Supplementary Table 4. Candidate NarP-regulated genes in gamma-proteobacteria. Scores and positions of NarP binding sites relative to the translation start are given. Notation : (*) the ortholog is not present in the genome; (-) no site is found in the upstream region. a. E. ņoli genes from the training set. b,c. Genes potentially regulated by NarP, identified by means of comparative analysis of regulation. The references report transcription to be redox-dependent in at least one of the four bacteria.

Gene

E. coli

Y. pestis

P. multocida

V. vulnificus

Reference

a. Training set

nrfA

-176; 4.67

-

-289; 4.45

-206; 4.35

-193; 4.78 1)

Wang and Gunsalus, 2000

-304; 5.05 2)

-109; 3.88 2)

napF

-128; 4.64

-184; 4.21 3)

-251; 3.87 3)

-99; 4.58 4)

-120; 4.56 3)

-147; 3.98 4)

Darwin et al., 1998

-159; 3.65 3)

-113; 4.49 4)

fdnG

-142; 4.52

*

-226; 3.62

*

Li et al., 1994

narK

-237; 4.37

*

*

*

Li et al., 1994

narG

-159; 4.29

*

*

*

Darwin et al., 1996

frdA

-100; 4.22

-

-141; 3.57

-

Kalman and Gunsalus, 1990

torC

-20; 3.91

*

-286; 4.14

-178; 3.93

Iuchi and Lin, 1987

adhE

-214; 3.91

-

-

-207; 3.82

Membrillo-Hernandez and Lin, 1999

dmsA

-234; 3.61

-

-

*

Bearson et al., 2002

b. Genes with conserved NarP-box

nirB

-102; 4.49

-99; 4.09

*

-17; 4.21

Wang and Gunsalus, 2000

dcuB

-351; 4.17

-

-

-48; 3.58

Golby et al., 1998

nqrA

*

-81; 3.46

-376; 4.05

-


-351; 3.82

moaA

-299; 3.88

-

-

-255; 3.92


-18; 3.60

c. Genes with non-conserved NarP-box

narQ

-

*

-

-188; 4.58 5)


narP

-

-

-

narXL

-117; 3.69

-

*

*

Darwin and Stewart , 1995

fdoG

-

-171; 3.77

*

*


ynfE

-93; 3.86

*

*

*


Changes in the operon structure are indicated by numbers: 1) site upstream of nrfA; 2) site upstream of nrfBCDEF; 3) site upstream of napF; 4) site upstream of ccm; 5) site upstream of narQP.

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. and Stewart,V. (1995) Expression of the narX, narL, narP, and narQ genes of Escherichia coli K-12: regulation of the regulators. J Bacteriol. 177(13). 3865-3869.

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.

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.