Essential Genes in E. coli
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This page was last updated March 2004. It provides links to data on essential genes in E. coli, and shows a short list of E. coli essential genes identified from the Neidhardt E. coli books (Neidhardt and Curtiss, 1996). I define essential genes as those genes which are required in WT strain MG1655 for the formation of colonies on solid rich medium within 24 hours of incubation at 37 degrees C. One method of establishing the essentiality of a gene is the the failure to obtain a null mutation in it. This approach is subject to both false postives and false negatives (see Gerdes et al. 2003 and Kang et al. 2004). In order to unequivocally identify an essential gene, a conditional lethal mutant must be made (see Herring and Blattner, 2004).
The best source of data on the identity of essential genes in E. coli is table # S2 made by Svetlana Gerdes and others from Integrated Genomics, associated with their recent paper (Gerdes et al. 2003). It is available here. It compares the essentiality determinations from 3 sources: the PEC database, the Blattner lab systematic Tn5 mutagenesis project, and their own work.
Another excellent source is the PEC database, which is lists essential genes identified from literature searches. It may also contain some experimental data, but this is not totally clear. PEC - E. coli essential genes (follow the link for Analyses, then Essential)
Another potential source is from the antisense mutants made by the folks at Elitra Pharmaceuticals. They have not published their work, but much of the data is available from U.S. patent application numbers 20020045592 and 20020022718, available here. Their work with Staphylococcus has been published (Forsyth et al. 2002).
....Please email me with suggestions or data on essential genes.
Partial list of essential genes identified from the Neidhardt E. coli and Salmonella books (Neidhardt and Curtiss, 1996). Note that in March 2004 I removed some of the genes previously listed (dinD, ftsE, ftsX, glmS, glmU, htrA, htrB, htrC, infC, lnt, nusB, rfaD, ribB, rpoE, surA, ) because they did not meet my definition of essential genes (they were only required under certain conditions, like high temperature or low salt). This data should be used with caution - extensive investigation of the primary references was NOT performed.
|study type||lethal condtion||strain||notes|
|b2316||accD||acetylCoA carboxylase, carboxytransferase component, beta subunit||enzyme; Fatty acid and phosphatidic acid biosynthesis||Mol Gen Genet 1991 Aug;228(1-2):62-4, "An essential gene of Escherichia coli that has sequence similarity to a chloroplast gene of unknown function"||AKA dedB, usg Questionable|
|b2563||acpS||CoA:apo-[acyl-carrier-protein] pantetheinephosphotransferase||enzyme; Fatty acid and phosphatidic acid biosynthesis||J Bacteriol 1992 Mar;174(5):1544-53, "Locating essential Escherichia coli genes by using mini-Tn10 transposons: the pdxJ operon"||AKA dpj|
|b3433||asd||aspartate-semialdehyde dehydrogenase||enzyme; Amino acid biosynthesis: Lysine|
|b2472||dapE||N-succinyl-diaminopimelate deacylase||enzyme; Amino acid biosynthesis: Lysine||J Bacteriol 1992 Aug;174(16):5258-64, "The essential Escherichia coli msgB gene, a multicopy suppressor of a temperature-sensitive allele of the heat shock gene grpE, is identical to dapE"||22 to 37 degrees||AKA msgB|
|b0015||dnaJ||chaperone with DnaK; heat shock protein||factor; Chaperones|
|b0014||dnaK||chaperone Hsp70; DNA biosynthesis; autoregulated heat shock proteins||factor; Chaperones|
|b2566||era||GTP-binding protein||factor; Global regulatory functions||J Bacteriol. 1989 May;171(5):2581-90 J Bacteriol. 1989 Sep;171(9):5017-24, "Temperature-sensitive lethal mutant of era, a G protein in Escherichia coli"||aka sdgE|
|b0172||frr||ribosome releasing factor||factor; Proteins - translation and modification||Proc Natl Acad Sci U S A 1994 May 10;91(10):4249-53, "Ribosome recycling factor (ribosome releasing factor) is essential for bacterial growth". Also Herring and Blattner, 2004.|
|b0084||ftsI||septum formation; penicillin-binding protein 3; peptidoglycan synthetase||enzyme; Cell division||J Bacteriol 1985 Aug;163(2):615-22, "Cell shape and division in Escherichia coli: experiments with shape and division mutants"||questionable|
