The last generation of bacterial growth in limiting nutrient

BMC Systems Biology

Uri Alon¹  Daniel Koster¹  Erez Dekel¹  Yuval Hart¹  Anat Bren¹ 

[1]Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel

关键词: Nitrogen assimilation;    Nutrient limitation;    Gene expression;    Monod law;    Bacterial growth;   

Others  :  1142947
DOI  :  10.1186/1752-0509-7-27

 received in 2012-10-23, accepted in 2013-03-12,  发布年份 2013

【 摘 要 】

Background

Bacterial growth as a function of nutrients has been studied for decades, but is still not fully understood. In particular, the growth laws under dynamically changing environments have been difficult to explore, because of the rapidly changing conditions. Here, we address this challenge by means of a robotic assay and measure bacterial growth rate, promoter activity and substrate level at high temporal resolution across the entire growth curve in batch culture. As a model system, we study E. coli growing under nitrogen or carbon limitation, and explore the dynamics in the last generation of growth where nutrient levels can drop rapidly.

Results

We find that growth stops abruptly under limiting nitrogen or carbon, but slows gradually when nutrients are not limiting. By measuring growth rate at a 3 min time resolution, and inferring the instantaneous substrate level, s, we find that the reduction in growth rate μ under nutrient limitation follows Monod’s law, View MathML">. By following promoter activity of different genes we found that the abrupt stop of growth under nitrogen or carbon limitation is accompanied by a pulse-like up-regulation of the expression of genes in the relevant nutrient assimilation pathways. We further find that sharp stop of growth is conditional on the presence of regulatory proteins in the assimilation pathway.

Conclusions

The observed sharp stop of growth accompanied by a pulsed expression of assimilation genes allows bacteria to compensate for the drop in nutrients, suggesting a strategy used by the cells to prolong exponential growth under limiting substrate.

【 授权许可】

   
2013 Bren et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

Figure 5.

