Dilution and the theoretical description of growth-rate dependent gene expression

Journal of Biological Engineering

Volumn 7, Issue 1, 2013, Pages

  Hintsche, Marius ^a   Klumpp, Stefan ^a  

^a MAX PLANCK INSTITUTE OF COLLOIDS AND INTERFACES   (Germany)

Author keywords

Bacterial growth; Dilution; Genetic circuits; Growth rate dependence; Modeling

Indexed keywords

ARTICLE; BACTERIAL CELL; BACTERIAL GROWTH; CELL GROWTH; DILUTION; GENE EXPRESSION; GROWTH RATE; MATHEMATICAL MODEL; NONHUMAN; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN SYNTHESIS;

BACTERIA (MICROORGANISMS);

EID: 84883815154     PISSN: None     EISSN: 17541611     Source Type: Journal    
DOI: 10.1186/1754-1611-7-22     Document Type: Article

References (14)

1. Klumpp S, Zhang Z, Hwa T. Growth rate-dependent global effects on gene expression in bacteria. Cell 2009, 139:1366-1375. 10.1016/j.cell.2009.12.001, 2818994, 20064380.
2. de Lorenzo V. Beware of metaphors: chasses and orthogonality in synthetic biology. Bioengineered bugs 2011, 2:3-7. 10.4161/bbug.2.1.13388, 21636982.
3. Kwok R. Five hard truths for synthetic biology. Nature 2010, 463:288-290. 10.1038/463288a, 20090726.
4. Bremer H, Dennis PP. Modulation of chemical composition and other pmeters of the cell by growth rate. Escherichia coli and Salmonella 1996, 1553-1569. Washington D.C: Neidhardt FC.
5. Tan C, Marguet P, You L. Emergent bistability by a growth-modulating positive feedback circuit. Nat Chem Biol 2009, 5:842-848. 10.1038/nchembio.218, 2908482, 19801994.
6. Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. Interdependence of cell growth and gene expression: origins and consequences. Science 2010, 330:1099-1102. 10.1126/science.1192588, 21097934.
7. Klumpp S. Growth-rate dependence reveals design principles of plasmid copy number control. PLoS One 2011, 6:e20403. 10.1371/journal.pone.0020403, 3103578, 21647376.
8. Berthoumieux S, de Jong H, Baptist G, Pinel C, Ranquet C, Ropers D, Geiselmann J. Shared control of gene expression in bacteria by transcription factors and global physiology of the cell. Mol Syst Biol 2013, 9:634. 3564261, 23340840.
9. Gerosa L, Kochanowski K, Heinemann M, Sauer U. Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol 2013, 9:658. 3658269, 23591774.
10. Nath K, Koch AL. Protein degradation in Escherichia coli. I. Measurement of rapidly and slowly decaying components. J Biol Chem 1970, 245:2889-2900.
11. Larrabee KL, Phillips JO, Williams GJ, Larrabee AR. The relative rates of protein synthesis and degradation in a growing culture of Escherichia coli. J Biol Chem 1980, 255:4125-4130.
12. Varshavsky A. The N-end rule: functions, mysteries, uses. Proc Natl Acad Sci USA 1996, 93:12142-12149. 10.1073/pnas.93.22.12142, 37957, 8901547.
13. Mandelstam J. The intracellular turnover of protein and nucleic acids and its role in biochemical differentiation. Bacteriological reviews 1960, 24:289-308. 441055, 13766080.
14. Klumpp S, Hwa T. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci USA 2008, 105:20245-20250. 10.1073/pnas.0804953105, 2629260, 19073937.