Alignment-based and alignment-free methods converge with experimental data on amino acids coded by stop codons at split between nuclear and mitochondrial genetic codes. (May 2018)

• Record Type: Journal Article
• Authors: Seligmann, Hervé
• Is Part Of: Bio systems. Volume 167(2018)
• Page Start: 33
• Page End: 46
• Publication Date: 2018-05
• Subjects: Start codon -- Stop codon -- Initiation codon -- Termination codon -- Phylogenetic reconstruction -- Codon ambiguity -- Antitermination -- Termination suppression; Biological systems -- Periodicals; Biology -- Periodicals; Biology -- Periodicals; Evolution -- Periodicals; Biologie -- Périodiques; Évolution -- Périodiques; 570
• DOI: 10.1016/j.biosystems.2018.03.002
• Languages: English
• ISSNs: 0303-2647

Abstract

Abstract: Genetic codes mainly evolve by reassigning punctuation codons, starts and stops. Previous analyses assuming that undefined amino acids translate stops showed greater divergence between nuclear and mitochondrial genetic codes. Here, three independent methods converge on which amino acids translated stops at split between nuclear and mitochondrial genetic codes: (a) alignment-free genetic code comparisons inserting different amino acids at stops; (b) alignment-based blast analyses of hypothetical peptides translated from non-coding mitochondrial sequences, inserting different amino acids at stops; (c) biases in amino acid insertions at stops in proteomic data. Hence short-term protein evolution models reconstruct long-term genetic code evolution. Mitochondria reassign stops to amino acids otherwise inserted at stops by codon-anticodon mismatches (near-cognate tRNAs). Hence dual function (translation termination and translation by codon-anticodon mismatch) precedes mitochondrial reassignments of stops to amino acids. Stop ambiguity increases coded information, compensates endocellular mitogenome reduction. Mitochondrial codon reassignments might prevent viral infections.