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Fig. S1. RT-PCR analysis of the pqsABCDE operon. A. Amplification of the individual pqs genes in PAO1. cDNA was synthesized from RNA extracted from P. aeruginosa PAO1 at various stages of growth (as determined by OD600). The corresponding RNA was amplified in parallel as a negative control, and the P. aeruginosa PAO1 genomic DNA was used as a positive control. B. Amplification of the pqsE gene in PAO1 pqsA and PAO1 pqsA pqsH mutants. cDNA was synthesized from RNA extracted from cells grown to OD600 1.5. Where indicated (+), strains were grown in presence of 40 µM HHQ and/or PQS. The corresponding RNA was amplified in parallel as a negative control, and the P. aeruginosa PAO1 genomic DNA was used as a positive control.

Fig. S2. Analysis of pqsE expression as a function of growth in the pqsEind strain. The fold change in pqsE transcript levels in the pqsEind strain grown to early exponential phase (OD600 = 0.5) and late exponential phase (OD600 = 1.5) was determined by qRT-PCR in the presence of absence of IPTG. The relative expression of pqsE is compared with that of the wild type at an OD600 of 0.5. Where indicated, IPTG (1 mM) was added to the growth medium.

Table S1. Genes regulated in the microarray experiments.

Table S2. Primers used in this work.

Appendix S1. Experimental procedures.

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