TABLE 2.

E. coli genes whose relative expression levels were increased or decreased by evgA amplification

Genea	b no.b	Functional classificationc	Known or predicted function	Effect of EvgA on gene expression (fold change)
Increased expression
hdeAd,e	b3510	Not known	Protein regulated by H-NS, chaperone	84.3
yfdX	b2375	Not known	Protein regulated by EvgA	54.4
hdeBd,e	b3509	Not known	Protein regulated by H-NS, predicted chaperone	42.2
evgAe	b2369	Regulation	Regurator of EvgAS two-component system	41.8
gadAd,e	b3517	Metabolism	Glutamate decarboxylase-alpha	41.4
ydePe	b1501	Metabolism	Putative reductase	15.3
yjfL	b4184	Cell structure	Putative membrane protein	9.2
yfdWe	b2374	Metabolism	Putative formyl-coenzyme A transferase	6.8
msyB	b1051	None	Acidic protein suppresses mutants lacking function of protein export	6.5
dpse	b0812	Adaptation (starvation)	Stress response DNA-binding protein	6.3
yhiEe	b3512	Regulation	Putative regulator	6.2
ybjR	b0867	Metabolism	Putative amidase	5.5
asr	b1597	Adaptation (stress)	Acid shock RNA controlled by phoBR	5.3
yfdM	b2359	Extrachromosomal (phage)	Putative transferase	5.2
gadC (xasA)d,e	b1492	Transport	Predicted amino acid transporter	5.2
ypeC	b2390	None	Function unknown	5.2
ycaC	b0897	Metabolism	Putative cysteine hydrolase	5.0
yahO	b0329	None	Function unknown	4.7
yfdO	b2358	Extrachromosomal (phage)	Putative replication protein	4.6
yhiV	b3514	Transport	Multidrug transport protein	4.4
ybaS	b0485	Metabolism	Putative glutaminase	4.3
mgtA	b4242	Transport	Magnesium transporter	4.1
yfdE	b2371	Metabolism	Putative formyl-coenzyme A transferase	4.0
Decreased expression
tnaA	b3708	Metabolism	Tryptophan deaminase	7.1
tnaL	b3707	Metabolism	Tryptophanase leader peptide	5.0
glpQ	b2239	Metabolism	Glycerophosphodiester phosphodiesterase	4.5

^aBased on information from the EcoGene database (http://bmb.med.miami.edu/ecogene/ecoweb/) (40).

^bBlattner number. Based on information from the E. coli Genome Project database (http://www.genome.wisc.edu/) (8).

^cBased on information from the Gene ProtEC database (http://genprotec.mbl.edu/) (38, 39).

^dPreviously shown to be important for acid survival.

^eExpression of these genes are increased in the H-NS-deficient strain (18).