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

Substrate and Stereochemical Control of Peptidoglycan Cross-Linking by Transpeptidation by Escherichia coli PBP1B

(2020) Anita C. Catherwood et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae

(2020) Alfonso Soler-Bistué et al.   BMC BIOLOGY

Theoretical investigation of a genetic switch for metabolic adaptation

(2020) Kathrin S. Laxhuber et al.   PLoS One

The Absence of (p)ppGpp Renders Initiation of Escherichia coli Chromosomal DNA Synthesis Independent of Growth Rates

(2020) Llorenç Fernández-Coll et al.   mBio

General quantitative relations linking cell growth and the cell cycle in Escherichia coli

(2020) Hai Zheng et al.   Nature Microbiology

Ribosome Composition Maximizes Cellular Growth Rates in E. coli

(2020) Sarah Kostinski et al.   PHYSICAL REVIEW LETTERS

Ranking essential bacterial processes by speed of mutant death

(2020) Larry A. Gallagher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

(2020) William T Ireland et al.   eLife

A Decrease in Transcription Capacity Limits Growth Rate upon Translation Inhibition

(2020) Qing Zhang et al.   mSystems

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

(2019) Manlu Zhu et al.   NUCLEIC ACIDS RESEARCH

Phosphate uptake by the phosphonate transport system PhnCDE

(2019) Raffaele Stasi et al.   BMC MICROBIOLOGY

Mechanistic Origin of Cell-Size Control and Homeostasis in Bacteria

(2019) Fangwei Si et al.   CURRENT BIOLOGY

Nucleoid Size Scaling and Intracellular Organization of Translation across Bacteria

(2019) William T. Gray et al.   CELL

The Stringent Response Inhibits DNA Replication Initiation in E. coli by Modulating Supercoiling of oriC

(2019) James A. Kraemer et al.   mBio

Surface-to-volume scaling and aspect ratio preservation in rod-shaped bacteria

(2019) Nikola Ojkic et al.   eLife

How to Build a Bacterial Cell: MreB as the Foreman of E. coli Construction

(2018) Handuo Shi et al.   CELL

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

(2018) M. Delarue et al.   CELL

Genomewide phenotypic analysis of growth, cell morphogenesis, and cell cycle events in Escherichia coli

(2018) Manuel Campos et al.   Molecular Systems Biology

Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria

(2018) Nathan M. Belliveau et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Surface Area to Volume Ratio: A Natural Variable for Bacterial Morphogenesis

(2018) Leigh K. Harris et al.   TRENDS IN MICROBIOLOGY

Slowdown of Translational Elongation in Escherichia coli under Hyperosmotic Stress

(2018) Xiongfeng Dai et al.   mBio

Visualizing Intracellular Organelle and Cytoskeletal Interactions at Nanoscale Resolution on Millisecond Timescales

(2018) Yuting Guo et al.   CELL

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

Homeostasis of protein and mRNA concentrations in growing cells

(2018) Jie Lin et al.   Nature Communications

Analysis of Interdependent Kinetic Controls of Fatty Acid Synthases

(2018) Alex Ruppe et al.   ACS Catalysis

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

Is cell size a spandrel?

(2017) Ariel Amir   eLife

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

(2017) Eyal Metzl-Raz et al.   eLife

Why Do Fast-Growing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis

(2017) Mariola Szenk et al.   Cell Systems

Pathways controlling dNTP pools to maintain genome stability

(2016) Sean G. Rudd et al.   DNA REPAIR

Aquaporin 4 as a NH3Channel

(2016) Mette Assentoft et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The physiology of growth arrest: uniting molecular and environmental microbiology

(2016) Megan Bergkessel et al.   NATURE REVIEWS MICROBIOLOGY

Transfer RNA is highly unstable during early amino acid starvation inEscherichia coli

(2016) Sine Lo Svenningsen et al.   NUCLEIC ACIDS RESEARCH

The EcoCyc database: reflecting new knowledge aboutEscherichia coliK-12

(2016) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Global characterization of in vivo enzyme catalytic rates and their correspondence to in vitrokcatmeasurements

