TABLE 1.

Operons that are responsive to S availability^a

b no.	Coding strand	Name	Description	Control	Reference(s)
b0197-b0199	−	metQIN	l- and d-methionine transport	MetJ	8, 28
b0260-b0261	+	mmuPM	S-Methylmethionine transport and metabolism	MetJb	50
b0365-b0368	+	tauABCD	Taurine transport and metabolism	CysB	54
				Cbl
b0605-b0606	+	ahpCF	Alkyl hydroperoxide reductasec	OxyR	59
b0775	+	bioBd	Biotin synthase	BirA	24
b0801	+	ybiC	?	?
b0828-b0830	+	iaaA-yliAB	Glutathione transport and metabolisme	CysB	34
				Cbl?
b0933-b0937	−	ssuBCDAE	Alkane sulfonate transport and metabolism	CysBf	4, 54
				Cbl
b1275	+	cysB	Positive regulator for Cys regulon	CysBf	20
b1287	−	yciWg	?	?
b1654	−	ydhD	Putative glutaredoxin	?
b1677	+	lpph	Murein lipoprotein structural gene	?
b1729	+	ydjN	?	?
b1823-b1824	−	cspC-yobF	Cold shock protein that affects rpoS expression and ?	?	35
b1919-b1920	−	dcyD-fliYi	Cystine transport and d-cysteine metabolism	Cbl	45, 54, 55
b1987	−	cblj	CysB-like regulator for responses to sulfate availability	CysB	17, 54
b2012-b2013	−	yeeDE	?	?
b2414	+	cysK	Cysteine synthase A	CysB	20, 54
				Cbl
b2421-b2425	−	cysMAWUP	Cysteine synthase B and sulfate/thiosulfate permeasek	CysB	20
b2528-b2530	−	iscAUSl	Synthesis of FeS clusters	IscR	39, 40
b2742	−	nlpDm	Lipoprotein	?
b2750-b2752	−	cysCNDn	Cysteine biosynthesis, sulfate reduction	CysB	20
b2762-b2764	−	cysHIJ	Cysteine biosynthesis, sulfate reduction	CysB	20
				Cbl?
b2903-b2905	−	gcvPHTo	Glycine cleavage, synthesis of 5, 10-methylene tetrahydrofolate	GcvRAp PurR LRP	46
b2913	−	serA	3-Phosphoglycerate dehydrogenase	Lrp	57
				Crp
b2942	+	metKq	SAM synthase	MetJ	10
b3008	+	metC	Synthesis of methionine	MetJ	10
b3207	+	yrbLr	?	?
b3661	−	nlpA	Lipoprotein in outer membrane	?
b3828	−	metRs	Positive regulator for metE and metH	MetJ	10
				MetRt
b3917	+	sbp	Periplasmic sulfate binding protein	CysB	20, 54
				Cbl
b3939-b3940	+	metBL	Synthesis of methionine	MetJ	10
b3941	+	metF	Synthesis of methionine	MetJ	10
b4013	+	metA	Synthesis of methionine	MetJ	10
b4135	−	yjdCu	?	?