【 参考文献 】

• [1]Jannasch HW, Egli T: Microbial growth kinetics: a historical perspective. Antonie Van Leeuwenhoek 1993, 63:213-224.
• [2]Ferenci T: ‘Growth of bacterial cultures’ 50 years on: towards an uncertainty principle instead of constants in bacterial growth kinetics. Res Microbiol 1999, 150:431-438.
• [3]Egli T: Growth kinetics, bacterial. In Encyclopedia of Microbiology. 3rd edition. Edited by Schaechter M. Oxford: Elsevier; 2009:180-193.
• [4]Scott M, Hwa T: Bacterial growth laws and their applications. Curr Opin Biotechnol 2011, 22:559-565.
• [5]Monod J: Recherches sur la croissance des cultures bacttriennes. Paris: Hermann and Cie; 1942.
• [6]Monod J: The growth of bacterial culture. Annual Reviews in Microbiology 1949, 3:371-394.
• [7]Dabes JN, Finn RK, Welke CR: Equations of substrate-limited growth: the case for blackman kinetics. Biotechnol Bioeng 1973, 15:1159-1177.
• [8]Westerhoff HV, Lolkema JS, Otto R, Hellingwerf KJ: Thermodynamics of growth. Non-equilibrium thermodynamics of bacterial growth. The phenomenological and the mosaic approach. Biochim Biophys Acta 1982, 683:181-220.
• [9]Shehata TE, Marr AG: Effect of nutrient concentration on the growth of Escherichia coli. J Bacteriol 1971, 107:210-216.
• [10]Koch AL: Multistep kinetics: choice of models for the growth of bacteria. J Theor Biol 1982, 98:401-417.
• [11]Owens JD, Legan JD: Determination of monod substrate saturating constant for microbila growth. FEMS Microbiol Rev 1987, 46:419-432.
• [12]Senn H, Lendenmann U, Snozzi M, Hamer G, Egli T: The growth of Escherichia coli in glucose-limited chemostat cultures: a re-examination of the kinetics. Biochim Biophys Acta 1994, 1201:424-436.
• [13]Koch AL, Wang CH: How close to the theoretical diffusion limit do bacterial uptake systems function? Arch Microbiol 1982, 131:36-42.
• [14]Wang CH, Koch AL: Constancy of growth on simple and complex media. J Bacteriol 1978, 136:969-975.
• [15]Ferenci T: Regulation by nutrient limitation. Curr Opin Microbiol 1999, 2:208-213.
• [16]Ferenci T: Hungry bacteria–definition and properties of a nutritional state. Environ Microbiol 2001, 3:605-611.
• [17]Gyaneshwar P, Paliy O, McAuliffe J, Popham DL, Jordan MI, Kustu S: Sulfur and nitrogen limitation in Escherichia coli K-12: specific homeostatic responses. J Bacteriol 2005, 187:1074-1090.
• [18]Atkinson MR, Blauwkamp TA, Bondarenko V, Studitsky V, Ninfa AJ: Activation of the glnA, glnK, and nac promoters as Escherichia coli undergoes the transition from nitrogen excess growth to nitrogen starvation. J Bacteriol 2002, 184:5358-5363.
• [19]Wanner U, Egli T: Dynamics of microbial growth and cell composition in batch culture. FEMS Microbiol Rev 1990, 6:19-43.
• [20]Chuang SE, Daniels DL, Blattner FR: Global regulation of gene expression in Escherichia coli. J Bacteriol 1993, 175:2026-2036.
• [21]Baranyi J, Roberts TA: A dynamic approach to predicting bacterial growth in food. Int J Food Microbiol 1994, 23:277-294.
• [22]Volkmer B, Heinemann M: Condition-dependent cell volume and concentration of Escherichia coli to facilitate data conversion for systems biology modeling. PLoS One 2011, 6:e23126.
• [23]Button DK: Kinetics of nutrient-limited transport and microbial growth. Microbiol Rev 1985, 49:270-297.
• [24]Lendenmann U, Egli T: Kinetic models for the growth of Escherichia coli with mixtures of sugars under carbon-limited conditions. Biotechnol Bioeng 1998, 59:99-107.
• [25]Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette MG, Alon U: A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 2006, 3:623-628.
• [26]Cormack BP, Valdivia RH, Falkow S: FACS-optimized mutants of the green fluorescent protein (GFP). Gene 1996, 173:33-38.
• [27]Ronen M, Rosenberg R, Shraiman BI, Alon U: Assigning numbers to the arrows: parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA 2002, 99:10555-10560.
• [28]Magasanik B: Regulation of transcription of the glnALG operon of Escherichia coli by protein phosphorylation. Biochimie 1989, 71:1005-1012.
• [29]Ninfa AJ, Magasanik B: Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc Natl Acad Sci USA 1986, 83:5909-5913.
• [30]Reitzer LJ, Magasanik B: Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter. Cell 1986, 45:785-792.
• [31]Javelle A, Severi E, Thornton J, Merrick M: Ammonium sensing in Escherichia coli. Role of the ammonium transporter AmtB and AmtB-GlnK complex formation. J Biol Chem 2004, 279:8530-8538.
• [32]Merrick M, Javelle A, Durand A, Severi E, Thornton J, Avent ND, Conroy MJ, Bullough PA: The Escherichia coli AmtB protein as a model system for understanding ammonium transport by Amt and Rh proteins. Transfus Clin Biol 2006, 13:97-102.
• [33]van Heeswijk WC, Hoving S, Molenaar D, Stegeman B, Kahn D, Westerhoff HV: An alternative PII protein in the regulation of glutamine synthetase in Escherichia coli. Mol Microbiol 1996, 21:133-146.
• [34]Kaplan S, Bren A, Zaslaver A, Dekel E, Alon U: Diverse two-dimensional input functions control bacterial sugar genes. Mol Cell 2008, 29:786-792.
• [35]Hengge R: the general stress response in gram negative bacteria. In Bacterial stress responses. 2nd edition. Edited by Storz G, Hengge R. Washington, DC: ASM press; 2012.
• [36]Kim M, Zhang Z, Okano H, Yan D, Groisman A, Hwa T: Need-based activation of ammonium uptake in Escherichia coli. Mol Syst Biol 2012, 8:616.
• [37]Muller PJ, von Frommannshausen B, Schutz H: Regulation of ammonia assimilation in ammonia-limited chemostat cultures of Escherichia coli ML 30: evidence of bistability. Z Allg Mikrobiol 1981, 21:361-372.
• [38]Hart Y, Madar D, Yuan J, Bren A, Mayo AE, Rabinowitz JD, Alon U: Robust control of nitrogen assimilation by a bifunctional enzyme in E. coli. Mol Cell 2011, 41:117-127.
• [39]Plumbridge J: Expression of ptsG, the gene for the major glucose PTS transporter in Escherichia coli, is repressed by Mlc and induced by growth on glucose. Mol Microbiol 1998, 29:1053-1063.
• [40]Plumbridge J: Regulation of gene expression in the PTS in Escherichia coli: the role and interactions of Mlc. Curr Opin Microbiol 2002, 5:187-193.
• [41]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.
• [42]Miyashiro T, Goulian M: High stimulus unmasks positive feedback in an autoregulated bacterial signaling circuit. Proc Natl Acad Sci USA 2008, 105:17457-17462.
• [43]Soupene E, van Heeswijk WC, Plumbridge J, Stewart V, Bertenthal D, Lee H, Prasad G, Paliy O, Charernnoppakul P, Kustu S: Physiological studies of Escherichia coli strain MG1655: growth defects and apparent cross-regulation of gene expression. J Bacteriol 2003, 185:5611-5626.
• [44]Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H: Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2006, 2:2006 0008.
• [45]Dekel E, Alon U: Optimality and evolutionary tuning of the expression level of a protein. Nature 2005, 436:588-592.
• [46]Zaslaver A, Mayo AE, Rosenberg R, Bashkin P, Sberro H, Tsalyuk M, Surette MG, Alon U: Just-in-time transcription program in metabolic pathways. Nat Genet 2004, 36:486-491.