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Molecular Basis of Coronavirus Virulence and Vaccine Design
1. MOLECULAR BASIS OF CORONAVIRUS
VIRULENCE AND VACCINE DESIGN TO
PROTECT AGAINST SARS
XRB. UNIVERSIDAD DE BARCELONA
13 JULIO 2012
LUIS ENJUANES
CNB-CSIC. MADRID
3. CORONAVIRUS INDUCED DISEASES
MAN
CENTRAL NERVOUS
SYSTEM
ANIMALS
EYE
UPPER AND LOWER AS IN HUMANS &
RESPIRATORY TRACT PERITONITIS
IMMUNE SYSTEM CELLS
HEPATITIS
NEPHRITIS
GASTROINTESTINAL CARDIOMIOPATHY
TRACT
5. MUTATION OF CORONAVIRUS EXON MOTIFS
MHV REP 1a REP 1b nsp14 CPD HE S 4a 4b 5a E M N An
I
C1 D89 E91 ZN F D242 D272 Q521
YEAST
MUT 1
..
AIDAEFV-103-
Zn F
.MUT 2.
VFVGHGLNNDFK-44-HDSIEDAHTAL
MHV-A59 GFDAEGA-111-VVCSVCTK-11-YGCWRHS-3-DYLYNPLIVDIQ-23-HVASSDAIMTR
SARS-CoV GFDVEGC-111-RTCCLCDK-11-YACWNHS-3-DYVYNPFMIDVQ-23-HVASCDAIMTR
HCoV-229E GMDVEGA-111-KHCQ-CGT-11-YCCFKHA-3-DYVYNPYVIDIQ-23-HVASGDAIMTR
TGEV GFDVEGA-111-QKCE-CGK-11-YACFKHA-3-DYLYNPYCIDIQ-23-HVASGDAIMTR
IBV GFDVEAT-111-QVCS-CGS-11-YACWKHC-3-DFVYNPLLVDIQ-23-HVASVDAIMTR
Eckerle et al., 2007, 2010
6. DISTRIBUTION OF MUTATIONS AFTER PASSAGE
MHV REP 1a REP 1b nsp14 CPD HE S 4a 4b 5a E M N An
I
WT p5 c1
c2
p17 c1
MUT 1 p1
c1
p5
c2
p17 c1
MUT 2 p1
c1
p5
c2
p17 c2
Eckerle et al., 2007
7. CORONAVIRUS STRUCTURE AND GENE
EXPRESSION
3b
ORF 1a ORF 1b S 3a E M N 7 UTR
+ CAP AAA
mRNA
+ AAA
- UUU
G
+ AAA
- UUU S
+ AAA
- UUU 3a
+ AAA
- UUU 3b
+ AAA
- UUU E
+ AAA
- UUU M
+ AAA
- UUU N
+ AAA
- UUU 7
8. TRANSCRIPTION MECHANISM
TEMPLATE SWITCH
A HIGH FREQUENCY RECOMBINATION
ENGINEERED AN INFECTIOUS cDNA CLONE
9. REGULATION OF sgmRNA LEVELS
TRS-L TRS-B
gRNA 5β L CS-L CS-B An 3β
5β An 3β + MULTIFACTOR REGULATION
1. TRS RNA STRUCTURE
3β cL cCS-B Un 5β -
2. TRS PRIMARY SEQUENCE
cTRS-B
3. LONG DISTANCE INTERACTIONS
4. PROTEIN-RNA BINDING
5β cCS-B 3β mRNA
.....................