|b0083||ftsL||cell division protein; ingrowth of wall at septum||phenotype; Cell division||J Bacteriol 1992 Dec;174(23):7716-28, "FtsL, an essential cytoplasmic membrane protein involved in cell division in Escherichia coli"|
|b3933||ftsN||essential cell division protein||phenotype; Cell division||J Bacteriol 1993 Jun;175(12):3790-7, "Cloning and characterization of ftsN, an essential cell division gene in Escherichia coli isolated as a multicopy suppressor of ftsA12(Ts)"|
|b0095||ftsZ||cell division; forms circumferential ring; tubulin-like GTP-binding protein and GTPase||enzyme; Cell division||J Bacteriol 1991 Jun;173(11):3500-6, "ftsZ is an essential cell division gene in Escherichia coli"|
|b2515||gcpE||orf, hypothetical protein||orf; Unknown||FEMS Microbiol Lett. 1992 Jul 1;73(1-2):175-80, "Sequence and characterization of the gcpE gene of Escherichia coli". Also Herring and Blattner, 2004.|
|b2614||grpE||phage lambda replication; host DNA synthesis; heat shock protein; protein repair||IS, phage, Tn; Phage-related functions and prophages|
|b3178||hflB||degrades sigma32, integral membrane peptidase, cell division protein||enzyme; Degradation of proteins, peptides, glyco||J Bacteriol. 1975 Dec;124(3):1502-7, "Isolation and characterization of a new temperature-sensitive cell division mutant of Escherichia coli K-12" J Bacteriol 1993 Mar;175(5):1344-51|
|b0884||infA||protein chain initiation factor IF-1||factor; Proteins - translation and modification||J. Bacteriol. 1994, 176:198?05, "Translation initiation factor IF1 is essential for cell viability in Escherichia coli"|
|b2828||lgt||phosphatidylglycerol prolipoprotein diacylglyceryl transferase; a major membrane phospholipid||enzyme; Macromolecule synthesis, modification: Phospholipids||J Bacteriol 1989 Jan;171(1):565-8, "Identification and genetic mapping of the structural gene for an essential Escherichia coli membrane protein"||AKA umpA|
|b0096||lpxC||UDP-3-O-acyl N-acetylglucosamine deacetylase; lipid A biosynthesis||enzyme; Surface polysaccharides & antigens||J Bacteriol 1987 Dec;169(12):5408-15, "Sequence analysis, transcriptional organization, and insertional mutagenesis of the envA gene of Escherichia coli". Also Herring and Blattner, 2004.||AKA envA|
|b0168||map||methionine aminopeptidase||enzyme; Proteins - translation and modification||J Bacteriol 1989 Jul;171(7):4071-2, "Methionine aminopeptidase gene of Escherichia coli is essential for cell growth". Also Herring and Blattner, 2004.||AKA pepM|
|b4143||mopA||GroEL, chaperone Hsp60, peptide-dependent ATPase, heat shock protein||factor; Chaperones||J. Bacteriol. 1989 171:1379?385. "The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures"||AKA groEL, groL|
|b4142||mopB||GroES, 10 Kd chaperone binds to Hsp60 in pres. Mg-ATP, suppressing its ATPase activity||factor; Chaperones||J. Bacteriol. 1989 171:1379?385. "The groES and groEL heat shock gene products of Escherichia coli are essential for bacterial growth at all temperatures"||AKA groES, groS|
|b0914||msbA||ATP-binding transport protein; multicopy suppressor of htrB||transport; Transport of small molecules: Other||Mol Microbiol 1993 Jan;7(1):69-79, "The essential Escherichia coli msbA gene, a multicopy suppressor of null mutations in the htrB gene, is related to the universally conserved family of ATP-dependent translocators"|
|b3189||murA||first step in murein biosynthesis;UDP-N-glucosamine 1-carboxyvinyltransferase||enzyme; Murein sacculus, peptidoglycan||J Bacteriol 1995 Jul;177(14):4194-7, "MurA (MurZ), the enzyme that catalyzes the first committed step in peptidoglycan biosynthesis, is essential in Escherichia coli". Also Herring and Blattner, 2004.|
|b3967||murI||glutamate racemase, required for biosynthesis of D-glutamate and peptidoglycan||enzyme; Murein sacculus, peptidoglycan||J Bacteriol 1993 May;175(10):2970-9, "The murI gene of Escherichia coli is an essential gene that encodes a glutamate racemase activity"|
|b1740||nadE||NAD synthetase, prefers NH3 over glutamine||enzyme; Biosynthesis of cofactors, carriers: Pyridine nucleotide||J Bacteriol 1992 Sep;174(17):5765-6, "An essential gene (efg) located at 38.1 minutes on the Escherichia coli chromosome"||AKA efg, ntrL Not Verified|
