Film-like organelles equip cells with multiple genetic codes

This article explores the material and digital culture of warfarin, one of the most commonly prescribed medications in the world. The author uses the drug’s 60-year history to describe its materiality and use, showing how and why it has become an informed material. Three ethnographic cases then show where warfarin has produced and is now reproduced by three types of information: NHS Trust guidelines, genetic codes and the INR (International Normalized Ratio). When a drug becomes so entangled with informational and digital technologies, it becomes reliant on them for its proper and safe use; it can no longer be just an informed material but is a digitally informed one.

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Refactoring the Genetic Code for Increased Evolvability

10.1101/128058 ◽

2017 ◽

Author(s):

Gur Pines ◽

James D. Winkler ◽

Assaf Pines ◽

Ryan T. Gill

Keyword(s):

Genetic Code ◽

Directed Evolution ◽

Single Gene ◽

Point Mutations ◽

Saturation Mutagenesis ◽

Mutagenic Potential ◽

Single Nucleotide ◽

Common Error ◽

Mutational Landscape ◽

Genetic Codes

AbstractThe standard genetic code is robust to mutations and base-pairing errors during transcription and translation. Point mutations are most likely to be synonymous or preserve the chemical properties of the original amino acid. Saturation mutagenesis experiments suggest that in some cases the best performing mutant requires a replacement of more than a single nucleotide within a codon. These replacements are essentially inaccessible to common error-based laboratory engineering techniques that alter single nucleotide per mutation event, due to the extreme rarity of adjacent mutations. In this theoretical study, we suggest a radical reordering of the genetic code that maximizes the mutagenic potential of single nucleotide replacements. We explore several possible genetic codes that allow a greater degree of accessibility to the mutational landscape and may result in a hyper-evolvable organism serving as an ideal platform for directed evolution experiments. We then conclude by evaluating potential applications for recoded organisms within the synthetic biology field.Significance StatementThe conservative nature of the genetic code prevents bioengineers from efficiently accessing the full mutational landscape of a gene using common error-prone methods. Here we present two computational approaches to generate alternative genetic codes with increased accessibility. These new codes allow mutational transition to a larger pool of amino acids and with a greater degree of chemical differences, using a single nucleotide replacement within the codon, thus increasing evolvability both at the single gene and at the genome levels. Given the widespread use of these techniques for strain and protein improvement along with more fundamental evolutionary biology questions, the use of recoded organisms that maximize evolvability should significantly improve the efficiency of directed evolution, library generation and fitness maximization.

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Are Proposed Early Genetic Codes Capable of Encoding Viable Proteins?

Journal of Molecular Evolution ◽

10.1007/s00239-014-9622-3 ◽

2014 ◽

Vol 78 (5) ◽

pp. 263-274 ◽

Cited By ~ 4

Author(s):

Annamária Franciska Ángyán ◽

Csaba Ortutay ◽

Zoltán Gáspári

Keyword(s):

Genetic Codes

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Comments on the entropies of genetic codes of DNA and proteins

Biophysical Chemistry ◽

10.1016/0301-4622(92)85037-5 ◽

1992 ◽

Vol 44 (1) ◽

pp. 77-78 ◽

Cited By ~ 1

Author(s):

Akiyoshi Wada

Keyword(s):

Genetic Codes

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Genomics Insights: The DNA Habitat and its RNA Inhabitants: At the Dawn of RNA Sociology

Genomics Insights ◽

10.4137/gei.s11490 ◽

2013 ◽

Vol 6 ◽

pp. GEI.S11490 ◽

Cited By ~ 20

Author(s):

Luis P. Villarreal ◽

Guenther Witzany

Keyword(s):

Genetic Code ◽

Evolutionary Novelty ◽

Agent Based ◽

Cellular Processes ◽

Genetic Codes ◽

Physical Chemical ◽

Persistent Viruses ◽

Virus Research ◽

Biological Concepts ◽

Regulatory Rnas

Most molecular biological concepts derive from physical chemical assumptions about the genetic code that are basically more than 40 years old. Additionally, systems biology, another quantitative approach, investigates the sum of interrelations to obtain a more holistic picture of nucleotide sequence order. Recent empirical data on genetic code compositions and rearrangements by mobile genetic elements and noncoding RNAs, together with results of virus research and their role in evolution, does not really fit into these concepts and compel a reexamination. In this review, we try to find an alternate hypothesis. It seems plausible now that if we look at the abundance of regulatory RNAs and persistent viruses in host genomes, we will find more and more evidence that the key players that edit the genetic codes of host genomes are consortia of RNA agents and viruses that drive evolutionary novelty and regulation of cellular processes in all steps of development. This agent-based approach may lead to a qualitative RNA sociology that investigates and identifies relevant behavioral motifs of cooperative RNA consortia. In addition to molecular biological perspectives, this may lead to a better understanding of genetic code evolution and dynamics.

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