title: Natural variability of Kozak sequences correlates with function in a zebrafish model.
abstract: In eukaryotes, targeting the small ribosomal subunit to the mRNA transcript requires a Kozak sequence at the translation initiation site. Despite the critical importance of the Kozak sequence to regulation of gene expression, there have been no correlation studies between its natural variance and efficiency of translation. Combining bioinformatics analysis with molecular biology techniques, and using zebrafish as a test case, we identify Kozak sequences based on their natural variance and characterize their function in vivo. Our data reveal that while the canonical Kozak sequence is efficient, in zebrafish it is neither the most common nor the most efficient translation initiation sequence. Rather, the most frequent natural variation of the Kozak sequence is almost twice as efficient. We conclude that the canonical Kozak sequence is a poor predictor of translation efficiency in different model organisms. Furthermore, our results provide an experimental approach to testing and optimizing an important tool for molecular biology.
authors.affiliation: Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Steven J
authors.initials: SJ
authors.lastname: Grzegorski
authors.affiliation: Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Estelle F
authors.initials: EF
authors.lastname: Chiari
authors.affiliation: Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Amy
authors.initials: A
authors.lastname: Robbins
authors.affiliation: Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Phillip E
authors.initials: PE
authors.lastname: Kish
authors.affiliation: Ophthalmology and Visual Sciences, Kellogg Eye Center, University of Michigan, Ann Arbor, Michigan, United States of America.
authors.forename: Alon
authors.initials: A
authors.lastname: Kahana
mesh_terms: D000818:Animals; D018387:Codon, Initiator; D016384:Consensus Sequence; D017124:Conserved Sequence; D017930:Genes, Reporter; D049452:Green Fluorescent Proteins / Q000032:analysis / Q000235:genetics; D010442:Peptide Chain Initiation, Translational / Q000235:genetics*; D012333:RNA, Messenger / Q000235:genetics*; D060888:Real-Time Polymerase Chain Reaction; D038621:Regulatory Sequences, Ribonucleic Acid; D020133:Reverse Transcriptase Polymerase Chain Reaction; D054682:Ribosome Subunits, Small, Eukaryotic / Q000378:metabolism; D013045:Species Specificity; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics*
chemical_list: D018387:Codon, Initiator; D012333:RNA, Messenger; D038621:Regulatory Sequences, Ribonucleic Acid; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins