Costs of accuracy determined by a maximal growth rate constraint

The present study is best understood as an extension and critique of two schools of thought. The first is that of Malloe and his students, among whom we number ourselves. It is to Maaloe that we are indebted for the idea that logarithmically growing bacteria assemble and use tibosomes in amounts that are optimally adjusted to yield the maximal growth rates supported by different media. Her, we begin our analysis by applying this optimization priciple to all the components of a logarithmically growing system. Our objective is to use the growth optimization constraint as a tool to explore the physiological limits on the accuracy of gene expression. This brings us to our second source of inspiration, which is Orgel's (1963) conception of a problem that Ninio (1982) has referred to as the ‘great error loop’.

[1]  L. Orgel,et al.  The maintenance of the accuracy of protein synthesis and its relevance to ageing. , 1963, Proceedings of the National Academy of Sciences of the United States of America.

[2]  C. Kurland,et al.  The distribution of soluble and ribosomal RNA as a function of growth rate , 1963 .

[3]  L E Orgel,et al.  The maintenance of the accuracy of protein synthesis and its relevance to ageing: a correction. , 1970, Proceedings of the National Academy of Sciences of the United States of America.

[4]  L. Gorini Ribosomal discrimination of tRNAs. , 1971, Nature: New biology.

[5]  R. Contreras,et al.  Recent progress in the sequence determination of bacteriophage MS2 RNA. , 1971, Biochimie.

[6]  J. Ninio A semi-quantitative treatment of missense and nonsense suppression in the strA and ram ribosomal mutants of Escherichia coli. Evaluation of some molecular parameters of translation in vivo. , 1974, Journal of molecular biology.

[7]  J. Hopfield Kinetic proofreading: a new mechanism for reducing errors in biosynthetic processes requiring high specificity. , 1974, Proceedings of the National Academy of Sciences of the United States of America.

[8]  J. Garel,et al.  Functional adaptation of tRNA population. , 1974, Journal of theoretical biology.

[9]  G W Hoffmann,et al.  On the origin of the genetic code and the stability of the translation apparatus. , 1974, Journal of molecular biology.

[10]  J. Ninio Kinetic amplification of enzyme discrimination. , 1975, Biochimie.

[11]  T B Kirkwood,et al.  The stability of the translation apparatus. , 1975, Journal of molecular biology.

[12]  M. Yčas,et al.  The error catastrophe hypothesis with reference to aging and the evolution of the protein synthesizing machinery. , 1975, Journal of theoretical biology.

[13]  D. Galas,et al.  Ribosome slowed by mutation to streptomycin resistance , 1976, Nature.

[14]  P. Dennis,et al.  Role of ribosomal protein S12 in peptide chain elongation: analysis of pleiotropic, streptomycin-resistant mutants of Escherichia coli , 1977, Journal of bacteriology.

[15]  T. Kirkwood Evolution of ageing , 1977, Nature.

[16]  F. Neidhardt,et al.  Chemical measurement of steady-state levels of ten aminoacyl-transfer ribonucleic acid synthetases in Escherichia coli , 1977, Journal of bacteriology.

[17]  A. Fersht Enzyme structure and mechanism , 1977 .

[18]  C. Kurland The role of guanine nucleotides in protein biosynthesis. , 1978, Biophysical journal.

[19]  G von Heijne,et al.  The concentration dependence of the error frequencies and some related quantities in protein synthesis. , 1979, Journal of theoretical biology.

[20]  O. Maaløe,et al.  Regulation of the Protein-Synthesizing Machinery—Ribosomes, tRNA, Factors, and So On , 1979 .

[21]  J. Gallant,et al.  Testing models of error propagation. , 1980, Journal of theoretical biology.

[22]  Free-energy dissipation constraints on the accuracy of enzymatic selections. , 1980, Quarterly reviews of biophysics.

[23]  C Blomberg,et al.  Thermodynamic constraints on kinetic proofreading in biosynthetic pathways. , 1980, Biophysical journal.

[24]  G. Churchward,et al.  Growth rate-dependent control of chromosome replication initiation in Escherichia coli , 1981, Journal of bacteriology.

[25]  R. Nussinov,et al.  Preferential codon usage in genes. , 1981, Gene.

[26]  T. Ikemura Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. , 1981, Journal of molecular biology.

[27]  J. Garel,et al.  Does quantitative tRNA adaptation to codon content in mRNA optimize the ribosomal translation efficiency? Proposal for a translation system model. , 1981, Biochimie.

[28]  Manolo Gouy,et al.  Codon catalog usage is a genome strategy modulated for gene expressivity , 1981, Nucleic Acids Res..

[29]  R. Thompson,et al.  The accuracy of protein biosynthesis is limited by its speed: high fidelity selection by ribosomes of aminoacyl-tRNA ternary complexes containing GTP[gamma S]. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[30]  W. Fiers,et al.  Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. , 1982, Gene.

[31]  G. Churchward,et al.  Macromolecular composition of bacteria. , 1982, Journal of theoretical biology.

[32]  M. Ehrenberg,et al.  Is there proofreading during polypeptide synthesis? , 1982, The EMBO journal.

[33]  Keith R. Yamamoto,et al.  Biological Regulation and Development , 1982, Springer US.

[34]  C. Kurland,et al.  Codon‐specific missense errors in vivo. , 1983, The EMBO journal.

[35]  C. Kurland,et al.  Does codon composition influence ribosome function? , 1984, The EMBO journal.