Table S2. Effect of mutations on the OMP response to NRES

ORF number / Gene name / Encoded protein/function / Fold-change in response to NRESa / Response of mutant to NRES / Source of mutant strainb
Genes induced in response to NRES
VC1712 / Hypothetical protein / 62.0 / WT / (1)
VC0481 / LysE/YggA family protein / 14.6 / WT / (1)
VC2698 / aspA / Aspartate ammonia lyase / 13.5 / WT / (1)
VC0706 / Putative Sigma-54 modulation protein / 12.8 / WT / (1)
VC0802 / Hypothetical protein / 10.5 / WT / (1)
VCA0952 / vpsT / Transcriptional regulator of biofilm genes VpsT / 5.8 / WT / (1)
VC0666 / Hypothetical protein / 5.2 / WT / (1)
VCA0124 / Hypothetical protein (T6SS?) / 3.7 / WT / (1)
VC0983 / toxS / Regulatory protein ToxS / 2.8 / No OMP switching / (2)c
VC0984 / toxR / Transcriptional Regulator of virulence genes ToxR / 2.7 / No OMP switching / (3)c
VC1213 / varA / Response regulator VarA / 2.5 / OmpU production in the absence of NRES / This studyd
VC0665 / vpsR / Sigma-54 dependent transcriptional regulator of biofilm genes VpsR / 2.4 / WT / (1)
VC2647 / aphA / Transcriptional regulator AphA / 1.8 / WT / (1)
Virulence-specific genes; not induced in response to NRES
VC2453 / varS / Sensor kinase VarS / 1.2 / OmpU production in the absence of NRES / (1)
VC0548 / csrA / Carbon storage regulatory protein CsrA / 0.9 / No OMP switching / This studyd
VC0583 / hapR / Regulatory protein HapR / Not detectede / WT / (1)
VC1021 / luxO / Quorum sensing regulatory protein LuxO / 0.9 / WT / (1)
VC1651 / vieB / Response regulator VieB / 1.0 / WT / (1)
VC1652 / vieA / Response regulator VieA / 1.2 / WT / (1)
VC1653 / vieS / Sensor histidine kinase VieS / 1.1 / WT / (1)
VC0838 / toxT / Transcriptional regulator ToxT / 1.0 / WT / (1)
VC0826 / tcpP / Transcriptional Regulator TcpP / 1.2 / WT / (1)
VC0827 / tcpH / Regulatory protein TcpH / 0.9 / WT / (1)
VC1049 / aphB / Transcriptional regulator AphB, / 1.3 / WT / (1)
VC2529 / rpoN / RNA polymerase factor Sigma-54 / 0.8 / Incomplete OMP switching / (1)

a Fold-change in expression in response to NRES compared with expression in T medium alone. The conditions for the microarray analysis are described in the legend to Table S1.

b Unless otherwise noted, mutant is in the V. cholerae C6706 background. C6706 shows a similar response to the NRES mix as N16961 (Fig. S4).

c Mutant is in the V. cholerae N16961 background.

d Mutant is in both the C6706 and the N16961 V. cholerae strain backgrounds.

e ORF is annoted as a pseudogene in strain N16961 and was therefore not included in microarray.

1. Cameron DE, Urbach JM, Mekalanos JJ. 2008. A defined transposon mutant library and its use in identifying motility genes in Vibrio cholerae. Proc Natl Acad Sci USA 105:8736-8741.

2. Mey AR, Craig SA, Payne SM. 2012. Effects of amino acid supplementation on porin expression and ToxR levels in Vibrio cholerae. Infect Immun 80:518-528.

3. Craig SA, Carpenter CD, Mey AR, Wyckoff EE, Payne SM. 2011. Positive Regulation of the Vibrio cholerae Porin OmpT by Iron and Fur. J Bacteriol 193:6505-6511.