An optimal regulation of fluxes dictates microbial growth in and out of steady state

ppGpp is a bacterial cell size regulator

(2022) Ferhat Büke et al.   CURRENT BIOLOGY

Cellular perception of growth rate and the mechanistic origin of bacterial growth law

(2022) Chenhao Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteome allocations change linearly with the specific growth rate of Saccharomyces cerevisiae under glucose limitation

(2022) Jianye Xia et al.   Nature Communications

Optimal proteome allocation and the temperature dependence of microbial growth laws

(2021) Francis Mairet et al.   npj Systems Biology and Applications

An alternative resource allocation strategy in the chemolithoautotrophic archaeon Methanococcus maripaludis

(2021) Albert L. Müller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulatory Themes and Variations by the Stress-Signaling Nucleotide Alarmones (p)ppGpp in Bacteria

(2021) Brent W. Anderson et al.   Annual Review of Genetics

Robust surface-to-mass coupling and turgor-dependent cell width determine bacterial dry-mass density

(2021) Enno R. Oldewurtel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2021) Nathan M. Belliveau et al.   Cell Systems

Suboptimal resource allocation in changing environments constrains response and growth in bacteria

(2021) Rohan Balakrishnan et al.   Molecular Systems Biology

Protein allocation and utilization in the versatile chemolithoautotroph Cupriavidus necator

(2021) Michael Jahn et al.   eLife

An analytical theory of balanced cellular growth

(2020) Hugo Dourado et al.   Nature Communications

Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift

(2020) Francesca Di Bartolomeo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ribosome Composition Maximizes Cellular Growth Rates in E. coli

(2020) Sarah Kostinski et al.   PHYSICAL REVIEW LETTERS

Growth-Optimized Aminoacyl-tRNA Synthetase Levels Prevent Maximal tRNA Charging

(2020) Darren J. Parker et al.   Cell Systems

The protein translation machinery is expressed for maximal efficiency in Escherichia coli

(2020) Xiao-Pan Hu et al.   Nature Communications

Nutrient-Dependent Trade-Offs between Ribosomes and Division Protein Synthesis Control Bacterial Cell Size and Growth

(2020) Diana Serbanescu et al.   Cell Reports

A bacterial size law revealed by a coarse-grained model of cell physiology

(2020) François Bertaux et al.   PLoS Computational Biology

Calibrating the Bacterial Growth Rate Speedometer: A Re-evaluation of the Relationship Between Basal ppGpp, Growth, and RNA Synthesis in Escherichia coli

(2020) Nicole C. E. Imholz et al.   Frontiers in Microbiology

Protein cost allocation explains metabolic strategies in Escherichia coli

(2020) Pranas Grigaitis et al.   JOURNAL OF BIOTECHNOLOGY

Growth suppression by altered (p)ppGpp levels results from non-optimal resource allocation in Escherichia coli

(2019) Manlu Zhu et al.   NUCLEIC ACIDS RESEARCH

Quantitative insights into the cyanobacterial cell economy

(2019) Tomáš Zavřel et al.   eLife

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

(2019) William T. Gray et al.   CELL

Protein synthesis rates and ribosome occupancies reveal determinants of translation elongation rates

(2019) Andrea Riba et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A quantitative screen for metabolic enzyme structures reveals patterns of assembly across the yeast metabolic network

(2019) Chalongrat Noree et al.   MOLECULAR BIOLOGY OF THE CELL

mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding

(2018) M. Delarue et al.   CELL

Fundamental principles in bacterial physiology—history, recent progress, and the future with focus on cell size control: a review

(2018) Suckjoon Jun et al.   REPORTS ON PROGRESS IN PHYSICS

A Bacterial Growth Law out of Steady State

(2018) Yael Korem Kohanim et al.   Cell Reports

Escherichia coli translation strategies differ across carbon, nitrogen and phosphorus limitation conditions

(2018) Sophia Hsin-Jung Li et al.   Nature Microbiology

Ribosome Hibernation

(2018) Thomas Prossliner et al.   Annual Review of Genetics

Growth of Cyanobacteria Is Constrained by the Abundance of Light and Carbon Assimilation Proteins

(2018) Michael Jahn et al.   Cell Reports

Ribosomes are optimized for autocatalytic production

(2017) Shlomi Reuveni et al.   NATURE

A global resource allocation strategy governs growth transition kinetics of Escherichia coli

