The origin of novel proteins by gene duplication: evolution of translation termination factors

1
The origin of novel proteins by gene duplication
evolution of translation termination factors
Galina Zhouravleva
Department of Genetics St. Petersburg State
University
2
Part 1. Mechanism of translation termination
3
Main steps in eukaryotic translation
Start codon
Stop codon
5
mRNA
3
UAA
AUG
CAP
AAAAAAA
3 UTR
5 UTR
Initiation
Elongation
Termination
Recycling
4
Main steps in eukaryotic translation
Start codon
Stop codon
5
mRNA
3
UAA
AUG
CAP
AAAAAAA
3 UTR
5 UTR
Initiation
Elongation
Termination
5
Translation termination in prokaryotes
Stop-codon recognition
? ? ?
? ? ?
RF1 (RF2) RF3
RF2 RF3
UGA
UGA
5
3
Translation termination factors - RF- factors
(Release Factors)
RF1 (essential) decodes UAA and UAG
36 amino acid identity
Class 1 release factors
RF2 (essential) decodes UAA and UGA
Class 2 release factor
RF3 - GTPase promotes RF1/2 release
(non-essential)
6
Translation termination in eukaryotes
Class 1 release factor
eRF1 (essential) UAA, UAG, UGA
(RF1 RF2)
Class 2 release factor
eRF3 (essential) - GTPase
(RF3)
7
Part 2. Translation termination factors
8
Class 1 release factors
Prokaryota
RF1 - UAA ? UAG
RF2 - UAA ? UGA
Homologous (30 of identity)
No sequence similarity
Class 2 release factors
Prokaryota
Archaea
RF3
Absent
No sequence similarity
9
The average similarity plot of RF sequences
A-G conserved regions
Ito et al., 1996
10
Comparison of the amino acid sequences of
prokaryotic RFs and EF-G of E.coli
Ito et al., 1996
11
tRNA-protein mimicry hypothesis
Ito et al., 1996
12
Phylogenetic tree of aRF1 and eRF1
Mulitcellular eukaryotes
Liu, 2005
Inagaki, Doolittle, 2000
13
Phylogenetic tree of eRF3
14
The phylogenetic tree showing the origin of
paralogs encoding the factors eRF3a and eRF3b in
higher eukaryotes
15
Difference in the organization of GSPT genes
GSPT1 15 introns
GSPT2 no introns
H.sapiens
? chromosome
16 chromosome
? chromosome
16 chromosome
M.musculus
16
A model of GSPT2 origin by reverse transcription
of a processed GSPT1 transcript and its
reintegration in X-chromosome
GSPT2 (X chromosome)
P2
5UTR/2
Retroposition
Splicing
P1
P2
5UTR/2
3UTR
5UTR/1
GSPT1 (16 chromosome)
P1, P2 promoter sequences
17
eRF3 family
Complementation of S. cerevisiae SUP35
disruption
N
M
C
S. cerevisiae Sup35
(1-685)
- - NT -
57
14
13
Amino acid identity between yeast Sup35 and human
GSPT1
(1-637)
Human GSPT1
(1-635)
Mouse GSPT1
Human GSPT2
NT
(1-632)
(1-632)
Mouse GSPT2
X. laevis Sup35
(1-573)
18
N-terminal domain of eRF3 is not conserved in
evolution
Identity ()
with yeast Sup35
with mouse GSPT1
Protein Yeast proteome ySup35 mGSPT1 mGSPT2
xSup35
GY () 8 33 10 5 9
QN () 10 45 8 4 18
- 100 10 7 14
- 10 100 49 11
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N-terminal domain of eRF3 is not conserved in
evolution
G-stretch
mGSPT1 -----------------MDPGSGGGGGGGGGGSSSSSDSAPDC
WDQTDME------------------
-----------------ccttccccccccccccccccccccccccccccc
------------------ mGSPT2 -----------------MDLGS--
-----------SNDSAPDCWDQVDME------------------
-----------------eeecc-------------cccccccccceee
ec------------------ xSup35 -----------------ITGTT
LFPPTWEVLPTLPTPCLTPSAPLIKQLV------------------
-----------------ecccccccccceecccccccccccccchh
heee------------------ ySup35 MSDSNQGNNQQNYQQYSQNG
NQQQGNNRYQGYQAYNAQAQPAGGYYQNYQGYSGYQQGGYQQYNPDAG
eccccccccccceeeeccccccccccccccchhhhhhtcccccc
ceecttccttcccttcccccttcc
. mGSPT1
APGPGPCGGG---GSGSGSMAAVAEAQR---ENLSAAFSRQLNVNAKPFV
PN--- cccccccccc---cccchhhhhhhhhhh---hhhhhh
hhhhhcccccccccc--- mGSPT2 GPGSAPSGDGIAPAAMAAAEAAEA
EAQR---KHLSLAFSSQLNIHAKPFVPS---
cccccccccccchhhhhhhhhhhhhhhh---hhhhhhhhhhccccccccc
cc--- xSup35 YPNPTHPEMDASDSAPDSWEQADMEATE---AQLNNS
MA-ALNVNAKPFVPN--- ccccccccccccccccchhhhhhh
hhhh---hhhhhhhh-hhhccccccccc--- ySup35
YQQQYNPQGGYQQYNPQGGYQQQFNPQGGRGNYKNFNYNNNLQGYQAGFQ
PQSQG ceeecccttccccccttccceeeccccccccceeeec
ccccccchettccccctt . .
. . .
QN-stretch
Oligopeptide (PQGGYQQ-YN) repeats
Pab1- interacting region
Oligopeptide (PQGGYQQ-YN) repeats
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/
20
Part 3. Prionization of translation termination
factor eRF3 in yeast
21
Composition of yeast eRF3 (Sup35)
1
254
685
124
C
M
N
PFD
Translation termination
EF1-A-like domain
6
33
97
PFD
R4
R6
R5
R1
R2
R3
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)
22
Evolutionary comparison of the N-terminal domains
of Sup35 proteins from budding and fission yeast
N-domain
QN-stretch
OR-region
Q()
N()
QN OR
132
D. hansenii
(GYQNYNQ)5.5

