Recent progress in the synthesis of advanced biofuel and bioproducts

BF Pfleger, R Takors - Current Opinion in Biotechnology, 2023 - Elsevier
Highlights●Why biofuels and bioproducts remain critical to society●What molecular
products can be made by biotechnology using available feedstocks●How new systems and …

Milligrams to kilograms: making microbes work at scale

WT Cordell, G Avolio, R Takors, BF Pfleger - Trends in Biotechnology, 2023 - cell.com
If biomanufacturing can become a sustainable route for producing chemicals, it will provide
a critical step in reducing greenhouse gas emissions to fight climate change. However …

Enzyme expression kinetics by Escherichia coli during transition from rich to minimal media depends on proteome reserves

C Wu, M Mori, M Abele, A Banaei-Esfahani… - Nature …, 2023 - nature.com
Bacterial fitness depends on adaptability to changing environments. In rich growth medium,
which is replete with amino acids, Escherichia coli primarily expresses protein synthesis …

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 …

Genomic footprinting uncovers global transcription factor responses to amino acids in Escherichia coli

J Trouillon, PF Doubleday, U Sauer - Cell Systems, 2023 - cell.com
Our knowledge of transcriptional responses to changes in nutrient availability comes
primarily from few well-studied transcription factors (TFs), often lacking an unbiased genome …

Proteome partitioning constraints in long-term laboratory evolution

M Mori, V Patsalo, C Euler, JR Williamson… - Nature …, 2024 - nature.com
Adaptive laboratory evolution experiments provide a controlled context in which the
dynamics of selection and adaptation can be followed in real-time at the single-nucleotide …

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

M Mori, C Cheng, BR Taylor, H Okano… - Nature Communications, 2023 - nature.com
Quantifying the contribution of individual molecular components to complex cellular
processes is a grand challenge in systems biology. Here we establish a general theoretical …

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 …

Understanding and computational design of genetic circuits of metabolic networks

A Berkvens, L Salinas, M Remeijer… - Essays in …, 2024 - portlandpress.com
The expression of metabolic proteins is controlled by genetic circuits, matching metabolic
demands and changing environmental conditions. Ideally, this regulation brings about a …

Deep mutational scanning reveals the molecular determinants of RNA polymerase-mediated adaptation and tradeoffs

A Choudhury, B Gachet, Z Dixit, R Faure, RT Gill… - Nature …, 2023 - nature.com
RNA polymerase (RNAP) is emblematic of complex biological systems that control multiple
traits involving trade-offs such as growth versus maintenance. Laboratory evolution has …