(2017) David W. Erickson et al.   NATURE

Microorganisms maintain crowding homeostasis

(2017) Jonas van den Berg et al.   NATURE REVIEWS MICROBIOLOGY

Quantifying the benefit of a proteome reserve in fluctuating environments

(2017) Matteo Mori et al.   Nature Communications

Optimality and sub-optimality in a bacterial growth law

(2017) Benjamin D. Towbin et al.   Nature Communications

Principles of cellular resource allocation revealed by condition-dependent proteome profiling

(2017) Eyal Metzl-Raz et al.   eLife

Quantitative mass spectrometry-based multiplexing compares the abundance of 5000 S. cerevisiae proteins across 10 carbon sources

(2016) Joao A. Paulo et al.   Journal of Proteomics

Dynamical Allocation of Cellular Resources as an Optimal Control Problem: Novel Insights into Microbial Growth Strategies

(2016) Nils Giordano et al.   PLoS Computational Biology

Reduction of translating ribosomes enables Escherichia coli to maintain elongation rates during slow growth

(2016) Xiongfeng Dai et al.   Nature Microbiology

How fast-growing bacteria robustly tune their ribosome concentration to approximate growth-rate maximization

(2015) Evert Bosdriesz et al.   FEBS Journal

Proteome-wide quantitative multiplexed profiling of protein expression: carbon-source dependency in Saccharomyces cerevisiae

(2015) Joao A. Paulo et al.   MOLECULAR BIOLOGY OF THE CELL

Proteome reallocation in Escherichia coli with increasing specific growth rate

(2015) Karl Peebo et al.   Molecular BioSystems

Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria

(2015) S. Hui et al.   Molecular Systems Biology

Inflating bacterial cells by increased protein synthesis

(2015) M. Basan et al.   Molecular Systems Biology

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Mechanistic links between cellular trade-offs, gene expression, and growth

(2015) Andrea Y. Weiße et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Universal and domain-specific sequences in 23S–28S ribosomal RNA identified by computational phylogenetics

(2015) Stephen M. Doris et al.   RNA

Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources

(2014) Gene-Wei Li et al.   CELL

Emergence of robust growth laws from optimal regulation of ribosome synthesis

(2014) M. Scott et al.   Molecular Systems Biology

Bacterial growth laws reflect the evolutionary importance of energy efficiency

(2014) Arijit Maitra et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Erosion Primarily Through Mutation Accumulation, and Not Tradeoffs, Drives Limited Evolution of Substrate Specificity in Escherichia coli

(2014) Nicholas Leiby et al.   PLOS BIOLOGY

What is the total number of protein molecules per cell volume? A call to rethink some published values

(2013) Ron Milo   BIOESSAYS

Promoter activity dynamics in the lag phase of Escherichia coli

(2013) Daniel Madar et al.   BMC Systems Biology

The last generation of bacterial growth in limiting nutrient

(2013) Anat Bren et al.   BMC Systems Biology

Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins

(2013) Kaspar Valgepea et al.   Molecular BioSystems

Coordination of bacterial proteome with metabolism by cyclic AMP signalling

(2013) Conghui You et al.   NATURE

Intracellular Water Exchange for Measuring the Dry Mass, Water Mass and Changes in Chemical Composition of Living Cells

(2013) Francisco Feijó Delgado et al.   PLoS One

Molecular crowding limits translation and cell growth

(2013) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Physical limits of cells and proteomes

(2011) K. A. Dill et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ppGpp is the major source of growth rate control in E. coli

(2010) Katarzyna Potrykus et al.   ENVIRONMENTAL MICROBIOLOGY

Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells

(2010) Y. Taniguchi et al.   SCIENCE

Interdependence of Cell Growth and Gene Expression: Origins and Consequences

(2010) M. Scott et al.   SCIENCE

A Comprehensive, Quantitative, and Genome-Wide Model of Translation

(2010) Marlena Siwiak et al.   PLoS Computational Biology

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

Absolute metabolite concentrations and implied enzyme active site occupancy in Escherichia coli

(2009) Bryson D Bennett et al.   Nature Chemical Biology

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

The evolving ribosome: from non-coded peptide bond formation to sophisticated translation machinery

(2009) Chen Davidovich et al.   RESEARCH IN MICROBIOLOGY

(p)ppGpp: Still Magical?

(2008) Katarzyna Potrykus et al.   Annual Review of Microbiology

Conservation of Bacterial Protein Synthesis Machinery: Initiation and Elongation inMycobacterium smegmatis†

(2008) Christian M. Bruell et al.   BIOCHEMISTRY

Control of bacterial transcription, translation and replication by (p)ppGpp

(2008) Anjana Srivatsan et al.   CURRENT OPINION IN MICROBIOLOGY