h/aca(like) srna in archaea
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![Page 1: H/ACA(like) sRNA in Archaea](https://reader035.vdocuments.net/reader035/viewer/2022062320/55cc8eeebb61ebec2c8b45d1/html5/thumbnails/1.jpg)
New Roles for Old ncRNAs in Archaeas ? Revisiting the Structure/Function
Relationships of H/ACA guide RNAs from Transcriptomics and Computational RNomics
Fabrice LeclercIGM - Orsay
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H/ACA & H/ACA-like motifsin Archaea
rRNA (tRNA)
Euryarchaea/Crenarchea (E/C)
C: PyrobaculumC: Thermoprotea
E: PyrococcusE: ThermococcusE: MethanococcusE: ArchaeoglobusE: Haloferax
C: SulfolobusC: Aeropyrum
H/ACA H/ACA-like
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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 ?
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“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
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10 H/ACA sRNA Genes,
10 H/ACA Motifs10 rRNA targets2 tRNA targets
“Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features”
Bernick et al., 2012
10 K-turn
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Structures of H/ACA RNAs & RNPs
(Pyrococcus furiosus)
5’
G
AA
GC
UGGG
GC
GGA
3’
stem H1
stem H2
K-loop
targetrRNA (tRNA)
guide
L7Ae
Nop10
Cbf5
ACA
PDB ID: 3LWO
Zhou et al., 2010
7-1
0b
p
14-1
6b
p9
-10
bp
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Structures of H/ACA RNAsfamily 10/5/9 (Pyrococcus)
10bp
9bp
5nt
10
5
9
PDB ID: 3LWO
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Structures of H/ACA RNAsfamily 10/6/9 (Pyrococcus)
10bp
9bp
6nt
10
6
9
PDB ID: 3HAX
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Subfamilies of H/ACA Motifs in Pyrococcus
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Representations of RNA guide/target pairs
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“Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in rRNAs”
Muller et al., NAR, 2008
non-productive
productive15 productive8 non-productive
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“Combined in silico and experimental identification of the Pyrococcus abyssi H/ACA sRNAs and their target sites in rRNAs”
Muller et al., NAR, 2008
![Page 13: H/ACA(like) sRNA in Archaea](https://reader035.vdocuments.net/reader035/viewer/2022062320/55cc8eeebb61ebec2c8b45d1/html5/thumbnails/13.jpg)
Structural Determinants in “Productive” H/ACA RNPs
(1)
productive
non-productive
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Structural Determinants in “Productive” H/ACA RNPs
(2)
productive
non-productive
![Page 15: H/ACA(like) sRNA in Archaea](https://reader035.vdocuments.net/reader035/viewer/2022062320/55cc8eeebb61ebec2c8b45d1/html5/thumbnails/15.jpg)
10 H/ACA sRNA Genes,
10 H/ACA Motifs10 K-turn Motifs
ANA Motif (?)
“Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features”
Bernick et al., RNA, 2012
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H/ACA Motifs (sR201, sR202) in Pyrobaculum
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H/ACA-like Motifs (sR203-206, sR208-210) in Pyrobaculum (1)
10
9
≥5}≥14
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H/ACA-like Motifs (sR203-206, sR208-210) in Pyrobaculum (2)
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10 H/ACA sRNA Genes,
10 H/ACA Motifs10 K-turn Motifs
ANA Motif (?)
“Discovery of Pyrobaculum small RNA families with atypical pseudouridine guide RNA features”
Bernick et al., RNA, 2012
non-productive
productive
![Page 20: H/ACA(like) sRNA in Archaea](https://reader035.vdocuments.net/reader035/viewer/2022062320/55cc8eeebb61ebec2c8b45d1/html5/thumbnails/20.jpg)
H/ACA-like Motif sR207 in Pyrobaculum: RNA fold
non-productive
12
9
4 }13
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H/ACA-like Motif sR207 in Pyrobaculum: RNA target
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H/ACA-like Motifs in Pyrococcus ?
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H/ACA-(like) Motifs in Pyrococcus
Toffano-Nioche et al., 2013
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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
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Pyrococcus, Thermococcus, Archaeoglobus, Haloferax, Methanocaldococcus
Pyrobaculum, Sulfolobus, Aeropyrum, Metalloshaera
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Acknowledgments
✤ Claire Toffano-Nioche
✤ Daniel Gautheret
Institut de Génétique & Microbiologie, Orsay