Fraction of Ribosomes Synthesizing Protein as a Function of Specific Growth Rate

Harvey, Richard J.

doi:10.1128/jb.114.1.287-293.1973

Cited by 46 publications

(21 citation statements)

References 25 publications

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“…The second school of thought suggests that ribosomes are substantially sub-saturated under all but the best conditions, often assuming a fraction of inactive ribosomes. Examples of this way of thinking can be found in work on upshifts by Koch (Koch, 1971(Koch, , 1988Koch and Deppe, 1971), Harvey (Harvey, 1973) and subsequent models and experiments (Borkowski et al, 2016;Dai et al, 2016;Metzl-Raz et al, 2017). The present study supports the second school.…”

Section: Discussionsupporting

confidence: 81%

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A bacterial growth law out of steady-state

Kohanim

Levi

Jona

et al. 2018

Preprint

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SummaryBacterial growth depends on numerous reactions, and yet follows surprisingly simple laws that inspired biologists for decades. Growth laws until now primarily dealt with steady-state exponential growth in constant conditions. However, bacteria in nature often face fluctuating environments, with nutritional upshifts and downshifts. We therefore ask whether there are growth laws that apply to changing environments. We derive a law for strong upshifts using an optimal resource-allocation model that was previously calibrated at steady-state growth: the post-shift growth rate equals the geometrical mean of the pre-shift growth rate and the growth rate on saturating carbon. We test this using chemostat and robotic batch culture experiments, as well as previous data from several species, and find good agreement with the model predictions. The increase in growth rate after an upshift indicates that ribosomes have spare capacity. We demonstrate theoretically that spare ribosomal capacity has the cost of slow steady-state growth, but is beneficial in fluctuating environments because it prevents large overshoots in intracellular metabolites after an upshift and allows rapid response to change. We also provide predictions for downshifts for future experimental tests. Spare capacity appears in diverse biological systems, and the present study quantifies the optimal degree of spare capacity, which rises the slower the growth rate, and suggests that it can be precisely regulated.

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Section: Discussionsupporting

confidence: 81%

“…The rapid increase in growth rate from 0 to 1 cannot be explained by synthesis of new ribosomes (Koch and Deppe, 1971). As suggested by Koch and others (Harvey, 1973;Koch, 1988), this hints that cells in slow growth have a higher translational capacity than is actually being used.…”

Section: Experimental Tests For Nutritional Upshifts Support the Squamentioning

confidence: 82%

A bacterial growth law out of steady-state

Kohanim

Levi

Jona

et al. 2018

Preprint

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“…Ifthe direct method ofobserving the sedimentation properties of the ribosome fraction yields estimates for the active fraction that are subject to considerable interference from artifacts, indirect methods to the same end are even more questionable. Harvey (1973) determined the number of 'mol' of nascent protein per total ribosome (leading to an estimation of the active fraction of ribosones) by pulse-labelling cells with radioactive leucine and then isolating the ribosome fraction, perfoming puromycin-induced chain termination and release from the ribosome fraction in vitro, pelleting the ribosomes, and determining the specific radioactivity of the supernatant, which presumably contained only the released nascent protein. This protocol involves so many different radioactivity and colorimetry measurements that its accuracy is difficult to evaluate; the results obtained are in several respects quite different from the results observed with more direct methods, especially that cp decreased continuously with increasing growth rate.…”

Section: Precision Of Resultsmentioning

confidence: 99%

Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate

Young

Bremer

1976

Biochemical Journal

167

120

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By evaluating the kinetics of radioactive labelling of nascent and finished polypeptides, the peptide-chain elongation rate for Escherichia coli B/r at three different growth rates (mu) was determined to be 17 amino acids/s for the fast-growing cells (mu equals 1.3 and 2.0 doublings/h) and 12 amino acids/s for slow-growing cells (mu equals 0.67 doublings/h). The results agree with the growth-rate-dependence of the rate of peptide-chain elongation found for the translation of newly induced beta-galactosidase messenger in this strain and under these conditions of growth [Dalbow & Young (1975) Biochem. J. 150, 13-20]. Together with the previously observed ribosome efficiency at these growth rates [Dennis & Bremer (1974) J. Mol. Biol. 84, 407-422] the results indicate that the fraction of ribosomes engaged in protein synthesis is about 0.8 at all three growth rates.

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“…Amino-terminal methionine and polypeptide chain growth periods were measured for total cell protein by methods previously described (14). The method used for measurement of the fraction of ribosomes in polyribosomes has also been described previously (15).…”

Section: Formate Acceptor Capacities Reaction Mixturesmentioning

confidence: 99%

Growth and Initiation of Protein Synthesis inEscherichia coliin the Presence of Trimethoprim

Harvey

1973

J Bacteriol

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Escherichia coli grew exponentially at a reduced rate in the presence of 50 or 100 ;&g of trimethoprim/ml if the low-molecular-weight products of folate metabolism or their precursors (thymidine, purines, methionine, glycine, and pantothenate) were supplied in the medium. Folate metabolism was inhibited 99.9% by these concentrations of trimethoprim, but a low level of formylation of methionyl transfer ribonucleic acid (met-tRNAF) could be detected. However, in a medium containing all major amino acids, nucleosides, and vitamins, formylation of met-tRNAF was undetectable in the presence of trimethoprim. No other amino-masked amino acids were detected, and methionine remained a major amino-terminal amino acid of mature proteins. met-tRNAF was rapidly labeled with exogenous methionine and was associated with 30s ribosomal subunits and 70s ribosomes. It was concluded that initiation of protein synthesis can occur with unformylated met-tRNAF in E. coli. Changes in macromolecular composition were associated with the lack of formylation, in particular a fourfold increase in both met-tRNAF and ribosomal subunits. These changes would tend to compensate for the low specific rate of initiation with unformylated met-tRNAF.

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Fraction of Ribosomes Synthesizing Protein as a Function of Specific Growth Rate

Cited by 46 publications

References 25 publications

A bacterial growth law out of steady-state

A bacterial growth law out of steady-state

Polypeptide-chain-elongation rate in Escherichia coli B/r as a function of growth rate

Growth and Initiation of Protein Synthesis inEscherichia coliin the Presence of Trimethoprim

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