. 2010 Dec 30;193(5):1098–1106. doi: 10.1128/JB.01027-10

TABLE 3.

Upregulated genes in BL21(DE3)ΔalrΔdadX^PR

Gene	2-D gel spot(s)^c	Function	SLR (log₂)^a
Gene	2-D gel spot(s)^c	Function	Mean^b	SD
asd	P9, P10	Aspartate-semialdehyde dehydrogenase	1.43	0.12
folE		GTP cyclohydrolase I	1.63	0.21
glyA	P3	Serine hydroxymethyltransferase	ND	ND
metA	P11	Homoserine transsuccinylase	2.43	0.31
metB	P13	Cystathionine gamma-synthase	2.20	0.56
metC		Cystathionine beta-lyase (beta-cystathionase)	2.27	0.40
metE	P1, P2, P15	Tetrahydropteroyltriglutamate methyltransferase	2.77	0.15
metF	P6, P7	5,10-Methylenetetrahydrofolate reductase	2.83	0.21
metI		d- and l-Methionine transport protein (ABC superfamily, membrane)	1.73	0.35
metK	P4	S-Adenosylmethionine synthetase	ND	ND
metL		Aspartokinase II and homoserine dehydrogenase II	2.27	0.75
metN		d- and l-Methionine transport protein (ABC superfamily, atp_bind)	2.00	0.53
metQ		d-Methionine transport protein (ABC superfamily, peri_bind)	1.57	0.32
rplJ	P14	Ribosomal protein L10	ND	ND
spf		Spot 42 RNA	1.63	0.31
trpA		Tryptophan synthase, alpha protein	1.23	0.23
trpB		Tryptophan synthase, beta protein	1.33	0.21
trpC		N-(5-phosphoribosyl) anthranilate isomerase and indole-3-glycerolphosphate synthetase	1.20	0.10
trpD		Anthranilate synthase component II, glutamine amido-transferase, and phosphoribosylanthranilate transferase	1.60	0.10
trpE		Anthranilate synthase component I	1.63	0.15
trpL		trp operon leader peptide	1.47	0.32
ybdH		Putative oxidoreductase	1.83	0.15
ybdL		Putative aminotransferase	1.30	0.17
yfcF		orf, hypothetical protein	1.53	0.35

An SLR (signal log ratio) is applied to reflect the change (n-fold) between the BL21(DE3)ΔalrΔdadX cell and its revertant. The SLR was calculated by taking the ratio of the signal intensity (difference of the log₂ value) between the two cells. Genes that showed at least a 2-fold increase in mRNA abundance relative to the control and had a present call by the Affymetrix algorithm were considered upregulated. ND, not determined.

An average value from three individual experiments.

“P” numbers denote proteins spots upregulated on 2-D gels and identified by peptide mass fingerprinting (Fig. 3B).