title: Codon usage and protein sequence pattern dependency in different organisms: A Bioinformatics approach.
abstract: Although it is known that synonymous codons are not chosen randomly, the role of the codon usage in gene regulation is not clearly understood, yet. Researchers have investigated the relation between the codon usage and various properties, such as gene regulation, translation rate, translation efficiency, mRNA stability, splicing, and protein domains. Recently, a universal codon usage based mechanism for gene regulation is proposed. We studied the role of protein sequence patterns on the codons usage by related genes. Considering a subsequence of a protein that matches to a pattern or motif, we showed that, parts of the genes, which are translated to this subsequence, use specific ratios of synonymous codons. Also, we built a multinomial logistic regression statistical model for codon usage, which considers the effect of patterns on codon usage. This model justifies the observed codon usage preference better than the classic organism dependent codon usage. Our results showed that the codon usage plays a role in controlling protein levels, for genes that participate in a specific biological function. This is the first time that this phenomenon is reported.
authors.affiliation: Department of Mathematical Sciences, Sharif University of Technology, Tehran, Iran.
authors.forename: Mohammad-Hadi
authors.initials: MH
authors.lastname: Foroughmand-Araabi
authors.forename: Bahram
authors.initials: B
authors.lastname: Goliaei
authors.forename: Kasra
authors.initials: K
authors.lastname: Alishahi
authors.forename: Mehdi
authors.initials: M
authors.lastname: Sadeghi
authors.forename: Sama
authors.initials: S
authors.lastname: Goliaei
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001482:Base Composition / Q000235:genetics; D003062:Codon / Q000235:genetics*; D019295:Computational Biology; D006801:Humans; D016015:Logistic Models; D014176:Protein Biosynthesis / Q000235:genetics; D011506:Proteins / Q000235:genetics*; D020871:RNA Stability; D017386:Sequence Homology, Amino Acid
chemical_list: D003062:Codon; D011506:Proteins
keywords: Codon usage; logistic regression model; protein sequence pattern; protein translation efficiency