• 39 15
• 43 17
• 35 30
• 16 22
• 26
• 12
• 38 9
• 45 14
• 15
• 39 7

Debaryomyces
137
K. lactis
(QGYNNAQQ)6
Kluyveromyces
P. methanolica
(NRGGYSNYN)5
161
Pichia
106
P. pastoris
(QGYQXY)4
S. cerevisiae
123
(PQGGYQQ-YN)5.5
Saccharomyces
Z. rouxii
103
(GGYGGY)5
Zygosaccharomyces
Y. lipolytica
157
(QGGYQGGYQGGY)5
Yarrowia
Ascomycota
S. ludwigii
(GYQAYQQYNAQPQQQ)4.5
121
Saccharomycodes
C. albicans
(GGYQQNYN)6.5
129
Candida
C. maltosa
144
(GGYQQNYNNR)4.5
Schizosaccharomyces
No repeats
No QN-stretch
S. pombe
112
23
Evolutionary origin of eRF3
Eukarya
eEF-2
Archaea
aEF-2
EF-G
EF-G
EF-G
RF3
Ancient GTPase
Eubacteria
EF-Tu
Archaea
aEF-1A
EF-Tu
eEF-1A
Eukarya
eEF-1A
eRF3
EF elongation factor, RF- release factor.
(1-465)
Giardia intestinalis Sup35
(1-685)
Saccharomyces cerevisiae Sup35
N
M
C
24
Part 4. Molecular mimicry translation
termination factors as tRNA
25
tRNA-protein mimicry hypothesis
Ito et al., 1996
26
Molecular Mimicry
EF-Tu
tRNA
tRNA-EF-Tu-GTP
EF-G-GTP
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(No Transcript)
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(Ramakrishnan 2002)
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Macromolecular mimicry in termination and
ribosome recycling
Human eRF1
Yeast tRNAPhe
E. coli RF2
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Part 5. Duplication in the evolutionary history
of translation elongation and termination factors
31
A scheme for the evolution of elongation and
release factors in Bacteria, Archaea, and
Eukarya.
(Inagaki and Ford, 2000)
32
The evolutionary origin of translation
termination factors
EF - elongation factors
EF-G
RF3
RF termination (release) factors
EF-G
eEF-2
Hbs1
RF1
EF
RF2
eRF1
Duplication
EF-Tu
Divergence
Hbs1
e - eukaryotic
EF-Tu
eRF3
eEF-1A