Search

Cyclic AMP, one of the earliest discovered and most intensely studied signalling molecules in molecular biology, is widely believed to signal the carbon status in mediating catabolite repression in bacteria; here a quantitative approach reveals a much broader physiological role for cAMP signalling, whereby it coordinates the allocation of proteomic resources with the global metabolic needs of the cell, including, for example, nitrogen or sulphur.

Bacterial colonies growing on solid surfaces can exhibit robust expansion kinetics, with constant radial growth and saturating vertical expansion. Here, the authors use modeling and experiments to show that colony growth dynamics are driven by an interplay of mechanical constraints and nutrient gradients arising from obligatory metabolic processes.

Pioneering bacterial cells use chemotaxis along self-generated attractant gradients to facilitate rapid colonization of nutrient-replete 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.

To successfully colonize a habitat in the presence of competing chemotactic bacterial populations, the winner is required to expand its range at a speed given by the habitat size and the population doubling time.

Chitin-degrading bacteria split into on- and away-from-particles subpopulations. Only on-particle cells grow and most disperse after replication, leaving chitinases behind. High dispersal is sustained by remaining cells thriving on leftover chitinases.

Using experimental proteomics and modelling in E. coli, the amount of protein needed to run respiration (per ATP produced) is shown to be twice as much as that needed to run fermentation; results demonstrate that overflow metabolism (known as the Warburg effect in cancer cells) is a necessary outcome of optimal bacterial growth, governed by a global resource allocation program, and that the methodology is directly applicable to synthetic biology and cancer research.

Antibiotics reduce the fraction of active ribosomes rather than slow translational elongation, a process also observed during E. coli adaptation to slow-growth conditions.

A micro-mechanical oscillator has been used, for the first time, to measure the dynamics of individual magnetic vortices threading a superconductor crystal. Predicting the behaviour of single vortex lines requires using a ‘1+1’-dimensional model from statistical mechanics — a tool that has wide applications, ranging from quantum mechanics to sequence alignment in genomics.

Mass spectrometry-based metabolomics is a powerful method for profiling large clinical cohorts but batch variations can obscure biologically meaningful differences. Here, the authors develop a computational workflow that removes unwanted data variation while preserving biologically relevant information.

A new approach to modelling bacterial growth removes the need to know kinetic parameters for metabolic and regulatory processes and can be used to model adaptive processes such as antibiotic responses and ecological dynamics.

How bacteria coordinate transcription and translation is incompletely understood. Here, ppGpp-dependent coordination between both processes is shown to occur under normal growth conditions and to be disrupted when translational elongation is slowed, a process that leads to premature transcriptional termination.

Microbes can cooperate and share resources via metabolic cross-feeding. Here, the authors show that excretion of key metabolites following acid stress provides a collaborative, inter-species mechanism of stress resistance.

Fast-growing bacteria produce many proteins in excess of what seems optimal for exponential growth. Here, the authors present a mathematical model and experimental evidence supporting that this overexpression serves as a strategic reserve to quickly meet demand upon sudden improvement in growth conditions.

The hierarchical consumption of carbon substrates by Escherichia coli is regulated by carbon-uptake flux rather than by the identity of the substrates, in a process controlled by cAMP–Crp signalling and fructose 1,6-bisphosphate.

Micro-scale microbial community dynamics can substantially alter the fate of sinking particulates in the ocean thus playing a key role in setting the vertical flux of particulate carbon in the ocean.

In this Review, Scott and Hwa describe how physiological constraints are sensed through metabolic fluxes and how flux-controlled regulation gives rise to simple empirical relations between protein levels and the rate of cell growth.

Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here, the authors present a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the synthesis of biomass building blocks.

Resource allocation in bacteria and adaptation to nutritional downshifts are characterized using a combination of quantitative proteomics and coarse-grained physiological modelling.

A model using data from culturing Escherichia coli in 32 different growth media sheds light on the relationship between bacterial cell growth and the cell cycle.