Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments
- Authors:
- Publication Date:
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1345285
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Published Article
- Journal Name:
- PLoS Computational Biology (Online)
- Additional Journal Information:
- Journal Name: PLoS Computational Biology (Online) Journal Volume: 12 Journal Issue: 6; Journal ID: ISSN 1553-7358
- Publisher:
- Public Library of Science (PLoS)
- Country of Publication:
- United States
- Language:
- English
Citation Formats
O’Brien, Edward J., Utrilla, Jose, Palsson, Bernhard O., and Maranas, ed., Costas D. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. United States: N. p., 2016.
Web. doi:10.1371/journal.pcbi.1004998.
O’Brien, Edward J., Utrilla, Jose, Palsson, Bernhard O., & Maranas, ed., Costas D. Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments. United States. https://doi.org/10.1371/journal.pcbi.1004998
O’Brien, Edward J., Utrilla, Jose, Palsson, Bernhard O., and Maranas, ed., Costas D. Tue .
"Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments". United States. https://doi.org/10.1371/journal.pcbi.1004998.
@article{osti_1345285,
title = {Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments},
author = {O’Brien, Edward J. and Utrilla, Jose and Palsson, Bernhard O. and Maranas, ed., Costas D.},
abstractNote = {},
doi = {10.1371/journal.pcbi.1004998},
journal = {PLoS Computational Biology (Online)},
number = 6,
volume = 12,
place = {United States},
year = {Tue Jun 28 00:00:00 EDT 2016},
month = {Tue Jun 28 00:00:00 EDT 2016}
}
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1371/journal.pcbi.1004998
https://doi.org/10.1371/journal.pcbi.1004998
Other availability
Cited by: 65 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
A Regulatory Trade-Off as a Source of Strain Variation in the Species Escherichia coli
journal, August 2004
- King, T.; Ishihama, A.; Kori, A.
- Journal of Bacteriology, Vol. 186, Issue 17
Strategies for cellular decision‐making
journal, January 2009
- Perkins, Theodore J.; Swain, Peter S.
- Molecular Systems Biology, Vol. 5, Issue 1
Optimality and evolutionary tuning of the expression level of a protein
journal, July 2005
- Dekel, Erez; Alon, Uri
- Nature, Vol. 436, Issue 7050
Microbial laboratory evolution in the era of genome‐scale science
journal, January 2011
- Conrad, Tom M.; Lewis, Nathan E.; Palsson, Bernhard Ø
- Molecular Systems Biology, Vol. 7, Issue 1
Prediction of Microbial Growth Rate versus Biomass Yield by a Metabolic Network with Kinetic Parameters
journal, July 2012
- Adadi, Roi; Volkmer, Benjamin; Milo, Ron
- PLoS Computational Biology, Vol. 8, Issue 7
Stress responses as determinants of antimicrobial resistance in Gram-negative bacteria
journal, May 2012
- Poole, Keith
- Trends in Microbiology, Vol. 20, Issue 5
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data
journal, February 2001
- Edwards, Jeremy S.; Ibarra, Rafael U.; Palsson, Bernhard O.
- Nature Biotechnology, Vol. 19, Issue 2
Using Genome-scale Models to Predict Biological Capabilities
journal, May 2015
- O’Brien, Edward J.; Monk, Jonathan M.; Palsson, Bernhard O.
- Cell, Vol. 161, Issue 5
Hierarchy of non-glucose sugars in Escherichia coli
journal, December 2014
- Aidelberg, Guy; Towbin, Benjamin D.; Rothschild, Daphna
- BMC Systems Biology, Vol. 8, Issue 1
Cost of Unneeded Proteins in E. coli Is Reduced after Several Generations in Exponential Growth
journal, June 2010
- Shachrai, Irit; Zaslaver, Alon; Alon, Uri
- Molecular Cell, Vol. 38, Issue 5
Genome-Scale In Silico Models of E. coli Have Multiple Equivalent Phenotypic States: Assessment of Correlated Reaction Subsets That Comprise Network States
journal, September 2004
- Reed, J. L.
- Genome Research, Vol. 14, Issue 9
Molecular crowding limits translation and cell growth
journal, September 2013
- Klumpp, S.; Scott, M.; Pedersen, S.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 42
The experimental evolution of specialists, generalists, and the maintenance of diversity: Experimental evolution in variable environments
journal, March 2002
- Kassen, R.
- Journal of Evolutionary Biology, Vol. 15, Issue 2
Functional and Metabolic Effects of Adaptive Glycerol Kinase (GLPK) Mutants in Escherichia coli
journal, May 2011
- Applebee, M. Kenyon; Joyce, Andrew R.; Conrad, Tom M.
- Journal of Biological Chemistry, Vol. 286, Issue 26
Protein costs do not explain evolution of metabolic strategies and regulation of ribosomal content: does protein investment explain an anaerobic bacterial Crabtree effect?: Protein costs and evolution of metabolic strategies
journal, May 2015
- Goel, Anisha; Eckhardt, Thomas H.; Puri, Pranav
- Molecular Microbiology, Vol. 97, Issue 1
The Interrelationship between Promoter Strength, Gene Expression, and Growth Rate
journal, October 2014
- Bienick, Matthew S.; Young, Katherine W.; Klesmith, Justin R.
- PLoS ONE, Vol. 9, Issue 10
Specific Growth Rate Determines the Sensitivity of Escherichia coli to Thermal, UVA, and Solar Disinfection
journal, April 2006
- Berney, M.; Weilenmann, H. -U.; Ihssen, J.
