DOI: 10.5061/dryad.vj35n
title: Data from: Linking system-wide impacts of RNA polymerase mutations to the fitness cost of rifampin resistance in Pseudomonas aeruginosa

description: Fitness costs play a key role in the evolutionary dynamics of antibiotic
 resistance in bacteria by generating selection against resistance in the
 absence of antibiotics. Although the genetic basis of antibiotic
 resistance is well understood, the precise molecular mechanisms linking
 the genetic basis of resistance to its fitness cost remain poorly
 characterized. Here, we examine how the system-wide impacts of mutations
 in the RNA polymerase (RNAP) gene rpoB shape the fitness cost of rifampin
 resistance in Pseudomonas aeruginosa. Rifampin resistance mutations reduce
 transcriptional efficiency, and this explains 76% of the variation in
 fitness among rpoB mutants. The pleiotropic consequence of rpoB mutations
 is that mutants show altered relative transcript levels of essential
 genes. We find no evidence that global transcriptional responses have an
 impact on the fitness cost of rifampin resistance as revealed by
 transcriptome sequencing (RNA-Seq). Global changes in the transcriptional
 profiles of rpoB mutants compared to the transcriptional profile of the
 rifampin-sensitive ancestral strain are subtle, demonstrating that the
 transcriptional regulatory network of P. aeruginosa is robust to the
 decreased transcriptional efficiency associated with rpoB mutations. On a
 smaller scale, we find that rifampin resistance mutations increase the
 expression of RNAP due to decreased termination at an attenuator upstream
 from rpoB, and we argue that this helps to minimize the cost of rifampin
 resistance by buffering against reduced RNAP activity. In summary, our
 study shows that it is possible to dissect the molecular mechanisms
 underpinning variation in the cost of rifampin resistance and highlights
 the importance of genome-wide buffering of relative transcript levels in
 providing robustness against resistance mutations. IMPORTANCE Antibiotic
 resistance mutations carry fitness costs. Relative to the characteristics
 of their antibiotic-sensitive ancestors, resistant mutants show reduced
 growth rates and competitive abilities. Fitness cost plays an important
 role in the evolution of antibiotic resistance in the absence of
 antibiotics; however, the molecular mechanisms underlying these fitness
 costs is not well understood. We applied a systems-level approach to
 dissect the molecular underpinnings of the fitness costs associated with
 rifampin resistance in P. aeruginosa and showed that most of the variation
 in fitness cost can be explained by the direct effect of resistance
 mutations on the enzymatic activity of the mutated gene. Pleiotropic
 changes in transcriptional profiles are subtle at a genome-wide scale,
 suggesting that the gene regulatory network of P. aeruginosa is robust in
 the face of the direct effects of resistance mutations.
description: PAO1::mini-Tn7-pLAC-lux
 ancestral strain RNA-SeqBAM files: RNA-Seq data
 for two biological replicates (BR) of the rifampin-sensitive
 PAO1::mini-Tn7-pLAC-lux ancestral strain.PAO1_ancestral_RNA-Seq.zipD521G rpoB mutant RNA-SeqBAM files: RNA-Seq data for two biological replicates (BR) of the rifampin-resistant D521G rpoB mutant, which was evolved from the PAO1::mini-Tn7-pLAC-lux ancestral strainH531R rpoB mutant RNA-SeqBAM files: RNA-Seq data for 2 biological replicates (BR) of the rifampin-resistant H531R rpoB mutant evolved from the PAO1::mini-Tn7-pLAC-lux ancestral strainGenome Sequence and AnnotationGenome sequence of the PAO1::mini-Tn7-pLAC-lux ancestral strain in FASTA format and the accompanying genome annotation file in GTF format.