al. (1972) Cell wall peptidoglycan mutants of Escherichia coli K-12: existence of two clusters of genes, mra and mrb, for cell wall peptidoglycan biosynthesis. J. Bacteriol. 112 950-8 PubMed

[PMID:4552998-25] Lugtenberg, EJ & v Schijndel-van Dam, A (1972) Temperature-sensitive mutants of Escherichia coli K-12 with low activities of the L-alanine adding enzyme and the D-alanyl-D-alanine adding enzyme. J. Bacteriol. 110 35-40 PubMed

[PMID:16153292-26] Stancek, M et al. (2005) Analysis of Escherichia coli nicotinate mononucleotide adenylyltransferase mutants in vivo and in vitro. BMC Biochem. 6 16 PubMed

[PMID:21219455-27] Schaub, RE & Hayes, CS (2011) Deletion of the RluD pseudouridine synthase promotes SsrA peptide tagging of ribosomal protein S7. Mol. Microbiol. 79 331-41 PubMed

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Essential genes: Difference between revisions

Latest revision as of 07:10, 28 May 2013

Contents

Introduction and caveats

Manually curating nonessential genes

Missing essential genes

The list (Edit this)

Evidence

See also

References

Navigation menu

@@ Line 1: / Line 1: @@
 == Introduction and caveats ==
-This page displays a list of ''E. coli'' genes that '''may''' be essential.  The list is generated by removing all genes where Keio deletions have been isolated, and all ins genes that are from insertion elements.  Genes can be removed from the list by editing the list of gene pages in the wikitext of this page
+A number of studies have attempted to determine the minimum number of essential genes in ''E. coli''<ref name='PMID:13129938'/><ref name='PMID:16738554'/><ref name='PMID:17700540'/>.  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 [[:Category:Gene List:MG1655|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.
 <pre>
 <nowiki>
@@ Line 10: / Line 16: @@
 </nowiki>
 </pre>
+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. <ref name='PMID:13129938'/> 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)==
 <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
+lysQ:Gene
+lysV:Gene
+lysW:Gene
+lysY:Gene
+lysZ:Gene
+lyx:Gene
 mazE:Gene
 mazF:Gene
-istR-1:Gene
+mdtQ:Gene
-istR-2:Gene
+metT:Gene
+metU:Gene
+metV:Gene
+metW:Gene
+metY:Gene
+metZ:Gene
+micA:Gene
+micC:Gene
+micF:Gene
+minD:Gene
+minE:Gene
+mnmG:Gene
+mokB:Gene
+mokC:Gene
+mraY:Gene
+mreD:Gene
+molR_3:Gene
+mug:Gene
+murA:Gene
+murB:Gene
+murF:Gene
+nadD:Gene
+nepI:Gene
+omrA:Gene
+omrB:Gene
+oriC:Gene
+orn:Gene
+oxyS:Gene
+pagP:Gene
+pgmB:Gene
+pheU:Gene
+pheV:Gene
+pinE:Gene
+pptA:Gene
+proK:Gene
+proL:Gene
+psrD:Gene
+psrN:Gene
+psrO:Gene
+ptrA:Gene
+purB:Gene
+qmcA:Gene
+queC:Gene
+queF:Gene
+racR:Gene
+raiA:Gene
+ravA:Gene
+rcnA:Gene
+rdlA:Gene
+rdlB:Gene
+rdlC:Gene
+rdlD:Gene
+rhaA:Gene
+rhaB:Gene
+rhaD:Gene
+rhaM:Gene
+rimN:Gene
+rlmG:Gene
+rlmL:Gene
+rluE:Gene
+rluF:Gene
+rnc:Gene
+rnlA:Gene
+rpoE:Gene
+rplP:Gene
+rplV:Gene
+rprA:Gene
+rpsF:Gene
+rpsG: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
+rseX:Gene
+rsmE:Gene
+rsmF:Gene
+rttR:Gene
+rutA:Gene
+rutD:Gene
+rutF:Gene
+rutR:Gene
+rybA:Gene
+rydB:Gene
+rydC:Gene
+ryeA:Gene
+ryeB:Gene
+ryeE:Gene
+rybB:Gene
+ryeC:Gene
+ryeD:Gene
+ryfA:Gene
