Document Detail

Near-critical behavior of aminoacyl-tRNA pools in E. coli at rate-limiting supply of amino acids.
MedLine Citation:
PMID:  15501947     Owner:  NLM     Status:  MEDLINE    
The rates of consumption of different amino acids in protein synthesis are in general stoichiometrically coupled with coefficients determined by codon usage frequencies on translating ribosomes. We show that when the rates of synthesis of two or more amino acids are limiting for protein synthesis and exactly matching their coupled rates of consumption on translating ribosomes, the pools of aminoacyl-tRNAs in ternary complex with elongation factor Tu and GTP are hypersensitive to a variation in the rate of amino acid supply. This high sensitivity makes a macroscopic analysis inconclusive, because it is accompanied by almost free and anticorrelated diffusion in copy numbers of ternary complexes. This near-critical behavior is relevant for balanced growth of Escherichia coli cells in media that lack amino acids and for adaptation of E. coli cells after downshifts from amino-acid-containing to amino-acid-lacking growth media. The theoretical results are used to discuss transcriptional control of amino acid synthesis during multiple amino acid limitation, the recovery of E. coli cells after nutritional downshifts and to propose a robust mechanism for the regulation of RelA-dependent synthesis of the global effector molecule ppGpp.
Johan Elf; Måns Ehrenberg
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Publication Detail:
Type:  Journal Article     Date:  2004-10-22
Journal Detail:
Title:  Biophysical journal     Volume:  88     ISSN:  0006-3495     ISO Abbreviation:  Biophys. J.     Publication Date:  2005 Jan 
Date Detail:
Created Date:  2005-01-05     Completed Date:  2005-07-11     Revised Date:  2013-06-09    
Medline Journal Info:
Nlm Unique ID:  0370626     Medline TA:  Biophys J     Country:  United States    
Other Details:
Languages:  eng     Pagination:  132-46     Citation Subset:  IM    
Department of Cell & Molecular Biology, BMC, Uppsala University, S-751 24 Uppsala, Sweden.
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MeSH Terms
Amino Acids / chemistry*
Biophysics / methods*
Computer Simulation
Culture Media / metabolism
Escherichia coli / metabolism,  physiology*
Guanosine Triphosphate / chemistry
Models, Biological
Models, Statistical
Monte Carlo Method
NF-kappa B / metabolism
Peptide Elongation Factor Tu / chemistry
Protein Binding
Protein Biosynthesis*
Proteins / chemistry
Sensitivity and Specificity
Time Factors
Transcription Factor RelA
Transcription, Genetic
Transfer RNA Aminoacylation*
Reg. No./Substance:
0/Amino Acids; 0/Codon; 0/Culture Media; 0/NF-kappa B; 0/Proteins; 0/Transcription Factor RelA; 86-01-1/Guanosine Triphosphate; EC 3.6.1.-/Peptide Elongation Factor Tu

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