Shaping bacterial gene expression by physiological and proteome allocation constraints

M Scott, T Hwa - Nature Reviews Microbiology, 2023 - nature.com
Networks of molecular regulators are often the primary objects of focus in the study of gene
regulation, with the machinery of protein synthesis tacitly relegated to the background …

Metabolomics and Microbial Metabolism: Toward a Systematic Understanding

D Holbrook-Smith, J Trouillon… - Annual Review of …, 2023 - annualreviews.org
Over the past decades, our understanding of microbial metabolism has increased
dramatically. Metabolomics, a family of techniques that are used to measure the quantities of …

The architecture of metabolic networks constrains the evolution of microbial resource hierarchies

S Takano, JCC Vila, R Miyazaki… - … Biology and Evolution, 2023 - academic.oup.com
Microbial strategies for resource use are an essential determinant of their fitness in complex
habitats. When facing environments with multiple nutrients, microbes often use them …

Synthetic robust perfect adaptation achieved by negative feedback coupling with linear weak positive feedback

Z Sun, W Wei, M Zhang, W Shi, Y Zong… - Nucleic Acids …, 2022 - academic.oup.com
Unlike their natural counterparts, synthetic genetic circuits are usually fragile in the face of
environmental perturbations and genetic mutations. Several theoretical robust genetic …

[HTML][HTML] Regulation of hierarchical carbon substrate utilization, nitrogen fixation, and root colonization by the Hfq/Crc/CrcZY genes in Pseudomonas stutzeri

F Lv, Y Zhan, W Lu, X Ke, Y Shao, Y Ma, J Zheng… - Iscience, 2022 - cell.com
Bacteria of the genus Pseudomonas consume preferred carbon substrates in nearly reverse
order to that of enterobacteria, and this process is controlled by RNA-binding translational …

[HTML][HTML] The importance of understanding the regulation of bacterial metabolism

R Moreno, F Rojo - Environmental microbiology, 2023 - ncbi.nlm.nih.gov
Many bacterial species have biotechnological applications, for example in the production of
compounds of interest by fermentation or biotransformation, the handling of waste and the …

Starvation responses impact interaction dynamics of human gut bacteria Bacteroides thetaiotaomicron and Roseburia intestinalis

B Liu, DR Garza, D Gonze, A Krzynowek… - The ISME …, 2023 - academic.oup.com
Bacterial growth often alters the environment, which in turn can impact interspecies
interactions among bacteria. Here, we used an in vitro batch system containing mucin beads …

Making sense of gene expression control by flux sensing

B Teusink, R Planqué, FJ Bruggeman - Nature Metabolism, 2025 - nature.com
Cells regulate metabolic fluxes by changing enzyme levels according to their needs, but
how do they regulate something that cannot be measured directly? In this issue of Nature …

Modeling interactions of Clostridium cadaveris and Clostridium sporogenes in anaerobic acidogenesis of glucose and peptone

MAH Jannat, SH Park, S Hwang - Bioresource Technology, 2024 - Elsevier
This study focuses on developing a mathematical model to assess interaction among
acidogenic bacteria during the anaerobic degradation of two substrates. Clostridium …

CRISPR/dCas12a knock-down of Acidithiobacillus ferrooxidans electron transport chain bc1 complexes enables enhanced metal sulfide bioleaching

H Jung, Y Inaba, S Banta - Journal of Biological Chemistry, 2024 - jbc.org
Acidithiobacillus ferrooxidans is an acidophilic chemolithoautotroph that plays an important
role in biogeochemical iron and sulfur cycling and is a member of the consortia used in …