Download Encoding and decoding translation efficiency

A genome-wide perspective on
translation of proteins
Dec 2012
Regulatory Genomics
Lecturer: Prof. Yitzhak Pilpel
Multiple codons for the same amino
acid: opportunities for sophisticated
control
C1 C2 C3 C4 C5 C6
Serine:
UCU UCC UCA UCG AGC AGU
Cysteine:
UGU UGC
Methionine: UGG
STOP: UAA,
UAG UGA
2
A simple model for translation efficiency
…
ATC
The tRNA Adaptation
Index (tAI)
CCA
AAA TCG
…
AAT
…
Wobble Interaction
Wi 
wi =
ni
 (1  s
ij
j 1
)tRNAij
Wi/Wmax
if Wi0
wmean
else
{
1/



tAIg  
w

i
k


dos Reis et al. NAR 2004
k1

g
g
3
Codon usage bias is correlated with
translation efficiency
r=-0.79 (p<0.001)
Mutation pattern
(neutral)
Selection
Codon bias
Selection of codons might affect:
Accuracy
Throughput
RNA-structure
Costs
Folding
kc
c+C
+
d
k’d
k’c
kd
dC
Kinetic proofreading –
the problem
vc
cC
AAc C – codon
c – Cognate tRNA
d – None-cognate tRNA
cC, dC – tRNA codon pair
AAc, AAd, correct and wrong
amino acid
Assumptions:
kc=kd,
k’d=100*k’c
vd=vc
vd
AAd
Error rate, Fo= AAd/AAc = dC/cC = k’c/k;d= 0.01
Yet in reality error rate is 10^-4… How can we explain
100 times more accurate translation
l’c
kc
c+C
+
l’d
d
k’d
k’c
kd
dC
m
d*C
Kinetic proofreading –
the solution
vc
m
cC
AAc
c*C
C – codon
C* – Modified Cognate tRNA
d* – Modified None-cognate tRNA
C*C, d*C – tRNA codon pair
m- rate of tRNA modification
l’c, l’d – rate of unidirectional reaction
in which the modified tRNAs
leave the site
Assumption:
l’c*100=l’d
vd
AAd
Corrected Error rate, F= (k’c/k’d) (l’c/l’d)= 10^-4
The energy landscape of kinetic proofreading
l’c
Free energy
d*C
l’d
c*C
c d
C
k’d
k’c
dC
cC
Fo
c
C
d
C
Analogy: from mating in yeast
A protease might help yeast find the right mate by
degrading the signal and the noise
No protease: large error
Barkai et al. Nature 1998
With protease: small error
Selection of codons might affect:
Accuracy
Throughput
RNA-structure
Costs
Folding
Programmed “errors” in amino acid loading
on tRNA in stress
Oxygen radicals – toxic !!!
A non-Met tRNA
As a result, in times of oxidative stress the cell is
more protected since it has more Met residues in
its proteins !!
(Netzer et al Nature 2009)
Open questions
• Does select act to tune the “desired” error
rate?
• How can we find places in genes where high
error rate is selected for/against?
• Does controlling tRNA availability serve as a
means to control error rate?
• Are there additional factors
(e.g. location of codon within a gene)?
Selection of codons might affect:
Accuracy
Throughput
RNA-structure
Costs
Folding
A simple model for translation efficiency
…
ATC
The tRNA Adaptation
Index (tAI)
CCA
AAA TCG
…
AAT
…
Wobble Interaction
Wi 
wi =
ni
 (1  s
ij
j 1
)tRNAij
Wi/Wmax
if Wi0
wmean
else
{
1/



tAIg  
w

i
k


dos Reis et al. NAR 2004
k1

g
g
15
Correlation does not imply causality!!
Measured protein
abundance
r=0.63
Z
Predicted translation efficiency
(Ghaemmaghami et al. Nature 2003)
Yet, mRNA also correlates with tAI… and with protein
levels…
mRNA
*
*
*
*
* *
*
tAI
tAI and protein levels correlate even among gene populations with same
mRNA levels
Deletion of a gene with a duplicate has
smaller effect on phenotype
(Gu et al Nature 2002)
•Single-copy
genes have a
tendency to be
essential
•Genes with
duplicates tend
to be more
dispensable
As always, correlation doesn’t
guarantee causality
Duplication
Dispensability
Z(??)
A synthetic library of GFP variants
Kudla et al. Science 2009
Protein
abundance
No correlation between CAI
and protein expression
Correlation does not imply causality!!
Measured protein
abundance
r=0.63
Predicted translation efficiency
(Ghaemmaghami et al. Nature 2003)
Protein
abundance
Tight RNA structure reduce
translation
The tightness at the 5’ matters
So if codon usage doesn’t affect protein level,
what does effect such levels? – It’s the RNA
structure and its tightness!
Is tightness important throughout, or just at
particular locations?
?
Natural sequences too show relaxed structure at 5’
Structural
tightness
Structural
tightness
(Tuller PNAS 2010)
Protein/mRNA
Yet, mRNA structure doesn’t predict expression at all
Structural Tightness
Bioinformatics vs. synthetic biology
Bioinformatics
Synthetic biology
Hundreds of thousands of
genes
Variability is controlled (few
confounding factors)
All passed through natural
selection
Protein
abundance
No correlation between CAI
and protein expression
Towards more sophisticated translation efficiency models