13. WT AND MUTANTS TRS-L STRUCTURES
U A U U A
U A U A U A C C A C
C C C A A A A
A A U A A A A A A A
C A A A A A A
A A A A A A A
A G C C G C
G C G C G C G
A A A G G
A C G
C G G C C G C G A A
A
U A A U U A
U A C G C G C A
C A A A C A A C A U A
C G A
A A C A A A U A U
A A A U A
U A U U A
A A U A C A U A U
A A A A U
C A C
U C U C U C U C G C G
U
C U C U C C U C G
U A U C G
A U A U A U
A U C G A U A U
C G C G C G U
C G A U C G
A U A U C G
A U A U A U
G C A U
G C G C G C
G C G U G C
G U G U G C
G U G U G U
G U
WT MS2 IL1 MS1 MS3 IL3 IL2
14. CONCLUSION
THE EXTENT OF sg mRNA SYNTHESIS:
CORRELATES WITH TRS-L STABILITY
WITH THE AVAILABILITY OF TRS-L
REQUIRES A SPECIFIC SECONDARY
STRUCTURE
15. TRANSCRIPTION MECHANISM
TEMPLATE SWITCH
A HIGH FREQUENCY RECOMBINATION
ENGINEERED AN INFECTIOUS cDNA CLONE
18. REQUIREMENT OF COMPLEMENTARITY BETWEEN
CS-L AND cCS-B FOR sgmRNA SYNTHESIS
CS-B MUTANTS CS-L MUTANTS
TITER* TITER*
5β C U A A A C 3β 5β C U A A A C 3β
B-C1G G 8x108 L-C1G G -
B-U2G G 1x107 L-U2G G -
B-A3C C 5x108 L-A3C C -
B-A4C C 6x108 L-A4C C 2x104
B-A5C C 3x108 L-A5C C 4x104
B-C6G G 4x108 L-C6G G 2x103
NON-WATSON-CRICK MUTANTS COMPLEMENTARY MUTANTS
TITER* TITER*
5β C U A A A C 3β 5β G U A A A C 3β
L-C1U U 2x103
D-C1G -
3β C A U U U G 5β
WT 5x108 -
L-A3U U 3x103 -
5x104 2x105
L-A4U U
L-A5U U 2x104 5β C U A A A G 3β 4x105
D-C6G
L-C6U U 1x108 3β G A U U U C 5β 2x10
3
* pfu/ml
19. MAIN CONCLUSION
Ξ
BASE-PAIRING (ΞG) IS A DRIVING FORCE
IN CoV TRANSCRIPTION
22. mRNA LEVELS AND BASE-PAIRING SCORE
110
90 BASE-PAIRING
RELATIVE UNITS
70
50
30
mRNA
10
S 3a E M N 7
mRNA
23. REGULATION OF sg mRNA-N LEVELS
TRS-L TRS-N
N-GENE
gRNA 5β L CS-L dE pE CS-N An 3β
460nt 7nt
5β
3β cL TAATGTATA
ATTACATAT An 3β +
cCS-N Un 5β -
cTRS-N
29. REQUIREMENT OF LONG DISTANCE INTERACTION
TRM
MUTANT AD dE pE CS-N N
REP-1
TRS-N
AD
AD-TRS-N
TRMopt
TRMopt-N
0 5 10 15
REP-1
TRS-N
AD-TRS-N
TRMopt-N
sgmRNA-N/gRNA
31. ACTIVE DOMAIN REGIONS REQUIREMENT
A 25
sgmRNA-N, RELATIVE UNITS
20
B 15
10
5
C
0 +
- ΞA ΞB ΞC
32. ACTIVE DOMAIN REGION C REQUIREMENT
ΞA ΞA-Cβ
25
sgmRNA-N, RELATIVE UNITS
B
20
15
10
C 5
0
ΞA ΞA-Cβ Ξ[A-B]
33. ACTIVE DOMAIN REGION B REQUIREMENT