|b3982||nusG||component in transcription antitermination||putative factor; RNA synthesis, modification, DNA transcription|
|b3019||parC||DNA topoisomerase IV subunit A||enzyme; DNA - replication, repair, restriction/modification||Cell 1990 Oct 19;63(2):393-404 "New topoisomerase essential for chromosome segregation in E. coli"||questionable|
|b4226||ppa||inorganic pyrophosphatase||enzyme; Central intermediary metabolism: Pool, multipurpose conversions||J. Bacteriol. 1990, 172:5686?689, "Pyrophosphatase is essential for growth of Escherichia coli". Also Herring and Blattner, 2004.|
|b0194||proS||proline tRNA synthetase||enzyme; Aminoacyl tRNA synthetases, tRNA modification||J Bacteriol 1990 Jan;172(1):281-6, "Identification and sequence of the drpA gene from Escherichia coli"||AKA drpA, questionable|
|b4245||pyrB||aspartate carbamoyltransferase, catalytic subunit||enzyme; Pyrimidine ribonucleotide biosynthesis||Arch Biochem Biophys 2000 Aug 1;380(1):78-84, "The Helicobacter pylori pyrB gene encoding aspartate carbamoyltransferase is essential for bacterial survival"|
|b0169||rpsB||30S ribosomal subunit protein S2||structural component; Ribosomal proteins - synthesis, modification||J Mol Biol 1979 Aug 5;132(2):219-33, "A conditionally lethal mutation of Escherichia coli affecting the gene coding for ribosomal protein S2 (rpsB)"|
|b3965||trmA||tRNA (uracil-5-)-methyltransferase||enzyme; Aminoacyl tRNA synthetases, tRNA modification||PNAS U S A 1992 May 1;89(9):3995-8, "The gene for a tRNA modifying enzyme, m5U54-methyltransferase, is essential for viability in Escherichia coli"|
|b0915||ycaH||putative EC 1.2 enzyme||putative enzyme; Not classified||Mol Microbiol 1993 Jan;7(1):69-79 J Biol Chem. 1997 Aug 29;272(35):21855-64||AKA orfE, lpxK|
|b1133||ycfB||orf, hypothetical protein||orf; Unknown||Nat Biotechnol 1998 Sep;16(9):851-6, "A genome-based approach for the identification of essential bacterial genes". Also Herring and Blattner, 2004.||LB||MG1655||questionable|
|b2602||yfiL||orf, hypothetical protein||orf; Unknown||Nat Biotechnol 1998 Sep;16(9):851-6, "A genome-based approach for the identification of essential bacterial genes"||LB||MG1655|
|b3064||ygjD||putative O-sialoglycoprotein endopeptidase||putative enzyme; Not classified||Nat Biotechnol 1998 Sep;16(9):851-6, "A genome-based approach for the identification of essential bacterial genes"||LB||MG1655|
|b3183||yhbZ||putative GTP-binding factor||putative factor; Not classified||Nat Biotechnol 1998 Sep;16(9):851-6, "A genome-based approach for the identification of essential bacterial genes"||LB||MG1655|
|b3865||yihA||orf, hypothetical protein||orf; Unknown||LB||MG1655|
|b4161||yjeQ||orf, hypothetical protein||orf; Unknown||LB||MG1655|
Other Essential Gene Sites:
DEG: Database of Essential Genes
Yeast Essential Genes
Yeast Genome Deletion Project
Yeast Eurofan Essential Genes
Forsyth, R.A., Haselbeck, R.J., Ohlsen, K.L., Yamamoto, R.T., Xu, H., Trawick, J.D., Wall, D., Wang, L., Brown-Driver, V., Froelich, J.M., C, K.G., King, P., McCarthy, M., Malone, C., Misiner, B., Robbins, D., Tan, Z., Zhu Zy, Z.Y., Carr, G., Mosca, D.A., Zamudio, C., Foulkes, J.G. and Zyskind, J.W.: A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Mol Microbiol 43 (2002) 1387-400.
Gerdes, S.Y., Scholle, M.D., Campbell, J.W., Balazsi, G., Ravasz, E., Daugherty, M.D., Somera, A.L., Kyrpides, N.C., Anderson, I., Gelfand, M.S., Bhattacharya, A., Kapatral, V., D'Souza, M., Baev, M.V., Grechkin, Y., Mseeh, F., Fonstein, M.Y., Overbeek, R., Barabasi, A.L., Oltvai, Z.N. and Osterman, A.L.: Experimental determination and system level analysis of essential genes in Escherichia coli MG1655. J Bacteriol 185 (2003) 5673-84.
Herring, C.D. and Blattner, F.R.: Conditional lethal amber mutations in essential Escherichia coli genes. Journal of Bacteriology 186 (2004).
Kang, Y., Durfee, T., Glasner, J.D., Qiu, Y., Frisch, D., Winterberg, K.M. and Blattner, F.R.: Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. In review (2004).
Neidhardt, F.C. and Curtiss, R.: Escherichia coli and Salmonella : cellular and molecular biology, 2nd ed. ASM Press, Washington, D.C., 1996.