The E-site story: Fundamental aspects of protein-synthesis Knud H. Nierhaus Max-Planck-Institute...
-
date post
20-Dec-2015 -
Category
Documents
-
view
214 -
download
0
Transcript of The E-site story: Fundamental aspects of protein-synthesis Knud H. Nierhaus Max-Planck-Institute...
The E-site story: Fundamental aspects of protein-synthesis
Knud H. Nierhaus Max-Planck-Institute für Molekulare Genetik
Berlin-Dahlem, Germany
Tucson, 14th September 2006
MPI MOLGEN, NH GROUP
The E-site story: New aspects of the protein-synthesis
1.Introduction: Three tRNA binding sitesFunctional elements of the ribosomal elongation The ribosomal working plane of protein synthesis
2. Role of the E site I: molecular recognition and the solution of the ribosomal decoding riddle
3. Role of the E site II:Maintenance of the reading frame
16S RNA
21 proteinsS1 - S21
33 proteinsL1 - L36*
23S RNA 5S RNA
L7 = N-acetylated L12L8 = (L7/L12) L10L26 = S20
4
*
MPI MOLGEN, NH GROUP
[C
]tRN
Abo
u nd
per
70S
1 4P
he
302010
1.0
2.0
3.0
040
tRNA
molar ratio tRNA:70S
plus mRNA
minus mRNA
Rheinberger, Sternbach & Nierhaus, 1980, PNAS 78:5310-5314
Hausner et al., 1988,J. Biol. Chem. 263:13103
MPI MOLGEN, NH GROUP
The ribosomal interface provides a plane area for protein synthesis
MPI MOLGEN, NH GROUP
The ribosomal interface provides a plane area for protein synthesis
MPI MOLGEN, NH GROUP
The ribosomal interface provides a plane area for protein synthesis
MPI MOLGEN, NH GROUP
Fitting of X-ray crystal structure of tRNA
MPI MOLGEN, NH GROUP
Elongation Cycle Movie!
PRE POST
30S
50S
Agrawal et al., 2000, J. Cell Biol. 150:447-459
The Ribosomal Elongation Cycle3. Elongation
Cycle
Zur Anzeige wird der QuickTime™ Dekompressor „Cinepak“
benötigt.
MPI MOLGEN, NH GROUP Agrawal et al., 2000, J. Cell Biol. 150:447-459
MPI MOLGEN, NH GROUP
The E-site story: New aspects of the protein-synthesis machinery
1.Introduction: Three tRNA binding sitesFunctional elements of the ribosomal elongation The ribosomal working plane of protein synthesis
2. Role of the E site I: molecular recognition and the solution of the ribosomal decoding riddle
3. Role of the E site II:Maintenance of the reading frame
Type I I I Type I Type I I
MPI MOLGEN, NH GROUP
Types of molecular recognition
Nierhaus, 1993,Molecular Microbiology 9: 661-669
A U G G U A A AC C U G A C C A A G
P AE
Leu
Lys
Ala
fMet
A U G G U A A AC C U G A C C A A G
P AE
Leu
Lys
Ala
fMet
ThrExplanations: aa–tRNA EF-Tu
Thr Ala Pro Ser Ser
Asn Ile Pro Pro Ser Ser Ala
Asp Cys Gly His Leu Phe Tyr
Val Arg Arg Ile Lys Met Arg
Arg Gln Gln Glu Gly Gly Leu
GTPGTP
GTP GTP GTP GTP GTP GTP GTP
GTP GTP GTP GTP GTP
GTP GTPGTP GTP GTP GTP GTP GTPGTPGTP
GTP GTP GTP GTP GTP GTP GTP
GTP GTP GTP GTP GTP GTP GTP
GTP GTP GTP GTP GTP GTP
Thr Thr
Leu Leu Trp ValLeu Sel-Cys
Nierhaus 74 Fig.2 /12.8.98
MPI MOLGEN, NH GROUP
Nierhaus, 1993,Molecular Microbiology 9: 661-669
E site free and affinity at A sitehigh
cognate(1 species)
near-cognate(2-4 species)
non-cognate(~50 species)
E site occupied and affinity at A sitelow
cognate
near-cognate
non-cognate
G°
cogn
ate
near
-cog
nate
non-
cogn
ate
cogn
ate
near
-cog
nate
non-
cogn
ate
G°,
free
ener
gy o
f A-s
it e bi
ndin
g
contribution bytRNA-mRNAinteraction(codon-anticodon)
contribution bytRNA-ribosomeand Tu-ribosomeinteractions(A-site)