βA βA-B*2r βA-B*1r βA-B*1r4 βA-B*1r3
B
25
sgmRNA-N, RELATIVE UNITS
20
15
10
5
0
βA βA-B*2r βA-B*1r βA-B*2r4 βA-B*1r3 (-)
34. INTRAGENOMIC RNA-RNA INTERACTIONS
INVOLVING B RNA MOTIF
cB-M B-M cB-M B-M
nt 218-229 nt 26408 - 26421 nt 477-489 nt 26408 - 26421
βG = -12.9 βG = -12.7
35. TGEV REPLICONS WITH MUTATED B AND cB RNA
MOTIFS
218-229 477-486 26,212-26,221
5β 3β
B dE pE N
wt/B 5β 3β
dE pE N
β
wt/βB 5β 3β
cB-218 dE pE N
* B
cB-218*/B 5β 3β
dE pE N
β
cB-218*/βB 5β * 3β
* B* dE pE N
cB-218*/B* 5β 3β
cB-477
B dE pE N
cB-477*/B 5β * 3β
dE pE N
β
cB-477*/βB 5β * 3β
B* dE pE N
cB-477*/B* 5β * 3β
B* dE pE N
cB-477*/B*-14 5β * 3β
36. sgmRNA N, RELATIVE UNITS
0
5
10
15
20
25
30
35
40
45
5β
w
t/B
w
t/β
B
218
477
cB
-2
18
cB * /B
-2
18
*/β
cB B
-2
18
* /B
*
cB
47
7*
cB /B
B
-4
26,212
77
*/β
cB B
dE
-4
cB 77
-4 */ B
pE
77 *
*/ B
N
*-
14
3β
TRANSCRIPTION AND COMPLEMENTARY LEVELS
38. RELEVANCE OF THE INTERACTION BETWEEN B AND
cB RNA MOTIFS ON sgmRNA AND VIRAL TITERS
39. MECHANISM OF DISCONTINUOUS TRANSCRIPTION
AD
cB-M
B-M
TRS-L
dE pE CS-N
5β(+) 3β(+)
pE CS-N
3β(+)
5β(-)
dE cCS-N
5β(+)
CS-L
B-M
cB-M
AD
cB-M
CS-L
5β(+)
40. CoV TRANSCRIPTION IS REGULATED
AT THREE LEVELS
TRS-L STABILITY AND SECONDARY STRUCTURE
COMPLEMENTARITY BETWEEN NASCENT
MINUS RNAs AND TRS-L
LONG DISTANCE RNA-RNA INTERACTIONS
41. TRM ACTIVITY WITHIN INFECTIOUS
VIRUSES
ORF 1a ORF 1b S 3a 3b E M N 7
wt-TGEV N N A
dE pE
0 2 4 6
CS
TRS-3a
AD dE pE CS
TRMopt-3a
TRMopt*-3a
TRMopt-19-3a
sgmRNA-3a/gRNA
45. SPREADING OF SARS
β¦JULY 5th, 03 END EPIDEMY BY WHO
NOV 02 JAN 03 FEB 03 DEC03 to JAN04
FOSHAN GUANGZHOU HONG KONG
FOUR LABORATORY CASES
Dr. A VIETNAM
CANADA FOUR NON-LABORATORY
MOST FIRST Nephro- ISOLATED CASES
SINGAPORE
RECENT MAJOR logist USA
COMMON OUTBREAK TWO ADDDITIONAL
ANCESTOR HOSPITAL HOTEL M SSE IN HK Beijin Apr F 26y, BSL-4
(>100 CONTACTS) Beijin Apr M 44y, BSL-4
48. ENGINEERING OF A SARS-CoV INFECTIOUS
cDNA CLONE AS A BAC
T by C T by A
10338 11163
8a
L 3b M 7a 8b 9b
CMV REP 1a REP 1b S 3a E 6 7b N
An
pBAC-SARS-CoV-URB*
49. BASIS OF SARS-CoV VIRULENCE
8a
3b M 7a 8b 9b
L REP 1a REP 1b S 3a E 6 7b N
An
DELETED GENE
Structural: E
Accessory: 6, 7a, 7b, 8a, 8b, 9b
