Codon usage bias Ref: Chapter 9

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Codon usage biasRef Chapter 9

• Xuhua Xia
• xxia_at_uottawa.ca
• http// dambe.bio.uottawa.ca

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Objectives

• Understand how codon usage bias affect
  translation efficiency and gene expression
• Biomedical relevance
• Protein drugs in pharmaceutical industry
• Transgenic experiments in agriculture
• Factors affecting codon usage bias
• Indices measuring codon usage bias
• Develop bioinformatic skills to study the genomic
  codon usage.

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Codon Usage Bias

• Observation Strongly biased codon usage in a
  variety of species ranging from viruses,
  mitochondria, plastids, prokaryotes and
  eukaryotes.
• Hypotheses
• Differential mutation hypothesis, e.g.,
  Transcriptional hypothesis of codon usage (Xia
  1996 Genetics 1441309-1320 )
• Different selection hypothesis, e.g., (Xia 1998
  Genetics 149 37-44)
• Predictions
• From mutation hypothesis Concordance between
  codon usage and mutation pressure
• From Selection hypothesis
• Concordance between differential availability of
  tRNA and differential codon usage.
• The concordance is stronger in highly expressed
  genes than lowly expressed genes (CAI is
  positively correlated with gene expression).

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Table 9-2, yeast
Xia 2007. Bioinformatics and the cell.
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Conflict Initiation and Elongation

• Met codon usage from the 12 CDSs AUA 214AUG
  37
• Possible tRNAMet/CAU, tRNAMet/UAU
• Vertebrate mitochondrial genome has only one
  tRNAMet. Which one to have?
• tRNAMet/CAU Good for initiation, but not
  efficient for AUA codons even with the C modified
  to 5-formylcytidine
• tRNAMet/UAU Good for AUA codons, but not good
  for initiation.
• anticodon CAU favoring the AUG codon
• Nature has chosen CAU All mitochondrial genomes
  with a single tRNAMet has a CAU anticodon.
• Problem with AUA codons in translation?

Xia et al. 2007. PLoS One
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Hypothesis and Predictions
Met Leu Glu Lys Gln Arg Trp
AUA UUA GAA AAA CAA AGA UGA
Favoured by mutation Also favoured by
tRNA-mediated selection the first (wobble)
position of tRNA is U.
Favoured by mutation, but not by tRNA-mediated
selection because the first (wobble) position in
tRNA anticodon is C.
Predictions 1. Proportion of A-ending codons
(or RSCU) should be smaller in the Met codon
family than in other R-ending codon
families PNNA NNNA/NNNG 2. Availability of
tRNAMet/UAU should increase PAUA.
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Selection against AUA codons
Carullo, M. and Xia, X. 2008 J Mol Evol
66484493.
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Fig. 5. Relationship between PAUA and PUUA,
highlighting the observation that PAUA is greater
when both a tRNAMet/CAU and a tRNAMet/UAU are
present than when only tRNAMet/CAU is present in
the mtDNA, for bivalve species (a) and chordate
species (b). The filled squares are for mtDNA
containing both tRNAMet/CAU and tRNAMet/UAU
genes, and the open triangles are for mtDNA
without a tRNAMet/UAU gene.
Xia, X. 2012. In RS Singh et al.. Evolution in
the fast lane Rapidly evolving genes and genetic
systems. Oxford University Press.
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Calculation of RSCU
RSCU and proportion Different scaling.
RSCU is codon-specific
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Calculation of CAI
N2,3,4 Number of 2-, 3-, 4-fold codon families
Compound 6- or 8-fold codon families should be
broken into two codon families CAI is
gene-specific. 0 ? CAI ? 1 CAI computed with
different reference sets are not comparable.
Problem with computing w as Fi/Fi.max Suppose
an amino acid is rarely used in highly expressed
genes, then there is little selection on it, and
the codon usage might be close to even, with wi ?
1. Now if we have a lowly expressed gene that
happen to be made of entire of this amino acid,
then the CAI for this lowly expressed gene would
be 1, which is misleading. There has been no good
alternative. Further research is needed.
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Weak mRNA predictive power
ENO1
FRS2
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Effect of Codon Usage Bias
ENO1
FRS2
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Problems with CAI

• Formulation
• Reference set
• w 0
• Implementation
• AUG
• UGG
• Multiple codon families for one amino acid
• Dependence on AT
• Solutions (Xia, X. 2007. Evolutionary
  Bioinformatics)

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RSCU (HIV-1 vs Human)
Fig. 1. Relative synonymous codon usage (RSCU) of
HIV-1 compared to RSCU of highly expressed human
genes. Data points for codons ending with A, C, G
or U are annotated with different combinations of
colors and symbols. A-ending codons exhibit
strong discordance in their usage between HIV-1
and human and are annotated with their coded
amino acids.
van Weringh et al. 2011. MBE.
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Research

• Observation on HIV-1
• Strong surplus of A-ending codon
• High mutation rate
• Hypothesis Strong A-biased mutation disrupting
  codon adaptation.
• Prediction
• Strong A-biased mutation (confirmed)
• If mutation rate is lower, then there will be
  better codon adaptation (The related HTLV-1
  parasitizes the same cell as HIV-1, but have
  lower mutation rate HTLV-1 genes should exhibit
  better codon adaptation)

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RSCU (HTLV-1 vs Human)
Relative synonymous codon usage (RSCU) of HTLV-1
compared to RSCU of highly expressed human genes.
Data points for codons ending with A, C, G or U
are annotated with different combinations of
colors and symbols. A-ending codons exhibit
strong discordance in their usage between HIV-1
and human and are annotated with their coded
amino acids.
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Any problem with the mutation hypothesis?
Table 2. Frequency of A residues, length and
codon adaptation index (CAI) for the three HIV-1
early (tat, rev and nef) and five late (gag-pol,
vif, vpu, vpr, and env) coding sequences (CDS).
Gene CDS (bp) CAI
tat 261 0.66875
rev 351 0.66211
nef 621 0.67523

gag 1503 0.62784
pol 3012 0.58139
vif 579 0.61941
vpr 291 0.64272
vpu 249 0.49068
env 2571 0.61924