Supplementary Table 3. E. coli genes used for construction of the NarP binding signal.

Name	Function	Reference	Experimental method
cydDC	Cytochrome bd-type terminal oxydase	Cook et al., 1997	Beta-Galactosidase assays
narK*	Nitrate-nitrite antiporter	Li et al., 1994	DNase I footprinting
fdnGHI	Formate dehydrogenase N
narGHJI*	Cytoplasmic nitrate reductase	Darwin et al., 1996	DNase I footprinting and other methods
nrfABCDEFG	Peryplasmic nitrite reductase	Wang and Gunsalus, 2000	Beta-Galactosidase assays
nirBDC-cysG	Cytoplasmic nitrite reductase
dmsABC*	Dimethyl sulfoxide reductase	Bearson et al., 2002	DNase I footprinting
focA-pflB	Formate transporter - pyruvate formate-lyase	Kaiser and Sawers, 1995	DNA binding assays and other methods
hyaABCDEF	Hydrogenase I	Richard et al., 1999	Beta-Galactosidase assays
hybOABCDEFG	Hydrogenase II
torCAD*	Trimethylamine-N-oxide reductase	Iuchi and Lin, 1987	Beta-Galactosidase assays
adhE*	alcohol dehydrogenase; acetaldehyde dehydrogenase; pyruvate formate-lyase deactivase	Membrillo-Hernandez and Lin, 1999	Beta-Galactosidase assays
napFDAGHBC-ccmABCDEF-dsbE-ccmH	Periplasmic nitrate reductase – heme exporter	Darwin et al., 1998	DNase I footprinting and other methods
dcuB-fumB*	Transporters for the uptake of C4-dicarboxylates and fumarase B	Golby et al., 1998	Beta-Galactosidase assays
frdABCD*	Fumarate reductase	Kalman and Gunsalus, 1990	Beta-Galactosidase assays
nuoABCDEFGHIJKLMN	NADH dehydrogenase I	Bongaerts et al., 1995	Beta-Galactosidase assays

* - only NarL-dependent regulation was shown.

References

Bearson,S.M., Albrecht,J.A. and Gunsalus,R.P. (2002) Oxygen and nitrate-dependent regulation of dmsABC operon expression in Escherichia coli: sites for Fnr and NarL protein interactions. BMC Microbiol. 2(1). 13-22.

Bongaerts,J., Zoske,S., Weidner,U. and Unden G. (1995) Transcriptional regulation of the proton translocating NADH dehydrogenase genes (nuoA-N) of Escherichia coli by electron acceptors, electron donors and gene regulators. Mol Microbiol., 16(3), 521-34.

Cook,G.M., Membrillo-Hernandez,J. and Poole R.K. (1997) Transcriptional regulation of the cydDC operon, encoding a heterodimeric ABC transporter required for assembly of cytochromes c and bd in Escherichia coli K-12: regulation by oxygen and alternative electron acceptors. J Bacteriol., 179(20), 6525-6530.

Darwin,A.J., Li,J. and Stewart,V. (1996) Analysis of nitrate regulatory protein NarL-binding sites in the fdnG and narG operon control regions of Escherichia coli K-12. Mol Microbiol. 20(3). 621-632.

Darwin,A.J., Ziegelhoffer,E.C., Kiley,P.J. and Stewart,V. (1998) Fnr, NarP, and NarL regulation of Escherichia coli K-12 napF (periplasmic nitrate reductase) operon transcription in vitro. J Bacteriol. 180(16). 4192-4198

Golby,P., Kelly,D.J., Guest,J.R. and Andrews,S.C. (1998) Transcriptional regulation and organization of the dcuA and dcuB genes, encoding homologous anaerobic C4-dicarboxylate transporters in Escherichia coli. J Bacteriol. 180(24), 6586-6596.

Iuchi,S., Lin,E.C. (1987) The narL gene product activates the nitrate reductase operon and represses the fumarate reductase and trimethylamine N-oxide reductase operons in Escherichia coli. Proc Natl Acad Sci U S A. 84(11). 3901-3905.

Kaiser,M., Sawers,G. (1997) Overlapping promoters modulate Fnr- and ArcA-dependent anaerobic transcriptional activation of the focApfl operon in Escherichia coli. Microbiology.143(3), 775-83.

Kalman,L.V. and Gunsalus,R.P. (1990) Nitrate- and molybdenum-independent signal transduction mutations in narX that alter regulation of anaerobic respiratory genes in Escherichia coli. J Bacteriol. 172(12). 7049-7056.

Li,J., Kustu,S. and Stewart,V. (1994) In vitro interaction of nitrate-responsive regulatory protein NarL with DNA target sequences in the fdnG, narG, narK and frdA operon control regions of Escherichia coli K-12. J Mol Biol. 241(2). 150-165.

Membrillo-Hernandez,J. and Lin,E.C. (1999) Regulation of expression of the adhE gene, encoding ethanol oxidoreductase in Escherichia coli: transcription from a downstream promoter and regulation by Fnr and RpoS. J Bacteriol. 181(24). 7571-7579.

Richard,D.J., Sawers,G., Sargent,F., McWalter,L. and Boxer,D.H. (1999) Transcriptional regulation in response to oxygen and nitrate of the operons encoding the [NiFe] hydrogenases 1 and 2 of Escherichia coli. Microbiology., 145(10), 2903-2912.

Wang,H. and Gunsalus,R.P. (2000) The nrfA and nirB nitrite reductase operons in Escherichia coli are expressed differently in response to nitrate than to nitrite. J Bacteriol. 182(20). 5813-5822.