Genome-scale identification of conditionally essential genes in E. coli by DNA microarrays.
Identifying the genes required for the growth or viability of an organism under a given condition is an important step toward understanding the roles these genes play in the physiology of the organism. Currently, the combination of global transposon mutagenesis with PCR-based mapping of transposon insertion sites is the most common method for determining conditional gene essentiality. In order to accelerate the detection of essential gene products, here we test the utility and reliability of a DNA microarray technology-based method for the identification of conditionally essential genes of the bacterium, Escherichia coli, grown in rich medium under aerobic or anaerobic growth conditions using two different DNA microarray platforms. Identification and experimental verification of five hypothetical E. coli genes essential for anaerobic growth directly demonstrated the utility of the method. However, the two different DNA microarray platforms yielded largely non-overlapping results after a two standard deviations cutoff and were subjected to high false positive background levels. Thus, further methodological improvements are needed prior to the use of DNA microarrays to reliably identify conditionally essential genes on genome-scale.
Department of Pathology, Northwestern University, Chicago, IL 60611, USA.
Xin
X
Tong
John W
JW
Campbell
Gábor
G
Balázsi
Krin A
KA
Kay
Barry L
BL
Wanner
Svetlana Y
SY
Gerdes
Zoltán N
ZN
Oltvai
D000332:Aerobiosis / Q000502:physiology; D000693:Anaerobiosis / Q000502:physiology; D002455:Cell Division; D018983:DNA Footprinting / Q000379:methods; D004926:Escherichia coli / Q000166:cytology / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000235:genetics* / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods; D015964:Gene Expression Regulation, Bacterial / Q000502:physiology*; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010100:Oxygen / Q000378:metabolism*; D023302:Protein Footprinting / Q000379:methods; D020543:Proteome / Q000235:genetics / Q000378:metabolism
D029968:Escherichia coli Proteins; D020543:Proteome; D010100:Oxygen