Overall controls on the biosynthesis of ribosomes in growing bacteria.
TL;DR: Experiments show that the “extra” RNA in the carbon-limited slow-growing cells is available in the cells in a form that can quickly function when the environment is enriched, implying strong physiological control at the level of RNA synthesis.
About: This article is published in Journal of Theoretical Biology.The article was published on 1970-08-01. It has received 86 citations till now. The article focuses on the topics: Ribosome & RNA.
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01 Jan 1999
1,102 citations
Additional excerpts
...Koch, A. 1970....
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...Norris, T., and A. Koch....
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...Similarly, Koch (82) and Daneo-Moore and Schockman (34) have used rate constants of RNA synthesis per DNA in models for the control of RNA synthesis or growth....
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...In G. Koch and D. Richter (ed.)...
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TL;DR: Evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations, and the complex and often contradictory relationships between rRNA, growth and activity are highlighted.
Abstract: Microbes exist in a range of metabolic states (for example, dormant, active and growing) and analysis of ribosomal RNA (rRNA) is frequently employed to identify the ‘active' fraction of microbes in environmental samples. While rRNA analyses are no longer commonly used to quantify a population's growth rate in mixed communities, due to rRNA concentration not scaling linearly with growth rate uniformly across taxa, rRNA analyses are still frequently used toward the more conservative goal of identifying populations that are currently active in a mixed community. Yet, evidence indicates that the general use of rRNA as a reliable indicator of metabolic state in microbial assemblages has serious limitations. This report highlights the complex and often contradictory relationships between rRNA, growth and activity. Potential mechanisms for confounding rRNA patterns are discussed, including differences in life histories, life strategies and non-growth activities. Ways in which rRNA data can be used for useful characterization of microbial assemblages are presented, along with questions to be addressed in future studies.
628 citations
Cites background from "Overall controls on the biosynthesi..."
...…under balanced growth conditions (that is, growing in an unchanging environment) (Schaechter et al., 1958; Neidhardt and Magasanik, 1960; Rosset et al., 1966; Koch, 1970; Kemp et al., 1993; Kerkhof and Ward, 1993; Poulsen et al., 1993; Wagner, 1994; Bremer and Dennis, 1996; Ramos et al., 2000)....
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07 Oct 2008
TL;DR: Five classes of growth-related parameters that are generally useful in describing or establishing the macromolecular composition of bacterial cultures are described in detail in this review.
Abstract: This review begins by briefly presenting the history of research on the chemical composition and other parameters of cells of E. coli and S. enterica at different exponential growth rates. Studies have allowed us to determine the in vivo strength of promoters and have allowed us to distinguish between factor-dependent transcriptional control of the promoter and changes in promoter activity due to changes in the concentration of free functional RNA polymerase associated with different growth conditions. The total, or bulk, amounts of RNA and protein are linked to the growth rate, because most bacterial RNA is ribosomal RNA (rRNA). Since ribosomes are required for protein synthesis, their number and their rate of function determine the rate of protein synthesis and cytoplasmic mass accumulation. Many mRNAs made in the presence of amino acids have strong ribosome binding sites whose presence reduces the expression of all other active genes. This implies that there can be profound differences in the spectrum of gene activities in cultures grown in different media that produce the same growth rate. Five classes of growth-related parameters that are generally useful in describing or establishing the macromolecular composition of bacterial cultures are described in detail in this review. A number of equations have been reported that describe the macromolecular composition of an average cell in an exponential culture as a function of the culture doubling time and five additional parameters: the C- and D-periods, protein per origin (PO), ribosome activity, and peptide chain elongation rate.
453 citations
TL;DR: Dynamic energy budget (DEB) models describe how individuals acquire and utilize energy, and can serve as a link between different levels of biological organization as mentioned in this paper, and show how the dynamics of individual organisms link to molecular processes, population dynamics, and (more tenuously) to ecosystem dynamics.
