Bacterial systems biology articles within Nature

Featured

• Article | 24 January 2024

  Transcription–replication interactions reveal bacterial genome regulation

  Single-cell expression data from bacteria are used to classify gene regulatory architectures in relation to gene expression dynamics and the cell cycle, revealing distinct categories of gene regulatory mechanisms.

  • Andrew W. Pountain
  • , Peien Jiang
  •  & Itai Yanai

• Article | 20 December 2023

  Discovery of a structural class of antibiotics with explainable deep learning

  An explainable deep learning model using a chemical substructure-based approach for the exploration of chemical compound libraries identified structural classes of compounds with antibiotic activity and low toxicity.

  • Felix Wong
  • , Erica J. Zheng
  •  & James J. Collins

• Article | 16 November 2022

  Enterococci enhance Clostridioides difficile pathogenesis

  Enterococci enhance the fitness and pathogenesis of Clostridioides difficile in the gut by altering the amino acid composition and providing signals that increase its virulence towards the host.

  • Alexander B. Smith
  • , Matthew L. Jenior
  •  & Joseph P. Zackular

• Article | 09 December 2020

  The functional proteome landscape of Escherichia coli

  Thermal proteome profiling combined with a reverse genetics approach provides insights into the abundance and thermal stability of the global proteome of Escherichia coli.

  • André Mateus
  • , Johannes Hevler
  •  & Mikhail M. Savitski

• Article | 15 July 2020

  A universal trade-off between growth and lag in fluctuating environments

  A model of sequential flux bottlenecks explains a universal trade-off between steady-state growth and physiological adaptation time in bacteria exposed to fluctuating growth conditions.

  • Markus Basan
  • , Tomoya Honda
  •  & Uwe Sauer

• Article | 21 October 2015

  Ion channels enable electrical communication in bacterial communities

  Ion channels in bacterial biofilms are shown to conduct long-range electrical signals within the biofilm community through the propagation of potassium ions; as predicted by a simple mathematical model, potassium channel gating is shown to coordinate metabolic states between distant cells via electrical communication.

  • Arthur Prindle
  • , Jintao Liu
  •  & Gürol M. Süel

• Article | 22 July 2015

  Metabolic co-dependence gives rise to collective oscillations within biofilms

  The emergence of long-range metabolic co-dependence within a biofilm drives oscillations in growth that resolve a social conflict between cooperation and competition, thereby increasing community-level fitness against chemical attack.

  • Jintao Liu
  • , Arthur Prindle
  •  & Gürol M. Süel

• Letter | 03 September 2014

  Stochasticity of metabolism and growth at the single-cell level

  The inherent stochasticity in metabolic reactions is a potent source of phenotypic heterogeneity in cell populations, with potentially fundamental implications for cancer research.

  • Daniel J. Kiviet
  • , Philippe Nghe
  •  & Sander J. Tans