{"database":"biostudies-literature","file_versions":[],"scores":null,"additional":{"omics_type":["Unknown"],"volume":["3(12)"],"submitter":["Barik S"],"pubmed_abstract":["A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes."],"journal":["Heliyon"],"pagination":["e00492"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/S-EPMC5772840"],"repository":["biostudies-literature"],"pubmed_title":["Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias."],"pmcid":["PMC5772840"],"pubmed_authors":["Barik S"],"additional_accession":[]},"is_claimable":false,"name":"Amino acid repeats avert mRNA folding through conservative substitutions and synonymous codons, regardless of codon bias.","description":"A significant number of proteins in all living species contains amino acid repeats (AARs) of various lengths and compositions, many of which play important roles in protein structure and function. Here, I have surveyed select homopolymeric single [(A)n] and double [(AB)n] AARs in the human proteome. A close examination of their codon pattern and analysis of RNA structure propensity led to the following set of empirical rules: (1) One class of amino acid repeats (Class I) uses a mixture of synonymous codons, some of which approximate the codon bias ratio in the overall human proteome; (2) The second class (Class II) disregards the codon bias ratio, and appears to have originated by simple repetition of the same codon (or just a few codons); and finally, (3) In all AARs (including Class I, Class II, and the in-betweens), the codons are chosen in a manner that precludes the formation of RNA secondary structure. It appears that the AAR genes have evolved by orchestrating a balance between codon usage and mRNA secondary structure. The insights gained here should provide a better understanding of AAR evolution and may assist in designing synthetic genes.","dates":{"release":"2017-01-01T00:00:00Z","publication":"2017 Dec","modification":"2026-05-03T09:39:33.641Z","creation":"2019-03-26T22:59:50Z"},"accession":"S-EPMC5772840","cross_references":{"pubmed":["29387823"],"doi":["10.1016/j.heliyon.2017.e00492"]}}