Global gene expression profiling in Escherichia coli K12: effects of oxygen availability and ArcA.
The ArcAB two-component system of Escherichia coli regulates the aerobic/anaerobic expression of genes that encode respiratory proteins whose synthesis is coordinated during aerobic/anaerobic cell growth. A genomic study of E. coli was undertaken to identify other potential targets of oxygen and ArcA regulation. A group of 175 genes generated from this study and our previous study on oxygen regulation (Salmon, K., Hung, S. P., Mekjian, K., Baldi, P., Hatfield, G. W., and Gunsalus, R. P. (2003) J. Biol. Chem. 278, 29837-29855), called our gold standard gene set, have p values <0.00013 and a posterior probability of differential expression value of 0.99. These 175 genes clustered into eight expression patterns and represent genes involved in a large number of cell processes, including small molecule biosynthesis, macromolecular synthesis, and aerobic/anaerobic respiration and fermentation. In addition, 119 of these 175 genes were also identified in our previous study of the fnr allele. A MEME/weight matrix method was used to identify a new putative ArcA-binding site for all genes of the E. coli genome. 16 new sites were identified upstream of genes in our gold standard set. The strict statistical analyses that we have performed on our data allow us to predict that 1139 genes in the E. coli genome are regulated either directly or indirectly by the ArcA protein with a 99% confidence level.
Salmon
Kirsty A
KA
Department of Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles, California 90095-1489, USA.
Hung
She-pin
SP
Steffen
Nicholas R
NR
Krupp
Rebecca
R
Baldi
Pierre
P
Hatfield
G Wesley
GW
Gunsalus
Robert P
RP
D000483:Alleles; D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000502:physiology*; D001665:Binding Sites; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000378:metabolism; D048168:Escherichia coli K12 / Q000235:genetics* / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism; D005285:Fermentation; D015964:Gene Expression Regulation, Bacterial; D005821:Genetic Techniques; D016680:Genome, Bacterial; D005810:Multigene Family; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D010100:Oxygen / Q000378:metabolism*; D025341:Principal Component Analysis; D012372:ROC Curve; D012097:Repressor Proteins / Q000737:chemistry / Q000502:physiology*; D012984:Software
D001425:Bacterial Outer Membrane Proteins; D018076:DNA, Complementary; D029968:Escherichia coli Proteins; D012097:Repressor Proteins; C041610:arcA protein, E coli; D010100:Oxygen