TABLE 1.

Transcriptional profile of genes whose TR values are ≤0.5^a

Gene (n = 40)	TR of β′ in expt:		NusA accumulationb in expt:		Transcriptc	Leader transcriptd	Binding factor or existence of terminatore	Figure no.f
	1	2	1	2
Known attenuators (n = 25)
ptsG	0.48	0.38	+	+	+	+	GlcT	36
glpD	0.15	0.17	+	+	+	+	GlpP	6
expZ (vmlR)	0.24	0.21	+	+	+	+	Unknown	12
proB	0.28	0.28	+	+	+	+	Unknown	15
valS	0.23	0.25	+	+	+	+	Unknown	10
ydaO	0.35	0.42	+	+	+	+	Unknown	25
yvbW	0.31	0.22	+	+	+	+	Unknown	22
mgtE (ykoK)	0.50	0.47	+	+	+	+	Mg2+	37
yusC	0.32	0.34	+	+	+	+	SAM	24
lysC	0.14	0.18	+	+	−	+	Lysine	3
mtnW (ykrW)	0.32	0.37	+	+	−	+	SAM	23
tenA	0.38	0.27	+	+	−	+	TPP	28
thiC	0.16	0.21	+	+	−	+	TPP	7
ykkC	0.26	0.45	+	+	−	+	Unknown	15
ykoY	0.45	0.37	+	+	−	+	Unknown	35
trpE	0.38	0.44	+	+	−	NC	TRAP	27
glpF	0.41	0.24	+	+	+	NC	GlpP	6
bglP	0.27	0.27	+	+	+	NC	LicT	18
queC (ykvJ)	0.24	0.40	+	+	+	NC	preQ1	12
thrS	0.36	0.42	+	+	+	NC	tRNA (Thr)	26
tyrS	0.42	0.44	+	+	+	NC	tRNA (Tyr)	32
alaS	0.29	0.33	+	+	+	NC	Unknown	19
glyQ	0.26	0.37	+	+	+	NC	Unknown	14
hisS	0.45	0.49	+	+	+	NC	Unknown	17
ileS	0.30	0.47	+	+	+	NC	Unknown	21
Candidates in this study (n = 15)
pheS	0.40	0.37	+	+	+	+	+	30
yyaE	0.44	0.41	+	+	+	+	+	33
ndhF	0.11	0.10	+	+	−	NC	+	2
ybgE	0.19	0.19	+	+	−	NC	+	8
prkA	0.14	0.17	+	+	−	NC	ND	4
ypbR	0.10	0.12	+	+	+	NC	+	1
yrhG	0.15	0.14	+	+	+	NC	+	5
thdF	0.45	0.39	−	−	+	NC	ND	34
yerA	0.30	0.30	−	−	+	NC	ND	20
yusL	0.22	0.25	Low	Low	−	NC	+	9
yktD	0.24	0.35	Low	Low	−	NC	ND	13
ylxS	0.40	0.41	Low	−	+	NC	+	31
ymcB	0.26	0.25	Low	Low	+	NC	ND	16
yfjO	0.39	0.48	Low	Low	+	NC	ND	29
mutS	0.42	0.46	Low	Low	+	NC	ND	16

^aOnly genes for which NusA binding was detected by our algorithm are shown. The full list of attenuators is shown in Table S3 in the supplemental data.

^bThe NusA peak was judged by visual inspection. +, accumulation at promoter-proximal site is detected (n = 32 for experiments 1 and 2); low, NusA signal is weak (n = 6 for experiment 1 and 5 for experiment 2); −, NusA is distributed constantly from promoter to coding region (n = 2 for experiment 1 and 3 for experiment 2).

^c+, transcript was detected at the coding region (n = 28); −, transcript not detected (n = 12).

^d+, transcript detected (n = 17); NC, not clear (n = 23).

^eFor known attenuators, the binding factor is indicated. TPP, thiamine pyrophosphate; SAM, S-adenosylmethionine; TRAP, trp RNA-binding attenuation protein; preQ1, 7-aminomethyl-7-deazaguanine; unknown, not reported. For new candidate attenuators. the existence of a terminator (+) was predicted by GENETYX-MAC (GENETYX Corporation). ND, not detected.

^fFigure number in Fig. S3 in the supplemental data.