Rewiring the keyboard: evolvability of the genetic code

Knight, Rob; Freeland, Stephen J.; Landweber, Laura F.

doi:10.1038/35047500

Cited by 387 publications

(363 citation statements)

References 74 publications

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“…Recent work [42] about evolvability of the genetic code suggests that the code is shaped by natural selection.…”

Section: Replicator Dynamics and Egtmentioning

confidence: 99%

Quantum Replicator Dynamics

Hidalgo

2006

Physica A: Statistical Mechanics and its Applications

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We propose quantization relationships which would let us describe and solution problems originated by conflicting or cooperative behaviors among the members of a system from the point of view of quantum mechanical interactions. The quantum analogue of the replicator dynamics is the equation of evolution of mixed states from quantum statistical mechanics. A system and all its members will cooperate and rearrange its states to improve their present condition. They strive to reach the best possible state for each of them which is also the best possible state for the whole system. This led us to propose a quantum equilibrium in which a system is stable only if it maximizes the welfare of the collective above the welfare of the individual. If it is maximized the welfare of the individual above the welfare of the collective the system gets unstable and eventually it collapses.

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“…Recent work [42] about evolvability of the genetic code suggests that the code is shaped by natural selection.…”

Section: Replicator Dynamics and Egtmentioning

confidence: 99%

Quantum Replicator Dynamics

Hidalgo

2006

Physica A: Statistical Mechanics and its Applications

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“…However, a standard genetic code (or just 'standard code') is common to all major domains of life on Earth, which is perhaps among the best evidence for their common ancestry. Alternative genetic codes are never different from the standard code in more than a few codons, and they are most parsimoniously explained as derived from the standard genetic code (Knight et al 2001). According to one estimate the standard genetic code is almost as old as life on Earth itself (Eigen et al 1989).…”

Section: Introductionmentioning

confidence: 99%

No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

Ardell

Sella

2002

Phil. Trans. R. Soc. Lond. B

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The standard genetic code poses a challenge in understanding the evolution of information processing at a fundamental level of biological organization. Genetic codes are generally coadapted with, or 'frozen' by, the protein-coding genes that they translate, and so cannot easily change by natural selection. Yet the standard code has a significantly non-random pattern that corrects common errors in the transmission of information in protein-coding genes. Because of the freezing effect and for other reasons, this pattern has been proposed not to be due to selection but rather to be incidental to other evolutionary forces or even entirely accidental.We present results from a deterministic population genetic model of code-message coevolution. We explicitly represent the freezing effect of genes on genetic codes and the perturbative effect of changes in genetic codes on genes. We incorporate characteristic patterns of mutation and translational error, namely, transition bias and positional asymmetry, respectively. Repeated selection over small successive changes produces genetic codes that are substantially, but not optimally, error correcting. In particular, our model reproduces the error-correcting patterns of the standard genetic code. Aspects of our model and results may be applicable to the general problem of adaptation to error in other natural information-processing systems.

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“…The most common one is a reassignment of the termination codon UGA to tryptophan (3). Thus, to decode the UGA tryptophan codon, mitochondria require a nonstandard tRNA Trp carrying a UCA instead of CCA anticodon.…”

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confidence: 99%

Dual targeting of a single tRNA ^Trp requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei

Charrière

Helgadöttir

Horn

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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The mitochondrion of Trypanosoma brucei does not encode any tRNAs. This deficiency is compensated for by the import of a small fraction of nearly all of its cytosolic tRNAs. Most trypanosomal aminoacyl-tRNA synthetases are encoded by single-copy genes, suggesting the use of the same enzyme in the cytosol and mitochondrion. However, the T. brucei genome contains two distinct genes for eukaryotic tryptophanyl-tRNA synthetase (TrpRS). RNA interference analysis established that both TrpRS1 and TrpRS2 are essential for growth and required for cytosolic and mitochondrial tryptophanyl-tRNA formation, respectively. Decoding the mitochondrial tryptophan codon UGA requires mitochondria-specific C3 U RNA editing in the anticodon of the imported tRNA Trp . In vitro charging assays with recombinant TrpRS enzymes demonstrated that the edited anticodon and the mitochondria-specific thiolation of U33 in the imported tRNA Trp act as antideterminants for the cytosolic TrpRS1. The existence of two TrpRS enzymes, therefore, can be explained by the need for a mitochondrial synthetase with extended substrate specificity to achieve aminoacylation of the imported thiolated and edited tRNA Trp . Thus, the notion that, in an organism, all nuclear-encoded tRNAs assigned to a given amino acid are charged by a single aminoacyl-tRNA synthetase, is not universally valid.genetic code ͉ mitochondria ͉ RNA editing ͉ aminoacyl-tRNA synthetase

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Rewiring the keyboard: evolvability of the genetic code

Cited by 387 publications

References 74 publications

Quantum Replicator Dynamics

Quantum Replicator Dynamics

No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

Dual targeting of a single tRNA ^Trp requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei

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Rewiring the keyboard: evolvability of the genetic code

Cited by 387 publications

References 74 publications

Quantum Replicator Dynamics

Quantum Replicator Dynamics

No accident: genetic codes freeze in error–correcting patterns of the standard genetic code

Dual targeting of a single tRNA Trp requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei

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Dual targeting of a single tRNA ^Trp requires two different tryptophanyl-tRNA synthetases in Trypanosoma brucei