Presentations text content in A genome-wide perspective on translation of proteins
Slide1
A genome-wide perspective on translation of proteins
Dec 2012Regulatory GenomicsLecturer: Prof. Yitzhak Pilpel
Slide2Teaching assistant: Idan Frumkin
idan.frumkin@weizmann.ac.ilSubmit Sunday at midnight
Slide3The Central Dogma of Molecular Biology
Expressing the genomeDNA
mRNA
Protein
f
f
Inactive
DNA
RNA
Slide4http://esg-www.mit.edu:8001/esgbio/pge/lac.html
In the presence of Lactose
The Lac Operon (Jacob and Monod)
4
Slide5Catabolism (breakdown of molecules, e.g. lactose)
Anabolism (synthesis of molecules, e.g. amino acids)Gene is ON when substrate is presentGene is OFF when substrate is absent
Gene is ON when substrate is absent
Gene is OFF when substrate is
present
The basic logic of metabolic control
Slide6A combined transcription -translation control switch
At the Attenuation mechanismCharles Yanofsky
Slide7The trp operon in
e. coli
Slide8A negative control at the transcription level (similar and different from the lac operon)
Slide9How not to make too much triptophene?
A fail safe mechanism complements transcription controlAt the translation level!
Slide10The up-stream ORF structure of the trp operon
An
uORF
Mutual palindromes
1-2 are complementary
2-3 are complementary
3-4 are complementary
Slide11The various palindromic pairings
1-2, and 3-4
2-3
Transcription
terminator!
Not a
terminator!
Slide12High Trp
Low
Trp
The structure of the Attenuation switch
Ribosome
Ribosome
RNA pol
RNA pol
Slide13Could that be implemented in eukaryotes as well?
No! because requires co transcription-translation
Slide14Where does translation take place?
Slide15Spatial organization of the flow of genetic
information in bacteria (Llopis Nature 2010)
DNA
=DNA
=mRNA
=Protein
Slide16Translation consists of initiation, elongation and termination
5’
3’
STOP
Codon
Anti-codon
Slide17The dynamics of translation
Slide18The ribosome reads nucleotide sequence and produces amino acid sequence based on the
genetic codeSome important properties of the codeThe code is (almost) universal
There are 61 amino acid codons, and 3 STOP codons
The code is “redundant” - many amino acids have more than one codon
The genetic code is optimal wrt to many properties, such as error tolerance
Slide19The tRNA
The generic form
A specific form
In 3D
Slide20Aminoacyl tRNA synthetase:The really “smart” part
20 amino acids, 61 codons, 20
Aminoacyl
tRNA
synthetases
Error rate: 1/10,000-1/100,000
(
in-vitro;
higher
in-vivo)
Slide21The 20 canonical amino acids
Slide22Possible mechanisms of translational regulation
optimality of ribosomal attachment sitemRNA secondary structurecodon usage
Slide23Multiple codons for the same amino acid
C1 C2 C3 C4 C5 C6Serine: UCU UCC UCA UCG AGC AGUCysteine: UGU UGCMethionine: UGG
STOP: UAA, UAG UGA
Slide24G T R Y E C Q A S F D
C1C1C1C1C1C1C1C1C1C1C1C2C2C2C2C2C2C2C2C2C2C2
C1C1
C2
C1C1
C2
C1C1
C2
C1C1
C2C2C2C2
C1C1C1C1C1C1C1
C1C1C1C1C1C1C1
C2C2C2C2
For a hypothetical protein of 300 amino acids with two-codon each,
There are
2^300
possible nucleotide sequences
These variants will code for the same protein, and are thus considered “synonymous”.
Indeed evolution would easily exchange between them
But are they all really equivalent??
Slide25The codon bias in genomes
Slide26Two potential types of sources for codon bias
Mutation pattern
(neutral)
Selection
Codon bias
Slide27The effect of (or on?) GC content
Nucleotide composition
Codon bias
Coding
Coding
Inter-
genic
Inter-genic composition (esp in bacteria) explain codon bias
Mutation
pressure
Selection
Amino acid
composition
Slide28Selection of codons might affect:
Accuracy
Throughput
Costs
Folding
RNA-structure
Slide29AAA
CCA
GAA
UCG
AAG
…
…
…
A simple model for translation efficiency
8 2 5 4 1
Average: 4
AA Codon Amount
Lys AAA 8
Asp AAC 6
Lys AAG 1
Asp AAU
Thr ACA
Thr ACC
.
.
Phe UUU
5’
3’
Slide30The same protein can be encoded in many ways…
amino acid sequence: M
P
KSNFRFGE
ATG
ATG
CCT
ATG
CCC
ATG
CCA
ATG
CCG
most efficient
least efficient
intermediate efficiency
intermediate efficiency
relative concentration of tRNA in the
cell
1
0
5
0
Slide31Scoring coding sequences for efficiency in translation
ATC
CCA
AAA
TCG
AAT
coding sequence translation efficiency score
( (geometric) average of all tRNA gene copy numbers)
…
…
…
…
Efficient
intermediate
non-efficient
10
10
7
2
6
tRNA
Gene copies
(
dos Reis et al.
Nucleic Acids Res
, 2004)
Slide32
W
i
/W
max
if
W
i
0
w
i
=
w
mean
else
{
dos Reis et al.
NAR
2004
The tRNA Adaptation Index (tAI)
ATC
CCA
AAA
TCG
AAT
…
…
…
A simple model for translation efficiency
Wobble Interaction
Slide33Correlation of tAI with experimentally determined protein levels
r=0.63
Predicted translation efficiency
Measured protein abundance
(Ghaemmaghami et al.
Nature 2003)
Physiological
Slide34The correlation is quite high, but why not even higher?
The limitations of the modeltRNA gene copy numbers Model only capture elongationDifference in mRNA levelsProtein are also degraded at different rates
Slide35The effective number of codons (Nc) - a measure of overall synonymous codon usage bias
AA
.
.
.
Gly
Gly
Gly
Gly
.
.
.
codon
.
.
.
GGT
GGC
GGA
GGG...
Codon count
.
..01200..
.
Highly biased synonymous codon usage (Nc=20)
Gene1
AA
.
.
.
Gly
Gly
Gly
Gly
.
.
.
codon
.
.
.
GGT
GGC
GGA
GGG
.
.
.
Codon count
.
.
.
3
3
3
3
.
.
.
No bias in synonymous codon usage (Nc≥61)
Gene2
Wright, F. (1990). "The 'effective number of codons' used in a gene." Gene 87(1): 23-9.
Slide36Codon usage bias is correlated with translation efficiency
r=-0.79 (p<0.001)
Mutation pattern
(neutral)
Selection
Codon bias
Slide37But not in all species
(e.g. A. gossypii)
r=-0.48 (p=0.218)
Mutation pattern
(neutral)
Selection
Codon bias
Slide38S. cerevisiae
S. bayanus
C. glabrata
A. gossypii
D. hansenii
C. albicans
Y. lipolytica
S. pombe
r
-0.79
-0.73
-0.79
-0.48
-0.75
-0.65
-0.84
-0.66
p
<0.001
<0.001
<0.001
0.218
<0.001
0.005
<0.001
<0.001
Translation selection acts in some but not all species
(e.g. debate on human…)
Slide39Correlation does not imply causality!!
r=0.63
Predicted translation efficiency
Measured protein abundance
(Ghaemmaghami et al.
Nature 2003)
Physiological
Evolutionary
Physiological
Z
A genome-wide perspective on translation of proteins
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