Abstract: Summary 1. Dynamic energy budget (DEB) models describe how individuals acquire and utilize energy, and can serve as a link between diAerent levels of biological organization. 2. We describe the formulation and testing of DEB models, and show how the dynamics of individual organisms link to molecular processes, to population dynamics, and (more tenuously) to ecosystem dynamics. 3. DEB models oAer mechanistic explanations of body-size scaling relationships. 4. DEB models constitute powerful tools for applications in toxicology and bio
418 citations
TL;DR: This chapter examines several aspects of its fitness for survival in the lower intestine and has shown that E. coli is designed for efficient growth in its high viscosity habitat with its sporadic nutrient input.
Abstract: Publisher Summary Escherichia coli (E. coli) is a creature adapted to its ecological niche. This chapter examines several aspects of its fitness for survival in the lower intestine and has shown that E. coli is designed for efficient growth in its high viscosity habitat with its sporadic nutrient input. Effective use of resources to produce functioning organisms implies that macromolecular synthesis is properly divided between structural and enzymic units on one hand and the means of production that include ribosomes and t-RNA on the other. In an expanding economy all elements must increase, but the manufacture of means of production themselves must be more sensitively geared to the rate of expansion than to the actual quantity of goods produced. E. coli are not constructed to be efficient at allocating resources for nucleic acid and protein synthesis from the point of view of an ideal, non-fluctuating continuous culture. An analysis of the efficiency of the transport machinery that allows E. coli to compete with its neighbors for carbon and nitrogen sources, growth factors, or trace elements is presented. It is concluded that the transport mechanisms for several compounds have evolved to the degree where diffusion through the viscous natural environment is limiting.
387 citations
References
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TL;DR: Cell mass, the average number of nuclei/cell and the content of RNA and DNA were studied in Salmonella typhimurium during balanced (steady state) growth in different media, indicating that this organism exists in one of a large number of possible stable physiological states.
Abstract: Cell mass, the average number of nuclei/cell and the content of RNA and DNA were studied in Salmonella typhimurium during balanced (steady state) growth in different media. These quantities could be described as exponential functions of the growth rates afforded by the various media at a given temperature. The size and chemical composition characteristic of a given medium were not influenced by the temperature of cultivation. Thus, under conditions of balanced growth, this organism exists in one of a large number of possible stable physiological states. The variations in mass/cell are due to changes in the number of nuclei/cell as well as in mass/nucleus. An increase in the number of ribonucleoprotein particles at higher growth rates could, it appears, largely account for the increase in mass/nucleus. Calculations indicate that the rate of protein synthesis per unit RNA is nearly the same at all growth rates.
1,419 citations
TL;DR: It is proposed that protein and/or RNA synthesis is necessary to initiate but not to sustain DNA replication, and that during renewed growth the acquired immunity to thymineless death is gradually lost and, in parallel, DNA synthesis is resumed.
571 citations
TL;DR: When cultures of Salmonella typhimurium undergoing balanced growth are shifted from one medium to another, a definite pattern of rate changes is observed and rate maintenance effect on DNA synthesis and cell division is discussed in terms of specific rate-controlling mechanisms.
Abstract: When cultures of Salmonella typhimurium undergoing balanced growth are shifted from one medium to another, a definite pattern of rate changes is observed. Shifts from a low to a high growth rate result in a strict succession of events: RNA synthesis is immediately affected and its rate rapidly increases to that characteristic of the new medium; the increase in optical density shows a lag of a few minutes before the new rate is attained; DNA synthesis and cell division, on the other hand, continue at the old rate for appreciable periods of time and then abruptly shift to the new rates. The times at which these shifts take place are, at 37°, invariably 20 and 70 min., regardless of the actual growth rates before and after the shift. This rate maintenance effect on DNA synthesis and cell division is discussed in terms of specific rate-controlling mechanisms.
372 citations
TL;DR: The results indicate that at a given temperature the RNA/protein ratio of a cultures is a direct function of the growth rate and that these two variables are linearly related at growth rates greater than 0.6 doublings per h.
317 citations
TL;DR: Britten, R. J., Roberts,R.
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283 citations