Figure 4. Alterations of the proteome and transcriptome implicate katG and the whiB7 regulon in the altered antibiotic sensitivity of the ribosomal mutants; restoration of wild-type KatG levels restores INH sensitivity.
(A) Hierarchical clustering of transcriptional alterations in representative ribosomal mutants, with lfrR-1 mutant included for comparison. For clustering, any genes whose expression is altered at least twofold and has an adjusted p value of <0.05 in any mutant is included. Source data are available as a Supplement. (B) Correlation between changes in RNA levels (x-axis) and protein levels (y-axis) in the rplO-1 mutant relative to wild type, plotted as log2 of fold change. Changes in both RNA and protein abundance are the averages of two replicate experiments. MSMEG_6384 (KatG) is highlighted in red and RplO (L15) is highlighted in green. Genes upregulated in MSMEG_6129 mutant (Bowman and Ghosh, 2014) (DOI: 10.1111/mmi.12448, supplementary file mmi12448-sup-0002-ts2.xls) are highlighted in yellow. See (C) Alterations in abundance of ribosomal proteins in the rplO-1 mutant relative to is parent strain as detected by iTRAQ (blue), and the corresponding changes in transcript abundance as determined by RNAseq (red). Student’s T-test used for comparing datasets. (D) Comparison of ribosomal preparations separated on 10–40% sucrose density gradient, revealing impaired ribosome assembly in the rplO-1 mutant (green line). (E) Western blot of KatG protein levels in rplO-1 (A–A13), rplO-1 allelic exchange mutant AX1G.1, and rplO-1 AX1G.1 expressing KatG from an AHT-inducible plasmid at various AHT concentrations, shown above a plot of INH MIC under those conditions. As the expression of KatG is restored to wild-type levels, INH susceptibility is also restored. (F) Deletion of whiB7 restores wild-type sensitivity to CIP and ETH but not INH or MER in an rplO-1 background. MICs (IC50) were calculated in PRISM using the ECAnything function to fit outgrowth across a 2-fold dilution series of each drug, and bars show mean ± SD of 2–4 biological replicates.
DOI: http://dx.doi.org/10.7554/eLife.20420.011
Figure 4—figure supplement 1. MA plots of the DESeq2 output relative to the parent for nine ribosomal mutants and lfrR mutant, highlighting whiB7 (yellow dot) and katG (purple dots).
Figure 4—figure supplement 2. Confirmation of transcriptional changes by PCR and impact of WhiB7 overexpression on antibiotic susceptibility.
Figure 4—figure supplement 3. Sucrose density gradient profiles of ribosomes isolated from rplF-1, rpsE-1 and rplY-1 mutants, methods as described in Figure 4D.