Combinations: E, 6, 7a, 7b, 8a, 8b, 9b
60. UNFOLDED PROTEIN RESPONSE
RE CYTOPLASM NUCLEUS
ACTIVATION
IN E VS WT-
Ξ
GRP78 GRP78
PERK eIF2 TRANSLATIONAL INFECTED CELLS
BLOCK
PERK eIF2
P
ATF4
TRANSLATION
ATTENUATION -
CHOP
GRP78
GENE
GRP78
CLEAVED
GRP78
CORRECT
ATF6
ATF6
EXPRESSION
PROTEIN
FOLDING
-
CHOP
GRP78
GRP78 GRP78
XBP1
IRE1 mRNA
IRE1 sXBP1
sXBP1
PROTEIN
DEGRADATION +
p58IPK
mRNA
61. EFFECT OF E PROTEIN ON THE STRESS PRODUCED
Ξ
BY SARS-CoV-ΞE INFECTION
E PROTEIN PROVIDED IN TRANS
12 HSP A1A HSP90 AA1 HSP H1 SERPIN H1 HSP E1 18S
E+
FOLD CHANGE, relative units
10 E-
8
6
4
2
62. SARS-CoV E PROTEIN AND STRESS PRODUCED
BY RSV INFECTION
E PROTEIN PROVIDED IN TRANS
350 7
HSP90 AA1 UBB HSP H1 SERPIN H1 HSP E1 18S
300 6
E+
FOLD CHANGE, relative units
250 5
E-
200
4
150
3
100
2
50
1
2 24 48 2 24 48 2 24 48 2 24 48 2 24 48 2 24 48
TIME POST-INFECTION, hours
63. CONCLUSION
E PROTEIN REDUCED CELLULAR STRESS
INDUCED BY:
SARS-CoV INFECTION
RSV INFECTION
THAPSIGARGIN - Ca++
TUNICAMYCIN - GLYCOSYLATION
65. MOUSE ADAPTED SARS-CoV
SARS-CoV-MA15
High titers in lungs
Viremia, extrapulmonary spread
Neutrophilia
Pathological changes in lungs
Death
K. SUBBARAO AND R. BARIC LABS
66. CONSTRUCTION OF A MOUSE ADAPTED SARS-CoV
8a
3b M 7a 8b 9b
L REP 1a REP 1b S 3a E 6 7b N
An
nsp5 nsp9
10384 12814
nsp13 S (RBD) M
16117 22797 26428
nsp5
10793
ENGINEERED MUTANTS wt
Ξ[6-9b]
ΞE
Ξ[E,6-9b]
67. CONCLUSION
Ξ
SARS-CoV-MA15-ΞE IS ATTENUATED AND
FULLY
PROTECTS BOTH YOUNG AND OLD MICE
THEREFORE IT IS A PROMISING VACCINE
Ξ
CANDIDATE, BETTER THAN SARS-CoV-ΞE
68. CNB. CSIC. MADRID COLLABORATORS
REPLICATION PROTEOMICS
FERNANDO ALMAZAN SILVIA JUAREZ. CNB-CSIC
AITOR NOGALES ALEXANDER AKOULICHEV. OXFORD
SILVIA MARQUEZ
GENOMICS
TRANSCRIPTION AND ASSEMBLY IRENE LOPEZ-VIDRIERO
ISABEL SOLA MARTA GODOY
PEDRO A. MATEOS JUAN CARLOS OLIVEROS
SONIA ZUΓIGA
MARTINA BECARES
ANIMAL MODELS
KANTA SUBBARAO. NIH
VIRUS-HOST INTERACTION: SARS
STANLEY PERLMAN. UNIV. IOWA
MARTA L. DeDIEGO
JOSE LUIS NIETO
JOSE MANUEL JIMENEZ ELECTRON MICROSCOPY
JOSE ANGEL REGLA MARIA TERESA REJAS. CBM, CSIC
RAUL FERNANDEZ CRISTINA PATIΓO. CNB. CSIC
CARLOS M. SANCHEZ
SARHAY ROS
LUIS ENJUANES MARGARITA GONZALEZ