1) The document describes a study using small angle neutron scattering (SANS) and molecular modeling to investigate the self-assembly and catalytic activity of a hammerhead ribozyme (HHR) from the pathogenic avocado sunblotch viroid (-) strand (ASBVd(-)). 2) The HHR was found to dimerize, with modeling revealing tertiary contacts between two HHR monomers that agree well with SANS data. Dimerization enhances the catalytic activity of the HHR. 3) Molecular dynamics simulations explored the influence of temperature on HHR monomer and dimer stability, finding decreased stability at higher temperatures due to disruption of tertiary interactions.

1. Self-Assembly
& Catalysis by HHR
from ASBVd(-)
A combined
SANS & Modeling
Study
G
G
A A
G
A
G
A
U
U
G
A
A
G
A
C
G
A
G
U
G
A
A
C
UAA
U
U
U
U
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U
U A A
U
A
A
A
A
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A
C
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A A
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G G A A A G
U C
G G A A
C A
G A C C U G G U
U U C
G U C
A A A
C A A
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G U U U A
A
U
C A
U
A
U C C U C
A
C U U C U U G U U
C
U
A A U
A
A
A C A A G
A
U
UUUGU
A
AAA
A
AACAAUGAAG
AUA
GAGGA
A
UAAAC
C
UUG
CGA
GAC
UC
AUCAGUGUU
C
UUCC
CAU
CUUUCC
C
U
GAA
G
A
GAC
GAA
GUG
A
UC
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210220230
240
249
79-nt
249-nt
HHRz
1

2. Outline
• What are viroids (ASBVd)?
• What role for ribozymes (HHR) in ASBVd ?
• HHR catalysis ?
• Self-association and Catalysis ?
2

3. Viroids: Replication
Rz: hammerhead ribozyme
Flores et al., Viruses, 20093

4. Viroids: 2D Structures
Vol. 20, No. 1, 2007
. 1. Secondary structures of representative viroids from the two viroid families, Avsunviroidae: Avocado sunblotch viroid (ASBVd) and Peach latent mo
id (PLMVd), and Pospiviroidae: Potato spindle tuber viroid (PSTVd). The transcription initiation sites on the viroid genomic RNAs are indicated. Note
ASBVd and PSTVd, these sites are mapped to terminal loops. The transcription initiation site for the (–)-PSTVd RNA template remains to be determined.
MVd, the dashed lines indicate kissing-loop interactions. For PSTVd, the five structural domains (Keese et al. 1985) are indicated. TL = left-terminal dom
central domain, and TR = right-terminal domain. HPII′ and HPII indicate nucleotide sequences that base pair to form the metastable hairpin II structure.
Ding & Itaya, Mol Plant Microbe Interact, 2007.
Pospiviroids
Avsunviroids
4

5. ASBVd: 2D Structures
esolving these issues is of great interest to broaden
wledge of the molecular processes in these organelles
rther our understanding of the molecular basis for the
of infectious RNAs.
zyme machinery for transcription. The DNA-depend-
polymerase II (Pol II) is generally accepted to be in-
the transcription of members of Pospiviroidae. Three
plate in vitro (Rackwitz et al. 1981). Second, α-amaniti
the replication of PSTVd (Mühlbach and Säng
Schindler and Mühlbach 1992), Cucumber pale fr
(Mühlbach and Sanger 1979), Hop stunt viroid
(Yoshikawa and Takahashi 1986), and CEVd (Flor
Flores and Semancik 1982; Rivera-Bustamante and S
1989; Semancik and Harper 1984). Low concentrati
Ding & Itaya, Mol Plant Microbe Interact, 2007.
5

