Biology subjects

Taylor, B. R.

Publications and source records attributed to Taylor, B. R..

5 recordsLinked to original sources

bioRxiv2023

Spatiotemporal development of growth and death zones in expanding bacterial colonies driven by emergent nutrient dynamics

Bacterial colony growth on hard agar is commonplace in microbiology; yet, what occurs inside a growing colony is complex even in the simplest cases. Robust colony expansion kinetics featuring a linear radial growth and a saturating vertical growth indicates a common developmental program which is elucidated here for Escherichia coli cells using a combination of modeling and experiments. Radial colony expansion is found to be limited by mechanical factors rather than nutrients as commonly assumed. In contrast, vertical expansion is limited by glucose depletion inside the colony, an effect compounded by reduced growth yield due to anaerobiosis. Carbon starvation in the colony interior results in substantial cell death within 1-2 days, with a distinct death zone that expands with the growing colony. Overall, the development of simple colonies lacking EPS production and differentiation is dictated by an interplay of mechanical constraints and emergent nutrient gradients arising from obligatory metabolic processes.

microbiology↗

bioRxiv2022

Functional Decomposition of Metabolism allows a system-level quantification of fluxes and protein allocation towards specific metabolic functions

Quantifying the contribution of individual molecular components to complex cellular processes is a grand challenge in systems biology. Here we establish a general theoretical framework (Functional Decomposition of Metabolism, FDM) to quantify the contribution of every metabolic reaction to metabolic functions, e.g. the biosynthesis of metabolic building blocks such as amino acids. This allows us to obtain a plethora of results for E. coli growing in different conditions. A detailed quantification of energetic costs for biosynthesis and biomass growth on glucose shows that ATP generated during de novo biosynthesis of building blocks almost balances the ATP costs of peptide chain polymerization, the single largest energy expenditure for growing cells. This leaves the bulk of energy generated by fermentation and respiration (consuming 1/3 of the glucose intake) during aerobic growth unaccounted for. FDM also enabled the quantification of protein allocated towards each metabolic function, unveiling linear enzyme-flux relations for biosynthesis. These results led us to derive a function-based coarse-grained model to capture global protein allocation and overflow metabolism, without relying on curated pathway annotation or clustering of gene expression data.

systems biology↗

bioRxiv2022

A Metabolic Sum Rule Dictates Bacterial Response to Short-Chain Fatty Acid Stress

Short-chain fatty acids (SCFAs) such as acetate accumulate in fermentative environments, inhibiting many types of bacteria. While it is known that cells accumulate SCFAs to high concentrations internally, the cause of SCFA toxicity is not understood. By forcing Escherichia coli cells to accumulate a variety of "useless metabolites", we establish via extensive omic analysis a metabolic sum rule, by which the accumulation of exogenous metabolites such as acetate forces the depletion of endogenous metabolites. The latter leads to bottlenecks in biosynthesis, manifested as a simple linear relation between useless metabolite accumulation and growth reduction. Guided by quantitative models, we show that acetate-stressed cells optimize growth by partially acidifying their own cytoplasm, which reduces acetate accumulation, restoring the endogenous metabolites as allowed by the sum rule.

microbiology↗

bioRxiv2021

A sensitive and specific genetically encodable biosensor for potassium ions

Potassium ions (K+) play a critical role as an essential electrolyte in all biological systems. Here we report the crystal structure-guided optimization and directed evolution of an improved genetically encoded fluorescent K+ biosensor, GINKO2. GINKO2 is highly sensitive and specific for K+ and enables in vivo detection of K+ dynamics in multiple species.

bioengineering↗

bioRxiv2021

Stress-induced cross-feeding of internal metabolites provides a dynamic mechanism of microbial cooperation

Metabolic cross-feeding plays vital roles in promoting ecological diversity. While some microbes depend on exchanges of essential nutrients for growth, forces driving the extensive cross-feeding needed to support the coexistence of free-living microbes are poorly understood. Here we characterize bacterial physiology under self-acidification, and establish that extensive excretion of key metabolites following acidification provides a collaborative, inter-species mechanism of stress resistance. This collaboration occurs not only between species isolated from the same community, but also between unrelated species with complementary (glycolytic vs. gluconeogenic) modes of metabolism. Cultures of such communities cycle through different phases in growth-dilution experiments, comprising of exponential growth, growth arrest upon acidification, collaborative stress relief, and growth recovery, with each phase involving distinct physiological states of individual species. Our findings challenge the static view of ecosystems commonly portrayed in ecological models, and offer an alternative dynamical view based on growth advantages of different species in different phases.

microbiology↗