The document discusses the structure-function relationships of h/aca guide RNAs in archaea, focusing on their identification and roles in various archaeal species such as Pyrococcus and Pyrobaculum. It highlights the presence of both productive and non-productive h/aca and h/aca-like guide RNAs, and their variations across euryarchaea and crenarchaea. Key findings include the discovery of unique small RNA families and the potential alternative functions of these guide RNAs.

1. New Roles for Old ncRNAs
in Archaeas ?
Revisiting the Structure/Function
Relationships of H/ACA guide RNAs from
Transcriptomics and Computational
RNomics
Fabrice Leclerc
IGM - Orsay
fabrice.leclerc@igmors.u-psud.fr

2. H/ACA & H/ACA-like motifs
in Archaea
rRNA (tRNA)
Euryarchaea/Crenarchea (E/C)
C: Pyrobaculum
C: Thermoprotea
E: Pyrococcus
E: Thermococcus
E: Methanococcus
E: Archaeoglobus
E: Haloferax
C: Sulfolobus
C: Aeropyrum
H/ACA H/ACA-like

3. Outline
✤ H/ACA(-like) structure function relationships (structural
determinants for RNA guide & target)
✤ Archaea: H/ACA (Euryarchaea + Crenarchaea) &
H/ACA-like (Crenarchaea): variations on the same theme
?
✤ Alternative function(s) in Archaea ?

4. “Combined in silico and experimental identification
of the Pyrococcus abyssi H/ACA sRNAs and their
target sites in rRNAs”
7 K-turn,
4 K-loop
Muller et al., 2008
7 H/ACA Genes,
11 H/ACA Motifs
23 rRNA targets

5. 10 H/ACA sRNA Genes,
10 H/ACA Motifs
10 rRNA targets
2 tRNA targets
“Discovery of Pyrobaculum small RNA families with
atypical pseudouridine guide RNA features”
Bernick et al., 2012
10 K-turn

6. Structures of H/ACA RNAs &
RNPs
(Pyrococcus furiosus)
5’
G
A
A
G
C
UGG
G
G
C
G
G
A
3’
stem H1
stem H2
K-loop
target
rRNA (tRNA)
guide
L7Ae
Nop10
Cbf5
ACA
PDB ID: 3LWO
Zhou et al., 2010
7-10bp
14-16bp
9-10bp

7. Structures of H/ACA RNAs
family 10/5/9 (Pyrococcus)
10bp
9bp
5nt
10
5
9
PDB ID: 3LWO

8. Structures of H/ACA RNAs
family 10/6/9 (Pyrococcus)
10bp
9bp
6nt
10
6
9
PDB ID: 3HAX

9. Subfamilies of H/ACA Motifs in
Pyrococcus

10. Representations of RNA
guide/target pairs

11. “Combined in silico and experimental identification
of the Pyrococcus abyssi H/ACA sRNAs and their
target sites in rRNAs”
Muller et al., NAR,
non-productive
productive

12. “Combined in silico and experimental identification
of the Pyrococcus abyssi H/ACA sRNAs and their
target sites in rRNAs”
Muller et al., NAR,

13. Structural Determinants in
“Productive” H/ACA RNPs (1)
productive
non-productive

14. Structural Determinants in
“Productive” H/ACA RNPs (2)
productive
non-productive

15. 10 H/ACA sRNA Genes,
10 H/ACA Motifs
10 K-turn Motifs
ANA Motif (?)
“Discovery of Pyrobaculum small RNA families with
atypical pseudouridine guide RNA features”
Bernick et al., RNA,

16. H/ACA Motifs (sR201, sR202) in
Pyrobaculum

17. H/ACA-like Motifs (sR203-206,
sR208-210) in Pyrobaculum (1)
10
9
≥5}≥14

18. H/ACA-like Motifs (sR203-206,
sR208-210) in Pyrobaculum (2)

19. 10 H/ACA sRNA Genes,
10 H/ACA Motifs
10 K-turn Motifs
ANA Motif (?)
“Discovery of Pyrobaculum small RNA families with
atypical pseudouridine guide RNA features”
Bernick et al., RNA,non-productive
productive

20. H/ACA-like Motif sR207 in
Pyrobaculum: RNA fold
non-productive
12
9
4 }13

21. H/ACA-like Motif sR207 in
Pyrobaculum: RNA target

22. H/ACA-like Motifs in Pyrococcus ?

23. H/ACA-(like) Motifs in
Pyrococcus
Toffano-Nioche et al.,

24. Conclusions
✤ H/ACA-like guide RNAs are expected to work in the
same way with a few specificities (ANA box,...)
✤ H/ACA-like motifs present in both Euryarchaea and
Crenarchaea
✤ productive H/ACA & H/ACA-like guide RNAs in
Pyrobaculum
✤ non-productive(?) H/ACA-like guide RNAs in
Pyrococcus

25. Pyrococcus, Thermococcus, Archaeoglobus,
Haloferax, Methanocaldococcus
Pyrobaculum, Sulfolobus,
Aeropyrum, Metalloshaera

26. Acknowledgments
✤ Claire Toffano-Nioche
✤ Daniel Gautheret
Institut de Génétique &
Microbiologie, Orsay