title: Different types of secondary information in the genetic code.
abstract: Whole-genome and functional analyses suggest a wealth of secondary or auxiliary genetic information (AGI) within the redundancy component of the genetic code. Although there are multiple aspects of biased codon use, we focus on two types of auxiliary information: codon-specific translational pauses that can be used by particular proteins toward their unique folding and biased codon patterns shared by groups of functionally related mRNAs with coordinate regulation. AGI is important to genetics in general and to human disease; here, we consider influences of its three major components, biased codon use itself, variations in the tRNAome, and anticodon modifications that distinguish synonymous decoding. AGI is plastic and can be used by different species to different extents, with tissue-specificity and in stress responses. Because AGI is species-specific, it is important to consider codon-sensitive experiments when using heterologous systems; for this we focus on the tRNA anticodon loop modification enzyme, CDKAL1, and its link to type 2 diabetes. Newly uncovered tRNAome variability among humans suggests roles in penetrance and as a genetic modifier and disease modifier. Development of experimental and bioinformatics methods are needed to uncover additional means of auxiliary genetic information.
authors.affiliation: Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: Richard J
authors.initials: RJ
authors.lastname: Maraia
authors.affiliation: Intramural Research Program on Genomics of Differentiation, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: James R
authors.initials: JR
authors.lastname: Iben
mesh_terms: D000818:Animals; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D005815:Genetic Code; D016678:Genome; D006801:Humans; D019683:Penetrance; D012333:RNA, Messenger / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics
chemical_list: D003062:Codon; D012333:RNA, Messenger; D012343:RNA, Transfer
keywords: anticodon; codons; silent mutation; tRNA modification