Download Class 2 release factors

The origin of novel proteins by gene
duplication: evolution of translation
termination factors
Galina Zhouravleva
Department of Genetics
St. Petersburg State University
Part 1. Mechanism
of translation termination
Main steps in eukaryotic translation
Start codon
5’
Stop codon
UAA
AUG
CAP
3’ UTR
5’ UTR
Initiation
mRNA
3’
AAAAAAA
Elongation
Recycling
Termination
Main steps in eukaryotic translation
Start codon
5’
Stop codon
UAA
AUG
CAP
3’ UTR
5’ UTR
Initiation
mRNA
3’
AAAAAAA
Elongation
Termination
Translation factors:
Prokariota:
IF-1, IF-2, IF-3
Eukaryota: eIF1, eIF1A, eIF2,
eIF2B, eIF3, eIF4A,
eIF4B, eIF4E,
eIF4G, eIF5
EF-Tu, EF-Ts, EF-G
RF1, RF2, RF3
eEF1А, eEF1В, eEF2
eRF1, eRF3
Translation termination in prokaryotes
Stop-codon recognition
Е Р А
Е Р А
RF1 (RF2) + RF3
UGA
RF2 + RF3
UGA
3’
5’
Translation termination factors - RF- factors (Release Factors):
Class 1 release factors
RF1 (essential) – decodes UAA and UAG
RF2 (essential) – decodes UAA and UGA
36% amino
acid identity
Class 2 release factor RF3 - GTPase; promotes RF1/2 release (non-essential)
Translation termination in eukaryotes
Stop-codon recognition
Е Р А
AAA
UUU
Е Р А
eRF1 + eRF3
UGA
AAA
UUU
GTP
UGA
Peptidyl-tRNA hydrolysis
Recycling?
Reinitiation?
Е Р А
AAA
UUU
UGA
3’
GTP hydrolysis
4G
4E
5’
Е Р А
AAA
UUU
GTP
UGA
Class 1 release factor
eRF1 (essential) – UAA, UAG, UGA
Class 2 release factor
eRF3 (essential) - GTPase
(RF1 + RF2)
(RF3)
Part 2. Translation termination factors
Class 1 release factors
Prokaryota
Eukaryota
RF1 - UAA и UAG
eRF1 – UAA, UAG, UGA
Archaea
aRF1 – all 3 stop codons (?)
RF2 - UAA и UGA
No sequence similarity
Homologous (30% of identity)
Class 2 release factors
Prokaryota
RF3
Eukaryota
Archaea
eRF3
Absent
No sequence similarity
The average similarity plot of RF sequences
A-G – conserved
regions
Ito et al., 1996
Comparison of the amino acid sequences
of prokaryotic RFs and EF-G of E.coli
Ito et al., 1996
tRNA-protein mimicry hypothesis
Ito et al., 1996
Phylogenetic tree of aRF1 and eRF1
Mulitcellular
eukaryotes
Inagaki, Doolittle, 2000
Liu, 2005
Phylogenetic tree of eRF3
The phylogenetic tree showing the origin of paralogs
encoding the factors eRF3a and eRF3b in higher eukaryotes
eRF3a
H. sapiens
Duplication
eRF3a
M. musculus
Divergence
eRF3b
H. sapiens
eRF3b
M. musculus
eRF3
lower eukaryotes
Duplication
Difference in the organization of GSPT genes
GSPT1 – 15 introns
GSPT2 – no introns
16 chromosome
H.sapiens
16 chromosome
M.musculus
Х chromosome
Х chromosome
A model of GSPT2 origin by reverse transcription of a
processed GSPT1 transcript and its reintegration
in X-chromosome
GSPT2 (X chromosome)
P2
5’UTR/2
Retroposition
Splicing
P1
P2
5’UTR/2
5’UTR/1
3’UTR
GSPT1 (16 chromosome)
P1, P2 – promoter sequences
eRF3 family
S. cerevisiae
Sup35
N
M
Complementation of
S. cerevisiae
SUP35 disruption
C
(1-685)
+
57%
14%
13%
Amino acid identity between yeast Sup35 and human GSPT1
Human GSPT1
(1-637)
-
Mouse GSPT1
(1-635)
-
Human GSPT2
(1-632)
Mouse GSPT2
(1-632)
+
X. laevis Sup35
(1-573)
-
NT
NT
N-terminal domain of eRF3 is not conserved in evolution
Identity (%)
Protein
with
yeast
Sup35
with
mouse
GSPT1
Q+N
(%)
G+Y
(%)
Yeast proteome
10
8
-
-
ySup35
45
33
100
10
mGSPT1
8
10
10
100
mGSPT2
4
5
7
49
xSup35
18
9
14
11
N-terminal domain of eRF3 is not conserved in evolution
G-stretch
mGSPT1 -----------------MDPGSGGGGGGGGGGSSSSSDSAPDCWDQTDME----------------------------------ccttccccccccccccccccccccccccccccc-----------------mGSPT2 -----------------MDLGS-------------SNDSAPDCWDQVDME----------------------------------eeecc-------------cccccccccceeeec-----------------xSup35 -----------------ITGTTLFPPTWEVLPTLPTPCLTPSAPLIKQLV----------------------------------ecccccccccceecccccccccccccchhheee-----------------ySup35 MSDSNQGNNQQNYQQYSQNGNQQQGNNRYQGYQAYNAQAQPAGGYYQNYQGYSGYQQGGYQQYNPDAG
eccccccccccceeeeccccccccccccccchhhhhhtccccccceecttccttcccttcccccttcc
.
*
:
QN-stretch
Oligopeptide (PQGGYQQ-YN) repeats
mGSPT1 APGPGPCGGG---GSGSGSMAAVAEAQR---ENLSAAFSRQLNVNAKPFVPN--cccccccccc---cccchhhhhhhhhhh---hhhhhhhhhhhcccccccccc--mGSPT2 GPGSAPSGDGIAPAAMAAAEAAEAEAQR---KHLSLAFSSQLNIHAKPFVPS--cccccccccccchhhhhhhhhhhhhhhh---hhhhhhhhhhccccccccccc--xSup35 YPNPTHPEMDASDSAPDSWEQADMEATE---AQLNNSMA-ALNVNAKPFVPN--ccccccccccccccccchhhhhhhhhhh---hhhhhhhh-hhhccccccccc--ySup35 YQQQYNPQGGYQQYNPQGGYQQQFNPQGGRGNYKNFNYNNNLQGYQAGFQPQSQG
ceeecccttccccccttccceeeccccccccceeeecccccccchettccccctt
.
.
:.
.
*:
* *.
Oligopeptide (PQGGYQQ-YN) repeats
Pab1interacting
region
Alpha helix – h, extended strand – e, random coil – c, beta turn - t
SOPM (Self-Optimized Prediction Method) - secondary structure prediction
method (Geourjon and Deleage, 1994) http://npsa-pbil.ibcp.fr/cgi-bin/
Part 3. Prionization
of translation termination factor eRF3 in
yeast
Composition of yeast eRF3 (Sup35)
1
124
N
254
685
M
PFD
C
Translation termination
EF1-A-like domain
6
33
97
PFD
R1 R2 R3 R4 R5 R6
QN
OR
QN: the N-terminal QN-rich stretch.
OR: R1-R6 – oligopeptide repeats of the consensus sequence PQGGYQQ-YN (P –
proline, Q – glutamine, G – glycine, Y – tyrosine, N – asparagine)
Evolutionary comparison of the N-terminal domains of Sup35
proteins from budding and fission yeast
N-domain
QN
Debaryomyces
QN-stretch
Q(%) N(%)
OR
Saccharomyces
Zygosaccharomyces
Yarrowia
Ascomycota
Saccharomycodes
Candida
Schizosaccharomyces
D. hansenii
39
15
(GYQNYNQ)5.5
K. lactis
43
17
(QGYNNAQQ)6
161 P. methanolica
35
30
(NRGGYSNYN)5
P. pastoris
16
22
(QGYQXY)4
S. cerevisiae
37
26
(PQGGYQQ-YN)5.5
Z. rouxii
40
12
(GGYGGY)5
38
9
132
137
Kluyveromyces
Pichia
OR-region
106
123
103
157 Y. lipolytica
(QGGYQGGYQGGY)5
121
S. ludwigii
45
14
(GYQAYQQYNAQPQQQ)4.5
129
C. albicans
52
15
(GGYQQNYN)6.5
144
C. maltosa
39
7
112
S. pombe
No QN-stretch
(GGYQQNYNNR)4.5
No repeats
Evolutionary origin of eRF3
EF-G
eEF-2
Eukarya
aEF-2
Archaea
EF-G
EF-G
RF3
Ancient GTPase
Eubacteria
EF-Tu
aEF-1A
EF-Tu
Archaea
eEF-1A
eEF-1A
eRF3
Eukarya
EF – elongation factor, RF- release factor.
(1-465)
Giardia intestinalis Sup35
(1-685)
Saccharomyces cerevisiae Sup35
N
M
C
Part 4. Molecular mimicry:
translation termination factors as tRNA
tRNA-protein mimicry hypothesis
Ito et al., 1996
Molecular Mimicry
EF-Tu
tRNA
tRNA-EF-Tu-GTP
EF-G-GTP
(Ramakrishnan 2002)
Macromolecular mimicry in termination
and ribosome recycling
Human eRF1
E. coli RF2
Yeast tRNAPhe
Part 5. Duplication
in the evolutionary history of translation
elongation and termination factors
A scheme for the evolution of elongation and
release factors in Bacteria, Archaea, and Eukarya.
(Inagaki and Ford, 2000)
The evolutionary origin of translation
termination factors
EF-G
RF3
EF-G
EF - elongation factors
RF – termination (release) factors
eEF-2
RF1
Hbs1
EF
RF2
eRF1
EF-Tu
Hbs1
EF-Tu
eRF3
eEF-1A
Duplication
Divergence
e - eukaryotic