Nierhaus, 1990,Biochemistry, 29:4997
MPI MOLGEN, NH GROUP
U
A C
G
E site free and affinity at A sitehigh
cognate(1 species)
near-cognate(2-4 species)
non-cognate(~50 species)
E site occupied and affinity at A sitelow
cognate
near-cognate
non-cognate
G°
cogn
ate
near
-cog
nate
non-
cogn
ate
cogn
ate
near
-cog
nate
non-
cogn
ate
G°,
free
ener
gy o
f A-s
it e bi
ndin
g
contribution bytRNA-mRNAinteraction(codon-anticodon)
contribution bytRNA-ribosomeand Tu-ribosomeinteractions(A-site)
Nierhaus, 1990,Biochemistry, 29:4997
MPI MOLGEN, NH GROUP
E site free and affinity at A sitehigh
cognate(1 species)
near-cognate(2-4 species)
non-cognate(~50 species)
E site occupied and affinity at A sitelow
cognate
near-cognate
non-cognate
G°
cogn
ate
near
-cog
nate
non-
cogn
ate
cogn
ate
near
-cog
nate
non-
cogn
ate
G°,
free
ener
gy o
f A-s
it e bi
ndin
g
contribution bytRNA-mRNAinteraction(codon-anticodon)
contribution bytRNA-ribosomeand Tu-ribosomeinteractions(A-site)
Nierhaus, 1990,Biochemistry, 29:4997
MPI MOLGEN, NH GROUP
Geigenmüller and Nierhaus., 1990,EMBO J. 9:4527
MPI MOLGEN, NH GROUP
6000
4000
2000
fractions
200
400
600
800
E P A
POST
E P A
Pi
AcPheAsp AcPhe2
dpm [ H] per fraction ( )
3
dpm [ C] per fraction ( )
14
•EF-Tu•GTP
•EF-Tu•GTP+
•EF-Tu•GTP
•EF-Tu•GTP+
dpm
[14
C]P
he p
er f
ract
ion
dpm [
3H] A
sp per f rac tion
MPI MOLGEN, NH GROUP
6000
4000
2000
fractions
200
400
600
800
E P A
POST
E P A
Pi
AcPheAsp AcPhe2
dpm [ H] per fraction ( )
3
dpm [ C] per fraction ( )
14
•EF-Tu•GTP
•EF-Tu•GTP+
•EF-Tu•GTP
•EF-Tu•GTP+
dpm
[14
C]P
he p
er f
ract
ion
dpm [
3H] A
sp per f rac tion
Geigenmüller and Nierhaus., 1990,EMBO J. 9:4527
6000
4000
2000
fractions
200
400
600
800
E P A
POST
E P A
Pi
AcPheAsp AcPhe2
dpm [ H] per fraction ( )
3
dpm [ C] per fraction ( )
14
•EF-Tu•GTP
•EF-Tu•GTP+
•EF-Tu•GTP
•EF-Tu•GTP+
MPI MOLGEN, NH GROUP
dpm
[14
C]P
he p
er f
ract
ion
dpm [
3H] A
sp per f rac tion
Geigenmüller and Nierhaus., 1990,EMBO J. 9:4527
A U G G U A A AC C U G A C C A A G
P AE
Leu
Lys
Ala
fMet
A U G G U A A AC C U G A C C A A G
P AE
Leu
Lys
Ala
fMet
ThrExplanations: aa–tRNA EF-Tu
Thr Ala Pro Ser Ser
Asn Ile Pro Pro Ser Ser Ala
Asp Cys Gly His Leu Phe Tyr
Val Arg Arg Ile Lys Met Arg
Arg Gln Gln Glu Gly Gly Leu
GTPGTP
GTP GTP GTP GTP GTP GTP GTP
GTP GTP GTP GTP GTP
GTP GTPGTP GTP GTP GTP GTP GTPGTPGTP
GTP GTP GTP GTP GTP GTP GTP
GTP GTP GTP GTP GTP GTP GTP
GTP GTP GTP GTP GTP GTP
Thr Thr
Leu Leu Trp ValLeu Sel-Cys
Nierhaus 74 Fig.2 /12.8.98
MPI MOLGEN, NH GROUP
Nierhaus, 1993,Molecular Microbiology 9: 661-669
Zur Anzeige wird der QuickTime™ Dekompressor „TIFF (LZW)“
benötigt.
Valle et al., 2002,EMBO J. 21:3557
MPI MOLGEN, NH GROUP
Conclusions 1: Importance of the E site for the decoding
The tRNA at the E site induces a low A-site affinity. This prevents the interference of non-cognate aa-tRNAs with the selection process. This means that a ribosome selects only one out of ≤4 aa-tRNAS (cognate+mis-cognate) instead of 1 out of ≈40.A mis-incorporation of a non-cognate aa-tRNA would be deleterious for the function of the corresponding protein in contrast to the mis-incorporation of a near-cognate aa-tRNA.Consequence of the E site effect: Selection of a near-cognate aa-tRNA destroys the function of a protein only 1 in 400 mis-incorporations due to the buffering of the codon lexicon.
