Machine learning-assisted discovery of growth decision elements by relating bacterial population dynamics to environmental diversity

H Aida, T Hashizume, K Ashino, BW Ying - Elife, 2022 - elifesciences.org
Microorganisms growing in their habitat constitute a complex system. How the individual
constituents of the environment contribute to microbial growth remains largely unknown. The …

Growth-optimized aminoacyl-tRNA synthetase levels prevent maximal tRNA charging

DJ Parker, JB Lalanne, S Kimura, GE Johnson… - Cell Systems, 2020 - cell.com
Aminoacyl-tRNA synthetases (aaRSs) serve a dual role in charging tRNAs. Their enzymatic
activities both provide protein synthesis flux and reduce uncharged tRNA levels. Although …

“Metabolic burden” explained: stress symptoms and its related responses induced by (over)expression of (heterologous) proteins in Escherichia coli

S Snoeck, C Guidi, M De Mey - Microbial Cell Factories, 2024 - Springer
Background Engineering bacterial strains to redirect the metabolism towards the production
of a specific product has enabled the development of industrial biotechnology. However …

Fundamental limits on the rate of bacterial growth and their influence on proteomic composition

NM Belliveau, G Chure, CL Hueschen, HG Garcia… - Cell Systems, 2021 - cell.com
Despite abundant measurements of bacterial growth rate, cell size, and protein content, we
lack a rigorous understanding of what sets the scale of these quantities and when protein …

(p) ppGpp: the magic governor of bacterial growth economy

M Zhu, Y Pan, X Dai - Current genetics, 2019 - Springer
A fundamental question in microbiology is how bacterial cells manage to coordinate gene
expression with cell growth during adapting to various environmental conditions. Although …

[HTML][HTML] Recent functional insights into the magic role of (p) ppGpp in growth control

H Mu, F Han, Q Wang, Y Wang, X Dai, M Zhu - … and structural biotechnology …, 2023 - Elsevier
Rapid growth and survival are two key traits that enable bacterial cells to thrive in their
natural habitat. The guanosine tetraphosphate and pentaphosphate [(p) ppGpp], also known …

Shaping of microbial phenotypes by trade-offs

M Zhu, X Dai - Nature Communications, 2024 - nature.com
Growth rate maximization is an important fitness strategy for microbes. However, the wide
distribution of slow-growing oligotrophic microbes in ecosystems suggests that rapid growth …

Feedforward growth rate control mitigates gene activation burden

C Barajas, HH Huang, J Gibson, L Sandoval… - Nature …, 2022 - nature.com
Heterologous gene activation causes non-physiological burden on cellular resources that
cells are unable to adjust to. Here, we introduce a feedforward controller that actuates …

Global transcriptional regulators fine-tune the translational and metabolic efficiency for optimal growth of Escherichia coli

MS Iyer, A Pal, S Srinivasan, PR Somvanshi… - Msystems, 2021 - Am Soc Microbiol
Global transcriptional regulators coordinate complex genetic interactions that bestow better
adaptability for an organism against external and internal perturbations. These …

Integrated control of bacterial growth and stress response by (p) ppGpp in Escherichia coli: A seesaw fashion

M Zhu, H Mu, X Dai - Iscience, 2024 - cell.com
To thrive in nature, bacteria have to reproduce efficiently under favorable conditions and
persist during stress. The global strategy that integrates the growth control and stress …