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Jump to search The Kozak consensus sequence (Kozak consensus or Kozak sequence) is a nucleic acid motif that functions as the protein translation initiation site in most mRNA (link) transcripts.[1] The sequence was named after the scientist who discovered it, Marilyn Kozak. Regarded as the optimum sequence for initiating translation in eukaryotes, the sequence is an integral aspect of protein regulation.[1] As it has become more studied, expansions of the nucleotide sequence, bases of importance, and notable exceptions have arisen.[1][2][3]

The Kozak Sequence was determined by sequencing of 699 vertebrate mRNAs and verified by site-directed mutagenesis.[4] While initially limited to a subset of vertebrates (i.e. human, cow, cat, dog, chicken, guinea pig, hamster, mouse, pig, rabbit, sheep, and Xenopus), subsequent studies confirmed its conservation in higher eukaryotes generally.[1] The sequence was defined as 5'-(gcc)gccRccAUGG-3' where:[4] The underlined nucleotides indicate the translation start codon, coding for Methionine. upper-case letters indicate highly conserved bases, i.e. the 'AUGG' sequence is constant or rarely, if ever, changes, with the exception being the IUPAC ambiguity code [5] 'R' indicates that a purine (adenine or guanine) is always observed at this position (with adenine being claimed by Kozak to be more frequent) a lower-case letter denotes the most common base at a position where the base can nevertheless vary the sequence in parentheses (gcc) is of uncertain significance.

Contents 1 Introduction 2 Mutations 3 Variations in the consensus sequence 4 See also 5 References 5.1 Further reading Introduction[edit] The ribosome assembles on the start codon (AUG), located within the Kozak sequence. Prior to translation initiation, scanning is done by the pre-initiation complex (PIC). The pre-initiation complex consists of the 40S (small ribosomal subunit) bound the to ternary complex, eIF2-GTP-intiatorMet tRNA (TC) to form the 43S ribosome. Assisted by several other initiation factors (eIF1 and eIF1A, eIF5, eIF3, polyA binding protein) it is recruited to the 5’ m7G cap of the mRNA. Once the PIC binds to the mRNA it scans until it reaches the first AUG codon in a Kozak sequence.[6][7] This scanning is stimulated by Dhx29 and Ded1 and eIF4 proteins.[1] Initiation at the first AUG from the 5' end of an mRNA is known as the “First AUG Rule.”[1] The AUG is most important because it is the actual initiation codon encoding a methionine amino acid at the N-terminus of the protein. (Rarely, GUG is used as an initiation codon, but methionine is still the first amino acid as it is the met-tRNA in the initiation complex that binds to the mRNA). Variation within the Kozak sequence alters the "strength" thereof. Kozak sequence strength refers to the favoribility of initiation, affecting how much protein is synthesized from a given mRNA.[2][8] The A nucleotide of the "AUG" is delineated as +1 in the Kozak sequence. For a 'strong' consensus, the nucleotides at positions +4 (i.e. G in the consensus) and -3 (i.e. either A or G in the consensus) relative to the +1 nucleotide must both match the consensus (there is no 0 position). An 'adequate' consensus has only 1 of these sites, while a 'weak' consensus has neither. The cc at -1 and -2 are not as conserved, but contribute to the overall strength.[9] There is also evidence that a G in the -6 position is important in the initiation of translation.[10] It is believed that the PIC is stalled at the Kozak sequence by interactions between eIF2 and the -3 and +4 nucleotides in the Kozak position.(3) This stalling allows the start codon and the corresponding anticodon time to form the correct hydrogen bonding. Once the codon:anticodon bonding occurs the 80S ribosome complex forms.The Kozak sequence is not to be confused with the ribosomal binding site (RBS), that being either the 5' cap of a messenger RNA or an Internal ribosome entry site (IRES). There are examples in vivo of each of these types of Kozak consensus, and they probably evolved as yet another mechanism of gene regulation. The first start codon closest to the 5’ end of the strand is not always recognized if it is not contained in a Kozak-like sequence. This is called “leaky scanning” and could be a potential way to control translation through initiation.[11] Lmx1b is an example of a gene with a weak Kozak consensus sequence.[12] For initiation of translation from such a site, other features are required in the mRNA sequence in order for the ribosome to recognize the initiation codon.

A sequence logo showing the most conserved bases around the initiation codon from 10 000 human mRNAs. Mutations[edit] Research has shown that a mutation of G—>C in the -6 position of the β-globin gene (β+45; human) disrupted the haematological and biosynthetic phenotype function. This was the first mutation found in the Kozak sequence and showed a 30% decrease in translational efficiency. It was found in a family from the Southeast Italy and they suffered from thalassaemia intermedia.[10]