MPI MOLGEN, NH GROUP
Nierhaus, 1993,Molecular Microbiology 9: 661-669
Ogle et al., 2001,Science 292:897
MPI MOLGEN, NH GROUP
The E-site story: New aspects of the protein-synthesis machinery
1.Introduction: Three tRNA binding sitesFunctional elements of the ribosomal elongation The ribosomal working plane of protein synthesis
2. Role of the E site I: molecular recognition and the solution of the ribosomal decoding riddle
3. Role of the E site II:Maintenance of the reading frame
The importance of frameshift maintenance
5’- UUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCUUCU -3’ 21 22 23 24 25 26
PhePhePhePhePhePhe
26 27 28 29 30 31 32
SerSerSerSerSerSerSer+1 frameshift
MPI MOLGEN, NH GROUP
The mRNA from termination factor RF2
CUUAGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU 5’- -3’ 21 22 23 24 25 26
26 27 28 29 30 31 32
Tyr LeuSTOP
Asp+1 frameshift
MPI MOLGEN, NH GROUP
CUUAGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU 5’- -3’ SD
21 22 23 24 25 26
26 27 28 29 30 31 32
Tyr LeuSTOP
Asp+1 frameshift
The mRNA from termination factor RF2
MPI MOLGEN, NH GROUP
AAACUGGUUCCUUAGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU
E P A
5’- -3’
Tyr Leu
SD
Termination: 25 aa peptide
+1 Frameshifting: Complete RF2 synthesis
A U A G A G
21 22 23 24 25 26
26 27 28 29 30 31 32
mRNA of the termination factor RF2
MPI MOLGEN, NH GROUP
Hypothesis concerning the extensive frameshifting of theRF2 mRNA: 1
MPI MOLGEN, NH GROUP
E P A
5’- -3’ 3‘-U C C U C C A’
Tyr Leu
SD A U A G A G
16S rRNA
ACUGGUUCCUUAGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU
Hypothesis concerning the extensive frameshifting of theRF2 mRNA: 2
MPI MOLGEN, NH GROUP
E P A
5’- -3’
Leu
SD G A G
Tyr
A U A
3‘-U C C U C C A’
16S rRNA
AAACUGGUUCCUUAGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU
Hypothesis concerning the extensive frameshifting of theRF2 mRNA: 3
5’-
MPI MOLGEN, NH GROUP
E P A
-3’ SD
G A G
Leu
C U G
Asp
+1 frameshift
3‘-U C C U C C A’
16S rRNA
AAACUGGUUCCUUAGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU
Models of mRNAS for testing frameshifting of the RF2-mRNA type
mRNA with SD
Oligo(Phe) Arg Met Lys Leu Val Leu Val Leu Arg Gly Tyr Leu Stop GG UUC (UUC)11 CGU AUG AAA CUG GUU CUU GUU CUU AGG GGG UAU CUU UGA CUC UGA UUC AAA AAG GGA U
SD Asp Ser Asp Ser Lys Arg Asp
mRNA without SD Arg Met Lys Leu Val Leu Val Leu Arg Gly Tyr Leu Stop
GG UUC (UUC)11 CGU AUG AAA CUG GUU CUU GUU CUU CGC GGC UAU CUU UGA CUC UGA UUC AAA AAG GGA U
Ac[3H]Pheincorporation Tyr-
[32P]tRNAbinding
[14C]Aspincorporation= frameshift
MPI MOLGEN, NH GROUP
Models of mRNAS for testing frameshifting of the RF2-mRNA type
Márquez et al., 2004, Cell 118:45-55
(UUC)12°°°°°°°°°°°°°°CGCGGCUAUCUUUGACUCUGAUUCAAAAAGGGAU
E P A3’-UCCUCCA
GAG
LeuTyr
AUA
mRNA
-SD
0
0.5
1
Aspincorporated
0.12 0.04
0.67 0.06
Synt
hesi
zed
pept
ide
chai
n (A
c[3 H
]Ph
e in
corp
orat
ion
)
E site tRNA[32P]
Frameshift[14C] Asp
incorporated
