Essential Genes

EGGS: Essential Genes on Genomic Scale

Data Curation

NMPDR curators have collated genome-scale essentiality datasets from published studies involving 10 bacterial species, including the priority pathogens Staphylococcus aureus, Streptococcus pneumoniae, Mycobacterium tuberculosis, Salmonella enterica, and Escherichia coli. The results of each of the studies cited below have been mapped onto only one genome. Projecting essentiality from one strain to another is problematic, so we have attributed essentiality only to genes in the complete genome that was both available in 2006 when these studies were reviewed, and that is most similar to the strain used for the in vivo experiment. While there are 16 studies cited, there is one strain (genome) annotated for each of 10 different organisms studied.

Establishing essentiality

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.

Analysis

Comparative analysis of these data across multiple organisms in a rich genomic, biochemical, and phylogenetic contexts provided by the collection of annotated Subsystems greatly facilitates their interpretation and practical applications, such as understanding of cellular networks, gene and pathway discovery, identification of novel drug targets, and strain engineering. 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.

Data

Data Curation		Experimental Conditions		Essentiality Assessment
Genome	Attribute Key	Mutagenesis	Outgrowth	ORFs tested	N	E	U	Ref
S. aureus N315 158879.1	SA_essential_Ji	random RNAi	clonal on undefined rich agar TSA, aerobic	2648	n/a	146	n/a	1
S. aureus N315 158879.1	SA_essential_Forsyth	random RNAi	clonal on undefined rich agar LB+0.2% glucose, 37°C, aerobic	2648	n/a	658*	n/a	2
S. aureus N315 158879.1	SA_essential_Ko	targeted deletion	clonal on undefined rich agar TSA+2% sheep blood, 37°C, microaerobic in 5% CO2	481	359*	123	216	3
S. pneumoniae R6 171101.1	SP_essential_Thanassi	targeted insertion	clonal on undefined rich agar Todd-Hewitt, 37°C, microaerobic growth in 5% CO2	347	234	113	n/a	4
S. pneumoniae R6 171101.1	SP_essential_Song	targeted deletion	clonal on undefined rich agar Todd-Hewitt, 37°C, microaerobic growth in 5% CO2	693	560	133		5
H. pylori 26695 85962.1	HP_candidate_essential_Salama	random insertion	population in undefined rich broth HB, 37°C, microaerobic in 10% CO2	1760	1178	344	54	6
M. genitalium 243273.1	MG_essential_Hutchison_2006	random insertion	clonal on undefined rich agar SP4, 37°C, microaerobic in 5% CO2	482	100	382	0	7
M. tuberculosis H37 Rv 83332.1	MT_contribute_to_fitness_Rubin	random insertion	population in defined rich broth OADC	3989	2567	614	808	8
H. influenzae KW20 Rd 71421.1	HI_contribute_to_fitness_Akerley	random insertion	population in undefined rich broth BHI, 37°C, aerobic	1657	602	670	385	9
P. aeruginosa PAO1 208964.1	PA_candidate_essential_Jacobs	random insertion	clonal on undefined rich agar LB, room temp, aerobic	5570	4783	787	0	10
P. aeruginosa PAO1 208964.1	PA_essential_PA14_PAO1_Liberati	random insertion	clonal on undefined rich agar LB, aerobic	5688	4,469	335	884	11
B. subtilis 168 224308.1	BS_essential_Kobayashi	targeted insertion	clonal on undefined rich agar LB, 37°C, aerobic	4105	3830	271	4	12
S. typhimurium LT2 99287.1	ST_essential_Knuth	random insertion	clonal on undefined rich agar LB, 30°C, aerobic	4425	n/a	257	n/a	13
E. coli K-12 83333.1	EC_contribute_to_fitness	random insertion	population in undefined rich broth LB, 37°C, aerobic	4308	3126	620	562	14
E. coli K-12 83333.1	EC_essential_Keio	targeted deletion	clonal on undefined rich agar LB, 37°C, aerobic	4390	3985	303	102	15
E. coli K-12 83333.1	EC_essential_Blattner	targeted insertion	clonal on undefined rich agar LB, 37°C, aerobic	4308	2001	n/a	2201	16

Mutagenesis and outgrowth conditions used in the studies are listed in brief. For complete details, see the published experiments. Results are recorded in NMPDR as attributes in key-value pairs. The attribute keys are listed. Values are N onessential, E ssential, or U ndetermined (or unreported). *Only partial data reported.

Published Experiments

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. 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. 11952893

3. Ko KS, Lee JY, Song JH, Baek JY, Oh WS, Chun J, Yoon HS. 2006 Screening of essential genes in Staphylococcus aureus N315 using comparative genomics and allelic replacement mutagenesis. J. Microbiol. Biotechnol. 16(4): 623%u2013632. journal ToC

4. 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. 12136097

5. 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. 15995353

6. Salama NR, Shepherd B, Falkow S. 2004 Global transposon mutagenesis and essential gene analysis of Helicobacter pylori. J Bacteriol 186: 7926-7935. 15547264

7. 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. 16407165

8. Sassetti CM, Boyd DH, Rubin EJ 2003 Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48: 77-84. 12657046

9. 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. 11805338

10. 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. 14617778

11. 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. 16477005

12. 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. 12682299

13. 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. 15009898

14. 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. 13129938

15. 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. 16738554

16. Kang Y, Durfee T, Glasner JD, Qiu Y, Frisch D, Winterberg KM, Blattner FR. 2004 Systematic mutagenesis of the Escherichia coli genome. J Bacteriol. 186: 8548. 15262929