^aThe table contains 35 operons. Thirty-five of the 64 genes in this table were found by all four methods of data assessment (numerical analysis of differentially expressed genes, k-means and hierarchical clustering of S and N shift experiments, and visual inspection of genome images). A single k-means cluster for shift experiments contained 41 of these genes, and 42 genes were present in two clusters of the hierarchical tree. The genes found in the k-means cluster but not in the hierarchical clusters were b2742 (nlpD), b2904 (gcvH), b2905 (gcvT), and b3008 (metC). The genes found in the two hierarchical clusters but not in the k-means cluster were b0261 (mmuM), b1919 (dcyD), b2012 (yeeD), b2423 (cysW), and b2764 (cysJ). The latter genes were in operons identified by k-means clustering. Numerical analysis indicated that most of the genes described were S related (see text). The genes supported numerically but not present in k-means or hierarchical clusters were b0197 (metQ), b0606 (ahpF), b0801 (ybiC), b0829 and b0830 (yliAB), b1654 (ydhD), b1677 (lpp), b1823 (cspC), b1987 (cbl), b2528 and b2529 (iscAU), b2903 (gcvP), b3828 (metR), and b1435 (yjdC). The genes that were not supported numerically were b0198 and b0199 (metIN), b1919 and b1920 (dcyD-fliY), b2012 and b2013 (yeeDE), b2423 (cysW), b2530 (iscS), and b3207 (yrbL). The genes that were identified only by visual inspection of genome images for shift experiments were b0198 and b0199 (metIN) and b2530 (iscS). These genes are members of operons identified by other criteria. See below for difficulties with operon organization and/or detection of all members of operons. Information on the genes was obtained from E. coli Entry Point (http://coli.berkeley.edu/cgi-bin/ecoli/coli_entry.pl), the Ecocyc database (http://ecocyc.org/), the ASAP database (http://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm), and primary references. Many references were obtained from the Ecocyc and Ecogene (http://bmb.med.miami.edu/EcoGene/EcoWeb) databases. The Ecocyc, ASAP, and Ecogene databases are among the databases directly accessible from E. coli Entry Point (60).

^bMetJ regulation was inferred from methionine regulation but was not demonstrated directly.

^cThe enzyme probably reduces H₂O₂ physiologically (41).

^dASAP and Ecocyc designate bioB a member of the bioBFCD operon, but the other members of this operon do not appear to be S controlled. BioB converts dethiobiotin to biotin and may also be under separate S control.

^eEcocyc designates yliABCD an ABC transporter.

^fCysB is a negative regulator.

^gASAP designates yciW a member of a 15-gene operon, but we saw no evidence for S control of the other genes.

^hASAP indicates that there is a two-gene operon consisting of b1676 and b1677. We saw no indication of S control for b1676 (pykF), which codes for a pyruvate kinase. Ecocyc designates b1676 a separate operon regulated by FruR.

ⁱfliY is now known to be a misnomer (37). ASAP designates fliY, yecS (b1918), and yecC (b1917) components of an ABC transporter and includes yecS and yecC in the operon. ASAP also includes b1921 (fliZ) and b1922 (fliA) in the operon, but these genes are known chemotaxis genes, and this is unlikely to be correct.

^jCbl constitutes a separate CysB-controlled operon and apparently also lies in an operon with b1988, which codes for the nitrogen regulator Nac. NtrC and Nac control the larger operon (61).

^kThe periplasmic sulfate binding protein, the product of b3917 (sbp), works with this system.

^lASAP includes b2531 (iscR) in the operon. It also includes an additional five genes with related functions (b2523 to b2527) in this operon, but Ecocyc does not. We have no indication that these genes are S regulated.

^mrpoS (b2741) is in an operon with nlpD and is also transcribed separately (22).

ⁿASAP places b2752 in a separate operon, but Ecocyc does not (20).

^ogcvPHT may be specific for glutathione (see text).

^pIncreased expression of the gcv operon may be a response to increased pools of glycine released from glutathione. The GcvRA system responds to glycine.

^qASAP incorrectly designates metK a member of a 10-gene operon.

^rASAP designates yrbL a member of a two-gene operon with b3208 (mtgA), encoding a putative monofunctional peptidoglycan transglycosylase. This gene has the opposite strand orientation, and we had no indication that it was S regulated.

^sASAP incorrectly designates metR a member of a two-gene operon with b3827, which has the opposite strand orientation.

^tRegulation by MetR is negative.

^uASAP lists b4135 as a member of a three-gene operon with b4136 (dipZ), encoding a transmembrane protein disulfide reductase, and b4137 (cutA), which is involved in copper sensitivity. Ecocyc shows cutA as a separate operon. It is not clear whether b4136 and b4137 are S controlled.