MPI MOLGEN, NH GROUP
0.88 0.07
0
0.5
1
tRNATyr
0 0.03
(UUC)12°°°°°°°°°°°°°°AGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU
E P A
3’-UCCUCCA
16S rRNA
SD GAG
Leu
Tyr
AUA
+SD
Márquez et al., 2004, Cell 118:45-55
(UUC)12°°°°°°°°°°°°°°CGCGGCUAUCUUUGACUCUGAUUCAAAAAGGGAU
E P A3’-UCCUCCA
GAG
LeuTyr
AUA
mRNA
-SD
(UUC)12°°°°°°°°°°°°°°AGGGGGUAUCUUUGACUCUGAUUCAAAAAGGGAU
E P A
16S rRNA
SD GAG
Leu
CUG
Asp
Tyr
AUA
+SD
0
0.5
1
0
0.5
1
tRNATyr Aspincorporated
0.88 0.07
0 0.03
0.12 0.04
0.67 0.06
Synt
hesi
zed
pept
ide
chai
n (A
c[3 H
]Ph
e in
corp
orat
ion
)
E site tRNA[32P]
Frameshift[14C] Asp
incorporated
MPI MOLGEN, NH GROUP
3’-UCCUCCA
Márquez et al., 2004, Cell 118:45-55
CUU GUU CUU AGG GGG UAU CUU UGA CUC 70 E P
SDCUU GUU CAG GGG GUA UAU CUU UGA CUC 0 E P
SDCUU AGG GGG UGU GUA UAU CUU UGA CUC 0 E P
no SDCUU GUU CUU CGC GGC UAU CUU UGA CUC 6 E P
mRNAsFrameshift ratio
Asp incorp./ act. Ribosome%
SD StopTyr Leu
Shifting SD sequence upstream away from frameshifting site
Márquez et al., 2004, Cell 118:45-55
Release of E-tRNA
Cause or Consequence?
gggaaaacaaaacaaaac- UAC-CUU-UGAC-aaaacaaaacaaaac
Tyr Leu Stop
YL stop mRNA
Asp
UAC C UUU GAC
E P AE site free
Fraction number
0 5 10 15 20 25 30 35 400
5
10
15
20
25
0
5
10
15
20
25
N-Ac[3H]Leu
[14C]Asp
(14 pmol)
N-Ac[3H]Leu-[14C]Asp
(38 pmol)
[14C
]Asp
[pm
ol]A
c[3 H
]Ph
e [p
mol
]
UAC CUU UGA C
E P A
?
+ GTP
GDP
?
Márquez et al., 2004, Cell 118:45-55
UAC CUU UGA CE P A
?
E site occupied
GTP+
Márquez et al., 2004, Cell 118:45-55
? UAC CUU U GAC
E P A
0 5 10 15 20 25 30 35 400
2
4
6
8
10
12
0
2
4
6
8
10
12
Fraction number
N-Ac[3H]Leu[14C]Asp
[14C
]Asp
[pm
ol]A
c[3 H
]Ph
e [p
mol
]
Conclusions 2: Importance of the E site for maintenance of the reading frame
The tRNA at the E site has to be removed in order to allow highly efficient frameshifting. The short spacer to the SD interaction blocks the –1 frameshift and probably fosters the +1 direction.Consequence: A tRNA at the E site and probably codon-anticodon interaction at the E site prevents mRNA slippage thus maintaining the reading frame.
Max-Planck-Institut für Molekulare Genetik,Berlin, Germany
Peter WurmbachHans-Jörg RheinbergerUte GeigenmüllerViter MarquezDaniel WilsonNils Burkhardt
Wadsworth Center, NY State Dept. of Health Albany, New York, USA
Joachim FrankRajendra AgrawalChristian SpahnMikel Valle
Pgggaaaacaaaacaaaac- UAC-UUC-UGAC-aaaacaaaacaaaac
Tyr Phe Stop
YF stop mRNAAsp
UAC UUC UGA C
E P A+ GTP UAC UUC U GAC
E P A
GDP
Fraction number
0 5 10 15 20 25 30 35 400
2
4
6
8
10
12
14
16
18
0
2
4
6
8
10
12
14
16
18N-Ac[3H]Phe
[14C]Asp
N-Ac[3H]Phe-[14C]Asp
E site free
Ac[
3 H]P
he
[pm
ol] [
14C]A
sp [p
mol]
ribosmal e
longation cycle
E P Aε δα
E P Aε α/δ
E P A
Tu•GTP
ε δα
POST
POST
PRE
PRE
E P Aε δα
E P Aε α/δ
TRANSLOC
ATION
TRAN
SFER
DECODING
•G GTP
• G GDP + Pi
•Tu GDP+Pi
Tu•GTPPOST
PRE POST
PRE
Dabrowski et al., 1998,J. Biol. Chem. 273:32793
RibosomalElongationCycle
MPI MOLGEN, NH GROUP