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Science 321 (5893): 1203-1206

Copyright © 2008 by the American Association for the Advancement of Science

Redox-Active Antibiotics Control Gene Expression and Community Behavior in Divergent Bacteria

Lars E. P. Dietrich1,3, Tracy K. Teal4, Alexa Price-Whelan1,4, and Dianne K. Newman1,2,3*

1 Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA.
2 Department of Earth and Planetary Science, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA.
3 Howard Hughes Medical Institute, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 01239, USA.
4 Division of Biology, California Institute of Technology, 1200 East California Boulevard, Pasadena, CA 91125, USA.

Figure 1 Fig. 1.. (A) Distribution of SoxR and SoxS among phyla of the domain Bacteria. A BLAST search for E. coli SoxR and SoxS was performed, and SoxS was found only in enterics. SoxR homologs were identified in 176 {alpha}-, β-, {delta}-, and {gamma}-Proteobacteria and Actinobacteria. All of these homologs contain the SoxR-specific cysteine motif CI[G/Q]CGC[L/M][S/L]XXXC required for binding of the [2Fe-2S] cluster (31). The number of hits within respective phyla are indicated, followed by the total number of genomes surveyed. Members of these phyla (in black) are noted for their ability to produce and excrete redox-active small molecules, such as phenazines (18) and actinorhodin (20). Representative structures are shown. The tree was constructed using the ARB neighbor joining method from 16S ribosomal RNAs of 604 bacterial species. The bar represents 0.1 base substitutions per nucleotide. (B) Gene categories regulated by SoxR. Only in enterics are soxRboxes located upstream of soxS, which confirms the uniqueness of this network. In all other soxR-containing Proteo- and Actinobacteria, soxRboxes are mainly found upstream of five gene types as indicated; 100% correspond to 16 {alpha}-Proetobacteria, 18 β-Proteobacteria, 27 enteric, 38 non-enteric {gamma}-Proteobacteria, or 22 Actinobacteria. "Dehydr." stands for putative dehydrogenases; "oxygen." for putative mono- or dioxygenases; "L-PSP" putative L-PSP endoribonucleases, a family of ribonucleases that share homology with the rat liver perchloric acid-soluble protein, L-PSP; and "methyl./acetylase" putative methyl- or acetyltransferases. Additional annotation information can be found at [View Larger Version of this Image (35K GIF file)]

Figure 2 Fig. 2.. The putative S. coelicolor A3(2) SoxR regulon is specifically up-regulated by pigments. (A) Genes predicted to be regulated by SoxR are shown in gray. (B) RNA extracted from plate-grown S. coelicolor A3(2) M145 and the pigment-null mutant M512 was used to generate cDNA for quantitative RT-PCR (15). Signals were standardized to SCO4548 (32). The experiment was done in triplicate, and data reported represent the mean ±SD. SoxR itself (SCO1697) was also tested for changes in gene expression. [View Larger Version of this Image (18K GIF file)]

Figure 3 Fig. 3.. Phenazine production modulates colony morphology in P. aeruginosa PA14. P. aeruginosa cultures were spotted onto agar plates containing Congo Red and Coomassie Blue, and incubated at 20°C for 6 days. The phenazine null strain ({Delta}phz) started to wrinkle on day 2, the wild type (wt) wrinkled on day 3, and the soxR and mexGHI-opmD deletion strains wrinkled on day 5, whereas a pyocyanin overproducer (DKN370) remained smooth and white after 6 days. [View Larger Version of this Image (50K GIF file)]

Figure 4 Fig. 4.. (A) Surface coverage of 35 colonies per strain monitored over 8 days (±SD). (B) Concentration of pyocyanin release from three colonies into 10 ml agar supplemented with Congo Red and Coomassie Blue. After 5 days of growth at room temperature, the cells were scraped off, pyocyanin was extracted from the agar using chloroform, and extracts were analyzed by high-performance liquid chromatography. The data reported represent the mean ±SD. (C) Spore suspensions of S. coelicolor A3(2) M145 and the pigment mutant M512 were spotted and incubated for 5 days on R5 medium at room temperature. The pigment mutant exhibits a wrinkled morphology, whereas the wild type takes on a smoother phenotype. Scale bar is 0.5 cm. [View Larger Version of this Image (18K GIF file)]

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