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Kozak sequences and yeast

Matthew Sachs msachs at bmb.ogi.edu
Fri Jul 13 18:11:47 EST 2001

For typical translation initiation in eukaryotes, there is not a ribosome
binding site such as is used by bacteria.  Ribosomes "scan" from the mRNA
5'-end and initiate translation when they encounter a start codon (generally
an AUG, though alternative codons can be used).  That is why the first AUG
in a eukaryotic mRNA sequence is generally considered the polypeptide
translational start site and downstream AUG codons are not.

The efficiency with which an AUG-codon can "capture" such a scanning
ribosome does depend on its context; in mammals, the optimal context is the
"Kozak consensus".  While the effects in yeast of initiation context have
not been as dramatic as in mammalian systems, they nevertheless exist and
can have important consequences for regulation and gene expression (e.g.,
ribosomes will bypass the first AUG in an mRNA if it is in a poor context
through so-called leaky scanning and initiate translation from sites

With respect to your specific question, a reference of interest is:

Miyasaka, H. (1999). The positive relationship between codon usage bias and
translation initiation AUG context in Saccharomyces cerevisiae. Yeast 15(8):
	Abstract:  The relationship between the codon usage bias and the sequence
context surrounding the AUG translation initiation codon was examined in 211
Saccharomyces cerevisiae mRNA sequences. The codon usage bias and the number
of matches to optimal AUG context, (A/U)A(A/C)AA(A/C)AUGUC(U/C), for
translation initiation showed a positive relationship, indicating that these
two factors are evolutionally under the similar natural selection constraint
at the translation level. A new index (AUGCAI = AUG Context Adaptation
Index) for the measure of optimal AUG context was devised, and the
importance of each position of AUG context was also examined.

Matthew S. Sachs, Ph.D.
Associate Professor
Department of Biochemistry and Molecular Biology
OGI School of Science and Engineering
Oregon Health & Science University
20000 N.W. Walker Road
Beaverton, OR  97006-8921
503 748-1487 phone
503 748-1464 fax
msachs at bmb.ogi.edu

> -----Original Message-----
> From: owner-yeast at hgmp.mrc.ac.uk [mailto:owner-yeast at hgmp.mrc.ac.uk]On
> Behalf Of Dr.Duncan Clark
> Sent: Friday, July 13, 2001 6:37 AM
> To: yeast at net.bio.net
> Subject: Kozak sequences and yeast
> Hi Folks,
> I am having to get involved with yeast expression and am not sure if I
> need both an rbs and a kozak sequence. We are planning to use the
> Invitrogen vector pYC6/CT but need to ensure that our gene starts with
> it's own ATG. The vector only has a GAL1 promoter so we
> presume we must
> design in the kozak sequence. Do we therefore need another rbs? I'm so
> used to expression in E.coli that I need to touch base on yeast.
> Many thanks
> Duncan
> --
> The problem with being on the cutting edge is that you
> occasionally get
> sliced from time to time....
> Duncan Clark
> GeneSys Ltd.
> Tel: +44(0)1252376288
> FAX: +44(0)8701640382
> ---

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