6. ASBVd(-): 2D Structures
A
G
G
A A
G
A
G
A
U
U
G
A
A
G
A
C
G
A
G
U
G
A
A
C
UAA
U
U
U
U
U
U
U A A
U
A
A
A
A
G
U
U
C
A
C C
A
C
G
A
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U
C
C
U
C
C
U
U
C
U
C
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C A C
A A
G U C
G
A
A A
C
U
C A
G
A
G
U
C
G G A A A G
U C
G G A A
C A
G A C C U G G U
U U C
G U C
A A A
C A A
A
G U U U A
A
U
C A
U
A
U C C U C
A
C U U C U U G U U
C
U
A A U
A
A
A C A A G
A
U
UUUGU
A
AAA
A
AACAAUGAAG
AUA
GAGGA
A
UAAAC
C
UUG
CGA
GAC
UC
AUCAGUGUU
C
UUCC
CAU
CUUUCC
C
U
GAA
G
A
GAC
GAA
GUG
A
UC
1
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210220230240
249
G G A A G A G A U U G A A G A C G A G U G A A C U A A U U U U U U U A A U A A A A G U U C A C C A C G A C U C C U C C U U C U C U C A C A A G U C G A A A C U C A G A G U C G G A A A G U C G G A A C A G A C C U G G U U U C G U C A A A C A A A G U U U A A U C A U A U C C U C A C U U C U U G U U C U A A U A A A C A A G A U U U U G U A A A A A A A C A A U G A A G A U A G A G G A A U A A A C C U U G C G A G A C U C A U C A G U G U U C U U C C C A U C U U U C C C U G A A G A G A C G A A G
1a 10a 20a 30a 40a 50a 60a 70a 80a 90a 100a 110a 120a 130a 140a 150a 160a 170a 180a 190a 200a 210a 220a 230a 240a
monomer 1
Rz
gguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
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c a
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u c
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c a
g a c c
u
g g u
u
u
c
g
u
c
1
10
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60
70
79
intra-molecular base-pairs
tertiary or inter-molecular contacts
nucleotide in tertiary contact
cleavage site
Rz
5'
3'
5' 3'
(-)
Leclerc et al., Sci. Rep., 2016.
(-)
3bps
(+)
2bps
Hammerhead (HHR)
6
Flores et al., Adv, Virus Res., 2000.

7. p
F
l
r
e
s
o
t
d
d
p
e
t
l
h
t
FIGURE 7. A folding scheme for the hammerhead ribozyme. Schematic to show the two-stage
folding scheme previously proposed for the hammerhead ribozyme. State U exists in the
absence of added metal ions, in which the three helical arms extend from an open central core.
Penedo et al.
Cold Son November 10, 2016 - Published byrnajournal.cshlp.orgDownloaded from
Penedo et al., RNA, 2004.
7
Loop-Loop interactions in
HHR folding

8. Minimum HHR, Tertiary
Contact and Catalysis
45-nt
O’Rourke et al., JMB, 2015 8

9. HHR morphing
O’Rourke et al., JMB, 2015
9

10. HHR morphing
O’Rourke et al., JMB, 2015
9

11. HHR: Active Conformation
and Metal Ions
66-nt Insert Table of Contents artwork here
Page 5 of 9 Biochemistry
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39
Mir et al., Biochem., 201510

