Conditionally unutilized proteins and their profound effects on growth and adaptation across microbial species

Quantifying the local adaptive landscape of a nascent bacterial community

(2023) Joao A. Ascensao et al.   Nature Communications

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

(2023) Chenhao Wu et al.   Nature Microbiology

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

(2023) Griffin Chure et al.   eLife

The landscape of transcriptional and 1translational changes over 22 years of bacterial adaptation

(2022) John S Favate et al.   eLife

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

Engineering of a robust Escherichia coli chassis and exploitation for large-scale production processes

(2021) Martin Ziegler et al.   METABOLIC ENGINEERING

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

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

CRISPRi enables fast growth followed by stable aerobic pyruvate formation in Escherichia coli without auxotrophy

(2021) Martin Ziegler et al.   ENGINEERING IN LIFE SCIENCES

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

A universal trade-off between growth and lag in fluctuating environments

(2020) Markus Basan et al.   NATURE

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

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

Quantitative insights into the cyanobacterial cell economy

(2019) Tomáš Zavřel et al.   eLife

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

(2019) Troy E. Sandberg et al.   METABOLIC ENGINEERING

Growth-rate dependent resource investment in bacterial motile behavior quantitatively follows potential benefit of chemotaxis

(2019) Bin Ni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Michael Jahn et al.   Cell Reports

The dynamics of molecular evolution over 60,000 generations

(2017) Benjamin H. Good et al.   NATURE

Quantifying the benefit of a proteome reserve in fluctuating environments

(2017) Matteo Mori et al.   Nature Communications

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

(2017) Eyal Metzl-Raz et al.   eLife

The quest for the minimal bacterial genome

(2016) Esteban Martínez-García et al.   CURRENT OPINION IN BIOTECHNOLOGY

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

(2016) Edward J. O’Brien et al.   PLoS Computational Biology

A Comparison of the Costs and Benefits of Bacterial Gene Expression

(2016) Morgan N. Price et al.   PLoS One

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

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

The quantitative and condition-dependent Escherichia coli proteome

(2015) Alexander Schmidt et al.   NATURE BIOTECHNOLOGY

Shifting Sugars and Shifting Paradigms

(2015) Mark L. Siegal   PLOS BIOLOGY

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

(2014) Gene-Wei Li et al.   CELL

Comprehensive Absolute Quantification of the Cytosolic Proteome ofBacillus subtilisby Data Independent, Parallel Fragmentation in Liquid Chromatography/Mass Spectrometry (LC/MSE)

(2014) Jan Muntel et al.   MOLECULAR & CELLULAR PROTEOMICS

Phycobilisome-Deficient Strains of Synechocystis sp. PCC 6803 Have Reduced Size and Require Carbon-Limiting Conditions to Exhibit Enhanced Productivity

(2014) D. J. Lea-Smith et al.   PLANT PHYSIOLOGY

Global epistasis makes adaptation predictable despite sequence-level stochasticity

(2014) S. Kryazhimskiy et al.   SCIENCE

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

Adaptive laboratory evolution – principles and applications for biotechnology

(2013) Martin Dragosits et al.   Microbial Cell Factories

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Multidimensional Optimality of Microbial Metabolism

(2012) R. Schuetz et al.   SCIENCE

Negative Epistasis Between Beneficial Mutations in an Evolving Bacterial Population

(2011) A. I. Khan et al.   SCIENCE

Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth

(2010) Irit Shachrai et al.   MOLECULAR CELL

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

Adaptive prediction of environmental changes by microorganisms

(2009) Amir Mitchell et al.   NATURE

Superpositioning of Deletions Promotes Growth of Escherichia coli with a Reduced Genome

(2008) H. Mizoguchi et al.   DNA RESEARCH

The Cost of Expression of Escherichia coli lac Operon Proteins Is in the Process, Not in the Products

(2008) D. M. Stoebel et al.   GENETICS