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Essential genes

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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)

294 candidates

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

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]


See also

PEC search essentials.jpg

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. 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 EcoliWiki page
  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 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. 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 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
  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 EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  21. Boyle, DS & Donachie, WD (1998) mraY is an essential gene for cell growth in Escherichia coli. J. Bacteriol. 180 6429-32 PubMed EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  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 EcoliWiki page
  26. Stancek, M et al. (2005) Analysis of Escherichia coli nicotinate mononucleotide adenylyltransferase mutants in vivo and in vitro. BMC Biochem. 6 16 PubMed EcoliWiki page
  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 EcoliWiki page