A genome-wide perspective on translation of proteins

Dec 2012Regulatory GenomicsLecturer: Prof. Yitzhak Pilpel

Multiple codons for the same amino acid: opportunities for sophisticated

control

C1 C2 C3 C4 C5 C6Serine: UCU UCC UCA UCG AGC AGUCysteine: UGU UGCMethionine: UGG

STOP: UAA, UAG UGA

2

in

jijiji tRNAsW

1

)1(

Wi/Wmax if Wi0wi = wmean else{

tAIg wikk1

g

1/g

dos Reis et al. NAR 2004

The tRNA Adaptation Index (tAI)

ATC CCA AAA TCG AAT … ……

A simple model for translation efficiency

Wobble Interaction

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:AccuracyThroughput

CostsFolding

RNA-structure

Kinetic proofreading – the problem

c + C AAc

d

dC

AAd

+cC C – codon

c – Cognate tRNAd – None-cognate tRNAcC, dC – tRNA codon pairAAc, AAd, correct and wrong

amino acidAssumptions:kc=kd,k’d=100*k’cvd=vc

Error rate, Fo= AAd/AAc = dC/cC = k’c/k;d= 0.01

Yet in reality error rate is 10^-4… How can we explain100 times more accurate translation

kc

k’c

vc

vd

kdk’d

Kinetic proofreading – the solution

c + C AAc

d

dC

AAd

+cC

C – codonC* – Modified Cognate tRNAd* – Modified None-cognate tRNAC*C, d*C – tRNA codon pairm- rate of tRNA modificationl’c, l’d – rate of unidirectional reaction

in which the modified tRNAsleave the site

Assumption:l’c*100=l’d

Corrected Error rate, F= (k’c/k’d) (l’c/l’d)= 10^-4

kc

k’c

vc

vd

kdk’d

c*C m

d*C m

l’c

l’d

Cc d

dC

cC

Fo

d*C

c*C

Free

ene

rgy

l’c

l’d

k’c

k’d

Cc C

d

The energy landscape of kinetic proofreading

Analogy: from mating in yeastA protease might help yeast find the right mate by degrading the signal and the noise

Barkai et al. Nature 1998

No protease: large error With protease: small error

Selection of codons might affect:AccuracyThroughput

CostsFolding

RNA-structure

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:AccuracyThroughput

CostsFolding

RNA-structure

in

jijiji tRNAsW

1

)1(

Wi/Wmax if Wi0wi = wmean else{

tAIg wikk1

g

1/g

dos Reis et al. NAR 2004

The tRNA Adaptation Index (tAI)

ATC CCA AAA TCG AAT … ……

A simple model for translation efficiency

Wobble Interaction

15

Correlation does not imply causality!!

r=0.63

Predicted translation efficiency

Mea

sure

d pr

otei

n ab

unda

nce

(Ghaemmaghami et al. Nature 2003)

Evolutionary

Physiological

Z

Yet, mRNA also correlates with tAI… and with protein levels…

*

*

*

*

*

*

*

tAI

mRNA

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

No correlation between CAI and protein expression

Pro

tein

ab

unda

nce

Correlation does not imply causality!!

r=0.63

Predicted translation efficiency

Mea

sure

d pr

otei

n ab

unda

nce

(Ghaemmaghami et al. Nature 2003)

Evolutionary

Physiological

Tight RNA structure reduce translation

Pro

tein

ab

unda

nce

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’ (Tuller PNAS 2010)

Stru

ctur

al ti

ghtn

ess

Stru

ctur

al ti

ghtn

ess

Yet, mRNA structure doesn’t predict expression at all

Structural Tightness

Pro

tein

/mR

NA

Bioinformatics vs. synthetic biology

Bioinformatics

Hundreds of thousands of genes

All passed through natural selection

Synthetic biology

Variability is controlled (few confounding factors)

No correlation between CAI and protein expression

Pro

tein

ab

unda

nce

Towards more sophisticated translation efficiency models