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 …

Root of the tree: the significance, evolution, and origins of the ribosome

JC Bowman, AS Petrov, M Frenkel-Pinter… - Chemical …, 2020 - ACS Publications
The ribosome is an ancient molecular fossil that provides a telescope to the origins of life.
Made from RNA and protein, the ribosome translates mRNA to coded protein in all living …

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

F Li, L Yuan, H Lu, G Li, Y Chen, MKM Engqvist… - Nature Catalysis, 2022 - nature.com
Enzyme turnover numbers (k cat) are key to understanding cellular metabolism, proteome
allocation and physiological diversity, but experimentally measured k cat data are sparse …

The bidirectional relationship between metabolism and cell cycle control

FF Diehl, KM Sapp, MG Vander Heiden - Trends in Cell Biology, 2024 - cell.com
The relationship between metabolism and cell cycle progression is complex and
bidirectional. Cells must rewire metabolism to meet changing biosynthetic demands across …

Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies

IE Elsemman, A Rodriguez Prado, P Grigaitis… - Nature …, 2022 - nature.com
When conditions change, unicellular organisms rewire their metabolism to sustain cell
maintenance and cellular growth. Such rewiring may be understood as resource re …

Homeostasis of protein and mRNA concentrations in growing cells

J Lin, A Amir - Nature communications, 2018 - nature.com
Many experiments show that the numbers of mRNA and protein are proportional to the cell
volume in growing cells. However, models of stochastic gene expression often assume …

Ribosome biogenesis and the cellular energy economy

D Shore, B Albert - Current Biology, 2022 - cell.com
Cell growth relies upon the ability to produce new proteins, which requires energy and
chemical precursors, and an adequate supply of the molecular machines for protein …

Adaptations in metabolism and protein translation give rise to the Crabtree effect in yeast

C Malina, R Yu, J Björkeroth… - Proceedings of the …, 2021 - National Acad Sciences
Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied
phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose …

Proteotoxicity from aberrant ribosome biogenesis compromises cell fitness

BW Tye, N Commins, LV Ryazanova, M Wühr… - elife, 2019 - elifesciences.org
To achieve maximal growth, cells must manage a massive economy of ribosomal proteins (r-
proteins) and RNAs (rRNAs) to produce thousands of ribosomes every minute. Although …

Escherichiacoli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions

SHJ Li, Z Li, JO Park, CG King, JD Rabinowitz… - Nature …, 2018 - nature.com
For cells to grow faster they must increase their protein production rate. Microorganisms
have traditionally been thought to accomplish this increase by producing more ribosomes to …