Codon Usage

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Codon Usage

• Dan Graur

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Codon-usage bias
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Measures of codon-usage bias
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The relative synonymous codon usage (RSCU) is the
number of times a codon appears in a gene divided
by the number of expected occurrences under equal
codon usage. n number of synonymous
codons (1 ? n ? 6) for the amino acid under
study, Xi number of occurrences of codon i. If
the synonymous codons of an amino acid are used
with equal frequencies, their RSCU values will
equal 1.
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The codon adaptation index (CAI) measures the
degree with which genes use preferred codons.
We first compile a table of RSCU values for
highly expressed genes. From this table, it is
possible to identify the codons that are most
frequently used for each amino acid. The relative
adaptiveness of a codon (wi) is computed
as where RSCUmax the RSCU value for the
most frequently used codon for an amino acid.
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The CAI value for a gene is calculated as the
geometric mean of wi values for all the codons
used in that gene. where L number of
codons.
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The effective number of codons (ENC) where Fi
(i 2, 3, 4, or 6) is the average probability
that two randomly chosen codons for an amino acid
with i codons will be identical. ENC values
range from 20 (the number of amino acids), which
means that the bias is at a maximum, and only one
codon is used from each synonymous-codon group,
to 61 (the number of sense codons), which
indicates no codon-usage bias.
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Universal and species-specific patterns of codon
usage
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The genome hypothesis All genes in a genome
tend to have the same coding strategy. That is,
they employ the codon catalog similarly and show
similar choices between synonymous codons.
Different taxa have different coding
strategies.
Richard Grantham
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Universal patterns Codons that contain the CG
dinucleotide are universally avoided (low-usage
codons). This phenomenon is particularly notable
as far as the arginine codons CGA and CGG are
concerned.
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Codon Usage is related to Translation Efficiency
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The translation efficiency of a codon is related
to the relative quantity of tRNA molecules that
recognize the particular codon.
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Codon Usage is related to Translation Efficiency
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Toshimishi Ikemura
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Rules determining choice of optimal codons in
unicellular organisms ____________________________
______ 1. tRNA availability. 2. Preference
for A over G when thiolated uridine or
5-carboxymethyl are at the anticodon wobble
position. 3. Preference for T and C over A
when inosine is at the anticodon wobble
position. 4. Codons of the AAN, ATN, TAN, and
TTN type prefer C in the third codon
position. __________________________________
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Codon usage in multicellular organisms
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Subramanian S. 2008. Genetics 1782429-2432