12. HHR: Metal Ions and
Catalysis
Mir & Golden, Biochem., 201511Leclerc, Molecules, 2010

13. ASBVd(-)/HHR(-): SANS
StudyASBVd(-) HHR(-)
Leclerc et al., Sci. Rep., 2016.12

14. HHR(-) dimerization/
catalysis
13 Leclerc et al., Sci. Rep., 2016.

15. HHR(-): 2D structures
monomer 1 monomeHI HII HIII
A
E
E
Egguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
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g
a
a a
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c a
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g g a a a g
u c
g g a a
c a
g a c c
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g g u
u
u
c
g
u
c
1
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79
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c
1a 10a 20a 30a 40a 50a 60a 70a 79a 1b
monomer 1 monomer 2HI HII HIII
A
B
Emonomer
(10ºC) = -26.9 kcal/mol
Emonomer
(25ºC) = -19.4 kcal/mol
Emonomer
(45ºC) = -9.6 kcal/molgguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
a a
c
u
c a
g
a
g
u
c
g g a a a g
u c
g g a a
c a
g a c c
u
g g u
u
u
c
g
u
c
1
10
20
30
40
50
60
70
79
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a
1a 10a 20a 30a 40a 50a 60a 70a 79a 10b 20b 30b1b
monomer 1 monomer 2HI HII HIII
A
Emonomer
(10ºC) = -26.9 kcal/mol
Emonomer
(25ºC) = -19.4 kcal/mol
Emonomer
(45ºC) = -9.6 kcal/molgguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
a a
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c a
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a
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g g a a a g
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g g a a
c a
g a c c
u
g g u
u
u
c
g
u
c
1
10
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30
40
50
60
70
79
intra-molecular base-pairs
tertiary or inter-molecular contacts
nucleotide in tertiary contact
cleavage site
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c
1a 10a 20a 30a 40a 50a 60a 70a 79a 10b 20b 30b 40b 50b 60b 70b 79b1b
14

16. 3D Modeling of HHR(-)
15

17. Modeling/SANS
dexp = 96.0Å
dcalc = 96.7Å
Rg
exp = 31Å
Rg
*calc = 31 (26)Å
16

18. HHR (-): dimerization
monomer 1 monomer 2HI HII HIII
A
B
Eint
(10ºC) = -9.3 kcal/mol
Eint
(25ºC) = -8.5 kcal/mol
Eint
(45ºC) = -5.8 kcal/mol
Edimer
(10ºC) = -47.1 kcal/mol
Edimer
(25ºC) = -33.6 kcal/mol
Edimer
(45ºC) = -15.7 kcal/mol
Emonomer
(10ºC) = -26.9 kcal/mol
Emonomer
(25ºC) = -19.4 kcal/mol
Emonomer
(45ºC) = -9.6 kcal/molgguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
a a
c
u
c a
g
a
g
u
c
g g a a a g
u c
g g a a
c a
g a c c
u
g g u
u
u
c
g
u
c
1
10
20
30
40
50
60
70
79
gguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
a a
c
u
c a
g
a
g
u
c
g g a a a g
u c
g g a a
c a
g a c c
u
g
g
u
u u c g
u
c
g g u u
c u u c c
c
a u
c u u u c c
c
u
g
a
a
g a g a
c
g
a
a
g
c
a
a
g
u
c
gaaa
c
u
ca
g
a
g
u
c
ggaaag
uc
ggaa
ca
gacc
u
g
g
u
u
ucgu
c
1a
10a
20a
30a
40a
50a
60a 70a
79a
10b
20b
30b
40b
50b
60b
70b
79b
1b
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c
1a 10a 20a 30a 40a 50a 60a 70a 79a 10b 20b 30b 40b 50b 60b 70b 79b1b
monomer 1 monomer 2HI HII HIII
intra-molecular base-pairs
tertiary or inter-molecular contacts
nucleotide in tertiary contact
cleavage site
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c
1a 10a 20a 30a 40a 50a 60a 70a 79a 10b 20b 30b 40b 50b 60b 70b 79b1b
17

