Essential Genes on Genomic Scale
NMPDR curators have collated genome-scale essentiality datasets from published studies involving 10 bacterial species, including the NMPDR pathogens Staphylococcus aureus and Streptococcus pneumoniae. Click on the red shaded portions of the bars below to explore the genes for which there is experimental evidence that the functions are essential in that organism. The remainder of the genes in the gray portion of the bars are either dispensable or untested. Experimental details of the studies are shown below the graph.
Proportion of total genes determined to be essential
mutagenesis |
R rna |
R rna |
T ins |
T del |
R ins |
R ins |
R ins |
R ins |
R ins |
R ins |
R ins |
R ins |
T del |
T ins |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
outgrowth |
clone |
clone |
clone |
clone |
pop |
clone |
pop |
pop |
clone |
clone |
clone |
clone |
clone |
clone |
reference |
The notion of essential for life is entirely dependent on the specific lifestyle and organism studied, that is, the environmental and genetic conditions surveyed. The methodology used to generate each dataset influences gene essentiality assessments as well. Bacterial genes may be inactivated with antisense RNAs or by deletion or insertional disruption, either randomly or in a specifically targeted manner. The important distinction between the techniques is whether the growth of each mutant occurs clonally or in a mixed population. Although in both strategies gene "essentiality" is deduced from the inability of a mutant cell to undergo a certain number of divisions, the passing threshold is much more stringent in mixed populations than in clonal studies. Thus, a mutant with substantially decreased fitness would be quickly selected against under the conditions of competitive outgrowth in planktonic culture, while it might still be capable of forming an isolated colony. The details of mutagenesis and outgrowth in the studies compiled here are indicated in the table, where T= targeted, R= random, rna= antisense RNA, ins= insertion, del= deletion, clone= clonal outgrowth on plates, pop= population outgrowth in liquid culture. For complete details, see the published studies.
These data may also be viewed and explored in the SEED. A comparative analysis of these essential genes in the context of functional subsystems has recently been published by our annotators, and here we make available the 
supplemental data tables discussed in the paper. Another resource is the Database of Essential Genes.
1. Ji YD, Zhang B, Van Horn SF, Warren P, Woodnutt G, Burnham MKR, Rosenberg M. 2001 Identification of critical staphylococcal genes using conditional phenotypes generated by antisense RNA. Science 293: 2266-2269. 
PMID 11567142
2. Forsyth RA, Haselbeck RJ, Ohlsen KL, Yamamoto RT, Xu H, Trawick JD, Wall D, Wang LS, Brown-Driver V, Froelich JM, et al. 2002 A genome-wide strategy for the identification of essential genes in Staphylococcus aureus. Molecular Microbiology 43: 1387-1400. PMID 11952893
3. Thanassi JA, Hartman-Neumann SL, Dougherty TJ, Dougherty BA, J. PM. 2002 Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae. Nucleic Acids Research 30: 3152-3162. PMID 12136097
4. Song JH, Ko KS, Lee JY, Baek JY, Oh WS, Yoon HS, Jeong JY, Chun J. 2005 Identification of essential genes in Streptococcus pneumoniae by allelic replacement mutagenesis. Mol Cells 19 365-374. PMID 15995353
5. Salama NR, Shepherd B, Falkow S. 2004 Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J Bacteriol 186: 7926-7935. PMID 15547264
6. Glass JI, Assad-Garcia N, Alperovich N, Yooseph S, Lewis MR, Maruf M, Hutchison CA, 3rd, Smith HO, Venter JC. 2006 Essential genes of a minimal bacterium. Proc Natl Acad Sci USA 103: 425-430. PMID 16407165
7. Sassetti CM, Boyd DH, Rubin EJ 2003 Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48: 77-84. PMID 12657046
8. Akerley BJ, Rubin EJ, Novick VL, Amaya K, Judson N, Mekalanos JJ. 2002 A genome-scale analysis for identification of genes required for growth or survival of Haemophilus influenzae. Proc Natl Acad Sci USA 99: 966-971. PMID 11805338
9. Jacobs MA, Alwood A, Thaipisuttikul I, Spencer D, Haugen E, Ernst S, Will O, Kaul R, Raymond C, Levy R, et al. 2003 Comprehensive transposon mutant library of Pseudomonas aeruginosa. Proc Natl Acad Sci USA 100: 14339-14344. PMID 14617778
10. Liberati NT, Urbach JM, Miyata S, Lee DG, Drenkard E, Wu G, Villanueva J, Wei T, Ausubel FM 2006 An ordered, nonredundant library of Pseudomonas aeruginosa strain PA14 transposon insertion mutants. Proc Natl Acad Sci USA 103 :2833-2838. PMID 16477005
11. Knuth K, Niesalla H, Hueck CJ, Fuchs TM 2004 Large-scale identification of essential Salmonella genes by trapping lethal insertions. Mol Microbiol 51: 1729-1744. PMID 15009898
12. Gerdes S, Scholle M, Campbell J, Balazsi G, Ravasz E, Daugherty M, Somera AL, Kyrpides N, Anderson I, Gelfand MS, et al. 2003 Experimental determination and system-level analysis of essential genes in E. coli MG1655. J Bacteriol 185: 5673-5684. PMID 13129938
13. Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H 2006 Construction of Escherichia coli K-12 in-frame, single-gene knock-out mutants: the Keio collection. Mol Systems Biol doi:10.1038/msb4100050. PMID 16738554
14. Kobayashi K, Ehrlich SD, Albertini A, Amati G, Andersen KK, Arnaud M, Asai K, Ashikaga S, Aymerich S, Bessieres P, et al. 2003 Essential Bacillus subtilis genes. Proc Natl Acad Sci USA 100: 4678-4683. PMID 12682299
