@article{19626,
  abstract     = {Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of nonfunctional “promoter leakiness,” merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the noncanonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g., control of costly-to-induce multidrug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multidrug resistance is crucial for effective public health measures.},
  author       = {Jain, Kirti and Hauschild, Robert and Bochkareva, Olga and Römhild, Roderich and Tkačik, Gašper and Guet, Calin C},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {15},
  publisher    = {National Academy of Sciences},
  title        = {{Pulsatile basal gene expression as a fitness determinant in bacteria}},
  doi          = {10.1073/pnas.2413709122},
  volume       = {122},
  year         = {2025},
}

@misc{19294,
  abstract     = {Active regulation of gene expression, orchestrated by complex interactions of activators and repressors at promoters, controls the fate of organisms. In contrast, basal expression at uninduced promoters is considered to be a dynamically inert mode of non-functional “promoter leakiness”, merely a byproduct of transcriptional regulation. Here, we investigate the basal expression mode of the mar operon, the main regulator of intrinsic multiple antibiotic resistance in Escherichia coli, and link its dynamic properties to the non-canonical, yet highly conserved start codon of marR across Enterobacteriaceae. Real-time, single-cell measurements across tens of generations reveal that basal expression consists of rare stochastic gene expression pulses, which maximize variability in wildtype and, surprisingly, transiently accelerate cellular elongation rates. Competition experiments show that basal expression confers fitness advantages to wildtype across several transitions between exponential and stationary growth by shortening lag times. The dynamically rich basal expression of the mar operon has likely been evolutionarily maintained for its role in growth homeostasis of Enterobacteria within the gut environment, thereby allowing other ancillary gene regulatory roles to evolve, e.g. control of costly-to-induce multi-drug efflux pumps. Understanding the complex selection forces governing genetic systems involved in intrinsic multi-drug resistance is crucial for effective public health measures.},
  author       = {Jain, Kirti and Hauschild, Robert and Bochkareva, Olga and Römhild, Roderich and Tkačik, Gašper and Guet, Calin C},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Data for "Pulsatile basal gene expression as a fitness determinant in bacteria"}},
  doi          = {10.15479/AT:ISTA:19294},
  year         = {2025},
}

@article{10812,
  abstract     = {Several promising strategies based on combining or cycling different antibiotics have been proposed to increase efficacy and counteract resistance evolution, but we still lack a deep understanding of the physiological responses and genetic mechanisms that underlie antibiotic interactions and the clinical applicability of these strategies. In antibiotic-exposed bacteria, the combined effects of physiological stress responses and emerging resistance mutations (occurring at different time scales) generate complex and often unpredictable dynamics. In this Review, we present our current understanding of bacterial cell physiology and genetics of responses to antibiotics. We emphasize recently discovered mechanisms of synergistic and antagonistic drug interactions, hysteresis in temporal interactions between antibiotics that arise from microbial physiology and interactions between antibiotics and resistance mutations that can cause collateral sensitivity or cross-resistance. We discuss possible connections between the different phenomena and indicate relevant research directions. A better and more unified understanding of drug and genetic interactions is likely to advance antibiotic therapy.},
  author       = {Römhild, Roderich and Bollenbach, Mark Tobias and Andersson, Dan I.},
  issn         = {1740-1534},
  journal      = {Nature Reviews Microbiology},
  keywords     = {General Immunology and Microbiology, Microbiology, Infectious Diseases},
  pages        = {478--490},
  publisher    = {Springer Nature},
  title        = {{The physiology and genetics of bacterial responses to antibiotic combinations}},
  doi          = {10.1038/s41579-022-00700-5},
  volume       = {20},
  year         = {2022},
}

@article{9046,
  author       = {Römhild, Roderich and Andersson, Dan I.},
  issn         = {1553-7374},
  journal      = {PLoS Pathogens},
  number       = {1},
  publisher    = {Public Library of Science},
  title        = {{Mechanisms and therapeutic potential of collateral sensitivity to antibiotics}},
  doi          = {10.1371/journal.ppat.1009172},
  volume       = {17},
  year         = {2021},
}

@article{9746,
  abstract     = {Evolutionary adaptation is a major source of antibiotic resistance in bacterial pathogens. Evolution-informed therapy aims to constrain resistance by accounting for bacterial evolvability. Sequential treatments with antibiotics that target different bacterial processes were previously shown to limit adaptation through genetic resistance trade-offs and negative hysteresis. Treatment with homogeneous sets of antibiotics is generally viewed to be disadvantageous, as it should rapidly lead to cross-resistance. We here challenged this assumption by determining the evolutionary response of Pseudomonas aeruginosa to experimental sequential treatments involving both heterogenous and homogeneous antibiotic sets. To our surprise, we found that fast switching between only β-lactam antibiotics resulted in increased extinction of bacterial populations. We demonstrate that extinction is favored by low rates of spontaneous resistance emergence and low levels of spontaneous cross-resistance among the antibiotics in sequence. The uncovered principles may help to guide the optimized use of available antibiotics in highly potent, evolution-informed treatment designs.},
  author       = {Batra, Aditi and Römhild, Roderich and Rousseau, Emilie and Franzenburg, Sören and Niemann, Stefan and Schulenburg, Hinrich},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{High potency of sequential therapy with only beta-lactam antibiotics}},
  doi          = {10.7554/elife.68876},
  volume       = {10},
  year         = {2021},
}