19. HHR (-): dimerizationmonomer 1 monomer 2HI HII HIII
B
Eint
(10ºC) = -9.3 kcal/mol
Eint
(25ºC) = -8.5 kcal/mol
Eint
(45ºC) = -5.8 kcal/mol
Edimer
(10ºC) = -47.1 kcal/mol
Edimer
(25ºC) = -33.6 kcal/mol
Edimer
(45ºC) = -15.7 kcal/mol
Edimer
(10ºC) = -53.7 kcal/mol
Edimer
(25ºC) = -38.9 kcal/mol
Edimer
(45ºC) = -19.2 kcal/mol
gguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
a a
c
u
c a
g
a
g
u
c
g g a a a g
u c
g g a a
c a
g a c c
u
g
g
u
u u c g
u
c
g g u u
c u u c c
c
a u
c u u u c c
c
u
g
a
a
g a g a
c
g
a
a
g
c
a
a
g
u
c
gaaa
c
u
ca
g
a
g
u
c
ggaaag
uc
ggaa
ca
gacc
u
g
g
u
u
ucgu
c
1a
10a
20a
30a
40a
50a
60a 70a
79a
10b
20b
30b
40b
50b
60b
70b
79b
1b
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c
1a 10a 20a 30a 40a 50a 60a 70a 79a 10b 20b 30b 40b 50b 60b 70b 79b1b
monomer 1 monomer 2HI HII HIII
gguu
c
uucc
cau
cuuucc
c
u
gaa
g
a
gac
ga
a
g
c
a a
g u c
g
a
a a
c
u
c a
g
a
g
u
c
g g a a a g
u c
g g a a
c a
g a c c
u
g
g
u
u u c g
u
c
g g u u
c u u c c
c
a u
c u u u c c
c
u
g
a a
g
a
g a c
g a
a
g
c
aa
guc
g
a
a
a
c
u
c
a
g
a
g
u
c
ggaaag
uc
ggaa
ca
gacc
u
g
g
u
u
ucgu
c
1a
10a
20a
30a
40a
50a
60a 70a
79a
10b
20b
30b
40b50b
60b
70b
79b
1b
C
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c
g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c g g u u c u u c c c a u c u u u c c c u g a a g a g a c g a a g c a a g u c g a a a c u c a g a g u c g g a a a g u c g g a a c a g a c c u g g u u u c g u c
1a 10a 20a 30a 40a 50a 60a 70a 79a 10b 20b 30b 40b 50b 60b 70b 79b1b
18

20. HHR(-)
dimer
19

21. HHR(-)
dimer
19

22. HHR(-): monomer 1
20

23. HHR(-): monomer 1
20

24. HHR(-): monomer 2
21

25. HHR(-): monomer 2
21

26. HHR(-): monomer seeds
22

27. HHR(-) monomers
23

28. Mir et al., Biochem., 2015
HHR: Monomer & Dimer
Figure S2. Crystal contacts involve intermolecular base pairs. A. In crystals of the RzB
PDB ID:
24

29. Rg & self-association
HIII
HII
HI/HII
core
R(exp)g ~ 50Å
Rg*=50.4Å
Rg*=44.6Å
Rg*=46.1Å25
HI
HI/HI

30. MD setup for HHR dimer
26
•~ 300 000 atoms
• K+ & Cl- (0.15M)
• T = (283K, 313K)
• NAMD

31. Dynamics of HHR(-) dimer
RMSD vs time (ns)
Rg vs time (ns)
Histogram of Rg
Histogram of RMSD
Rg (monomer 1) vs time (ns)
Rg (monomer 2) vs time (ns)
Histogram of Rg (monomer 1)
Histogram of Rg (monomer 2)
RMSD(Å)
0
5
10
15
Rg(Å)
25
30
35
40
45
time (ns)
0 10 20 30 40 50 0 2500 5000 7500 10000125001500017500
27

32. Conclusions
28
• Self-assembly of HHR(-)
controls self-cleavage
• Self-assembly of ASBVd(-) …
• Self-assembly depends on
temperature
• impact of day/night cycle on
viroid replication and virulence

33. Conclusions
28
• Self-assembly of HHR(-)
controls self-cleavage
• Self-assembly of ASBVd(-) …
• Self-assembly depends on
temperature
• impact of day/night cycle on
viroid replication and virulence

34. Acknowledgments
•Zdenek Chval (University of South Bohemia, CK)
•Daniela Chvalová (University of South Bohemia, CK)
•Xavier Lopez (Euskal Herriko Unibertsitatea, SP)
•Annick Dejaegere (ESBS Strasbourg)
•Darrin M. York (Rutgers University, USA)
•Martin Karplus (Harvard University, USA)
•Giuseppe Zaccai (IBS, Grenoble)
•Jacques Vergne (MNHN, Paris)
•Anne Martel (ILL, Grenoble)
•Martina Rihova (Institute of Physics, Prague, CK)
•Marie-Christine Maurel (MNHN, Paris)
•William G. Scott (UCSC, Santa-Cruz, USA)
29
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