Robust genetic codes enhance protein evolvability. 2024

Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
Institute of Integrative Biology, ETH Zürich, Zürich, Switzerland.

The standard genetic code defines the rules of translation for nearly every life form on Earth. It also determines the amino acid changes accessible via single-nucleotide mutations, thus influencing protein evolvability-the ability of mutation to bring forth adaptive variation in protein function. One of the most striking features of the standard genetic code is its robustness to mutation, yet it remains an open question whether such robustness facilitates or frustrates protein evolvability. To answer this question, we use data from massively parallel sequence-to-function assays to construct and analyze 6 empirical adaptive landscapes under hundreds of thousands of rewired genetic codes, including those of codon compression schemes relevant to protein engineering and synthetic biology. We find that robust genetic codes tend to enhance protein evolvability by rendering smooth adaptive landscapes with few peaks, which are readily accessible from throughout sequence space. However, the standard genetic code is rarely exceptional in this regard, because many alternative codes render smoother landscapes than the standard code. By constructing low-dimensional visualizations of these landscapes, which each comprise more than 16 million mRNA sequences, we show that such alternative codes radically alter the topological features of the network of high-fitness genotypes. Whereas the genetic codes that optimize evolvability depend to some extent on the detailed relationship between amino acid sequence and protein function, we also uncover general design principles for engineering nonstandard genetic codes for enhanced and diminished evolvability, which may facilitate directed protein evolution experiments and the bio-containment of synthetic organisms, respectively.

UI MeSH Term Description Entries
D008957 Models, Genetic Theoretical representations that simulate the behavior or activity of genetic processes or phenomena. They include the use of mathematical equations, computers, and other electronic equipment. Genetic Models,Genetic Model,Model, Genetic
D009154 Mutation Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations. Mutations
D011506 Proteins Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein. Gene Products, Protein,Gene Proteins,Protein,Protein Gene Products,Proteins, Gene
D003062 Codon A set of three nucleotides in a protein coding sequence that specifies individual amino acids or a termination signal (CODON, TERMINATOR). Most codons are universal, but some organisms do not produce the transfer RNAs (RNA, TRANSFER) complementary to all codons. These codons are referred to as unassigned codons (CODONS, NONSENSE). Codon, Sense,Sense Codon,Codons,Codons, Sense,Sense Codons
D005815 Genetic Code The meaning ascribed to the BASE SEQUENCE with respect to how it is translated into AMINO ACID SEQUENCE. The start, stop, and order of amino acids of a protein is specified by consecutive triplets of nucleotides called codons (CODON). Code, Genetic,Codes, Genetic,Genetic Codes
D014176 Protein Biosynthesis The biosynthesis of PEPTIDES and PROTEINS on RIBOSOMES, directed by MESSENGER RNA, via TRANSFER RNA that is charged with standard proteinogenic AMINO ACIDS. Genetic Translation,Peptide Biosynthesis, Ribosomal,Protein Translation,Translation, Genetic,Protein Biosynthesis, Ribosomal,Protein Synthesis, Ribosomal,Ribosomal Peptide Biosynthesis,mRNA Translation,Biosynthesis, Protein,Biosynthesis, Ribosomal Peptide,Biosynthesis, Ribosomal Protein,Genetic Translations,Ribosomal Protein Biosynthesis,Ribosomal Protein Synthesis,Synthesis, Ribosomal Protein,Translation, Protein,Translation, mRNA,mRNA Translations
D015202 Protein Engineering Procedures by which protein structure and function are changed or created in vitro by altering existing or synthesizing new structural genes that direct the synthesis of proteins with sought-after properties. Such procedures may include the design of MOLECULAR MODELS of proteins using COMPUTER GRAPHICS or other molecular modeling techniques; site-specific mutagenesis (MUTAGENESIS, SITE-SPECIFIC) of existing genes; and DIRECTED MOLECULAR EVOLUTION techniques to create new genes. Genetic Engineering of Proteins,Genetic Engineering, Protein,Proteins, Genetic Engineering,Engineering, Protein,Engineering, Protein Genetic,Protein Genetic Engineering
D058615 Synthetic Biology A field of biological research combining engineering in the formulation, design, and building (synthesis) of novel biological structures, functions, and systems. Biologies, Synthetic,Biology, Synthetic,Synthetic Biologies
D019143 Evolution, Molecular The process of cumulative change at the level of DNA; RNA; and PROTEINS, over successive generations. Molecular Evolution,Genetic Evolution,Evolution, Genetic

Related Publications

Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
March 2016, PLoS computational biology,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
May 2024, PLoS biology,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
April 2003, Journal of experimental zoology. Part B, Molecular and developmental evolution,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
March 2015, Bio Systems,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
April 2009, Science (New York, N.Y.),
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
April 2006, Proceedings of the National Academy of Sciences of the United States of America,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
January 1967, Guy's Hospital reports,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
September 2023, Trends in biochemical sciences,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
January 1987, Nature,
Hana Rozhoňová, and Carlos Martí-Gómez, and David M McCandlish, and Joshua L Payne
March 1962, Nature,
Copied contents to your clipboard!