+ryfB:Gene
+ryfC:Gene
+ryfD:Gene
+rygC:Gene
+rygD:Gene
+rygE:Gene
+ryhA:Gene
+ryhB:Gene
+ryiA:Gene
+glmZ:Gene
+ryjA:Gene
+ryjB:Gene
+ryjC:Gene
+selC:Gene
+serU:Gene
+serV:Gene
+serW:Gene
+serX:Gene
+sgrS:Gene
+skp:Gene
+sokA:Gene
+sokB:Gene
+sokC:Gene
+spf:Gene
+sraA:Gene
+sroA:Gene
+sroB:Gene
+sroC:Gene
+sroD:Gene
+sroF:Gene
+sroG:Gene
+sroH:Gene
+ssrA:Gene
+ssrS:Gene
+suhB:Gene
+tadA:Gene
+tdcF:Gene
+tff:Gene
+thrT:Gene
+thrV:Gene
+thrW:Gene
+tisA:Gene
+tisB:Gene
+tp2:Gene
+tpke70:Gene
+trpH:Gene
+tusB:Gene
+tusC:Gene
+tusD:Gene
+tusE:Gene
+tyrT:Gene
+tyrU:Gene
+tyrV:Gene
+ubiB:Gene
+ubiD:Gene
+uof:Gene
+uspB:Gene
+valT:Gene
+valU:Gene
+valV:Gene
+valW:Gene
+valX:Gene
+valY:Gene
+valZ:Gene
+ves:Gene
+waaU:Gene
+wbbL_1:Gene
+wzyE:Gene
+xni:Gene
+yabQ:Gene
+yadR:Gene
+yafF:Gene
+yagG:Gene
+ybhU:Gene
+ybfK:Gene
+yccB:Gene
+yceM:Gene
+ycgH_2:Gene
+ychE_2:Gene
+ychG_1:Gene
+ychO:Gene
+ychS:Gene
+yciY:Gene
+yciZ:Gene
+ydbA_2:Gene
+ydfB:Gene
+ydfN:Gene
+ydgU:Gene
+ydiL:Gene
+yedN_1:Gene
+yedS_3:Gene
+yeeL_1:Gene
+yefM:Gene
+yegZ:Gene
+yejM:Gene
+yfaS_1:Gene
+yfdT:Gene
+yffL:Gene
+yffN:Gene
+yffP:Gene
+yffQ:Gene
+yffM:Gene
+yffO:Gene
+yffR:Gene
+yffS:Gene
+ygdT:Gene
+ygiA:Gene
+ygiD:Gene
+ygiT:Gene
+yhbV:Gene
+yhhQ:Gene
+yi82_1:Gene
+ylbE_2:Gene
+yibJ:Gene
+yibV:Gene
+yigP:Gene
+yjgX_1:Gene
+yjbS:Gene
+yjbT:Gene
+yjdP:Gene
+yjhW:Gene
+yjjL:Gene
+ykfM:Gene
+ykgO:Gene
+ylbG:Gene
+ylcH:Gene
+ylcI:Gene
+yliL:Gene
+ymfK:Gene
+ymgI:Gene
+ymgJ:Gene
+yncK_2:Gene
+yncL:Gene
+yneM:Gene
+ynhF:Gene
+yoaI:Gene
+yojO:Gene
+ypaB:Gene
+ypfM:Gene
+ypjK:Gene
+yqgD:Gene
+yraL:Gene
+yrbB:Gene
+yrfF:Gene
+yrhD:Gene
+ytcA:Gene
+ytjA:Gene
+ysaA:Gene
 </essentialGenes>
@@ Line 29: / Line 443: @@
 *
 ****************************************************************************************** -->
-{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
+{|   id="M48ae3191b3b22"  class=" tableEdit "
 |-
 !|Gene!!Reference(s)!!Comments
@@ Line 36: / Line 450: @@
 [[folA]]
 |
-[[PMID:8423162]]<ref name=PMID:8423162/>
+PMID:8423162
+|
+|-
+|
+micF
+|
+PMID:15466019
+|
+|-
+|
+rpsF, rpsI, rpsM, rpsO, rpsQ, and rpsT
+|
+PMID:17277072
+|
+precise gene knockout by recombineering
+|-
+|
+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, alaT, alaU, alaV, alaW, alaX, argQ, argV, argW, argY, argZ, asnT, asnU, asnV, asnW, aspT, aspU, aspV, bcsB, cydA, cydC, dicA, dicF, entS, fadJ, fadK, feoC,fruL, gadY,gcvB,ghrA, ghrB, glnW, gltT, gltU, gltV, gltW, glyU, glyV, glyW, glyX, glyY, gmm, gsiA, gsiB, gsiD,gspB, hofM, hspQ, isrA, isrB, isrC, kilR, ldrA, ldrB, ldrC, ldrD, leuP, leuQ, leuT, lysQ, lysV, lysW, lysY, lysZ, mdtQ, metT, metU, metV, metW, metY, metZ, micA, micC, minD, minE, mnmG, mokB, mokC, nepI, omrA, omrB, pagP, pheU, pheV, proK, proL, psrD, psrN, psrO, racR, rdlA, rdlB, rdlC, rdlD, rhaA, rhaB, rhaD, rhaM, rnc, rpoE, rprA, rseX, rutD,rutF, rutR, rybA, rydB, rydC, ryeA, ryeB, ryeE, ryfA, ryfB, ryfC, ryfD, ryhA, ryhB, ryiA, ryjA, ryjB, ryjC, selC, serW, serX, sgrS, skp, sokA, sokB, sokC, spf, sraA, sroA, sroB, sroC, sroD, sroF, sroG, sroH, ssrS, tadA, tdcF, tff, thrT, thrV, thrW, tisA, tisB, rttR, tpke70, tp2, tyrU, tyrV, ubiB
