A multiobjective approach to the genetic code adaptability problem

• Published in: BMC bioinformatics Vol. 16; no. 1; p. 52
• Main Authors: de Oliveira, Lariza Laura, de Oliveira, Paulo S L, Tinós, Renato
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 19-02-2015; BioMed Central
• Subjects: Algorithms; Amino acids; Amino Acids - genetics; Analysis; Codon; Evolution; Evolution, Molecular; Genetic Code; Humans; Journalism; Models, Genetic; Mutation - genetics; Protein Biosynthesis; Selection, Genetic - genetics
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-015-0480-9

The organization of the canonical code has intrigued researches since it was first described. If we consider all codes mapping the 64 codes into 20 amino acids and one stop codon, there are more than 1.51×10(84) possible genetic codes. The main question related to the organization of the genetic code is why exactly the canonical code was selected among this huge number of possible genetic codes. Many researchers argue that the organization of the canonical code is a product of natural selection and that the code's robustness against mutations would support this hypothesis. In order to investigate the natural selection hypothesis, some researches employ optimization algorithms to identify regions of the genetic code space where best codes, according to a given evaluation function, can be found (engineering approach). The optimization process uses only one objective to evaluate the codes, generally based on the robustness for an amino acid property. Only one objective is also employed in the statistical approach for the comparison of the canonical code with random codes. We propose a multiobjective approach where two or more objectives are considered simultaneously to evaluate the genetic codes.
In order to test our hypothesis that the multiobjective approach is useful for the analysis of the genetic code adaptability, we implemented a multiobjective optimization algorithm where two objectives are simultaneously optimized. Using as objectives the robustness against mutation with the amino acids properties polar requirement (objective 1) and robustness with respect to hydropathy index or molecular volume (objective 2), we found solutions closer to the canonical genetic code in terms of robustness, when compared with the results using only one objective reported by other authors.
Using more objectives, more optimal solutions are obtained and, as a consequence, more information can be used to investigate the adaptability of the genetic code. The multiobjective approach is also more natural, because more than one objective was adapted during the evolutionary process of the canonical genetic code. Our results suggest that the evaluation function employed to compare genetic codes should consider simultaneously more than one objective, in contrast to what has been done in the literature.