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Measuring the dynamics of E. coli ribosome biogenesis using pulse-labeling and quantitative mass spectrometry.
Chen SS, Sperling E, Silverman JM, Davis JH, Williamson JR. Chen SS, et al. Among authors: williamson jr. Mol Biosyst. 2012 Oct 30;8(12):3325-34. doi: 10.1039/c2mb25310k. Mol Biosyst. 2012. PMID: 23090316 Free PMC article.
Additionally, we observe anomalously large precursor pools for specific r-proteins with known extra-ribosomal functions, as well as three r-proteins that apparently turnover during steady-state growth. Taken together, this highly precise, time-dependent proteomic qMS appro …
Additionally, we observe anomalously large precursor pools for specific r-proteins with known extra-ribosomal functions, as well as three r- …
Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria.
Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR. Hui S, et al. Among authors: williamson jr. Mol Syst Biol. 2015 Feb 12;11(1):784. doi: 10.15252/msb.20145697. Mol Syst Biol. 2015. PMID: 25678603 Free PMC article.
The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual dependencies can be characterized by a simple flux model involving only two effective parameters. The success and apparent generality of this …
The growth rate-dependent components of the proteome fractions comprise about half of the proteome by mass, and their mutual d …
Measuring Food Intake and Nutrient Absorption in Caenorhabditis elegans.
Gomez-Amaro RL, Valentine ER, Carretero M, LeBoeuf SE, Rangaraju S, Broaddus CD, Solis GM, Williamson JR, Petrascheck M. Gomez-Amaro RL, et al. Among authors: williamson jr. Genetics. 2015 Jun;200(2):443-54. doi: 10.1534/genetics.115.175851. Epub 2015 Apr 21. Genetics. 2015. PMID: 25903497 Free PMC article.
The first method is a microtiter plate-based bacterial clearing assay that measures food intake by quantifying the change in the optical density of bacteria over time. The second method, termed pulse feeding, measures the absorption of food by tracking de novo protein synt …
The first method is a microtiter plate-based bacterial clearing assay that measures food intake by quantifying the change in the opti …
A global resource allocation strategy governs growth transition kinetics of Escherichia coli.
Erickson DW, Schink SJ, Patsalo V, Williamson JR, Gerland U, Hwa T. Erickson DW, et al. Among authors: williamson jr. Nature. 2017 Nov 2;551(7678):119-123. doi: 10.1038/nature24299. Epub 2017 Oct 25. Nature. 2017. PMID: 29072300 Free PMC article.
Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models from steady-state growth into the kinetic regime. Using only qualitative knowledge of the underlying regulatory processes and imposing the condition of flux ba …
Here we develop a top-down approach, expanding the recently established coarse-grained proteome allocation models from steady-state g …
Characterization of the ribosome biogenesis landscape in E. coli using quantitative mass spectrometry.
Chen SS, Williamson JR. Chen SS, et al. Among authors: williamson jr. J Mol Biol. 2013 Feb 22;425(4):767-79. doi: 10.1016/j.jmb.2012.11.040. Epub 2012 Dec 7. J Mol Biol. 2013. PMID: 23228329 Free PMC article.
The model-free clustering analysis of the resultant protein levels for the different ribosomal particles produced four 30S assembly groups that correlate very well with previous in vitro assembly studies of the small ribosomal subunit and six 50S assembly groups that clearly defi …
The model-free clustering analysis of the resultant protein levels for the different ribosomal particles produced four 30S assembly groups t …
ArcA overexpression induces fermentation and results in enhanced growth rates of E. coli.
Basan M, Hui S, Williamson JR. Basan M, et al. Among authors: williamson jr. Sci Rep. 2017 Sep 19;7(1):11866. doi: 10.1038/s41598-017-12144-6. Sci Rep. 2017. PMID: 28928483 Free PMC article.
As recently suggested, overflow metabolism can be understood in terms of proteome allocation, since fermentation has lower proteome cost for energy production than respiration. ...
As recently suggested, overflow metabolism can be understood in terms of proteome allocation, since fermentation has lower proteom …