TABLE 3.

Relative real-time RT-PCR gene expression (mRNA) levels for different strains grown with or without Phe or Trp

Row	Strain and culture conditionsa	Expression level of gene (Trp residues/totalb)						% Trp-tRNATrpe
		rtpA (0/53)	ycbK (5/312)	trpE (2/515)	trpG (0/194)	trpS (1/330)	mtrB (0/75)
	−Phe
	Wild type
1	−Trp	1c	1	1	1	1	1	85
2	+Trp	1	1	1	1	1	0.9	88
	ΔrtpA
3	−Trp	NAd	NA	1	1	1	0.9	80
4	+Trp	NA	NA	1	1	1	0.8	87
	+Phe
	Wild type
5	−Trp	2.5	2.5	10	1	2	1	47
6	+Trp	1	1.5	2	0.7	0.6	0.7	89
	ΔrtpA
7	−Trp	NA	NA	5	0.4	2.8	0.8	28
8	+Trp	NA	NA	2	0.5	0.4	0.8	89
	ΔmtrB
9	−Trp	0.5	2.3	110	2	0.4	NA	87
10	+Trp	0.5	1.5	90	2	0.4	NA	92
	↑AT
11	−Trp	5	NA	120	2	0.4	0.7	88
12	+Trp	3.8	NA	70	2	0.4	0.7	94

^aRNA was extracted from cultures grown in minimal medium with the supplements indicated (see Materials and Methods). +, present; −, absent.

^bNumber of Trp residues relative to the total number of residues in each polypeptide.

^cAs a reference, we used the relative mRNA concentration calculated from wild-type cultures grown in the presence of Phe (see Materials and Methods). trpP, a Trp transporter (27) was not included in these analyses. Three parallel experiments were performed, and the averaged results are presented. The values obtained in the repeated analyses varied by less than 15 percent.

^dNA, not applicable because these genes have been deleted from the chromosome of the corresponding strain.

^eThe percent Trp-tRNA^Trp corresponds to the amount of Trp-charged tRNA^Trp in an extract divided by the total amount of tRNA^Trp. The amounts of charged and uncharged tRNA^Trp in each sample were determined by using Northern blot analyses (see Materials and Methods).