+valT, valU, valV, valW, valX, valY, valZ, waaU, wzyE, yafF, yagG, ybhU, yccB, ydfB, ydfN, ydgU, yffM, yffO, yffR, yffS, ygiD, ygiT, yhhQ, yibV, yjbS, yjbT, yjdP, yjhW, ykfM, ykgO, ylbG, ylcH, ylcI, yliL, ymfK, ymgI, ymgJ, yncL, yneM, ynhF, yoaI, yojO, ypaB, ypfM, yqgD, yrhD, ytcA, ytjA
+|
+|
+Covered by deletions (see PEC)
+|-
+|
+suhB
+|
+PMID:17652087
+|
+precise gene knockout by recombineering
-|-class='sortbottom'
+|- class="tableEdit_footer"
-|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&page=136300&pagename={{FULLPAGENAMEE}}&type=0&template= edit table] || ||
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22&page=136300&pagename={{FULLPAGENAMEE}}&type=0&template= edit table]</span> || ||
 |}
 <!--box uid=63ce1649aab8b3180235b0af7618f667.136300.M48ae3191b3b22--></protect>
+Add evidence for essentiality here:
+<protect><!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a-->
+<!--
+******************************************************************************************
+*
+*   ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
+*
+****************************************************************************************** -->
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y48ae47a0bea4a"  class=" tableEdit "
+|-
+!|Gene!!Reference(s)!!Comments
+|-
+|
+nusA
+|
+PMID:17277072
+|
+|-
+|
+rpoD
+|
+|
+Ts mutants and depletion studies
+|-
+|
+nusE
+|
+PMID:17277072
+|
+|-
+|
+nusG
+|
+PMID:17277072
+|
+|-
+|
+ffh
+|
+PMID:7559342
+|
+|-
+|
+rpsU
+|
+PMID:17277072
+|
+|-
+|
+accD
+|
+PMID:1886618
+|
+|-
+|
+degS
+|
+PMID:11442831
+|
+|-
+|
+fldA
+|
+PMID:15978585
+|
+|-
+|
+ftsN
+|
+PMID:8509333
+|
+|-
+|
+hflB
+|
+PMID:1104589
+|
+|-
+|
+lolA
+|
+PMID:9849875
+|
+|-
+|
+mraY
+|
+PMID:9829961
+|
+|-
+|
+mreD
+|
+PMID:15612918
+|
+|-
+|
+murA
+|
+PMID:7608103
+|
+|-
+|
+murB
+|
+PMID:4563986
+|
+|-
+|
+murF
+|
+PMID:4552998
+|
+|-
+|
+nadD
+|
+PMID:16153292
+|
+|-
+|
+rplV
+|
+no Keio or PEC deletion
+|
+|-
+|
+rpsG
+|
+PMID:21219455
+|
+|- class="tableEdit_footer"
+|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a&page=136300&pagename={{FULLPAGENAMEE}}&type=0&template= edit table]</span> || ||
+|}
+<!--box uid=63ce1649aab8b3180235b0af7618f667.136300.Y48ae47a0bea4a--></protect>
+== See also ==
+[[Image:PEC search essentials.jpg|thumb]]
+* Baba et al [http://www.nature.com/msb/journal/v2/n1/suppinfo/msb4100050_S1.html supplemental data]
+* Gerdes et al [http://www.integratedgenomics.com/online_material/gerdes/supplementary_table.html supplemental data]
+* [http://www.shigen.nig.ac.jp/ecoli/pec/ PEC] ([[PEC|EcoliWiki page]]).  PEC is a curated database that focuses on phenotypes of ''E. coli'' genes. To display essential genes, go to the [http://www.shigen.nig.ac.jp/ecoli/pec/genes.jsp PEC gene search] and uncheck nonessential, unknown, and Kohara phage (See figure).
+* Kato (2007)<ref name='PMID:17700540'/> identified 303 essential genes
 == References ==
 {{RefHelp}}
 <references/>

Essential genes: Difference between revisions

Latest revision as of 07:10, 28 May 2013

Introduction and caveats

Manually curating nonessential genes

Missing essential genes

The list (Edit this)

Evidence

See also

References

Navigation menu

Search