- Applied and Environmental Microbiology, Vol. 72, Issue 4
The Moderately Efficient Enzyme: Evolutionary and Physicochemical Trends Shaping Enzyme Parameters
journal, May 2011
- Bar-Even, Arren; Noor, Elad; Savir, Yonatan
- Biochemistry, Vol. 50, Issue 21
Nitrogen Assimilation and Global Regulation in Escherichia coli
journal, October 2003
- Reitzer, Larry
- Annual Review of Microbiology, Vol. 57, Issue 1
Predictive Behavior Within Microbial Genetic Networks
journal, June 2008
- Tagkopoulos, I.; Liu, Y. -C.; Tavazoie, S.
- Science, Vol. 320, Issue 5881
Condition-Dependent Cell Volume and Concentration of Escherichia coli to Facilitate Data Conversion for Systems Biology Modeling
journal, July 2011
- Volkmer, Benjamin; Heinemann, Matthias
- PLoS ONE, Vol. 6, Issue 7
Lean-Proteome Strains – Next Step in Metabolic Engineering
journal, February 2015
- Valgepea, Kaspar; Peebo, Karl; Adamberg, Kaarel
- Frontiers in Bioengineering and Biotechnology, Vol. 3
Quantifying Absolute Protein Synthesis Rates Reveals Principles Underlying Allocation of Cellular Resources
journal, April 2014
- Li, Gene-Wei; Burkhardt, David; Gross, Carol
- Cell, Vol. 157, Issue 3
Coordination of microbial metabolism
journal, March 2014
- Chubukov, Victor; Gerosa, Luca; Kochanowski, Karl
- Nature Reviews Microbiology, Vol. 12, Issue 5
The effects of alternate optimal solutions in constraint-based genome-scale metabolic models
journal, October 2003
- Mahadevan, R.; Schilling, C. H.
- Metabolic Engineering, Vol. 5, Issue 4
Escherichia coli achieves faster growth by increasing catalytic and translation rates of proteins
journal, January 2013
- Valgepea, Kaspar; Adamberg, Kaarel; Seiman, Andrus
- Molecular BioSystems, Vol. 9, Issue 9
Coordination of bacterial proteome with metabolism by cyclic AMP signalling
journal, August 2013
- You, Conghui; Okano, Hiroyuki; Hui, Sheng
- Nature, Vol. 500, Issue 7462
Different Levels of Catabolite Repression Optimize Growth in Stable and Variable Environments
journal, January 2014
- New, Aaron M.; Cerulus, Bram; Govers, Sander K.
- PLoS Biology, Vol. 12, Issue 1
The Growth of Bacterial Cultures
journal, October 1949
- Monod, J.
- Annual Review of Microbiology, Vol. 3, Issue 1
Bacterial Growth: Constant Obsession withdN/dt
journal, December 1999
- Neidhardt, Frederick C.
- Journal of Bacteriology, Vol. 181, Issue 24
Omic data from evolved E. coli are consistent with computed optimal growth from genome‐scale models
journal, January 2010
- Lewis, Nathan E.; Hixson, Kim K.; Conrad, Tom M.
- Molecular Systems Biology, Vol. 6, Issue 1
Novel Roles of cAMP Receptor Protein (CRP) in Regulation of Transport and Metabolism of Carbon Sources
journal, June 2011
- Shimada, Tomohiro; Fujita, Nobuyuki; Yamamoto, Kaneyoshi
- PLoS ONE, Vol. 6, Issue 6
Interdependence of Cell Growth and Gene Expression: Origins and Consequences
journal, November 2010
- Scott, M.; Gunderson, C. W.; Mateescu, E. M.
- Science, Vol. 330, Issue 6007
Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol
journal, January 2014
- Cheng, Kian-Kai; Lee, Baek-Seok; Masuda, Takeshi
- Nature Communications, Vol. 5, Issue 1
Adaptive prediction of environmental changes by microorganisms
journal, June 2009
- Mitchell, Amir; Romano, Gal H.; Groisman, Bella
- Nature, Vol. 460, Issue 7252
Global transcription machinery engineering: A new approach for improving cellular phenotype
journal, May 2007
- Alper, H.; Stephanopoulos, G.
- Metabolic Engineering, Vol. 9, Issue 3, p. 258-267
Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms
journal, May 2014
- Zarecki, Raphy; Oberhardt, Matthew A.; Yizhak, Keren
- PLoS ONE, Vol. 9, Issue 5
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth
journal, November 2002
- Ibarra, Rafael U.; Edwards, Jeremy S.; Palsson, Bernhard O.
- Nature, Vol. 420, Issue 6912
Computing the functional proteome: recent progress and future prospects for genome-scale models
journal, August 2015
- O’Brien, Edward J.; Palsson, Bernhard O.
- Current Opinion in Biotechnology, Vol. 34
EcoCyc: fusing model organism databases with systems biology
journal, November 2012
- Keseler, Ingrid M.; Mackie, Amanda; Peralta-Gil, Martin
- Nucleic Acids Research, Vol. 41, Issue D1
Specific Growth Rate Determines the Sensitivity of Escherichia coli to Lactic Acid Stress: Implications for Predictive Microbiology
journal, January 2014
- Lindqvist, Roland; Barmark, Gunilla
- BioMed Research International, Vol. 2014