(2016) Dan Davidi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Exploiting rRNA operon copy number to investigate bacterial reproductive strategies

(2016) Benjamin R. K. Roller et al.   Nature Microbiology

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

(2016) Xiongfeng Dai et al.   Nature Microbiology

Free RNA polymerase in Escherichia coli

(2015) Michael Patrick et al.   BIOCHIMIE

Cell-Size Control and Homeostasis in Bacteria

(2015) Sattar Taheri-Araghi et al.   CURRENT BIOLOGY

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

(2015) Evert Bosdriesz et al.   FEBS Journal

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

Recent functional insights into the role of (p)ppGpp in bacterial physiology

(2015) Vasili Hauryliuk et al.   NATURE REVIEWS MICROBIOLOGY

RegulonDB version 9.0: high-level integration of gene regulation, coexpression, motif clustering and beyond

(2015) Socorro Gama-Castro et al.   NUCLEIC ACIDS RESEARCH

The bioenergetic costs of a gene

(2015) Michael Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RodZ links MreB to cell wall synthesis to mediate MreB rotation and robust morphogenesis

(2015) Randy M. Morgenstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Simultaneous regulation of cell size and chromosome replication in bacteria

(2015) Po-Yi Ho et al.   Frontiers in Microbiology

Characterization of the E. coli proteome and its modifications during growth and ethanol stress

(2015) Boumediene Soufi et al.   Frontiers in Microbiology

The Escherichia coli CysZ is a pH dependent sulfate transporter that can be inhibited by sulfite

(2014) Li Zhang et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES

Hierarchy of non-glucose sugars in Escherichia coli

(2014) Guy Aidelberg et al.   BMC Systems Biology

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

(2014) Gene-Wei Li et al.   CELL

Bacterial growth: global effects on gene expression, growth feedback and proteome partition

(2014) Stefan Klumpp et al.   CURRENT OPINION IN BIOTECHNOLOGY

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

Regulation of crp Gene Expression by the Catabolite Repressor/Activator, Cra, in Escherichia coli

(2014) Zhongge Zhang et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Emergence of robust growth laws from optimal regulation of ribosome synthesis

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

Visual account of protein investment in cellular functions

(2014) W. Liebermeister et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Nitrogen Assimilation in Escherichia coli: Putting Molecular Data into a Systems Perspective

(2013) W. C. van Heeswijk et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

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

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

Structural Perspective of Peptidoglycan Biosynthesis and Assembly

(2012) Andrew L. Lovering et al.   Annual Review of Biochemistry

Current knowledge of the Escherichia coli phosphoenolpyruvate–carbohydrate phosphotransferase system: peculiarities of regulation and impact on growth and product formation

(2012) Adelfo Escalante et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

An integrated computational and experimental study for overproducing fatty acids in Escherichia coli

(2012) Sridhar Ranganathan et al.   METABOLIC ENGINEERING

Organization of ribonucleoside diphosphate reductase during multifork chromosome replication in Escherichia coli

(2011) M. A. Sanchez-Romero et al.   MICROBIOLOGY-SGM

Economics of membrane occupancy and respiro-fermentation

(2011) K. Zhuang et al.   Molecular Systems Biology

Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling

(2011) Benjamin Volkmer et al.   PLoS One

In vitro reconstitution and steady-state analysis of the fatty acid synthase from Escherichia coli

(2011) X. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome-derived minimal metabolic models for Escherichia coli MG1655 with estimated in vivo respiratory ATP stoichiometry

(2010) Hilal Taymaz-Nikerel et al.   BIOTECHNOLOGY AND BIOENGINEERING

Using buoyant mass to measure the growth of single cells

(2010) Michel Godin et al.   NATURE METHODS

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

Shifts in growth strategies reflect tradeoffs in cellular economics

(2009) Douwe Molenaar et al.   Molecular Systems Biology

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

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

A Contemporary Microbially Maintained Subglacial Ferrous "Ocean"

(2009) J. A. Mikucki et al.   SCIENCE

Growth-rate-dependent partitioning of RNA polymerases in bacteria

(2008) S. Klumpp et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA